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Sample records for abundant taxonomic groups

  1. Annual trend patterns of phytoplankton species abundance belie homogeneous taxonomical group responses to climate in the NE Atlantic upwelling.

    PubMed

    Bode, Antonio; Estévez, M Graciela; Varela, Manuel; Vilar, José A

    2015-09-01

    Phytoplankton is a sentinel of marine ecosystem change. Composed by many species with different life-history strategies, it rapidly responds to environment changes. An analysis of the abundance of 54 phytoplankton species in Galicia (NW Spain) between 1989 and 2008 to determine the main components of temporal variability in relation to climate and upwelling showed that most of this variability was stochastic, as seasonality and long term trends contributed to relatively small fractions of the series. In general, trends appeared as non linear, and species clustered in 4 groups according to the trend pattern but there was no defined pattern for diatoms, dinoflagellates or other groups. While, in general, total abundance increased, no clear trend was found for 23 species, 14 species decreased, 4 species increased during the early 1990s, and only 13 species showed a general increase through the series. In contrast, series of local environmental conditions (temperature, stratification, nutrients) and climate-related variables (atmospheric pressure indices, upwelling winds) showed a high fraction of their variability in deterministic seasonality and trends. As a result, each species responded independently to environmental and climate variability, measured by generalized additive models. Most species showed a positive relationship with nutrient concentrations but only a few showed a direct relationship with stratification and upwelling. Climate variables had only measurable effects on some species but no common response emerged. Because its adaptation to frequent disturbances, phytoplankton communities in upwelling ecosystems appear less sensitive to changes in regional climate than other communities characterized by short and well defined productive periods. PMID:26283032

  2. Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities.

    PubMed

    Smith, Renee J; Paterson, James S; Sibley, Cally A; Hutson, John L; Mitchell, James G

    2015-01-01

    Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices. PMID:26083532

  3. Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities

    PubMed Central

    Sibley, Cally A.; Hutson, John L.; Mitchell, James G.

    2015-01-01

    Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices. PMID:26083532

  4. A realistic assessment of the indicator potential of butterflies and other charismatic taxonomic groups.

    PubMed

    Fleishman, Erica; Murphy, Dennis D

    2009-10-01

    Charismatic groups of animals and plants often are proposed as sentinels of environmental status and trends. Nevertheless, many claims that a certain taxonomic group can provide more-general information on environmental quality are not evaluated critically. To address several of the many definitions of indicator species, we used butterflies to explore in some detail the attributes that affect implementation of indicators generically. There probably are few individual species, or sets of species, that can serve as scientifically valid, cost-effective measures of the status or trend of an environmental phenomenon that is difficult to measure directly. Nevertheless, there are species with distributions, abundances, or demographic characteristics that are responsive to known environmental changes. In this context, single or multiple species can serve as indicators when targets are defined explicitly, ecological relationships between the target and the putative indicators are well understood, and data are sufficient to differentiate between deterministic and stochastic responses. Although these situations exist, they are less common than might be apparent from an extensive and often confounded literature on indicators. Instead, the public appeal of charismatic groups may be driving much of their acclaim as indicators. The same taxon may not be appropriate for marketing a general conservation mission and for drawing strong inference about specific environmental changes. To provide insights into the progress of conservation efforts, it is essential to identify scientific and practical criteria for selection and application of indicators and then to examine whether a given taxonomic group meets those criteria. PMID:19459893

  5. Phi Class of Glutathione S-transferase Gene Superfamily Widely Exists in Nonplant Taxonomic Groups

    PubMed Central

    Munyampundu, Jean-Pierre; Xu, You-Ping; Cai, Xin-Zhong

    2016-01-01

    Glutathione S-transferases (GSTs) constitute a superfamily of enzymes involved in detoxification of noxious compounds and protection against oxidative damage. GST class Phi (GSTF), one of the important classes of plant GSTs, has long been considered as plant specific but was recently found in basidiomycete fungi. However, the range of nonplant taxonomic groups containing GSTFs remains unknown. In this study, the distribution and phylogenetic relationships of nonplant GSTFs were investigated. We identified GSTFs in ascomycete fungi, myxobacteria, and protists Naegleria gruberi and Aureococcus anophagefferens. GSTF occurrence in these bacteria and protists correlated with their genome sizes and habitats. While this link was missing across ascomycetes, the distribution and abundance of GSTFs among ascomycete genomes could be associated with their lifestyles to some extent. Sequence comparison, gene structure, and phylogenetic analyses indicated divergence among nonplant GSTFs, suggesting polyphyletic origins during evolution. Furthermore, in silico prediction of functional partners suggested functional diversification among nonplant GSTFs. PMID:26884677

  6. [Taxonomic revision of the Haplothrips-Karnyothrips group (Thysanoptera: Phlaeothripidae)].

    PubMed

    Retana-Salazar, Axel P; Soto-Rodríguez, Gerardo A

    2007-06-01

    The generic group ("ensemble") Haplothrips-Karnyothrips is reviewed, following the most recently published criteria for distinguishing generic characters. We establish a new diagnosis for each genus. A review of a Central American collection is included and a new genus of Phlaeothripidae is described from the Central Pacific of Costa Rica from specimens collected on Cyperaceae flowers during the dry season. The genus can be distinguished by widely separated maxillary stylets, absent maxillary bridge, pelta shape and the setae B1, which measures two thirds of the tube length. We include a key based on characters of phylogenetic importance. PMID:19069772

  7. Dynamics of extinction debt across five taxonomic groups.

    PubMed

    Halley, John M; Monokrousos, Nikolaos; Mazaris, Antonios D; Newmark, William D; Vokou, Despoina

    2016-01-01

    Species extinction following habitat loss is well documented. However, these extinctions do not happen immediately. The biodiversity surplus (extinction debt) declines with some delay through the process of relaxation. Estimating the time constants of relaxation, mainly the expected time to first extinction and the commonly used time for half the extinction debt to be paid off (half-life), is crucial for conservation purposes. Currently, there is no agreement on the rate of relaxation and the factors that it depends on. Here we find that half-life increases with area for all groups examined in a large meta-analysis of extinction data. A common pattern emerges if we use average number of individuals per species before habitat loss as an area index: for mammals, birds, reptiles and plants, the relationship has an exponent close to a half. We also find that the time to first determined extinction is short and increases slowly with area. PMID:27452815

  8. Dynamics of extinction debt across five taxonomic groups

    PubMed Central

    Halley, John M.; Monokrousos, Nikolaos; Mazaris, Antonios D.; Newmark, William D.; Vokou, Despoina

    2016-01-01

    Species extinction following habitat loss is well documented. However, these extinctions do not happen immediately. The biodiversity surplus (extinction debt) declines with some delay through the process of relaxation. Estimating the time constants of relaxation, mainly the expected time to first extinction and the commonly used time for half the extinction debt to be paid off (half-life), is crucial for conservation purposes. Currently, there is no agreement on the rate of relaxation and the factors that it depends on. Here we find that half-life increases with area for all groups examined in a large meta-analysis of extinction data. A common pattern emerges if we use average number of individuals per species before habitat loss as an area index: for mammals, birds, reptiles and plants, the relationship has an exponent close to a half. We also find that the time to first determined extinction is short and increases slowly with area. PMID:27452815

  9. 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

  10. 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

  11. 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

  12. The pattern of serotonin and FMRFamide in cercaria from different taxonomic groups--a preliminary study.

    PubMed

    Tolstenkov, O O; Terenina, Nadezhda; Gustafsson, Margaretha; Serbina, Elena; Kreshchenko, Natalia D; Maklakova, Ludmila; Jashina, Alexandra

    2008-01-01

    Serotoninergic and FMRFamidergic components of the nervous system were examined in cercaria from different types using immunocytochemical techniques interfaced with confocal scanning laser microscopy. Cercariae from 9 families were studied - Opisthorchis felineus, Parafasciolopsis fasciolaemorpha, Echinochasmus coaxatus, Echinoparyphium aconiatum, Notocotylus attenuatus, Psilotrema tuberculata, Plagiorchis sp., Cyathocotyle bithyniae, Diplostomum chromatophorum. The results show that 5-HT-IR and FMRFamide-IR occur in all types of cercariae, regardless of what morphological, taxonomic and biological group they belong to. Small differences in the patterns of 5-HT-IR and FMRFamide-IR were observed. PMID:18652395

  13. Taxonomic review of the Dichotomius (Luederwaldtinia) assifer (Eschscholtz) species-group (Coleoptera: Scarabaeidae).

    PubMed

    Nunes, Rafael V; Carvalho, Marcela S G; Vaz-de-Mello, Fernando Z

    2016-01-01

    The Dichotomius assifer species-group, a component of Dichotomius (Luederwaldtinia) is taxonomically revised. The group now contains five species: D. angeloi sp. nov. (Holotype male deposited in CEMT: BRAZIL, Minas Gerais State, Vargem Bonita, Parque Nacional Serra da Canastra. Mata de Galeria, 28º18'39"S, 46º31'30"W. 865 m a.s.l., 02.XI.2011, MF Souza leg.), and D. louzadai sp. nov. (Holotype male deposited in CEMT: BRAZIL, Minas Gerais State, Lima Duarte, Parque Estadual Ibitipoca, VI.2001, FZ Vaz-de-Mello leg.) are described; D. assifer and D. affinis are redescribed and lectotypes are designated. D. machadoi is diagnosed. Illustrations, distributional records, diagnosis and a key for identification of the species in the group are provided. Some aspects of the natural history and biogeography of species in the assifer group are also discussed. PMID:27395977

  14. 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

  15. Taxonomic minimalism.

    PubMed

    Beattle, A J; Oliver, I

    1994-12-01

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

  16. Phylogenetic relationships within the Callicebus cupreus species group (Pitheciidae: Primates): Biogeographic and taxonomic implications.

    PubMed

    Hoyos, Manuel; Bloor, Paul; Defler, Thomas; Vermeer, Jan; Röhe, Fabio; Farias, Izeni

    2016-09-01

    The genus Callicebus (Thomas, 1903) is one of the most diverse of Neotropical primate genera and the only extant member of the Callicebinae subfamily. It has a widespread distribution from Colombia to Brazil, Bolivia, Peru and northern Paraguay. Coat colouring and colour pattern vary substantially within the genus, and this has led to the description of numerous species and subspecies, as well as numerous species groups. However, a lack of molecular phylogenetic analyses on the genus means that phylogenetic relationships and biogeographic history of species are poorly understood. Here, we examined phylogenetic relationships and patterns of diversification within the Callicebus cupreus species Group (sensu Kobayashi, 1995) using complete mitochondrial DNA cytochrome b gene sequence. Analyses indicate that the Callicebus cupreus Group underwent recent and extensive diversification. The common ancestor appears to have emerged some 2.3 million years ago (Ma) from a centre of origin in the western Amazon region, followed by diversification of the group between about 1.5 and 1.2Ma. Phylogenetic analyses were able to recover most previously described species (including the recently described Colombian endemic Callicebus caquetensis). However, there are some notable inconsistences between the obtained phylogeny and current taxonomy. Some previously recognized taxa were not separated by our data (e.g., Callicebus caligatus and Callicebus dubius), while currently unrecognized species diversity was uncovered within C. cupreus in the form of two divergent lineages: one of which exhibited greater phylogenetic similarity to species from the C. moloch Group. Based on the present study, we challenge current taxonomic arrangements for the C. cupreus species Group and call for a thorough taxonomic revision within the genus Callicebus. PMID:27235549

  17. Long-term warming alters richness and composition of taxonomic and functional groups of arctic fungi.

    PubMed

    Geml, József; Morgado, Luis N; Semenova, Tatiana A; Welker, Jeffrey M; Walker, Marilyn D; Smets, Erik

    2015-08-01

    Fungi, including symbionts, pathogens and decomposers, play crucial roles in community dynamics and nutrient cycling in terrestrial ecosystems. Despite their ecological importance, the response of most arctic fungi to climate warming is unknown, so are their potential roles in driving the observed and predicted changes in tundra communities. We carried out deep DNA sequencing of soil samples to study the long-term effects of experimental warming on fungal communities in dry heath and moist tussock tundra in Arctic Alaska. The data presented here indicate that fungal community composition responds strongly to warming in the moist tundra, but not in the dry tundra. While total fungal richness was not significantly affected by warming, there were clear correlations among operational taxonomic unit richness of various ecological and taxonomic groups and long-term warming. Richness of ectomycorrhizal, ericoid mycorrhizal and lichenized fungi generally decreased with warming, while richness of saprotrophic, plant and animal pathogenic, and root endophytic fungi tended to increase in the warmed plots. More importantly, various taxa within these functional guilds followed opposing trends that highlight the importance of species-specific responses to warming. We recommend that species-level ecological differences be taken into account in climate change and nutrient cycling studies that involve arctic fungi. PMID:26253509

  18. Chemical abundances of massive stars in Local Group galaxies

    NASA Astrophysics Data System (ADS)

    Venn, Kim A.; Kaufer, Andreas; Tolstoy, Eline; Kudritzki, Rolf-Peter; Przybilla, Norbert; Smartt, Stephen J.; Lennon, Daniel J.

    The relative abundances of elements in galaxies can provide valuable information on the stellar and chemical evolution of a galaxy. While nebulae can provide abundances for a variety of light elements, stars are the only way to directly determine the abundances of iron-group and s-process and r-process elements in a galaxy. The new 8m and 10m class telescopes and high-efficiency spectrographs now make high-quality spectral observations of bright supergiants possible in dwarf galaxies in the Local Group. We have been concentrating on elemental abundances in the metal-poor dwarf irregular galaxies, NGC 6822, WLM, Sextants A, and GR 8. Comparing abundance ratios to those predicted from their star formation histories, determined from color-magnitude diagrams, and comparing those ratios between these galaxies can give us new insights into the evolution of these dwarf irregular galaxies. Iron-group abundances also allow us to examine the metallicities of the stars in these galaxies directly, which affects their inferred mass loss rates and predicted stellar evolution properties.

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

    PubMed

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

    2016-01-01

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

  20. 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

  1. Inordinate Spinescence: Taxonomic Revision and Microtomography of the Pheidole cervicornis Species Group (Hymenoptera, Formicidae).

    PubMed

    Sarnat, Eli M; Fischer, Georg; Economo, Evan P

    2016-01-01

    The ant genus Pheidole-for all of its hyperdiversity and global ubiquity-is remarkably conservative with regard to morphological disparity. A striking exception to this constrained morphology is the spinescent morphotype, which has evolved multiple times across distantly related lineages of Indoaustralian Pheidole. The Pheidole cervicornis group contains perhaps the most extraordinary spinescent forms of all Pheidole. Here we present a taxonomic revision of the P. cervicornis group, and use microtomographic scanning technology to investigate the internal anatomy of the thoracic spines. Our findings suggest the pronotal spines of Pheidole majors, are possibly skeletomuscular adaptations for supporting their disproportionately large heads. The 'head support hypothesis' is an alternative to the mechanical defense hypothesis most often used to explain spinescence in ants. The P. cervicornis group is known only from New Guinea and is represented by the following four species, including two described here as new: P. barumtaun Donisthorpe, P. drogon sp. nov., P. cervicornis Emery, and P. viserion sp. nov. The group is most readily identified by the minor worker caste, which has extremely long pronotal spines and strongly bifurcating propodeal spines. The major and minor workers of all species are illustrated with specimen photographs, with the exception of the major worker of P. cervicornis, which is not known. PMID:27463644

  2. Inordinate Spinescence: Taxonomic Revision and Microtomography of the Pheidole cervicornis Species Group (Hymenoptera, Formicidae)

    PubMed Central

    Sarnat, Eli M.; Fischer, Georg; Economo, Evan P.

    2016-01-01

    The ant genus Pheidole—for all of its hyperdiversity and global ubiquity—is remarkably conservative with regard to morphological disparity. A striking exception to this constrained morphology is the spinescent morphotype, which has evolved multiple times across distantly related lineages of Indoaustralian Pheidole. The Pheidole cervicornis group contains perhaps the most extraordinary spinescent forms of all Pheidole. Here we present a taxonomic revision of the P. cervicornis group, and use microtomographic scanning technology to investigate the internal anatomy of the thoracic spines. Our findings suggest the pronotal spines of Pheidole majors, are possibly skeletomuscular adaptations for supporting their disproportionately large heads. The ‘head support hypothesis’ is an alternative to the mechanical defense hypothesis most often used to explain spinescence in ants. The P. cervicornis group is known only from New Guinea and is represented by the following four species, including two described here as new: P. barumtaun Donisthorpe, P. drogon sp. nov., P. cervicornis Emery, and P. viserion sp. nov. The group is most readily identified by the minor worker caste, which has extremely long pronotal spines and strongly bifurcating propodeal spines. The major and minor workers of all species are illustrated with specimen photographs, with the exception of the major worker of P. cervicornis, which is not known. PMID:27463644

  3. The magnitude of spatial and temporal variation in δ15N and δ13C differs between taxonomic groups: Implications for food web studies

    NASA Astrophysics Data System (ADS)

    Hyndes, Glenn A.; Hanson, Christine E.; Vanderklift, Mathew A.

    2013-03-01

    Understanding variability in stable isotope abundance is essential for effective hypothesis testing and evaluating food sources, trophic levels and food web structure. The magnitude and sources of variability are likely to differ among taxonomic and functional groups. We aimed to quantify variability of δ13C and δ15N for 16 species representing seven distinct taxonomic groups of benthic invertebrates and autotrophs in a marine ecosystem. We quantified the magnitude of variability among individuals or shoots separated by metres, among eight sites separated by kilometres, and between two survey occasions separated by months. δ13C varied by as much as 7‰ for primary producers, 4‰ for consumers, while δ15N varied by as much as 9‰ and 2‰ respectively. Variation in δ15N of seagrass was largely accounted for by differences among sites, while variation in δ13C was mainly attributable to shoots collected a few metres apart. Compared to seagrasses, variation in macroalgae was mainly explained by differences between the two survey occasions for δ15N and among individuals collected a few metres apart for δ13C. Variation was generally lower for consumers and typically explained by differences among individuals for δ15N but displayed inconsistent patterns for δ13C. Dual isotope Bayesian mixing models showed that the potential contributions of food sources for herbivorous consumers varied among sites and between survey occasions, and also that there was high variability or uncertainty in the contributions of sources within sites. The relative consistency in the main sources of variation among broad taxonomic groups in autotrophs suggests that aspects of physiology that are phylogenetically conserved might be important influences on variation in natural abundances of stable isotopes. In comparison, the sources of variability were less consistent within and among broad consumer groups, suggesting complex interactions between consumers and their food sources.

  4. New Abundant Microbial Groups in Aquatic Hypersaline Environments

    PubMed Central

    Ghai, Rohit; Pašić, Lejla; Fernández, Ana Beatriz; Martin-Cuadrado, Ana-Belen; Mizuno, Carolina Megumi; McMahon, Katherine D.; Papke, R. Thane; Stepanauskas, Ramunas; Rodriguez-Brito, Beltran; Rohwer, Forest; Sánchez-Porro, Cristina; Ventosa, Antonio; Rodríguez-Valera, Francisco

    2011-01-01

    We describe the microbiota of two hypersaline saltern ponds, one of intermediate salinity (19%) and a NaCl saturated crystallizer pond (37%) using pyrosequencing. The analyses of these metagenomes (nearly 784 Mb) reaffirmed the vast dominance of Haloquadratum walsbyi but also revealed novel, abundant and previously unsuspected microbial groups. We describe for the first time, a group of low GC Actinobacteria, related to freshwater Actinobacteria, abundant in low and intermediate salinities. Metagenomic assembly revealed three new abundant microbes: a low-GC euryarchaeon with the lowest GC content described for any euryarchaeon, a high-GC euryarchaeon and a gammaproteobacterium related to Alkalilimnicola and Nitrococcus. Multiple displacement amplification and sequencing of the genome from a single archaeal cell of the new low GC euryarchaeon suggest a photoheterotrophic and polysaccharide-degrading lifestyle and its relatedness to the recently described lineage of Nanohaloarchaea. These discoveries reveal the combined power of an unbiased metagenomic and single cell genomic approach. PMID:22355652

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

    PubMed

    Ahrens, Dirk; Liu, Wan-Gang; Fabrizi, Silvia; Bai, Ming; Yang, Xing-Ke

    2014-01-01

    The present paper revises the species belonging to the Neoserica (sensu lato) abnormis group, so far known only with two nominal species. Twenty new species are herein described from Indochina and southern China: N. abnormoides sp. n. (Vietnam, China), N. allolaotica sp. n., N. namthaensis sp. n., N. simplicissima sp. n. (Laos), N. thailandensis sp. n. (Thailand), N. alloputaoana sp. n., N. kanphantensis sp. n., N. natmatoungensis sp. n., N. putaoana sp. n., N. taunggyiana sp. n. (Myanmar), N. lamellosa sp. n., N. tonkinea sp. n. (Vietnam), N. bairailingshanica sp. n., N. euyunnanica sp. n., N. huangi sp. n., N. jiangxiensis sp. n., N. trifida sp. n., N. yaoi sp. n., N. yingjiangensis sp. n. (China), N. cardamomensis sp. n. (Indochina and southern China). One new combination is established: Neoserica ponderosa Arrow, 1946, comb. n. The lectotypes of Neoserica abnormis Moser, 1908 and the taxonomically uncertain N. inclinata Brenske, 1898, which very likely also belongs to this species group, are designated herein. A key to the species and to species groups is given, the genitalia of all species including their habitus are illustrated. Maps of species distribution are included. PMID:25317056

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

    PubMed Central

    Ahrens, Dirk; Liu, Wan-Gang; Fabrizi, Silvia; Bai, Ming; Yang, Xing-Ke

    2014-01-01

    Abstract The present paper revises the species belonging to the Neoserica (sensu lato) abnormis group, so far known only with two nominal species. Twenty new species are herein described from Indochina and southern China: N. abnormoides sp. n. (Vietnam, China), N. allolaotica sp. n., N. namthaensis sp. n., N. simplicissima sp. n. (Laos), N. thailandensis sp. n. (Thailand), N. alloputaoana sp. n., N. kanphantensis sp. n., N. natmatoungensis sp. n., N. putaoana sp. n., N. taunggyiana sp. n. (Myanmar), N. lamellosa sp. n., N. tonkinea sp. n. (Vietnam), N. bairailingshanica sp. n., N. euyunnanica sp. n., N. huangi sp. n., N. jiangxiensis sp. n., N. trifida sp. n., N. yaoi sp. n., N. yingjiangensis sp. n. (China), N. cardamomensis sp. n. (Indochina and southern China). One new combination is established: Neoserica ponderosa Arrow, 1946, comb. n. The lectotypes of Neoserica abnormis Moser, 1908 and the taxonomically uncertain N. inclinata Brenske, 1898, which very likely also belongs to this species group, are designated herein. A key to the species and to species groups is given, the genitalia of all species including their habitus are illustrated. Maps of species distribution are included. PMID:25317056

  7. Comparing Amino Acid Abundances and Distributions Across Carbonaceous Chondrite Groups

    NASA Technical Reports Server (NTRS)

    Burton, Aaron S.; Callahan, Michael P.; Glavin, Daniel P.; Elsila, Jamie E.; Dworkin, Jason P.

    2012-01-01

    Meteorites are grouped according to bulk properties such as chemical composition and mineralogy. These parameters can vary significantly among the different carbonaceous chondrite groups (CI, CM, CO, CR, CH, CB, CV and CK). We have determined the amino acid abundances of more than 30 primary amino acids in meteorites from each of the eight groups, revealing several interesting trends. There are noticeable differences in the structural diversity and overall abundances of amino acids between meteorites from the different chondrite groups. Because meteorites may have been an important source of amino acids to the prebiotic Earth and these organic compounds are essential for life as we know it, the observed variations of these molecules may have been important for the origins of life.

  8. New species, redescription and taxonomic notes in the Dichotomius (Luederwaldtinia) batesi (Harold) species-group (Coleoptera: Scarabaeidae: Scarabaeinae).

    PubMed

    Vaz-de-Mello, Fernando Z; Nunes, Rafael V

    2016-01-01

    This paper deals with taxonomic issues of the Dichotomius (Luederwaldtinia) batesi (Harold) species-group. We describe Dichotomius benesi n. sp. from Panama, and redescribe and designate a lectotype for Dichotomius ocellatopunctatus (Felsche) from Venezuela, both hemi-brachypterous species. We also do brief comments on the taxonomy of this species-group. Dichotomius joelus, previously assigned to this group, is here considered to be a new synonym of D. opacipennis and then to belong to Dichotomius geminatus species-group. PMID:27470806

  9. Lead and uranium group abundances in cosmic rays

    NASA Technical Reports Server (NTRS)

    Yadav, J. S.; Perelygin, V. P.

    1985-01-01

    The importance of Lead and Uranium group abundances in cosmic rays is discussed in understanding their evolution and propagation. The electronic detectors can provide good charge resolution but poor data statistics. The plastic detectors can provide somewhat better statistics but charge resolution deteriorates. The extraterrestrial crystals can provide good statistics but with poor charge resolution. Recent studies of extraterrestrial crystals regarding their calibration to accelerated uranium ion beam and track etch kinetics are discussed. It is hoped that a charge resolution of two charge units can be achieved provided an additional parameter is taken into account. The prospects to study abundances of Lead group, Uranium group and superheavy element in extraterrestrial crystals are discussed, and usefulness of these studies in the light of studies with electronic and plastic detectors is assessed.

  10. 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...

  11. Fish otoliths: do sizes correlate with taxonomic group, habitat and/or luminescence?

    PubMed

    Paxton, J R

    2000-09-29

    Otoliths are dense structures in the ears of fishes that function in hearing and gravity perception. Otolith (sagitta) diameters, as percentages of standard length (% SL), are calculated for 247 marine fish species in 147 families and compared by taxonomic group (usually order), habitat and presence or absence of luminescence. Otolith sizes range from 0.4-31.4 mm and 0.08-11.2% SL. The eel and spiny eel orders Anguilliformes and Notacanthiformes have small to very small otoliths, as do the triggerfish order Tetraodontiformes, pipefish order Gasterosteiformes, billfish suborder Scombroidei and many of the dragonfish order Stomiiformes. The soldierfish order Beryciformes has moderate to very large otoliths. The perch order Perciformes has a wide range of otolith sizes but most have small to moderate otoliths 2-5% SL. Only 16 out of the 247 species have the relatively largest otoliths, over 7% SL. Seven out of these 16 species are also luminous from a variety of habitats. Luminous species have slightly to much larger otoliths than non-luminous species in the same family Both beryciforms and luminous fishes live in low-light environments, where acute colour vision is probably impossible. Most fishes of the epipelagic surface waters have very small otoliths, perhaps due to background noise and/or excessive movement of heavy otoliths in rough seas. Bathypelagic species usually have small otoliths and regressed or absent swimbladders. Other habitats have species with a range of otolith sizes. While the relationship between hearing ability and otolith length is unknown, at least some groups with modified swim-bladders have larger otoliths, which may be associated with more acute hearing. PMID:11079419

  12. Fish otoliths: do sizes correlate with taxonomic group, habitat and/or luminescence?

    PubMed Central

    Paxton, J R

    2000-01-01

    Otoliths are dense structures in the ears of fishes that function in hearing and gravity perception. Otolith (sagitta) diameters, as percentages of standard length (% SL), are calculated for 247 marine fish species in 147 families and compared by taxonomic group (usually order), habitat and presence or absence of luminescence. Otolith sizes range from 0.4-31.4 mm and 0.08-11.2% SL. The eel and spiny eel orders Anguilliformes and Notacanthiformes have small to very small otoliths, as do the triggerfish order Tetraodontiformes, pipefish order Gasterosteiformes, billfish suborder Scombroidei and many of the dragonfish order Stomiiformes. The soldierfish order Beryciformes has moderate to very large otoliths. The perch order Perciformes has a wide range of otolith sizes but most have small to moderate otoliths 2-5% SL. Only 16 out of the 247 species have the relatively largest otoliths, over 7% SL. Seven out of these 16 species are also luminous from a variety of habitats. Luminous species have slightly to much larger otoliths than non-luminous species in the same family Both beryciforms and luminous fishes live in low-light environments, where acute colour vision is probably impossible. Most fishes of the epipelagic surface waters have very small otoliths, perhaps due to background noise and/or excessive movement of heavy otoliths in rough seas. Bathypelagic species usually have small otoliths and regressed or absent swimbladders. Other habitats have species with a range of otolith sizes. While the relationship between hearing ability and otolith length is unknown, at least some groups with modified swim-bladders have larger otoliths, which may be associated with more acute hearing. PMID:11079419

  13. The Heavy Element Abundance in Groups of Galaxies

    NASA Technical Reports Server (NTRS)

    David, Laurence

    2000-01-01

    Over the past few years we have analyzed a sample of clusters observed by the Advanced Spacecraft for Cosmology Astrophysics (ASCA) X-ray satellite. We performed spatially resolved X-ray spectroscopy of a sample of 18 relaxed clusters of galaxies with gas temperatures below 4 keV. The spectral analysis was done using ASCA/SIS (Solid state Imaging Spectrometer) data combined with imaging data from ROSAT/PSPC (German acronym for X-ray satellite/Position Sensitive Proportional Counter) and Einstein/IPC (Imaging Proportional Counter) observations. We derived temperature profiles using single-temperature fits for all of the clusters in the sample, and also corrected for the presence of cold gas in the center of so-called 'cooling flow' clusters. For all of the clusters in the sample we derived Si and Fe abundance profiles. For a few of the clusters we also were able to derive Ne and S abundance profiles. We compared the elemental abundances derived at similar overdensities in all of the clusters in the sample. We also compared element mass-to-light ratios for the entire sample. We concluded that the preferential accretion of low entropy, low abundance gas into the potentials of groups and cold clusters can explain most of the observed trends in metallicity. In addition, we discussed the importance of preheating of the intracluster medium by Type II supernovae on the cluster scaling relations.

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

    PubMed

    Fisher, Jenny C; Eren, A Murat; Green, Hyatt C; Shanks, Orin C; Morrison, Hilary G; Vineis, Joseph H; Sogin, Mitchell L; McLellan, Sandra L

    2015-10-01

    Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but the gut microbiota of humans and other animals contain organisms from an array of other taxonomic groups that might provide indicators of fecal pollution sources. To discern between human and nonhuman fecal sources, we compared the V6 regions of the 16S rRNA genes detected in fecal samples from six animal hosts to those found in sewage (as a proxy for humans). We focused on 10 abundant genera and used oligotyping, which can detect subtle differences between rRNA gene sequences from ecologically distinct organisms. Our analysis showed clear patterns of differential oligotype distributions between sewage and animal samples. Over 100 oligotypes of human origin occurred preferentially in sewage samples, and 99 human oligotypes were sewage specific. Sequences represented by the sewage-specific oligotypes can be used individually for development of PCR-based assays or together with the oligotypes preferentially associated with sewage to implement a signature-based approach. Analysis of sewage from Spain and Brazil showed that the sewage-specific oligotypes identified in U.S. sewage have the potential to be used as global alternative indicators of human fecal pollution. Environmental samples with evidence of prior human fecal contamination had consistent ratios of sewage signature oligotypes that corresponded to the trends observed for sewage. Our methodology represents a promising approach to identifying new bacterial taxa for MST applications and further highlights the potential of the family Lachnospiraceae to provide human-specific markers. In addition to source tracking applications, the patterns of the fine-scale population structure within fecal taxa suggest a fundamental relationship between bacteria and their hosts. PMID:26231648

  15. 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

  16. Platinum-group element abundance patterns in different mantle environments

    SciTech Connect

    Rehkaemper, M.; Halliday, A.N.; Barfod, D.; Fitton, J.G.; Dawson, J.B.

    1997-11-28

    Mantle-derived xenoliths from the Cameroon Line and northern Tanzania display differences in their platinum-group element (PGE) abundance patterns. The Cameroon Line lherzolites have uniform PGE patterns indicating a homogeneous upper mantle over several hundreds of kilometers, with approximately chondritic PGE ratios. The PGE patterns of the Tanzanian peridotites are similar to the PGE systematics of ultramafic rocks from ophiolites. The differences can be explained if the northern Tanzanian lithosphere developed in a fluid-rich suprasubduction zone environment, whereas the Cameroon Line lithosphere only experienced melt extraction from anhydrous periodotites. 32 refs., 2 figs., 1 tab.

  17. Population modelling to compare chronic external radiotoxicity between individual and population endpoints in four taxonomic groups.

    PubMed

    Alonzo, Frédéric; Hertel-Aas, Turid; Real, Almudena; Lance, Emilie; Garcia-Sanchez, Laurent; Bradshaw, Clare; Vives I Batlle, Jordi; Oughton, Deborah H; Garnier-Laplace, Jacqueline

    2016-02-01

    soil invertebrates. These predictions suggested that proposed reference benchmarks from the literature for different taxonomic groups protected all simulated species against population extinction. A generic reference benchmark of 10 μGy h(-1) protected all simulated species against 10% of the effect causing population extinction. Finally, a risk of pseudo-extinction was predicted from 2.0 μGy h(-1) in mammals to 970 μGy h(-1) in soil invertebrates, representing a slight but statistically significant population decline, the importance of which remains to be evaluated in natural settings. PMID:26630040

  18. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data.

    PubMed

    Spring, Stefan; Scheuner, Carmen; Göker, Markus; Klenk, Hans-Peter

    2015-01-01

    In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov. PMID:25914684

  19. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data

    PubMed Central

    Spring, Stefan; Scheuner, Carmen; Göker, Markus; Klenk, Hans-Peter

    2015-01-01

    In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov. PMID:25914684

  20. Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups.

    PubMed

    Le, Huong T; Ho, Cuong T; Trinh, Quan H; Trinh, Duc A; Luu, Minh T N; Tran, Hai S; Orange, Didier; Janeau, Jean L; Merroune, Asmaa; Rochelle-Newall, Emma; Pommier, Thomas

    2016-01-01

    Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as

  1. Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups

    PubMed Central

    Le, Huong T.; Ho, Cuong T.; Trinh, Quan H.; Trinh, Duc A.; Luu, Minh T. N.; Tran, Hai S.; Orange, Didier; Janeau, Jean L.; Merroune, Asmaa; Rochelle-Newall, Emma; Pommier, Thomas

    2016-01-01

    Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as

  2. Is sociality required for the evolution of communicative complexity? Evidence weighed against alternative hypotheses in diverse taxonomic groups

    PubMed Central

    Ord, Terry J.; Garcia-Porta, Joan

    2012-01-01

    Complex social communication is expected to evolve whenever animals engage in many and varied social interactions; that is, sociality should promote communicative complexity. Yet, informal comparisons among phylogenetically independent taxonomic groups seem to cast doubt on the putative role of social factors in the evolution of complex communication. Here, we provide a formal test of the sociality hypothesis alongside alternative explanations for the evolution of communicative complexity. We compiled data documenting variations in signal complexity among closely related species for several case study groups—ants, frogs, lizards and birds—and used new phylogenetic methods to investigate the factors underlying communication evolution. Social factors were only implicated in the evolution of complex visual signals in lizards. Ecology, and to some degree allometry, were most likely explanations for complexity in the vocal signals of frogs (ecology) and birds (ecology and allometry). There was some evidence for adaptive evolution in the pheromone complexity of ants, although no compelling selection pressure was identified. For most taxa, phylogenetic null models were consistently ranked above adaptive models and, for some taxa, signal complexity seems to have accumulated in species via incremental or random changes over long periods of evolutionary time. Becoming social presumably leads to the origin of social communication in animals, but its subsequent influence on the trajectory of signal evolution has been neither clear-cut nor general among taxonomic groups. PMID:22641820

  3. Chaetopteryx bucari sp. n., a new species from the Chaetopteryx rugulosa group from Croatia (Insecta, Trichoptera, Limnephilidae) with molecular, taxonomic and ecological notes on the group

    PubMed Central

    Kučinić, Mladen; Szivák, Ildikó; Pauls, Steffen U.; Bálint, Miklós; Delić, Antun; Vučković, Ivan

    2013-01-01

    Abstract We describe a new autumnal caddisfly species Chaetopteryx bucari sp. n. from 8 localities in the Banovina region of Croatia. We also present molecular, taxonomic and ecological notes (emergence, sex ratio and seasonal dynamics) on the new species and discuss the distribution of Chaetopteryx species in general and the Chaetopteryx rugulosa group in particular. Based on Bayesian phylogenetic analysis Chaetopteryx rugulosa schmidi was separated from the clade containing the other subspecies of Chaetopteryx rugulosa. Thus the subspecies Chaetopteryx rugulosa schmidi is here raised to species level, Chaetopteryx schmidi, as it was described originally. We further present distribution data on rare species in the genus Chaetopteryx in Croatia. PMID:23950680

  4. Abundance trends in kinematical groups of the Milky Way's disk

    NASA Astrophysics Data System (ADS)

    Soubiran, C.; Girard, P.

    2005-07-01

    We have compiled a large catalogue of metallicities and abundance ratios from the literature in order to investigate abundance trends of several alpha and iron peak elements in the thin disk and the thick disk of the Galaxy. The catalogue includes 743 stars with abundances of Fe, O, Mg, Ca, Ti, Si, Na, Ni and Al in the metallicity range -1.30 < [Fe/H] < +0.50. We have checked that systematic differences between abundances measured in the different studies were lower than random errors before combining them. Accurate distances and proper motions from Hipparcos and radial velocities from several sources have been retreived for 639 stars and their velocities (U, V, W) and galactic orbits have been computed. Ages of 322 stars have been estimated with a Bayesian method of isochrone fitting. Two samples kinematically representative of the thin and thick disks have been selected, taking into account the Hercules stream which is intermediate in kinematics, but with a probable dynamical origin. Our results show that the two disks are chemically well separated, they overlap greatly in metallicity and both show parallel decreasing alpha elements with increasing metallicity, in the interval -0.80 < [Fe/H] < -0.30. The Mg enhancement with respect to Fe of the thick disk is measured to be 0.14 dex. An even larger enhancement is observed for Al. The thick disk is clearly older than the thin disk with tentative evidence of an AMR over 2-3 Gyr and a hiatus in star formation before the formation of the thin disk. We do not observe a vertical gradient in the metallicity of the thick disk. The Hercules stream has properties similar to that of the thin disk, with a wider range of metallicity. Metal-rich stars assigned to the thick disk and super-metal-rich stars assigned to the thin disk appear as outliers in all their properties.

  5. New brachypterous species of Dichotomius (Selenocopris) Burmeister (Coleoptera: Scarabaeidae: Scarabaeinae) with the definition of species groups and taxonomic notes in the subgenus.

    PubMed

    Nunes, Rafael V; Vaz-de-Mello, Fernando Z

    2016-01-01

    Five species groups of Dichotomius (Selenocopris) are defined and separated in an illustrated key in the first effective attempt of systematization of the subgenus. Four new brachypterous species of Selenocopris are described and the also brachypterous Dichotomius ingens (Luederwaldt) is redescribed. These species are diagnosed, illustrated and assigned to the quadraticeps species group. Taxonomic issues on the subgenus are discussed. PMID:27470786

  6. H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups

    PubMed Central

    Piché-Choquette, Sarah; Tremblay, Julien; Tringe, Susannah G.

    2016-01-01

    Soil microbial communities are continuously exposed to H2 diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2 exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2 oxidation activity in soil changed drastically upon elevated H2 exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2 exposure, suggesting that H2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities. PMID:26989620

  7. A taxonomic review of the Neoserica (sensu lato) septemlamellata group (Coleoptera, Scarabaeidae, Sericini)

    PubMed Central

    Ahrens, Dirk; Liu, Wan-Gang; Fabrizi, Silvia; Bai, Ming; Yang, Xing-Ke

    2014-01-01

    Abstract In the present paper the species belonging to the Neoserica (sensu lato) septemlamellata group, that included so far only four known species, are revised. Here we describe eleven new species originating mainly from Indochina and Southern China: N. daweishanica sp. n., N. gaoligongshanica sp. n., N. guangpingensis sp. n., N. igori sp. n., N. jiulongensis sp. n., N. plurilamellata sp. n., N. weishanica sp. n., N. yanzigouensis sp. n. (China) N. sapaensis sp. n. (China, Vietnam), N. bansongchana sp. n., N. takakuwai sp. n. (Laos). The lectotypes of Neoserica septemlamellata Brenske, 1898 and N. septemfoliata Moser, 1915 are designated. Keys to the species and species groups are given, the genitalia of all species and their habitus are illustrated and distribution maps are included. PMID:24843263

  8. Taxonomic revision of the species group rubripes of Corinna Koch, 1842 (Araneae; Corinnidae).

    PubMed

    Rodrigues, Bruno V B; Bonaldo, Alexandre B

    2014-01-01

    The species of the group rubripes, which harbors the type species of the genus Corinna C. L. Koch, 1842, are revised, including 20 Neotropical species. Three previously known species are re-diagnosed: Corinna rubripes C. L. Koch, 1842, Corinna nitens (Keyserling, 1891) and Corinna mourai Bonaldo, 2000. New records of Corinna nitens are provided, including the first ones from Peru and Bolivia. Seventeen new species, all from Brazil, were described: C. aechmea n. sp., C. balacobaco n. sp., C. caatinga n. sp., C. demersa n. sp., C. escalvada n. sp., C. hyalina n. sp., C. jecatatu n. sp., C. kuryi n. sp., C. loiolai n. sp., C. maracas n. sp., C. regii n. sp., C. telecoteco n. sp., C. tranquilla n. sp., C. vesperata n. sp., C. vilanovae n. sp., C. zecarioca n. sp. and C. ziriguidum n. sp. A key for all twenty species of the group is presented. PMID:24943629

  9. A taxonomic study of Chinese species of the alberti group of Metaphycus (Hymenoptera, Encyrtidae)

    PubMed Central

    Wang, Ying; Li, Cheng-De; Zhang, Yan-Zhou

    2013-01-01

    Abstract Ten alberti-group species of the genus Metaphycus Mercet from China are reviewed. Six species Metaphycus dorsalis sp. n., Metaphycus chinensis sp. n., Metaphycus wui sp. n., Metaphycus stylatus sp. n., Metaphycus fusiscapus sp. n. and Metaphycus fusiformis sp. n. are described as new to science. Four known species from China are redescribed. A key to the females of the Chinese species is given and photomicrographs are provided to illustrate morphological characters of these species. All specimens unless otherwise specified are deposited in the National Zoological Museum of China Institute of Zoology Chinese Academy of Sciences Beijing. PMID:23798896

  10. 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

  11. 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

  12. Genetic diversity of European phytoplasmas of the 16SrV taxonomic group and proposal of 'Candidatus Phytoplasma rubi'.

    PubMed

    Malembic-Maher, Sylvie; Salar, Pascal; Filippin, Luisa; Carle, Patricia; Angelini, Elisa; Foissac, Xavier

    2011-09-01

    In addition to the grapevine flavescence dorée phytoplasmas, other members of taxonomic group 16SrV phytoplasmas infect grapevines, alders and species of the genera Clematis and Rubus in Europe. In order to investigate which phytoplasmas constitute discrete, species-level taxa, several strains were analysed by comparing their 16S rRNA gene sequences and a set of five housekeeping genes. Whereas 16S rRNA gene sequence similarity values were >97.5 %, the proposed threshold to distinguish two 'Candidatus Phytoplasma' taxa, phylogenetic analysis of the combined sequences of the tuf, rplV-rpsC, rplF-rplR, map and uvrB-degV genetic loci showed that two discrete phylogenetic clusters could be clearly distinguished. The first cluster grouped flavescence dorée (FD) phytoplasmas, alder yellows (AldY) phytoplasmas, Clematis (CL) phytoplasmas and the Palatinate grapevine yellows (PGY) phytoplasmas. The second cluster comprised Rubus stunt (RS) phytoplasmas. In addition to the specificity of the insect vector, the Rubus stunt phytoplasma contained specific sequences in the 16S rRNA gene. Hence, the Rubus stunt phytoplasma 16S rRNA gene was sufficiently differentiated to represent a novel putative taxon: 'Candidatus Phytoplasma rubi'. PMID:20889771

  13. Climatic and Catchment-Scale Predictors of Chinese Stream Insect Richness Differ between Taxonomic Groups

    PubMed Central

    Tonkin, Jonathan D.; Shah, Deep Narayan; Kuemmerlen, Mathias; Li, Fengqing; Cai, Qinghua; Haase, Peter; Jähnig, Sonja C.

    2015-01-01

    Little work has been done on large-scale patterns of stream insect richness in China. We explored the influence of climatic and catchment-scale factors on stream insect (Ephemeroptera, Plecoptera, Trichoptera; EPT) richness across mid-latitude China. We assessed the predictive ability of climatic, catchment land cover and physical structure variables on genus richness of EPT, both individually and combined, in 80 mid-latitude Chinese streams, spanning a 3899-m altitudinal gradient. We performed analyses using boosted regression trees and explored the nature of their influence on richness patterns. The relative importance of climate, land cover, and physical factors on stream insect richness varied considerably between the three orders, and while important for Ephemeroptera and Plecoptera, latitude did not improve model fit for any of the groups. EPT richness was linked with areas comprising high forest cover, elevation and slope, large catchments and low temperatures. Ephemeroptera favoured areas with high forest cover, medium-to-large catchment sizes, high temperature seasonality, and low potential evapotranspiration. Plecoptera richness was linked with low temperature seasonality and annual mean, and high slope, elevation and warm-season rainfall. Finally, Trichoptera favoured high elevation areas, with high forest cover, and low mean annual temperature, seasonality and aridity. Our findings highlight the variable role that catchment land cover, physical properties and climatic influences have on stream insect richness. This is one of the first studies of its kind in Chinese streams, thus we set the scene for more in-depth assessments of stream insect richness across broader spatial scales in China, but stress the importance of improving data availability and consistency through time. PMID:25909190

  14. Climatic and Catchment-Scale Predictors of Chinese Stream Insect Richness Differ between Taxonomic Groups.

    PubMed

    Tonkin, Jonathan D; Shah, Deep Narayan; Kuemmerlen, Mathias; Li, Fengqing; Cai, Qinghua; Haase, Peter; Jähnig, Sonja C

    2015-01-01

    Little work has been done on large-scale patterns of stream insect richness in China. We explored the influence of climatic and catchment-scale factors on stream insect (Ephemeroptera, Plecoptera, Trichoptera; EPT) richness across mid-latitude China. We assessed the predictive ability of climatic, catchment land cover and physical structure variables on genus richness of EPT, both individually and combined, in 80 mid-latitude Chinese streams, spanning a 3899-m altitudinal gradient. We performed analyses using boosted regression trees and explored the nature of their influence on richness patterns. The relative importance of climate, land cover, and physical factors on stream insect richness varied considerably between the three orders, and while important for Ephemeroptera and Plecoptera, latitude did not improve model fit for any of the groups. EPT richness was linked with areas comprising high forest cover, elevation and slope, large catchments and low temperatures. Ephemeroptera favoured areas with high forest cover, medium-to-large catchment sizes, high temperature seasonality, and low potential evapotranspiration. Plecoptera richness was linked with low temperature seasonality and annual mean, and high slope, elevation and warm-season rainfall. Finally, Trichoptera favoured high elevation areas, with high forest cover, and low mean annual temperature, seasonality and aridity. Our findings highlight the variable role that catchment land cover, physical properties and climatic influences have on stream insect richness. This is one of the first studies of its kind in Chinese streams, thus we set the scene for more in-depth assessments of stream insect richness across broader spatial scales in China, but stress the importance of improving data availability and consistency through time. PMID:25909190

  15. THE ABUNDANCE OF BULLET GROUPS IN ΛCDM

    SciTech Connect

    Fernández-Trincado, J. G.; Forero-Romero, J. E.; Foex, G.; Motta, V.; Verdugo, T. E-mail: je.forero@uniandes.edu.co

    2014-06-01

    We estimate the expected distribution of displacements between the two dominant dark matter (DM) peaks (DM-DM displacements) and between the DM and gaseous baryon peak (DM-gas displacements) in DM halos with masses larger than 10{sup 13} h {sup –1} M {sub ☉}. As a benchmark, we use the observation of SL2S J08544–0121, which is the lowest mass system (1.0 × 10{sup 14} h {sup –1} M {sub ☉}) observed so far, featuring a bi-modal DM distribution with a dislocated gas component. We find that (50 ± 10)% of the DM halos with circular velocities in the range 300-700 km s{sup –1} (groups) show DM-DM displacements equal to or larger than 186 ± 30 h {sup –1} kpc as observed in SL2S J08544–0121. For DM halos with circular velocities larger than 700 km s{sup –1} (clusters) this fraction rises to (70 ± 10)%. Using the same simulation, we estimate the DM-gas displacements and find that 0.1%-1.0% of the groups should present separations equal to or larger than 87 ± 14 h {sup –1} kpc, corresponding to our observational benchmark; for clusters, this fraction rises to (7 ± 3)%, consistent with previous studies of DM to baryon separations. Considering both constraints on the DM-DM and DM-gas displacements, we find that the number density of groups similar to SL2S J08544–0121 is ∼6.0 × 10{sup –7} Mpc{sup –3}, three times larger than the estimated value for clusters. These results open up the possibility for a new statistical test of ΛCDM by looking for DM-gas displacements in low mass clusters and groups.

  16. Iron-group Abundances in the Metal-poor Main-Sequence Turnoff Star HD~84937

    NASA Astrophysics Data System (ADS)

    Sneden, Christopher; Cowan, John J.; Kobayashi, Chiaki; Pignatari, Marco; Lawler, James E.; Den Hartog, Elizabeth A.; Wood, Michael P.

    2016-01-01

    We have derived new, very accurate abundances of the Fe-group elements Sc through Zn (Z = 21-30) in the bright main-sequence turnoff star HD 84937 based on high-resolution spectra covering the visible and ultraviolet spectral regions. New or recent laboratory transition data for 14 species of seven elements have been used. Abundances from more than 600 lines of non-Fe species have been combined with about 550 Fe lines in HD 84937 to yield abundance ratios of high precision. The abundances have been determined from both neutral and ionized transitions, which generally are in agreement with each other. We find no substantial departures from the standard LTE Saha ionization balance in this [Fe/H] = -2.32 star. Noteworthy among the abundances are [Co/Fe] = +0.14 and [Cu/Fe] = -0.83, in agreement with past studies of abundance trends in this and other low-metallicity stars, and < [{{Sc,Ti,V/Fe}}]> = +0.31, which has not been noted previously. A detailed examination of scandium, titanium, and vanadium abundances in large-sample spectroscopic surveys reveals that they are positively correlated in stars with [Fe/H] < -2 HD 84937 lies at the high end of this correlation. These trends constrain the synthesis mechanisms of Fe-group elements. We also examine the Galactic chemical evolution abundance trends of the Fe-group elements, including a new nucleosynthesis model with jet-like explosion effects.

  17. The pattern of change in the abundances of specific bacterioplankton groups is consistent across different nutrient-enriched habitats in Crete.

    PubMed

    Fodelianakis, Stilianos; Papageorgiou, Nafsika; Pitta, Paraskevi; Kasapidis, Panagiotis; Karakassis, Ioannis; Ladoukakis, Emmanuel D

    2014-07-01

    A common source of disturbance for coastal aquatic habitats is nutrient enrichment through anthropogenic activities. Although the water column bacterioplankton communities in these environments have been characterized in some cases, changes in α-diversity and/or the abundances of specific taxonomic groups across enriched habitats remain unclear. Here, we investigated the bacterial community changes at three different nutrient-enriched and adjacent undisturbed habitats along the north coast of Crete, Greece: a fish farm, a closed bay within a town with low water renewal rates, and a city port where the level of nutrient enrichment and the trophic status of the habitat were different. Even though changes in α-diversity were different at each site, we observed across the sites a common change pattern accounting for most of the community variation for five of the most abundant bacterial groups: a decrease in the abundance of the Pelagibacteraceae and SAR86 and an increase in the abundance of the Alteromonadaceae, Rhodobacteraceae, and Cryomorphaceae in the impacted sites. The abundances of the groups that increased and decreased in the impacted sites were significantly correlated (positively and negatively, respectively) with the total heterotrophic bacterial counts and the concentrations of dissolved organic carbon and/or dissolved nitrogen and chlorophyll α, indicating that the common change pattern was associated with nutrient enrichment. Our results provide an in situ indication concerning the association of specific bacterioplankton groups with nutrient enrichment. These groups could potentially be used as indicators for nutrient enrichment if the pattern is confirmed over a broader spatial and temporal scale by future studies. PMID:24747897

  18. The Pattern of Change in the Abundances of Specific Bacterioplankton Groups Is Consistent across Different Nutrient-Enriched Habitats in Crete

    PubMed Central

    Fodelianakis, Stilianos; Papageorgiou, Nafsika; Pitta, Paraskevi; Kasapidis, Panagiotis; Karakassis, Ioannis

    2014-01-01

    A common source of disturbance for coastal aquatic habitats is nutrient enrichment through anthropogenic activities. Although the water column bacterioplankton communities in these environments have been characterized in some cases, changes in α-diversity and/or the abundances of specific taxonomic groups across enriched habitats remain unclear. Here, we investigated the bacterial community changes at three different nutrient-enriched and adjacent undisturbed habitats along the north coast of Crete, Greece: a fish farm, a closed bay within a town with low water renewal rates, and a city port where the level of nutrient enrichment and the trophic status of the habitat were different. Even though changes in α-diversity were different at each site, we observed across the sites a common change pattern accounting for most of the community variation for five of the most abundant bacterial groups: a decrease in the abundance of the Pelagibacteraceae and SAR86 and an increase in the abundance of the Alteromonadaceae, Rhodobacteraceae, and Cryomorphaceae in the impacted sites. The abundances of the groups that increased and decreased in the impacted sites were significantly correlated (positively and negatively, respectively) with the total heterotrophic bacterial counts and the concentrations of dissolved organic carbon and/or dissolved nitrogen and chlorophyll α, indicating that the common change pattern was associated with nutrient enrichment. Our results provide an in situ indication concerning the association of specific bacterioplankton groups with nutrient enrichment. These groups could potentially be used as indicators for nutrient enrichment if the pattern is confirmed over a broader spatial and temporal scale by future studies. PMID:24747897

  19. Taxonomic review of catsharks of the Scyliorhinus haeckelii group, with the description of a new species (Chondrichthyes: Carcharhiniformes: Scyliorhinidae).

    PubMed

    Soares, Karla D A; Gomes, Ulisses L; Carvalho, Marcelo R De

    2016-01-01

    Sharks of the genus Scyliorhinus from the southwestern Atlantic are reviewed; identification problems and taxonomic misinformation given in the literature are rectified. After extensive examination of the external and internal morphology of specimens collected mostly off southeastern and southern Brazil, Scyliorhinus besnardi Springer & Sadowsky, 1970 is placed in the synonymy of S. haeckelii (Miranda Ribeiro, 1907), which is thoroughly redescribed. Additionally, a new species, Scyliorhinus cabofriensis, sp. nov., is described from the state of Rio de Janeiro, distinguished from all southwestern Atlantic congeners by its color pattern, clasper and neurocranial morphology, and proportional measurements. A key to Scyliorhinus species occurring in the southwestern Atlantic is also provided. PMID:27395851

  20. CHEMICAL ABUNDANCES OF SEVEN IRREGULAR AND THREE TIDAL DWARF GALAXIES IN THE M81 GROUP

    SciTech Connect

    Croxall, Kevin V.; Van Zee, Liese; Lee, Henry; Miller, Bryan W.; Skillman, Evan D.; Lee, Janice C.; Cote, Stephanie; Kennicutt, Robert C. E-mail: vanzee@astro.indiana.ed E-mail: skillman@astro.umn.ed E-mail: stephanie.cote@nrc-cnrc.gc.c E-mail: bmiller@gemini.ed

    2009-11-01

    We have derived nebular abundances for 10 dwarf galaxies belonging to the M81 Group, including several galaxies which do not have abundances previously reported in the literature. For each galaxy, multiple H II regions were observed with GMOS-N at the Gemini Observatory in order to determine abundances of several elements (oxygen, nitrogen, sulfur, neon, and argon). For seven galaxies, at least one H II region had a detection of the temperature sensitive [O III] lambda4363 line, allowing a 'direct' determination of the oxygen abundance. No abundance gradients were detected in the targeted galaxies, and the observed oxygen abundances are typically in agreement with the well-known metallicity-luminosity relation. However, three candidate 'tidal dwarf' galaxies lie well off this relation: UGC 5336, Garland, and KDG 61. The nature of these systems suggests that UGC 5336 and Garland are indeed recently formed systems, whereas KDG 61 is most likely a dwarf spheroidal galaxy which lies along the same line of sight as the M81 tidal debris field. We propose that these H II regions formed from previously enriched gas which was stripped from nearby massive galaxies (e.g., NGC 3077 and M81) during a recent tidal interaction.

  1. Fe-Group Elements in the Metal-Poor Star HD 84937: Abundances and their Implications

    NASA Astrophysics Data System (ADS)

    Sneden, Chris; Cowan, John J.; Kobayashi, Chiaki; Pignatari, Marco; Lawler, James E.; Den Hartog, Elizabeth; Wood, Michael P.

    2016-01-01

    We have derived accurate relative abundances of the Fe-group elements Sc through Zn in the very metal-poor main-sequence turnoff star HD 84937. For this study we analyzed high resolution, high signal-to-noise HST/STIS and VLT/UVES spectra over a total wavelength range 2300-7000 Å. We employed only recent or newly-applied reliable laboratory transition data for all species. Abundances from more than 600 lines of non-Fe species were combined with about 550 Fe lines in HD 84937 to yield abundance ratios of high precision. From parallel analyses of solar photospheric spectra we also derived new solar abundances of these elements. This in turn yielded internally-consistent relative HD 84937 abundances with respect to the Sun. For seven of the ten Fe-group elements the HD 84937 abundances were from both neutral and ionized transitions. In all of these cases the neutral and ionized species yield the same abundances within the measurement uncertainties. Therefore standard Saha ionization balance appears to hold in the HD 84937 atmosphere. We derived metallicity [Fe/H] = -2.32 with sample standard deviation of 0.06. Solid evidence is seen for departures from the solar abundance mix in HD 84937, for example [Co/Fe] = +0.14, [Cu/Fe] = -0.83, and <[Sc,Ti,V/Fe]> = +0.31. Combining our Sc, Ti, and V abundances for this star with those from large-sample spectroscopic surveys suggests that these elements are positively correlated in stars with [Fe/H] < -2. HD 84937 is unusually enriched in Sc, Ti, and V. Our analysis strongly suggests that different types of supernovae with a large scatter of explosion energies and asymmetries contributed to the creation of the Fe-group elements early in the Galaxy's history.This work has been supported in part by NASA grant NNX10AN93G (J.E.L.), by NSF grants AST-1211055 (J.E.L.), AST-1211585 (C.S.), PHY-1430152 (through JINA, J.J.C. and M.P.), EU MIRGCT-2006-046520 (M.P.), and by the ``Lendlet-2014'' Programme of the Hungarian Academy of

  2. Surface composition and taxonomic classification of a group of near-Earth and Mars-crossing asteroids

    NASA Astrophysics Data System (ADS)

    Sanchez, Juan A.; Michelsen, René; Reddy, Vishnu; Nathues, Andreas

    2013-07-01

    In the past, constraining the surface composition of near-Earth asteroids (NEAs) has been difficult due to the lack of high quality near-IR spectral data (0.7-2.5 μm) that contain mineralogically diagnostic absorption bands. Here we present visible (˜0.43-0.95 μm) and near-infrared (˜0.7-2.5 μm) spectra of nine NEAs and five Mars-crossing asteroids (MCs). The studied NEAs are: 4055 Magellan, 19764 (2000 NF5), 89830 (2002 CE), 138404 (2000 HA24), 143381 (2003 BC21), 159609 (2002 AQ3), 164121 (2003 YT1), 241662 (2000 KO44) and 2007 ML13. The studied MCs are: 1656 Suomi, 2577 Litva, 5407 (1992 AX), 22449 Ottijeff and 47035 (1998 WS). The observations were conducted with the NTT at La Silla, Chile, the 2.2 m telescope at Calar Alto, Spain, and the IRTF on Mauna Kea, Hawai'i. The taxonomic classification (Bus system) of asteroids showed that all observed MC asteroids belong to the S-complex, including the S, Sr and Sl classes. Seven of the NEAs belong to the S-complex, including the S, Sa, Sk and Sl classes, and two NEAs were classified as V-types. The classification of the NEA 164121 (2003 YT1) as a V-type was made on the basis of its near-infrared spectrum since no visible spectrum is available for this asteroid. A mineralogical analysis was performed on six of the asteroids (those for which near-IR spectra were obtained or previously available). We found that three asteroids (241662 (2000 KO44), 19764 (2000 NF5), 138404 (2000 HA24)) have mafic silicate compositions consistent with ordinary chondrites, while three others (4055 Magellan, 164121 (2003 YT1), 5407 (1992 AX)) are pyroxene-dominated basaltic achondrite assemblages. In the case of 5407 (1992 AX) we found that its basaltic surface composition contrasts its taxonomic classification as a S-type.

  3. Population Signatures in Planetary Nebulae from Abundances of Fe-group and Neutron-Capture Elements

    NASA Astrophysics Data System (ADS)

    Dinerstein, Harriet L.; Geballe, Thomas R.; Sterling, N. C.

    2015-08-01

    There are two categories of elements for which abundances are measured in planetary nebulae (PNe). The first are species whose abundances may be modified by nuclear reactions in the star prior to PN formation, such as He, C, N, and nuclei made by slow neutron captures (Karakas & Lattanzio 2014, PASA, 31, 30). In contrast, elements unaffected by evolution should indicate the star’s initial composition. These include S, Ar, Cl, and (with certain exceptions) O and Ne, most of which are alpha species. A long-missing piece of the puzzle has been the abundances of the Fe-group elements. We cannot determine a meaningful elemental abundance from the gas-phase Fe lines seen in PNe, since Fe is heavily depleted into dust. Another approach is to use a different element as a proxy for Fe. Dinerstein & Geballe (2001, ApJ, 562, 515) identified a line at 3.625 μm as due to Zn, the least refractory Fe-group element. Observations of this line in Milky Way PNe yield -1 ≤ [Zn/H] ≤ 0 (Smith, Zijlstra, & Dinerstein 2014, MNRAS, 441, 3161; Dinerstein et al. 2015, in preparation). Substituting Zn for Fe, PNe can be placed in the [alpha/Fe] vs. [Fe/H] diagram used to characterize stellar populations. Dividing our sample into probable thin and thick disk members using the kinematic criterion of Peimbert’s Type II and III classes (1978, IAU Symp. 76, 215), we find that they occupy similar regions in [alpha/Fe] vs. [Fe/H] phase space as the stars of those populations. Elevated [alpha/Fe] values at subsolar [Fe/H], which tend to be higher for thick than thin disk PNe, cause degeneracies that make alpha species ambiguous metallicity indicators. This is important for self-enrichment studies, since if the initial abundance of an element is lower than projected from an alpha species, internal synthesis may be required to produce even a solar final abundance. Low observed abundances of the n-capture element Se suggest that many Type III PNe may have subsolar initial abundances of n

  4. Comparison of the peptidome and insecticidal activity of venom from a taxonomically diverse group of theraphosid spiders.

    PubMed

    Gentz, Margaret C; Jones, Alun; Clement, Herlinda; King, Glenn F

    2009-04-01

    We screened a panel of theraphosid venoms in two orders of insect in order to determine whether these bioassays would help in the selection of candidate venoms for future discovery of insecticidal toxins. Venoms from six different theraphosid genera were compared with venom from the Australian funnel-web spider Hadronyche infensa (Hexathelidae). The tarantulas included were Coremiocnemis tropix, Selenocosmia crossipes, and Selenotholus foelschei from Australia and Brachypelma albiceps and Brachypelma hamorii from Mexico. The insects assayed, Tenebrio molitor (Coleoptera: Tenebrionidae) and Acheta domesticus (Orthoptera: Gryllidae), were selected because of their relevance as model holometabolous and hemimetabolous insects, respectively, as well as their taxonomic relationship to economically important pest insects. Despite significant differences in their peptide/protein profiles as determined using SDS-PAGE, HPLC, and mass spectrometry, all of the theraphosid venoms exhibited remarkably similar LD50 values of 46-126 microg/g for crickets and 0.5-4.0 microg/g for mealworms. Notably, mealworms were on average 50-fold more susceptible than crickets to each of the crude theraphosid venoms and consequently they provide an excellent bioassay system when venom supply is limited. This study indicates that even closely related spiders have evolved quite different toxin repertoires that nevertheless have comparable efficiency with respect to killing their primary prey, namely insects. PMID:19673095

  5. Taxonomic review of the major larval pests of bolete fungi (Boletaceae) in Europe: The Pegomya fulgens, furva and tabida species groups (Diptera: Anthomyiidae).

    PubMed

    Michelsen, Verner

    2015-01-01

    A taxonomic review of the European species of the Pegomya fulgens, furva and tabida species groups is given with emphasis on characters of importance for the identification of males and females. These Pegomya species groups are represented in Europe by two, two and nine species, respectively. Their mycophagous larvae may all feed exclusively on bolete sporocarps of Leccinum and Boletus aff. edulis. Their relationships and biology are summarized. Each species is given a selective list of references and synonymy, richly illustrated descriptions of males and females, a list or summary of the examined material, and a synopsis of the known distribution and biology. Pegomya ringdahli sp. nov., previously confused with P. scapularis (Zetterstedt, 1846), is described from Fennoscandia. Lectotypes are designated for Anthomyia fulgens Meigen, 1826 and Pegomyia (Pegomyia) furva Ringdahl, 1938. An identification key is given to all 17 species (males and females) of Pegomya that supposedly feed as larvae on sporocarps of Boletaceae and Suillaceae in Europe. PMID:26624089

  6. Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments

    PubMed Central

    Kubo, Kyoko; Lloyd, Karen G; F Biddle, Jennifer; Amann, Rudolf; Teske, Andreas; Knittel, Katrin

    2012-01-01

    Members of the highly diverse Miscellaneous Crenarchaeotal Group (MCG) are globally distributed in various marine and continental habitats. In this study, we applied a polyphasic approach (rRNA slot blot hybridization, quantitative PCR (qPCR) and catalyzed reporter deposition FISH) using newly developed probes and primers for the in situ detection and quantification of MCG crenarchaeota in diverse types of marine sediments and microbial mats. In general, abundance of MCG (cocci, 0.4 μm) relative to other archaea was highest (12–100%) in anoxic, low-energy environments characterized by deeper sulfate depletion and lower microbial respiration rates (P=0.06 for slot blot and P=0.05 for qPCR). When studied in high depth resolution in the White Oak River estuary and Hydrate Ridge methane seeps, changes in MCG abundance relative to total archaea and MCG phylogenetic composition did not correlate with changes in sulfate reduction or methane oxidation with depth. In addition, MCG abundance did not vary significantly (P>0.1) between seep sites (with high rates of methanotrophy) and non-seep sites (with low rates of methanotrophy). This suggests that MCG are likely not methanotrophs. MCG crenarchaeota are highly diverse and contain 17 subgroups, with a range of intragroup similarity of 82 to 94%. This high diversity and widespread distribution in subsurface sediments indicates that this group is globally important in sedimentary processes. PMID:22551871

  7. Galaxy interactions in compact groups - II. Abundance and kinematic anomalies in HCG 91c

    NASA Astrophysics Data System (ADS)

    Vogt, Frédéric P. A.; Dopita, Michael A.; Borthakur, Sanchayeeta; Verdes-Montenegro, Lourdes; Heckman, Timothy M.; Yun, Min S.; Chambers, Kenneth C.

    2015-07-01

    Galaxies in Hickson Compact Group 91 (HCG 91) were observed with the WiFeS integral field spectrograph as part of our ongoing campaign targeting the ionized gas physics and kinematics inside star-forming members of compact groups. Here, we report the discovery of H II regions with abundance and kinematic offsets in the otherwise unremarkable star-forming spiral HCG 91c. The optical emission line analysis of this galaxy reveals that at least three H II regions harbour an oxygen abundance ˜0.15 dex lower than expected from their immediate surroundings and from the abundance gradient present in the inner regions of HCG 91c. The same star-forming regions are also associated with a small kinematic offset in the form of a lag of 5-10 km s-1 with respect to the local circular rotation of the gas. H I observations of HCG 91 from the Very Large Array and broad-band optical images from Pan-STARRS (Panoramic Survey Telescope And Rapid Response System) suggest that HCG 91c is caught early in its interaction with the other members of HCG 91. We discuss different scenarios to explain the origin of the peculiar star-forming regions detected with WiFeS, and show that evidence points towards infalling and collapsing extraplanar gas clouds at the disc-halo interface, possibly as a consequence of long-range gravitational perturbations of HCG 91c from the other group members. As such, HCG 91c provides evidence that some of the perturbations possibly associated with the early phase of galaxy evolution in compact groups impact the star-forming disc locally, and on sub-kpc scales.

  8. ‘Live’ (stained) deep-sea benthic foraminiferans in the western Weddell Sea: trends in abundance, diversity and taxonomic composition along a depth transect

    NASA Astrophysics Data System (ADS)

    Cornelius, Nils; Gooday, Andrew J.

    2004-07-01

    'Entire' live foraminiferal assemblages (i.e. including soft-walled species) were analysed using replicate subcores (3.45 cm 2 surface area, 0-1 cm layer; >63 μm fraction) from multiple corer samples collected along a transect (1100-5000 m water depth) of the continental slope and rise and adjacent abyssal plain to the east of the Antarctic Peninsula. Foraminiferans usually accounted for 61-83% of all meiofaunal organisms. Mean densities were highest (576 individuals (indiv.)10 cm -2) at 2100 m water depth and declined to 240 indiv. 10 cm -2 at 5000 m, although there was considerable variability between replicates at some stations (e.g., 304, 333, 1090 indiv. 10 cm -2 at 2100 m). Foraminiferan and metazoan meiofaunal densities were broadly coherent across the depth range sampled. A total of 158 live foraminiferal species was recognized. Assemblages were most diverse on the lower slope, with species numbers peaking at 3100 m and the Fisher α diversity index at 3100-4100 m. Monothalamous taxa increased in relative abundance from 8% at 1100 m to 33% at 4975 m, and there was a corresponding decrease in the proportion of calcareous taxa from 65% to 16%. On the continental slope (1100-3100 m), the most abundant hard-walled species were Epistominella exigua, Adercotryma glomeratum, Alabaminella weddellensis and Stetsonia hovarthi. In the deeper samples (4100-5000 m), A. glomeratum became the dominant hard-walled species. Important soft-walled species included Tinogullmia riemanni and Bathyallogromia weddellensis. In some samples from 1100 and 2100 m, more than a third of the live assemblage was hidden within phytodetrital aggregates; species such as E. exigua, A. weddellensis and T. riemanni were concentrated within these microhabitats. Many of the Weddell Sea species are typical bathyal and abyssal forms well known from the North Atlantic and elsewhere. The phytodetrital assemblages are strikingly similar to those reported from abyssal sites in the North Atlantic. Our

  9. Redescriptions of the Oxyethira aeola Group species in North America (Trichoptera:Hydroptilidae): Clarification of a taxonomic enigma

    USGS Publications Warehouse

    Moulton, S.R., II; Harris, S.C.

    1999-01-01

    The Oxyethira aeola Group at present contains 8 species distributed among Nearctic, Palaearctic, and Neotropical regions. The 4 North American species of this group, O. abacatia Denning, O. aeola Ross, O. anabola Blickle, and O. mirabills Morton, are similar and difficult to identify. The males of each of the 4 species are redescribed, illustrated, and keyed to clarify the confusing taxonomy.

  10. Taxonomic revision of the genus Callimerus Gorham s. l. (Coleoptera, Cleridae). Part I. latifrons species-group

    PubMed Central

    Yang, Gan-Yan; Montreuil, Olivier; Yang, Xing-Ke

    2013-01-01

    Abstract The latifrons species-group (=Brachycallimerus sensu Chapin 1924, Corporaal 1950; = flavofasciatus-group sensu Kolibáč 1998) of Callimerus Gorham is redefined and revised. Five species are recognized including one new species Callimerus cacuminis Yang & Yang sp. n. (type locality: Yunnan, China). Callimerus flavofasciatus Schenkling, 1902 is newly synonymized with Callimerus latifrons Gorham, 1876. Callimerus trifasciatus Schenkling, 1899a is transferred to the genus Corynommadius Schenkling, 1899a. Callimerus gorhami Corporaal, 1949 and Callimerus pallidus Gorham, 1892 are excluded from the latifrons species-group (their assignment to a species-group will be dealt with in a subsequent paper). A key to species of the latifrons species-group is given and habitus of each type specimen, male terminalia, and other diagnostic characters are illustrated. PMID:23794870

  11. Expanded haloes, abundance matching and too-big-to-fail in the Local Group

    NASA Astrophysics Data System (ADS)

    Brook, Chris B.; Di Cintio, Arianna

    2015-07-01

    Observed kinematical data of 40 Local Group (LG) members are used to derive the dark matter halo mass of such galaxies. Haloes are selected from the theoretically expected LG mass function and two different density profiles are assumed, a standard universal cuspy model and a mass-dependent profile which accounts for the effects of baryons in modifying the dark matter distribution within galaxies. The resulting relations between stellar and halo mass are compared with expectations from abundance matching. Using a universal cuspy profile, the ensemble of LG galaxies is fit in relatively low-mass haloes, leaving `dark' many massive haloes of Mhalo ≳ 1010 M⊙: this reflects the `too-big-to-fail' problem and results in a Mstar-Mhalo relation that differs from abundance matching predictions. Moreover, the star formation efficiency of isolated LG galaxies increases with decreasing halo mass when adopting a cuspy model. By contrast, using the mass-dependent density profile, dwarf galaxies with Mstar ≳ 106 M⊙ are assigned to more massive haloes, which have a central cored distribution of dark matter: the `too-big-to-fail' problem is alleviated, the resultant Mstar-Mhalo relation follows abundance matching predictions down to the completeness limit of current surveys, and the star formation efficiency of isolated members decreases with decreasing halo mass, in agreement with theoretical expectations. Finally, the cusp/core space of LG galaxies is presented, providing a framework to understand the non-universality of their density profiles.

  12. Life strategies of a ubiquitous and abundant subsurface archaeal group Bathyarchaeota

    NASA Astrophysics Data System (ADS)

    He, Y.; Li, M.; Perumal, V.; Feng, X.; Sievert, S. M.; Wang, F.

    2015-12-01

    Archaea belonging to the Miscellaneous Crenarchaeota Group (MCG, "Candidatus Bathyarchaeota") are widespread and abundant in the deep biosphere, yet their life strategies and ecological roles remain elusive. Metagenomic sequencing of a sample enriched in Bathyarchaeota (up to 74%) that originated from Guaymas Basin deep-sea vent sediments revealed 6 partial to nearly completed Bathyarchaeota genomic bins. ranging ~900kb-3.3Mb. The Bathyarchaeota bin size ranged from approximately 0.9 to 3.3 Mb, with coverage ranging from approximately 10× to 28×. The phylogeny based on 110 concatenated conserved archaeal single copy genes confirmed the placement of Bathyarchaeota into a novel archaeal phylum. Genes encoding for enzymes involved in the degradation of organic polymers such as protein, cellulose, chitin, and aromatic compounds, were identified. In addition, genes encoding glycolysis/gluconeogenesis, beta-oxidation pathways and the tricarboxylic acid cycle (except citrate synthase) were present in all genomic bins highlighting the heterotrophic life style of Bathyarchaeota. The presence of a wide variety of transporters of organic compounds further supports the versatile heterotrophic metabolism of Bathyarchaeota. This study highlights the life strategies of a ubiquitous and abundant subsurface archaeal group that thrives under energy-limited conditions, and expands the metabolic potentials of Archaea that play important roles in carbon cycling in marine sediments.

  13. Density and abundance of badger social groups in England and Wales in 2011-2013

    NASA Astrophysics Data System (ADS)

    Judge, Johanna; Wilson, Gavin J.; MacArthur, Roy; Delahay, Richard J.; McDonald, Robbie A.

    2014-01-01

    In the United Kingdom, European badgers Meles meles are a protected species and an important wildlife reservoir of bovine tuberculosis. We conducted a survey of badger dens (main setts) in 1614 1 km squares across England and Wales, between November 2011 and March 2013. Using main setts as a proxy for badger social groups, the estimated mean density of badger social groups in England and Wales was 0.485 km-2 (95% confidence interval 0.449-0.521) and the estimated abundance of social groups was 71,600 (66,400-76,900). In the 25 years since the first survey in 1985-88, the annual rate of increase in the estimated number of badger social groups was 2.6% (2.2-2.9%), equating to an 88% (70-105%) increase across England and Wales. In England, we estimate there has been an increase of 103% (83-123%) in badger social groups, while in Wales there has been little change (-25 to +49%).

  14. The Tetramorium tortuosum species group (Hymenoptera, Formicidae, Myrmicinae) revisited - taxonomic revision of the Afrotropical T. capillosum species complex

    PubMed Central

    Garcia, Francisco Hita; Fisher, Brian L.

    2013-01-01

    Abstract In this study we revise the taxonomy of the Tetramorium tortuosum species group members encountered in the Afrotropical region, which we have placed in its own subgroup: the Tetramorium capillosum species complex. We re-describe the two previously known species Tetramorium capillosum Bolton and Tetramorium tabarum Bolton, and describe the new species Tetramorium hecate sp. n. The geographic distribution of the three species appears to be restricted to the equatorial rainforests of Central Africa. We provide a diagnosis of the Tetramorium capillosum species complex, an illustrated identification key to species level, and worker-based species descriptions, which include diagnoses, discussions, high-quality montage images, and distribution maps. Furthermore, we discuss biogeography and composition of the globally distributed Tetramorium tortuosum group. PMID:23794889

  15. Taxonomic revision of the Carpathian endemic Pedicia (Crunobia) staryi species–group (Diptera, Pediciidae) based on morphology and molecular data

    PubMed Central

    Dénes, Avar-Lehel; Kolcsár, Levente-Péter; Török, Edina; Keresztes, Lujza

    2016-01-01

    Abstract Three new species of the genus Pedicia, subgenus Crunobia (Diptera: Pediciidae) belonging to the staryi group are described on the basis of a combination of molecular and morphology datasets, and a key to discriminate between species of the subgenus Crunobia is added. Geographic projection of the identified taxa suggests insular-like distribution and shows the importance of the Carpathians as a genetic center which is home to an exceptionally high aquatic diversity in Europe. PMID:27110152

  16. Testing surrogacy assumptions: can threatened and endangered plants be grouped by biological similarity and abundances?

    PubMed

    Che-Castaldo, Judy P; Neel, Maile C

    2012-01-01

    There is renewed interest in implementing surrogate species approaches in conservation planning due to the large number of species in need of management but limited resources and data. One type of surrogate approach involves selection of one or a few species to represent a larger group of species requiring similar management actions, so that protection and persistence of the selected species would result in conservation of the group of species. However, among the criticisms of surrogate approaches is the need to test underlying assumptions, which remain rarely examined. In this study, we tested one of the fundamental assumptions underlying use of surrogate species in recovery planning: that there exist groups of threatened and endangered species that are sufficiently similar to warrant similar management or recovery criteria. Using a comprehensive database of all plant species listed under the U.S. Endangered Species Act and tree-based random forest analysis, we found no evidence of species groups based on a set of distributional and biological traits or by abundances and patterns of decline. Our results suggested that application of surrogate approaches for endangered species recovery would be unjustified. Thus, conservation planning focused on individual species and their patterns of decline will likely be required to recover listed species. PMID:23240051

  17. Species discrimination in the subfamily Ostertagiinae of Northern China: assessment of DNA barcode in a taxonomically challenging group.

    PubMed

    Lv, Jizhou; Zhang, Yongning; Feng, Chunyan; Yuan, Xiangfen; Sun, Degang; Deng, Junhua; Wang, Caixia; Wu, Shaoqiang; Lin, Xiangmei

    2016-03-01

    Gastrointestinal nematodes within the subfamily Ostertagiinae (Teladorsagia, Ostertagia, and Marshallagia et al.) are among the most common infections of domesticated livestock. These parasites are of particular interest, as many of the species within this group are of economic importance worldwide. Traditionally, nematode species designations have been based on morphological criteria. However, this group possesses poorly defined species. There is an urgent need to develop a reliable technique that can distinguish species of Ostertagiinae. DNA barcoding has been proved to be a powerful tool to identify species of birds, mammals, and arthropods, but this technique has not yet been examined for identifying species of Ostertagiinae. In this study, a total of 138 mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) sequences from individuals representing 11 species of Ostertagiinae were acquired by PCR for the first time. The specimens were collected from pastoral area of northern China. Genetic divergence analyses showed that mean interspecific Kimura two-parameter distances of COI (13.61 %) were about four times higher than the mean value of the intraspecific divergence (3.69 %). Then, the performance of the COI to identify species of Ostertagiinae was evaluated by identification success rates using nearest neighbor (NN) and BLASTn. The results indicated that the rates of correct sequence identification for COI were high (>80 %) when using the NN and BLASTn methods. Besides, the deep lineage divergences are detected in Teladorsagia circumcincta. Meanwhile, the analyses also detected no genetic differentiation between some species such as Ostertagia hahurica and Ostertagia buriatica. These results indicate that the traditional status of species within Ostertagiinae should be closely examined based on the molecular data. PMID:26584827

  18. Taxonomic and strain-specific identification of the probiotic strain Lactobacillus rhamnosus 35 within the Lactobacillus casei group.

    PubMed

    Coudeyras, Sophie; Marchandin, Hélène; Fajon, Céline; Forestier, Christiane

    2008-05-01

    Lactobacilli are lactic acid bacteria that are widespread in the environment, including the human diet and gastrointestinal tract. Some Lactobacillus strains are regarded as probiotics because they exhibit beneficial health effects on their host. In this study, the long-used probiotic strain Lactobacillus rhamnosus 35 was characterized at a molecular level and compared with seven reference strains from the Lactobacillus casei group. Analysis of rrn operon sequences confirmed that L. rhamnosus 35 indeed belongs to the L. rhamnosus species, and both temporal temperature gradient gel electrophoresis and ribotyping showed that it is closer to the probiotic strain L. rhamnosus ATCC 53103 (also known as L. rhamnosus GG) than to the species type strain. In addition, L. casei ATCC 334 gathered in a coherent cluster with L. paracasei type strains, unlike L. casei ATCC 393, which was closer to L. zeae; this is evidence of the lack of relatedness between the two L. casei strains. Further characterization of the eight strains by pulsed-field gel electrophoresis repetitive DNA element-based PCR identified distinct patterns for each strain, whereas two isolates of L. rhamnosus 35 sampled 40 years apart could not be distinguished. By subtractive hybridization using the L. rhamnosus GG genome as a driver, we were able to isolate five L. rhamnosus 35-specific sequences, including two phage-related ones. The primer pairs designed to amplify these five regions allowed us to develop rapid and highly specific PCR-based identification methods for the probiotic strain L. rhamnosus 35. PMID:18326671

  19. Differential Abundance of Microbial Functional Groups along the Elevation Gradient from the Coast to the Luquillo Mountains

    EPA Science Inventory

    Microbial communities respond to multiple abiotic and biotic factors that change along elevation gradients. We compare changes in microbial community composition in soil and review previous research on differential abundance of microbial functional groups along an elevation gradi...

  20. DNA polymerase gene sequences indicate western and forest tent caterpillar viruses form a new taxonomic group within baculoviruses.

    PubMed

    Nielsen, Cydney B; Cooper, Dawn; Short, Steven M; Myers, Judith H; Suttle, Curtis A

    2002-11-01

    Baculoviruses infect larval lepidopterans, and thus have potential value as microbial controls of agricultural and forest pests. Understanding their genetic relatedness and host specificity is relevant to the risk assessment of viral insecticides if non-target impacts are to be avoided. DNA polymerase gene sequences have been demonstrated to be useful for inferring genetic relatedness among dsDNA viruses. We have adopted this approach to examine the relatedness among natural isolates of two uncharacterized caterpillar-infecting baculoviruses, Malacosoma californicum pluviale nucleopolyhedrovirus (McplMNPV) and Malacosoma disstria nucleopolyhedrovirus (MadiMNPV), which infect two closely related host species with little to no cross-infectivity. We designed two degenerate primers (BVP1 and BVP2) based on protein motifs conserved among baculoviruses. McplMNPV and MadiMNPV viral DNA was obtained from naturally infected caterpillars collected from geographically distinct sites in the Southern Gulf Islands and Prince George regions of British Columbia, Canada. Sequencing of 0.9 kb PCR amplicons from six McplMNPV and six MadiMNPV isolates obtained from a total of eight sites, revealed very low nucleotide variation among McplMNPV isolates (99.2-100% nucleotide identity) and among MadiMNPV isolates (98.9-100% nucleotide identity). Greater nucleotide variation was observed between viral isolates from the two different caterpillar species (only 84.7-86.1% nucleotide identity). Both maximum parsimony and maximum likelihood phylogenetic analyses support placement of McplMNPV and MadiMNPV in a clade that is distinct from other groups of baculoviruses. PMID:12507483

  1. The abundance and organization of polypeptides associated with antigens of the Rh blood group system.

    PubMed

    Gardner, B; Anstee, D J; Mawby, W J; Tanner, M J; von dem Borne, A E

    1991-06-01

    Twelve murine monoclonal antibodies, which react with human red cells of common Rh phenotype but give weak or negative reactions with Rh null erythrocytes, were used in quantitative binding assays and competitive binding assays to investigate the abundance and organization of polypeptides involved in the expression of antigens of the Rh blood group system. Antibodies of the R6A-type (R6A, BRIC-69, BRIC-207) and the 2D10-type (MB-2D10, LA18.18, LA23.40) recognize related structures and 100,000-200,000 molecules of each antibody bind maximally to erythrocytes of common Rh phenotype. Antibodies of the BRIC-125 type (BRICs 32, 122, 125, 126, 168, 211) recognize structures that are unrelated to those recognized by R6A-type and 2D10-type antibodies and between 10,000 and 50,000 antibody molecules bind maximally to erythrocytes of the common Rh phenotype. The binding of antibodies of the R6A-type and the 2D10-type, but not of antibodies of the BRIC-125-type could be partially inhibited by human anti-D antibodies (polyclonal and monoclonal) and a murine anti-e-like antibody. These results are consistent with evidence (Moore & Green 1987; Avent et al., 1988b) that the Rh blood group antigens are associated with a complex that comprises two groups of related polypeptides of M(r) 30,000 and M(r) 35,000-100,000, respectively, and suggest that there are 1-2 x 10(5) copies of this complex per erythrocyte. The polypeptide recognized by antibodies of the BRIC-125 type is likely to be associated with this complex. PMID:9259831

  2. A volume-limited sample of X-ray galaxy groups and clusters - III. Central abundance drops

    NASA Astrophysics Data System (ADS)

    Panagoulia, E. K.; Sanders, J. S.; Fabian, A. C.

    2015-02-01

    We present the results of a search and study of central abundance drops in a volume-limited sample (z ≤ 0.071) of 101 X-ray galaxy groups and clusters. These are best observed in nearby, and so best resolved, groups and clusters, making our sample ideal for their detection. Out of the 65 groups and clusters in our sample for which we have abundance profiles, 8 of them have certain central abundance drops, with possible central abundance drops in another 6. All sources with central abundance drops have X-ray cavities, and all bar one exception have a central cooling time of ≤1 Gyr. These central abundance drops can be generated if the iron injected by stellar mass-loss processes in the core of these sources is in grains, which then become incorporated in the central dusty filaments. These, in turn, are dragged outwards by the bubbling feedback process in these sources. We find that data quality significantly affects the detection of central abundance drops, inasmuch as a higher number of counts in the central 20 kpc of a source makes it easier to detect a central abundance drop, as long as these counts are more than ˜13 000. On the other hand, the magnitude of the central abundance drop does not depend on the number of these counts, though the statistical significance of the measured drop does. Finally, in line with the scenario briefly outlined above, we find that, for most sources, the location of X-ray cavities acts as an upper limit to the location of the peak in the radial metallicity distribution.

  3. The integripennis species group of Geocharidius Jeannel, 1963 (Carabidae, Bembidiini, Anillina) from Nuclear Central America: a taxonomic review with notes about biogeography and speciation.

    PubMed

    Sokolov, Igor M; Kavanaugh, David H

    2014-01-01

    Our review recognizes 15 species of the integripennis species group of Geocharidius from Nuclear Central America, include three species previously described (Geocharidiusgimlii Erwin, Geocharidiusintegripennis (Bates) and Geocharidiuszullinii Vigna Taglianti) and 12 described here as new. They are: Geocharidiusandersoni sp. n. (type locality: Chiapas, Chiapas Highlands, Cerro Huitepec) and Geocharidiusvignatagliantii sp. n. (type locality: Chiapas, Motozintla, Sierra Madre de Chiapas, Benito Juárez) from Mexico; Geocharidiusantigua sp. n. (type locality: Sacatepéquez, 5 km SE of Antigua), Geocharidiusbalini sp. n. (type locality: Suchitepéquez, 4 km S of Volcan Atitlán), Geocharidiuserwini sp. n. (type locality: Quiché Department, 7 km NE of Los Encuentros), Geocharidiusjalapensis sp. n. (type locality: Jalapa Department, 4 km E of Mataquescuintla), Geocharidiuslonginoi, sp. n. (type locality: El Progreso Department, Cerro Pinalón), and Geocharidiusminimus sp. n. (type locality: Sacatepéquez Department, 5 km SE of Antigua) from Guatemala; and Geocharidiuscelaquensis sp. n. (type locality: Lempira Department, Celaque National Park), Geocharidiuscomayaguanus sp. n. (type locality: Comayagua Department, 18 km ENE of Comayagua), Geocharidiusdisjunctus sp. n. (type locality: Francisco Morazán, La Tigra National Park), and Geocharidiuslencanus sp. n. (type locality: Lempira Department, Celaque National Park) from Honduras. For all members of the group, adult structural characters, including male and female genitalia, are described, and a taxonomic key for all members of the integripennis species group is presented based on these characters. Behavioral and biogeographical aspects of speciation in the group are discussed, based on the morphological analysis. In all cases of sympatry, pairs of closely related species show greater differences in sizes than pairs of more remotely related species. Integripennis group species occupy six different montane areas at

  4. The integripennis species group of Geocharidius Jeannel, 1963 (Carabidae, Bembidiini, Anillina) from Nuclear Central America: a taxonomic review with notes about biogeography and speciation

    PubMed Central

    Sokolov, Igor M.; Kavanaugh, David H.

    2014-01-01

    Abstract Our review recognizes 15 species of the integripennis species group of Geocharidius from Nuclear Central America, include three species previously described (Geocharidius gimlii Erwin, Geocharidius integripennis (Bates) and Geocharidius zullinii Vigna Taglianti) and 12 described here as new. They are: Geocharidius andersoni sp. n. (type locality: Chiapas, Chiapas Highlands, Cerro Huitepec) and Geocharidius vignatagliantii sp. n. (type locality: Chiapas, Motozintla, Sierra Madre de Chiapas, Benito Juárez) from Mexico; Geocharidius antigua sp. n. (type locality: Sacatepéquez, 5 km SE of Antigua), Geocharidius balini sp. n. (type locality: Suchitepéquez, 4 km S of Volcan Atitlán), Geocharidius erwini sp. n. (type locality: Quiché Department, 7 km NE of Los Encuentros), Geocharidius jalapensis sp. n. (type locality: Jalapa Department, 4 km E of Mataquescuintla), Geocharidius longinoi, sp. n. (type locality: El Progreso Department, Cerro Pinalón), and Geocharidius minimus sp. n. (type locality: Sacatepéquez Department, 5 km SE of Antigua) from Guatemala; and Geocharidius celaquensis sp. n. (type locality: Lempira Department, Celaque National Park), Geocharidius comayaguanus sp. n. (type locality: Comayagua Department, 18 km ENE of Comayagua), Geocharidius disjunctus sp. n. (type locality: Francisco Morazán, La Tigra National Park), and Geocharidius lencanus sp. n. (type locality: Lempira Department, Celaque National Park) from Honduras. For all members of the group, adult structural characters, including male and female genitalia, are described, and a taxonomic key for all members of the integripennis species group is presented based on these characters. Behavioral and biogeographical aspects of speciation in the group are discussed, based on the morphological analysis. In all cases of sympatry, pairs of closely related species show greater differences in sizes than pairs of more remotely related species. Integripennis group species occupy six different

  5. DISTINCTIVE LOCALIZATION OF GROUP 3 LATE EMBRYOGENESIS ABUNDANT SYNTHESIZING CELLS DURING BRINE SHRIMP DEVELOPMENT.

    PubMed

    Kim, Bo Yong; Song, Hwa Young; Kim, Mi Young; Lee, Bong Hee; Kim, Kyung Joo; Jo, Kyung Jin; Kim, Suhng Wook; Lee, Seung Gwan; Lee, Boo Hyung

    2015-07-01

    Despite numerous studies on late embryogenesis abundant (LEA) proteins, their functions, roles, and localizations during developmental stages in arthropods remain unknown. LEA proteins protect crucial proteins against osmotic stress during the development and growth of various organisms. Thus, in this study, fluorescence in situ hybridization was used to determine the crucial regions protected against osmotic stress as well as the distinctive localization of group 3 (G3) LEA(+) cells during brine shrimp development. Several cell types were found to synthesize G3 LEA RNA, including neurons, muscular cells, APH-1(+) cells, and renal cells. The G3 LEA(+) neuronal cell bodies outside of the mushroom body projected their axonal bundles to the central body, but those inside the mushroom body projected their axonal bundles toward the deutocerebrum without innervating the central body. The cell bodies inside the mushroom body received axons of the G3 LEA(+) sensory cells at the medial ventral cup of the nauplius eye. Several glands were found to synthesize G3 LEA RNA during the nauplius stages of brine shrimp, including the sinus, antennal I and II, salt, and three ectodermal glands. This study provides the first demonstration of the formation of G3 LEA(+) sinus glands at the emergence stages of brine shrimp. These results suggest that G3 LEA protein is synthesized in several cell types. In particular, specific glands play crucial roles during the emergence and nauplius stages of brine shrimp. PMID:25781424

  6. Few apparent short-term effects of elevated soil temperature and increased frequency of summer precipitation on the abundance and taxonomic diversity of desert soil micro- and meso-fauna

    USGS Publications Warehouse

    Darby, B.J.; Neher, D.A.; Housman, D.C.; Belnap, J.

    2011-01-01

    Frequent hydration and drying of soils in arid systems can accelerate desert carbon and nitrogen mobilization due to respiration, microbial death, and release of intracellular solutes. Because desert microinvertebrates can mediate nutrient cycling, and the autotrophic components of crusts are known to be sensitive to rapid desiccation due to elevated temperatures after wetting events, we studied whether altered soil temperature and frequency of summer precipitation can also affect the composition of food web consumer functional groups. We conducted a two-year field study with experimentally-elevated temperature and frequency of summer precipitation in the Colorado Plateau desert, measuring the change in abundance of nematodes, protozoans, and microarthropods. We hypothesized that microfauna would be more adversely affected by the combination of elevated temperature and frequency of summer precipitation than either effect alone, as found previously for phototrophic crust biota. Microfauna experienced normal seasonal fluctuations in abundance, but the effect of elevated temperature and frequency of summer precipitation was statistically non-significant for most microfaunal groups, except amoebae. The seasonal increase in abundance of amoebae was reduced with combined elevated temperature and increased frequency of summer precipitation compared to either treatment alone, but comparable with control (untreated) plots. Based on our findings, we suggest that desert soil microfauna are relatively more tolerant to increases in ambient temperature and frequency of summer precipitation than the autotrophic components of biological soil crust at the surface.

  7. The Abundances of the Fe Group Elements in Early B Stars in the Magellanic Clouds and Bridge

    NASA Astrophysics Data System (ADS)

    Peters, Geraldine J.; Adelman, Saul J.

    2016-01-01

    The abundances of three Fe Group elements (V, Cr, and Fe) in 9 early main-sequence band B stars in the LMC, 7 in the SMC , and two in the Magellanic Bridge have been determined from archival FUSE observations and the Hubeny/Lanz NLTE programs TLUSTY/SYNSPEC. Lines from the Fe group elements, except for a few weak multiplets of Fe III, are not observable in the optical spectral region. The best set of lines in the FUSE spectral region are Fe III (UV1), V III 1150 Å, and Cr III 1137 Å. The abundances of these elements in early B stars are a marker for recent SNe Ia activity, as a single exploding white dwarf can deliver 0.5 solar masses of Ni-56 that decays into Fe to the ISM. The Fe group abundances in an older population of stars primarily reflect SNe II activity, in which a single explosion delivers only 0.07 solar masses of Ni-56 to the ISM (the rest remains trapped in the neutron star). The abundances of the Fe group elements in early B stars not only track SNe Ia activity but are also important for computing evolutionary tracks for massive stars. In general, the Fe abundance relative to the sun's value is comparable to the mean abundances for the lighter elements in the Clouds/Bridge but the values of [V,Cr/Fe]sun are smaller. This presentation will discuss the spatial distribution of the Fe Group elements in the Magellanic Clouds, and compare it with our galaxy in which the abundance of Fe declines with radial distance from the center. Support from NASA grants NAG5-13212, NNX10AD66G, STScI HST-GO-13346.22, and USC's Women in Science and Engineering (WiSE) program is greatly appreciated.

  8. [Metagenomic analysis of taxonomic and functional changes in gut microbiota of patients with alcoholic dependence syndrome].

    PubMed

    Dubinkina, V B; Tyakht, A V; Ilina, E N; Ischenko, D S; Kovarsky, B A; Yarygin, K S; Pavlenko, A V; Popenko, A S; Alexeev, D G; Taraskina, A E; Nasyrova, R F; Krupitski, E M; Skorodumova, L O; Larin, A K; Kostryukova, E S; Govorun, V M

    2015-01-01

    Here we present the first metagenomic study of gut microbiota in patients with alcohol dependence syndrome (ADS) performed in the whole-genome ("shotgun") format. Taxonomic analysis highlighted changes in community "drivers" abundance previously associated with inflammatory processes (including increase in Ruminococcus gnavus and torques, as well as decrease in Faecalibacterium and Akkermansia). Microbiota of alcoholics manifested presence of specific opportunistic pathogens rarely detected in healthy control subjects of the world. Differential analysis of metabolic potential basing on changes in KEGG Orthology groups abundance revealed increase in pathways associated with response to oxidative stress. Analysis of two specific gene groups--alcohol metabolism and virulence factors--also showed increase in comparison with the control groups. We suggest that gut microbiota distinct in alcoholics by both taxonomic and functional composition plays role in modulating the effect of alcohol on host organism. PMID:26716747

  9. Integrating macroecological metrics and community taxonomic structure.

    PubMed

    Harte, John; Rominger, Andrew; Zhang, Wenyu

    2015-10-01

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

  10. The Abundances of the Fe Group Elements in Three Early B Stars in the Large Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    Peters, G. J.; Adelman, S. J.

    2005-12-01

    The photospheric abundances of V, Cr, and Fe have been determined for three sharp-lined early B stars in the Large Magellanic Cloud using FUV spectra obtained from the Far Ultraviolet Spectroscopic Explorer (FUSE) and the Kurucz LTE model atmosphere/spectrum synthesis codes ATLAS9/SYNTHE. The program stars include NGC1818/D1, NGC2004/B15, and NGC2004/B30 (star designations are from Robertson 1974, A&AS, 15, 261). The calculations were carried through with model parameters close to those adopted by Korn et al. (2000, A&A, 353, 655). Values of Teff, log g, ξ T, and v sin I are 25000/4.0/0/30, 20000/3.1/6/25, and 23500/3.3/14/30 for NGC1818/D1, NGC2004/B15, and NGC2004/B30, respectively. The abundances quoted below are in sequence for the latter stars. The vanadium abundances, [V/H], determined from V III λ λ 1150,1152 (UV 2), are -0.6, -0.9, and -0.9 dex. Cr was determined from Cr III λ λ 1118,1136. Values of -0.5, -0.8, and -0.7 dex were found. Uncertainties in the V and Cr abundances are ˜0.3 dex. The Fe abundance is primarily from 7 lines of Fe III (UV 1) in the region λ λ 1122-32. Values are -0.8±0.3, ˜-1.1, and -0.4±0.3. Since there is no evidence for N enhancement in the program stars ([N/H] ˜ -0.9, -1.0, and -0.6 from the N III doublet at 1183,1184 Å) the photospheric abundances have probably not been altered by mixing of processed material from the star's interior and the derived abundances represent pristine values for the two young clusters in the LMC. It should be noted that the N and Fe abundances derived for NGC1818/D1 are about 0.5 dex lower than those determined by Korn et al. from much weaker optical lines. We will discuss possible reasons for the discrepancy. The generally low abundances for the Fe group elements in these young cluster B stars imply that supernova activity has been minimal in the regions of the LMC in which the stars were formed. GJP appreciates support from NASA grant NAG5-13212.

  11. Platinum group element abundances in the upper continental crust revisited - New constraints from analyses of Chinese loess

    NASA Astrophysics Data System (ADS)

    Park, Jung-Woo; Hu, Zhaochu; Gao, Shan; Campbell, Ian H.; Gong, Hujun

    2012-09-01

    Platinum group element (PGE) abundances in the upper continental crust (UCC) are poorly constrained with published values varying by up to an order of magnitude. We evaluated the validity of using loess to estimate PGE abundances in the UCC by measuring these elements in seven Chinese loess samples using a precise method that combines NiS fire assay with isotope dilution. Major and trace elements of the Chinese loess show a typical upper crustal composition and PGE abundances are consistent with literature data on Chinese loess, except for Ru, which is a factor of 10 lowe than published values. We suggest that the high Ru data and RuN/IrN values of Chinese loess reported by Peucker-Ehrenbrink and Jahn (2001) (Geochem. Geophys. Geosys.2, 2001GC000172) are an analytical artifact, rather than a true geochemical characteristic of loess because likely sources of loess are not significantly enriched in Ru and transport and deposition processes cannot preferentially enrich Ru in loess. The effect of eolian fractionation on PGE abundances in loess appears to be limited because Chinese loess from different locations shows similar PGE patterns and concentrations. This conclusion is supported by strong positive correlations between the PGE (except for Pt) and other compatible elements such as Fe2O3, Ni, Cr, Co. Using a compilation of PGE data for loess from China, Argentina and Europe, including our data but excluding one sample with an anomalously high Pt content, we propose average PGE abundances for global loess of Ir = 0.022 ppb (ng/g), Ru = 0.030 ppb, Rh = 0.018 ppb, Pt = 0.599 ppb, and Pd = 0.526 ppb, and suggest that these are the best current estimates for the PGE abundances of the UCC.

  12. Abundance and Relative Distribution of Frankia Host Infection Groups Under Actinorhizal Alnus glutinosa and Non-actinorhizal Betula nigra Trees.

    PubMed

    Samant, Suvidha; Huo, Tian; Dawson, Jeffrey O; Hahn, Dittmar

    2016-02-01

    Quantitative polymerase chain reaction (qPCR) was used to assess the abundance and relative distribution of host infection groups of the root-nodule forming, nitrogen-fixing actinomycete Frankia in four soils with similar physicochemical characteristics, two of which were vegetated with a host plant, Alnus glutinosa, and two with a non-host plant, Betula nigra. Analyses of DAPI-stained cells at three locations, i.e., at a distance of less than 1 m (near stem), 2.5 m (middle crown), and 3-5 m (crown edge) from the stems of both tree species revealed no statistically significant differences in abundance. Frankiae generally accounted for 0.01 to 0.04 % of these cells, with values between 4 and 36 × 10(5) cells (g soil)(-1). In three out of four soils, abundance of frankiae was significantly higher at locations "near stem" and/or "middle crown" compared to "crown edge," while numbers at these locations were not different in the fourth soil. Frankiae of the Alnus host infection group were dominant in all samples accounting for about 75 % and more of the cells, with no obvious differences with distance to stem. In three of the soils, all of these cells were represented by strain Ag45/Mut15. In the fourth soil that was vegetated with older A. glutinosa trees, about half of these cells belonged to a different subgroup represented by strain ArI3. In all soils, the remaining cells belonged to the Elaeagnus host infection group represented by strain EAN1pec. Casuarina-infective frankiae were not found. Abundance and relative distribution of Frankia host infection groups were similar in soils under the host plant A. glutinosa and the non-host plant B. nigra. Results did thus not reveal any specific effects of plant species on soil Frankia populations. PMID:26143359

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

    PubMed

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

    2014-08-01

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

  14. 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

  15. Two-dimensional gel electrophoresis analysis of the abundance of virulent exoproteins of group A streptococcus caused by environmental changes.

    PubMed

    Nakamura, Tadahiro; Hasegawa, Tadao; Torii, Keizo; Hasegawa, Yoshinori; Shimokata, Kaoru; Ohta, Michio

    2004-01-01

    Group A streptococci regulate the expression of virulence factors in response to environmental change. In order to investigate this mechanism, the growth of group A streptococci and the abundance of virulent exoprotein production in culture supernatant were analyzed by two-dimensional gel electrophoresis (2-D electrophoresis) under several culture conditions. Judging from alterations in their growth, group A streptococci were affected by various environmental stresses. Under high O(2) and low CO(2 )concentrations, streptococcal pyrogenic exotoxin B (SpeB) and streptococcal pyrogenic exotoxin F (SpeF) significantly decreased, and the streptococcal inhibitor of complement (Sic) increased. At 30 degrees C, increases in endo-beta- N-acetylglucosaminidase (EndoS) and alpha-amylase were also detected, while at 41 degrees C EndoS became undetectable and SpeB and SpeF decreased. Sic, SpeF and mitogenic factor 3 (Mf3) decreased when cells were cultured in higher NaCl concentrations, and EndoS disappeared following culture of the cells in high glucose concentration. An increase in acid phosphatase and a decrease in several other proteins were detected when the cells were cultivated in high iron concentrations. These results suggest that group A streptococci have a versatile adaptation system that responds to several environmental stresses by altering the level of exoprotein production. PMID:14673516

  16. Sniffing for Clues to the Dinosaurs Demise: Measurement of Osmium Isotope Compositions and Platinum Group Element Abundances in Volcanic Emissions

    NASA Astrophysics Data System (ADS)

    Sims, K. W.; Peucker-Ehrenbrink, B.; Mather, T.; Pyle, D.; Martin, R.; Gauthier, P.; Aiuppa, A.

    2005-12-01

    Platinum Group Elements (PGE: Os, Ir, Rh, Ru, Pt, Pd) and osmium isotopes measured in marine and terrestrial sediment, snow and ice records are important paleo-tracers of riverine, hydrothermal, extraterrestrial, volcanic and anthropogenic inputs into the global surficial environment. For instance, the marine Os isotope record across the Cretaceous-Tertiary Boundary (KTB) indicates that the onset of the main phase of Deccan volcanism and the transient late Maastrichtian warming preceded the large extraterrestrial impact and the related KTB mass extinction by several hundred thousand years [Ravizza and Peucker-Ehrenbrink, 2003]. Distinguishing extraterrestrial from volcanic PGE sources has been difficult due to the similarity in Os isotopic compositions, complex PGE fractionations, and our lack of knowledge of the Os isotopic composition and PGE abundances in volcanic aerosols. These difficulties have fueled vigorous debate about extraterrestrial vs. volcanic triggers of mass extinctions in the geologic record. To assess the volcanic contribution to the global Re-Os-PGE cycle we have initiated a study of Os isotopic compositions and PGE abundances in volcanic emissions from volcanoes around the globe. Here we report preliminary data on PGE abundances and Os isotopes measured in gas and aerosol filter samples from Vulcan Masaya, Nicaragua and Mt Etna, Italy. Samples were analyzed by ID-ICPMS (ThermoFinnigan ELEMENT 2 and NEPTUNE) at the Woods Hole Oceanographic Institution. Osmium isotope compositions of the filters are unradiogenic (0.1272 to 0.187). Osmium concentrations range from 28 to 97 pg/cubic meter and are 3-4 orders of magnitude lower than those measured by Krahenbuhl et al. [1992] during the spring 1984 eruption of Mauna Loa just after the lava fountaining phase. Normalized PGE abundance patterns are fractionated relative to carbonaceous chondrites and two important features distinguish the pattern from other important PGE sources: 1) Os/Ir is much higher

  17. Study of model systems to test the potential function of Artemia group 1 late embryogenesis abundant (LEA) proteins.

    PubMed

    Warner, Alden H; Guo, Zhi-hao; Moshi, Sandra; Hudson, John W; Kozarova, Anna

    2016-01-01

    Embryos of the brine shrimp, Artemia franciscana, are genetically programmed to develop either ovoviparously or oviparously depending on environmental conditions. Shortly upon their release from the female, oviparous embryos enter diapause during which time they undergo major metabolic rate depression while simultaneously synthesize proteins that permit them to tolerate a wide range of stressful environmental events including prolonged periods of desiccation, freezing, and anoxia. Among the known stress-related proteins that accumulate in embryos entering diapause are the late embryogenesis abundant (LEA) proteins. This large group of intrinsically disordered proteins has been proposed to act as molecular shields or chaperones of macromolecules which are otherwise intolerant to harsh conditions associated with diapause. In this research, we used two model systems to study the potential function of the group 1 LEA proteins from Artemia. Expression of the Artemia group 1 gene (AfrLEA-1) in Escherichia coli inhibited growth in proportion to the number of 20-mer amino acid motifs expressed. As well, clones of E. coli, transformed with the AfrLEA-1 gene, expressed multiple bands of LEA proteins, either intrinsically or upon induction with isopropyl-β-thiogalactoside (IPTG), in a vector-specific manner. Expression of AfrLEA-1 in E. coli did not overcome the inhibitory effects of high concentrations of NaCl and KCl but modulated growth inhibition resulting from high concentrations of sorbitol in the growth medium. In contrast, expression of the AfrLEA-1 gene in Saccharomyces cerevisiae did not alter the growth kinetics or permit yeast to tolerate high concentrations of NaCl, KCl, or sorbitol. However, expression of AfrLEA-1 in yeast improved its tolerance to drying (desiccation) and freezing. Under our experimental conditions, both E. coli and S. cerevisiae appear to be potentially suitable hosts to study the function of Artemia group 1 LEA proteins under environmentally

  18. A taxonomic revision of the Cymindis (Pinacodera) limbata species group (Coleoptera, Carabidae, Lebiini), including description of a new species from Florida, U.S.A.

    PubMed Central

    Hunting, Wesley M.

    2013-01-01

    Abstract The Cymindis (Pinacodera) limbata species group (Coleoptera, Carabidae, Lebiini) is a precinctive New World taxon with ranges extended from portions of temperate southeastern Canada and the U.S.A. through the montane regions of Mexico, south to the Isthmus of Tehuantepec. The group is distinguishable from all other members of the subgenus Pinacodera by males possessing a distinctive sclerite (endophallic plate) at the apex of the endophallus. In the past, a lack of material and misunderstandings of range of variation within species have contributed to confusion about how many species there really are. This revision of the limbata species group includes a classification, a key to groups within the subgenus Pinacodera and species within the limbata group, descriptions of species, re-rankings and new synonymies. In total 10 taxa are treated, with 6 new synonyms proposed, 1 new combination introduced and 1 new species described: Cymindis (Pinacodera) rufostigma (type locality: Archbold Biological Station, Highlands County, Florida, U.S.A.). Each taxon is characterized in terms of structural features of adults, habitat, geographical distribution, and chorological affinities. Available ecological information and treatments of variation are included. PMID:23653501

  19. 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.

  20. The ant genus Tetramorium Mayr in the Afrotropical region (Hymenoptera, Formicidae, Myrmicinae): synonymisation of Decamorium Forel under Tetramorium, and taxonomic revision of the T. decem species group

    PubMed Central

    Hita Garcia, Francisco; Fisher, Brian L.

    2014-01-01

    Abstract In this study we synonymise the genus Decamorium Forel under Tetramorium Mayr, revise the new T. decem species group by providing a diagnosis of the group, an illustrated identification key to species level, and worker-based species descriptions for all five species, which include diagnoses, discussions, images, and distribution maps. The following species are revised in this study: T. decem Forel, comb. r., T. raptor sp. n., T. uelense Santschi, comb. r., T. ultor Forel, comb. r., stat. r. & stat. n., and T. venator sp. n. In addition, we also designate lectotypes for T. decem, T. uelense, and T. ultor. PMID:24899856

  1. 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

  2. Phylogeny of Protopolybia Ducke, 1905 and taxonomic revision of the Protopolybia exigua species-group (Hymenoptera: Vespidae, Polistinae), with description of four new species.

    PubMed

    Dos Santos Junior, José N A; Silveira, Orlando T; Carpenter, James M

    2015-01-01

    A first phylogenetic hypothesis is proposed for Protopolybia Ducke, 1905 based on cladistic analysis of 31 species. New evidence in support of monophyly of the genus is presented. A revision of the Protopolybia exigua species-group is also presented. Protopolybia diligens (Smith, 1857), stat. resurr. is revalidated. Four new species are described: P. collombiana Santos, Silveira & Carpenter, sp. nov., P. clypeata Santos, Silveira & Carpenter, sp. nov., P. similis Santos, Silveira & Carpenter, sp. nov., and P. potiguara Santos, Silveira & Carpenter, sp. nov. Protopolybia holoxantha (Ducke, 1904) and P. rubrithorax Bequaert, 1944 are redescribed. New synonymy is proposed for P. bituberculata Silveira & Carpenter, 1995 =Polybia nana Cameron, 1912 (nom. praeocc., nec de Saussure 1863), syn. nov. New records and description of the male genitalia are provided for some of the species of the P. exigua species-group. PMID:26248912

  3. Taxonomic and morphological survey of the Lygephila lusoria (Linnaeus, 1758) species-group with description of a new species (Lepidoptera, Erebidae, Toxocampinae)

    PubMed Central

    Pekarsky, Oleg

    2013-01-01

    Abstract The taxa of the Lygephila lusoria (Linnaeus, 1758) species-group are revised. The genital features of all known taxa are described and illustrated with special reference to the structure of vesica. The male genitalia of L. pallida pallida (Bang-Haas, 1907) are described and illustrated for the first time. L. pallida subpicata (Wiltshire, 1971) is treated here as a species, L. pallida subpicata (Wiltshire, 1971), stat. n., distinct from L. pallida. A new species, L. minima, sp. n.,from South Russia is described. Illustrations of the holotype and its genitalia are provided; a diagnostic comparison with L. pallida is given. L. alaica Remm, 1983 is included in the L. lusoria species-group for the first time. PMID:24294088

  4. TIPP: taxonomic identification and phylogenetic profiling

    PubMed Central

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

    2014-01-01

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

  5. Taxonomic abstraction in psychobiology.

    PubMed

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

    1984-10-01

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

  6. Characterization of mycobacteria from a major Brazilian outbreak suggests that revision of the taxonomic status of members of the Mycobacterium chelonae-M. abscessus group is needed.

    PubMed

    Leao, Sylvia Cardoso; Tortoli, Enrico; Viana-Niero, Cristina; Ueki, Suely Yoko Mizuka; Lima, Karla Valeria Batista; Lopes, Maria Luiza; Yubero, Jesus; Menendez, Maria Carmen; Garcia, Maria Jesus

    2009-09-01

    An outbreak of postsurgical infections caused by rapidly growing mycobacteria has been ongoing in Brazil since 2004. The degrees of similarity of the rpoB and hsp65 sequences from the clinical isolates and the corresponding sequences from both the Mycobacterium massiliense and the M. bolletii type strains were above the accepted limit for interspecies variability, leading to conflicting identification results. Therefore, an extensive characterization of members of the M. chelonae-M. abscessus group was carried out. The M. abscessus, M. chelonae, M. immunogenum, M. massiliense, and M. bolletii type strains and a subset of clinical isolates were analyzed by biochemical tests, high-performance liquid chromatography, drug susceptibility testing, PCR-restriction enzyme analysis of hsp65 (PRA-hsp65), rpoB, and hsp65 gene sequencing and analysis of phylogenetic trees, DNA-DNA hybridization (DDH), and restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene (RFLP-16S rRNA). The clinical isolates and the M. abscessus, M. massiliense, and M. bolletii type strains could not be separated by phenotypic tests and were grouped in the phylogenetic trees obtained. The results of DDH also confirmed the >70% relatedness of the clinical isolates and the M. abscessus, M. massiliense, and M. bolletii type strains; and indistinguishable RFLP-16S rRNA patterns were obtained. On the contrary, the separation of clinical isolates and the M. abscessus, M. massiliense, and M. bolletii type strains from M. chelonae and M. immunogenum was supported by the results of PRA-hsp65, DDH, and RFLP-16S rRNA and by the rpoB and hsp65 phylogenetic trees. Taken together, these results led to the proposition that M. abscessus, M. massiliense, and M. bolletii represent a single species, that of M. abscessus. Two subspecies are also proposed, M. abscessus subsp. abscessus and M. abscessus subsp. massiliense, and these two subspecies can be distinguished by two different PRA-hsp65 patterns

  7. 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

  8. Taxonomic revision of the Malagasy members of the Nesomyrmex angulatus species group using the automated morphological species delineation protocol NC-PART-clustering

    PubMed Central

    Fisher, Brian L.

    2016-01-01

    Background. Applying quantitative morphological approaches in systematics research is a promising way to discover cryptic biological diversity. Information obtained through twenty-first century science poses new challenges to taxonomy by offering the possibility of increased objectivity in independent and automated hypothesis formation. In recent years a number of promising new algorithmic approaches have been developed to recognize morphological diversity among insects based on multivariate morphometric analyses. These algorithms objectively delimit components in the data by automatically assigning objects into clusters. Method. In this paper, hypotheses on the diversity of the Malagasy Nesomyrmex angulatus group are formulated via a highly automated protocol involving a fusion of two algorithms, (1) Nest Centroid clustering (NC clustering) and (2) Partitioning Algorithm based on Recursive Thresholding (PART). Both algorithms assign samples into clusters, making the class assignment results of different algorithms readily inferable. The results were tested by confirmatory cross-validated Linear Discriminant Analysis (LOOCV-LDA). Results. Here we reveal the diversity of a unique and largely unexplored fragment of the Malagasy ant fauna using NC-PART-clustering on continuous morphological data, an approach that brings increased objectivity to taxonomy. We describe eight morphologically distinct species, including seven new species: Nesomyrmex angulatus (Mayr, 1862), N. bidentatus sp. n., N. clypeatus sp. n., N. devius sp. n., N. exiguus sp. n., N. fragilis sp. n., N. gracilis sp. n., and N. hirtellus sp. n.. An identification key for their worker castes using morphometric data is provided. Conclusions. Combining the dimensionality reduction feature of NC clustering with the assignment of samples into clusters by PART advances the automatization of morphometry-based alpha taxonomy. PMID:26989630

  9. Group 3 late embryogenesis abundant proteins from embryos of Artemia franciscana: structural properties and protective abilities during desiccation.

    PubMed

    Boswell, Leaf C; Menze, Michael A; Hand, Steven C

    2014-01-01

    Group 3 late embryogenesis abundant (LEA) proteins are highly hydrophilic, and their expression is associated with desiccation tolerance in both plants and animals. Here we show that two LEA proteins from embryos of Artemia franciscana, AfrLEA2 and AfrLEA3m, are intrinsically disordered in solution but upon desiccation gain secondary structure, as measured by circular dichroism. Trifluoroethanol and sodium dodecyl sulfate are both shown to induce α-helical structure in AfrLEA2 and AfrLEA3m. Bioinformatic predictions of secondary-structure content for both proteins correspond most closely to conformations measured in the dry state. Because some LEA proteins afford protection to desiccation-sensitive proteins during drying and subsequent rehydration, we tested for this capacity in AfrLEA2 and AfrLEA3m. The protective capacities vary, depending on the target enzyme. For the cytoplasmic enzyme lactate dehydrogenase, neither AfrLEA2 nor AfrLEA3m, with or without trehalose present, was able to afford protection better than that provided by bovine serum albumin (BSA) under the same conditions. However, for another cytoplasmic enzyme, phosphofructokinase, both AfrLEA2 and AfrLEA3m in the presence of trehalose were able to afford protection far greater than that provided by BSA with trehalose. Finally, for the mitochondrial enzyme citrate synthase, 400-μg/mL AfrLEA3m without trehalose provided significantly more protection than the same concentration of either AfrLEA2 or BSA. PMID:25244376

  10. 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

  11. Richness and abundance of the cardini group of Drosophila (Diptera, Drosophilidae) in the Caatinga and Atlantic Forest biomes in northeastern Brazil.

    PubMed

    Rohde, Cláudia; Silva, Diva Maria Izabel O; Oliveira, Geórgia F; Monteiro, Liv S; Montes, Martín A; Garcia, Ana Cristina L

    2014-12-01

    Brazil has a high diversity of flies of the genus Drosophila, and part of this richness is represented by the cardini group. We analyzed the fluctuations in the richness and abundance of this group, in environments that had never previously been studied in the northeastern region of Brazil. Among the 28,204 drosophilids sampled, 1,294 belonged to the cardini group and were represented by D. polymorpha, D. cardini, D. neocardini and D. cardinoides. Occurrences of D. neocardini and D. cardinoides were registered for the first time in the Caatinga. In this biome, D. cardini stood out as having the highest abundance, and D. polymorpha was not observed. In the coastal Atlantic Forest, D. cardini was not registered, but D. polymorpha was found in all the localities investigated. Mangrove swamps were the environment with the lowest abundance and richness of the cardini group. The High-altitude Forest presented the highest richness of this group. We suggest that the high abundance of D. polymorpha in the High-altitude Forest and in the coastal Atlantic Forest may be a reflection of the historical relationship between these two environments. PMID:25590710

  12. Richness and abundance of the cardini group of Drosophila (Diptera, Drosophilidae) in the Caatinga and Atlantic Forest biomes in northeastern Brazil.

    PubMed

    Rohde, Cláudia; Silva, Diva Maria Izabel O; Oliveira, Geórgia F; Monteiro, Liv S; Montes, Martín A; Garcia, Ana Cristina L

    2014-11-11

    Brazil has a high diversity of flies of the genus Drosophila, and part of this richness is represented by the cardini group. We analyzed the fluctuations in the richness and abundance of this group, in environments that had never previously been studied in the northeastern region of Brazil. Among the 28,204 drosophilids sampled, 1,294 belonged to the cardini group and were represented by D. polymorpha, D. cardini, D. neocardini and D. cardinoides. Occurrences of D. neocardini and D. cardinoides were registered for the first time in the Caatinga. In this biome, D. cardini stood out as having the highest abundance, and D. polymorpha was not observed. In the coastal Atlantic Forest, D. cardini was not registered, but D. polymorpha was found in all the localities investigated. Mangrove swamps were the environment with the lowest abundance and richness of the cardini group. The High-altitude Forest presented the highest richness of this group. We suggest that the high abundance of D. polymorpha in the High-altitude Forest and in the coastal Atlantic Forest may be a reflection of the historical relationship between these two environments. PMID:25387390

  13. Platinum-group element abundance and distribution in chromite deposits of the Acoje Block, Zambales Ophiolite Complex, Philippines

    USGS Publications Warehouse

    Bacuta, G.C., Jr.; Kay, R.W.; Gibbs, A.K.; Lipin, B.R.

    1990-01-01

    Platinum-group elements (PGE) occur in ore-grade concentration in some of the chromite deposits related to the ultramafic section of the Acoje Block of the Zambales Ophiolite Complex. The deposits are of three types: Type 1 - associated with cumulate peridotites at the base of the crust; Type 2 - in dunite pods from the top 1 km of mantle harzburgite; and Type 3 - like Type 2, but in deeper levels of the harzburgite. Most of the deposites have chromite compositions that are high in Cr with Cr/(Cr + Al) (expressed as chromium index, Cr#) > 0.6; high-Al (Cr# Pd, thought to be characteristic of PGE-barren deposits) and positive slope (Ir < Pd, characteristic of PGE-rich deposits). Iridium, Ru and Os commonly occur as micron-size laurite (sulfide) inclusions in unfractured chromite. Laurite and native Os are also found as inclusions in interstitial sulfides. Platinum and Pd occur as alloy inclusions (and possibly as solid solution) in interstitial Ni-Cu sulfides and as tellurobismuthides in serpentine and altered sulfides. Variability of PGE distribution may be explained by alteration, crystal fractionation or partial melting processes. Alteration and metamorphism were ruled out, because PGE contents do not correlate with degree of serpentinization or the abundance and type (hydroxyl versus non-hydroxyl) of silicate inclusions in chromite. Preliminary Os isotopic data do not support crustal contamination as a source of the PGEs in the Acoje deposits. The anomalous PGE concentrations in Type 1 high-Cr chromite deposits are attributed to two stages of enrichment: an early enrichment of their mantle source from previous melting events and a later stage of sulfide segregation accompanying chromite crystallization. High-Al chromite deposits which crystallized from basalts derived from relatively low degrees of melting owe their low PGE content to partitioning of PGEs in sulfides and alloys that remain in the mantle. High-Cr deposits crystallized from melts that were

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

    PubMed Central

    Page, Roderic DM

    2005-01-01

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

  15. Platinum Group Element (PGE) Abundances in Lava Flows Generated by the Hawaiian Plume: Insights into Plume Evolution

    NASA Astrophysics Data System (ADS)

    Shafer, J. T.; Neal, C. R.

    2003-12-01

    Picritic and high-MgO (7.7-24 wt.%) basalt samples from Detroit (/sim81-76 Ma) and Koko (/sim48 Ma) Seamounts along the ESC have been analyzed for PGEs (Ru, Rh, Pd, Ir, and Pt) allowing an examination of how the PGEs in lavas from the Hawaiian plume have changed over time. Major and trace element (including the PGEs) concentrations were quantified by ICP methods at the University of Notre Dame. See Ely et al. (1999, Chem. Geol. 157:219) for the PGE analytical method. Bennett et al. (2000) analyzed Hawaiian picrites and found PGE abundances slightly greater than average MORB and comparable to the low-PGE basaltic komatiites. These authors modeled the PGE abundances of these picrites by using variable amounts of residual sulfide during melting, such that Koolau (low PGE contents) formed from a relatively sulfide-rich source and Loihi (high PGEs) from a sulfide-poor source. Our PGE data from Detroit Seamount show slightly higher PGE abundances than Loihi and Kilauea, suggesting these picrites formed from a source lacking residual sulfide. These results suggest that, if the model of Bennett et al. (2000) is correct, the dilution of plume lava with MORB source, as hypothesized on the basis of depleted isotope ratios and lower trace element abundances than modern Hawaii (Keller et al., 2000, Nature 405:603; Kinman & Neal, 2002, Eos 83:F1282; Regelous et al., 2003, JPet 44:113), was not the controlling factor in PGE abundances. However, since MORB PGE concentrations are not substantially different than low-PGE Hawaiian picrites, incorporation of MORB material within the Hawaiian plume at Detroit Seamount would not have drastically reduced the PGE abundances. Koko Seamount has relatively high PGE concentrations (/sim3-12 times greater than those from Detroit lavas). This may be the result of a lack of residual sulfide facilitated by higher degrees of partial melting. Although our initial data are consistent with variable degrees of partial melting and/or source

  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. THE ABUNDANCES OF HYDROCARBON FUNCTIONAL GROUPS IN THE INTERSTELLAR MEDIUM INFERRED FROM LABORATORY SPECTRA OF HYDROGENATED AND METHYLATED POLYCYCLIC AROMATIC HYDROCARBONS

    SciTech Connect

    Steglich, M.; Jäger, C.; Huisken, F.; Friedrich, M.; Plass, W.; Räder, H.-J.; Müllen, K.; Henning, Th.

    2013-10-01

    Infrared (IR) absorption spectra of individual polycyclic aromatic hydrocarbons (PAHs) containing methyl (-CH{sub 3}), methylene (CH{sub 2}), or diamond-like CH groups and IR spectra of mixtures of methylated and hydrogenated PAHs prepared by gas-phase condensation were measured at room temperature (as grains in pellets) and at low temperature (isolated in Ne matrices). In addition, the PAH blends were subjected to an in-depth molecular structure analysis by means of high-performance liquid chromatography, nuclear magnetic resonance spectroscopy, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Supported by calculations at the density functional theory level, the laboratory results were applied to analyze in detail the aliphatic absorption complex of the diffuse interstellar medium at 3.4 μm and to determine the abundances of hydrocarbon functional groups. Assuming that the PAHs are mainly locked in grains, aliphatic CH {sub x} groups (x = 1, 2, 3) would contribute approximately in equal quantities to the 3.4 μm feature (N {sub CHx}/N {sub H} ≈ 10{sup –5}-2 × 10{sup –5}). The abundances, however, may be two to four times lower if a major contribution to the 3.4 μm feature comes from molecules in the gas phase. Aromatic ≅CH groups seem to be almost absent from some lines of sight, but can be nearly as abundant as each of the aliphatic components in other directions (N{sub ≅CH}/N {sub H} ∼< 2 × 10{sup –5}; upper value for grains). Due to comparatively low binding energies, astronomical IR emission sources do not display such heavy excess hydrogenation. At best, especially in protoplanetary nebulae, CH{sub 2} groups bound to aromatic molecules, i.e., excess hydrogens on the molecular periphery only, can survive the presence of a nearby star.

  18. Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River

    PubMed Central

    Ruiz-González, Clara; Salazar, Guillem; Logares, Ramiro; Proia, Lorenzo; Gasol, Josep M.; Sabater, Sergi

    2015-01-01

    Deductions about the ecology of high taxonomic bacterial ranks (i.e., phylum, class, order) are often based on their abundance patterns, yet few studies have quantified how accurately variations in abundance of these bacterial groups represent the dynamics of the taxa within them. Using 454-pyrosequencing of the 16S rRNA gene, we investigated whether the changes in abundance of six dominant bacterial classes (Actinobacteria, Beta-/Alpha-/Gamma-proteobacteria, Flavobacteria, and Sphingobacteria) along a large dam-regulated river are reflected by those of their constituent Operational Taxonomic Units (OTUs; 97% similarity level). The environmental impact generated by the reservoirs promoted clear compositional shifts in all bacterial classes that resulted from changes in the abundance of individual OTUs rather than from the appearance of new taxa along the river. Abundance patterns at the class level represented the dynamics of only a small but variable proportion of their constituting OTUs, which were not necessarily the most abundant ones. Within most classes, we detected sub-groups of OTUs showing contrasting responses to reservoir-induced environmental changes. Overall, we show that the patterns observed at the class level fail to capture the dynamics of a significant fraction of their constituent members, calling for caution when the ecological attributes of high-ranks are to be interpreted. PMID:26635761

  19. A new strategy for integrating abundant oxygen functional groups into carbon felt electrode for vanadium redox flow batteries

    PubMed Central

    Kim, Ki Jae; Lee, Seung-Wook; Yim, Taeeun; Kim, Jae-Geun; Choi, Jang Wook; Kim, Jung Ho; Park, Min-Sik; Kim, Young-Jun

    2014-01-01

    The effects of surface treatment combining corona discharge and hydrogen peroxide (H2O2) on the electrochemical performance of carbon felt electrodes for vanadium redox flow batteries (VRFBs) have been thoroughly investigated. A high concentration of oxygen functional groups has been successfully introduced onto the surface of the carbon felt electrodes by a specially designed surface treatment, which is mainly responsible for improving the energy efficiency of VRFBs. In addition, the wettability of the carbon felt electrodes also can be significantly improved. The energy efficiency of the VRFB cell employing the surface modified carbon felt electrodes is improved by 7% at high current density (148 mA cm−2). Such improvement is attributed to the faster charge transfer and better wettability allowed by surface-active oxygen functional groups. Moreover, this method is much more competitive than other surface treatments in terms of processing time, production costs, and electrochemical performance. PMID:25366060

  20. A new strategy for integrating abundant oxygen functional groups into carbon felt electrode for vanadium redox flow batteries

    NASA Astrophysics Data System (ADS)

    Kim, Ki Jae; Lee, Seung-Wook; Yim, Taeeun; Kim, Jae-Geun; Choi, Jang Wook; Kim, Jung Ho; Park, Min-Sik; Kim, Young-Jun

    2014-11-01

    The effects of surface treatment combining corona discharge and hydrogen peroxide (H2O2) on the electrochemical performance of carbon felt electrodes for vanadium redox flow batteries (VRFBs) have been thoroughly investigated. A high concentration of oxygen functional groups has been successfully introduced onto the surface of the carbon felt electrodes by a specially designed surface treatment, which is mainly responsible for improving the energy efficiency of VRFBs. In addition, the wettability of the carbon felt electrodes also can be significantly improved. The energy efficiency of the VRFB cell employing the surface modified carbon felt electrodes is improved by 7% at high current density (148 mA cm-2). Such improvement is attributed to the faster charge transfer and better wettability allowed by surface-active oxygen functional groups. Moreover, this method is much more competitive than other surface treatments in terms of processing time, production costs, and electrochemical performance.

  1. A new strategy for integrating abundant oxygen functional groups into carbon felt electrode for vanadium redox flow batteries.

    PubMed

    Kim, Ki Jae; Lee, Seung-Wook; Yim, Taeeun; Kim, Jae-Geun; Choi, Jang Wook; Kim, Jung Ho; Park, Min-Sik; Kim, Young-Jun

    2014-01-01

    The effects of surface treatment combining corona discharge and hydrogen peroxide (H2O2) on the electrochemical performance of carbon felt electrodes for vanadium redox flow batteries (VRFBs) have been thoroughly investigated. A high concentration of oxygen functional groups has been successfully introduced onto the surface of the carbon felt electrodes by a specially designed surface treatment, which is mainly responsible for improving the energy efficiency of VRFBs. In addition, the wettability of the carbon felt electrodes also can be significantly improved. The energy efficiency of the VRFB cell employing the surface modified carbon felt electrodes is improved by 7% at high current density (148 mA cm(-2)). Such improvement is attributed to the faster charge transfer and better wettability allowed by surface-active oxygen functional groups. Moreover, this method is much more competitive than other surface treatments in terms of processing time, production costs, and electrochemical performance. PMID:25366060

  2. The Abundances of Hydrocarbon Functional Groups in the Interstellar Medium Inferred from Laboratory Spectra of Hydrogenated and Methylated Polycyclic Aromatic Hydrocarbons

    NASA Astrophysics Data System (ADS)

    Steglich, M.; Jäger, C.; Huisken, F.; Friedrich, M.; Plass, W.; Räder, H.-J.; Müllen, K.; Henning, Th.

    2013-10-01

    Infrared (IR) absorption spectra of individual polycyclic aromatic hydrocarbons (PAHs) containing methyl (\\sbondCH3), methylene (\\protect{\\epsfbox{art/apjs484229un01.eps}}CH2), or diamond-like \\protect{\\epsfbox{art/apjs484229un02.eps}}CH groups and IR spectra of mixtures of methylated and hydrogenated PAHs prepared by gas-phase condensation were measured at room temperature (as grains in pellets) and at low temperature (isolated in Ne matrices). In addition, the PAH blends were subjected to an in-depth molecular structure analysis by means of high-performance liquid chromatography, nuclear magnetic resonance spectroscopy, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Supported by calculations at the density functional theory level, the laboratory results were applied to analyze in detail the aliphatic absorption complex of the diffuse interstellar medium at 3.4 μm and to determine the abundances of hydrocarbon functional groups. Assuming that the PAHs are mainly locked in grains, aliphatic CH x groups (x = 1, 2, 3) would contribute approximately in equal quantities to the 3.4 μm feature (N CHx /N H ≈ 10-5-2 × 10-5). The abundances, however, may be two to four times lower if a major contribution to the 3.4 μm feature comes from molecules in the gas phase. Aromatic \\epsfbox{art/apjs484229un03.eps} CH groups seem to be almost absent from some lines of sight, but can be nearly as abundant as each of the aliphatic components in other directions (N_{\\epsfbox{art/apjs484229un03.eps} CH}/N H lsim 2 × 10-5 upper value for grains). Due to comparatively low binding energies, astronomical IR emission sources do not display such heavy excess hydrogenation. At best, especially in protoplanetary nebulae, \\protect{\\epsfbox{art/apjs484229un01.eps}}CH2 groups bound to aromatic molecules, i.e., excess hydrogens on the molecular periphery only, can survive the presence of a nearby star.

  3. Model-measurement comparison of functional group abundance in α-pinene and 1,3,5-trimethylbenzene secondary organic aerosol formation

    NASA Astrophysics Data System (ADS)

    Ruggeri, Giulia; Bernhard, Fabian A.; Henderson, Barron H.; Takahama, Satoshi

    2016-07-01

    Secondary organic aerosol (SOA) formed by α-pinene and 1,3,5-trimethylbenzene photooxidation under different NOx regimes is simulated using the Master Chemical Mechanism v3.2 (MCM) coupled with an absorptive gas-particle partitioning module. Vapor pressures for individual compounds are estimated with the SIMPOL.1 group contribution model for determining apportionment of reaction products to each phase. We apply chemoinformatic tools to harvest functional group (FG) composition from the simulations and estimate their contributions to the overall oxygen to carbon ratio. Furthermore, we compare FG abundances in simulated SOA to measurements of FGs reported in previous chamber studies using Fourier transform infrared spectroscopy. These simulations qualitatively capture the dynamics of FG composition of SOA formed from both α-pinene and 1,3,5-trimethylbenzene in low-NOx conditions, especially in the first hours after start of photooxidation. Higher discrepancies are found after several hours of simulation; the nature of these discrepancies indicates sources of uncertainty or types of reactions in the condensed or gas phase missing from current model implementation. Higher discrepancies are found in the case of α-pinene photooxidation under different NOx concentration regimes, which are reasoned through the domination by a few polyfunctional compounds that disproportionately impact the simulated FG abundance in the aerosol phase. This manuscript illustrates the usefulness of FG analysis to complement existing methods for model-measurement evaluation.

  4. A Taxonomic Approach to the Gestalt Theory of Perls

    ERIC Educational Resources Information Center

    Raming, Henry E.; Frey, David H.

    1974-01-01

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

  5. Millimeter-scale variations of stable isotope abundances in carbonates from banded iron-formations in the Hamersley Group of Western Australia.

    PubMed

    Baur, M E; Hayes, J M; Studley, S A; Walter, M R

    1985-01-01

    Several diamond drill cores from formations within the Hamersley Group of Western Australia have been studied for evidence of short-range variations in the isotopic compositions of the carbonates. For a set of 32 adjacent microbands analyzed in a specimen from the Marra Mamba Iron Formation, carbon isotope compositions of individual microbands ranged from -2.8 to -19.8 per mil compared to PDB and oxygen isotope compositions ranged from 10.2 to 20.8 per mil compared to SMOW. A pattern of alternating abundances was present, with the average isotopic contrasts between adjacent microbands being 3.0 per mil for carbon and 3.1 per mil for oxygen. Similar results were obtained for a suite of 34 microbands (in four groups) from the Bruno's Band unit of the Mount Sylvia Formation. Difficulties were experienced in preparing samples of single microbands from the Dales Gorge Member of the Brockman Iron Formation, but overall isotopic compositions were in good agreement with values reported by previous authors. Chemical analyses showed that isotopically light carbon and oxygen were correlated with increased concentrations of iron. The preservation of these millimeter-scale variations in isotopic abundances is interpreted as inconsistent with a metamorphic origin for the isotopically light carbon in the BIF carbonates. A biological origin is favored for the correlated variations in 13C and Fe, and it is suggested that the 13C-depleted carbonates may derive either from fermentative metabolism or from anaerobic respiration. A model is presented in which these processes occur near the sediment-water interface and are coupled with an initial oxidative precipitation of the iron. PMID:11539027

  6. Millimeter-scale variations of stable isotope abundances in carbonates from banded iron-formations in the Hamersley Group of Western Australia

    NASA Technical Reports Server (NTRS)

    Baur, M. E.; Hayes, J. M.; Studley, S. A.; Walter, M. R.

    1985-01-01

    Several diamond drill cores from formations within the Hamersley Group of Western Australia have been studied for evidence of short-range variations in the isotopic compositions of the carbonates. For a set of 32 adjacent microbands analyzed in a specimen from the Marra Mamba Iron Formation, carbon isotope compositions of individual microbands ranged from -2.8 to -19.8 per mil compared to PDB and oxygen isotope compositions ranged from 10.2 to 20.8 per mil compared to SMOW. A pattern of alternating abundances was present, with the average isotopic contrasts between adjacent microbands being 3.0 per mil for carbon and 3.1 per mil for oxygen. Similar results were obtained for a suite of 34 microbands (in four groups) from the Bruno's Band unit of the Mount Sylvia Formation. Difficulties were experienced in preparing samples of single microbands from the Dales Gorge Member of the Brockman Iron Formation, but overall isotopic compositions were in good agreement with values reported by previous authors. Chemical analyses showed that isotopically light carbon and oxygen were correlated with increased concentrations of iron. The preservation of these millimeter-scale variations in isotopic abundances is interpreted as inconsistent with a metamorphic origin for the isotopically light carbon in the BIF carbonates. A biological origin is favored for the correlated variations in 13C and Fe, and it is suggested that the 13C-depleted carbonates may derive either from fermentative metabolism or from anaerobic respiration. A model is presented in which these processes occur near the sediment-water interface and are coupled with an initial oxidative precipitation of the iron.

  7. The Unstructured N-terminal Region of Arabidopsis Group 4 Late Embryogenesis Abundant (LEA) Proteins Is Required for Folding and for Chaperone-like Activity under Water Deficit.

    PubMed

    Cuevas-Velazquez, Cesar L; Saab-Rincón, Gloria; Reyes, José Luis; Covarrubias, Alejandra A

    2016-05-13

    Late embryogenesis abundant (LEA) proteins are a conserved group of proteins widely distributed in the plant kingdom that participate in the tolerance to water deficit of different plant species. In silico analyses indicate that most LEA proteins are structurally disordered. The structural plasticity of these proteins opens the question of whether water deficit modulates their conformation and whether these possible changes are related to their function. In this work, we characterized the secondary structure of Arabidopsis group 4 LEA proteins. We found that they are disordered in aqueous solution, with high intrinsic potential to fold into α-helix. We demonstrate that complete dehydration is not required for these proteins to sample ordered structures because milder water deficit and macromolecular crowding induce high α-helix levels in vitro, suggesting that prevalent conditions under water deficit modulate their conformation. We also show that the N-terminal region, conserved across all group 4 LEA proteins, is necessary and sufficient for conformational transitions and that their protective function is confined to this region, suggesting that folding into α-helix is required for chaperone-like activity under water limitation. We propose that these proteins can exist as different conformers, favoring functional diversity, a moonlighting property arising from their structural dynamics. PMID:27006402

  8. Testing the effects of ant invasions on non-ant arthropods with high-resolution taxonomic data.

    PubMed

    Hanna, Cause; Naughton, Ida; Boser, Christina; Holway, David

    2015-10-01

    Invasions give rise to a wide range of ecological effects. Many invasions proceed without noticeable impacts on the resident biota, whereas others shift species composition and even alter ecosystem function. Ant invasions generate a broad spectrum of ecological effects, but controversy surrounds the extent of these impacts, especially with regard to how other arthropods are affected. This uncertainty in part results from the widespread use of low-resolution taxonomic data, which can mask the presence of other introduced species and make it difficult to isolate the effects of ant invasions on native species. Here, we use high-resolution taxonomic data to examine the effects of Argentine ant invasions on arthropods on Santa Cruz Island, California. We sampled arthropods in eight pairs of invaded and uninvaded plots and then collaborated with taxonomic experts to identify taxa in four focal groups: spiders, bark lice, beetles, and ants. Spiders, bark lice, and beetles made up ~40% of the 9868 non-ant arthropod individuals sampled; the majority of focal group arthropods were putatively native taxa. Although our results indicate strong negative effects of the Argentine ant on native ants, as is well documented, invaded and uninvaded plots did not differ with respect to the richness, abundance, or species composition of spiders, bark lice, and beetles. One common, introduced species of bark louse was more common in uninvaded plots than in invaded plots, and including this species into our analyses changed the relationship between bark louse richness vs. L. humile abundance from no relationship to a significant negative relationship. This case illustrates how failure to differentiate native and introduced taxa can lead to erroneous conclusions about the effects of ant invasions. Our results caution against unqualified assertions about the effects of ant invasions on non-ant arthropods, and more generally demonstrate that accurate assessments of invasion impacts depend on

  9. 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

  10. 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

  11. Facile one-step coating approach to magnetic submicron particles with poly(ethylene glycol) coats and abundant accessible carboxyl groups

    PubMed Central

    Long, Gaobo; Yang, Xiao-lan; Zhang, Yi; Pu, Jun; Liu, Lin; Liu, Hong-bo; Li, Yuan-li; Liao, Fei

    2013-01-01

    Purpose Magnetic submicron particles (MSPs) are pivotal biomaterials for magnetic separations in bioanalyses, but their preparation remains a technical challenge. In this report, a facile one-step coating approach to MSPs suitable for magnetic separations was investigated. Methods Polyethylene glycol) (PEG) was derived into PEG-bis-(maleic monoester) and maleic monoester-PEG-succinic monoester as the monomers. Magnetofluids were prepared via chemical co-precipitation and dispersion with the monomers. MSPs were prepared via one-step coating of magnetofluids in a water-in-oil microemulsion system of aerosol-OT and heptane by radical co-polymerization of such monomers. Results The resulting MSPs contained abundant carboxyl groups, exhibited negligible nonspecific adsorption of common substances and excellent suspension stability, appeared as irregular particles by electronic microscopy, and had submicron sizes of broad distribution by laser scattering. Saturation magnetizations and average particle sizes were affected mainly by the quantities of monomers used for coating magnetofluids, and steric hindrance around carboxyl groups was alleviated by the use of longer monomers of one polymerizable bond for coating. After optimizations, MSPs bearing saturation magnetizations over 46 emu/g, average sizes of 0.32 μm, and titrated carboxyl groups of about 0.21 mmol/g were obtained. After the activation of carboxyl groups on MSPs into N-hydroxysuccinimide ester, biotin was immobilized on MSPs and the resulting biotin-functionalized MSPs isolated the conjugate of streptavidin and alkaline phosphatase at about 2.1 mg/g MSPs; streptavidin was immobilized at about 10 mg/g MSPs and retained 81% ± 18% (n = 5) of the specific activity of the free form. Conclusion The facile approach effectively prepares MSPs for magnetic separations. PMID:23589687

  12. A group 6 late embryogenesis abundant protein from common bean is a disordered protein with extended helical structure and oligomer-forming properties.

    PubMed

    Rivera-Najera, Lucero Y; Saab-Rincón, Gloria; Battaglia, Marina; Amero, Carlos; Pulido, Nancy O; García-Hernández, Enrique; Solórzano, Rosa M; Reyes, José L; Covarrubias, Alejandra A

    2014-11-14

    Late embryogenesis-abundant proteins accumulate to high levels in dry seeds. Some of them also accumulate in response to water deficit in vegetative tissues, which leads to a remarkable association between their presence and low water availability conditions. A major sub-group of these proteins, also known as typical LEA proteins, shows high hydrophilicity and a high percentage of glycine and other small amino acid residues, distinctive physicochemical properties that predict a high content of structural disorder. Although all typical LEA proteins share these characteristics, seven groups can be distinguished by sequence similarity, indicating structural and functional diversity among them. Some of these groups have been extensively studied; however, others require a more detailed analysis to advance in their functional understanding. In this work, we report the structural characterization of a group 6 LEA protein from a common bean (Phaseolus vulgaris L.) (PvLEA6) by circular dichroism and nuclear magnetic resonance showing that it is a disordered protein in aqueous solution. Using the same techniques, we show that despite its unstructured nature, the addition of trifluoroethanol exhibited an intrinsic potential in this protein to gain helicity. This property was also promoted by high osmotic potentials or molecular crowding. Furthermore, we demonstrate that PvLEA6 protein is able to form soluble homo-oligomeric complexes that also show high levels of structural disorder. The association between PvLEA6 monomers to form dimers was shown to occur in plant cells by bimolecular fluorescence complementation, pointing to the in vivo functional relevance of this association. PMID:25271167

  13. A Group 6 Late Embryogenesis Abundant Protein from Common Bean Is a Disordered Protein with Extended Helical Structure and Oligomer-forming Properties*

    PubMed Central

    Rivera-Najera, Lucero Y.; Saab-Rincón, Gloria; Battaglia, Marina; Amero, Carlos; Pulido, Nancy O.; García-Hernández, Enrique; Solórzano, Rosa M.; Reyes, José L.; Covarrubias, Alejandra A.

    2014-01-01

    Late embryogenesis-abundant proteins accumulate to high levels in dry seeds. Some of them also accumulate in response to water deficit in vegetative tissues, which leads to a remarkable association between their presence and low water availability conditions. A major sub-group of these proteins, also known as typical LEA proteins, shows high hydrophilicity and a high percentage of glycine and other small amino acid residues, distinctive physicochemical properties that predict a high content of structural disorder. Although all typical LEA proteins share these characteristics, seven groups can be distinguished by sequence similarity, indicating structural and functional diversity among them. Some of these groups have been extensively studied; however, others require a more detailed analysis to advance in their functional understanding. In this work, we report the structural characterization of a group 6 LEA protein from a common bean (Phaseolus vulgaris L.) (PvLEA6) by circular dichroism and nuclear magnetic resonance showing that it is a disordered protein in aqueous solution. Using the same techniques, we show that despite its unstructured nature, the addition of trifluoroethanol exhibited an intrinsic potential in this protein to gain helicity. This property was also promoted by high osmotic potentials or molecular crowding. Furthermore, we demonstrate that PvLEA6 protein is able to form soluble homo-oligomeric complexes that also show high levels of structural disorder. The association between PvLEA6 monomers to form dimers was shown to occur in plant cells by bimolecular fluorescence complementation, pointing to the in vivo functional relevance of this association. PMID:25271167

  14. Remote sensing data to classify functional groups of vegetation and their distribution and abundance in a semiarid mountain watershed, Idaho, USA

    NASA Astrophysics Data System (ADS)

    Loughridge, R. E.; Benner, S. G.; McNamara, J. P.; Flores, A. N.

    2012-12-01

    In water-limited montane ecosystems, topography is a significant driver of energy balance and soil moisture and therefore governs the distribution and abundance of terrestrial vegetation. Few studies have made a concerted effort to quantify spatial patterns in vegetation along physiographic gradients that control microclimate such as slope, elevation, and aspect. Furthermore, spectral mixing of different vegetation species within individual visible and near-infrared remote sensing pixels makes it difficult to constrain the temporal growth and senescence of individual plant functional types. We report on a study that seeks to understand the interacting roles of topography, soil moisture, and solar radiation on the distribution of different plant functional types within the Dry Creek Experimental Watershed (DCEW). Boise State University maintains the 27 km2 watershed which is located in the Boise Front Mountains of southwest Idaho. It is qualitatively observed in DCEW that low elevations are dominated by sage-steppe ecosystems and high elevations transition to conifer forests. It is also observed that aspect has a major control in which sage-steppe is evident at high elevations on south facing slopes conversely from north facing slopes. To quantify these trends we measured percent ground cover of functional groups (i.e. forbs, grass, shrubs, etc.) at 77 sites within DCEW spanning a large gradient in the controlling biophysiographic variables. In addition, vegetation water content (VWC) and spectral reflectance from the 325 to 1075 nm wavelengths was collected for specific vegetation types at eight permanent soil moisture monitoring sites contained in DCEW throughout the 2012 green-up/senescence transition. To develop a watershed-wide classification we built a supervised multilayer perceptron (MLP) backpropagating artificial neural network (ANN) using temporal Landsat 5 images to classify 4 major groups: sage-steppe, Douglas fir, ponderosa pine, and deciduous trees

  15. Variations of the relative abundances of He, (C,N,O) and Fe-group nuclei in solar cosmic rays and their relationship to solar particle acceleration

    NASA Technical Reports Server (NTRS)

    Bertsch, D. L.; Biswas, S.; Fichtel, C. E.; Pellerin, C. J.; Reames, D. V.

    1973-01-01

    Measurements of the flux of helium nuclei in the 24 January 1971 event and of helium and (C,N,O) nuclei in the 1 September 1971 event are combined with previous measurements to obtain the relative abundances of helium, (C,N,O), and Fe-group nuclei in these events. These data are then summarized together with previously reported results to show that, even when the same detector system using a dE/dx plus range technique is used, differences in the He/(C,N,O) value in the same energy/nucleon interval are observed in solar cosmic ray events. Further, when the He/(C,N,O) value is lower the He/(Fe-group nuclei) value is also systematically lower in these large events. When solar particle acceleration theory is analyzed, it is seen that the results suggest that, for large events, Coulomb energy loss probably does not play a major role in determining solar particle composition at higher energies (10 MeV). The variations in multicharged nuclei composition are more likely due to partial ionization during the acceleration phase.

  16. Commonly Rare and Rarely Common: Comparing Population Abundance of Invasive and Native Aquatic Species

    PubMed Central

    Hansen, Gretchen J. A.; Vander Zanden, M. Jake; Blum, Michael J.; Clayton, Murray K.; Hain, Ernie F.; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S.; McIntyre, Peter B.; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D.; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies. PMID:24194883

  17. Commonly rare and rarely common: comparing population abundance of invasive and native aquatic species.

    PubMed

    Hansen, Gretchen J A; Vander Zanden, M Jake; Blum, Michael J; Clayton, Murray K; Hain, Ernie F; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S; McIntyre, Peter B; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies. PMID:24194883

  18. Effect of Leaf Type and Pesticide Exposure on Abundance of Bacterial Taxa in Mosquito Larval Habitats

    PubMed Central

    Muturi, Ephantus J.; Orindi, Benedict O.; Kim, Chang-Hyun

    2013-01-01

    Lentic freshwater systems including those inhabited by aquatic stages of mosquitoes derive most of their carbon inputs from terrestrial organic matter mainly leaf litter. The leaf litter is colonized by microbial communities that provide the resource base for mosquito larvae. While the microbial biomass associated with different leaf species in container aquatic habitats is well documented, the taxonomic composition of these microbes and their response to common environmental stressors is poorly understood. We used indoor aquatic microcosms to determine the abundances of major taxonomic groups of bacteria in leaf litters from seven plant species and their responses to low concentrations of four pesticides with different modes of action on the target organisms; permethrin, malathion, atrazine and glyphosate. We tested the hypotheses that leaf species support different quantities of major taxonomic groups of bacteria and that exposure to pesticides at environmentally relevant concentrations alters bacterial abundance and community structure in mosquito larval habitats. We found support for both hypotheses suggesting that leaf litter identity and chemical contamination may alter the quality and quantity of mosquito food base (microbial communities) in larval habitats. The effect of pesticides on microbial communities varied significantly among leaf types, suggesting that the impact of pesticides on natural microbial communities may be highly complex and difficult to predict. Collectively, these findings demonstrate the potential for detritus composition within mosquito larval habitats and exposure to pesticides to influence the quality of mosquito larval habitats. PMID:23940789

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

    PubMed

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

    2016-04-01

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

  20. 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.

  1. Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats.

    PubMed

    Jiao, Jinzhen; Huang, Jinyu; Zhou, Chuanshe; Tan, Zhiliang

    2015-05-15

    Understanding of the colonization process of epithelial bacteria attached to the rumen tissue during rumen development is very limited. Ruminal epithelial bacterial colonization is of great significance for the relationship between the microbiota and the host and can influence the early development and health of the host. MiSeq sequencing of 16S rRNA genes and quantitative real-time PCR (qPCR) were applied to characterize ruminal epithelial bacterial diversity during rumen development in this study. Seventeen goat kids were selected to reflect the no-rumination (0 and 7 days), transition (28 and 42 days), and rumination (70 days) phases of animal development. Alpha diversity indices (operational taxonomic unit [OTU] numbers, Chao estimate, and Shannon index) increased (P < 0.01) with age, and principal coordinate analysis (PCoA) revealed that the samples clustered together according to age group. Phylogenetic analysis revealed that Proteobacteria, Firmicutes, and Bacteroidetes were detected as the dominant phyla regardless of the age group, and the abundance of Proteobacteria declined quadratically with age (P < 0.001), while the abundances of Bacteroidetes (P = 0.088) and Firmicutes (P = 0.009) increased with age. At the genus level, Escherichia (80.79%) dominated at day zero, while Prevotella, Butyrivibrio, and Campylobacter surged (linearly; P < 0.01) in abundance at 42 and 70 days. qPCR showed that the total copy number of epithelial bacteria increased linearly (P = 0.013) with age. In addition, the abundances of the genera Butyrivibrio, Campylobacter, and Desulfobulbus were positively correlated with rumen weight, rumen papilla length, ruminal ammonia and total volatile fatty acid concentrations, and activities of carboxymethylcellulase (CMCase) and xylanase. Taking the data together, colonization by ruminal epithelial bacteria is age related (achieved at 2 months) and might participate in the anatomic and functional development of the rumen. PMID:25769827

  2. Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats

    PubMed Central

    Jiao, Jinzhen; Huang, Jinyu; Zhou, Chuanshe

    2015-01-01

    Understanding of the colonization process of epithelial bacteria attached to the rumen tissue during rumen development is very limited. Ruminal epithelial bacterial colonization is of great significance for the relationship between the microbiota and the host and can influence the early development and health of the host. MiSeq sequencing of 16S rRNA genes and quantitative real-time PCR (qPCR) were applied to characterize ruminal epithelial bacterial diversity during rumen development in this study. Seventeen goat kids were selected to reflect the no-rumination (0 and 7 days), transition (28 and 42 days), and rumination (70 days) phases of animal development. Alpha diversity indices (operational taxonomic unit [OTU] numbers, Chao estimate, and Shannon index) increased (P < 0.01) with age, and principal coordinate analysis (PCoA) revealed that the samples clustered together according to age group. Phylogenetic analysis revealed that Proteobacteria, Firmicutes, and Bacteroidetes were detected as the dominant phyla regardless of the age group, and the abundance of Proteobacteria declined quadratically with age (P < 0.001), while the abundances of Bacteroidetes (P = 0.088) and Firmicutes (P = 0.009) increased with age. At the genus level, Escherichia (80.79%) dominated at day zero, while Prevotella, Butyrivibrio, and Campylobacter surged (linearly; P < 0.01) in abundance at 42 and 70 days. qPCR showed that the total copy number of epithelial bacteria increased linearly (P = 0.013) with age. In addition, the abundances of the genera Butyrivibrio, Campylobacter, and Desulfobulbus were positively correlated with rumen weight, rumen papilla length, ruminal ammonia and total volatile fatty acid concentrations, and activities of carboxymethylcellulase (CMCase) and xylanase. Taking the data together, colonization by ruminal epithelial bacteria is age related (achieved at 2 months) and might participate in the anatomic and functional development of the rumen. PMID:25769827

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

    PubMed

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

    2016-06-01

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

  4. 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

  5. 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...

  6. Abundance of broad bacterial taxa in the sargasso sea explained by environmental conditions but not water mass.

    PubMed

    Sjöstedt, Johanna; Martiny, Jennifer B H; Munk, Peter; Riemann, Lasse

    2014-05-01

    To explore the potential linkage between distribution of marine bacterioplankton groups, environmental conditions, and water mass, we investigated the factors determining the abundance of bacterial taxa across the hydrographically complex Subtropical Convergence Zone in the Sargasso Sea. Based on information from 16S rRNA gene clone libraries from various locations and two depths, abundances of the predominant taxa (eubacteria, Archaea, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and the Roseobacter, SAR11, and SAR86 clades) were quantified by real-time PCR. In addition, the abundances of Synechococcus, Prochlorococcus, and picoalgae were determined by flow cytometry. Linear multiple-regression models determining the relative effects of eight environmental variables and of water mass explained 35 to 86% of the variation in abundance of the quantified taxa, even though only one to three variables were significantly related to any particular taxon's abundance. Most of the variation in abundance was explained by depth and chlorophyll a. The predominant phototrophs, Prochlorococcus and picoalgae, were negatively correlated with phosphate, whereas eubacteria, heterotrophic bacteria, and SAR86 were negatively correlated with nitrite. Water mass showed limited importance for explaining the abundance of the taxonomical groups (significant only for Roseobacter, explaining 14% of the variation). The results suggest the potential for predicting the abundance of broad bacterioplankton groups throughout the Sargasso Sea using only a few environmental parameters. PMID:24561593

  7. 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

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

    PubMed Central

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

    2014-01-01

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

  9. Assessing introduction risk using species' rank-abundance distributions.

    PubMed

    Chan, Farrah T; Bradie, Johanna; Briski, Elizabeta; Bailey, Sarah A; Simard, Nathalie; MacIsaac, Hugh J

    2015-01-22

    Mixed-species assemblages are often unintentionally introduced into new ecosystems. Analysing how assemblage structure varies during transport may provide insights into how introduction risk changes before propagules are released. Characterization of introduction risk is typically based on assessments of colonization pressure (CP, the number of species transported) and total propagule pressure (total PP, the total abundance of propagules released) associated with an invasion vector. Generally, invasion potential following introduction increases with greater CP or total PP. Here, we extend these assessments using rank-abundance distributions to examine how CP : total PP relationships change temporally in ballast water of ocean-going ships. Rank-abundance distributions and CP : total PP patterns varied widely between trans-Atlantic and trans-Pacific voyages, with the latter appearing to pose a much lower risk than the former. Responses also differed by taxonomic group, with invertebrates experiencing losses mainly in total PP, while diatoms and dinoflagellates sustained losses mainly in CP. In certain cases, open-ocean ballast water exchange appeared to increase introduction risk by uptake of new species or supplementation of existing ones. Our study demonstrates that rank-abundance distributions provide new insights into the utility of CP and PP in characterizing introduction risk. PMID:25473007

  10. Assessing introduction risk using species’ rank-abundance distributions

    PubMed Central

    Chan, Farrah T.; Bradie, Johanna; Briski, Elizabeta; Bailey, Sarah A.; Simard, Nathalie; MacIsaac, Hugh J.

    2015-01-01

    Mixed-species assemblages are often unintentionally introduced into new ecosystems. Analysing how assemblage structure varies during transport may provide insights into how introduction risk changes before propagules are released. Characterization of introduction risk is typically based on assessments of colonization pressure (CP, the number of species transported) and total propagule pressure (total PP, the total abundance of propagules released) associated with an invasion vector. Generally, invasion potential following introduction increases with greater CP or total PP. Here, we extend these assessments using rank-abundance distributions to examine how CP : total PP relationships change temporally in ballast water of ocean-going ships. Rank-abundance distributions and CP : total PP patterns varied widely between trans-Atlantic and trans-Pacific voyages, with the latter appearing to pose a much lower risk than the former. Responses also differed by taxonomic group, with invertebrates experiencing losses mainly in total PP, while diatoms and dinoflagellates sustained losses mainly in CP. In certain cases, open-ocean ballast water exchange appeared to increase introduction risk by uptake of new species or supplementation of existing ones. Our study demonstrates that rank-abundance distributions provide new insights into the utility of CP and PP in characterizing introduction risk. PMID:25473007

  11. Body Size Versus Depth: Regional and Taxonomical Variation in Deep-Sea Meio- and Macrofaunal Organisms.

    PubMed

    van der Grient, Jesse M A; Rogers, Alex D

    2015-01-01

    Body size (weight per individual) is an important concept in ecology. It has been studied in the deep sea where a decrease in size with increasing depth has often been found. This has been explained as an adaptation to food limitation where size reduction results in a lowered metabolic rate and a decreased energetic requirement. However, observations vary, with some studies showing an increase in size with depth, and some finding no depth correlation at all. Here, we collected data from peer-reviewed studies on macro- and meiofaunal abundance and biomass, creating two datasets allowing statistical comparison of factors expected to influence body size in meio- and macrofaunal organisms. Our analyses examined the influence of region, taxonomic group and sampling method on the body size of meiofauna and macrofauna in the deep sea with increasing depth, and the resulting models are presented. At the global scale, meio- and macrofaunal communities show a decrease in body size with increasing depth as expected with the food limitation hypothesis. However, at the regional scale there were differences in trends of body size with depth, either showing a decrease (e.g. southwest Pacific Ocean; meio- and macrofauna) or increase (e.g. Gulf of Mexico; meiofauna only) compared to a global mean. Taxonomic groups also showed differences in body size trends compared to total community average (e.g. Crustacea and Bivalvia). Care must be taken when conducting these studies, as our analyses indicated that sampling method exerts a significant influence on research results. It is possible that differences in physiology, lifestyle and life history characteristics result in different responses to an increase in depth and/or decrease in food availability. This will have implications in the future as food supply to the deep sea changes as a result of climate change (e.g. increased ocean stratification at low to mid latitudes and reduced sea ice duration at high latitudes). PMID:26320616

  12. [Bats (Chiroptera: Mammalia) from Yurubí National Park, Venezuela: taxonomic list and community study].

    PubMed

    Delgado-Jaramillo, Mariana; Machado, Marjorie; García, Franger J; Ochoa, José

    2011-12-01

    Bats represent a key component in the dynamics of many terrestrial ecosystems, and one of the groups of mammals with the highest levels of diversification in the Neotropics. Here we describe the results of a study of the bat fauna from Yurubí National Park (mountain area in Northern Venezuela), that includes a taxonomic list and the characterization of some community attributes in forested areas. Data was collected from zoological collections and diversified sampling methods from February to July of 2009 in an altitudinal gradient (100-1 500m), with three principal ecological units: semideciduous, evergreen and cloud forests. We recorded 64 species grouped in five families (63% of the bats known from La Cordillera de la Costa), of which Phyllostomidae was the dominant taxa (42 species; 66% of total), followed by Vespertilionidae, Molossidae, Emballonuridae and Mormoopidae. The community with the highest taxonomic diversification was found in the lowest elevation range, while the lowest number of species was found at the highest range. Eleven trophic guilds were identified; the insectivorous guild was the richest, whereas the frugivorous was the most abundant. Our results allow us to indicate these forest ecosystems have an appropriate conservation status, taking into account the presence of a relatively high proportion of species from the subfamily Phyllostominae, as well as the presence of other species with conservation priorities. All these aspects, and the fact that this represents a reservoir of the biological diversity of the forest ecosystems of La Cordillera de la Costa, make this protected area of an essential conservation value, in a highly endangered bioregion by neighboring socio-economic growth. PMID:22208091

  13. The hyper-diverse ant genus Tetramorium Mayr (Hymenoptera, Formicidae) in the Malagasy region taxonomic revision of the T. naganum, T. plesiarum, T. schaufussii, and T. severini species groups

    PubMed Central

    Hita Garcia, Francisco; Fisher, Brian L.

    2014-01-01

    Abstract The taxonomy of the Tetramorium naganum, T. plesiarum, T. schaufussii, and T. severini species groups are revised for the Malagasy region. A total of 31 species are treated, of which 22 are newly described and nine redescribed. This increases the richness of the hyper-diverse genus Tetramorium in the Malagasy region to 106 species, which makes it the most species-rich genus in the region. Twenty-nine of the treated species are endemic to Madagascar, one is endemic to the Comoros, and one species is found predominantly in Madagascar but also on the island of Reunion. The T. naganum species group contains five species, which are mainly distributed in the rainforests and montane rainforests of eastern and northern Madagascar: T. alperti sp. n., T. dalek sp. n., T. enkidu sp. n., T. gilgamesh sp. n., and T. naganum Bolton, 1979. The T. plesiarum species group holds five species: T. bressleri sp. n., T. hobbit sp. n., T. gollum sp. n., T. mars sp. n., and T. plesiarum Bolton, 1979. All five are arid-adapted species occurring in the southwest and west of Madagascar. The second-most species-rich group in the region is the T. schaufussii species group with 20 species, most of which inhabit rainforests or montane rainforests of eastern and northern Madagascar. This group includes two species complexes each containing ten species: the T. cognatum complex with the species T. aspis sp. n., T. camelliae sp. n., T. cognatum Bolton, 1979, T. freya sp. n., T. gladius sp. n., T. karthala sp. n., T. myrmidon sp. n., T. proximum Bolton, 1979, T. rumo sp. n., and T. tenuinode sp. n.; and the T. schaufussii complex with the species T. merina sp. n., T. monticola sp. n., T. nassonowii Forel, 1892 stat. n., T. obiwan sp. n., T. pseudogladius sp. n., T. rala sp. n., T. schaufussii Forel, 1891, T. sikorae Forel, 1892 (= T. latior (Santschi, 1926)), T. scutum sp. n., T. xanthogaster Santschi, 1911. The last group treated in this study is the T. severini species group, which

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

    PubMed Central

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

    1997-01-01

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

  15. Taxonomic revision and biogeography of the Tamarix-feeding Diorhabda elongata (Brulle, 1832) species group (Coleoptera: Chrysomelidae: Galerucinae: Galerucini) and analysis of their potential in biological control of Tamarisk

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The primarily Palearctic Diorhabda elongata species group is established for five Tamarix-feeding sibling species (tamarisk beetles): D. elongata (Brullé, 1832), D. carinata (Faldermann, 1837), D. sublineata (Lucas, 1849) REVISED STATUS, D. carinulata (Desbrochers, 1869), and D. meridionalis Berti &...

  16. [Taxonomic status of the Burana virus (BURV) (Bunyaviridae, Nairovirus, Tamdy group) isolated from the ticks Haemaphysalis punctata Canestrini et Fanzago, 1877 and Haem. concinna Koch, 1844 (Ixodidae, Haemaphysalinae) in Kyrgyzstan].

    PubMed

    L'vov, D K; Al'khovskiĭ, S V; Shchelkanov, M Iu; Shchetinin, A M; Deriabin, P G; Gitel'man, A K; Aristova, V A; Botikov, A G

    2014-01-01

    Complete genome sequence of the Burana virus (BURV) was determined using the next-generation sequencing approach (ID GenBank KF801651). The prototype strain of BURV LEIV-Krg760 was originally isolated from the ticks Haemaphysalis punctata Canestrini et Fanzago, 1877 (Ixodidae, Haemaphysalinae), collected from cows in Tokmak wildlife sanctuary, eastern part of the Chu valley (43 degrees 10' N, 74 degrees 40' E) near Burana village, Kirgizia, in April 1971. Molecular genetics and phylogenetic analyses showed that the BURV belonged to the Nairovirus genus, Bunyaviridae and is related to Tamdy virus (TAMV) that is also associated with the ixodidae ticks of pasture biocenosis in Central Asia. Previous studies showed that TAMV is the prototypic virus of new phylogenetic Tamdy group in the Nairovirus genus. Thus, BURV was classified as a new virus of the Tamdy group, Nairovirus, Bunyaviridae. PMID:25549462

  17. Protein covalent immobilization via its scarce thiol versus abundant amine groups: Effect on orientation, cell binding domain exposure and conformational lability.

    PubMed

    Ba, O M; Hindie, M; Marmey, P; Gallet, O; Anselme, K; Ponche, A; Duncan, A C

    2015-10-01

    Quantity, orientation, conformation and covalent linkage of naturally cell adhesive proteins adsorbed or covalently linked to a surface, are known to influence the preservation of their subsequent long term cell adhesion properties and bioactivity. In the present work, we explore two different strategies for the covalent linking of plasma fibronectin (pFN) - used as a cell adhesive model protein, onto a polystyrene (PS) surface. One is aimed at tethering the protein to the surface in a semi-oriented fashion (via one of the 4 free thiol reactive groups on the protein) with a heterofunctional coupling agent (SSMPB method). The other aims to immobilize the protein in a more random fashion by reaction between the abundant pendant primary amine bearing amino acids of the pFN and activated carboxylic surface functions obtained after glutaric anhydride surface treatment (GA method). The overall goal will be to verify the hypothesis of a correlation between covalent immobilization of a model cell adhesive protein to a PS surface in a semi-oriented configuration (versus randomly oriented) with promotion of enhanced exposure of the protein's cell binding domain. This in turn would lead to enhanced cell adhesion. Ideally the goal is to elaborate substrates exhibiting a long term stable protein monolayer with preserved cell adhesive properties and bioactivity for biomaterial and/or cell adhesion commercial plate applications. However, the initial restrictive objective of this paper is to first quantitatively and qualitatively investigate the reversibly (merely adsorbed) versus covalently irreversibly bound protein to the surface after the immobilization procedure. Although immobilized surface amounts were similar (close to the monolayer range) for all immobilization approaches, covalent grafting showed improved retention and stronger "tethering" of the pFN protein to the surface (roughly 40%) after SDS rinsing compared to that for mere adsorption (0%) suggesting an added value

  18. 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

  19. 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

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

    PubMed

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

    2013-10-01

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

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

    PubMed

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

    2013-06-25

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

  2. Reconciling more than 150 years of taxonomic confusion: the true identity of Moenkhausia lepidura, with a key to the species of the M. lepidura group (Characiformes: Characidae).

    PubMed

    Marinho, Manoela M F; Langeani, Francisco

    2016-01-01

    Moenkhausia lepidura (Kner) is redescribed based on the examination of the type and other specimens from several localities of the Amazon and Orinoco basins. The species is readly diagnosed from congeners by a combination of a dark blotch on the upper caudal-fin lobe, lower lobe hyaline, and by the arrangement of predorsal scales, in which scales of anterior portion of predorsal area are arranged in pairs, followed by a single median row of scales extending to dorsal-fin origin. The analysis of the type material of Gymnotichthys hildae Fernández-Yépez and Knodus calliurus Ahl demonstrated the former is a junior synonym of Moenkhausia lepidura, whereas the latter should be removed from its synonymy. An identification key to the Moenkhausia lepidura-group is provided. PMID:27394824

  3. Abundances of platinum group elements in native sulfur condensates from the Niuatahi-Motutahi submarine volcano, Tonga rear arc: Implications for PGE mineralization in porphyry deposits

    NASA Astrophysics Data System (ADS)

    Park, Jung-Woo; Campbell, Ian H.; Kim, Jonguk

    2016-02-01

    Some porphyry Cu-Au deposits, which are enriched in Pd, are potentially an economic source of Pd. Magmatic volatile phases are thought to transport the platinum group elements (PGEs) from the porphyry source magma to the point of deposition. However, the compatibilities of the PGEs in magmatic volatile phases are poorly constrained. We report PGE and Re contents in native sulfur condensates and associated altered dacites from the Niuatahi-Motutahi submarine volcano, Tonga rear arc, in order to determine the compatibility of PGEs and Re in magmatic volatile phases, and their mobility during secondary hydrothermal alteration. The native sulfur we analyzed is the condensate of a magmatic volatile phase exsolved from the Niuatahi-Motutahi magma. The PGEs are moderately enriched in the sulfur condensates in comparison to the associated fresh dacite, with enrichment factors of 11-285, whereas Au, Cu and Re are strongly enriched with enrichment factors of ∼20,000, ∼5000 and ∼800 respectively. Although the PGEs are moderately compatible into magmatic volatile phases, their compatibility is significantly lower than that of Au, Cu and Re. Furthermore, the compatibility of PGEs decrease in the order: Ru > Pt > Ir > Pd. This trend is also observed in condensates and sublimates from other localities. PGE mineralization in porphyry Cu-Au deposits is characterized by substantially higher Pd/Pt (∼7-60) and Pd/Ir (∼100-10,500) than typical orthomagmatic sulfide deposits (e.g. Pd/Pt ∼0.6 and Pd/Ir ∼20 for the Bushveld). It has previously been suggested that the high mobility of Pd, relative to the other PGEs, may account for the preferential enrichment of Pd in porphyry Cu-Au deposits. However, the low compatibility of Pd in the volatile phase relative to the other PGEs, shown in this study, invalidates this explanation. We suggest that the PGE geochemistry of Pd-rich Cu-Au deposits is principally derived from the PGE characteristics of the magma from which the ore

  4. [Taxonomic status of the Chim virus (CHIMV) (Bunyaviridae, Nairovirus, Qalyub group) isolated from the Ixodidae and Argasidae ticks collected in the great gerbil (Rhombomys opimus Lichtenstein, 1823) (Muridae, Gerbillinae) burrows in Uzbekistan and Kazakhstan].

    PubMed

    L'vov, D K; Al'khovskiĭ, S V; Shchelkanov, M Iu; Shchetinin, A M; Aristova, V A; Morozova, T N; Gitel'man, A K; Deriabin, P G; Botikov, A G

    2014-01-01

    Full-length genome of the Chim virus (CHIMV) (strain LEIV-858Uz) was sequenced using the next-generation sequencing approach (ID GenBank: KF801656). The CHIMV/LEIV-858Uz was isolated from the Ornithodoros tartakovskyi Olenev, 1931 ticks collected in the great gerbil (Rhombomys opimus Lichtenstein, 1823) burrow in Uzbekistan near Chim town (Kashkadarinsky region) in July of 1971. Later, four more CHIMV strains were isolated from the O. tartakovskyi, O. papillipes Birula, 1895, Rhipicephalus turanicus Pomerantsev, 1936 collected in the great gerbil burrows in Kashkadarinsky, Bukhara, and Syrdarya regions of Uzbekistan, and three strains--from the Hyalomma asiaticum Schulze et Schlottke, 1930 from the great gerbil burrows in Dzheskazgan region of Kazakhstan. The virus is a potential pathogen of humans and camels. The phylogenetic analysis revealed that the CHIMV is a novel member of the Nairovirus genus (Bunyaviridae) and closely related to the Qalyub virus (QYBV), which is prototype for the group of the same name. The amino acid homology between the CHIMV and QYBV is 87% for the RdRp catalytic center (L-segment) that is coincident with both QYBV and CHIMV associated with the Ornithodoros ticks and burrow of rodents as well. The CHIMV homologies with other nairoviruses are 30-40% for the amino acid sequences of precursor polyprotein GnGc (M-segment), whereas 50%--for the nucleocapsid N (S-segment). The data obtained permit to classify the CHIMV as a member of the QYBV group in the genus of Nairovirus (Bunyaviridae). PMID:25335414

  5. Bifidobacteria Abundance-Featured Gut Microbiota Compositional Change in Patients with Behcet’s Disease

    PubMed Central

    Shimizu, Jun; Kubota, Takao; Takada, Erika; Takai, Kenji; Fujiwara, Naruyoshi; Arimitsu, Nagisa; Ueda, Yuji; Wakisaka, Sueshige; Suzuki, Tomoko; Suzuki, Noboru

    2016-01-01

    Gut microbiota compositional alteration may have an association with immune dysfunction in patients with Behcet’s disease (BD). We conducted a fecal metagenomic analysis of BD patients. We analyzed fecal microbiota obtained from 12 patients with BD and 12 normal individuals by sequencing of 16S ribosomal RNA gene. We compared the relative abundance of bacterial taxa. Direct comparison of the relative abundance of bacterial taxa demonstrated that the genera Bifidobacterium and Eggerthella increased significantly and the genera Megamonas and Prevotella decreased significantly in BD patients compared with normal individuals. A linear discriminant analysis of bacterial taxa showed that the phylum Actinobacteria, including Bifidobacterium, and the family Lactobacillaceae exhibited larger positive effect sizes than other bacteria in patients with BD. The phylum Firmicutes and the class Clostridia had large effect sizes in normal individuals. There was no significant difference in annotated species numbers (as numbers of operational taxonomic unit; OTU) and bacterial diversity of each sample (alpha diversity) between BD patients and normal individuals. We next assigned each sample to a position using three axes by principal coordinates analysis of the OTU table. The two groups had a significant distance as beta diversity in the 3-axis space. Fecal sIgA concentrations increased significantly in BD patients but did not correlate with any bacterial taxonomic abundance. These data suggest that the compositional changes of gut microbes may be one type of dysbiosis (unfavorable microbiota alteration) in patients with BD. The dysbiosis may have an association with the pathophysiology of BD. PMID:27105322

  6. 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…

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

    PubMed

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

    2012-08-01

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

  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. Patterns of taxonomic diversity among terrestrial isopods

    PubMed Central

    Sfenthourakis, Spyros; Taiti, Stefano

    2015-01-01

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

  10. Diversity and abundance of invertebrate epifaunal assemblages associated with gorgonians are driven by colony attributes

    NASA Astrophysics Data System (ADS)

    Cúrdia, João; Carvalho, Susana; Pereira, Fábio; Guerra-García, José Manuel; Santos, Miguel N.; Cunha, Marina R.

    2015-06-01

    The present study aimed to explicitly quantify the link between the attributes of shallow-water gorgonian colonies (Octocorallia: Alcyonacea) and the ecological patterns of associated non-colonial epifaunal invertebrates. Based on multiple regression analysis, we tested the contribution of several attributes (colony height, width, and area, fractal dimension as a measure of colony complexity, lacunarity as a measure of the heterogeneity, and "colonial" epibiont cover) to abundance and taxonomic richness of associated assemblages. The results highlight the variation in the response of epifaunal assemblages to the gorgonian colony characteristics. The nature and intensity of the relationships were gorgonian species-dependent and varied from one taxonomic group to another. For both gorgonian species analyzed, the strongest predictor of species richness and abundance of the epifaunal assemblages was "colonial" epibiont cover, possibly due to a trophic effect (direct or indirect enhancement of food availability) combined with the surface available for colonization (species-area effect). Although structural complexity is usually indicated as the main driver for rich and abundant coral-associated assemblages, no significant relationship was observed between fractal dimension and the community descriptors; lacunarity, which reflects the sizes of the inter-branch spaces, was only linked to taxonomic richness in the assemblages associated with Leptogorgia lusitanica. The validity of the paradigm that structural complexity enhances biodiversity may be scale-dependent. In the case of gorgonians, the effect of complexity at the "garden" level may be more relevant than at the individual colony level. This reinforces the need for the conservation of gorgonian aggregation areas as a whole in order to preserve host diversity and size structure.

  11. Comparison and Interpretation of Taxonomical Structure of Bacterial Communities in Two Types of Lakes on Yun-Gui plateau of China

    PubMed Central

    Han, Maozhen; Gong, Yanhai; Zhou, Chunyu; Zhang, Junqian; Wang, Zhi; Ning, Kang

    2016-01-01

    Bacterial communities from freshwater lakes are shaped by various factors such as nutrients, pH value, temperature, etc. Their compositions and relative abundances would undergo changes to adapt the changing environments, and in turn could affect the environments of freshwater lakes. Analyses of the freshwater lake’s bacterial communities under different environments would be of pivotal importance to monitor the condition of waterbody. In this study, we have collected freshwater samples from two lakes on Yun-Gui plateau of China, Lake Dianchi and Lake Haixihai, and analyzed the bacterial community structures from these samples based on 16S rRNA sequencing. Results have shown that: Firstly, the bacterial community of these samples have very different taxonomical structures, not only between two lakes but also among the intra-groups for samples collected from Dianchi. Secondly, the differences between samples from two lakes are highly associated with the chemical-geographical properties of the two lakes. Thirdly, for samples of Dianchi and Haixihai, analytical results of physicochemical, taxonomical structure and relative abundance of community revealed that extreme physicochemical factors caused by human activities have strongly affected the bacterial ecosystem in Dianchi. These results have clearly indicated the importance of combining biological profiling and chemical-geographical properties for monitoring Chinese plateau freshwater bacterial ecosystem, which could provide clues for Chinese freshwater ecosystem remediation on plateau. PMID:27461070

  12. Comparison and Interpretation of Taxonomical Structure of Bacterial Communities in Two Types of Lakes on Yun-Gui plateau of China.

    PubMed

    Han, Maozhen; Gong, Yanhai; Zhou, Chunyu; Zhang, Junqian; Wang, Zhi; Ning, Kang

    2016-01-01

    Bacterial communities from freshwater lakes are shaped by various factors such as nutrients, pH value, temperature, etc. Their compositions and relative abundances would undergo changes to adapt the changing environments, and in turn could affect the environments of freshwater lakes. Analyses of the freshwater lake's bacterial communities under different environments would be of pivotal importance to monitor the condition of waterbody. In this study, we have collected freshwater samples from two lakes on Yun-Gui plateau of China, Lake Dianchi and Lake Haixihai, and analyzed the bacterial community structures from these samples based on 16S rRNA sequencing. Results have shown that: Firstly, the bacterial community of these samples have very different taxonomical structures, not only between two lakes but also among the intra-groups for samples collected from Dianchi. Secondly, the differences between samples from two lakes are highly associated with the chemical-geographical properties of the two lakes. Thirdly, for samples of Dianchi and Haixihai, analytical results of physicochemical, taxonomical structure and relative abundance of community revealed that extreme physicochemical factors caused by human activities have strongly affected the bacterial ecosystem in Dianchi. These results have clearly indicated the importance of combining biological profiling and chemical-geographical properties for monitoring Chinese plateau freshwater bacterial ecosystem, which could provide clues for Chinese freshwater ecosystem remediation on plateau. PMID:27461070

  13. 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

  14. 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.

  15. CNO abundances in H II regions of the Magellanic clouds and the galaxy with implications regarding the nucleosynthesis of the CNO element group

    NASA Technical Reports Server (NTRS)

    Dufour, R. J.; Shields, G. A.

    1982-01-01

    Final abundance results of IUE observations of the UV spectra of three H II regions in the Small Magellanic Cloud and four H II regions in the Large Magellanic Cloud are presented. Calculated yields of carbon and oxygen derived are y(C)=.00063 and y(O)=.0016. The nucleosynthetic origin of nitrogen was evaluated as being predominantly a secondary element produced from carbon as its seed. Plotting log N/C versus log C/H yielded the rather unexpected result that log N/C decreases with lo C/H over the SMC-LMC-Orion range. The cause of this relationship is discussed.

  16. Abundances in dwarf irregular galaxies

    NASA Technical Reports Server (NTRS)

    Dufour, Reginald J.

    1986-01-01

    The results of abundance studies of dwarf irregular galaxies and similar objects are reviewed with special attention to variations in the CNO element group. Observations of the forbidden N II and semiforbidden C III lines in the most metal-poor galaxy known, IZw 18, are presented for the first time and CNO abundances are derived via a photoionization model and discussed in the context of the abundances found in other metal-poor H II regions and galaxies.

  17. Taxonomic changes in Solanum section Petota

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  18. Taxonomic revision of Ustilago, Sporisorium and Macalpinomyces.

    PubMed

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

    2012-12-01

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

  19. Mechanisms of Innovation Diffusion under Information Abundance and Information Scarcity--On the Contribution of Social Networks in Group vs. Individual Extension Approaches in Semi-Arid Kenya

    ERIC Educational Resources Information Center

    Darr, Dietrich; Pretzsch, Jurgen

    2008-01-01

    Purpose: The objective of this paper is to assess the effectiveness of innovation diffusion under group-oriented and individual-oriented extension. Current theoretical notions of innovation diffusion in social networks shall be briefly reviewed, and the concepts of "search" and "innovation" vis-a-vis "transfer" and "imitation" mechanisms (Hansen,…

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

    PubMed

    Borkenhagen, Kai; Krupp, Friedhelm

    2013-01-01

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

  1. 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

  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. Partial Knowledge of Word Meanings: Thematic and Taxonomic Representations

    ERIC Educational Resources Information Center

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

    2004-01-01

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

  4. 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

  5. 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

  6. 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

  7. Abundance of Jackfruit ( Artocarpus heterophyllus) Affects Group Characteristics and Use of Space by Golden-Headed Lion Tamarins ( Leontopithecus chrysomelas) in Cabruca Agroforest

    NASA Astrophysics Data System (ADS)

    Oliveira, Leonardo C.; Neves, Leonardo G.; Raboy, Becky E.; Dietz, James M.

    2011-08-01

    Cabruca is an agroforest of cacao trees shaded by native forest trees. It is the predominant vegetation type throughout eastern part of the range of the golden-headed lion tamarins, Leontopithecus chrysomelas, an endangered primate endemic to Atlantic Forest. Understanding how lion tamarins use this agroforest is a conservation priority. To address this question, we documented the diet, home range size, group sizes and composition, density, number of litters and body condition of lion tamarins living in cabruca, and other habitats. Jackfruit, Artocarpus heterophyllus, was the most used species used by lion tamarins in cabruca and was widely available and used throughout the year. In cabruca, home range size was the smallest (22-28 ha) and density of lion tamarins was the highest (1.7 ind/ha) reported for the species. Group size averaged 7.4 individuals and was not significantly different among the vegetation types. In cabruca, groups produced one or two litters a year, and all litters were twins. Adult males in cabruca were significantly heavier than males in primary forest. Our study is the first to demonstrate that breeding groups of golden-headed lion tamarins can survive and reproduce entirely within cabruca agroforest. Jackfruit proved to be a keystone resource for lion tamarins in cabruca, and bromeliads were important as an animal prey foraging microhabitat. In cases where cabruca contains concentrated resources, such as jackfruit and bromeliads, lion tamarins may not only survive and reproduce but may fare better than in other forest types, at least for body condition and reproduction.

  8. 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

  9. Abundance and novel lineages of thraustochytrids in Hawaiian waters.

    PubMed

    Li, Qian; Wang, Xin; Liu, Xianhua; Jiao, Nianzhi; Wang, Guangyi

    2013-11-01

    Thraustochydrids has been known for their ubiquitous distribution in the ocean. However, a few efforts have been made to investigate their ecology. In this study, we have applied molecular method, acriflavine direct detection, and classical oceanographic methods to investigate the abundance and diversity of thraustochytrids in the North Pacific subtropical gyre. Our results revealed interesting temporal and spatial variations of their population. Out of three seasons (spring, summer, and fall), cruise Hawaii Ocean Time-series (HOT)-216 during November 2009 obtained the highest abundance of thraustochytrids ranging from 1,890 (Station S1C1, 45 m) to 630,000 (Station S2C12, 100 m) cells L(-1) of seawater, which accounted for a 0.79 to 281.0 % biomass ratio to that of bacteria in terms of gram carbon per liter. A patchy distribution of these organisms was widely observed in the water column and they were somehow related to the maximum chlorophyll layers. A total of 25 operational taxonomic units (OTUs) from cruise HOT-216 formed four phylogroups in the specific labyrinthulomycetes 18S rRNA-based phylogenetic tree, with the largest group of 20 OTUs fell into the Aplanochytrium cluster and the others aligned with uncultured clones or none, thus appeared to be undescribed. This study indicates the presence of new thraustochytrids lineages and their quantitative importance in the marine water column. PMID:23942794

  10. Analyzing fractal property of species abundance distribution and diversity indexes.

    PubMed

    Su, Qiang

    2016-03-01

    Community diversity is usually characterized by numerical indexes; however it indeed depends on the species abundance distribution (SAD). Diversity indexes and SAD are based on the same information but treating as separate themes. Ranking species abundance from largest to smallest, the decreasing pattern can give the information about the SAD. Frontier proposed such SAD might be a fractal structure, and first applied the Zipf-Mandelbrot model to the SAD study. However, this model fails to include the Zipf model, and also fails to ensure an integer rank. In this study, a fractal model of SAD was reconstructed, and tested with 104 community samples from 8 taxonomic groups. The results show that there was a good fit of the presented model. Fractal parameter (p) determines the SAD of a community. The ecological significance of p relates to the "dominance" of a community. The correlation between p and classical diversity indexes show that Shannon index decreases and Simpson index increases as p increases. The main purpose of this paper is not to compare with other SADs models; it simply provides a new interpretation of SAD model construction, and preliminarily integrates diversity indexes and SAD model into a broader perspective of community diversity. PMID:26746388

  11. 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.

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

    PubMed

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

    2015-02-28

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

  13. Spatiotemporal Changes in the Structure and Composition of a Less-Abundant Bacterial Phylum (Planctomycetes) in Two Perialpine Lakes ▿ †

    PubMed Central

    Pollet, Thomas; Tadonléké, Rémy D.; Humbert, Jean François

    2011-01-01

    We used fingerprinting and cloning-sequencing to study the spatiotemporal dynamics and diversity of Planctomycetes in two perialpine lakes with contrasting environmental conditions. Planctomycetes, which are less-abundant bacteria in freshwater ecosystems, appeared to be structured in the same way as the entire bacterial community in these ecosystems. They were more diversified and displayed fewer temporal variations in the hypolimnia than in the epilimnia. Like the more-abundant bacterial groups in aquatic systems, Planctomycetes communities seem to be composed of a very small number of abundant and widespread operational taxonomic units (OTUs) and a large number of OTUs that are present at low abundance. This indicates that the concept of “abundant or core” and “rare” bacterial phylotypes could also be applied to less-abundant freshwater bacterial phyla. The richness and diversity of Planctomycetes were mainly driven by pH and were similar in both of the lakes studied, whereas the composition of the Planctomycetes community seemed to be determined by a combination of factors including temperature, pH, and nutrients. The relative abundances of the dominant OTUs varied over time and were differently associated with abiotic factors. Our findings demonstrate that less-abundant bacterial phyla, such as Planctomycetes, can display strong spatial and seasonal variations linked to environmental conditions and suggest that their functional role in the lakes studied might be attributable mainly to a small number of phylotypes and vary over space and time in the water column. PMID:21602381

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

    PubMed

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

    2015-03-01

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

  15. 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

  16. 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.

  17. 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).

  18. Stellar Oxygen Abundances

    NASA Astrophysics Data System (ADS)

    King, Jeremy

    1994-04-01

    . [1989, ARAA, 27, 279], persists despite the addition of more O data and may betray the occurrence of a hiatus in star formation between the end of halo formation and the beginning of star formation in the disk. It is noted that the slope of the [O/Fe] versus [Fe/H] relation for [Fe/H] >/= -1 depends on the statistical regression utilized. Hence, alleged "observed" [O/H] - age relations, which do not use truly observed O abundances (but, rather, adopt O abundances based on Fe abundances), should be regarded with caution. Systematic effects on O abundances derived from the 6300A [O I] and 7774A O I lines are considered next. While our Solar observations confirm the disagreement between the observed 7774A O I equivalent widths and LTE model calculations at low microns, we stress that Solar O abundance determinations made from flux spectra are in very good agreement with the meteoritic value. We find the 6300A [O I] equivalent width value appears to be uncertain for the Sun. Given this uncertainty, the inability of authors to reproduce each others' 6300A O abundances, and the results of recent quasi-two-stream calculations, we do not believe it can be readily claimed (as is usually done) that these abundances are more reliable than those derived from the 7774A O I triplet. In a sample of relatively metal-rich F and G dwarfs, we find no systematic difference between the 6300 and 7774A O abundances for Teff abundances are also determined for 8 open clusters or moving groups. A very clear relation between cluster age and O abundance is seen; this is in stark contrast to the lack of any relation between age and Fe abundance in the same clusters. Hence, despite possible a priori objections, O abundances may prove to be a superior chronometer (as others have suggested) in the study of Galactic chemical evolution. Somewhat surprisingly, our our [O/Fe] ratios appear to be larger for the

  19. Glucosinolates in Diplotaxis and Eruca leaves: diversity, taxonomic relations and applied aspects.

    PubMed

    D'Antuono, L Filippo; Elementi, Simona; Neri, Roberta

    2008-01-01

    Leaf glucosinolates of 42 Diplotaxis and 21 Eruca accessions were studied. Total content ranged from 0.25 to more than 70 g kg(-1) dry wt. The 13 clusters, defined on the basis of glucosinolate composition, belonged to two glucosinolate-rich groups, characterised by the prevalence of a single component, and one low-glucosinolate group, with a profile not dominated by any individual component. A sinigrin-rich cluster (D. ibicensis, D. berthautii, D. ilorcitana, D. siettiana, D. tenuisiliqua, D. brevisiliqua, and D. virgata) and a gluconapin-rich cluster (D. catholica, D.siifolia, D. virgata, and D. ollivieri) included all the species previously classified in the nigra phylogenetic lineage. D. virgata was confirmed to be a critical taxon, with one accession slightly diverging from the others. D. siifolia subsp. vicentina was separated from the others in a glucobrassicin-rich cluster. D. harra, a rather isolated representative of sub-genus Hesperidium, clustered together D. assurgens in a sinalbin-rich cluster. Another well defined cluster was represented by D. brachycarpa (gluconasturtin). The two sub-species of D. erucoides were well differentiated by their glucosinolate profile. The low glucosinolate species: D. tenuifolia, D. viminea, D. cretacea, D. muralis (subgenus Diplotaxis), and E. vesicaria, all previously included in the rapa/oleracea lineage, belonged to seven less defined clusters, mainly differing on the presence/absence or the relative abundance of some components (glucoraphanin, glucolepidin, 4-hydroxy-glucobrassicin, 4-phenylbutyl gls, glucoerucin and neoglucobrassicin). The data support previous taxonomic works. Glucosinolate-rich taxa, with well characterised profiles may be suitable for industrial uses, whereas the variability of edible D. tenuifolia and E. vesicaria may represent a basis for breeding horticultural types. PMID:17669448

  20. Contrasting soil fungal community responses to experimental nitrogen addition using the large subunit rRNA taxonomic marker and cellobiohydrolase I functional marker.

    PubMed

    Mueller, Rebecca C; Balasch, Monica M; Kuske, Cheryl R

    2014-09-01

    Human activities have resulted in increased nitrogen inputs into terrestrial ecosystems, but the impact of nitrogen on ecosystem function, such as nutrient cycling, will depend at least in part on the response of soil fungal communities. We examined the response of soil fungi to experimental nitrogen addition in a loblolly pine forest (North Carolina, USA) using a taxonomic marker (large subunit rDNA, LSU) and a functional marker involved in a critical step of cellulose degradation (cellobiohydrolase, cbhI) at five time points that spanned fourteen months. Sampling date had no impact on fungal community richness or composition for either gene. Based on the LSU, nitrogen addition led to increased fungal community richness, reduced relative abundance of fungi in the phylum Basidiomycota and altered community composition; however, similar shifts were not observed with cbhI. Fungal community dissimilarity of the LSU and cbhI genes was significantly correlated in the ambient plots, but not in nitrogen-amended plots, suggesting either functional redundancy of fungi with the cbhI gene or shifts in other functional groups in response to nitrogen addition. To determine whether sequence similarity of cbhI could be predicted based on taxonomic relatedness of fungi, we conducted a phylogenetic analysis of publically available cbhI sequences from known isolates and found that for a subset of isolates, similar cbhI genes were found within distantly related fungal taxa. Together, these findings suggest that taxonomic shifts in the total fungal community do not necessarily result in changes in the functional diversity of fungi. PMID:25039479

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  3. 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

  4. 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

  5. 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

  6. Spatial and temporal variability of planktonic archaeal abundance in the Humboldt Current System off Chile

    NASA Astrophysics Data System (ADS)

    Quiñones, Renato A.; Levipan, Héctor A.; Urrutia, Homero

    2009-07-01

    The latest advances in the field of microbial ecology have shown that planktonic Archaea are one of the most abundant unicellular microorganisms of the oceans. However, no information is available on the contribution this group makes to the prokaryote assemblages that inhabit the eastern South Pacific Ocean. Here, we describe the relative abundance and vertical distribution of planktonic Archaea off northern and central-southern Chile. Data come from several cruises and a 45-month time series at a station located on the shelf off central-southern Chile. Both the taxonomic composition of the prokaryote community and its relative abundance were determined using quantitative dot blot 16S-rRNA hybridizations. Total Archaea in central-southern Chile made up 6-87% of the prokaryote rRNA in the water column and did not present evidence of any seasonal pattern. Crenarchaea were the most abundant archaeal group at this site and were significantly associated with the ammonium concentration ( r2=0.16, p=0.0003, n=80). Archaeal abundance in the time series was usually greater in the deeper layer (>50 m), with contributions reaching up to ˜90% of the prokaryote rRNA on certain occasions, and decreasing towards the surface. Important increments in the relative abundance of total Archaea were observed on given dates at the surface of the time-series station off central-southern Chile. Off northern Chile, total Archaea normally contributed from ˜10% to 50% of the prokaryote rRNA found between 10 and 1000 m, and were generally important in the mesopelagic realm. Our results indicate that Archaea constitute an important fraction of the prokaryote assemblage in the water column of the Humboldt Current System, especially in the oxygen minimum zone.

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

    PubMed

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

    2016-06-01

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

  8. Rumen Methanogenic Genotypes Differ in Abundance According to Host Residual Feed Intake Phenotype and Diet Type

    PubMed Central

    Carberry, CIara A.; Kenny, David A.; Creevey, Christopher J.

    2014-01-01

    Methane is an undesirable end product of rumen fermentative activity because of associated environmental impacts and reduced host feed efficiency. Our study characterized the rumen microbial methanogenic community in beef cattle divergently selected for phenotypic residual feed intake (RFI) while offered a high-forage (HF) diet followed by a low-forage (LF) diet. Rumen fluid was collected from 14 high-RFI (HRFI) and 14 low-RFI (LRFI) animals at the end of both dietary periods. 16S rRNA gene clone libraries were used, and methanogen-specific tag-encoded pyrosequencing was carried out on the samples. We found that Methanobrevibacter spp. are the dominant methanogens in the rumen, with Methanobrevibacter smithii being the most abundant species. Differences in the abundance of Methanobrevibacter smithii and Methanosphaera stadtmanae genotypes were detected in the rumen of animals offered the LF compared to the HF diet while the abundance of Methanobrevibacter smithii genotypes was different between HRFI and LRFI animals irrespective of diet. Our results demonstrate that while a core group of methanogen operational taxonomic units (OTUs) exist across diet and phenotype, significant differences were observed in the distribution of genotypes within those OTUs. These changes in genotype abundance may contribute to the observed differences in methane emissions between efficient and inefficient animals. PMID:24212580

  9. Annual cycle of zooplankton abundance and species composition in Izmit Bay (the northeastern Marmara Sea)

    NASA Astrophysics Data System (ADS)

    Isinibilir, Melek; Kideys, Ahmet E.; Tarkan, Ahmet N.; Yilmaz, I. Noyan

    2008-07-01

    The monthly abundance, biomass and taxonomic composition of zooplankton of Izmit Bay (the northeastern Marmara Sea) were studied from October 2001 to September 2002. Most species within the zooplankton community displayed a clear pattern of succession throughout the year. Generally copepods and cladocerans were the most abundant groups, while the contribution of meroplankton increased at inner-most stations and dominated the zooplankton. Both species number ( S) and diversity ( H') were positively influenced by the increase in salinity of upper layers ( r = 0.30 and r = 0.31, p < 0.001, respectively), while chlorophyll a was negatively affected ( r = -0.36, p < 0.001). Even though Noctiluca scintillans had a significant seasonality ( F11,120 = 8.45, p < 0.001, ANOVA), abundance was not related to fluctuations in temperature and only chlorophyll a was adversely correlated ( r = -0.35, p < 0.001). In general, there are some minor differences in zooplankton assemblages of upper and lower layers. A comparison of the species composition and abundance of Izmit Bay with other Black Sea bays reveals a high similarity between them.

  10. Indirect consequences of fishing: reduction of coralline algae suppresses juvenile coral abundance

    NASA Astrophysics Data System (ADS)

    O'Leary, J. K.; Potts, D. C.; Braga, J. C.; McClanahan, T. R.

    2012-06-01

    Removing predatory fishes has effects that cascade through ecosystems via interactions between species and functional groups. In Kenyan reef lagoons, fishing-induced trophic cascades produce sea urchin-dominated grazing communities that greatly reduce the overall cover of crustose coralline algae (CCA). Certain species of CCA enhance coral recruitment by chemically inducing coral settlement. If sea urchin grazing reduces cover of settlement-inducing CCA, coral recruitment and hence juvenile coral abundance may also decline on fished reefs. To determine whether fishing-induced changes in CCA influence coral recruitment and abundance, we compared (1) CCA taxonomic compositions and (2) taxon-specific associations between CCA and juvenile corals under three fisheries management systems: closed, gear-restricted, and open-access. On fished reefs (gear-restricted and open-access), abundances of two species of settlement-inducing CCA, Hydrolithon reinboldii and H. onkodes, were half those on closed reefs. On both closed and fished reefs, juveniles of four common coral families (Poritidae, Pocilloporidae, Agariciidae, and Faviidae) were more abundant on Hydrolithon than on any other settlement substrate. Coral densities were positively correlated with Hydrolithon spp. cover and were significantly lower on fished than on closed reefs, suggesting that fishing indirectly reduces coral recruitment or juvenile success over large spatial scales via reduction in settlement-inducing CCA. Therefore, managing reefs for higher cover of settlement-inducing CCA may enhance coral recruitment or juvenile survival and help to maintain the ecological and structural stability of reefs.

  11. Rumen methanogenic genotypes differ in abundance according to host residual feed intake phenotype and diet type.

    PubMed

    Carberry, Ciara A; Waters, Sinéad M; Waters, Sinead M; Kenny, David A; Creevey, Christopher J

    2014-01-01

    Methane is an undesirable end product of rumen fermentative activity because of associated environmental impacts and reduced host feed efficiency. Our study characterized the rumen microbial methanogenic community in beef cattle divergently selected for phenotypic residual feed intake (RFI) while offered a high-forage (HF) diet followed by a low-forage (LF) diet. Rumen fluid was collected from 14 high-RFI (HRFI) and 14 low-RFI (LRFI) animals at the end of both dietary periods. 16S rRNA gene clone libraries were used, and methanogen-specific tag-encoded pyrosequencing was carried out on the samples. We found that Methanobrevibacter spp. are the dominant methanogens in the rumen, with Methanobrevibacter smithii being the most abundant species. Differences in the abundance of Methanobrevibacter smithii and Methanosphaera stadtmanae genotypes were detected in the rumen of animals offered the LF compared to the HF diet while the abundance of Methanobrevibacter smithii genotypes was different between HRFI and LRFI animals irrespective of diet. Our results demonstrate that while a core group of methanogen operational taxonomic units (OTUs) exist across diet and phenotype, significant differences were observed in the distribution of genotypes within those OTUs. These changes in genotype abundance may contribute to the observed differences in methane emissions between efficient and inefficient animals. PMID:24212580

  12. Habitat fragmentation and effects of herbivore (howler monkey) abundances on bird species richness.

    PubMed

    Feeley, Kenneth J; Terborgh, John W

    2006-01-01

    Habitat fragmentation can alter herbivore abundances, potentially causing changes in the plant community that can propagate through the food web and eventually influence other important taxonomic groups such as birds. Here we test the relationship between the density of red howler monkeys (Alouatta seniculus) and bird species richness on a large set of recently isolated land-bridge islands in Lago Guri, Venezuela (n = 29 islands). Several of these islands host relict populations of howler monkeys at densities up to more than 30 times greater than those on the mainland. These "hyperabundant" herbivores previously have been shown to have a strong positive influence on aboveground plant productivity. We predicted that this should lead to a positive, indirect effect of howler monkey density on bird species richness. After accounting for passive sampling (the tendency for species richness to be positively associated with island area, regardless of differences in habitat quality) we found a significant positive correlation between howler monkey density and bird species richness. A path analysis incorporating data on tree growth rates from a subset of islands (n = 9) supported the hypothesis that the effect of howler monkeys on the resident bird communities is indirect and is mediated through changes in plant productivity and habitat quality. These results highlight the potential for disparate taxonomic groups to be related through indirect interactions and trophic cascades. PMID:16634305

  13. What are the taxonomic and evolutionary relationships of the Protozoa to the Protista?

    PubMed

    Corliss, J O

    1981-01-01

    In order to consider the problems of protist-protozoan interrelationships in proper perspective, a new "packaging" of phyla within the great kingdom Protista is proposed. Although it is based largely on historical groupings and is admittedly "unnatural" (nor are taxonomic names proposed for my five supraphyletic groupings), the arrangement may clarify some long-persisting problems, especially with regard to mixed algal-protozoan groups and/or phylogenies. Some three dozen phyla are recognized as comprising the kingdom, with the number that might be considered as "protozoan" ranging from 10 to 25, depending on one's viewpoint. No taxon should have the formal name "Protozoa", "Phytoflagellate" and "zooflagellate" are also misleading categories. Taxonomic and evolutionary relationships of phyla containing protozoa (with small "p") are inextricably intermeshed with those of other protist phyla, and thus no unified protozoan super-group exists. PMID:7337817

  14. Charting taxonomic knowledge through ontologies and ranking algorithms

    NASA Astrophysics Data System (ADS)

    Huber, Robert; Klump, Jens

    2009-04-01

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

  15. Spatial distribution and abundance of ammonia-oxidizing microorganisms in deep-sea sediments of the Pacific Ocean.

    PubMed

    Luo, Zhu-Hua; Xu, Wei; Li, Meng; Gu, Ji-Dong; Zhong, Tian-Hua

    2015-08-01

    Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is performed by nitrifying microbes including ammonia-oxidizing bacteria (AOB) and archaea (AOA). In the current study, the phylogenetic diversity and abundance of AOB and AOA in deep-sea sediments of the Pacific Ocean were investigated using ammonia monooxygenase subunit A (amoA) coding genes as molecular markers. The study uncovered 3 AOB unique operational taxonomic units (OTUs, defined at sequence groups that differ by ≤5 %), which indicates lower diversity than AOA (13 OTUs obtained). All AOB amoA gene sequences were phylogenetically related to amoA sequences similar to those found in marine Nitrosospira species, and all AOA amoA gene sequences were affiliated with the marine sediment clade. Quantitative PCR revealed similar archaeal amoA gene abundances [1.68 × 10(5)-1.89 × 10(6) copies/g sediment (wet weight)] among different sites. Bacterial amoA gene abundances ranged from 5.28 × 10(3) to 2.29 × 10(6) copies/g sediment (wet weight). The AOA/AOB amoA gene abundance ratios ranged from 0.012 to 162 and were negatively correlated with total C and C/N ratio. These results suggest that organic loading may be a key factor regulating the relative abundance of AOA and AOB in deep-sea environments of the Pacific Ocean. PMID:26014493

  16. Contrasting soil ciliate species richness and abundance between two tropical plant species: a test of the plant effect.

    PubMed

    Acosta-Mercado, D; Lynn, D H

    2006-05-01

    We still have a rudimentary understanding about the mechanism by which plant roots may stimulate soil microbial interactions. A biochemical model involving plant-derived biochemical fractions, such as exudates, has been used to explain this "rhizosphere effect" on bacteria. However, the variable response of other soil microbial groups, such as protozoa, to the rhizosphere suggests that other factors could be involved in shaping their communities. Thus, two experiments were designed to: (1) determine whether stimulatory and/or inhibiting factors associated with particular plant species regulate ciliate diversity and abundance and (2) obtain a better understanding about the mechanism by which these plant factors operate in the rhizosphere. Bacterial and chemical slurries were reciprocally exchanged between two plant species known to differ in terms of ciliate species richness and abundance (i.e., Canella winterana and plantation Tectona grandis). Analysis of variance showed that the bacteria plus nutrients and the nutrients only treatment had no significant effect on overall ciliate species richness and abundance when compared to the control treatment. However, the use of only colpodean species increased the taxonomic resolution of treatment effects revealing that bacterial slurries had a significant effect on colpodean ciliate species richness. Thus, for particular rhizosphere ciliates, biological properties, such as bacterial diversity or abundance, may have a strong influence on their diversity and possibly abundance. These results are consistent with a model of soil bacteria-mediated mutualisms between plants and protozoa. PMID:16645921

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

    PubMed

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

    2013-01-01

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

  18. 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

  19. Taxonomic etymology - in search of inspiration.

    PubMed

    Jóźwiak, Piotr; Rewicz, Tomasz; Pabis, Krzysztof

    2015-01-01

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

  20. Flexible taxonomic assignment of ambiguous sequencing reads

    PubMed Central

    2011-01-01

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

  1. 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

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

    PubMed

    Tóth, Peter; Undas, Anna K; Verstappen, Francel; Bouwmeester, Harro

    2016-01-01

    The holoparasitic broomrapes, Orobanche spp. and Phelipanche spp. (Orobanchaceae), are root parasites that completely depend on a host plant for survival and reproduction. There is considerable controversy on the taxonomy of this biologically and agronomically important family. Flowers of over 25 parasitic Orobanchaceae and a number of close, parasitic and non-parasitic, relatives emitted a complex blend of volatile organic compounds (VOCs), consisting of over 130 VOCs per species. Floral VOC blend-based phylogeny supported the known taxonomy in internal taxonomic grouping of genus and eliminated the uncertainty in some taxonomical groups. Moreover, phylogenetic analysis suggested separation of the broomrapes into two main groups parasitizing annual and perennial hosts, and for the annual hosts, into weedy and non-weedy broomrapes. We conclude that floral VOCs are a significant tool in species identification and possibly even in defining new species and can help to improve controversial taxonomy in the Orobanchaceae. PMID:27014329

  3. 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

  4. 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

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

    ERIC Educational Resources Information Center

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

    2008-01-01

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

  7. A Test of Taxonomic and Biogeographic Predictivity: Resistance to Potato Virus Y in Wild Relatives of the Cultivated Potato

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A major justification for taxonomic research is its assumed ability to predict the presence of traits in a group for which the trait has been observed in a representative subset of the group. Such predictors are regularly used by breeders interested in choosing potential sources of disease and pest...

  8. Tests of Taxonomic and Biogeographic Predictivity: Resistance to Multiple Disease and Insect Pests in Wild Relatives of Cultivated Potato

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A major justification for taxonomic and biogeographic research is its assumed ability to predict the presence of traits in a group for which the trait has been observed in only a representative subset of the group. Such predictors are regularly used by breeders interested in choosing potential sourc...

  9. 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

  10. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

    PubMed Central

    Segata, Nicola; Börnigen, Daniela; Morgan, Xochitl C.; Huttenhower, Curtis

    2013-01-01

    New microbial genomes are constantly being sequenced, and it is crucial to accurately determine their taxonomic identities and evolutionary relationships. Here we report PhyloPhlAn, a new method to assign microbial phylogeny and putative taxonomy using >400 proteins optimized from among 3,737 genomes. This method measures the sequence diversity of all clades, classifies genomes from deep-branching candidate divisions through closely-related subspecies, and improves consistency between phylogenetic and taxonomic groupings. PhyloPhlAn improved taxonomic accuracy for existing and newly-sequenced genomes, detecting 157 erroneous labels, correcting 46, and placing or refining 130 new genomes. We provide examples of accurate classifications from subspecies (Sulfolobus spp.) to phyla, and of preliminary rooting of deep-branching candidate divisions, including consistent statistical support for Caldiserica (formerly candidate division OP5). PhyloPhlAn will thus be useful for both phylogenetic assessment and taxonomic quality control of newly-sequenced genomes. The final phylogenies, conserved protein sequences, and open-source implementation are available online. PMID:23942190

  11. 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.

  12. Taxonomic and functional metagenomic analysis of anodic communities in two pilot-scale microbial fuel cells treating different industrial wastewaters.

    PubMed

    Kiseleva, Larisa; Garushyants, Sofya K; Ma, Hongwu; Simpson, David J W; Fedorovich, Viatcheslav; Cohen, Michael F; Goryanin, Igor

    2015-01-01

    The combined processes of microbial biodegradation accompanied by extracellular electron transfer make microbial fuel cells (MFCs) a promising new technology for cost-effective and sustainable wastewater treatment. Although a number of microbial species that build biofilms on the anode surfaces of operating MFCs have been identified, studies on the metagenomics of entire electrogenic communities are limited. Here we present the results of whole-genome metagenomic analysis of electrochemically active robust anodic microbial communities, and their anaerobic digester (AD) sludge inocula, from two pilot-scale MFC bioreactors fed with different distillery wastewaters operated under ambient conditions in distinct climatic zones. Taxonomic analysis showed that Proteobacteria, Bacteroidetes and Firmicutes were abundant in AD sludge from distinct climatic zones, and constituted the dominant core of the MFC microbiomes. Functional analysis revealed species involved in degradation of organic compounds commonly present in food industry wastewaters. Also, accumulation of methanogenic Archaea was observed in the electrogenic biofilms, suggesting a possibility for simultaneous electricity and biogas recovery from one integrated wastewater treatment system. Finally, we found a range of species within the anode communities possessing the capacity for extracellular electron transfer, both via direct contact and electron shuttles, and show differential distribution of bacterial groups on the carbon cloth and activated carbon granules of the anode surface. Overall, this study provides insights into structural shifts that occur in the transition from an AD sludge to an MFC microbial community and the metabolic potential of electrochemically active microbial populations with wastewater-treating MFCs. PMID:26673789

  13. Chironomus group classification according to the mapping of polytene chromosomes

    NASA Astrophysics Data System (ADS)

    Salleh, Syafinaz; Kutty, Ahmad Abas

    2013-11-01

    Chironomus is one of the important genera in Chironomidae family since they are widely diverse and abundance in aquatic ecosystem. Since Chironomus is very diverse, taxonomic work on this genus is very difficult and incomplete. Objective of this study is to form group classification of Chironomus according to the polytene chromosome mapping. The specific characteristics of polytene chromosomes in the salivary gland appeared to be particularly promising for taxonomic diagnosis of chironomid species. Chironomid larvae were collected from pristine sites at Sg. Langat and cultured in laboratory to reach fourth instar stage. The salivary glands were removed from larvae and chromosomes were stained with aceto orcein. Results showed that polytene chromosomes of Chironomus comprise of three long metacentric or submetacentric arms (BF, CD and AE arms) and one short acrocentric (G arm). In regards to nucleolar organizing region (NOR), Balbiani ring (BR), puffings and chromosome rearrangement, a number of four groups of different banding patterns were found. Two groups called as G group A and B have common NOR on arm BF and BR on arm G. However, group A has rearrangement pattern on arm CD and not in group B. This makes group B separated from group A. Another two groups called as groups C and D do not have common NOR on arm BF and also BR on arm G. Groups C and D were separated using arms G and arm AE. At arm G, only group C rearrangement pattern at unit 23c whereas group D was found to have large NOR at arm G and as well as arm AE, only group D has rearrangement pattern at unit 12c. This study indicates that chromosome arrangement could aid in revealing Chironomus diversity.

  14. Contribution of different functional groups to the diet of major predatory fishes at a seagrass meadow in northeastern Japan

    NASA Astrophysics Data System (ADS)

    Yamada, Katsumasa; Hori, Masakazu; Tanaka, Yoshiyuki; Hasegawa, Natsuki; Nakaoka, Masahiro

    2010-01-01

    We examined the variation in habitat use and diet of three dominant fish species ( Myoxocephalus brandti, Pholidapus dybowskii, and Pholis crassispina) in a seagrass meadow in the Akkeshi-ko estuary in northeastern Japan, where broad and dense Zostera marina beds exist, using a semi-quantitative census of the fishes and analyses of their stomach contents. Differences among the three fish species in the temporal variation in abundance of each age class (mainly 1- and 2-year age classes) indicated that the temporal pattern of utilization of the seagrass meadow were different among them. In the semi-quantitative dietary analysis, two prey categories, i.e., taxonomic group (order and suborder) and functional group, were used to explain the variation in prey composition with size-dependent changes. The six prey functional groups were classified based on the ecological traits of the prey, i.e., trophic level, size, and life type (habitat and behavior). Ontogenetic shifts in prey of the three fish species could be fully explained by a combination of the two prey categories, and not by the use of only one category (taxonomic or functional group). The pattern of ontogenetic shifts in prey differed among the fish species and size (age) classes. These results indicate that segregation of habitat (seagrass meadow) and prey group (taxonomic and functional group) is performed among the three species, which may contribute to their coexistence in this estuary.

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

    PubMed

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

    2014-06-01

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

  16. 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

  17. A taxonomic survey of comet composition 1985-2004 using CCD spectroscopy

    NASA Astrophysics Data System (ADS)

    Fink, Uwe

    2009-05-01

    A summary is presented of our spectroscopic survey of comets extending for roughly 19 years from 1985 to 2004 comprising data for 92 comets of which 50 showed good emissions. All data were re-analyzed using consistent reduction techniques. Our observations of comets over several apparitions and comets observed over an extended period indicate no major changes in compositional classification. To our regret, no major unidentified cometary features were found in our surveyed spectral region of 5200-10400 Å. Absolute production rates for the dominant parent molecule H 2O and the daughter species C 2, NH 2 and CN are determined within the limits of the Haser model as are values for the dust continuum, Afρ. From these data, production rate ratios are calculated for C 2/H 2O, NH 2/H 2O, CN/H 2O and Afρ/H 2O. Excluding the odd Comets Yanaka (1988r), 43P/Wolf-Harrington and 19P/Borrelly, with unusual spectra, our set of comets exhibited relatively uniform composition. Detailed analyses of our data resulted in four taxonomic classes: Comets of typical composition (˜70%); exhibiting typical ratios with respect to water of C 2, NH 2, and CN. Tempel 1 type (˜22%); having a deficiency in C 2 but normal NH 2 abundance. G-Z type (˜6%); having both low C 2 and NH 2 ratios. The unusual object Yanaka (1988r) (˜2%?); no detectable C 2 or CN emission but normal NH 2. It is uncertain whether there is a clear separation between the comets of typical composition and those with C 2 depletion, or whether the latter consists of a group showing a continuum of decreasing C 2/CN ratios. Our spectroscopic investigations result in a visual record of the various compositional classes, which are illustrated in a number of figures. Production rate comparisons with the comet photometry program of Schleicher and A'Hearn [A'Hearn, M.F., and 4 colleagues, 1995. Icarus 118, 223-270] for 13 comets in common yielded good agreement once the different scale lengths are taken into account. An

  18. 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.

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

    PubMed

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

    2015-01-01

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

  20. 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

  1. 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.

  2. Effect of taxonomic resolution on ecological and palaeoecological inference - a test using testate amoeba water table depth transfer functions

    NASA Astrophysics Data System (ADS)

    Mitchell, Edward A. D.; Lamentowicz, Mariusz; Payne, Richard J.; Mazei, Yuri

    2014-05-01

    Sound taxonomy is a major requirement for quantitative environmental reconstruction using biological data. Transfer function performance should theoretically be expected to decrease with reduced taxonomic resolution. However for many groups of organisms taxonomy is imperfect and species level identification not always possible. We conducted numerical experiments on five testate amoeba water table (DWT) transfer function data sets. We sequentially reduced the number of taxonomic groups by successively merging morphologically similar species and removing inconspicuous species. We then assessed how these changes affected model performance and palaeoenvironmental reconstruction using two fossil data sets. Model performance decreased with decreasing taxonomic resolution, but this had only limited effects on patterns of inferred DWT, at least to detect major dry/wet shifts. Higher-resolution taxonomy may however still be useful to detect more subtle changes, or for reconstructed shifts to be significant.

  3. 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

  4. Taxonomic and Functional Resilience of Grasshoppers (Orthoptera, Caelifera) to Fire in South Brazilian Grasslands.

    PubMed

    Ferrando, C P R; Podgaiski, L R; Costa, M K M; Mendonça, M D S

    2016-08-01

    Fire is a frequent disturbance in grassland ecosystems enabling variability in habitat characteristics and creating important environmental filters for community assembly. Changes in vegetation have a large influence on herbivore insect assemblages. Here, we explored the responses of grasshoppers to disturbance by fire in grasslands of southern Brazil through a small-scale experiment based in paired control and burned plots. The resilience of grasshoppers was assessed by monitoring changes to their abundance, taxonomic, and functional parameters along time. Burned patches have been already recolonized by grasshoppers 1 month after fire and did not differ in terms of abundance and richness from control areas in any evaluated time within 1 year. Simpson diversity decreased 1 month after fire due to the increased dominance of Dichroplus misionensis (Carbonell) and Orphulella punctata (De Geer). In this period, grasshoppers presented in average a smaller body and a larger relative head size; these are typically nymph characteristics, which are possibly indicating a preference of juveniles for the young high-quality vegetation, or a diminished vulnerability to predation in open areas. Further, at 6 months after fire grasshoppers with smaller relative hind femur and thus lower dispersal ability seemed to be benefitted in burned patches. Finally, 1 year after fire grasshoppers became more similar to each other in relation to their set of traits. This study demonstrates how taxonomic and functional aspects of grasshopper assemblages can be complementary tools to understand their responses to environmental change. PMID:26957086

  5. Slope and deep-sea abundance across scales: Southern Ocean isopods show how complex the deep sea can be

    NASA Astrophysics Data System (ADS)

    Kaiser, Stefanie; Barnes, David K. A.; Brandt, Angelika

    2007-08-01

    How animals are distributed in the world's largest surface environment, the deep sea, is poorly understood. The ANDEEP (ANtarctic benthic DEEP-sea biodiversity, colonisation history and recent community patterns) III cruise probed richness and abundance of one group, peracarid crustaceans (isopods, amphipods, cumaceans, tanaidaceans, mysidaceans), as a model of deep-sea fauna across Southern Ocean (SO) sites. Analysis of samples from the ANDEEP cruises reveals SO isopods to be highly abundant, rich and endemic as many other taxa in the region are known to be. Samples taken across three spatial scales include sites tens, hundreds and thousands of kilometers apart, sites stretching from the Southern Cape Basin (South Atlantic) to continental Antarctica and including depths from 1030 to 5000 m. Across these spatial scales we investigated ecological success (abundance) of peracarids at order, family, and species levels. Remarkably no significant relationship was found between abundance and spatial scale at any taxonomic level. That is, the variability in abundance at major regional scale is no different to that across just tens of kilometres. Most taxa were represented in only a few samples, but we suggest most inhabitants of the deep Weddell Sea environment to be very patchy rather than rare. Separate plots of family, genus, and species abundance by sample number revealed this to be true—nearly all genera and species are an order of magnitude more abundant than 'background' levels in just one or two samples. Our isopod and amphipod samples reveal the Atlantic sector of the SO, one of the most dynamic and important regions influencing the global deep-sea environment, to be highly complex. Our study suggests that, at least with regard to the study taxa and area, the typical comparisons of regions that are made by ecologists miss the scale at which crucial ecological variability happens. Even without ice scours creating topographical complexity (as on the shelf) the

  6. Abundance, depth distribution, and composition of aerobic bacteriochlorophyll a-producing bacteria in four basins of the central Baltic Sea.

    PubMed

    Salka, Ivette; Moulisová, Vladimíra; Koblízek, Michal; Jost, Günter; Jürgens, Klaus; Labrenz, Matthias

    2008-07-01

    The abundance, vertical distribution, and diversity of aerobic anoxygenic phototrophic bacteria (AAP) were studied at four basins of the Baltic Sea. AAP were enumerated by infrared epifluorescence microscopy, and their diversity was analyzed by using pufM gene clone libraries. In addition, numbers of CFU containing the pufM gene were determined, and representative strains were isolated. Both approaches indicated that AAP reached maximal abundance in the euphotic zone. Maximal AAP abundance was 2.5 x 10(5) cells ml(-1) (11% of total prokaryotes) or 1.0 x 10(3) CFU ml(-1) (9 to 10% of total CFU). Environmental pufM clone sequences were grouped into 11 operational taxonomic units phylogenetically related to cultivated members of the Alpha-, Beta-, and Gammaproteobacteria. In spite of varying pufM compositions, five clones were present in all libraries. Of these, Jannaschia-related clones were always found in relative abundances representing 25 to 30% of the total AAP clones. The abundances of the other clones varied. Clones potentially affiliated with typical freshwater Betaproteobacteria sequences were present at three Baltic Sea stations, whereas clones grouping with Loktanella represented 40% of the total cell numbers in the Gotland Basin. For three alphaproteobacterial clones, probable pufM phylogenetic relationships were supported by 16S rRNA gene analyses of Baltic AAP isolates, which showed nearly identical pufM sequences. Our data indicate that the studied AAP assemblages represented a mixture of marine and freshwater taxa, thus characterizing the Baltic Sea as a "melting pot" of abundant, polyphyletic aerobic photoheterotrophic bacteria. PMID:18502937

  7. Predicting taxonomic and thematic relational responding

    PubMed Central

    Osborne, J. Grayson; Heath, John

    2003-01-01

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

  8. Nitrogen and phosphorus additions impact arbuscular mycorrhizal abundance and molecular diversity in a tropical montane forest.

    PubMed

    Camenzind, Tessa; Hempel, Stefan; Homeier, Jürgen; Horn, Sebastian; Velescu, Andre; Wilcke, Wolfgang; Rillig, Matthias C

    2014-12-01

    Increased nitrogen (N) depositions expected in the future endanger the diversity and stability of ecosystems primarily limited by N, but also often co-limited by other nutrients like phosphorus (P). In this context a nutrient manipulation experiment (NUMEX) was set up in a tropical montane rainforest in southern Ecuador, an area identified as biodiversity hotspot. We examined impacts of elevated N and P availability on arbuscular mycorrhizal fungi (AMF), a group of obligate biotrophic plant symbionts with an important role in soil nutrient cycles. We tested the hypothesis that increased nutrient availability will reduce AMF abundance, reduce species richness and shift the AMF community toward lineages previously shown to be favored by fertilized conditions. NUMEX was designed as a full factorial randomized block design. Soil cores were taken after 2 years of nutrient additions in plots located at 2000 m above sea level. Roots were extracted and intraradical AMF abundance determined microscopically; the AMF community was analyzed by 454-pyrosequencing targeting the large subunit rDNA. We identified 74 operational taxonomic units (OTUs) with a large proportion of Diversisporales. N additions provoked a significant decrease in intraradical abundance, whereas AMF richness was reduced significantly by N and P additions, with the strongest effect in the combined treatment (39% fewer OTUs), mainly influencing rare species. We identified a differential effect on phylogenetic groups, with Diversisporales richness mainly reduced by N additions in contrast to Glomerales highly significantly affected solely by P. Regarding AMF community structure, we observed a compositional shift when analyzing presence/absence data following P additions. In conclusion, N and P additions in this ecosystem affect AMF abundance, but especially AMF species richness; these changes might influence plant community composition and productivity and by that various ecosystem processes. PMID:24764217

  9. 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

  10. 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

  11. Solar abundance of osmium

    PubMed Central

    Jacoby, George; Aller, Lawrence H.

    1976-01-01

    The abundance parameter, log gfA, where g is the statistical weight of the lower level, f is the oscillator strength, and A is the abundance (by numbers of atoms with respect to hydrogen), has been derived for three lines of osmium by a method of spectrum synthesis. An apparent discordance of the derived abundance with that found from the carbonaceous chondrites is probably to be attributed primarily to errors in the f-values, and blending with unknown contributors. PMID:16592314

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

    ERIC Educational Resources Information Center

    Vogt, Kenneth D.

    1993-01-01

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

  13. Lightcurve Analysis of Five Taxonomic A-class Asteroids

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

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

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

    PubMed Central

    Mirman, Daniel; Graziano, Kristen M.

    2011-01-01

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

  15. 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.

  16. Influence of Top-Down and Bottom-Up Manipulations on the R-BT065 Subcluster of β-Proteobacteria, an Abundant Group in Bacterioplankton of a Freshwater Reservoir

    PubMed Central

    Šimek, Karel; Horňák, Karel; Jezbera, Jan; Mašín, Michal; Nedoma, Jiří; Gasol, Josep M.; Schauer, Michael

    2005-01-01

    We studied the effects of nutrient availability and protistan grazing on bacterial dynamics and community composition (BCC) in different parts of the canyon-shaped Římov reservoir (Czech Republic). The effects of protistan grazing on BCC were examined using a size fractionation approach. Water from the dam area with only bacteria (<0.8 μm), bacteria and heterotrophic nanoflagellates (<5 μm), or whole water were incubated in situ inside dialysis bags. Top-down or predator manipulations (size fractionation) were also combined with bottom-up or resource manipulations, i.e., transplantation of samples to the middle and upper inflow parts of the reservoir with increased phosphorus availability. Significant genotypic shifts in BCC occurred with transplantation as indicated by denaturing gradient gel electrophoresis. Using different probes for fluorescence in situ hybridization, we found that 10 to 50% of total bacteria were members of the phylogenetically small cluster of β-proteobacteria (targeted with the probe R-BT065). These rod-shaped cells of very uniform size were vulnerable to predation but very fast growing and responded markedly to the different experimental manipulations. In all the grazer-free treatments, the members of the R-BT065 cluster showed the highest net growth rates of all studied bacterial groups. Moreover, their relative abundance was highly correlated with bacterial bulk parameters and proportions of bacteria with high nucleic acid (HNA) content. In contrast, increasing protistan bacterivory yielded lower proportions of R-BT065-positive and HNA bacteria substituted by increasing proportions of the class Actinobacteria, which profited from the enhanced protistan bacterivory. PMID:15870325

  17. 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.

  18. Population density and taxonomic composition of bacterial nanoforms in soils of Russia

    NASA Astrophysics Data System (ADS)

    Lysak, L. V.; Lapygina, E. V.; Konova, I. A.; Zvyagintsev, D. G.

    2010-07-01

    The population density, physiological state, and taxonomic composition of bacterial nanoforms were first studied in soils of Russia. It was demonstrated with the help of fluorescent microscopy that the populations of nanoforms in the studied soils are very high and comprise tens and hundreds of millions of cells per 1 g of soil. The portion of cells with undamaged cell membranes was significantly higher in the nanoforms (95-98%) than in the cells of common size (about 50%), and this fact suggests the viability of the nanoforms. The taxonomic diversity of the nanoforms is great; the representatives of the main phylogenetic groups widespread in the soils were found among the nanoforms, namely, Archaea, Actinobacteria, Cytophaga, and Proteobacteria. The results allow assuming that the transformation of the cells into nanoforms is a relatively common event in the life of soil bacteria, allowing them to remain viable under unfavorable conditions and participate actively in soil processes.

  19. 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

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

    PubMed

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

    2016-06-20

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

  1. A Test of Taxonomic and Biogeographic Predictivity: Resistance to Potato Virus Y in Wild Relatives of the Cultivated Potato

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A major justification for taxonomic research is its assumed ability to predict traits in a group for which the trait has been observed in a representative subset. In this study, we evaluated potato virus Y resistance using 135 accessions of potato to determine whether we can predict the distributio...

  2. The Taxonomic Instruction Project: A Manual of Principles and Practices Pertaining to the Content of Instruction. First Report.

    ERIC Educational Resources Information Center

    Reichart, Sandford; And Others

    Presented is the first of three reports on taxonomic instruction, which is defined as a method of systematizing strategies and substances of instruction for purposes of diagnostic teaching. The target population is a group of behaviorally disordered, underachieving boys, aged 10 to 15, and the instructional content is reading, which is divided…

  3. Physical and biological control of protistan community composition, distribution and abundance in the seasonal ice zone of the Southern Ocean between 30 and 80°E

    NASA Astrophysics Data System (ADS)

    Davidson, Andrew T.; Scott, Fiona J.; Nash, Geraldine V.; Wright, Simon W.; Raymond, Ben

    2010-05-01

    Protists are critical components of the Antarctic marine ecosystem as they comprise most of the living carbon and are the base of the Antarctic food web. They are also key determinants of vertical carbon flux and mediate draw-down of atmospheric CO 2 by the ocean. The community composition, abundance and distribution of marine protists (phytoplankton and protozoa) was studied during the Baseline Research on Oceanography, Krill and the Environment-West (BROKE-West) survey, in the seasonal ice zone during the 2005-2006 austral summer between 30°E and 80°E. Light and electron microscopy were used to determine the protistan composition and abundance in samples obtained at 30 sites from surface waters and at 26 sites from the depth of the maximum in situ chlorophyll fluorescence (Chl max). Cluster analysis was used to identify 5 groups of sample sites at the surface and 5 at the Chl max that were of similar protist composition and abundance. The physical characteristics, taxonomic composition, indicator taxa, and taxonomic diversity were determined for each group. In the southwest, a bloom of colonial Phaeocystis antarctica dominated the protistan community composition and biomass amongst the receding ice, but this was replaced by the flagellate life stage/s of this haptophyte in waters to the north. In the southeast, a diatom bloom had the highest diversity of protist taxa observed during the survey and centric diatoms dominated the biomass. Outside these blooms, grazing by krill probably reduced the composition and abundance of large diatoms and autotrophic dinoflagellates in coastal to mid-inshore waters. Only in offshore waters did large diatoms and dinoflagellates increase in abundance and diversity, despite low concentrations of iron and silicate at many of these sites. This increase was probably due to reduced top-down control by krill and other large zooplankton. Large diatoms dominated in offshore waters, despite other coincident studies showing that the

  4. Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria.

    PubMed

    Farrant, Gregory K; Doré, Hugo; Cornejo-Castillo, Francisco M; Partensky, Frédéric; Ratin, Morgane; Ostrowski, Martin; Pitt, Frances D; Wincker, Patrick; Scanlan, David J; Iudicone, Daniele; Acinas, Silvia G; Garczarek, Laurence

    2016-06-14

    Prochlorococcus and Synechococcus are the two most abundant and widespread phytoplankton in the global ocean. To better understand the factors controlling their biogeography, a reference database of the high-resolution taxonomic marker petB, encoding cytochrome b6, was used to recruit reads out of 109 metagenomes from the Tara Oceans expedition. An unsuspected novel genetic diversity was unveiled within both genera, even for the most abundant and well-characterized clades, and 136 divergent petB sequences were successfully assembled from metagenomic reads, significantly enriching the reference database. We then defined Ecologically Significant Taxonomic Units (ESTUs)-that is, organisms belonging to the same clade and occupying a common oceanic niche. Three major ESTU assemblages were identified along the cruise transect for Prochlorococcus and eight for Synechococcus Although Prochlorococcus HLIIIA and HLIVA ESTUs codominated in iron-depleted areas of the Pacific Ocean, CRD1 and the yet-to-be cultured EnvB were the prevalent Synechococcus clades in this area, with three different CRD1 and EnvB ESTUs occupying distinct ecological niches with regard to iron availability and temperature. Sharp community shifts were also observed over short geographic distances-for example, around the Marquesas Islands or between southern Indian and Atlantic Oceans-pointing to a tight correlation between ESTU assemblages and specific physico-chemical parameters. Together, this study demonstrates that there is a previously overlooked, ecologically meaningful, fine-scale diversity within some currently defined picocyanobacterial ecotypes, bringing novel insights into the ecology, diversity, and biology of the two most abundant phototrophs on Earth. PMID:27302952

  5. Structure and taxonomic composition of free-living nematode and macrofaunal assemblages in a eutrophic subtropical harbour, Hong Kong.

    PubMed

    Xu, W Z; Cheung, S G; Shin, Paul K S

    2014-08-30

    The spatial and seasonal taxonomic composition patterns of macrofauna and nematodes in a eutrophic subtropical harbour, previously suffered from sewage pollution, were studied in relation to a number of sediment parameters. In the polluted, inner-harbour area, levels of organic contents and heavy metals were high, whereas species number, abundance and diversity of nematodes and macrofauna were the lowest in comparison to the cleaner, outer-harbour area. Different taxonomic composition patterns of nematodes and macrofaunal assemblages were found between inner-harbour and outer-harbour area, which was highly correlated with sediment nutrient levels. Different responses of macrofaunal and nematode communities to sewage pollution suggested that macrofauna might be more tolerant than nematodes to eutrophic conditions due to their ability to modify the sediment. The present findings indicated the usefulness of studying both nematode and macrofaunal communities, in order to reveal different aspects of the benthic ecosystems in response to organic enrichment. PMID:24467853

  6. Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis

    PubMed Central

    Manor, Ohad; Levy, Roie; Pope, Christopher E.; Hayden, Hillary S.; Brittnacher, Mitchell J.; Carr, Rogan; Radey, Matthew C.; Hager, Kyle R.; Heltshe, Sonya L.; Ramsey, Bonnie W.; Miller, Samuel I.; Hoffman, Lucas R.; Borenstein, Elhanan

    2016-01-01

    Cystic fibrosis (CF) results in inflammation, malabsorption of fats and other nutrients, and obstruction in the gastrointestinal (GI) tract, yet the mechanisms linking these disease manifestations to microbiome composition remain largely unexplored. Here we used metagenomic analysis to systematically characterize fecal microbiomes of children with and without CF, demonstrating marked CF-associated taxonomic dysbiosis and functional imbalance. We further showed that these taxonomic and functional shifts were especially pronounced in young children with CF and diminished with age. Importantly, the resulting dysbiotic microbiomes had significantly altered capacities for lipid metabolism, including decreased capacity for overall fatty acid biosynthesis and increased capacity for degrading anti-inflammatory short-chain fatty acids. Notably, these functional differences correlated with fecal measures of fat malabsorption and inflammation. Combined, these results suggest that enteric fat abundance selects for pro-inflammatory GI microbiota in young children with CF, offering novel strategies for improving the health of children with CF-associated fat malabsorption. PMID:26940651

  7. Diverse Effects of a Seven-Year Experimental Grassland Fragmentation on Major Invertebrate Groups.

    PubMed

    Braschler, Brigitte; Baur, Bruno

    2016-01-01

    Habitat fragmentation is a major driver of biodiversity loss, but observed effects vary and may depend on the group examined. Time since fragmentation may explain some differences between taxonomical groups, as some species and thus species composition respond with a delay to changes in their environment. Impacts of drivers of global change may thus be underestimated in short-term studies. In our study we experimentally fragmented nutrient-poor dry calcareous grasslands and studied the response of species richness, individual density and species composition of various groups of invertebrates (gastropods, ants, ground beetles, rove beetles, orthoptera, spiders, woodlice) in 12 small (1.5 m * 1.5 m) and 12 large (4.5 m * 4.5 m) fragments and their corresponding control plots after 7 years. We further examined responses to fragmentation in relation to body size and habitat preferences. Responses to fragmentation varied between taxonomical groups. While spider species richness and individual density were lower in fragments, the opposite was true for an orthopteran species and woodlice. Species composition and β-diversity differed between fragments and control plots for some groups. However, the interaction treatment*plot size was rarely significant. Species with high occupancy rates in undisturbed control plots responded more negatively to the fragmentation, while species with large body size were relatively more abundant in fragments in some groups. No effect of the fragmentation was found for ants, which may have the longest lag times because of long-lived colonies. However, relationships between abundance and the species' preferences for environmental factors affected by edge effects indicate that ant diversity too may be affected in the longer-term. Our results show the importance of considering different groups in conservation management in times of widespread fragmentation of landscapes. While species richness may respond slowly, changes in abundance related to

  8. Diverse Effects of a Seven-Year Experimental Grassland Fragmentation on Major Invertebrate Groups

    PubMed Central

    Braschler, Brigitte; Baur, Bruno

    2016-01-01

    Habitat fragmentation is a major driver of biodiversity loss, but observed effects vary and may depend on the group examined. Time since fragmentation may explain some differences between taxonomical groups, as some species and thus species composition respond with a delay to changes in their environment. Impacts of drivers of global change may thus be underestimated in short-term studies. In our study we experimentally fragmented nutrient-poor dry calcareous grasslands and studied the response of species richness, individual density and species composition of various groups of invertebrates (gastropods, ants, ground beetles, rove beetles, orthoptera, spiders, woodlice) in 12 small (1.5 m * 1.5 m) and 12 large (4.5 m * 4.5 m) fragments and their corresponding control plots after 7 years. We further examined responses to fragmentation in relation to body size and habitat preferences. Responses to fragmentation varied between taxonomical groups. While spider species richness and individual density were lower in fragments, the opposite was true for an orthopteran species and woodlice. Species composition and β-diversity differed between fragments and control plots for some groups. However, the interaction treatment*plot size was rarely significant. Species with high occupancy rates in undisturbed control plots responded more negatively to the fragmentation, while species with large body size were relatively more abundant in fragments in some groups. No effect of the fragmentation was found for ants, which may have the longest lag times because of long-lived colonies. However, relationships between abundance and the species’ preferences for environmental factors affected by edge effects indicate that ant diversity too may be affected in the longer-term. Our results show the importance of considering different groups in conservation management in times of widespread fragmentation of landscapes. While species richness may respond slowly, changes in abundance related

  9. 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

  10. 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

  11. 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

  12. 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

  13. [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

  14. 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

  15. Geographical Range and Local Abundance of Tree Species in China

    PubMed Central

    Ren, Haibao; Condit, Richard; Chen, Bin; Mi, Xiangcheng; Cao, Min; Ye, Wanhui; Hao, Zhanqing; Ma, Keping

    2013-01-01

    Most studies on the geographical distribution of species have utilized a few well-known taxa in Europe and North America, with little research in China and its wide range of climate and forest types. We assembled large datasets to quantify the geographic ranges of tree species in China and to test several biogeographic hypotheses: 1) whether locally abundant species tend to be geographically widespread; 2) whether species are more abundant towards their range-centers; and 3) how abundances are correlated between sites. Local abundances of 651 species were derived from four tree plots of 20–25 ha where all individuals ≥1 cm in stem diameter were mapped and identified taxonomically. Range sizes of these species across China were then estimated from over 460,000 geo-referenced records; a Bayesian approach was used, allowing careful measures of error of each range estimate. The log-transformed range sizes had a bell-shaped distribution with a median of 703,000 km2, and >90% of 651 species had ranges >105 km2. There was no relationship between local abundance and range size, and no evidence for species being more abundant towards their range-centers. Finally, species’ abundances were positively correlated between sites. The widespread nature of most tree species in China suggests few are vulnerable to global extinction, and there is no indication of the double-peril that would result if rare species also had narrow ranges. PMID:24130772

  16. Microbial distribution and abundance in the digestive system of five shipworm species (Bivalvia: Teredinidae).

    PubMed

    Betcher, Meghan A; Fung, Jennifer M; Han, Andrew W; O'Connor, Roberta; Seronay, Romell; Concepcion, Gisela P; Distel, Daniel L; Haygood, Margo G

    2012-01-01

    Marine bivalves of the family Teredinidae (shipworms) are voracious consumers of wood in marine environments. In several shipworm species, dense communities of intracellular bacterial endosymbionts have been observed within specialized cells (bacteriocytes) of the gills (ctenidia). These bacteria are proposed to contribute to digestion of wood by the host. While the microbes of shipworm gills have been studied extensively in several species, the abundance and distribution of microbes in the digestive system have not been adequately addressed. Here we use Fluorescence In-Situ Hybridization (FISH) and laser scanning confocal microscopy with 16S rRNA directed oligonucleotide probes targeting all domains, domains Bacteria and Archaea, and other taxonomic groups to examine the digestive microbiota of 17 specimens from 5 shipworm species (Bankia setacea, Lyrodus pedicellatus, Lyrodus massa, Lyrodus sp. and Teredo aff. triangularis). These data reveal that the caecum, a large sac-like appendage of the stomach that typically contains large quantities of wood particles and is considered the primary site of wood digestion, harbors only very sparse microbial populations. However, a significant number of bacterial cells were observed in fecal pellets within the intestines. These results suggest that due to low abundance, bacteria in the caecum may contribute little to lignocellulose degradation. In contrast, the comparatively high population density of bacteria in the intestine suggests a possible role for intestinal bacteria in the degradation of lignocellulose. PMID:23028923

  17. Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities.

    PubMed

    Paula, Fabiana S; Rodrigues, Jorge L M; Zhou, Jizhong; Wu, Liyou; Mueller, Rebecca C; Mirza, Babur S; Bohannan, Brendan J M; Nüsslein, Klaus; Deng, Ye; Tiedje, James M; Pellizari, Vivian H

    2014-06-01

    Land use change in the Amazon rainforest alters the taxonomic structure of soil microbial communities, but whether it alters their functional gene composition is unknown. We used the highly parallel microarray technology GeoChip 4.0, which contains 83,992 probes specific for genes linked nutrient cycling and other processes, to evaluate how the diversity, abundance and similarity of the targeted genes responded to forest-to-pasture conversion. We also evaluated whether these parameters were reestablished with secondary forest growth. A spatially nested scheme was employed to sample a primary forest, two pastures (6 and 38 years old) and a secondary forest. Both pastures had significantly lower microbial functional genes richness and diversity when compared to the primary forest. Gene composition and turnover were also significantly modified with land use change. Edaphic traits associated with soil acidity, iron availability, soil texture and organic matter concentration were correlated with these gene changes. Although primary and secondary forests showed similar functional gene richness and diversity, there were differences in gene composition and turnover, suggesting that community recovery was not complete in the secondary forest. Gene association analysis revealed that response to ecosystem conversion varied significantly across functional gene groups, with genes linked to carbon and nitrogen cycling mostly altered. This study indicates that diversity and abundance of numerous environmentally important genes respond to forest-to-pasture conversion and hence have the potential to affect the related processes at an ecosystem scale. PMID:24806276

  18. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China

    NASA Astrophysics Data System (ADS)

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-11-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g-1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.

  19. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China

    PubMed Central

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-01-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to −25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g−1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments. PMID:26522086

  20. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China.

    PubMed

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-01-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 10(4) to 8.5 × 10(9) copies g(-1)), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments. PMID:26522086

  1. Microbial Distribution and Abundance in the Digestive System of Five Shipworm Species (Bivalvia: Teredinidae)

    PubMed Central

    Betcher, Meghan A.; Fung, Jennifer M.; Han, Andrew W.; O’Connor, Roberta; Seronay, Romell; Concepcion, Gisela P.; Distel, Daniel L.; Haygood, Margo G.

    2012-01-01

    Marine bivalves of the family Teredinidae (shipworms) are voracious consumers of wood in marine environments. In several shipworm species, dense communities of intracellular bacterial endosymbionts have been observed within specialized cells (bacteriocytes) of the gills (ctenidia). These bacteria are proposed to contribute to digestion of wood by the host. While the microbes of shipworm gills have been studied extensively in several species, the abundance and distribution of microbes in the digestive system have not been adequately addressed. Here we use Fluorescence In-Situ Hybridization (FISH) and laser scanning confocal microscopy with 16S rRNA directed oligonucleotide probes targeting all domains, domains Bacteria and Archaea, and other taxonomic groups to examine the digestive microbiota of 17 specimens from 5 shipworm species (Bankia setacea, Lyrodus pedicellatus, Lyrodus massa, Lyrodus sp. and Teredo aff. triangularis). These data reveal that the caecum, a large sac-like appendage of the stomach that typically contains large quantities of wood particles and is considered the primary site of wood digestion, harbors only very sparse microbial populations. However, a significant number of bacterial cells were observed in fecal pellets within the intestines. These results suggest that due to low abundance, bacteria in the caecum may contribute little to lignocellulose degradation. In contrast, the comparatively high population density of bacteria in the intestine suggests a possible role for intestinal bacteria in the degradation of lignocellulose. PMID:23028923

  2. Resolving microbial membership using Abundance and Variability In Taxonomy ('AVIT ).

    PubMed

    Chakrabarti, Anirikh; Siddharth, Jay; Lauber, Christian L; Membrez, Mathieu; Betrisey, Bertrand; Loyer, Carole; Chou, Chieh Jason; Pataky, Zoltan; Golay, Alain; Parkinson, Scott J

    2016-01-01

    Development of NGS has revolutionized the analysis in microbial ecology contributing to our deeper understanding of microbiota in health and disease. However, the quality, quantity and confidence of summarized taxonomic abundances are in need of further scrutiny due to sample dependent and independent effects. In this article we introduce 'AVIT (Abundance and Variability In Taxonomy), an unbiased method to enrich for assigned members of microbial communities. As opposed to using a priori thresholds, 'AVIT uses inherent abundance and variability of taxa in a dataset to determine the inclusion or rejection of each taxa for further downstream analysis. Using in-vitro and in-vivo studies, we benchmarked performance and parameterized 'AVIT to establish a framework for investigating the dynamic range of microbial community membership in clinically relevant scenarios. PMID:27530237

  3. OXYGEN ABUNDANCES IN CEPHEIDS

    SciTech Connect

    Luck, R. E.; Andrievsky, S. M.; Korotin, S. N.; Kovtyukh, V. V. E-mail: serkor@skyline.od.ua E-mail: scan@deneb1.odessa.ua

    2013-07-01

    Oxygen abundances in later-type stars, and intermediate-mass stars in particular, are usually determined from the [O I] line at 630.0 nm, and to a lesser extent, from the O I triplet at 615.7 nm. The near-IR triplets at 777.4 nm and 844.6 nm are strong in these stars and generally do not suffer from severe blending with other species. However, these latter two triplets suffer from strong non-local thermodynamic equilibrium (NLTE) effects and thus see limited use in abundance analyses. In this paper, we derive oxygen abundances in a large sample of Cepheids using the near-IR triplets from an NLTE analysis, and compare those abundances to values derived from a local thermodynamic equilibrium (LTE) analysis of the [O I] 630.0 nm line and the O I 615.7 nm triplet as well as LTE abundances for the 777.4 nm triplet. All of these lines suffer from line strength problems making them sensitive to either measurement complications (weak lines) or to line saturation difficulties (strong lines). Upon this realization, the LTE results for the [O I] lines and the O I 615.7 nm triplet are in adequate agreement with the abundance from the NLTE analysis of the near-IR triplets.

  4. Structural and taxonomic components of habitat selection in the neotropical folivore Lamponius portoricensis (Phasmetodea: Phasmatidae)

    SciTech Connect

    Willig, M.R.; Sandlin, E.A. Univ. of Arizona, Tucson ); Gannon, M.R. )

    1993-06-01

    Lamponius portoricensis Rhen is a folivorous neotropical walkingstick that is a common light-gap inhabitant of the tabonuco forest in Puerto Rico. Little is known concerning the spatial distribution of this phasmatid or the manner in which it selects habitats. Based on multiple regression analysis of a suite of taxonomic and structural characteristics of understory flora, we determined that the density of walkingsticks was associated with patches that exhibit high apparency values for Piper treleaseanum Britton Wilson and Symplocos martinicensis Jacq., and low apparency values for Dryopteris deltoidea (Sw.) Kuntze. The total development of the understory regardless of taxonomic composition at 76 cm (2.5 ft) and 107 cm (3.5 ft) also contributes to high walkingstick density, based on correlative analyses. Moreover, nonparametric analysis suggests that L. portoricensis disproportionately occurs on P. treleaseanum (approximately twice as often as expected based on plant apparency). Despite these associations, only a third of the variation in walkingstick density is accounted for by this suite of floral characteristics. The low vagility of L. portoricensis may result in its having incomplete information about the abundance and distribution of forage plants, whereas patch-dynamic processes involving changes in quality of forage can confound the significance of apparency alone in predicting density. The production of aromatic attractants by Piper may act as the proximate cue affecting patch selection.

  5. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

    PubMed Central

    Luo, Chengwei; Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T.

    2014-01-01

    Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across the fields of environmental, clinical and evolutionary microbiology. Here, we introduce MyTaxa, a homology-based bioinformatics framework to classify metagenomic and genomic sequences with unprecedented accuracy. The distinguishing aspect of MyTaxa is that it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power at a given taxonomic level and frequency of horizontal gene transfer. MyTaxa also implements a novel classification scheme based on the genome-aggregate average amino acid identity concept to determine the degree of novelty of sequences representing uncharacterized taxa, i.e. whether they represent novel species, genera or phyla. Application of MyTaxa on in silico generated (mock) and real metagenomes of varied read length (100–2000 bp) revealed that it correctly classified at least 5% more sequences than any other tool. The analysis also showed that ∼10% of the assembled sequences from human gut metagenomes represent novel species with no sequenced representatives, several of which were highly abundant in situ such as members of the Prevotella genus. Thus, MyTaxa can find several important applications in microbial identification and diversity studies. PMID:24589583

  6. Richness and Abundance of Ichneumonidae in a Fragmented Tropical Rain Forest.

    PubMed

    Ruiz-Guerra, B; Hanson, P; Guevara, R; Dirzo, R

    2013-10-01

    Because of the magnitude of land use currently occurring in tropical regions, the local loss of animal species due to habitat fragmentation has been widely studied, particularly in the case of vertebrates. Many invertebrate groups and the ichneumonid wasps in particular, however, have been poorly studied in this context, despite the fact that they are one of the most species-rich groups and play an important role as regulators of other insect populations. Here, we recorded the taxonomic composition of ichneumonid parasitoids and assessed their species richness, abundance, similarity, and dominance in the Los Tuxtlas tropical rain forest, Mexico. We compared two forest types: a continuous forest (640 ha) and a forest fragment (19 ha). We sampled ichneumonids using four malaise traps in both forest types during the dry (September-October) and rainy (March-April) seasons. A total of 104 individuals of Ichneumonidae belonging to 11 subfamilies, 18 genera, and 42 species were collected in the continuous forest and 11 subfamilies, 15 genera, and 24 species were collected in the forest fragment. Species richness, abundance, and diversity of ichneumonids were greater in the continuous forest than in the forest fragment. We did not detect differences between seasons. Species rank/abundance curves showed that the ichneumonid community between the forest types was different. Species similarity between forest types was low. The most dominant species in continuous forest was Neotheronia sp., whereas in the forest fragment, it was Orthocentrus sp. Changes in the ichneumonid wasp community may compromise important tropical ecosystem processes. PMID:23949980

  7. 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

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

    PubMed

    Baab, Karen L

    2008-06-01

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

  9. Zooplankton abundance, biovolume and size spectra at western boundary currents in the subtropical North Pacific during winter 2012

    NASA Astrophysics Data System (ADS)

    Dai, Luping; Li, Chaolun; Yang, Guang; Sun, Xiaoxia

    2016-03-01

    Horizontal changes in mesozooplankton abundance, biovolume and size spectra at western boundary currents in the subtropical North Pacific during winter 2012 were evaluated by ZooScan measurement on samples collected by net towing from 23 stations. Zooplankton abundance and biovolume ranged from 35.1 to 456.8 ind. m- 3 and 4.3 to 231.7 mm3 m- 3, respectively. Copepoda were the most dominant species, followed by Chaetognatha and Tunicata. According to the Bray-Curtis cluster analysis based on biovolume of zooplankton size classes of each taxonomic group at intervals of 1 (log2 mm3 ind.- 1) between - 6 and 12 and considering the effect of regional factors, zooplankton communities were classified into four groups, which basically coincided with the geographical patterns of different currents: the North Equatorial Current (NEC), the North Equatorial Counter Current (NECC), the Kuroshio Current (KC), and the Mindanao Eddy (ME), respectively. The largest and lowest biovolumes were observed in the NECC region and the NEC region, respectively, and both were dominated by the 0.3 to 1 mm equivalent spherical diameter (ESD) size class, while the ME region was dominant by the 1 to 2 mm ESD size class. The slopes of the normalized biovolume size spectra for each group were slightly lower than - 1 (range from - 0.85 to - 0.92), which indicates that zooplankton communities in the study area were characterized by low productivity and high energy transfer efficiency.

  10. Characterization of the Vaginal Microbiota among Sexual Risk Behavior Groups of Women with Bacterial Vaginosis

    PubMed Central

    Muzny, Christina A.; Sunesara, Imran R.; Kumar, Ranjit; Mena, Leandro A.; Griswold, Michael E.; Martin, David H.; Lefkowitz, Elliot J.; Schwebke, Jane R.

    2013-01-01

    Background The pathogenesis of bacterial vaginosis (BV) remains elusive. BV may be more common among women who have sex with women (WSW). The objective of this study was to use 454 pyrosequencing to investigate the vaginal microbiome of WSW, women who have sex with women and men (WSWM), and women who have sex with men (WSM) with BV to determine if there are differences in organism composition between groups that may inform new hypotheses regarding the pathogenesis of BV. Methods Vaginal swab specimens from eligible women with BV at the Mississippi State Department of Health STD Clinic were used. After DNA extraction, 454 pyrosequencing of PCR-amplified 16S rRNA gene sequences was performed. Sequence data was classified using the Ribosomal Database Program classifer. Complete linkage clustering analysis was performed to compare bacterial community composition among samples. Differences in operational taxonomic units with an abundance of ≥2% between risk behavior groups were determined. Alpha and beta diversity were measured using Shannon’s Index implemented in QIIME and Unifrac analysis, respectively. Results 33 WSW, 35 WSWM, and 44 WSM were included. The vaginal bacterial communities of all women clustered into four taxonomic groups with the dominant taxonomic group in each being Lactobacillus, Lachnospiraceae, Prevotella, and Sneathia. Regarding differences in organism composition between risk behavior groups, the abundance of Atopobium (relative ratio (RR)=0.24; 95%CI 0.11-0.54) and Parvimonas (RR=0.33; 95%CI 0.11-0.93) were significantly lower in WSW than WSM, the abundance of Prevotella was significantly higher in WSW than WSWM (RR=1.77; 95%CI 1.10-2.86), and the abundance of Atopobium (RR=0.41; 95%CI 0.18-0.88) was significantly lower in WSWM than WSM. Overall, WSM had the highest diversity of bacterial taxa. Conclusion The microbiology of BV among women in different risk behavior groups is heterogeneous. WSM in this study had the highest diversity of

  11. Evaluating predictors of local dabbling duck abundance during migration: Managing the spectrum of conditions faced by migrants

    USGS Publications Warehouse

    Aagaard, Kevin; Crimmins, Shawn M.; Thogmartin, Wayne E.; Tavernia, Brian; Lyons, James E.

    2015-01-01

    The development of robust modelling techniques to derive inferences from large-scale migratory bird monitoring data at appropriate scales has direct relevance to their management. The Integrated Waterbird Management and Monitoring programme (IWMM) represents one of the few attempts to monitor migrating waterbirds across entire flyways using targeted local surveys. This dataset included 13,208,785 waterfowl (eight Anas species) counted during 28,000 surveys at nearly 1,000 locations across the eastern United States between autumn 2010 and spring 2013 and was used to evaluate potential predictors of waterfowl abundance at the wetland scale. Mixed-effects, log-linear models of local abundance were built for the Atlantic and Mississippi flyways during spring and autumn migration to identify factors relating to habitat structure, forage availability, and migration timing that influence target dabbling duck species abundance. Results indicated that migrating dabbling ducks responded differently to environmental factors. While the factors identified demonstrated a high degree of importance, they were inconsistent across species, flyways and seasons. Furthermore, the direction and magnitude of the importance of each covariate group considered here varied across species. Given our results, actionable policy recommendations are likely to be most effective if they consider species-level variation within targeted taxonomic units and across management areas. The methods implemented here can easily be applied to other contexts, and serve as a novel investigation into local-level population patterns using data from broad-scale monitoring programmes.

  12. Taxonomic and functional annotation of gut bacterial communities of Eisenia foetida and Perionyx excavatus.

    PubMed

    Singh, Arjun; Singh, Dushyant P; Tiwari, Rameshwar; Kumar, Kanika; Singh, Ran Vir; Singh, Surender; Prasanna, Radha; Saxena, Anil K; Nain, Lata

    2015-06-01

    Epigeic earthworms can significantly hasten the decomposition of organic matter, which is known to be mediated by gut associated microflora. However, there is scanty information on the abundance and diversity of the gut bacterial flora in different earthworm genera fed with a similar diet, particularly Eisenia foetida and Perionyx excavatus. In this context, 16S rDNA based clonal survey of gut metagenomic DNA was assessed after growth of these two earthworms on lignocellulosic biomass. A set of 67 clonal sequences belonging to E. foetida and 75 to P. excavatus were taxonomically annotated using MG-RAST and RDP pipeline servers. Highest number of sequences were annotated to Proteobacteria (38-44%), followed by unclassified bacteria (14-18%) and Firmicutes (9.3-11%). Comparative analyses revealed significantly higher abundance of Actinobacteria and Firmicutes in the gut of P. excavatus. The functional annotation for the 16S rDNA clonal libraries of both the metagenomes revealed a high abundance of xylan degraders (12.1-24.1%). However, chitin degraders (16.7%), ammonia oxidizers (24.1%) and nitrogen fixers (7.4%) were relatively higher in E. foetida, while in P. excavatus; sulphate reducers and sulphate oxidizers (12.1-29.6%) were more abundant. Lignin degradation was detected in 3.7% clones of E. foetida, while cellulose degraders represented 1.7%. The gut microbiomes showed relative abundance of dehalogenators (17.2-22.2%) and aromatic hydrocarbon degraders (1.7-5.6%), illustrating their role in bioremediation. This study highlights the significance of differences in the inherent microbiome of these two earthworms in shaping the metagenome for effective degradation of different types of biomass under tropical conditions. PMID:25813857

  13. Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters

    PubMed Central

    Jia, Yangyang; Wilkins, David; Lu, Hongyuan; Cai, Mingwei

    2015-01-01

    Cellulose and xylan are two major components of lignocellulosic biomass, which represents a potentially important energy source, as it is abundant and can be converted to methane by microbial action. However, it is recalcitrant to hydrolysis, and the establishment of a complete anaerobic digestion system requires a specific repertoire of microbial functions. In this study, we maintained 2-year enrichment cultures of anaerobic digestion sludge amended with cellulose or xylan to investigate whether a cellulose- or xylan-digesting microbial system could be assembled from sludge previously used to treat neither of them. While efficient methane-producing communities developed under mesophilic (35°C) incubation, they did not under thermophilic (55°C) conditions. Illumina amplicon sequencing results of the archaeal and bacterial 16S rRNA genes revealed that the mature cultures were much lower in richness than the inocula and were dominated by single archaeal (genus Methanobacterium) and bacterial (order Clostridiales) groups, although at finer taxonomic levels the bacteria were differentiated by substrates. Methanogenesis was primarily via the hydrogenotrophic pathway under all conditions, although the identity and growth requirements of syntrophic acetate-oxidizing bacteria were unclear. Incubation conditions (substrate and temperature) had a much greater effect than inoculum source in shaping the mature microbial community, although analysis based on unweighted UniFrac distance found that the inoculum still determined the pool from which microbes could be enriched. Overall, this study confirmed that anaerobic digestion sludge treating nonlignocellulosic material is a potential source of microbial cellulose- and xylan-digesting functions given appropriate enrichment conditions. PMID:26712547

  14. Using plant functional traits as a link between land use and bee foraging abundance

    NASA Astrophysics Data System (ADS)

    Pakeman, R. J.; Stockan, J.

    2013-07-01

    Many recent studies have shown that plant functional traits can be used to predict the response of plant assemblages to management or other environmental change. A further challenge is to use them to predict changes in the assemblages of other groups. Using data from a study of the impact of land use on biodiversity, the linkages between management drivers, a range of plant functional traits and the overall foraging numbers and assemblage of bees was assessed. Bee foraging numbers were only weakly predicted by plant traits, though bee foraging assemblage was closely related to a number of different groups of plant traits (flower colour and Forage Index, as well as taxonomic group). In turn, the selected traits were significantly correlated to some of the response traits that linked the plant assemblage to management, indicating that there was a predictive pathway from management to bee abundance and assemblage structure. However, models developed with just the environmental drivers proved superior at predicting both bee numbers and assemblage. Plant traits proved to be a moderately effective predictor of bee assemblage structure. However, the use of plant traits as a link between the bees and management did not offer any improvement on models directly developed from management variables. This suggests that the bee assemblage is responding to traits that have not been quantified and that developing these trophic linkage models may have to take a different approach.

  15. Application of functional data analysis to investigate seasonal progression with interannual variability in plankton abundance in the Bay of Fundy, Canada

    NASA Astrophysics Data System (ADS)

    Ikeda, Takayoshi; Dowd, Michael; Martin, Jennifer L.

    2008-06-01

    The statistical technique of functional data analysis (FDA) is applied to a time series analysis of plankton monitoring data. The analysis is focused on revealing patterns in the seasonal cycle to assess interannual variability of several different taxonomic groups of plankton. Cell concentrations of diatom, dinoflagellate and zooplankton abundances from the Bay of Fundy, Canada provide the observations for analysis. FDA was performed on the log-transformed abundance data as a new approach for treating such types of sparse and noisy data. Differences in the seasonal progression were seen, with peak numbers, timings and abundance levels varying for the three groups as determined by curve registration and higher order derivatives using the objectively fit FDA curves. Nonmetric multidimensional scaling was used to capture seasonal variation among years. These results were further assessed in terms of dominant species and the relationships between groups for different seasons and years. It is anticipated that the easy to use, general and flexible technique of FDA could be applied to a wide variety of marine ecological data that are characterized by missing values and non-Gaussian distributions.

  16. Solar abundance of platinum

    PubMed Central

    Burger, Harry; Aller, Lawrence H.

    1975-01-01

    Three lines of neutral platinum, located at λ 2997.98 Å, λ 3064.71 Å, and λ 3301.86 Å have been used to determine the solar platinum abundance by the method of spectral synthesis. On the scale, log A(H) = 12.00, the thus-derived solar platinum abundance is 1.75 ± 0.10, in fair accord with Cameron's value of log A(Pt) = 1.69 derived by Mason from carbonaceous chondrites and calculated on the assumption that log A(Si) = 7.55 in the sun. PMID:16592278

  17. Determining the Diversity and Species Abundance Patterns in Arctic Soils using Rational Methods for Exploring Microbial Diversity

    NASA Astrophysics Data System (ADS)

    Ovreas, L.; Quince, C.; Sloan, W.; Lanzen, A.; Davenport, R.; Green, J.; Coulson, S.; Curtis, T.

    2012-12-01

    Arctic microbial soil communities are intrinsically interesting and poorly characterised. We have inferred the diversity and species abundance distribution of 6 Arctic soils: new and mature soil at the foot of a receding glacier, Arctic Semi Desert, the foot of bird cliffs and soil underlying Arctic Tundra Heath: all near Ny-Ålesund, Spitsbergen. Diversity, distribution and sample sizes were estimated using the rational method of Quince et al., (Isme Journal 2 2008:997-1006) to determine the most plausible underlying species abundance distribution. A log-normal species abundance curve was found to give a slightly better fit than an inverse Gaussian curve if, and only if, sequencing error was removed. The median estimates of diversity of operational taxonomic units (at the 3% level) were 3600-5600 (lognormal assumed) and 2825-4100 (inverse Gaussian assumed). The nature and origins of species abundance distributions are poorly understood but may yet be grasped by observing and analysing such distributions in the microbial world. The sample size required to observe the distribution (by sequencing 90% of the taxa) varied between ~ 106 and ~105 for the lognormal and inverse Gaussian respectively. We infer that between 5 and 50 GB of sequencing would be required to capture 90% or the metagenome. Though a principle components analysis clearly divided the sites into three groups there was a high (20-45%) degree of overlap in between locations irrespective of geographical proximity. Interestingly, the nearest relatives of the most abundant taxa at a number of most sites were of alpine or polar origin. Samples plotted on first two principal components together with arbitrary discriminatory OTUs

  18. The Impact of Land Abandonment on Species Richness and Abundance in the Mediterranean Basin: A Meta-Analysis

    PubMed Central

    Plieninger, Tobias; Hui, Cang; Gaertner, Mirijam; Huntsinger, Lynn

    2014-01-01

    Land abandonment is common in the Mediterranean Basin, a global biodiversity hotspot, but little is known about its impacts on biodiversity. To upscale existing case-study insights to the Pan-Mediterranean level, we conducted a meta-analysis of the effects of land abandonment on plant and animal species richness and abundance in agroforestry, arable land, pastures, and permanent crops of the Mediterranean Basin. In particular, we investigated (1) which taxonomic groups (arthropods, birds, lichen, vascular plants) are more affected by land abandonment; (2) at which spatial and temporal scales the effect of land abandonment on species richness and abundance is pronounced; (3) whether previous land use and current protected area status affect the magnitude of changes in the number and abundance of species; and (4) how prevailing landforms and climate modify the impacts of land abandonment. After identifying 1240 potential studies, 154 cases from 51 studies that offered comparisons of species richness and abundance and had results relevant to our four areas of investigation were selected for meta-analysis. Results are that land abandonment showed slightly increased (effect size  = 0.2109, P<0.0001) plant and animal species richness and abundance overall, though results were heterogeneous, with differences in effect size between taxa, spatial-temporal scales, land uses, landforms, and climate. In conclusion, there is no “one-size-fits-all” conservation approach that applies to the diverse contexts of land abandonment in the Mediterranean Basin. Instead, conservation policies should strive to increase awareness of this heterogeneity and the potential trade-offs after abandonment. The strong role of factors at the farm and landscape scales that was revealed by the analysis indicates that purposeful management at these scales can have a powerful impact on biodiversity. PMID:24865979

  19. The impact of land abandonment on species richness and abundance in the Mediterranean Basin: a meta-analysis.

    PubMed

    Plieninger, Tobias; Hui, Cang; Gaertner, Mirijam; Huntsinger, Lynn

    2014-01-01

    Land abandonment is common in the Mediterranean Basin, a global biodiversity hotspot, but little is known about its impacts on biodiversity. To upscale existing case-study insights to the Pan-Mediterranean level, we conducted a meta-analysis of the effects of land abandonment on plant and animal species richness and abundance in agroforestry, arable land, pastures, and permanent crops of the Mediterranean Basin. In particular, we investigated (1) which taxonomic groups (arthropods, birds, lichen, vascular plants) are more affected by land abandonment; (2) at which spatial and temporal scales the effect of land abandonment on species richness and abundance is pronounced; (3) whether previous land use and current protected area status affect the magnitude of changes in the number and abundance of species; and (4) how prevailing landforms and climate modify the impacts of land abandonment. After identifying 1240 potential studies, 154 cases from 51 studies that offered comparisons of species richness and abundance and had results relevant to our four areas of investigation were selected for meta-analysis. Results are that land abandonment showed slightly increased (effect size  = 0.2109, P<0.0001) plant and animal species richness and abundance overall, though results were heterogeneous, with differences in effect size between taxa, spatial-temporal scales, land uses, landforms, and climate. In conclusion, there is no "one-size-fits-all" conservation approach that applies to the diverse contexts of land abandonment in the Mediterranean Basin. Instead, conservation policies should strive to increase awareness of this heterogeneity and the potential trade-offs after abandonment. The strong role of factors at the farm and landscape scales that was revealed by the analysis indicates that purposeful management at these scales can have a powerful impact on biodiversity. PMID:24865979

  20. Seasonal Abundance of Culex tarsalis and Culex pipiens Complex Mosquitoes (Diptera: Culicidae) in California

    PubMed Central

    BARKER, CHRISTOPHER M.; ELDRIDGE, BRUCE F.; REISEN, WILLIAM K.

    2010-01-01

    Large-scale patterns in the seasonal abundance profiles of the arboviral mosquito vectors Culex tarsalis Coquillett and the species of the Culex pipiens complex were described based on a decade of counts from 868 New Jersey light traps located throughout the urban and agricultural areas of California. Mean seasonal abundance profiles varied markedly among hydrologic regions. For all species, abundance increased earlier and declined later in drier, warmer southern regions, but variation could not be explained fully by latitude. The observed patterns may be driven by temperature, availability of larval habitats, and for the Cx. pipiens complex, the taxonomic composition of local populations. PMID:20939368

  1. MetaBoot: a machine learning framework of taxonomical biomarker discovery for different microbial communities based on metagenomic data

    PubMed Central

    Wang, Xiaojun; Su, Xiaoquan

    2015-01-01

    As more than 90% of species in a microbial community could not be isolated and cultivated, the metagenomic methods have become one of the most important methods to analyze microbial community as a whole. With the fast accumulation of metagenomic samples and the advance of next-generation sequencing techniques, it is now possible to qualitatively and quantitatively assess all taxa (features) in a microbial community. A set of taxa with presence/absence or their different abundances could potentially be used as taxonomical biomarkers for identification of the corresponding microbial community’s phenotype. Though there exist some bioinformatics methods for metagenomic biomarker discovery, current methods are not robust, accurate and fast enough at selection of non-redundant biomarkers for prediction of microbial community’s phenotype. In this study, we have proposed a novel method, MetaBoot, that combines the techniques of mRMR (minimal redundancy maximal relevance) and bootstrapping, for discover of non-redundant biomarkers for microbial communities through mining of metagenomic data. MetaBoot has been tested and compared with other methods on well-designed simulated datasets considering normal and gamma distribution as well as publicly available metagenomic datasets. Results have shown that MetaBoot was robust across datasets of varied complexity and taxonomical distribution patterns and could also select discriminative biomarkers with quite high accuracy and biological consistency. Thus, MetaBoot is suitable for robustly and accurately discover taxonomical biomarkers for different microbial communities. PMID:26213658

  2. MetaBoot: a machine learning framework of taxonomical biomarker discovery for different microbial communities based on metagenomic data.

    PubMed

    Wang, Xiaojun; Su, Xiaoquan; Cui, Xinping; Ning, Kang

    2015-01-01

    As more than 90% of species in a microbial community could not be isolated and cultivated, the metagenomic methods have become one of the most important methods to analyze microbial community as a whole. With the fast accumulation of metagenomic samples and the advance of next-generation sequencing techniques, it is now possible to qualitatively and quantitatively assess all taxa (features) in a microbial community. A set of taxa with presence/absence or their different abundances could potentially be used as taxonomical biomarkers for identification of the corresponding microbial community's phenotype. Though there exist some bioinformatics methods for metagenomic biomarker discovery, current methods are not robust, accurate and fast enough at selection of non-redundant biomarkers for prediction of microbial community's phenotype. In this study, we have proposed a novel method, MetaBoot, that combines the techniques of mRMR (minimal redundancy maximal relevance) and bootstrapping, for discover of non-redundant biomarkers for microbial communities through mining of metagenomic data. MetaBoot has been tested and compared with other methods on well-designed simulated datasets considering normal and gamma distribution as well as publicly available metagenomic datasets. Results have shown that MetaBoot was robust across datasets of varied complexity and taxonomical distribution patterns and could also select discriminative biomarkers with quite high accuracy and biological consistency. Thus, MetaBoot is suitable for robustly and accurately discover taxonomical biomarkers for different microbial communities. PMID:26213658

  3. Abundance, Depth Distribution, and Composition of Aerobic Bacteriochlorophyll a-Producing Bacteria in Four Basins of the Central Baltic Sea▿ †

    PubMed Central

    Salka, Ivette; Moulisová, Vladimíra; Koblížek, Michal; Jost, Günter; Jürgens, Klaus; Labrenz, Matthias

    2008-01-01

    The abundance, vertical distribution, and diversity of aerobic anoxygenic phototrophic bacteria (AAP) were studied at four basins of the Baltic Sea. AAP were enumerated by infrared epifluorescence microscopy, and their diversity was analyzed by using pufM gene clone libraries. In addition, numbers of CFU containing the pufM gene were determined, and representative strains were isolated. Both approaches indicated that AAP reached maximal abundance in the euphotic zone. Maximal AAP abundance was 2.5 × 105 cells ml−1 (11% of total prokaryotes) or 1.0 × 103 CFU ml−1 (9 to 10% of total CFU). Environmental pufM clone sequences were grouped into 11 operational taxonomic units phylogenetically related to cultivated members of the Alpha-, Beta-, and Gammaproteobacteria. In spite of varying pufM compositions, five clones were present in all libraries. Of these, Jannaschia-related clones were always found in relative abundances representing 25 to 30% of the total AAP clones. The abundances of the other clones varied. Clones potentially affiliated with typical freshwater Betaproteobacteria sequences were present at three Baltic Sea stations, whereas clones grouping with Loktanella represented 40% of the total cell numbers in the Gotland Basin. For three alphaproteobacterial clones, probable pufM phylogenetic relationships were supported by 16S rRNA gene analyses of Baltic AAP isolates, which showed nearly identical pufM sequences. Our data indicate that the studied AAP assemblages represented a mixture of marine and freshwater taxa, thus characterizing the Baltic Sea as a “melting pot” of abundant, polyphyletic aerobic photoheterotrophic bacteria. PMID:18502937

  4. Seasonality, Dietary Overlap and the Role of Taxonomic Resolution in the Study of the Diet of Three Congeneric Fishes from a Tropical Bay

    PubMed Central

    Pombo, Maíra; Denadai, Márcia Regina; Turra, Alexander

    2013-01-01

    Not only seasonality but also taxonomic resolution of prey categories has been shown to affect diet studies. We analyzed the stomach contents of three sympatric species, Stellifer rastrifer, S. brasiliensis and S. stellifer, sampled monthly from August 2003 to October 2004 in Caraguatatuba Bay, southeastern Brazil. General characteristics and similarities among their diets were evaluated by considering high taxonomic ranks of all prey groups, and also the lower taxonomic ranks of the main prey groups. Dietary similarity was relatively high among species and low between seasons, and both evaluation criteria gave the equivalent results. The rare items, however, provided information about resource partition, and the species compositions of the most important groups were apparently good indicators of food availability. PMID:23405256

  5. The Development of Taxonomic Structure in Lexical Memory.

    ERIC Educational Resources Information Center

    Blewitt, Pamela; Toppino, Thomas C.

    1991-01-01

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

  6. Taxonomic scheme for the identification of marine bacteria

    NASA Astrophysics Data System (ADS)

    Oliver, James D.

    1982-06-01

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

  7. 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…

  8. Abundances of light elements.

    PubMed Central

    Pagel, B E

    1993-01-01

    Recent developments in the study of abundances of light elements and their relevance to cosmological nucleosynthesis are briefly reviewed. The simplest model, based on standard cosmology and particle physics and assuming homogeneous baryon density at the relevant times, continues to stand up well. PMID:11607388

  9. The taxonomic value of fruit wing types in the order Apiales.

    PubMed

    Liu, Mei Rebecca; Plunkett, Gregory M; Lowry, Porter P; Wyk, Ben-Erik Van; Tilney, Patricia M

    2006-09-01

    This study shows that structural data, when carefully examined, can provide valuable characters for delimiting monophyletic groups and can complement DNA with observable features to recognize and circumscribe taxa. In the angiosperm order Apiales, traditional classification has relied heavily (often exclusively) on fruit characters. Recent molecular systematic studies, however, provided a radically different picture of relationships, calling into question the utility of fruit characters. We have studied fruit anatomy from 18 genera (Annesorhiza, Asteriscium, Astrotricha, Choritaenia, Dasispermum, Elaeoselinum, Heptaptera, Hermas, Heteromorpha, Laretia, Molopospermum, Myodocarpus, Pachypleurum, Peucedanum, Polemanniopsis, Polylophium, Rouya, and Tordylium) that represent all major taxonomic groups of Apiales characterized by winged fruits and the full range of wing types. Fruit anatomy closely corresponded with the phylogenetic position of these genera, as suggested by molecular studies. Fruit features of taxonomic importance include developmental origin of the wings, carpel shape, presence of vittae, woodiness of the endocarp, position of crystals, and type of carpophores. Despite the long history of recognizing umbellifers as a "natural group," few studies have been able to provide structural characters to help circumscribe the clades identified by molecular data. The interpretations presented are an important step toward erecting a stable system of classification for this difficult family. PMID:21642200

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

    PubMed

    Brown-Elliott, Barbara A; Wallace, Richard J

    2002-10-01

    The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are reviewed. Community-acquired disease and health care-associated disease are highlighted for each species. The latter grouping includes health care-associated outbreaks and pseudo-outbreaks as well as sporadic disease cases. Treatment recommendations for each species and type of disease are also described. Special emphasis is on the Mycobacterium fortuitum group, including M. fortuitum, M. peregrinum, and the unnamed third biovariant complex with its recent taxonomic changes and newly recognized species (including M. septicum, M. mageritense, and proposed species M. houstonense and M. bonickei). The clinical and taxonomic status of M. chelonae, M. abscessus, and M. mucogenicum is also detailed, along with that of the closely related new species, M. immunogenum. Additionally, newly recognized species, M. wolinskyi and M. goodii, as well as M. smegmatis sensu stricto, are included in a discussion of the M. smegmatis group. Laboratory diagnosis of RGM using phenotypic methods such as biochemical testing and high-performance liquid chromatography and molecular methods of diagnosis are also discussed. The latter includes PCR-restriction fragment length polymorphism analysis, hybridization, ribotyping, and sequence analysis. Susceptibility testing and antibiotic susceptibility patterns of the RGM are also annotated, along with the current recommendations from the National Committee for Clinical Laboratory Standards (NCCLS) for mycobacterial susceptibility testing. PMID:12364376

  11. Clinical and Taxonomic Status of Pathogenic Nonpigmented or Late-Pigmenting Rapidly Growing Mycobacteria

    PubMed Central

    Brown-Elliott, Barbara A.; Wallace, Richard J.

    2002-01-01

    The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are reviewed. Community-acquired disease and health care-associated disease are highlighted for each species. The latter grouping includes health care-associated outbreaks and pseudo-outbreaks as well as sporadic disease cases. Treatment recommendations for each species and type of disease are also described. Special emphasis is on the Mycobacterium fortuitum group, including M. fortuitum, M. peregrinum, and the unnamed third biovariant complex with its recent taxonomic changes and newly recognized species (including M. septicum, M. mageritense, and proposed species M. houstonense and M. bonickei). The clinical and taxonomic status of M. chelonae, M. abscessus, and M. mucogenicum is also detailed, along with that of the closely related new species, M. immunogenum. Additionally, newly recognized species, M. wolinskyi and M. goodii, as well as M. smegmatis sensu stricto, are included in a discussion of the M. smegmatis group. Laboratory diagnosis of RGM using phenotypic methods such as biochemical testing and high-performance liquid chromatography and molecular methods of diagnosis are also discussed. The latter includes PCR-restriction fragment length polymorphism analysis, hybridization, ribotyping, and sequence analysis. Susceptibility testing and antibiotic susceptibility patterns of the RGM are also annotated, along with the current recommendations from the National Committee for Clinical Laboratory Standards (NCCLS) for mycobacterial susceptibility testing. PMID:12364376

  12. Functional and Taxonomic Diversity of Stinging Wasps in Brazilian Atlantic Rainforest Areas.

    PubMed

    Dos Santos, E F; Noll, F B; Brandão, C R F

    2014-04-01

    Vespoidea are the most functionally diverse superfamily of Hymenoptera. Ecological studies involving this family are primarily based on eusocial groups, including ants and social paper wasps. In the present study, we examine stinging wasp (Vespoidea) faunal diversity in the Atlantic Rain Forest, which is one of the most diverse and threatened ecosystems in the World. Three conservation areas were sampled employing a standardized sample protocol. Families and functional groups of Vespoidea were collected in each area, with the exception ants (Formicidae), and analyzed using diversity analyses, to generate taxonomic diversity and distinctness indices. Results indicated Pompilidae was the most diverse family, and the idiobiont parasitoid type was the most diverse functional group in the three study areas. Núcleo Picinguaba of the Parque Estadual da Serra do Mar was taxonomically and functionally the most diverse and species rich area. Parque Estadual Intervales showed the highest number of dominant species and diversity of koinobiont parasitoids, while the Rebio Sooretama exhibited a decrease in several diversity parameters. PMID:27193515

  13. Taxonomic and geographic patterns of decline for threatened and endangered species in the United States.

    PubMed

    Leidner, Allison K; Neel, Maile C

    2011-08-01

    Species listed under the U.S. Endangered Species Act (i.e., listed species) have declined to the point that the probability of their extinction is high. The decline of these species, however, may manifest itself in different ways, including reductions in geographic range, number of populations, or overall abundance. Understanding the pattern of decline can help managers assess extinction probability and define recovery objectives. Although quantitative data on changes in geographic range, number of populations, and abundance usually do not exist for listed species, more often qualitative data can be obtained. We used qualitative data in recovery plans for federally listed species to determine whether each listed species declined in range size, number of populations, or abundance relative to historical levels. We calculated the proportion of listed species in each state (or equivalent) that declined in each of those ways. Nearly all listed species declined in abundance, and range size or number of populations declined in approximately 80% of species for which those data were available. Patterns of decline, however, differed taxonomically and geographically. Declines in range were more common among vertebrates than plants, whereas population extirpations were more common among plants. Invertebrates had high incidence of range and population declines. Narrowly distributed plants and invertebrates may be subject to acute threats that may result in population extirpations, whereas vertebrates may be affected by chronic threats that reduce the extent and size of populations. Additionally, in the eastern United States and U.S. coastal areas, where the level of land conversion is high, a greater percentage of species' ranges declined and more populations were extirpated than in other areas. Species in the Southwest, especially plants, had fewer range and population declines than other areas. Such relations may help in the selection of species' recovery criteria. PMID

  14. Taxonomic revision of Rochefortia Sw. (Ehretiaceae, Boraginales)

    PubMed Central

    Irimia, Ramona-Elena

    2016-01-01

    Abstract Background Rochefortia is a small taxon of woody plants in the Ehretiaceae (Boraginales) exhibiting coriaceous leaves with cystoliths, small whitish flowers and drupaceous fruits containing four pyrenes. It shares the dioecious sex distribution with its sister group Lepidocordia and can be delimited from the latter (and all other Ehretiaceae) by the presence of thorns. Neotropical Rochefortia is distributed over most Caribbean islands, Central America and northern South America. Twenty-eight validly published names (corresponding to twenty-one typified taxa at the species level and below) are available in Rochefortia, but the precise number of species to be accepted has been elusive before this revision. New information In the course of the present revision, 353 herbarium collections, comprising approximately 540 Rochefortia specimens, were entried into a BRAHMS data base providing information about protologues and types and retrospective georeferences if possible. Based on the combination of molecular and morphological data we propose to recognise nine species of Rochefortia, namely R. acanthophora, R. bahamensis, R. barloventensis, R. cubensis, R. cuneata, R. lundellii, R. oblongata, R. spinosa and R. stellata (the remaining nineteen validly published names are synonymised under such names). Morphological description of each species and an identification key are provided. PMID:27346952

  15. Taxonomic review and phylogenetic analysis of Enchodontoidei.

    PubMed

    Silva, Hilda M A; Gallo, Valéria

    2011-06-01

    Enchodontoidei are extinct marine teleost fishes with a long temporal range and a wide geographic distribution. As there has been no comprehensive phylogenetic study of this taxon, we performed a parsimony analysis using a data matrix with 87 characters, 31 terminal taxa for ingroup, and three taxa for outgroup. The analysis produced 93 equally parsimonious trees (L = 437 steps; CI = 0. 24; RI = 0. 49). The topology of the majority rule consensus tree was: (Sardinioides + Hemisaurida + (Nardorex + (Atolvorator + (Protostomias + Yabrudichthys ) + (Apateopholis + (Serrilepis + (Halec + Phylactocephalus ) + (Cimolichthys + (Prionolepis + ( (Eurypholis + Saurorhamphus ) + (Enchodus + (Paleolycus + Parenchodus ))))))) + ( (Ichthyotringa + Apateodus ) + (Rharbichthys + (Trachinocephalus + ( (Apuliadercetis + Brazilodercetis ) + (Benthesikyme + (Cyranichthys + Robertichthys ) + (Dercetis + Ophidercetis )) + (Caudadercetis + (Pelargorhynchus + (Nardodercetis + (Rhynchodercetis + (Dercetoides + Hastichthys )))))). The group Enchodontoidei is not monophyletic. Dercetidae form a clade supported by the presence of very reduced neural spines and possess a new composition. Enchodontidae are monophyletic by the presence of middorsal scutes, and Rharbichthys was excluded. Halecidae possess a new composition, with the exclusion of Hemisaurida. This taxon and Nardorex are Aulopiformes incertae sedis. PMID:21670874

  16. Taxonomic and developmental aspects of radiosensitivity

    SciTech Connect

    Harrison, F.L.; Anderson, S.L.

    1996-11-01

    Considerable information is available on the effects of radioactivity on adult and early life stages of organisms. The preponderance of data is on mortality after a single irradiation with relatively high doses. Unfortunately, because experiments were carried out under different conditions and for different time periods, the validity of comparing the results from different laxonomic groups is questionable. In general, the conclusions are that there is a relationship (1) between radioresistance to high doses of acute radiation and taxonomy of the organism, primitive forms being more radioresistant than complex vertebrates and (2) between radiosensitivity and developmental stage, early life stages being more sensitive than later stages. The first conclusion may be related to the capability of the organism to repopulate cells and to differentiate and redifferentiate them; the second to the rate of cellular division and to the degree of differentiation. In question, however, is the relevance of the responses from high levels of acute radiation to that of the responses to long-term exposure to low levels of radiation, which are ecologically of more interest. Data from studies of the effects of acute and chronic exposure on development of gametes and zygotes indicate that, for some fishes and invertebrates, responses at the cellular and molecular levels show effect levels comparable to those observed in some mammals. Acute doses between 0,05 and 0.5Cy and dose rates between 0.02 to 0.2mCy/h appear to define critical ranges in which detrimental effects on fertility are first observed in a variety of radiosensitive organisms. To better understand inherent radiosensitivity, we need more information on the ability of cells to repopulate and differentiate and to prevent or repair damage to biological critical molecules, such as DNA, because these factors may alter significantly organisms` responses to radiation.

  17. Silicon abundances in population I giants

    NASA Technical Reports Server (NTRS)

    Boehm-Vitense, Erika

    1992-01-01

    Silicon to carbon abundance ratios for population I giants were determined from emission lines originating in the transition layers between stellar chromospheres and coronae. For effective temperatures larger than 6200 K we find a group of stars with increased silicon to carbon but normal nitrogen to carbon abundance ratios. These stars are presumably descendents from Ap stars with increased surface silicon to carbon abundance ratios. For G stars this anomaly disappears as is to be expected due to the increased depth of the convection zone and therefore deeper mixing which dilutes the surface overabundances. The disappearance of the abundance anomalies proves that the anomalous abundances observed for the F giants are indeed only a surface phenomenon. It also proves that the same holds for their progenitors, the Ap and Am stars, as has been generally believed. Unexplained is the increased silicon to carbon abundance ratio observed for several stars cooler than 5100 L. RS CVn and related stars do not show this increased abundance ratio. There are also some giants which appear to be enriched in carbon, perhaps due to a helium flash with some mixing if the star is a clump star.

  18. Solar abundance of iridium

    PubMed Central

    Drake, Stephen; Aller, Lawrence H.

    1976-01-01

    By a method of spectrum synthesis, which yields log gfA, where g is the statistical weight of the lower level, f is the oscillator strength, and A is the abundance, an attempt is made to deduce the solar iridium abundance from one relatively unblended, but fairly weak IrI line, λ 3220.78 Å. If the Corliss-Bozman f-value for this line is adopted, we find log A(Ir) = 0.82 on the scale log A(H) = 12.00. The discordance with the value found from carbonaceous chondrites may arise from faulty f-values or from difficulties arising from line blending in this far ultraviolet domain of the solar spectrum. PMID:16578735

  19. Geographic distribution and possible taxonomic distinction of Callicebus torquatus populations (Pitheciidae: Primates) in Peruvian Amazonia.

    PubMed

    Aquino, Rolando; Terrones, Wagner; Cornejo, Fanny; Heymann, Eckhard W

    2008-12-01

    Population densities of yellow-handed titi monkey (Callicebus torquatus) were estimated using transect census methods. Densities were 2.8 individuals/km(2 )in the upper Rio Itaya basin and 2.5 individuals/km(2) in the lower Rio Algodón basin. Group size varied from two to five individuals, with an average of 2.9 individuals per group at the Rio Itaya. Groups were generally composed of two adults, probably the reproductive pair, with progeny from one to three previous birth seasons. Although the Rio Itaya population is phenotypically identical to populations from the rivers Nanay and Tigre, it differs from population on the rivers Napo and Putumayo. This suggests the existence of two disjunct populations of C. torquatus in Peruvian Amazonia whose taxonomic status warrants further examination. PMID:18767122

  20. Derivation of the Secondary Structure of the ITS-1 Transcript in Volvocales and its Taxonomic Correlations.

    PubMed

    Coleman, A W; Maria Preparata, R; Mehrotra, B; Mai, J C

    1998-05-01

    Knowledge of secondary structure, formed by the gene spacer regions of the primary transcript of nuclear rDNA cistrons, is lacking for most phyla of eukaryotes. We have sequenced the first internal transcribed spacer region (ITS-1) of multiple representatives of the Volvocales, and from comparisons of these, derived a secondary structure common to the entire group. The secondary structure model is supported by numerous compensating base pair changes located within the paired regions of the stem-loops. Within the morphological species, such as those of Astrephomene and Gonium, the three basal nucleotide pairs of helices are highly conserved in primary sequence, and the single stranded region rich in CCAA is identical in sequence, even when isolates come from all continents of the earth. In other Volvocacean species known to include many pairs of mating types, this same level of conservation is found to correlate with the mating subgroups of the species. Thus a comparable degree of sequence similarity appears to characterize all isolates of a "biological" species; this is valid for taxonomic species only where the biological and taxonomic species levels coincide. In addition, the ITS-1 contains information useful for population analyses, and spacer secondary structure may have additional phylogenetic utility at the level of class or subclass when that information becomes available for other protistan groups. PMID:23196163

  1. Taxonomic and Functional Metagenomic Signature of Turfs in the Abrolhos Reef System (Brazil)

    PubMed Central

    Walter, Juline M.; Tschoeke, Diogo A.; Meirelles, Pedro M.; de Oliveira, Louisi; Leomil, Luciana; Tenório, Márcio; Valle, Rogério; Salomon, Paulo S.; Thompson, Cristiane C.; Thompson, Fabiano L.

    2016-01-01

    Turfs are widespread assemblages (consisting of microbes and algae) that inhabit reef systems. They are the most abundant benthic component in the Abrolhos reef system (Brazil), representing greater than half the coverage of the entire benthic community. Their presence is associated with a reduction in three-dimensional coral reef complexity and decreases the habitats available for reef biodiversity. Despite their importance, the taxonomic and functional diversity of turfs remain unclear. We performed a metagenomics and pigments profile characterization of turfs from the Abrolhos reefs. Turf microbiome primarily encompassed Proteobacteria (mean 40.57% ± s.d. 10.36, N = 1.548,192), Cyanobacteria (mean 35.04% ± s.d. 15.5, N = 1.337,196), and Bacteroidetes (mean 11.12% ± s.d. 4.25, N = 424,185). Oxygenic and anoxygenic phototrophs, chemolithotrophs, and aerobic anoxygenic phototrophic (AANP) bacteria showed a conserved functional trait of the turf microbiomes. Genes associated with oxygenic photosynthesis, AANP, sulfur cycle (S oxidation, and DMSP consumption), and nitrogen metabolism (N2 fixation, ammonia assimilation, dissimilatory nitrate and nitrite ammonification) were found in the turf microbiomes. Principal component analyses of the most abundant taxa and functions showed that turf microbiomes differ from the other major Abrolhos benthic microbiomes (i.e., corals and rhodoliths) and seawater. Taken together, these features suggest that turfs have a homogeneous functional core across the Abrolhos Bank, which holds diverse microbial guilds when comparing with other benthic organisms. PMID:27548380

  2. Taxonomic and Functional Metagenomic Signature of Turfs in the Abrolhos Reef System (Brazil).

    PubMed

    Walter, Juline M; Tschoeke, Diogo A; Meirelles, Pedro M; de Oliveira, Louisi; Leomil, Luciana; Tenório, Márcio; Valle, Rogério; Salomon, Paulo S; Thompson, Cristiane C; Thompson, Fabiano L

    2016-01-01

    Turfs are widespread assemblages (consisting of microbes and algae) that inhabit reef systems. They are the most abundant benthic component in the Abrolhos reef system (Brazil), representing greater than half the coverage of the entire benthic community. Their presence is associated with a reduction in three-dimensional coral reef complexity and decreases the habitats available for reef biodiversity. Despite their importance, the taxonomic and functional diversity of turfs remain unclear. We performed a metagenomics and pigments profile characterization of turfs from the Abrolhos reefs. Turf microbiome primarily encompassed Proteobacteria (mean 40.57% ± s.d. 10.36, N = 1.548,192), Cyanobacteria (mean 35.04% ± s.d. 15.5, N = 1.337,196), and Bacteroidetes (mean 11.12% ± s.d. 4.25, N = 424,185). Oxygenic and anoxygenic phototrophs, chemolithotrophs, and aerobic anoxygenic phototrophic (AANP) bacteria showed a conserved functional trait of the turf microbiomes. Genes associated with oxygenic photosynthesis, AANP, sulfur cycle (S oxidation, and DMSP consumption), and nitrogen metabolism (N2 fixation, ammonia assimilation, dissimilatory nitrate and nitrite ammonification) were found in the turf microbiomes. Principal component analyses of the most abundant taxa and functions showed that turf microbiomes differ from the other major Abrolhos benthic microbiomes (i.e., corals and rhodoliths) and seawater. Taken together, these features suggest that turfs have a homogeneous functional core across the Abrolhos Bank, which holds diverse microbial guilds when comparing with other benthic organisms. PMID:27548380

  3. Evolutionary and Taxonomic Implications of Variation in Nuclear Genome Size: Lesson from the Grass Genus Anthoxanthum (Poaceae)

    PubMed Central

    Chumová, Zuzana; Krejčíková, Jana; Mandáková, Terezie; Suda, Jan; Trávníček, Pavel

    2015-01-01

    The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x–18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus. PMID:26207824

  4. Evolutionary and Taxonomic Implications of Variation in Nuclear Genome Size: Lesson from the Grass Genus Anthoxanthum (Poaceae).

    PubMed

    Chumová, Zuzana; Krejčíková, Jana; Mandáková, Terezie; Suda, Jan; Trávníček, Pavel

    2015-01-01

    The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x-18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus. PMID:26207824

  5. bioOTU: An Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences.

    PubMed

    Chen, Shi-Yi; Deng, Feilong; Huang, Ying; Jia, Xianbo; Liu, Yi-Ping; Lai, Song-Jia

    2016-04-01

    Clustering of 16s rRNA amplicon sequences into operational taxonomic units (OTUs) is the most common bioinformatics pipeline for investigating microbial community by high-throughput sequencing technologies. However, the existing algorithms of OTUs clustering still remain to be improved at reliability. Here we propose an improved method (bioOTU) that first assigns taxonomy to unique tags at genus level for separating the error-free sequences of known species in reference database from artifacts, and then cluster them into OTUs by different strategies. The remaining tags, which fail to be clustered in the previous step, are further subjected to independent OTUs clustering by the optimized algorithm of heuristic clustering. The performance tests on both mock and real communities revealed that bioOTU is powerful for recovering the underlying profiles at both microbial composition and abundance, and it also produces comparable or less number of OTUs in comparison with the prevailing tools of Mothur and UPARSE. The bioOTU is implemented in C and Python languages with source codes freely available on the GitHub repository. PMID:26950196

  6. Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site.

    PubMed

    Baltar, Federico; Palovaara, Joakim; Vila-Costa, Maria; Salazar, Guillem; Calvo, Eva; Pelejero, Carles; Marrasé, Cèlia; Gasol, Josep M; Pinhassi, Jarone

    2015-06-01

    Bacterioplankton communities are made up of a small set of abundant taxa and a large number of low-abundant organisms (i.e. 'rare biosphere'). Despite the critical role played by bacteria in marine ecosystems, it remains unknown how this large diversity of organisms are affected by human-induced perturbations, or what controls the responsiveness of rare compared to abundant bacteria. We studied the response of a Mediterranean bacterioplankton community to two anthropogenic perturbations (i.e. nutrient enrichment and/or acidification) in two mesocosm experiments (in winter and summer). Nutrient enrichment increased the relative abundance of some operational taxonomic units (OTUs), e.g. Polaribacter, Tenacibaculum, Rhodobacteraceae and caused a relative decrease in others (e.g. Croceibacter). Interestingly, a synergistic effect of acidification and nutrient enrichment was observed on specific OTUs (e.g. SAR86). We analyzed the OTUs that became abundant at the end of the experiments and whether they belonged to the rare (<0.1% of relative abundance), the common (0.1-1.0% of relative abundance) or the abundant (>1% relative abundance) fractions. Most of the abundant OTUs at the end of the experiments were abundant, or at least common, in the original community of both experiments, suggesting that ecosystem alterations do not necessarily call for rare members to grow. PMID:26032602

  7. 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

  8. 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

  9. 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

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

    PubMed

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

    2012-04-01

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

  11. BOTUX: Bayesian-like operational taxonomic unit examiner

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Kajihara, Hiroshi

    2007-04-01

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

  13. Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome.

    PubMed

    Hurwitz, Bonnie L; Brum, Jennifer R; Sullivan, Matthew B

    2015-02-01

    Microbes drive myriad ecosystem processes, and their viruses modulate microbial-driven processes through mortality, horizontal gene transfer, and metabolic reprogramming by viral-encoded auxiliary metabolic genes (AMGs). However, our knowledge of viral roles in the oceans is primarily limited to surface waters. Here we assess the depth distribution of protein clusters (PCs) in the first large-scale quantitative viral metagenomic data set that spans much of the pelagic depth continuum (the Pacific Ocean Virome; POV). This established 'core' (180 PCs; one-third new to science) and 'flexible' (423K PCs) community gene sets, including niche-defining genes in the latter (385 and 170 PCs are exclusive and core to the photic and aphotic zones, respectively). Taxonomic annotation suggested that tailed phages are ubiquitous, but not abundant (<5% of PCs) and revealed depth-related taxonomic patterns. Functional annotation, coupled with extensive analyses to document non-viral DNA contamination, uncovered 32 new AMGs (9 core, 20 photic and 3 aphotic) that introduce ways in which viruses manipulate infected host metabolism, and parallel depth-stratified host adaptations (for example, photic zone genes for iron-sulphur cluster modulation for phage production, and aphotic zone genes for high-pressure deep-sea survival). Finally, significant vertical flux of photic zone viruses to the deep sea was detected, which is critical for interpreting depth-related patterns in nature. Beyond the ecological advances outlined here, this catalog of viral core, flexible and niche-defining genes provides a resource for future investigation into the organization, function and evolution of microbial molecular networks to mechanistically understand and model viral roles in the biosphere. PMID:25093636

  14. 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

  15. Taxonomic identification of Lower Pleistocene fossil hominins based on distal humeral diaphyseal cross-sectional shape

    PubMed Central

    2015-01-01

    The coexistence of multiple hominin species during the Lower Pleistocene has long presented a challenge for taxonomic attribution of isolated postcrania. Although fossil humeri are well-suited for studies of hominin postcranial variation due to their relative abundance, humeral articular morphology has thus far been of limited value for differentiating Paranthropus from Homo. On the other hand, distal humeral diaphyseal shape has been used to justify such generic distinctions at Swartkrans. The potential utility of humeral diaphyseal shape merits larger-scale quantitative analysis, particularly as it permits the inclusion of fragmentary specimens lacking articular morphology. This study analyzes shape variation of the distal humeral diaphysis among fossil hominins (c. 2-1 Ma) to test the hypothesis that specimens can be divided into distinct morphotypes. Coordinate landmarks were placed on 3D laser scans to quantify cross-sectional shape at a standardized location of the humeral diaphysis (proximal to the olecranon fossa) for a variety of fossil hominins and extant hominids. The fossil sample includes specimens attributed to species based on associated craniodental remains. Mantel tests of matrix correlation were used to assess hypotheses about morphometric relationships among the fossils by comparing empirically-derived Procrustes distance matrices to hypothetical model matrices. Diaphyseal shape variation is consistent with the hypothesis of three distinct morphotypes (Paranthropus, Homo erectus, non-erectus early Homo) in both eastern and southern Africa during the observed time period. Specimens attributed to non-erectus early Homo are unique among hominids with respect to the degree of relative anteroposterior flattening, while H. erectus humeri exhibit morphology more similar to that of modern humans. In both geographic regions, Paranthropus is characterized by a morphology that is intermediate with respect to those morphological features that differentiate

  16. Taxonomic identification of Lower Pleistocene fossil hominins based on distal humeral diaphyseal cross-sectional shape.

    PubMed

    Lague, Michael R

    2015-01-01

    The coexistence of multiple hominin species during the Lower Pleistocene has long presented a challenge for taxonomic attribution of isolated postcrania. Although fossil humeri are well-suited for studies of hominin postcranial variation due to their relative abundance, humeral articular morphology has thus far been of limited value for differentiating Paranthropus from Homo. On the other hand, distal humeral diaphyseal shape has been used to justify such generic distinctions at Swartkrans. The potential utility of humeral diaphyseal shape merits larger-scale quantitative analysis, particularly as it permits the inclusion of fragmentary specimens lacking articular morphology. This study analyzes shape variation of the distal humeral diaphysis among fossil hominins (c. 2-1 Ma) to test the hypothesis that specimens can be divided into distinct morphotypes. Coordinate landmarks were placed on 3D laser scans to quantify cross-sectional shape at a standardized location of the humeral diaphysis (proximal to the olecranon fossa) for a variety of fossil hominins and extant hominids. The fossil sample includes specimens attributed to species based on associated craniodental remains. Mantel tests of matrix correlation were used to assess hypotheses about morphometric relationships among the fossils by comparing empirically-derived Procrustes distance matrices to hypothetical model matrices. Diaphyseal shape variation is consistent with the hypothesis of three distinct morphotypes (Paranthropus, Homo erectus, non-erectus early Homo) in both eastern and southern Africa during the observed time period. Specimens attributed to non-erectus early Homo are unique among hominids with respect to the degree of relative anteroposterior flattening, while H. erectus humeri exhibit morphology more similar to that of modern humans. In both geographic regions, Paranthropus is characterized by a morphology that is intermediate with respect to those morphological features that differentiate

  17. 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

  18. Abundance of field galaxies

    NASA Astrophysics Data System (ADS)

    Klypin, Anatoly; Karachentsev, Igor; Makarov, Dmitry; Nasonova, Olga

    2015-12-01

    We present new measurements of the abundance of galaxies with a given circular velocity in the Local Volume: a region centred on the Milky Way Galaxy and extending to distance ˜10 Mpc. The sample of ˜750 mostly dwarf galaxies provides a unique opportunity to study the abundance and properties of galaxies down to absolute magnitudes MB ≈ -10 and virial masses M_vir= 109{ M_{⊙}}. We find that the standard Λ cold dark matter (ΛCDM) model gives remarkably accurate estimates for the velocity function of galaxies with circular velocities V ≳ 70 kms-1 and corresponding virial masses M_vir≳ 5× 10^{10}{ M_{⊙}}, but it badly fails by overpredicting ˜5 times the abundance of large dwarfs with velocities V = 30-40 kms-1. The warm dark matter (WDM) models cannot explain the data either, regardless of mass of WDM particle. Just as in previous observational studies, we find a shallow asymptotic slope dN/dlog V ∝ Vα, α ≈ -1 of the velocity function, which is inconsistent with the standard ΛCDM model that predicts the slope α = -3. Though reminiscent to the known overabundance of satellite problem, the overabundance of field galaxies is a much more difficult problem. For the standard ΛCDM model to survive, in the 10 Mpc radius of the Milky Way there should be 1000 not yet detected galaxies with virial mass M_vir≈ 10^{10}{ M_{⊙}}, extremely low surface brightness and no detectable H I gas. So far none of this type of galaxies have been discovered.

  19. Macroinvertebrate Abundance and Biomass: 2007 Data, BPA-51; Preliminary Report, February 10, 2009..

    SciTech Connect

    Holderman, Charles

    2009-02-10

    Four Excel files containing information on the 2007 macroinvertebrate data were initially provided to Statistical Consulting Services (SCS) by EcoAnalysts on 1/27/2009. These data files contained information on abundance and biomass data at the level of taxonomic groups. The data were subsequently reformatted and compiled, and aggregated for analysis by SCS. All descriptions and analyses below relate to this compiled data. Computations were carried out separately for each site over all sample periods. Basic summary information for both the abundance and biomass data is presented in Print Out No.2. The 14 sites varied widely in their minimum, mean, maximum and variance values. The number of observations ranged from 10 to 18. Some large abundance values (abundance > 40,000) were noted for sites KR6 and KR13. A more detailed summary of each site is given in Print Out No.3. Site KR3, for example, had a mean abundance of 6914 with a sample size of 17. The variance was 4591991 and the standard error of the mean was 1643. The skewness value, a measure of symmetry for the frequency distribution, was moderately large at 1.29 indicating an asymmetric distribution. Biomass for KR3 had a mean value of 0.87 g/m{sup 2} with 17 observations. The variance was 0.8872 and the standard error was 0.228 g/m{sup 2}. Skewness for biomass was also high at 1.29. Further examination of the quantiles and frequency plots for abundance and biomass also indicate considerable skewness. The stem and leaf diagram (frequency plot) for abundance in KR3 shows most of the data centered on smaller values with a few very large counts. The distribution for biomass has a similar pattern. Statistical tests for normality are significant for both response variables in KR3, thus, the hypothesis that the data originates from a symmetric normal distribution is rejected. Because sample size estimation and statistical inference assume normally distributed data, a transformation of the data is required prior to

  20. 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

  1. Late embryogenesis abundant proteins

    PubMed Central

    Olvera-Carrillo, Yadira; Reyes, José Luis

    2011-01-01

    Late Embryogenesis Abundant (LEA) proteins accumulate at the onset of seed desiccation and in response to water deficit in vegetative plant tissues. The typical LEA proteins are highly hydrophilic and intrinsically unstructured. They have been classified in different families, each one showing distinctive conserved motifs. In this manuscript we present and discuss some of the recent findings regarding their role in plant adaptation to water deficit, as well as those concerning to their possible function, and how it can be related to their intrinsic structural flexibility. PMID:21447997

  2. 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

  3. 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

  4. Flare Plasma Iron Abundance

    NASA Technical Reports Server (NTRS)

    Dennis, Brian R.; Dan, Chau; Jain, Rajmal; Schwartz, Richard A.; Tolbert, Anne K.

    2008-01-01

    The equivalent width of the iron-line complex at 6.7 keV seen in flare X-ray spectra suggests that the iron abundance of the hottest plasma at temperatures >approx.10 MK may sometimes be significantly lower than the nominal coronal abundance of four times the photospheric value that is commonly assumed. This conclusion is based on X-ray spectral observations of several flares seen in common with the Ramaty High Energy Solar Spectroscopic Imager (RHESSI) and the Solar X-ray Spectrometer (SOXS) on the second Indian geostationary satellite, GSAT-2. The implications of this will be discussed as it relates to the origin of the hot flare plasma - either plasma already in the corona that is directly heated during the flare energy release process or chromospheric plasma that is heated by flare-accelerated particles and driven up into the corona. Other possible explanations of lower-than-expected equivalent widths of the iron-line complex will also be discussed.

  5. Taxonomically Important Features on the Surface of Floatoblasts in Plumatella (Bryozoa)

    NASA Astrophysics Data System (ADS)

    Reynolds, Kevin T.

    2000-05-01

    : At the species level, bryozoans (class Phylactolaemata) in the family Plumatellidae are difficult to organize taxonomically. Of principal concern is the absence of consistent distinguishing features due mainly to plasticity of the group, a common problem with soft-bodied invertebrates. Yet, within the last three decades, analysis of distinctive chitinous statoblasts—using scanning electron microscopy—has resolved certain taxonomic questions. I examined statoblasts from 30 similar collections, the majority from the midwestern United States, and identified four distinct subgroups. Also, nine new statoblast surface features were identified: fold, polar grooves, bead, cave, demarcation, parasutural zone, ridge, sutural band, and sutural knob. The surface features of floating statoblasts (floatoblasts) provide useful data for species identification. Most consistently useful in plumatellids is a suture which varies from one species to the next. Mound-like tubercles and net-like ridges are next in the extent of variability. Finally, folds and polar grooves are present but vary even within floatoblasts from the same colony. Analysis of the suture in PLUMATELLA FUNGOSA, over a 5-day germination period, reveals all features at the site remain intact regardless of the initial age of the floatoblast. Only the suture line itself splits lengthwise to permit emergence of the new animal.

  6. Testing Taxonomic Predictivity of Foliar and Tuber Resistance to Phytophthora infestans in Wild Relatives of Potato.

    PubMed

    Khiutti, A; Spooner, D M; Jansky, S H; Halterman, D A

    2015-09-01

    Potato late blight, caused by the oomycete phytopathogen Phytophthora infestans, is a devastating disease found in potato-growing regions worldwide. Long-term management strategies to control late blight include the incorporation of host resistance to predominant strains. However, due to rapid genetic changes within pathogen populations, rapid and recurring identification and integration of novel host resistance traits is necessary. Wild relatives of potato offer a rich source of desirable traits, including late blight resistance, but screening methods can be time intensive. We tested the ability of taxonomy, ploidy, crossing group, breeding system, and geography to predict the presence of foliar and tuber late blight resistance in wild Solanum spp. Significant variation for resistance to both tuber and foliar late blight was found within and among species but there was no discernable predictive power based on taxonomic series, clade, ploidy, breeding system, elevation, or geographic location. We observed a moderate but significant correlation between tuber and foliar resistance within species. Although previously uncharacterized sources of both foliar and tuber resistance were identified, our study does not support an assumption that taxonomic or geographic data can be used to predict sources of late blight resistance in wild Solanum spp. PMID:25871860

  7. Discovery, taxonomic distribution, and phenotypic characterization of a gene required for 3-methylhopanoid production

    PubMed Central

    Welander, Paula V.; Summons, Roger E.

    2012-01-01

    Hopanoids methylated at the C-3 position are a subset of bacterial triterpenoids that are readily preserved in modern and ancient sediments and in petroleum. The production of 3-methylhopanoids by extant aerobic methanotrophs and their common occurrence in modern and fossil methane seep communities, in conjunction with carbon isotope analysis, has led to their use as biomarker proxies for aerobic methanotrophy. In addition, these lipids are also produced by aerobic acetic acid bacteria and, lacking carbon isotope analysis, are more generally used as indicators for aerobiosis in ancient ecosystems. However, recent genetic studies have brought into question our current understanding of the taxonomic diversity of methylhopanoid-producing bacteria and have highlighted that a proper interpretation of methylhopanes in the rock record requires a deeper understanding of their cellular function. In this study, we identified and deleted a gene, hpnR, required for methylation of hopanoids at the C-3 position in the obligate methanotroph Methylococcus capsulatus strain Bath. Bioinformatics analysis revealed that the taxonomic distribution of HpnR extends beyond methanotrophic and acetic acid bacteria. Phenotypic analysis of the M. capsulatus hpnR deletion mutant demonstrated a potential physiological role for 3-methylhopanoids; they appear to be required for the maintenance of intracytoplasmic membranes and cell survival in late stationary phase. Therefore, 3-methylhopanoids may prove more useful as proxies for specific environmental conditions encountered during stationary phase rather than a particular bacterial group. PMID:22826256

  8. Enhancing protein function prediction with taxonomic constraints--The Argot2.5 web server.

    PubMed

    Lavezzo, Enrico; Falda, Marco; Fontana, Paolo; Bianco, Luca; Toppo, Stefano

    2016-01-15

    Argot2.5 (Annotation Retrieval of Gene Ontology Terms) is a web server designed to predict protein function. It is an updated version of the previous Argot2 enriched with new features in order to enhance its usability and its overall performance. The algorithmic strategy exploits the grouping of Gene Ontology terms by means of semantic similarity to infer protein function. The tool has been challenged over two independent benchmarks and compared to Argot2, PANNZER, and a baseline method relying on BLAST, proving to obtain a better performance thanks to the contribution of some key interventions in critical steps of the working pipeline. The most effective changes regard: (a) the selection of the input data from sequence similarity searches performed against a clustered version of UniProt databank and a remodeling of the weights given to Pfam hits, (b) the application of taxonomic constraints to filter out annotations that cannot be applied to proteins belonging to the species under investigation. The taxonomic rules are derived from our in-house developed tool, FunTaxIS, that extends those provided by the Gene Ontology consortium. The web server is free for academic users and is available online at http://www.medcomp.medicina.unipd.it/Argot2-5/. PMID:26318087

  9. Discovery, taxonomic distribution, and phenotypic characterization of a gene required for 3-methylhopanoid production.

    PubMed

    Welander, Paula V; Summons, Roger E

    2012-08-01

    Hopanoids methylated at the C-3 position are a subset of bacterial triterpenoids that are readily preserved in modern and ancient sediments and in petroleum. The production of 3-methylhopanoids by extant aerobic methanotrophs and their common occurrence in modern and fossil methane seep communities, in conjunction with carbon isotope analysis, has led to their use as biomarker proxies for aerobic methanotrophy. In addition, these lipids are also produced by aerobic acetic acid bacteria and, lacking carbon isotope analysis, are more generally used as indicators for aerobiosis in ancient ecosystems. However, recent genetic studies have brought into question our current understanding of the taxonomic diversity of methylhopanoid-producing bacteria and have highlighted that a proper interpretation of methylhopanes in the rock record requires a deeper understanding of their cellular function. In this study, we identified and deleted a gene, hpnR, required for methylation of hopanoids at the C-3 position in the obligate methanotroph Methylococcus capsulatus strain Bath. Bioinformatics analysis revealed that the taxonomic distribution of HpnR extends beyond methanotrophic and acetic acid bacteria. Phenotypic analysis of the M. capsulatus hpnR deletion mutant demonstrated a potential physiological role for 3-methylhopanoids; they appear to be required for the maintenance of intracytoplasmic membranes and cell survival in late stationary phase. Therefore, 3-methylhopanoids may prove more useful as proxies for specific environmental conditions encountered during stationary phase rather than a particular bacterial group. PMID:22826256

  10. Discovery, taxonomic distribution, and phenotypic characterization of a gene required for 3-methylhopanoid production

    NASA Astrophysics Data System (ADS)

    Welander, Paula V.; Summons, Roger E.

    2012-08-01

    Hopanoids methylated at the C-3 position are a subset of bacterial triterpenoids that are readily preserved in modern and ancient sediments and in petroleum. The production of 3-methylhopanoids by extant aerobic methanotrophs and their common occurrence in modern and fossil methane seep communities, in conjunction with carbon isotope analysis, has led to their use as biomarker proxies for aerobic methanotrophy. In addition, these lipids are also produced by aerobic acetic acid bacteria and, lacking carbon isotope analysis, are more generally used as indicators for aerobiosis in ancient ecosystems. However, recent genetic studies have brought into question our current understanding of the taxonomic diversity of methylhopanoid-producing bacteria and have highlighted that a proper interpretation of methylhopanes in the rock record requires a deeper understanding of their cellular function. In this study, we identified and deleted a gene, hpnR, required for methylation of hopanoids at the C-3 position in the obligate methanotroph Methylococcus capsulatus strain Bath. Bioinformatics analysis revealed that the taxonomic distribution of HpnR extends beyond methanotrophic and acetic acid bacteria. Phenotypic analysis of the M. capsulatus hpnR deletion mutant demonstrated a potential physiological role for 3-methylhopanoids; they appear to be required for the maintenance of intracytoplasmic membranes and cell survival in late stationary phase. Therefore, 3-methylhopanoids may prove more useful as proxies for specific environmental conditions encountered during stationary phase rather than a particular bacterial group.

  11. The histo structure of galls induced by aphids as a useful taxonomic character: the case of Rectinasus (Hemiptera, Aphididae, Eriosomatinae).

    PubMed

    Álvarez, Rafael; Molist, Pilar; González-Sierra, Silvia; Martinez, Jean Jacques Itzhak; Nafría, Juan M Nieto

    2014-01-01

    Morphological differentiation of gall tissues induced on plants may play a role to characterize the real taxonomic position of the gall inducer. We verified this hypothesis with galls induced by Rectinasus buxtoni on Pistacia palaestina. There is controversy about the taxonomic localization of genus Rectinasus: in one classification it is situated with the genera Forda and Paracletus while in another it is linked to the genera Geoica and Baizongia. Histological examination of the walls of the galls reveals the presence of two opposed vascular bundles and an inner surface of the gall with cavities. These features place Rectinasus in the same group as Geoica and Baizongia, and not with Paracletus and Forda, whose galls have a different histological structure, as generally admitted. PMID:25283424

  12. Multi-locus analysis supports the taxonomic validity of Arborophila gingica guangxiensis Fang Zhou & Aiwu Jiang, 2008

    PubMed Central

    Chen, De; Liu, Qiong; Chang, Jiang; Jiang, Aiwu; Zhou, Fang; Zhang, Yanyun; Zhang, Zhengwang

    2016-01-01

    Abstract The taxonomic status of subspecies has long been debated, especially in conservation biology. Some proposed subspecies must be evolutionarily distinct to be considered conservation units. White-necklaced Partridge (Arborophila gingica) comprises two subspecies, Arborophila gingica gingica and Arborophila gingica guangxiensis. Arborophila gingica guangxiensis, restricted to three isolated small areas in Guangxi, China, with limited population sizes, is a newly discovered subspecies based on recently identified geographic and phenotypic differences between Arborophila gingica gingica; however, evidence is lacking that can effectively identify whether the subspecies is evolutionarily distinct. Here, three mitochondrial DNA segments and four nuclear introns were used to test whether the two subspecies are reciprocally monophyletic, which has been proposed as an objective method to evaluate evolutionary distinctiveness. The results indicate that the two subspecies are genetically divergent and form reciprocal monophyletic groups. Therefore, this study further supports the taxonomic validity and distinctiveness of Arborophila gingica guangxiensis and suggests that this subspecies be considered as a conservation unit. PMID:26877690

  13. Oxygen abundance and convection

    NASA Astrophysics Data System (ADS)

    Van't Veer, C.; Cayrel, R.

    The triplet IR lines of O I near 777 nm are computed with the Kurucz's code, modified to accept several convection models. The program has been run with the MLT algorithm, with l/H = 1.25 and 0.5, and with the Canuto-Mazzitelli and Canuto-Goldman-Mazzitelli approaches, on a metal-poor turnoff-star model atmosphere with Teff=6200 K, log g = 4.3, [Fe/H]= -1.5. The results show that the differences in equivalent widths for the 4 cases do not exceed 2 per cent (0.3 mA). The convection treatment is therefore not an issue for the oxygen abundance derived from the permitted lines.

  14. Marine Actinobacteria from the Gulf of California: diversity, abundance and secondary metabolite biosynthetic potential

    PubMed Central

    Becerril-Espinosa, Amayaly; Freel, Kelle C.; Jensen, Paul R.

    2015-01-01

    The Gulf of California is a coastal marine ecosystem characterized as having abundant biological resources and a high level of endemism. In this work we report the isolation and characterization of Actinobacteria from different sites in the western Gulf of California. We collected 126 sediment samples and isolated on average 3.1–38.3 Actinobacterial strains from each sample. Phylogenetic analysis of 136 strains identified them as members of the genera Actinomadura, Micromonospora, Nocardiopsis, Nonomuraea, Saccharomonospora, Salinispora, Streptomyces and Verrucosispora. These strains were grouped into 26–56 operational taxonomic units (OTUs) based on 16S rRNA gene sequence identities of 98–100 %. At 98 % sequence identity, three OTUs appear to represent new taxa while nine (35 %) have only been reported from marine environments. Sixty-three strains required seawater for growth. These fell into two OTUs at the 98 % identity level and include one that failed to produce aerial hyphae and was only distantly related (≤95.5 % 16S identity) to any previously cultured Streptomyces sp. Phylogenetic analyses of ketosynthase domains associated with polyketide synthase genes revealed sequences that ranged from 55 to 99 % nucleotide identity to experimentally characterized biosynthetic pathways suggesting that some may be associated with the production of new secondary metabolites. These results indicate that marine sediments from the Gulf of California harbor diverse Actinobacterial taxa with the potential to produce new secondary metabolites. PMID:23229438

  15. The Bias-Corrected Taxonomic Distribution of Mission-Accessible Small Near-Earth Objects

    NASA Astrophysics Data System (ADS)

    Hinkle, Mary L.; Moskovitz, Nicholas; Trilling, David; Binzel, Richard P.; Thomas, Cristina; Christensen, Eric; DeMeo, Francesca; Person, Michael J.; Polishook, David; Willman, Mark

    2015-11-01

    Although they are thought to compose the majority of the Near-Earth object (NEO) population, the small (d < 1 km) near-Earth asteroids (NEAs) have not yet been studied as thoroughly as their larger cousins. Sub-kilometer objects are amongst the most abundant newly discovered NEOs and are often targets of opportunity, observable for only a few days to weeks after their discovery. Even at their brightest (V ~ 18), these asteroids are faint enough that they must be observed with large ground-based telescopes.The Mission Accessible Near-Earth Object Survey (MANOS) began in August 2013 as a multi-year physical characterization survey that was awarded survey status by NOAO. MANOS will target several hundred mission-accessible NEOs across visible and near-infrared wavelengths, ultimately providing a comprehensive catalog of physical properties (astrometry, light curves, spectra).Fifty-seven small, mission-accessible NEAs were observed between mid 2013 and mid 2015 using GMOS at Gemini North & South observatories as well as the DeVeny spectrograph at Lowell Observatory's Discovery Channel Telescope. Archival data of 43 objects from the MIT-UH-IRTF Joint Campaign for NEO Spectral Reconnaissance (PI R. Binzel) were also used. Taxonomic classifications were obtained by fitting our spectra to the mean reflectance spectra of the Bus asteroid taxonomy (Bus & Binzel 2002). Small NEAs are the likely progenitors of meteorites; an improved understanding of the abundance of meteorite parent body types in the NEO population improves understanding of how the two populations are related as well as the biases Earth's atmosphere imposes upon the meteorite collection.We present classifications for these objects as well as results for the debiased distribution of taxa(as a proxy for composition) as a function of object size and compare to the observed fractions of ordinary chondritemeteorites and asteroids with d > 1 km. Amongst the smallest NEOs we find an unexpected distribution of

  16. Selection of a taxonomic level for soil mapping using diversity and map purity indices: A case study from an Iranian arid region

    NASA Astrophysics Data System (ADS)

    Jafari, A.; Ayoubi, S.; Khademi, H.; Finke, P. A.; Toomanian, N.

    2013-11-01

    There is a growing demand for digital soil maps for environmental planning, modeling and management. If mapped soil classes are taken from a hierarchical taxonomic system, a question arises: which taxonomic level is most appropriate to be depicted on the map with a given sample size, available environmental covariates and the strength of predictive relations between covariates and the soil classes? Pedodiversity, the study and measurement of soil diversity, can be considered as a framework to analyze spatial patterns depicted on soil maps. This paper discusses the selection of the taxonomic level for soil mapping in an arid region in southeast Iran on the basis of (1) the purity of a digital soil class map derived from an artificial neural network (ANN) prediction method using environmental covariates and (2) pedodiversity indices of these soil maps. The prediction of soil classes and the calculation of diversity indices were carried out for taxonomic categories of order, suborder, great group, and subgroup. Using the feed forward back-propagation algorithm, three-layer ANNs with input, hidden and output layers were trained for soil class prediction at each category level. In most predictions, the combined use of terrain attributes and geomorphic surfaces provided the best results. When the taxonomic level changed from order to subgroup, the purity decreased, whereas the values of the diversity indices increased. The highest purity and lowest diversity are observed at the order level, indicating a good quality map in terms of its purity, but reflecting only little soil diversity, thus with a low usage potential. On the other hand, soil maps at the level of subgroup illustrate high diversity and low purity, so that the predicted map units are highly uncertain. This map is also inappropriate for users. We introduced an index combining the diversity and purity which indicated that the best taxonomic level for soil mapping in the study area is the great group, with

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

    PubMed

    Le Péchon, Timothée; Gigord, Luc D B

    2014-01-01

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

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

    PubMed Central

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

    2005-01-01

    contain a thorough sampling of taxonomically well-annotated sequences. Taxonomy, held by some to be an old-fashioned trade, has accordingly never been more important. emerencia does not automate the taxonomic process, but it does allow researchers to focus their efforts elsewhere than countless manual BLAST runs and arduous sieving of BLAST hit lists. The emerencia system is available on an open source basis for local installation with any organism and gene group as targets. PMID:16022740

  19. 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

  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. PMID:22063815

  1. Actinide abundances in ordinary chondrites

    NASA Technical Reports Server (NTRS)

    Hagee, B.; Bernatowicz, T. J.; Podosek, F. A.; Johnson, M. L.; Burnett, D. S.

    1990-01-01

    Measurements of actinide and light REE (LREE) abundances and of phosphate abundances in equilibrated ordinary chondrites were obtained and were used to define the Pu abundance in the solar system and to determine the degree of variation of actinide and LREE abundances. The results were also used to compare directly the Pu/U ratio with the earlier obtained ratio determined indirectly, as (Pu/Nd)x(Nd/U), assuming that Pu behaves chemically as a LREE. The data, combined with high-accuracy isotope-dilution data from the literature, show that the degree of gram-scale variability of the Th, U, and LREE abundances for equilibrated ordinary chondrites is a factor of 2-3 for absolute abundances and up to 50 percent for relative abundances. The observed variations are interpreted as reflecting the differences in the compositions and/or proportions of solar nebula components accreted to ordinary chondrite parent bodies.

  2. Capella: Structure and Abundances

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy S.

    1999-01-01

    This grant covers the analysis of EUVE spectra of the cool star binary system Capella. This project has also required the analysis of simultaneous Advanced Satellite for Cosmology and Astrophysics (ASCA) data. The ASCA spectrum of Capella could not be fit with standard models; by imposing models based on strong lines observed with EUVE, a problem wavelength region was identified. Correcting the problem required calculations of atomic collision strengths of higher principal quantum number than had ever been calculated. With these new models applied to the ASCA spectrum, better fits were obtained. Findings are that: (1) ASCA and EUVE spectra are both dominated by a region at 6 x 10(exp 6) K. (2) The high energy cut-off of the ASCA spectrum is consistent with emission from the highest ionization stages of EUVE, namely Fe XXIV. (3) EUVE requires a continuous emission measure distribution with more than two temperatures. (4) The ASCA spectra are of such high statistical significance that systematic uncertainties dominate, including atomic physics issues and calibration issues. (5) While the ASCA spectral fits achieve lower Chi(exp 2 with two-temperature fits, the EUVE-derived emission measure distribution models are also consistent with the spectra. (6) The Fe/H ratio obtained from the ASCA fit is within 20 % of the Fe/H abundance obtained from the summed spectra of Capella over 5 EUVE pointings, as well as the 1996 EUVE data. This result confirms our claims that quasi-continua composed of weak emission lines in the short wavelength spectrometer of EUVE are not major contributors to the measured Capella continuum. Other abundance ratios are also determined from the ASCA data, using models derived with EUVE. Si, Si, and Mg appear to be close to solar photospheric values, while the ratio of Ne/Fe is three to four times lower than solar photospheric values. Whether there is a general First Ionization Potential (FIP) effect or a specific neon anomaly cannot be determined

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

    PubMed

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

    2016-01-01

    Quantifying changes to coral reef fish assemblages in the wake of cyclonic disturbances is challenging due to spatial variability of damage inherent in such events. Often, fish abundance appears stable at one spatial scale (e.g. reef-wide), but exhibits substantial change at finer scales (e.g. site-specific decline or increase). Taxonomic resolution also plays a role; overall stability at coarse taxonomic levels (e.g. family) may mask species-level turnover. Here we document changes to reef fish communities after severe Tropical Cyclone Ita crossed Lizard Island, Great Barrier Reef. Coral and reef fish surveys were conducted concurrently before and after the cyclone at four levels of exposure to the prevailing weather. Coral cover declined across all exposures except sheltered sites, with the largest decline at exposed sites. There was no significant overall reduction in the total density, biomass and species richness of reef fishes between 2011 and 2015, but individual fish taxa (families and species) changed in complex and unpredictable ways. For example, more families increased in density and biomass than decreased following Cyclone Ita, particularly at exposed sites whilst more fish families declined at lagoon sites even though coral cover did not decline. All sites lost biomass of several damselfish species, and at most sites there was an increase in macroinvertivores and grazers. Overall, these results suggest that the degree of change measured at coarse taxonomic levels masked high species-level turnover, although other potential explanations include that there was no impact of the storm, fish assemblages were impacted but underwent rapid recovery or that there is a time lag before the full impacts become apparent. This study confirms that in high-complexity, high diversity ecosystems such as coral reefs, species level analyses are essential to adequately capture the consequences of disturbance events. PMID:27285160

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

    PubMed Central

    Ceccarelli, Daniela M.

    2016-01-01

    Quantifying changes to coral reef fish assemblages in the wake of cyclonic disturbances is challenging due to spatial variability of damage inherent in such events. Often, fish abundance appears stable at one spatial scale (e.g. reef-wide), but exhibits substantial change at finer scales (e.g. site-specific decline or increase). Taxonomic resolution also plays a role; overall stability at coarse taxonomic levels (e.g. family) may mask species-level turnover. Here we document changes to reef fish communities after severe Tropical Cyclone Ita crossed Lizard Island, Great Barrier Reef. Coral and reef fish surveys were conducted concurrently before and after the cyclone at four levels of exposure to the prevailing weather. Coral cover declined across all exposures except sheltered sites, with the largest decline at exposed sites. There was no significant overall reduction in the total density, biomass and species richness of reef fishes between 2011 and 2015, but individual fish taxa (families and species) changed in complex and unpredictable ways. For example, more families increased in density and biomass than decreased following Cyclone Ita, particularly at exposed sites whilst more fish families declined at lagoon sites even though coral cover did not decline. All sites lost biomass of several damselfish species, and at most sites there was an increase in macroinvertivores and grazers. Overall, these results suggest that the degree of change measured at coarse taxonomic levels masked high species-level turnover, although other potential explanations include that there was no impact of the storm, fish assemblages were impacted but underwent rapid recovery or that there is a time lag before the full impacts become apparent. This study confirms that in high-complexity, high diversity ecosystems such as coral reefs, species level analyses are essential to adequately capture the consequences of disturbance events. PMID:27285160

  5. Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial communities in the sediments of Hangzhou Bay.

    PubMed

    Dai, Tianjiao; Zhang, Yan; Tang, Yushi; Bai, Yaohui; Tao, Yile; Huang, Bei; Wen, Donghui

    2016-10-01

    Coastal areas are land-sea transitional zones with complex natural and anthropogenic disturbances. Microorganisms in coastal sediments adapt to such disturbances both individually and as a community. The microbial community structure changes spatially and temporally under environmental stress. In this study, we investigated the microbial community structure in the sediments of Hangzhou Bay, a seriously polluted bay in China. In order to identify the roles and contribution of all microbial taxa, we set thresholds as 0.1% for rare taxa and 1% for abundant taxa, and classified all operational taxonomic units into six exclusive categories based on their abundance. The results showed that the key taxa in differentiating the communities are abundant taxa (AT), conditionally abundant taxa (CAT), and conditionally rare or abundant taxa (CRAT). A large population in conditionally rare taxa (CRT) made this category collectively significant in differentiating the communities. Both bacteria and archaea demonstrated a distance decay pattern of community similarity in the bay, and this pattern was strengthened by rare taxa, CRT and CRAT, but weakened by AT and CAT. This implied that the low abundance taxa were more deterministically distributed, while the high abundance taxa were more ubiquitously distributed. PMID:27402713

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

    NASA Astrophysics Data System (ADS)

    Carvano, J.; Davallos, J.

    2014-07-01

    Asteroid taxonomy is the effort of grouping asteroids into classes based on similarities of a number of their observational properties. The most used properties include measurements of their spectral reflectance (by means of low-resolution spectra, spectro-photometry, or colors), and geometric albedo. The usefulness of asteroid taxonomic classes derived in this way relies on the assumption that the classes bear some correspondence to the mineralogy of the asteroids, and on the fact that such classification can be made using types of observations that presently are available to a large number of asteroids. Therefore, asteroid taxonomy can be used to infer trends in the distribution of compositions in the main belt and other populations, as an additional parameter in defining asteroid families, and as a selection tool to identify candidates for more detailed observations. However, the fact that the correspondence between taxonomic class and composition is far from perfect is still sometimes overlooked in the literature. Indeed, although a taxonomic classification narrows down the possible mineralogies of a given asteroid, it will seldom point univocally to one particular mineralogy. This happens for a number of reasons, some linked to the intrinsic difficulty involved in the remote characterization of the mineralogy of an asteroid, since it depends on the presence of absorption bands in its reflectance spectrum which may be absent or not completely sampled by the observations used to derive taxonomy. Other problem here is the exposure of the material on the surface of the asteroid to space-weathering effects, such as solar wind implantation and micro-meteorite bombardment, which can change the optical properties of the material. Finally, the overall shape of the reflectance spectrum of an asteroid is also affected by the geometry of the observation, as well as by its shape. In this work, we analyze how the classification of asteroids observed by the Sloan Digital Sky

  7. Taxonomic composition and physiological and biochemical properties of bacteria in the digestive tracts of earthworms

    NASA Astrophysics Data System (ADS)

    Byzov, B. A.; Tikhonov, V. V.; Nechitailo, T. Yu.; Demin, V. V.; Zvyagintsev, D. G.

    2015-03-01

    Several hundred bacterial strains belonging to different taxa were isolated and identified from the digestive tracts of soil and compost earthworms. Some physiological and biochemical properties of the bacteria were characterized. The majority of intestinal bacteria in the earthworms were found to be facultative anaerobes. The intestinal isolates as compared to the soil ones had elevated activity of proteases and dehydrogenases. In addition, bacteria associated with earthworms' intestines are capable of growth on humic acids as a sole carbon source. Humic acid stimulated the growth of the intestinal bacteria to a greater extent than those of the soil ones. In the digestive tracts, polyphenol oxidase activity was found. Along with the data on the taxonomic separation of the intestinal bacteria, the features described testified to the presence of a group of bacteria in the earthworms intestines that is functionally characteristic and is different from the soil bacteria.

  8. Taxonomic revision of Australian long-horn moths of the genus Nemophora (Lepidoptera: Adelidae).

    PubMed

    Kozlov, Mikhail V

    2016-01-01

    The taxonomic revision of Australian species of the genus Nemophora Hoffmannsegg is based on investigation of type materials of all described taxa. Lectotypes are designated for Nemotois opalina Meyrick, 1912; N. panaeola Turner, 1913; N. sparsella Walker, 1863; N. topazias Meyrick, [1893]; N. orichalcias Meyrick, [1893]; and N. selasphora Turner, 1913. N. topazias Meyrick, syn. nov. and N. selasphora Turner, syn. n. are synonymized with Nemophora laurella (Newman, 1856). Two new species, Nemophora doddi sp. nov. and N. turneri sp. nov., are described from Queensland. The fauna of Australia currently includes seven valid species of Nemophora, which form a monophyletic laurella species-group. Keys to species based on external characters and on male genitalia are provided; adults and male genitalia are described and illustrated. PMID:27394526

  9. Taxonomic status and phylogenetic relationship of tits based on mitogenomes and nuclear segments.

    PubMed

    Li, Xuejuan; Lin, Liliang; Cui, Aiming; Bai, Jie; Wang, Xiaoyang; Xin, Chao; Zhang, Zhen; Yang, Chao; Gao, Ruirui; Huang, Yuan; Lei, Fumin

    2016-11-01

    The phylogeny of tits has been studied using various molecular markers, but their phylogenetic relationships remain controversial. To further investigate their taxonomic status and phylogenetic relationships, the entire mitochondrial genomes (mitogenomes) and five nuclear segments were sequenced from 10 species of tits and two outgroups (Sylviparus modestus and Remiz consobrinus), followed by the comparison of mitogenomic characteristics and reconstruction of phylogenetic relationship based on the different datasets. The results revealed the following: the mitogenomes of 10 ingroup tits, each 16,758-16,799bp in length, displayed typical mitogenome organization and the gene order found in most previously determined Passeriformes mitogenomes; close relationships existed between Parus major and P. monticolus, between P. montanus and P. palustris, and between P. ater and P. venustulus; and Pseudopodoces humilis was a sister group to P. spilonotus, P. cyanus, or the clade containing P. major and P. monticolus. PMID:27444707

  10. 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.

  11. Phytoplankton Composition and Abundance in Restored Maltański Reservoir under the Influence of Physico-Chemical Variables and Zooplankton Grazing Pressure

    PubMed Central

    Kozak, Anna; Gołdyn, Ryszard; Dondajewska, Renata

    2015-01-01

    In this paper we present the effects of environmental factors and zooplankton food pressure on phytoplankton in the restored man-made Maltański Reservoir (MR). Two methods of restoration: biomanipulation and phosphorus inactivation have been applied in the reservoir. Nine taxonomical groups of phytoplankton represented in total by 183 taxa were stated there. The richest groups in respect of taxa number were green algae, cyanobacteria and diatoms. The diatoms, cryptophytes, chrysophytes, cyanobacteria, green algae and euglenophytes dominated in terms of abundance and/or biomass. There were significant changes among environmental parameters resulting from restoration measures which influenced the phytoplankton populations in the reservoir. These measures led to a decrease of phosphorus concentration due to its chemical inactivation and enhanced zooplankton grazing as a result of planktivorous fish stocking. The aim of the study is to analyse the reaction of phytoplankton to the restoration measures and, most importantly, to determine the extent to which the qualitative and quantitative composition of phytoplankton depends on variables changing under the influence of restoration in comparison with other environmental variables. We stated that application of restoration methods did cause significant changes in phytoplankton community structure. The abundance of most phytoplankton taxa was negatively correlated with large zooplankton filter feeders, and positively with zooplankton predators and concentrations of ammonium nitrogen and partly of phosphates. However, restoration was insufficient in the case of decreasing phytoplankton abundance. The effects of restoration treatments were of less importance for the abundance of phytoplankton than parameters that were independent of the restoration. This was due to the continuous inflow of large loads of nutrients from the area of the river catchment. PMID:25906352

  12. Phytoplankton Composition and Abundance in Restored Maltański Reservoir under the Influence of Physico-Chemical Variables and Zooplankton Grazing Pressure.

    PubMed

    Kozak, Anna; Gołdyn, Ryszard; Dondajewska, Renata

    2015-01-01

    In this paper we present the effects of environmental factors and zooplankton food pressure on phytoplankton in the restored man-made Maltański Reservoir (MR). Two methods of restoration: biomanipulation and phosphorus inactivation have been applied in the reservoir. Nine taxonomical groups of phytoplankton represented in total by 183 taxa were stated there. The richest groups in respect of taxa number were green algae, cyanobacteria and diatoms. The diatoms, cryptophytes, chrysophytes, cyanobacteria, green algae and euglenophytes dominated in terms of abundance and/or biomass. There were significant changes among environmental parameters resulting from restoration measures which influenced the phytoplankton populations in the reservoir. These measures led to a decrease of phosphorus concentration due to its chemical inactivation and enhanced zooplankton grazing as a result of planktivorous fish stocking. The aim of the study is to analyse the reaction of phytoplankton to the restoration measures and, most importantly, to determine the extent to which the qualitative and quantitative composition of phytoplankton depends on variables changing under the influence of restoration in comparison with other environmental variables. We stated that application of restoration methods did cause significant changes in phytoplankton community structure. The abundance of most phytoplankton taxa was negatively correlated with large zooplankton filter feeders, and positively with zooplankton predators and concentrations of ammonium nitrogen and partly of phosphates. However, restoration was insufficient in the case of decreasing phytoplankton abundance. The effects of restoration treatments were of less importance for the abundance of phytoplankton than parameters that were independent of the restoration. This was due to the continuous inflow of large loads of nutrients from the area of the river catchment. PMID:25906352

  13. Taxonomic turmoil down-under: recent developments in Australian orchid systematics

    PubMed Central

    Hopper, Stephen D.

    2009-01-01

    Background The issue of determining the most appropriate rank for each accepted taxon fuels ongoing controversy throughout systematics. The particularly marked escalation of such issues in modern Australian orchid systematics merits examination, not only because of wider implications in taxonomy but also because of direct effects on studies of comparative biology and conservation management. Scope This paper briefly reviews the causes of recent taxonomic turmoil for Australian orchids and outlines new research opportunities and conservation implications arising from an improved understanding of their molecular phylogenetics. Conclusions DNA sequencing and intensified field work have contributed towards a much improved understanding of Australian orchid systematics. Great progress has been made in discerning monophyletic groups or clades. Fresh interpretations of morphological evolution have been made possible by comparisons with the results of DNA analyses. Significant conceptual shifts from polymorphic species concepts to biological and phylogenetic concepts have also elevated the discovery and description of new species. Consequently, over the past decade, the number of Australian orchid species recognized by taxonomists has risen from approx. 900 to 1200. Similarly, the number of genera recognized by some taxonomists has increased from 110 to 192, resulting in 45% of Australian species/subspecies being assigned a new generic epithet since 2000. At higher taxonomic levels, much of the recent controversy in Australian orchid systematics reflects a divergence in views about where to split and assign formal names within unequivocally monophyletic groups. Differences regarding typification in the case of Caladenia have added additional confusion and complexity. However, new insights into and research opportunities concerning speciation processes in orchids have arisen from the wealth of new data and discrimination of species. Robustly supported molecular analyses of

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

    PubMed

    Trojan, Daniela; Schreiber, Lars; Bjerg, Jesper T; Bøggild, Andreas; Yang, Tingting; Kjeldsen, Kasper U; Schramm, Andreas

    2016-07-01

    Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exact phylogeny is uncertain, as most studies so far have reported only short partial 16S rRNA sequences or have relied on identification by a combination of filament morphology and 16S rRNA-targeted fluorescence in situ hybridization with a Desulfobulbaceae-specific probe. In this study, nearly full-length 16S rRNA gene sequences of 16 individual cable bacteria filaments from freshwater, salt marsh, and marine sites of four geographic locations are presented. These sequences formed a distinct, monophyletic sister clade to the genus Desulfobulbus and could be divided into six coherent, species-level clusters, arranged as two genus-level groups. The same grouping was retrieved by phylogenetic analysis of full or partial dsrAB genes encoding the dissimilatory sulfite reductase. Based on these results, it is proposed to accommodate cable bacteria within two novel candidate genera: the mostly marine "Candidatus Electrothrix", with four candidate species, and the mostly freshwater "Candidatus Electronema", with two candidate species. This taxonomic framework can be used to assign environmental sequences confidently to the cable bacteria clade, even without morphological information. Database searches revealed 185 16S rRNA gene sequences that affiliated within the clade formed by the proposed cable bacteria genera, of which 120 sequences could be assigned to one of the six candidate species, while the remaining 65 sequences indicated the existence of up to five additional species. PMID:27324572

  15. Mercury in feathers from Chilean birds: Influence of location, feeding strategy, and taxonomic affiliation

    USGS Publications Warehouse

    Ochoa-Acua, H.; Sepulveda, M.S.; Gross, T.S.

    2002-01-01

    This study reports baseline concentrations of mercury (Hg) in feathers from different species of birds sampled at various locations off the Chilean coast (Southeastern Pacific). Hg concentrations were evaluated in relation to geographic location, taxonomic affiliation, and feeding strategies. Between January and March of 1995, we collected mature contour feathers from 116 birds belonging to 22 species, mostly seabirds. Birds were collected from 10 different locations (26??09???S, 70??40???W to 54??56???S, 67??37???W). Feather Hg concentrations ranged from 0.11 to 13 ??gg-1 dry weight. We found differences in feather Hg concentrations across taxonomic groups, with highest concentrations in petrels, shearwaters, and albatrosses (Procellaridae), followed by boobies (Sulidae), gulls, terns, skuas (Laridae) and cormorants (Phalacrocoracidae). Ibises and oystercatchers (Threskiornithidae and Charadriidae) had intermediate values, whereas ducks and geese (Anatidae) contained the least amount of Hg. Oceanic species preying on mesopelagic fish (the Procellariformes albatrosses, petrels, and fulmars) had over twice as much Hg (overall average of 3.9 ??gg-1) when compared to the rest of the species sampled (overall average of 1.5 ??gg-1). We did not find higher Hg concentrations in birds inhabiting the more heavily industrialized and urbanized areas of the country (central and northern regions), but in birds inhabiting the remote Juan Ferna??ndez Archipelago. This is not surprising, since all the Procellariformes (the group with highest Hg values in this study) were collected from these islands. Except for Hg in Kermadec petrels (mean of 12 ??gg-1), the range of Hg values reported here (0.11-7.3 ??gg-1) fell below those known to cause adverse health and reproductive effects in birds. ?? 2002 Elsevier Science Ltd. All rights reserved.

  16. Mercury in feathers from Chilean birds: Influence of location, feeding strategy and taxonomic affiliation

    USGS Publications Warehouse

    Ochoa-Acuna, H.G.; Sepulveda, M.S.; Gross, T.S.

    2002-01-01

    This study reports baseline concentrations of mercury (Hg) in feathers from different species of birds sampled at various locations off the Chilean coast (Southeastern Pacific). Hg concentrations were evaluated in relation to geographic location, taxonomic affiliation, and feeding strategies. Between January and March of 1995, we collected mature contour feathers from 116 birds belonging to 22 species, mostly seabirds. Birds were collected from 10 different locations (26?09'S, 70?40'W to 54?56'S, 67?37'W). Feather Hg concentrations ranged from 0.11 to 13 ?g g-1 dry weight. We found differences in feather Hg concentrations across taxonomic groups, with highest concentrations in petrels, shearwaters, and albatrosses (Procellaridae), followed by boobies (Sulidae), gulls, terns, skuas (Laridae) and cormorants (Phalacrocoracidae). Ibises and oystercatchers (Threskiornithidae and Charadriidae) had intermediate values, whereas ducks and geese (Anatidae) contained the least amount of Hg. Oceanic species preying on mesopelagic fish (the Procellariformes albatrosses, petrels, and fulmars) had over twice as much Hg (overall average of 3.9 ?g g-1) when compared to the rest of the species sampled (overall average of 1.5 ?g g-1). We did not find higher Hg concentrations in birds inhabiting the more heavily industrialized and urbanized areas of the country (central and northern regions), but in birds inhabiting the remote Juan Fernandez Archipelago. This is not surprising, since all the Procellariformes (the group with highest Hg values in this study) were collected from these islands. Except for Hg in Kermadec petrels (mean of 12 ?g g-1), the range of Hg values reported here (0.11-7.3 ?g g-1) fell below those known to cause adverse health and reproductive effects in birds.

  17. Capella: Structure and Abundances

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy S.

    1999-01-01

    This grant covers the analysis of ASCA spectra of the cool star binary system Capella. This project has also required the analysis of simultaneous EUVE data. The ASCA spectrum of Capella could not be fit with standard models; by imposing models based on strong lines observed with EUVE, a problem wavelength region was identified. Correcting the problem required calculations of atomic collision strengths of higher principal quantum number than had ever been calculated, resulting in a paper in process by Liedahl and Brickhouse. With these new models applied to the ASCA spectrum, better fits were obtained. While solar abundance ratios are generally consistent with the ASCA data, the ratio of Ne/Fe is three to four times lower than solar photospheric values. Whether there is a general First Ionization Potential (FIP) effect or a specific neon anomaly cannot be determined from these data. Detailed discussion has been provided to NASA in the most recent annual report (1997). Two poster presentations have been made regarding modeling requirements. A substantial paper is in the final revision form, following review by six co-authors. The results of this work have wide implications, since the newly calculated emission lines almost certainly contribute to other problems in fitting not only other stellar spectra, but also composite supernova remnants, galaxies, and cooling flow clusters of galaxies. Furthermore, Liedahl and Brickhouse have identified other species for which lines of a similar nature (high principal quantum number) will contribute significant flux. For moderate resolution X-ray spectra, lines left out of the models in relatively isolated bands, will be attributed to continuum flux by spectral fitting engines, causing errors in line-to-continuum ratios. Thus addressing the general theoretical problem is of crucial importance.

  18. Taxonomic, Spatial and Temporal Patterns of Bleaching in Anemones Inhabited by Anemonefishes

    PubMed Central

    Hobbs, Jean-Paul A.; Frisch, Ashley J.; Ford, Benjamin M.; Thums, Michele; Saenz-Agudelo, Pablo; Furby, Kathryn A.; Berumen, Michael L.

    2013-01-01

    Background Rising sea temperatures are causing significant destruction to coral reef ecosystems due to coral mortality from thermally-induced bleaching (loss of symbiotic algae and/or their photosynthetic pigments). Although bleaching has been intensively studied in corals, little is known about the causes and consequences of bleaching in other tropical symbiotic organisms. Methodology/Principal Findings This study used underwater visual surveys to investigate bleaching in the 10 species of anemones that host anemonefishes. Bleaching was confirmed in seven anemone species (with anecdotal reports of bleaching in the other three species) at 10 of 19 survey locations spanning the Indo-Pacific and Red Sea, indicating that anemone bleaching is taxonomically and geographically widespread. In total, bleaching was observed in 490 of the 13,896 surveyed anemones (3.5%); however, this percentage was much higher (19–100%) during five major bleaching events that were associated with periods of elevated water temperatures and coral bleaching. There was considerable spatial variation in anemone bleaching during most of these events, suggesting that certain sites and deeper waters might act as refuges. Susceptibility to bleaching varied between species, and in some species, bleaching caused reductions in size and abundance. Conclusions/Significance Anemones are long-lived with low natural mortality, which makes them particularly vulnerable to predicted increases in severity and frequency of bleaching events. Population viability will be severely compromised if anemones and their symbionts cannot acclimate or adapt to rising sea temperatures. Anemone bleaching also has negative effects to other species, particularly those that have an obligate relationship with anemones. These effects include reductions in abundance and reproductive output of anemonefishes. Therefore, the future of these iconic and commercially valuable coral reef fishes is inextricably linked to the ability of

  19. Distribution, abundance and diversity of crustose coralline algae on the Great Barrier Reef

    NASA Astrophysics Data System (ADS)

    Dean, Angela J.; Steneck, Robert S.; Tager, Danika; Pandolfi, John M.

    2015-06-01

    The Great Barrier Reef (GBR) is the world's largest coral reef ecosystem. Crustose coralline algae (CCA) are important contributors to reef calcium carbonate and can facilitate coral recruitment. Despite the importance of CCA, little is known about species-level distribution, abundance, and diversity, and how these vary across the continental shelf and key habitat zones within the GBR. We quantified CCA species distributions using line transects ( n = 127) at 17 sites in the northern and central regions of the GBR, distributed among inner-, mid-, and outer-shelf regions. At each site, we identified CCA along replicate transects in three habitat zones: reef flat, reef crest, and reef slope. Taxonomically, CCA species are challenging to identify (especially in the field), and there is considerable disagreement in approach. We used published, anatomically based taxonomic schemes for consistent identification. We identified 30 CCA species among 12 genera; the most abundant species were Porolithon onkodes, Paragoniolithon conicum (sensu Adey), Neogoniolithon fosliei, and Hydrolithon reinboldii. Significant cross-shelf differences were observed in CCA community structure and CCA abundance, with inner-shelf reefs exhibiting lower CCA abundance than outer-shelf reefs. Shelf position, habitat zone, latitude, depth, and the interaction of shelf position and habitat were all significantly associated with variation in composition of CCA communities. Collectively, shelf position, habitat, and their interaction contributed to 22.6 % of the variation in coralline communities. Compared to mid- and outer-shelf sites, inner-shelf sites exhibited lower relative abundances of N. fosliei and Lithophyllum species. Reef crest habitats exhibited greater abundance of N. fosliei than reef flat and reef slope habitats. Reef slope habitats exhibited lower abundance of P. onkodes, but greater abundance of Neogoniolithon clavycymosum than reef crest and reef slope habitats. These findings

  20. Effect of Lake Trophic Status and Rooted Macrophytes on Community Composition and Abundance of Ammonia-Oxidizing Prokaryotes in Freshwater Sediments▿

    PubMed Central

    Herrmann, Martina; Saunders, Aaron M.; Schramm, Andreas

    2009-01-01

    Communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in freshwater sediments and those in association with the root system of the macrophyte species Littorella uniflora, Juncus bulbosus, and Myriophyllum alterniflorum were compared for seven oligotrophic to mesotrophic softwater lakes and acidic heathland pools. Archaeal and bacterial ammonia monooxygenase alpha-subunit (amoA) gene diversity increased from oligotrophic to mesotrophic sites; the number of detected operational taxonomic units was positively correlated to ammonia availability and pH and negatively correlated to sediment C/N ratios. AOA communities could be grouped according to lake trophic status and pH; plant species-specific communities were not detected, and no grouping was apparent for AOB communities. Relative abundance, determined by quantitative PCR targeting amoA, was always low for AOB (<0.05% of all prokaryotes) and slightly higher for AOA in unvegetated sediment and AOA in association with M. alterniflorum (0.01 to 2%), while AOA accounted for up to 5% in the rhizospheres of L. uniflora and J. bulbosus. These results indicate that (i) AOA are at least as numerous as AOB in freshwater sediments, (ii) aquatic macrophytes with substantial release of oxygen and organic carbon into their rhizospheres, like L. uniflora and J. bulbosus, increase AOA abundance; and (iii) AOA community composition is generally determined by lake trophy, not by plant species-specific interactions. PMID:19304820

  1. Effects of insecticide-treated and Lepidopteran-active Bt transgenic sweet corn on the abundance and diversity of arthropods.

    PubMed

    Rose, Robyn; Dively, Galen P

    2007-10-01

    A field study was conducted over 2 yr to determine the effects of transgenic sweet corn containing a gene from the bacterium Bacillus thuringiensis (Bt) on the diversity and abundance of nontarget arthropods. The Bt hybrid (expressing Cry1Ab endotoxin for lepidopteran control) was compared with near-isogenic non-Bt and Bt hybrids treated with a foliar insecticide and with a near-isogenic non-Bt hybrid without insecticides. Plant inspections, sticky cards, and pitfall traps were used to sample a total of 573,672 arthropods, representing 128 taxonomic groups in 95 families and 18 orders. Overall biodiversity and community-level responses were not significantly affected by the transgenic hybrid. The Bt hybrid also had no significant adverse effects on population densities of specific nontarget herbivores, decomposers, and natural enemies enumerated at the family level during the crop cycle. As expected, the insecticide lambda-cyhalothrin had broad negative impacts on the abundance of many nontarget arthropods. One insecticide application in the Bt plots reduced the overall abundance of the natural enemy community by 21-48%. Five applications in the non-Bt plots reduced natural enemy communities by 33-70%. Nontarget communities affected in the insecticide-treated Bt plots exhibited some recovery, but communities exposed to five applications showed no trends toward recovery during the crop cycle. This study clearly showed that the nontarget effects of Bt transgenic sweet corn on natural enemies and other arthropods were minimal and far less than the community-level disruptions caused by lambda-cyhalothrin. PMID:18284751

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

    PubMed Central

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

    2015-01-01

    Abstract The African species of the genus Laccophilus Leach, 1815, are revised, on the basis of study of adult specimens. In all, 105 species are now recognized. A phenetic character-analysis was undertaken, which resulted in a split of the genus into 17 species groups. Diagnoses and a description of each species are given together with keys for identification of species groups and species. We also provide habitus photos, illustration of male genitalia and distribution maps for all species. New species are described as follows: Laccophilus grossus sp. n. (Angola, Namibia), Laccophilus rocchii sp. n. (Tanzania, Namibia, Botswana, Mozambique), Laccophilus ferrugo sp. n. (Mozambique), Laccophilus furthi sp. n. (Madagascar), Laccophilus isamberti sp. n. (Madagascar), Laccophilus inobservatus sp. n. (Gambia, Senegal, Mali, Niger, Sudan, Chad, Ethiopia, Burkina Faso, Ivory Coast, Ghana, Nigeria, Cameroon, Zaire and Asia: Yemen), Laccophilus cryptos sp. n. (Zaire, Mozambique, Zimbabwe, Namibia, Botswana, South Africa), Laccophilus enigmaticus sp. n. (Nigeria, Sudan), Laccophilus bellus sp. n. (Benin, Nigeria), Laccophilus guentheri sp. n. (Guinea, Ghana), Laccophilus guineensis sp. n. (Guinea), Laccophilus decorosus sp. n. (Uganda), Laccophilus empheres sp. n. (Kenya), Laccophilus inconstans sp. n. (Guinea, Ivory Coast, Ghana, Nigeria, Cameroon), Laccophilus brancuccii sp. n. (Central African Republic), Laccophilus incomptus sp. n. (Cameroon), Laccophilus australis sp. n. (Tanzania, South Africa), Laccophilus minimus sp. n. (Namibia), Laccophilus eboris sp. n. (Ivory Coast), Laccophilus insularum sp. n. (Madagascar), Laccophilus occidentalis sp. n. (Gambia, Senegal, Mali, Guinea, Sierra Leone, Ivory Coast, Ghana, Benin, Nigeria, Central African Republic, Zaire) and Laccophilus transversovittatus sp. n. (Madagascar). Laccophilus restrictus Sharp, 1882, is restored as good species; not junior synonym of Laccophilus pictipennis Sharp, 1882. New synonyms are established as

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

    PubMed

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

    2012-08-01

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

  4. 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

  5. Abundance coefficients, a new method for measuring microorganism relative abundance

    USGS Publications Warehouse

    Forester, R.M.

    1977-01-01

    A new method of measuring the relative abundance of microorganisms by using a set of interrelated coefficients, termed 'abundance coefficients' or 'AC', is proposed. These coefficients provide a means of recording abundance for geometric density categories, and each density measurement represents an approximation of the Poisson parameter ??t. The AC is the natural logarithm of a 'characteristic value,' which is a particular number for each geometric density category. The 'characteristic values' are based upon a probabilistic error statement derived from the Poisson formula, and they present evidence for separation of the geometric category boundaries by e = 2.71828. The proposed AC provide a means for recording species abundance in a manner suitable for arithmetic manipulation, for population structure studies, and for the determination of practical limits for defining the presence or absence of a species. Further, these coefficients provide for both intrasample and intersample abundance comparisons. ?? 1977 Plenum Publishing Corporation.

  6. Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water.

    PubMed

    Narciso-da-Rocha, Carlos; Manaia, Célia M

    2016-09-01

    The environment is the original and most ancient source of the antibiotic resistance determinants that threat the human health nowadays. In the environment, water is a privileged habitat and mode of dissemination of bacteria of different origins. Freshwater bodies that cross urban areas are supposed to hold a complex mixture of both human/animal origin and strictly environmental bacteria. In this study, we were interested in unveiling the bacterial diversity in urban river transects and, simultaneously, investigate the occurrence of antibiotic resistant bacteria, in particular the multidrug resistant (MDR). With this aim, water and sediments of two rivers were sampled from an urban transect and the bacterial diversity was assessed based on 16S rRNA gene-based community analysis and, simultaneously, total heterotrophic bacteria were isolated in the presence and in the absence of antibiotics. The three predominant phyla were Proteobacteria, Bacteroidetes and Actinobacteria, in water, or Acidobacteria, in sediments. MDR bacteria were observed to belong to the predominant phyla observed in water, mostly of the classes Gamma- and Betaproteobacteria (Proteobacteria) and Sphingobacteriia and Flavobacteriia (Bacteroidetes) and belonged to genera of ubiquitous (Pseudomonas, Acinetobacter, Stenotrophomonas) or mainly environmental (Chitinophaga, Chryseobacterium) bacteria. The observation that MDR bacteria are widespread in the environment and over distinct phylogenetic lineages has two relevant implications: i) the potential of environmental bacteria as source or facilitators for antibiotic resistance acquisition; ii) the need to complement culture-independent methods with culture-based approaches in order to identify major sources of MDR profiles. PMID:27131885

  7. USING MULTIPILE TAXONOMIC GROUPS TO INDEX THE ECOLOGICAL CONDITION OF LAKES

    EPA Science Inventory

    Biological indicators of communities typically reflect a common environmental signal reflecting the general condition of the ecosystem, as well as individual signals by indicators differentially sensitive to particular environmental conditions. We describe here a method of integ...

  8. Enterotoxin production in relation to taxonomic grouping and source of isolation of Aeromonas species.

    PubMed

    Turnbull, P C; Lee, J V; Miliotis, M D; Van de Walle, S; Koornhof, H J; Jeffery, L; Bryant, T N

    1984-02-01

    A total of 19 of 20 (95%) strains of Aeromonas hydrophila biovar hydrophila and 16 of 17 (94%) strains of Aeromonas sobria isolated from a variety of clinical and environmental sources were found to be enterotoxin positive. Only 2 of 18 (11%) A. hydrophila biovar anaerogenes and 2 of 13 (15%) unidentified Aeromonas strains from a similar variety of sources produced enterotoxin. No association was apparent between the source of isolation, in particular diarrheal stools, and enterotoxigenicity; 41% of the isolates from diarrheal stools were enterotoxin negative. A strong correlation was noted between ability to produce enterotoxin and positive results in six characters: lysine decarboxylase and Voges-Proskauer reactions, production of gas from glucose, gluconate oxidation, xanthine hydrolysis, and hemolysis of human erythrocytes. In the majority of cases (35 of 39 strains), enterotoxigenicity was detected using cell-free filtrates of brain heart infusion broth cultures grown at 36 degrees C for 15; however, the other four positive isolates were detected after growth in the same broth at 30 degrees C or in Casamino Acids-yeast extract broth at 30 or 37 degrees C. It is recommended that for enterotoxin tests, strains should be grown in both media at both temperatures. The infant mouse test was found to be a simple and reliable method for detection of the enterotoxin. The toxin proved to be heat labile and not neutralized by cholera antitoxin. PMID:6699147

  9. Taxonomic hypotheses regarding the genus Gerbillus (Rodentia, Muridae, Gerbillinae) based on molecular analyses of museum specimens.

    PubMed

    Ndiaye, Arame; Tatard, Caroline; Stanley, William; Granjon, Laurent

    2016-01-01

    Methodological improvements now allow routine analyses of highly degraded DNA samples as found in museum specimens. Using these methods could be useful in studying such groups as rodents of the genus Gerbillus for which i) the taxonomy is still highly debated, ii) collection of fresh specimens may prove difficult. Here we address precise taxonomic questions using a small portion of the cytochrome b gene obtained from 45 dry skin/skull museum samples (from 1913 to 1974) originating from two African and three Asian countries. The specimens were labelled Gerbillus gerbillus, Gerbillus andersoni, Gerbillus nanus, Gerbillus amoenus, Gerbillus perpallidus and Gerbillus pyramidum, and molecular results mostly confirmed these assignations. The close relationship between Gerbillus nanus (Asian origin) and Gerbillus amoenus (African origin) confirmed that they represent vicariant sibling species which differentiated in allopatry on either side of the Red Sea. In the closely related Gerbillus perpallidus and Gerbillus pyramidum, specimens considered as belonging to one Gerbillus pyramidum subspecies (Gerbillus pyramidum floweri) appeared closer to Gerbillus perpallidus suggesting that they (Gerbillus pyramidum floweri and Gerbillus perpallidus) may represent a unique species, distributed on both sides of the Nile River, for which the correct name should be Gerbillus floweri. Furthermore, the three other Gerbillus pyramidum subspecies grouped together with no apparent genetic structure suggesting that they may not yet represent genetically differentiated lineages. This study confirms the importance of using these methods on museum samples, which can open new perspectives in this particular group as well as in other groups of interest. PMID:27047247

  10. Taxonomic hypotheses regarding the genus Gerbillus (Rodentia, Muridae, Gerbillinae) based on molecular analyses of museum specimens

    PubMed Central

    Ndiaye, Arame; Tatard, Caroline; Stanley, William; Granjon, Laurent

    2016-01-01

    Abstract Methodological improvements now allow routine analyses of highly degraded DNA samples as found in museum specimens. Using these methods could be useful in studying such groups as rodents of the genus Gerbillus for which i) the taxonomy is still highly debated, ii) collection of fresh specimens may prove difficult. Here we address precise taxonomic questions using a small portion of the cytochrome b gene obtained from 45 dry skin/skull museum samples (from 1913 to 1974) originating from two African and three Asian countries. The specimens were labelled Gerbillus gerbillus, Gerbillus andersoni, Gerbillus nanus, Gerbillus amoenus, Gerbillus perpallidus and Gerbillus pyramidum, and molecular results mostly confirmed these assignations. The close relationship between Gerbillus nanus (Asian origin) and Gerbillus amoenus (African origin) confirmed that they represent vicariant sibling species which differentiated in allopatry on either side of the Red Sea. In the closely related Gerbillus perpallidus and Gerbillus pyramidum, specimens considered as belonging to one Gerbillus pyramidum subspecies (Gerbillus pyramidum floweri) appeared closer to Gerbillus perpallidus suggesting that they (Gerbillus pyramidum floweri and Gerbillus perpallidus) may represent a unique species, distributed on both sides of the Nile River, for which the correct name should be Gerbillus floweri. Furthermore, the three other Gerbillus pyramidum subspecies grouped together with no apparent genetic structure suggesting that they may not yet represent genetically differentiated lineages. This study confirms the importance of using these methods on museum samples, which can open new perspectives in this particular group as well as in other groups of interest. PMID:27047247

  11. Erratum: Interstellar Abundance Standards Revisited

    NASA Astrophysics Data System (ADS)

    Sofia, U. J.; Meyer, D. M.

    2001-09-01

    In the Letter ``Interstellar Abundance Standards Revisited'' by U. J. Sofia and D. M. Meyer (ApJ, 554, L221 [2001]), Table 2 and its footnotes contain several typographical errors. The corrected table is shown below. We note that the solar reference standard now implies a positive abundance of nitrogen in halo dust.

  12. Taxonomic Study of the Genus Abundisporus in Korea.

    PubMed

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

    2015-09-01

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

  13. Taxonomic Study of the Genus Abundisporus in Korea

    PubMed Central

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

    2015-01-01

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

  14. 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

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

    NASA Astrophysics Data System (ADS)

    Harrison, Terry; Msuya, Charles P.

    2005-04-01

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

  16. 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

  17. Taxonomic consequences of cryptic speciation in the Golden Whistler Pachycephala pectoralis complex in mainland southern Australia.

    PubMed

    Joseph, Leo; Nyári, Árpád S; Andersen, Michael J

    2014-01-01

    The Golden Whistler (Aves: Passeriformes: Pachycephalidae) Pachycephala pectoralis sensu lato has long played a key role in the development of the theory of allopatric speciation (Mayr 1932a, b; Mayr 1942; Galbraith 1956). The P. pectoralis species complex formerly comprised 60-70 nominal subspecies and so had a distribution spanning the Indo-Pacific (Boles 2007). More recent taxonomic treatments consider the complex as multiple species-level taxa largely circumscribed by geography (Dickinson and Christidis 2014; Gill and Donsker 2014). In Australia, the endemic species P. pectoralis sensu stricto is sympatric with the closely related Mangrove Golden Whistler P. melanura. However, as the latter's English name suggests, P. melanura is closely tied to mangroves in Australia, southeast New Guinea, and islets in the Bismarck Archipelago. Diagnostic plumage traits separating the two species are subtle: males of P. melanura have more extensively black tails and a greyer upper surface to the remiges, and females are usually yellower ventrally. All Pachycephala species, especially those in the P. pectoralis-melanura species complex, have recently become the focus of DNA sequence-based studies (Jønsson et al. 2008, 2014; Andersen et al. 2014). Data from most populations have now been analysed phylogenetically to better understand relationships and thus the history of evolution and speciation processes within and between both species. This has also been used in studies of the group's historical biogeography to provide information as to the age of taxa and their spread across oceanic archipelagos and continents (Jønsson et al. 2014). Here we discuss the taxonomic implications of a result that has emerged consistently and independently in these studies, concerning the systematics of the southern Australian populations in south-eastern and south-western Australia, both of which have been ascribed to P. p. fuliginosa since Galbraith (1956), and we show that the name P

  18. Molecular phylogenetics of the avian genus Pipilo and a biogeographic argument for taxonomic uncertainty.

    PubMed

    Zink, R M; Weller, S J; Blackwell, R C

    1998-10-01

    We sequenced 1709 base pairs (bp) of mitochondrial DNA including parts of cytochrome b, ND 2, and the control region (CR I, II) for seven members of the avian genus Pipilo (towhees), Melozone kieneri (rusty-crowned ground-sparrow), and Arremonops rufivirgatus (olive sparrow). A total of 457 bp was variable and 257 bp were potentially phylogenetically informative. All gene regions were similarly variable (20.2 to 28.4%) except for CR II (38.4%); third position transitions were as common as substitutions in the CR. Tree topology was sensitive to choice of outgroup(s) and individual sequences used as exemplars. Six trees were considered viable phylogenetic hypotheses based on maximum parsimony and maximum likelihood analyses. These trees generally supported two groups of towhees (rufous-sided group, brown towhee group), a sister taxon relationship for P. aberti and P. crissalis, and a sister taxon relationship for P. ocai and P. maculatus. The occurrence of M. kiernei within Pipilo in three trees challenges the monophyly of the latter; the other species of Melozone and other outgroups require study to resolve Pipilo monophyly. The relationships of P. albicollis and P. fuscus were ambiguous, as they were with previous data sets (allozymes, mtDNA restriction sites); they could be sister species or either one could be the basal species in the brown towhee group. We suggest that this taxonomic uncertainty obtains from the contemporaneous origin of P. fuscus, P. albicollis, and the ancestor of P. aberti/P. crissalis. We favor a "star" phylogeny because species in unrelated lineages found in the same region as P. albicollis are similarly difficult to resolve phylogenetically. Synapomorphies from coding genes and the CR did not preferentially support basal and terminal nodes, and hence did not provide different windows of taxonomic resolution, which might be expected from the apparent rapid rate of CR evolution. Phylogenetic trees inferred from allozymes, restriction sites

  19. 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…

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

    ERIC Educational Resources Information Center

    Blum, Abraham

    1989-01-01

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

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

  2. Taxonomic distribution of cryptic diversity among metazoans: not so homogeneous after all.

    PubMed

    Pérez-Ponce de León, Gerardo; Poulin, Robert

    2016-08-01

    Cryptic diversity plagues estimates of biodiversity, conservation efforts and attempts to control diseases and invasive species. Here, we re-visit a decade-old assessment of whether or not cryptic species are homogeneously reported among higher metazoan taxa. We compiled information from an extensive survey of the literature to recover all reports of cryptic species among metazoans. After correcting for currently known species richness and research effort per taxon, we find that cryptic species are over-reported in some taxa and under-reported in others. Although several taxa showing either a lack or an excess of reported cryptic species were poorly studied invertebrate groups, we found that cryptic species were over-reported in amphibians, reptiles and crustaceans, all relatively well-studied groups. The observed heterogeneity in the distribution of reported cryptic species may reflect taxon-specific properties affecting either the propensity for cryptic species to be formed or their likelihood of being detected by conventional taxonomy. Either way, the implications of cryptic diversity may not apply equally across all taxonomic groups. PMID:27555648

  3. Influence of edge on predator prey distribution and abundance

    NASA Astrophysics Data System (ADS)

    Ferguson, Steven H.

    2004-03-01

    I investigated the effect of spatial configuration on distribution and abundance of invertebrate trophic groups by counting soil arthropods under boxes (21 × 9.5 cm) arranged in six different patterns that varied in the amount of edge (137-305 cm). I predicted fewer individuals from the consumer trophic group (Collembola) in box groups with greater amount of edge. This prediction was based on the assumption that predators (mites, ants, spiders, centipedes) select edge during foraging and thereby reduce abundance of the less mobile consumer group under box patterns with greater edge. Consumer abundance (Collembola) was not correlated with amount of edge. Among the predator groups, mite, ant and centipede abundance related to the amount of edge of box groups. However, in contrast to predictions, abundance of these predators was negatively correlated with amount of edge in box patterns. All Collembola predators, with the exception of ants, were less clumped in distribution than Collembola. The results are inconsistent with the view that predators used box edges to predate the less mobile consumer trophic group. Alternative explanations for the spatial patterns other than predator-prey relations include (1) a negative relationship between edge and moisture, (2) a positive relationship between edge and detritus decomposition (i.e. mycelium as food for the consumer group), and (3) a negative relationship between edge and the interstices between adjacent boxes. Landscape patterns likely affect microclimate, food, and predator-prey relations and, therefore, future experimental designs need to control these factors individually to distinguish among alternative hypotheses.

  4. Geographical and seasonal variations in mesozooplankton abundance and biomass in relation to environmental parameters in Lake Shinji Ohashi River Lake Nakaumi brackish-water system, Japan

    NASA Astrophysics Data System (ADS)

    Uye, S.; Shimazu, T.; Yamamuro, M.; Ishitobi, Y.; Kamiya, H.

    2000-10-01

    We measured the abundance and biomass of the major taxonomic groups of mesozooplankton at six stations in Lake Shinji-Ohashi River-Lake Nakaumi brackish-water system, Japan, monthly for three full years (1995-1997), except for one station (for 1 year and 9 months). Over the entire area, copepods overwhelmingly dominated the zooplankton community both in terms of abundance (mean: 87.9%) and biomass (83.4%). The remaining taxa were cladocerans (i.e. Diphanosoma brachyurum, Evadone tergestina, Penilia avirostris, Podon leuckarti and Podon polyphemoides), appendicularians ( Oikopleura dioica and Oikopleura longicauda), chaetognaths ( Sagitta crassa) and the larvae of benthos (e.g. polychaetes, bivalves, gastropods and malacostracans). The geographical and seasonal variations of the mesozooplankton community were therefore principally explained by the variations of the copepod community. The geographical difference in copepod species composition was associated with salinity preference or tolerance of respective species. In Lake Shinji, where the salinity was lowest (mean: 4.0), Sinocalanus tenellus was monospecifically abundant with sporadic occurrence of Pseudodiaptomus inopinus. In Ohashi River (mean salinity: 9.9), Acartia hudsonica, Acartia sinjiensis, Eurytemora pacifica and Oithona davisae added to the community. At central and southeast Lake Nakaumi and in Honjo District, where mean salinity ranged from 16.4 to 21.7, these four species became more important than S. tenellus and P. inopinus. At the entrance of Sakai Strait, where the salinity was highest (mean: 24.0), Paracalanus spp. constituted a significant component. Due to large temperature fluctuation with season, the copepods showed remarkable seasonal variations in abundance and biomass, with enormous annual peaks in winter-spring. These annual peaks might be attributed to scarce occurrence of predators.

  5. The plankton community in Norwegian coastal waters—abundance, composition, spatial distribution and diel variation

    NASA Astrophysics Data System (ADS)

    Bratbak, Gunnar; Jacquet, Stéphan; Larsen, Aud; Pettersson, Lasse H.; Sazhin, Andrey F.; Thyrhaug, Runar

    2011-09-01

    The purpose of the present study was to explore the composition and variation of the pico-, nano- and micro-plankton communities in Norwegian coastal waters and Skagerrak, and the co-occurrence of bacteria and viruses. Samples were collected along three cruise transects from Jæren, Lista and Oksøy on the south coast of Norway and into the North Sea and Skagerrak. We also followed a drifting buoy for 55 h in Skagerrak in order to observe diel variations. Satellite ocean color images (SeaWiFS) of the chlorophyll a (chl a) distribution compared favorably to in situ measurements in open waters, while closer to the shore remote sensing chl a data was overestimated compared to the in situ data. Using light microscopy, we identified 49 micro- and 15 nanoplankton sized phototrophic forms as well as 40 micro- and 12 nanoplankton sized heterotrophic forms. The only picoeukaryote (0.2-2.0 μm) we identified was Resultor micron (Pedinophyceae ). Along the transects a significant variation in the distribution and abundance of different plankton forms were observed, with Synechococcus spp and autotrophic picoeukaryotes as the most notable examples. There was no correlation between viruses and chl a, but between viruses and bacteria, and between viruses and some of the phytoplankton groups, especially the picoeukaryotes. Moreover, there was a negative correlation between nutrients and small viruses (Low Fluorescent Viruses) but a positive correlation between nutrients and large viruses (High Fluorescent Viruses). The abundance of autotrophic picoplankton, bacteria and viruses showed a diel variation in surface waters with higher values around noon and late at night and lower values in the evening. Synechococcus spp were found at 20 m depth 25-45 nautical miles from shore apparently forming a bloom that stretched out for more than 100 nautical miles from Skagerrak and up the south west coast of Norway. The different methods used for assessing abundance, distribution and

  6. Taxonomic complexity in the halophyte Limonium vulgare and related taxa (Plumbaginaceae): insights from analysis of morphological, reproductive and karyological data

    PubMed Central

    Cortinhas, Ana; Erben, Matthias; Paula Paes, Ana; Espírito Santo, Dalila; Guara-Requena, Miguel; Caperta, Ana D.

    2015-01-01

    Background and Aims Limonium is a well-known example of a group of plants that is taxonomically complex due to certain biological characteristics that hamper species' delineation. The closely related polyploid species Limonium vulgare Mill., L. humile Mill. and L. narbonense Mill. are defined species and can be used for studying patterns of morphological and reproductive variation. The first two taxa are usually found in Atlantic Europe and the third in the Mediterranean region, but a number of intermediate morphological forms may be present alongside typical examples of these species. This study attempts to elucidate morphological, floral and karyological diversity representative of these taxa in the Iberian Peninsula. Methods The extent of morphological differentiation was tested through comparison of 197 specimens from both Portugal and Spain using 17 descriptive morphological characters and 19 diagnostic morphometric characters. Analyses of floral morphisms (heterostyly and pollen–stigma dimorphism) and karyological determinations were also conducted. Key Results and Conclusions Discriminant analysis using morphometric variables reliably assigned individuals in natural populations to their respective groups. In addition, the results provide the first direct evidence that L. narbonense and a new species, Limonium maritimum Caperta, Cortinhas, Paes, Guara, Espírito-Santo and Erben, sp. nov., related to L. vulgare are present on Portuguese coasts. Most of these species are found together in mixed populations, especially L. vulgare and L. narbonense. It is hypothesized that taxonomic biodiversity found in sites where distinct species co-occur facilitates the evolutionary processes of hybridization, introgression and apomixis. This study therefore contributes to the elucidation of the taxonomic diversity in L. vulgare-related species and may also help in implementing future conservation programmes to maintain the evolutionary processes generating biodiversity

  7. Aerial survey estimates of fallow deer abundance

    USGS Publications Warehouse

    Gogan, Peter J.; Gates, Natalie B.; Lubow, Bruce C.; Pettit, Suzanne

    2012-01-01

    Reliable estimates of the distribution and abundance of an ungulate species is essential prior to establishing and implementing a management program. We used ground surveys to determine distribution and ground and aerial surveys and individually marked deer to estimate the abundance of fallow deer (Dama dama) in north-coastal California. Fallow deer had limited distribution and heterogeneous densities. Estimated post-rut densities across 4 annual surveys ranged from a low of 1.4 (SE=0.2) deer/km2 to a high of 3.3 (se=0.5) deer/km2 in a low density stratum and from 49.0 (SE=8.3) deer/km2 to 111.6 deer/km2 in a high density stratum. Sightability was positively influenced by the presence of white color-phase deer in a group and group size, and varied between airial and ground-based observers and by density strata. Our findings underscore the utility of double-observer surveys and aerial surveys with individually marked deer, both incorporating covariates to model sightability, to estimate deer abundance.

  8. The boron abundance of Procyon

    NASA Technical Reports Server (NTRS)

    Lemke, Michael; Lambert, David L.; Edvardsson, Bengt

    1993-01-01

    The B I 2496.8 A resonance line and HST/GHRS echelle spectra are used with model atmospheres and synthetic spectra to derive the B abundance of the F dwarfs Procyon (Alpha Canis Minoris), Theta Ursae Majoris, and Iota Pegasi. The B abundance of Theta UMa and Iota Peg is similar to that derived by Boesgaard and Heacox (1978) from the B II resonance line in spectra of A- and B-type stars. These two dwarfs show normal abundances of Li, Be, and B. Procyon, which is highly depleted in Li and Be, is depleted in B by a factor of at least 3. Comparison of the spectra of Procyon and the halo dwarf HD 140283 shows that the B abundance assigned by Duncan et al. (1992) to three halo dwarfs is not greatly overestimated as a result of contamination of the B I line by an unidentified line.

  9. The activated sludge ecosystem contains a core community of abundant organisms

    PubMed Central

    Saunders, Aaron M; Albertsen, Mads; Vollertsen, Jes; Nielsen, Per H

    2016-01-01

    Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the choice of organisms should be prioritized to those that are frequently abundant (core) or transiently abundant, which are therefore putatively make the greatest contribution to carbon turnover in the system. We analyzed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S ribosomal RNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level operational taxonomic units (OTUs) that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to three plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily because of immigration with the wastewater. Transiently abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants, which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal. PMID:26262816

  10. Resolving microbial membership using Abundance and Variability In Taxonomy (‘AVIT )

    PubMed Central

    Chakrabarti, Anirikh; Siddharth, Jay; Lauber, Christian L.; Membrez, Mathieu; Betrisey, Bertrand; Loyer, Carole; Chou, Chieh Jason; Pataky, Zoltan; Golay, Alain; Parkinson, Scott J.

    2016-01-01

    Development of NGS has revolutionized the analysis in microbial ecology contributing to our deeper understanding of microbiota in health and disease. However, the quality, quantity and confidence of summarized taxonomic abundances are in need of further scrutiny due to sample dependent and independent effects. In this article we introduce ‘AVIT (Abundance and Variability In Taxonomy), an unbiased method to enrich for assigned members of microbial communities. As opposed to using a priori thresholds, ‘AVIT uses inherent abundance and variability of taxa in a dataset to determine the inclusion or rejection of each taxa for further downstream analysis. Using in-vitro and in-vivo studies, we benchmarked performance and parameterized ‘AVIT to establish a framework for investigating the dynamic range of microbial community membership in clinically relevant scenarios. PMID:27530237

  11. 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

  12. 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

  13. 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

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

    PubMed

    Rosas, A; Bermúdez de Castro, J M

    1998-10-01

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

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

    PubMed Central

    Holcomb, Linda S.

    2015-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

    Rubio, Gonzalo D; Ramírez, Martín J

    2015-01-01

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

  18. Taxonomic homogenization of woodland plant communities over 70 years

    PubMed Central

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

    2009-01-01

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

  19. 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

  20. 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.

  1. Autofluorescence of atmospheric bioaerosols: spectral fingerprints and taxonomic trends of pollen

    NASA Astrophysics Data System (ADS)

    Pöhlker, C.; Huffman, J. A.; Förster, J.-D.; Pöschl, U.

    2013-12-01

    Primary biological aerosol particles (PBAP) are important factors in atmospheric cycling, climate, and public health. Pollen is a major fraction of PBAP and is receiving increasing attention due to its high allergenic potential and the associated impacts on personal life quality and economy. Recently, autofluorescence-based techniques have proven to be valuable tools for real time, in situ quantification and classification of PBAP. First studies suggest that the autofluorescence of pollen may be sufficiently selective to be utilized for an automated and real-time monitoring of pollen in ambient air. However, the degree of selectivity autofluorescence can provide is still in question and actively debated. This study addresses the origin, properties, and selectivity of autofluorescence from natural pollen by fluorescence microscopy and spectroscopy measurements along with a systematic synthesis of related literature. We show that dry pollen reveals characteristic and reproducible autofluorescence signatures which are shaped by cell wall associated fluorophores, such as phenolic compounds and carotenoid pigments. In addition, fluorescence signals from proteins and chlorophyll a were observed in some species. The abundance and intensity of the individual fluorescence signals show certain taxonomic trends and allow systematic differentiation from bacteria and fungal spores due to the lack of proteins on the grain surface. Principal component analysis was used to explore the discrimination potential of pollen autofluorescence, in combination with size and shape, revealing a differentiation of pollen on family level. Our results help explore the levels of selectivity that autofluorescence-based techniques can provide to PBAP analysis and will support the development and application of autofluorescence-based detectors for monitoring of allergenic pollen in the atmosphere.

  2. Autofluorescence of atmospheric bioaerosols - spectral fingerprints and taxonomic trends of native pollen

    NASA Astrophysics Data System (ADS)

    Pöhlker, C.; Huffman, J. A.; Förster, J.-D.; Pöschl, U.

    2013-06-01

    Primary biological aerosol particles (PBAP) are important factors in atmospheric cycling, climate, and public health. Pollen is a major fraction of PBAP and is receiving increasing attention due to its high allergenic potential and the associated severe impacts on personal life quality and economy. Recently, autofluorescence-based techniques have proven to be valuable tools for real-time, in-situ quantification and classification of PBAP. First studies suggest that the autofluorescence of pollen may be sufficiently selective to be utilized for an automated and real-time monitoring of pollen in ambient air. However, the degree of selectivity autofluorescence can provide is still in question and actively debated. This study addresses the origin, properties, and selectivity of autofluorescence from native pollen (undamaged and chemically untreated) by providing fluorescence microscopy and spectroscopy measurements along with a systematic synthesis of related literature. We show that dry, native pollen reveals characteristic and reproducible autofluorescence signatures which are shaped by cell wall associated fluorophores, such as phenolic compounds and carotenoid pigments. In addition, fluorescence signals from proteins and chlorophyll a were observed occasionally. The abundance and intensity of the individual fluorescence signals show certain taxonomic trends and allow systematic differentiation from bacteria and fungal spores due to the lack of protein fluorescence from the grain surface. Principal component analysis was used to explore the discrimination potential of pollen autofluorescence and revealed a differentiation of pollen on family level. Our results help explore the levels of selectivity that autofluorescence-based techniques can provide to PBAP analysis and will support the development and application of autofluorescence-based detectors for monitoring of allergenic pollen in the atmosphere.

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

    PubMed

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

    2013-11-01

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

  4. Taxonomic status and ecologic function of methanogenic bacteria isolated from the oral cavity of humans

    SciTech Connect

    Kemp, C.W.

    1985-01-01

    The detection of methane gas in samples of dental plaque and media inoculated with dental plaque was attributed to the presence of methane-producing bacteria in the plaque microbiota. The results of a taxonomic analysis of the 12 methanogenic isolates obtained from human dental plaque, (ABK1-ABK12), placed the organisms in the genus Methanobrevibacter. A DNA-DNA hybridization survey established three distinct genetic groups of oral methanogens based on percent homology values. The groups exhibited less than 32% homology between themselves and less than 17% homology with the three known members of the genus methanobrevibacter. The ecological role of the oral methanogens was established using mixed cultures of selected methanogenic isolates (ABK1, ABK4, ABK6, or ABK7) with oral heterotrophic bacteria. Binary cultures of either Streptococcus mutans, Streptococcus sanguis, Veillonella rodentium, Lactobacillus casei, or Peptostreptococcus anaerobius together with either methanogenic isolates ABK6 or ABK7 were grown to determine the effect of the methanogens on the distribution of carbon end products produced by the heterotrophs. Binary cultures of S. mutans and ABK7 exhibited a 27% decrease in lactic acid formation when compared to pure culture of S. mutans. The decrease in lactic acid production was attributed to the removal of formate by the methanogen, (ABK7), which caused an alteration in the distribution of carbon end products by S. mutans.

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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…

  10. 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.

  11. 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

  12. Molecular phylogenetics of subfamily Ornithogaloideae (Hyacinthaceae) based on nuclear and plastid DNA regions, including a new taxonomic arrangement

    PubMed Central

    Martínez-Azorín, Mario; Crespo, Manuel B.; Juan, Ana; Fay, Michael F.

    2011-01-01

    Background and Aims The taxonomic arrangement within subfamily Ornithogaloideae (Hyacinthaceae) has been a matter of controversy in recent decades: several new taxonomic treatments have been proposed, based exclusively on plastid DNA sequences, and these have resulted in classifications which are to a great extent contradictory. Some authors have recognized only a single genus Ornithogalum for the whole subfamily, including 250–300 species of variable morphology, whereas others have recognized many genera. In the latter case, the genera are inevitably much smaller and they are better defined morphologically. However, some are not monophyletic as circumscribed. Methods Phylogenetic analyses of Ornithogaloideae were based on nucleotide sequences of four plastid regions (trnL intron, trnL-F spacer, rbcL and matK) and a nuclear region (ITS). Eighty species covering all relevant taxonomic groups previously recognized in the subfamily were sampled. Parsimony and Bayesian analyses were performed. The molecular data were compared with a matrix of 34 morphological characters. Key Results Combinations of plastid and nuclear data yielded phylogenetic trees which are better resolved than those obtained with any plastid region alone or plastid regions in combination. Three main clades are found, corresponding to the previously recognized tribes Albuceae, Dipcadieae and Ornithogaleae. In these, up to 19 clades are described which are definable by morphology and biogeography. These mostly correspond to previously described taxa, though some need recircumscription. Morphological characters are assessed for their diagnostic value for taxonomy in the subfamily. Conclusions On the basis of the phylogenetic analyses, 19 monophyletic genera are accepted within Ornithogaloideae: Albuca, Avonsera, Battandiera, Cathissa, Coilonox, Dipcadi, Eliokarmos, Elsiea, Ethesia, Galtonia, Honorius, Loncomelos, Melomphis, Neopatersonia, Nicipe, Ornithogalum, Pseudogaltonia, Stellarioides and

  13. Regional species richness of families and the distribution of abundance and rarity in a local community of forest Hymenoptera

    NASA Astrophysics Data System (ADS)

    Ulrich, Werner

    2005-09-01

    Recent investigations about the relationship between the number of species of taxonomic lineages and regional patterns of species abundances gave indecisive results. Here, it is shown that mean densities of species of a species-rich community of forest Hymenoptera (673 species out of 25 families) were positively related to the number of European species per family. The fraction of abundant species per family declined and the fraction of rare species increased with species richness. Species rich families contained relatively more species, which were present in only one study year (occasional species), and relatively fewer species present during the whole study period (frequent species).

  14. Metagenomic abundance estimation and diagnostic testing on species level

    PubMed Central

    Lindner, Martin S.; Renard, Bernhard Y.

    2013-01-01

    One goal of sequencing-based metagenomic community analysis is the quantitative taxonomic assessment of microbial community compositions. In particular, relative quantification of taxons is of high relevance for metagenomic diagnostics or microbial community comparison. However, the majority of existing approaches quantify at low resolution (e.g. at phylum level), rely on the existence of special genes (e.g. 16S), or have severe problems discerning species with highly similar genome sequences. Yet, problems as metagenomic diagnostics require accurate quantification on species level. We developed Genome Abundance Similarity Correction (GASiC), a method to estimate true genome abundances via read alignment by considering reference genome similarities in a non-negative LASSO approach. We demonstrate GASiC’s superior performance over existing methods on simulated benchmark data as well as on real data. In addition, we present applications to datasets of both bacterial DNA and viral RNA source. We further discuss our approach as an alternative to PCR-based DNA quantification. PMID:22941661

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

    PubMed

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

    2015-12-01

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

  16. Solar and stellar photospheric abundances

    NASA Astrophysics Data System (ADS)

    Allende Prieto, Carlos

    2016-07-01

    The determination of photospheric abundances in late-type stars from spectroscopic observations is a well-established field, built on solid theoretical foundations. Improving those foundations to refine the accuracy of the inferred abundances has proven challenging, but progress has been made. In parallel, developments on instrumentation, chiefly regarding multi-object spectroscopy, have been spectacular, and a number of projects are collecting large numbers of observations for stars across the Milky Way and nearby galaxies, promising important advances in our understanding of galaxy formation and evolution. After providing a brief description of the basic physics and input data involved in the analysis of stellar spectra, a review is made of the analysis steps, and the available tools to cope with large observational efforts. The paper closes with a quick overview of relevant ongoing and planned spectroscopic surveys, and highlights of recent research on photospheric abundances.

  17. 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

  18. Use of a Hierarchical Oligonucleotide Primer Extension Approach for Multiplexed Relative Abundance Analysis of Methanogens in Anaerobic Digestion Systems

    PubMed Central

    Chuang, Hui-Ping; Hsu, Mao-Hsuan; Chen, Wei-Yu

    2013-01-01

    In this study, we established a rapid multiplex method to detect the relative abundances of amplified 16S rRNA genes from known cultivatable methanogens at hierarchical specificities in anaerobic digestion systems treating industrial wastewater and sewage sludge. The method was based on the hierarchical oligonucleotide primer extension (HOPE) technique and combined with a set of 27 primers designed to target the total archaeal populations and methanogens from 22 genera within 4 taxonomic orders. After optimization for their specificities and detection sensitivity under the conditions of multiple single-nucleotide primer extension reactions, the HOPE approach was applied to analyze the methanogens in 19 consortium samples from 7 anaerobic treatment systems (i.e., 513 reactions). Among the samples, the methanogen populations detected with order-level primers accounted for >77.2% of the PCR-amplified 16S rRNA genes detected using an Archaea-specific primer. The archaeal communities typically consisted of 2 to 7 known methanogen genera within the Methanobacteriales, Methanomicrobiales, and Methanosarcinales and displayed population dynamic and spatial distributions in anaerobic reactor operations. Principal component analysis of the HOPE data further showed that the methanogen communities could be clustered into 3 distinctive groups, in accordance with the distribution of the Methanosaeta, Methanolinea, and Methanomethylovorans, respectively. This finding suggested that in addition to acetotrophic and hydrogenotrophic methanogens, the methylotrophic methanogens might play a key role in the anaerobic treatment of industrial wastewater. Overall, the results demonstrated that the HOPE approach is a specific, rapid, and multiplexing platform to determine the relative abundances of targeted methanogens in PCR-amplified 16S rRNA gene products. PMID:24077716

  19. Robust Abundance Estimation in Animal Abundance Surveys with Imperfect Detection

    EPA Science Inventory

    Surveys of animal abundance are central to the conservation and management of living natural resources. However, detection uncertainty complicates the sampling process of many species. One sampling method employed to deal with this problem is depletion (or removal) surveys in whi...

  20. Abundance Inequality in Freshwater Communities Has an Ecological Origin.

    PubMed

    Passy, Sophia I

    2016-04-01

    The hollow-shaped species abundance distribution (SAD) and its allied rank abundance distribution (RAD)-showing that abundance is unevenly distributed among species-are some of the most studied patterns in ecology. To explain the nature of abundance inequality, I developed a novel framework identifying environmental favorability, which controls the balance between reproduction and immigration, as the ultimate source and species stress tolerance as a proximate factor. Thus, under harsh conditions, only a few tolerant species can reproduce, while some sensitive species can be present in low numbers due to chance immigration. This would lead to high abundance inequality between the two groups of species. Under benign conditions, both groups can reproduce and give rise to higher abundance equality. To test these ideas, I examined the variability in the parameters of a Poisson lognormal fit of the SAD and a square root fit of the RAD in diatom and fish communities across US streams. Indeed, as environmental favorability increased, more sensitive forms were able to establish large populations, diminishing the abundance disparity between locally common and rare species. Finally, it was demonstrated that in diatoms, the RAD belonged to the same family of relationships as those of population density with body size and regional distribution. PMID:27028078

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

    NASA Astrophysics Data System (ADS)

    Wahl, E. R.; Schoelzel, C.

    2010-12-01

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

  2. Coronal abundances and their variation

    NASA Technical Reports Server (NTRS)

    Saba, Julia L. R.

    1995-01-01

    This contract supports the investigation of elemental abundances in the solar corona, principally through analysis of high-resolution soft X-ray spectra from the Flat Crystal Spectrometer on the Solar Maximum Mission. The goals of the study are a characterization of the mean values of relative abundances of elements accessible in the FCS data, and information on the extent and circumstances of their variability. This report is a summation of the data analysis and reporting activities which occurred during the period of 15 April 1994 to 15 April 1995.

  3. The solar abundance of beryllium

    NASA Technical Reports Server (NTRS)

    Ross, J. E.; Aller, L. H.

    1974-01-01

    The solar abundance of beryllium is deduced from high-resolution Kitt Peak observations of the 3130.43- and 3131.08-A lines of Be II interpreted by the method of spectrum synthesis. The results are in good agreement with those previously obtained by Grevesse (1968) and by Hauge and Engvold (1968) and indicate that in the photospheric layers, beryllium is depleted below the chondritic value by a factor of about two. It is found that the beryllium abundance is equal to logN(Be)/N(H) + 12 = 1.08 plus or minus 0.05.

  4. Chemical Abundances of Symbiotic Giants

    NASA Astrophysics Data System (ADS)

    Gałan, C.; Mikołajewska, J.; Hinkle, K. H.; Joyce, R. R.

    2015-12-01

    High resolution (R ˜ 50000), near-IR spectra were used to measure photospheric abundances of CNO and elements around the iron peak for 24 symbiotic giants. Spectrum synthesis was employed using local thermal equilibrium and hydrostatic model atmospheres. The metallicities are distributed in a wide range with maximum around [Fe/H] ˜-0.4 - - 0.3 dex. Enrichment in 14N indicates that all the sample giants have experienced the first dredge-up. The relative abundance of [Ti/Fe] is generally large in red symbiotic systems.

  5. Coronal Abundances and Their Variation

    NASA Technical Reports Server (NTRS)

    Saba, Julia L. R.

    1996-01-01

    This contract supported the investigation of elemental abundances in the solar corona, principally through analysis of high-resolution soft X-ray spectra from the Flat Crystal Spectrometer on NASA's Solar Maximum Mission. The goals of the study were a characterization of the mean values of relative abundances of elements accessible in the FCS data, and information on the extent and circumstances of their variability. This is the Final Report, summarizing the data analysis and reporting activities which occurred during the period of performance, June 1993 - December 1996.

  6. SOLAR MODELS WITH REVISED ABUNDANCE

    SciTech Connect

    Bi, S. L.; Li, T. D.; Yang, W. M.; Li, L. H.

    2011-04-20

    We present new solar models in which we use the latest low abundances and further include the effects of rotation, magnetic fields, and extra-mixing processes. We assume that the extra-element mixing can be treated as a diffusion process, with the diffusion coefficient depending mainly on the solar internal configuration of rotation and magnetic fields. We find that such models can well reproduce the observed solar rotation profile in the radiative region. Furthermore, the proposed models can match the seismic constraints better than the standard solar models, also when these include the latest abundances, but neglect the effects of rotation and magnetic fields.

  7. 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

  8. 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

  9. Patterns of plastid and nuclear variation among apomictic polyploids of Hieracium: evolutionary processes and taxonomic implications

    PubMed Central

    Tyler, Torbjörn; Jönsson, Jane

    2013-01-01

    Background and Aims Apomictic species (with asexual seed production) make up for 20–50 % of all taxonomically recognized species in northern Europe, but the phylogenetic relationships of apomictic species and the mode of evolution and speciation remain largely unknown and their taxonomy is consequently disputed. Methods In the present study, plastid psbD-trnT sequences (349 accessions) and 12 nuclear microsatellite loci (478 accessions) were used to create an overview of the molecular variation in (mainly) northern European members of the most species-rich of all plant genera, Hieracium s.s. The results are discussed and interpreted in the context of morphological and cytological data on the same species. Key Results and Conclusions The complete psbD-trnT alignment was 1243 bp and 50 polymorphisms defined 40 haplotypes. All haplotypes found in the sections of the genus distributed in the northern European lowlands fell into one of two main groups, group H and group V, mutually separated by seven or eight polymorphisms. All accessions belonging to H. sects. Foliosa, Hieracioides (viz. H. umbellatum) and Tridentata and all but one accession of triploid species of H. sects. Oradea and Vulgata showed haplotypes of group V. Haplotypes of group H were found in all accessions of H. sects. Bifida and Hieracium and in all tetraploid representatives of H. sects. Oreadea and Vulgata. Additional haplotypes were found in accessions of the genus Pilosella and in southern European and Alpine sections of Hieracium. In contrast, the distribution of individual haplotypes in the two major groups appeared uncorrelated with morphology and current taxonomy, but polymorphisms within species were only rarely encountered. In total, 160 microsatellite alleles were identified. Levels of variation were generally high with only nine pairs of accessions being identical at all loci (in all cases representing accessions of the same species). In the neighbor-joining analysis based on the

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

    EPA Science Inventory

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

  11. 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...

  12. 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.

  13. THE SOLAR FLARE IRON ABUNDANCE

    SciTech Connect

    Phillips, K. J. H.; Dennis, B. R. E-mail: Brian.R.Dennis@nasa.gov

    2012-03-20

    The abundance of iron is measured from emission line complexes at 6.65 keV (Fe line) and 8 keV (Fe/Ni line) in RHESSI X-ray spectra during solar flares. Spectra during long-duration flares with steady declines were selected, with an isothermal assumption and improved data analysis methods over previous work. Two spectral fitting models give comparable results, viz., an iron abundance that is lower than previous coronal values but higher than photospheric values. In the preferred method, the estimated Fe abundance is A(Fe) = 7.91 {+-} 0.10 (on a logarithmic scale, with A(H) = 12) or 2.6 {+-} 0.6 times the photospheric Fe abundance. Our estimate is based on a detailed analysis of 1898 spectra taken during 20 flares. No variation from flare to flare is indicated. This argues for a fractionation mechanism similar to quiet-Sun plasma. The new value of A(Fe) has important implications for radiation loss curves, which are estimated.

  14. Taxonomic and Geographic Bias in Conservation Biology Research: A Systematic Review of Wildfowl Demography Studies.

    PubMed

    Roberts, Beth E I; Harris, W Edwin; Hilton, Geoff M; Marsden, Stuart J

    2016-01-01

    Demographic data are important to wildlife managers to gauge population health, to allow populations to be utilised sustainably, and to inform conservation efforts. We analysed published demographic data on the world's wildfowl to examine taxonomic and geographic biases in study, and to identify gaps in knowledge. Wildfowl (order: Anseriformes) are a comparatively well studied bird group which includes 169 species of duck, goose and swan. In all, 1,586 wildfowl research papers published between 1911 and 2010 were found using Web of Knowledge (WoK) and Google Scholar. Over half of the research output involved just 15 species from seven genera. Research output was strongly biased towards 'high income' countries, common wildfowl species, and measures of productivity, rather than survival and movement patterns. There were significantly fewer demographic data for the world's 31 threatened wildfowl species than for non-threatened species. Since 1994, the volume of demographic work on threatened species has increased more than for non-threatened species, but still makes up only 2.7% of total research output. As an aid to research prioritisation, a metric was created to reflect demographic knowledge gaps for each species related to research output for the species, its threat status, and availability of potentially useful surrogate data from congeneric species. According to the metric, the 25 highest priority species include thirteen threatened taxa and nine species each from Asia and South America, and six from Africa. PMID:27166624

  15. Taxonomic and Geographic Bias in Conservation Biology Research: A Systematic Review of Wildfowl Demography Studies

    PubMed Central

    2016-01-01

    Demographic data are important to wildlife managers to gauge population health, to allow populations to be utilised sustainably, and to inform conservation efforts. We analysed published demographic data on the world’s wildfowl to examine taxonomic and geographic biases in study, and to identify gaps in knowledge. Wildfowl (order: Anseriformes) are a comparatively well studied bird group which includes 169 species of duck, goose and swan. In all, 1,586 wildfowl research papers published between 1911 and 2010 were found using Web of Knowledge (WoK) and Google Scholar. Over half of the research output involved just 15 species from seven genera. Research output was strongly biased towards ‘high income’ countries, common wildfowl species, and measures of productivity, rather than survival and movement patterns. There were significantly fewer demographic data for the world’s 31 threatened wildfowl species than for non-threatened species. Since 1994, the volume of demographic work on threatened species has increased more than for non-threatened species, but still makes up only 2.7% of total research output. As an aid to research prioritisation, a metric was created to reflect demographic knowledge gaps for each species related to research output for the species, its threat status, and availability of potentially useful surrogate data from congeneric species. According to the metric, the 25 highest priority species include thirteen threatened taxa and nine species each from Asia and South America, and six from Africa. PMID:27166624

  16. Taxonomic Identity, Geographic Distribution, and Commercial Exploitation of the Culinary-Medicinal Mushroom Pleurotus nebrodensis (Basidiomycetes).

    PubMed

    Venturella, Giuseppe; Zervakis, Georgios I; Polemis, Elias; Gargano, Maria Letizia

    2016-01-01

    An updated overview of the outcome of studies conducted on the culinary-medicinal mushroom Pleurotus nebrodensis is presented by placing emphasis on the clarification of the taxonomic identity of P. nebrodensis and other related taxa possessing entirely white to cream basidiomes, which grow in association with different plants of the family Apiaceae. Cultivation techniques, quality of the product sold and sales price, as well as nutritional and medicinal aspects are discussed. Taking also into consideration the high economic importance of P. nebrodensis, it is essential to proceed with the verification of the commercial strains currently available in the international market under the name of "P. nebrodensis" since it is very probable that many (or most) of them do not represent the real P. nebrodensis. TO confirm this hypothesis, an in silico analysis was conducted on a large of number of ITS1-5.8S-ITS2 rRNA sequences deposited in the National Center for Biotechnology Information database under the name P. nebrodensis. Results demonstrated that all "P nebrodensis" material examined from China (plus several sequences of no reported origin) corresponded to P. eryngii subsp. tuoliensis, with only 2 exceptions, which were grouped within P. eryngii sensu stricto. The real P. nebrodensis biological material from Italy and Greece is certified and is available upon request by the authors at the University of Palermo and the Agricultural University of Athens. PMID:27279445

  17. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016).

    PubMed

    Adams, Michael J; Lefkowitz, Elliot J; King, Andrew M Q; Harrach, Balázs; Harrison, Robert L; Knowles, Nick J; Kropinski, Andrew M; Krupovic, Mart; Kuhn, Jens H; Mushegian, Arcady R; Nibert, Max; Sabanadzovic, Sead; Sanfaçon, Hélène; Siddell, Stuart G; Simmonds, Peter; Varsani, Arvind; Zerbini, Francisco Murilo; Gorbalenya, Alexander E; Davison, Andrew J

    2016-10-01

    This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2016.Changes to virus taxonomy (the Universal Scheme of Virus Classification of the International Committee on Taxonomy of Viruses [ICTV]) now take place annually and are the result of a multi-stage process. In accordance with the ICTV Statutes ( http://www.ictvonline.org/statutes.asp ), proposals submitted to the ICTV Executive Committee (EC) undergo a review process that involves input from the ICTV Study Groups (SGs) and Subcommittees (SCs), other interested virologists, and the EC. After final approval by the EC, proposals are then presented for ratification to the full ICTV membership by publication on an ICTV web site ( http://www.ictvonline.org/ ) followed by an electronic vote. The latest set of proposals approved by the EC was made available on the ICTV website by January 2016 ( https://talk.ictvonline.org/files/proposals/ ). A list of these proposals was then emailed on 28 March 2016 to the 148 members of ICTV, namely the EC Members, Life Members, ICTV Subcommittee Members (including the SG chairs) and ICTV National Representatives. Members were then requested to vote on whether to ratify the taxonomic proposals (voting closed on 29 April 2016). PMID:27424026

  18. A molecular phylogeny for the order Clathrinida rekindles and refines Haeckel's taxonomic proposal for calcareous sponges.

    PubMed

    Klautau, Michelle; Azevedo, Fernanda; Cóndor-Luján, Báslavi; Rapp, Hans Tore; Collins, Allen; Russo, Claudia Augusta de Moraes

    2013-09-01

    Most biological groups are still longing for a phylogenetically sound taxonomic organization. In this article, we aimed to verify the consistency of morphological characters in calcarean sponges of the well-known non-monophyletic order Clathrinida using a molecular phylogeny. For this we included 50 species, including six type species, currently assigned to eight different genera. A maximum likelihood topology was generated for the nuclear ITS marker using the General Time Reversible model and the bootstrap reliability test. Our topology indicated 10 clathrinid clades that included species with consistent morphological characters. In the present study, we defined nine of these clades as clathrinid genera, including four newly described and two newly diagnosed genera. Recent studies have indicated that not much phylogenetic information may be found in morphology, but our findings contradict this general assertion. Our study confirms the suitability of skeleton and body anastomosis as valid characters in a phylogenetically sound taxonomy for the order. Interestingly, we have also found that, apart from the Calcinea/Calcaronea split and a few minor details, Haeckel's original proposal is remarkably similar to our own, which was based on a molecular phylogeny 140 years later. PMID:23704365

  19. Phylogenetic relationships of corallinaceae (Corallinales, Rhodophyta): taxonomic implications for reef-building corallines.

    PubMed

    Rösler, Anja; Perfectti, Francisco; Peña, Viviana; Braga, Juan Carlos

    2016-06-01

    A new, more complete, five-marker (SSU, LSU, psbA, COI, 23S) molecular phylogeny of the family Corallinaceae, order Corallinales, shows a paraphyletic grouping of seven well-supported monophyletic clades. The taxonomic implications included the amendment of two subfamilies, Neogoniolithoideae and Metagoniolithoideae, and the rejection of Porolithoideae as an independent subfamily. Metagoniolithoideae contained Harveylithon gen. nov., with H. rupestre comb. nov. as the generitype, and H. canariense stat. nov., H. munitum comb. nov., and H. samoënse comb. nov. Spongites and Pneophyllum belonged to separate clades. The subfamily Neogoniolithoideae included the generitype of Spongites, S. fruticulosus, for which an epitype was designated. Pneophyllum requires reassesment. The generitype of Hydrolithon, H. reinboldii, was a younger heterotypic synonym of H. boergesenii. The evolutionary novelty of the subfamilies Hydrolithoideae, Metagoniolithoideae, and Lithophylloideae was the development of tetra/bisporangial conceptacle roofs by filaments surrounding and interspersed among the sporangial initials. PMID:27273534

  20. Taxonomic status of Syngamus nematodes parasitizing passeriform hosts from Central Europe: Morphological, morphometric and molecular identification.

    PubMed

    Kanarek, Gerard; Zaleśny, Grzegorz; Sitko, Jiljí; Rząd, Izabella

    2016-10-01

    The systematic position and validity of species within genus Syngamus have always been controversial. In this present work, we evaluated the taxonomic status and phylogenetic relationships between three species of Syngamus nematodes (Syngamus trachea, Syngamus taiga and Syngamus merulae) and one taxa, determined only to the generic level, collected from respiratory tracts of passeriform hosts from Central Europe using newly obtained sequences of 2 nuclear markers (internal transcribed spacers 1 and 2 [ITS1, ITS2]) and a fragment of mitochondrial cytochrome oxidase I [COI] gene. Our results clearly showed that S. trachea, S. taiga and S. merulae are valid, molecularly and morphologically distinct species. Moreover, molecular analysis of adult female of Syngamus sp. collected from tracheae of the European robin Erithacus rubecula clearly indicate that these comprise separate species. In the derived phylogeny, the Syngamus clade is divided into two sub-clades: one comprised Syngamus species with a characteristic, well-developed cuticular collar around the oral opening (S. trachea and S. taiga) and a second that groups taxa without or with rudimentary collar (S. merulae and currently sequenced Syngamus sp. from Erithacus rubecula). These results clearly suggest that the degree of collar development (well-developed vs. rudimentary/absent) may be an important phylogenetic feature for determining the structure of the genus Syngamus on subgeneric level. Additionally, our results support historical division of the genus Syngamus into two subgenera S. (Syngamus) and S. (Ornithogamus). PMID:27353021

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

    PubMed

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

    2013-01-01

    The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus of 800 abstracts, which were manually annotated after the development of the tool. The corpus comprises abstracts from journals selected to represent many taxonomic groups, which gives insights into which types of organism names are hard to detect and which are easy. Finally, we have tagged org