Sample records for taxonomic units including

  1. Taxonomic classification of world map units in crop producing areas of Argentina and Brazil with representative US soil series and major land resource areas in which they occur

    NASA Technical Reports Server (NTRS)

    Huckle, H. F. (Principal Investigator)

    1980-01-01

    The most probable current U.S. taxonomic classification of the soils estimated to dominate world soil map units (WSM)) in selected crop producing states of Argentina and Brazil are presented. Representative U.S. soil series the units are given. The map units occurring in each state are listed with areal extent and major U.S. land resource areas in which similar soils most probably occur. Soil series sampled in LARS Technical Report 111579 and major land resource areas in which they occur with corresponding similar WSM units at the taxonomic subgroup levels are given.

  2. PESI - a taxonomic backbone for Europe.

    PubMed

    de Jong, Yde; 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

    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. This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.

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

    PubMed Central

    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

    2016-01-01

    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

  4. 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

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

    PubMed

    Pavlinov, I Ia

    2012-01-01

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

  6. 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. Copyright © 1994. Published by Elsevier Ltd.

  7. Parallel changes of taxonomic interaction networks in lacustrine bacterial communities induced by a polymetallic perturbation

    PubMed Central

    Laplante, Karine; Sébastien, Boutin; Derome, Nicolas

    2013-01-01

    Heavy metals released by anthropogenic activities such as mining trigger profound changes to bacterial communities. In this study we used 16S SSU rRNA gene high-throughput sequencing to characterize the impact of a polymetallic perturbation and other environmental parameters on taxonomic networks within five lacustrine bacterial communities from sites located near Rouyn-Noranda, Quebec, Canada. The results showed that community equilibrium was disturbed in terms of both diversity and structure. Moreover, heavy metals, especially cadmium combined with water acidity, induced parallel changes among sites via the selection of resistant OTUs (Operational Taxonomic Unit) and taxonomic dominance perturbations favoring the Alphaproteobacteria. Furthermore, under a similar selective pressure, covariation trends between phyla revealed conservation and parallelism within interphylum interactions. Our study sheds light on the importance of analyzing communities not only from a phylogenetic perspective but also including a quantitative approach to provide significant insights into the evolutionary forces that shape the dynamic of the taxonomic interaction networks in bacterial communities. PMID:23789031

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

    PubMed

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

    2006-12-01

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

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

    USGS Publications Warehouse

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

    2006-01-01

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

  10. 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

  11. Whartonacarus floridensis sp. nov. (Acari: Trombiculidae), with a taxonomic review and the first record of Whartonacarus chiggers in the continental United States.

    PubMed

    Mertins, James W; Hanson, Britta A; Corn, Joseph L

    2009-11-01

    Among several unusual species collected during surveillance of ectoparasites on wildlife hosts in the southeastern United States and Caribbean Region, the larvae of a new species of Whartonacarus were encountered in 2003 on a cattle egret, Bubulcus ibis (L.), in the Florida Keys. This is the first record for a member of Whartonacarus in the continental United States. The mite is described and named as Whartonacarus floridensis Mertins, and the possible significance of this discovery with respect to the "tropical bont tick," Amblyomma variegatum (F.), is discussed. A brief taxonomic review of Whartonacarus raises questions about the putative synonymy of Whartonacarus nativitatis (Hoffmann) and Whartonacarus thompsoni (Brennan) and suggests that Whartonacarus shiraii (Sasa et al.) may include two distinct taxa. Whartonacarus is redefined, and a revised key to the known taxa is provided. Toritrombicula oceanica Brennan & Amerson is placed in the genus Whartonacarus. Also, Whartonacarus palenquensis (Hoffman) is rejected as a member of this genus and placed in its own new genus, Longisetacarus Mertins.

  12. Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

    PubMed Central

    Schmidt, Thomas S. B.; Matias Rodrigues, João F.; von Mering, Christian

    2014-01-01

    Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate ‘true’ microbial taxa. Here, we explore the ecological consistency of OTUs – based on the assumption that, like true microbial taxa, they should show measurable habitat preferences (niche conservatism). In a global and comprehensive survey of available microbial sequence data, we systematically parse sequence annotations to obtain broad ecological descriptions of sampling sites. Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency. However, different OTU clustering methods result in marked differences in the strength of this signal. Assuming that ecological consistency can serve as an objective external benchmark for cluster quality, we conclude that hierarchical complete linkage clustering, which provided the most ecologically consistent partitions, should be the default choice for OTU clustering. To our knowledge, this is the first approach to assess cluster quality using an external, biologically meaningful parameter as a benchmark, on a global scale. PMID:24763141

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

    PubMed

    Törnroos, Anna; Nordström, Marie C; Bonsdorff, Erik

    2013-01-01

    Due to human impact, there is extensive degradation and loss of marine habitats, which calls for measures that incorporate taxonomic as well as functional and trophic aspects of biodiversity. Since such data is less easily quantifiable in nature, the use of habitats as surrogates or proxies for biodiversity is on the rise in marine conservation and management. However, there is a critical gap in knowledge of whether pre-defined habitat units adequately represent the functional and trophic structure of communities. We also lack comparisons of different measures of community structure in terms of both between- (β) and within-habitat (α) variability when accounting for species densities. Thus, we evaluated a priori defined coastal habitats as surrogates for traditional taxonomic, functional and trophic zoobenthic community structure. We focused on four habitats (bare sand, canopy-forming algae, seagrass above- and belowground), all easily delineated in nature and defined through classification systems. We analyzed uni- and multivariate data on species and trait diversity as well as stable isotope ratios of benthic macrofauna. A good fit between habitat types and taxonomic and functional structure was found, although habitats were more similar functionally. This was attributed to within-habitat heterogeneity so when habitat divisions matched the taxonomic structure, only bare sand was functionally distinct. The pre-defined habitats did not meet the variability of trophic structure, which also proved to differentiate on a smaller spatial scale. The quantification of trophic structure using species density only identified an epi- and an infaunal unit. To summarize the results we present a conceptual model illustrating the match between pre-defined habitat types and the taxonomic, functional and trophic community structure. Our results show the importance of including functional and trophic aspects more comprehensively in marine management and spatial planning.

  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. Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures.

    PubMed

    Schloss, Patrick D; Handelsman, Jo

    2006-10-01

    The recent advent of tools enabling statistical inferences to be drawn from comparisons of microbial communities has enabled the focus of microbial ecology to move from characterizing biodiversity to describing the distribution of that biodiversity. Although statistical tools have been developed to compare community structures across a phylogenetic tree, we lack tools to compare the memberships and structures of two communities at a particular operational taxonomic unit (OTU) definition. Furthermore, current tests of community structure do not indicate the similarity of the communities but only report the probability of a statistical hypothesis. Here we present a computer program, SONS, which implements nonparametric estimators for the fraction and richness of OTUs shared between two communities.

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

    PubMed Central

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

    2014-01-01

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

  17. Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae)

    PubMed Central

    Francisco, Jessica Nayara Carvalho; Lohmann, Lúcia G.

    2018-01-01

    Abstract Pachyptera DC. is a small genus of neotropical lianas included in tribe Bignonieae (Bignoniaceae). The genus has a complicated taxonomic history but currently includes species distributed from Belize to Southern Amazon. Pachyptera is characterised by four main synapomorphies, namely, a papery peeling bark, prophylls of the axillary buds organised in a series of three, patelliform glands arranged in lines in the upper portions of the calyx and corolla tube. Furthermore, members of the genus also have stems with four phloem wedges in cross-section and conspicuous extrafloral nectaries between the interpetiolar region and at the petiole apex, although these characters are also shared with other genera of tribe Bignonieae. Here, we present a taxonomic revision of Pachyptera, which includes a complete list of synonyms, detailed morphological descriptions of species and an identification key, as well as information on the habitat, distribution and phenology, nomenclatural notes, taxonomic comments and illustrations of all the species. In addition, we designate three lectotypes, propose one new combination, raise one variety to species status and describe a new species. After these adjustments, a Pachyptera with five well-defined species is recognised. PMID:29416412

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

    PubMed

    Francisco, Jessica Nayara Carvalho; Lohmann, Lúcia G

    2018-01-01

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

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

    USGS Publications Warehouse

    Walsh, Stephen Joseph; Meador, Michael R.

    1998-01-01

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

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

    Treesearch

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

    2011-01-01

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

  1. Increasing numbers of bird species result from taxonomic progress, not taxonomic inflation

    PubMed Central

    Sangster, George

    2009-01-01

    The impact and significance of modern taxonomy on other fields in biology have been subjects of much debate. It has been proposed that increasing numbers of vertebrate species are largely owing to ‘taxonomic inflation’. According to this hypothesis, newly recognized species result from reinterpretations of species limits based on phylogenetic species concepts (PSCs) rather than from new discoveries. Here, I examine 747 proposals to change the taxonomic rank of birds in the period 1950–2007. The trend to recognize more species of birds started at least two decades before the introduction of PSCs. Most (84.6%) newly recognized species were supported by new taxonomic data. Proposals to recognize more species resulted from application of all six major taxonomic criteria. Many newly recognized species (63.4%) were not based exclusively on PSC-based criteria (diagnosability, monophyly and exclusive coalescence of gene trees). Therefore, this study finds no empirical support for the idea that the increase in species is primarily epistemological rather than data-driven. This study shows that previous claims about the causes and effects of taxonomic inflation lack empirical support. I argue that a more appropriate term for the increase in species is ‘taxonomic progress’. PMID:19520805

  2. 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

  3. Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

    PubMed

    He, Yan; Caporaso, J Gregory; Jiang, Xiao-Tao; Sheng, Hua-Fang; Huse, Susan M; Rideout, Jai Ram; Edgar, Robert C; Kopylova, Evguenia; Walters, William A; Knight, Rob; Zhou, Hong-Wei

    2015-01-01

    The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses. Here, we report that many hierarchical and greedy clustering methods produce unstable OTUs, with membership that depends on the number of sequences clustered. If OTUs are regenerated with additional sequences or samples, sequences originally assigned to a given OTU can be split into different OTUs. Alternatively, sequences assigned to different OTUs can be merged into a single OTU. This OTU instability affects alpha-diversity analyses such as rarefaction curves, beta-diversity analyses such as distance-based ordination (for example, Principal Coordinate Analysis (PCoA)), and the identification of differentially represented OTUs. Our results show that the proportion of unstable OTUs varies for different clustering methods. We found that the closed-reference method is the only one that produces completely stable OTUs, with the caveat that sequences that do not match a pre-existing reference sequence collection are discarded. As a compromise to the factors listed above, we propose using an open-reference method to enhance OTU stability. This type of method clusters sequences against a database and includes unmatched sequences by clustering them via a relatively stable de novo clustering method. OTU stability is an important consideration when analyzing microbial diversity and is a feature that should be taken into account during the development of novel OTU clustering methods.

  4. Rapid evolution in lekking grouse: Implications for taxonomic definitions

    USGS Publications Warehouse

    Oyler-McCance, Sara J.; St. John, Judy; Quinn, Thomas W.

    2010-01-01

    Species and subspecies delineations were traditionally defined by morphological and behavioral traits, as well as by plumage characteristics. Molecular genetic data have more recently been used to assess these classifications and, in many cases, to redefine them. The recent practice of utilizing molecular genetic data to examine taxonomic questions has led some to suggest that molecular genetic methods are more appropriate than traditional methods for addressing taxonomic uncertainty and management units. We compared the North American Tetraoninae—which have been defined using plumage, morphology, and behavior—and considered the effects of redefinition using only neutral molecular genetic data (mitochondrial control region and cytochrome oxidase subunit 1). Using the criterion of reciprocal monophyly, we failed to recognize the five species whose mating system is highly polygynous, with males displaying on leks. In lek-breeding species, sexual selection can act to influence morphological and behavioral traits at a rate much faster than can be tracked genetically. Thus, we suggest that at least for lek-breeding species, it is important to recognize the possibility that morphological and behavioral changes may occur at an accelerated rate compared with the processes that led to reciprocal monophyly of putatively neutral genetic markers. Therefore, it is particularly important to consider the possible disconnect between such lines of evidence when making taxonomic revisions and definitions of management units.

  5. Current Taxonomical Situation of Streptococcus suis

    PubMed Central

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

    2016-01-01

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

  6. Current Taxonomical Situation of Streptococcus suis.

    PubMed

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

    2016-06-24

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

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

    EPA Pesticide Factsheets

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

  8. Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit

    PubMed Central

    2014-01-01

    Background The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. Results We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Conclusions Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning. PMID:24708438

  9. Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit.

    PubMed

    Hoefman, Sven; van der Ha, David; Boon, Nico; Vandamme, Peter; De Vos, Paul; Heylen, Kim

    2014-04-04

    The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning.

  10. Taxonomic indexing--extending the role of taxonomy.

    PubMed

    Patterson, David J; Remsen, David; Marino, William A; Norton, Cathy

    2006-06-01

    Taxonomic indexing refers to a new array of taxonomically intelligent network services that use nomenclatural principles and elements of expert taxonomic knowledge to manage information about organisms. Taxonomic indexing was introduced to help manage the increasing amounts of digital information about biology. It has been designed to form a near basal layer in a layered cyberinfrastructure that deals with biological information. Taxonomic Indexing accommodates the special problems of using names of organisms to index biological material. It links alternative names for the same entity (reconciliation), and distinguishes between uses of the same name for different entities (disambiguation), and names are placed within an indefinite number of hierarchical schemes. In order to access all information on all organisms, Taxonomic indexing must be able to call on a registry of all names in all forms for all organisms. NameBank has been developed to meet that need. Taxonomic indexing is an area of informatics that overlaps with taxonomy, is dependent on the expert input of taxonomists, and reveals the relevance of the discipline to a wide audience.

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

    PubMed

    Horton, Matthew; Bodenhausen, Natacha; Bergelson, Joy

    2010-02-15

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

  13. A Framework for Inferring Taxonomic Class of Asteroids.

    NASA Technical Reports Server (NTRS)

    Dotson, J. L.; Mathias, D. L.

    2017-01-01

    Introduction: Taxonomic classification of asteroids based on their visible / near-infrared spectra or multi band photometry has proven to be a useful tool to infer other properties about asteroids. Meteorite analogs have been identified for several taxonomic classes, permitting detailed inference about asteroid composition. Trends have been identified between taxonomy and measured asteroid density. Thanks to NEOWise (Near-Earth-Object Wide-field Infrared Survey Explorer) and Spitzer (Spitzer Space Telescope), approximately twice as many asteroids have measured albedos than the number with taxonomic classifications. (If one only considers spectroscopically determined classifications, the ratio is greater than 40.) We present a Bayesian framework that provides probabilistic estimates of the taxonomic class of an asteroid based on its albedo. Although probabilistic estimates of taxonomic classes are not a replacement for spectroscopic or photometric determinations, they can be a useful tool for identifying objects for further study or for asteroid threat assessment models. Inputs and Framework: The framework relies upon two inputs: the expected fraction of each taxonomic class in the population and the albedo distribution of each class. Luckily, numerous authors have addressed both of these questions. For example, the taxonomic distribution by number, surface area and mass of the main belt has been estimated and a diameter limited estimate of fractional abundances of the near earth asteroid population was made. Similarly, the albedo distributions for taxonomic classes have been estimated for the combined main belt and NEA (Near Earth Asteroid) populations in different taxonomic systems and for the NEA population specifically. The framework utilizes a Bayesian inference appropriate for categorical data. The population fractions provide the prior while the albedo distributions allow calculation of the likelihood an albedo measurement is consistent with a given taxonomic

  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 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. © 2011

  16. 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

  17. 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

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

    PubMed

    Stahlschmidt, Zachary R

    2011-01-01

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

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

    PubMed Central

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

    2018-01-01

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

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

    PubMed

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

    2015-09-01

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

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

    PubMed

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

    2014-04-01

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

  2. MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

    PubMed

    Albanese, Davide; Fontana, Paolo; De Filippo, Carlotta; Cavalieri, Duccio; Donati, Claudio

    2015-05-19

    The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project.

  3. 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

  4. 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…

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

    PubMed Central

    Mateus, Octávio; Benson, Roger B.J.

    2015-01-01

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

  6. Increasing fish taxonomic and functional richness affects ecosystem properties of small headwater prairie streams

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Martin, Erika C.; Gido, Keith B.; Bello, Nora

    Stream fish can regulate their environment through direct and indirect pathways, and the relative influence of communities with different taxonomic and functional richness on ecosystem properties likely depends on habitat structure. Given this complexity, it is not surprising that observational studies of how stream fish communities influence ecosystems have shown mixed results. In this study, we evaluated the effect of an observed gradient of taxonomic (zero, one, two or three species) and functional (zero, one or two groups) richness of fishes on several key ecosystem properties in experimental stream mesocosms. Our study simulated small (less than two metres wide) headwatermore » prairie streams with a succession of three pool-riffle structures (upstream, middle and downstream) per mesocosm. Additionally, ecosystem responses included chlorophyll a from floating algal mats and benthic algae, benthic organic matter, macroinvertebrates (all as mass per unit area), algal filament length and stream metabolism (photosynthesis and respiration rate). Ecosystem responses were analysed individually using general linear mixed models. Significant treatment (taxonomic and functional richness) by habitat (pools and riffles) interactions were found for all but one ecosystem response variable. After accounting for location (upstream, middle and downstream) effects, the presence of one or two grazers resulted in shorter mean algal filament lengths in pools compared to no-fish controls. These observations suggest grazers can maintain short algal filaments in pools, which may inhibit long filaments from reaching the surface. Accordingly, floating algal mats decreased in mid- and downstream locations in grazer treatment relative to no-fish controls. At the scale of the entire reach, gross primary productivity and respiration were greater in treatments with two grazer species compared to mixed grazer/insectivore or control treatments. Lastly, the distribution of stream resources

  7. Increasing fish taxonomic and functional richness affects ecosystem properties of small headwater prairie streams

    DOE PAGES

    Martin, Erika C.; Gido, Keith B.; Bello, Nora; ...

    2016-04-06

    Stream fish can regulate their environment through direct and indirect pathways, and the relative influence of communities with different taxonomic and functional richness on ecosystem properties likely depends on habitat structure. Given this complexity, it is not surprising that observational studies of how stream fish communities influence ecosystems have shown mixed results. In this study, we evaluated the effect of an observed gradient of taxonomic (zero, one, two or three species) and functional (zero, one or two groups) richness of fishes on several key ecosystem properties in experimental stream mesocosms. Our study simulated small (less than two metres wide) headwatermore » prairie streams with a succession of three pool-riffle structures (upstream, middle and downstream) per mesocosm. Additionally, ecosystem responses included chlorophyll a from floating algal mats and benthic algae, benthic organic matter, macroinvertebrates (all as mass per unit area), algal filament length and stream metabolism (photosynthesis and respiration rate). Ecosystem responses were analysed individually using general linear mixed models. Significant treatment (taxonomic and functional richness) by habitat (pools and riffles) interactions were found for all but one ecosystem response variable. After accounting for location (upstream, middle and downstream) effects, the presence of one or two grazers resulted in shorter mean algal filament lengths in pools compared to no-fish controls. These observations suggest grazers can maintain short algal filaments in pools, which may inhibit long filaments from reaching the surface. Accordingly, floating algal mats decreased in mid- and downstream locations in grazer treatment relative to no-fish controls. At the scale of the entire reach, gross primary productivity and respiration were greater in treatments with two grazer species compared to mixed grazer/insectivore or control treatments. Lastly, the distribution of stream resources

  8. Taxonomic and Thematic Semantic Systems

    PubMed Central

    Mirman, Daniel; Landrigan, Jon-Frederick; Britt, Allison E.

    2017-01-01

    Object concepts are critical for nearly all aspects of human cognition, from perception tasks like object recognition, to understanding and producing language, to making meaningful actions. Concepts can have two very different kinds of relations: similarity relations based on shared features (e.g., dog – bear), which are called “taxonomic” relations, and contiguity relations based on co-occurrence in events or scenarios (e.g., dog – leash), which are called “thematic” relations. Here we report a systematic review of experimental psychology and cognitive neuroscience evidence of this distinction in the structure of semantic memory. We propose two principles that may drive the development of distinct taxonomic and thematic semantic systems: (1) differences between which features determine taxonomic vs. thematic relations and (2) differences in the processing required to extract taxonomic vs. thematic relations. This review brings together distinct threads of behavioral, computational, and neuroscience research on semantic memory in support of a functional and neural dissociation, and defines a framework for future studies of semantic memory. PMID:28333494

  9. MICCA: a complete and accurate software for taxonomic profiling of metagenomic data

    PubMed Central

    Albanese, Davide; Fontana, Paolo; De Filippo, Carlotta; Cavalieri, Duccio; Donati, Claudio

    2015-01-01

    The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project. PMID:25988396

  10. Taxonomic synopsis of invasive and native Spartina (Poaceae, Chloridoideae) in the Pacific Northwest (British Columbia, Washington and Oregon), including the first report of Spartina ×townsendii for British Columbia, Canada

    PubMed Central

    Saarela, Jeffery M.

    2012-01-01

    Abstract Five species of the grass genus Spartina are invading salt marshes along the Pacific coast of North America, of which three have been documented in British Columbia, Canada, in only the last decade. A taxonomic synopsis of the two native (Spartina gracilis, Spartina pectinata) and five introduced Spartina taxa (Spartina anglica, Spartina alterniflora, Spartina densiflora, Spartina patens, Spartina ×townsendii) in the Pacific Northwest is presented to facilitate their identification, including nomenclature, a new taxonomic key, new descriptions for a subset of taxa, and representative specimens. Spartina ×townsendii is newly reported for the flora of British Columbia. The non-coastal species Spartina pectinata is reported from an urban site in British Columbia, the first confirmed report of the taxon for the province. Lectotypes are newly designated for Spartina anglica C.E. Hubb., Spartina maritima subvar. fallax St.-Yves, and Spartina cynosuroides f. major St.-Yves. PMID:22461730

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

    PubMed

    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.

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

    PubMed Central

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

    2015-01-01

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

  13. A Synopsis of the Taxonomic Revisions in the Genus Ceratocystis Including a Review of Blue-Staining Species Associated with Dendroctonus Bark Beetles

    Treesearch

    Thelma J. Perry

    1991-01-01

    Taxonomic revisions in both the teleomorphic (sexual) and anamorphic (asexual) forms of the genus Ceratocystis Ellis & Halstead are chronicled in this review. Recognized species associated with Dendroctonus Erichson bark beetles are summarized, and several species that have been published as recombinations, species that were...

  14. Unbiased Taxonomic Annotation of Metagenomic Samples

    PubMed Central

    Fosso, Bruno; Pesole, Graziano; Rosselló, Francesc

    2018-01-01

    Abstract The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under the receiver operating characteristic (ROC) curve and F-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample. PMID:29028181

  15. Identifying taxonomic and functional surrogates for spring biodiversity conservation.

    PubMed

    Jyväsjärvi, Jussi; Virtanen, Risto; Ilmonen, Jari; Paasivirta, Lauri; Muotka, Timo

    2018-02-27

    Surrogate approaches are widely used to estimate overall taxonomic diversity for conservation planning. Surrogate taxa are frequently selected based on rarity or charisma, whereas selection through statistical modeling has been applied rarely. We used boosted-regression-tree models (BRT) fitted to biological data from 165 springs to identify bryophyte and invertebrate surrogates for taxonomic and functional diversity of boreal springs. We focused on these 2 groups because they are well known and abundant in most boreal springs. The best indicators of taxonomic versus functional diversity differed. The bryophyte Bryum weigelii and the chironomid larva Paratrichocladius skirwithensis best indicated taxonomic diversity, whereas the isopod Asellus aquaticus and the chironomid Macropelopia spp. were the best surrogates of functional diversity. In a scoring algorithm for priority-site selection, taxonomic surrogates performed only slightly better than random selection for all spring-dwelling taxa, but they were very effective in representing spring specialists, providing a distinct improvement over random solutions. However, the surrogates for taxonomic diversity represented functional diversity poorly and vice versa. When combined with cross-taxon complementarity analyses, surrogate selection based on statistical modeling provides a promising approach for identifying groundwater-dependent ecosystems of special conservation value, a key requirement of the EU Water Framework Directive. © 2018 Society for Conservation Biology.

  16. Taxonomic bias in biodiversity data and societal preferences.

    PubMed

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

    2017-08-22

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

  17. The identity of three South American “smiliine” treehoppers (Hemiptera: Membracidae) and related taxonomic changes, including description of a new genus in Thuridini

    USDA-ARS?s Scientific Manuscript database

    Based on examination of holotype or interpretation of original descriptions, four taxonomic changes are proposed for South American species erroneously placed in the tribe Smiliini: Flynnia, n. gen. (Thuridini) and F. fascipennis (Funkhouser), n. comb. from Bolivia; Antianthe atromarginata (Goding),...

  18. Florisitic summary of 'Manual of Vascular Plants of Northeastern United States and Adjacent Canada', second edition

    USGS Publications Warehouse

    Bennett, J.P.

    1996-01-01

    The second edition of the Manual of Vascular Plants of Northeastern United States and Adjacent Canada by Gleason and Cronquist (1991) is the most recent and up-to-date taxonomic treatment of the flora of that region. Since no floristic summary of the Manual was included in the publication, a computer analysis of the taxonomic data of the Manual was performed in order to generate a floristic summary. Totals of 4285 species, 1091 genera, and 191 families were tabulated. The largest genus was Carex, with 230 species; the largest family was the Asteraceae, with 528 species. Comparisons made with earlier floras of the same region indicated small declines on the order of 10% for these taxonomic groups.

  19. High-throughput amplicon sequencing and stream benthic bacteria: identifying the best taxonomic level for multiple-stressor research

    PubMed Central

    Salis, R. K.; Bruder, A.; Piggott, J. J.; Summerfield, T. C.; Matthaei, C. D.

    2017-01-01

    Disentangling the individual and interactive effects of multiple stressors on microbial communities is a key challenge to our understanding and management of ecosystems. Advances in molecular techniques allow studying microbial communities in situ and with high taxonomic resolution. However, the taxonomic level which provides the best trade-off between our ability to detect multiple-stressor effects versus the goal of studying entire communities remains unknown. We used outdoor mesocosms simulating small streams to investigate the effects of four agricultural stressors (nutrient enrichment, the nitrification inhibitor dicyandiamide (DCD), fine sediment and flow velocity reduction) on stream bacteria (phyla, orders, genera, and species represented by Operational Taxonomic Units with 97% sequence similarity). Community composition was assessed using amplicon sequencing (16S rRNA gene, V3-V4 region). DCD was the most pervasive stressor, affecting evenness and most abundant taxa, followed by sediment and flow velocity. Stressor pervasiveness was similar across taxonomic levels and lower levels did not perform better in detecting stressor effects. Community coverage decreased from 96% of all sequences for abundant phyla to 28% for species. Order-level responses were generally representative of responses of corresponding genera and species, suggesting that this level may represent the best compromise between stressor sensitivity and coverage of bacterial communities. PMID:28327636

  20. Vertebrate species introductions in the United States and its territories

    USGS Publications Warehouse

    Witmer, Gary W.; Fuller, Pam L.

    2011-01-01

    At least 1,065 introduced vertebrate species have been introduced in the United States and its territories, including at least 86 mammalian, 127 avian, 179 reptilian/amphibian, and 673 fish species. Examples in each major taxonomic group include domestic cat, small Indian mongoose, red fox, goat, pig, rabbit, rats, house mouse, gray squirrel, nutria, starling, Indian common myna, red-vented bulbul, brown treesnake, red-eared slider, brown trout, tilapia, and grass carp. We briefly review some of these species and the types of damage they cause. We then review the basic types of methods used for control or eradication of each taxonomic group, including physical, chemical, biological, and cultural methods. We discuss some of the challenges in managing these species, including issues with the use of toxicants, land access, public attitudes, and monitoring difficulties. Finally, we list some ongoing research and future research needs, including improved detection methods, improved attractants, improved barriers, improved capture methods, fertility control, and risk assessment methods.

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

    PubMed Central

    Kekkonen, Mari; Hebert, Paul D N

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Skorobogatova, O. N.

    2018-03-01

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

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

    PubMed

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

    2016-12-05

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

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

    PubMed

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

    2017-01-01

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

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

    PubMed Central

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

    2017-01-01

    We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280–460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520–600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation. PMID:29236767

  11. A taxonomic revision of Herminium L. (Orchidoideae, Orchidaceae)

    PubMed Central

    Raskoti, Bhakta Bahadur; Schuiteman, André; Jin, Wei-Tao; Jin, Xiao-Hua

    2017-01-01

    Abstract Herminium (Orchidaceae, Orchidoideae) is a medium-sized genus widespread in the northern hemisphere, with a clear centre of diversity in the Himalayas. We present a comprehensive taxonomic revision of Herminium based on field observations and morphological studies, for which we examined about 2500 specimens. We recognize 49 species grouped into six formal sections, including one new species, Herminium tibeticum, from Tibet. We provide an identification key to the species, descriptions of the species, notes on ecology and distribution, and complete nomenclature for each species, including typifications. We here designate lectotypes for five species and reduce four taxa to synonymy. PMID:28794677

  12. 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…

  13. 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…

  14. TRUSS DETAILS. United Engineering Company Ltd., Alameda Shipyard. Includes crane ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    TRUSS DETAILS. United Engineering Company Ltd., Alameda Shipyard. Includes crane girder section. No architect noted. Drawn by Penney. Plan no. 2-N-7. March 10, 1942, no revisions. U.S. Navy, Bureau of Yards & Docks, Contract no. bs 76, item no. 22A. Approved for construction October 9, 1943. blueprint - United Engineering Company Shipyard, Warehouse, 2900 Main Street, Alameda, Alameda County, CA

  15. Three operational taxonomic units of Eimeria are common in Nigerian chickens and may undermine effective molecular diagnosis of coccidiosis.

    PubMed

    Jatau, Isa D; Lawal, Idris A; Kwaga, Jacob K P; Tomley, Fiona M; Blake, Damer P; Nok, Andrew J

    2016-06-04

    Chicken is fast becoming the world's most consumed meat. As a consequence poultry health is more important now than ever before, with pathogens of chickens recognised as serious threats to food security. One such threat are Eimeria species parasites, protozoa which can cause the disease coccidiosis. Eimeria can compromise economic poultry production and chicken welfare, and have serious consequences for poor livestock keepers. Seven Eimeria species that infect chickens are recognised with a global enzootic distribution. More recently three cryptic Operational Taxonomic Units (OTUx, y and z) have been described in populations of Eimeria recovered from chickens in Australia. Two of the three OTUs have also been detected in sub-Saharan Africa, but their occurrence, pathology and the risk they pose is largely unknown. Nigeria has witnessed a dramatic expansion in poultry production and is now the largest poultry producer in Africa. Here, faecal samples collected from nine of 12 commercial chicken farms sampled in Kaduna state, Nigeria, were found to contain eimerian oocysts. After amplification by in vivo propagation all three cryptic OTU genotypes were detected using polymerase chain reaction (PCR), including OTUy for the first time outside of Australia. Comparison with a widely used, established Eimeria species-specific PCR assay revealed failure to detect the OTU genotypes. All three of the Eimeria OTU genotypes appear to be common in north-western Nigeria. The failure of a leading species-specific molecular assay to detect these genotypes indicates a risk of false negative Eimeria diagnosis when using molecular tools and suggests that the spatial occurrence of each OTU may be far wider than has been recognised. The risk posed by these novel genotypes is unknown, but it is clear that a better understanding of Eimeria occurrence is required together with the validation of effective diagnostics.

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

    PubMed

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

    2010-11-22

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

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

    PubMed Central

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

    2010-01-01

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

  18. 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

  19. 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

  20. Neuroanatomical dissociation for taxonomic and thematic knowledge in the human brain

    PubMed Central

    Schwartz, Myrna F.; Kimberg, Daniel Y.; Walker, Grant M.; Brecher, Adelyn; Faseyitan, Olufunsho K.; Dell, Gary S.; Mirman, Daniel; Coslett, H. Branch

    2011-01-01

    It is thought that semantic memory represents taxonomic information differently from thematic information. This study investigated the neural basis for the taxonomic-thematic distinction in a unique way. We gathered picture-naming errors from 86 individuals with poststroke language impairment (aphasia). Error rates were determined separately for taxonomic errors (“pear” in response to apple) and thematic errors (“worm” in response to apple), and their shared variance was regressed out of each measure. With the segmented lesions normalized to a common template, we carried out voxel-based lesion-symptom mapping on each error type separately. We found that taxonomic errors localized to the left anterior temporal lobe and thematic errors localized to the left temporoparietal junction. This is an indication that the contribution of these regions to semantic memory cleaves along taxonomic-thematic lines. Our findings show that a distinction long recognized in the psychological sciences is grounded in the structure and function of the human brain. PMID:21540329

  1. An Overview of Marine Biodiversity in United States Waters

    PubMed Central

    Fautin, Daphne; Dalton, Penelope; Incze, Lewis S.; Leong, Jo-Ann C.; Pautzke, Clarence; Rosenberg, Andrew; Sandifer, Paul; Sedberry, George; Tunnell, John W.; Abbott, Isabella; Brainard, Russell E.; Brodeur, Melissa; Eldredge, Lucius G.; Feldman, Michael; Moretzsohn, Fabio; Vroom, Peter S.; Wainstein, Michelle; Wolff, Nicholas

    2010-01-01

    Marine biodiversity of the United States (U.S.) is extensively documented, but data assembled by the United States National Committee for the Census of Marine Life demonstrate that even the most complete taxonomic inventories are based on records scattered in space and time. The best-known taxa are those of commercial importance. Body size is directly correlated with knowledge of a species, and knowledge also diminishes with distance from shore and depth. Measures of biodiversity other than species diversity, such as ecosystem and genetic diversity, are poorly documented. Threats to marine biodiversity in the U.S. are the same as those for most of the world: overexploitation of living resources; reduced water quality; coastal development; shipping; invasive species; rising temperature and concentrations of carbon dioxide in the surface ocean, and other changes that may be consequences of global change, including shifting currents; increased number and size of hypoxic or anoxic areas; and increased number and duration of harmful algal blooms. More information must be obtained through field and laboratory research and monitoring that involve innovative sampling techniques (such as genetics and acoustics), but data that already exist must be made accessible. And all data must have a temporal component so trends can be identified. As data are compiled, techniques must be developed to make certain that scales are compatible, to combine and reconcile data collected for various purposes with disparate gear, and to automate taxonomic changes. Information on biotic and abiotic elements of the environment must be interactively linked. Impediments to assembling existing data and collecting new data on marine biodiversity include logistical problems as well as shortages in finances and taxonomic expertise. PMID:20689852

  2. An overview of marine biodiversity in United States waters

    USGS Publications Warehouse

    Fautin, Daphne G.; Delton, Penelope; Incze, Lewis S.; Leong, Jo-Ann C.; Pautzke, Clarence; Rosenberg, Andrew A.; Sandifer, Paul; Sedberry, George R.; Tunnell, John W.; Abbott, Isabella; Brainard, Russell E.; Brodeur, Melissa; Eldredge, Lucius G.; Feldman, Michael; Moretzsohn, Fabio; Vroom, Peter S.; Wainstein, Michelle; Wolff, Nicholas

    2010-01-01

    Marine biodiversity of the United States (U.S.) is extensively documented, but data assembled by the United States National Committee for the Census of Marine Life demonstrate that even the most complete taxonomic inventories are based on records scattered in space and time. The best-known taxa are those of commercial importance. Body size is directly correlated with knowledge of a species, and knowledge also diminishes with distance from shore and depth. Measures of biodiversity other than species diversity, such as ecosystem and genetic diversity, are poorly documented. Threats to marine biodiversity in the U.S. are the same as those for most of the world: overexploitation of living resources; reduced water quality; coastal development; shipping; invasive species; rising temperature and concentrations of carbon dioxide in the surface ocean, and other changes that may be consequences of global change, including shifting currents; increased number and size of hypoxic or anoxic areas; and increased number and duration of harmful algal blooms. More information must be obtained through field and laboratory research and monitoring that involve innovative sampling techniques (such as genetics and acoustics), but data that already exist must be made accessible. And all data must have a temporal component so trends can be identified. As data are compiled, techniques must be developed to make certain that scales are compatible, to combine and reconcile data collected for various purposes with disparate gear, and to automate taxonomic changes. Information on biotic and abiotic elements of the environment must be interactively linked. Impediments to assembling existing data and collecting new data on marine biodiversity include logistical problems as well as shortages in finances and taxonomic expertise.

  3. An overview of marine biodiversity in United States waters.

    PubMed

    Fautin, Daphne; Dalton, Penelope; Incze, Lewis S; Leong, Jo-Ann C; Pautzke, Clarence; Rosenberg, Andrew; Sandifer, Paul; Sedberry, George; Tunnell, John W; Abbott, Isabella; Brainard, Russell E; Brodeur, Melissa; Eldredge, Lucius G; Feldman, Michael; Moretzsohn, Fabio; Vroom, Peter S; Wainstein, Michelle; Wolff, Nicholas

    2010-08-02

    Marine biodiversity of the United States (U.S.) is extensively documented, but data assembled by the United States National Committee for the Census of Marine Life demonstrate that even the most complete taxonomic inventories are based on records scattered in space and time. The best-known taxa are those of commercial importance. Body size is directly correlated with knowledge of a species, and knowledge also diminishes with distance from shore and depth. Measures of biodiversity other than species diversity, such as ecosystem and genetic diversity, are poorly documented. Threats to marine biodiversity in the U.S. are the same as those for most of the world: overexploitation of living resources; reduced water quality; coastal development; shipping; invasive species; rising temperature and concentrations of carbon dioxide in the surface ocean, and other changes that may be consequences of global change, including shifting currents; increased number and size of hypoxic or anoxic areas; and increased number and duration of harmful algal blooms. More information must be obtained through field and laboratory research and monitoring that involve innovative sampling techniques (such as genetics and acoustics), but data that already exist must be made accessible. And all data must have a temporal component so trends can be identified. As data are compiled, techniques must be developed to make certain that scales are compatible, to combine and reconcile data collected for various purposes with disparate gear, and to automate taxonomic changes. Information on biotic and abiotic elements of the environment must be interactively linked. Impediments to assembling existing data and collecting new data on marine biodiversity include logistical problems as well as shortages in finances and taxonomic expertise.

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

    PubMed

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

    2015-04-01

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

  5. Taxonomic revision of Neotropical Murdannia Royle (Commelinaceae)

    PubMed Central

    Pellegrini, Marco Octávio de Oliveira; Faden, Robert B.; de Almeida, Rafael Felipe

    2016-01-01

    Abstract This study provides a taxonomic revision for the Neotropical species of the genus Murdannia. Six species are recognized as native, including a new species and a new combination, while two Asian species are recognized as invasive. We present an identification key, a table summarizing the morphologic differences among the species, a new synonym, six lectotypifications, a distribution map, and descriptions, comments and photographic plates for each species. We also provide comments on the morphology of the Neotropical species of Murdannia, comparing them with the Paleotropical species, and a discussion of inflorescence architecture in the genus as a whole. PMID:28127236

  6. 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

  7. Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific

    PubMed Central

    Larkin, Alyse A; Blinebry, Sara K; Howes, Caroline; Lin, Yajuan; Loftus, Sarah E; Schmaus, Carrie A; Zinser, Erik R; Johnson, Zackary I

    2016-01-01

    The distribution of major clades of Prochlorococcus tracks light, temperature and other environmental variables; yet, the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. We examined high light (HL) adapted Prochlorococcus communities across spatial and temporal environmental gradients in the Pacific Ocean to determine the ecological drivers of population structure and diversity across taxonomic ranks. We show that the Prochlorococcus community has the highest diversity at low latitudes, but seasonality driven by temperature, day length and nutrients adds complexity. At finer taxonomic resolution, some ‘sub-ecotype' clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Intriguingly, biogeographies of the HL-I sub-ecotypes are driven by unique combinations of environmental traits, rather than through trait hierarchy, while the HL-II sub-ecotypes appear ecologically similar, thus demonstrating differences among these dominant HL ecotypes. Examining biodiversity across taxonomic ranks reveals high-resolution dynamics of Prochlorococcus evolution and ecology that are masked at phylogenetically coarse resolution. Spatial and seasonal trends of Prochlorococcus communities suggest that the future ocean may be comprised of different populations, with implications for ecosystem structure and function. PMID:26800235

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

    PubMed

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

    2016-03-01

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

  9. Extraction of phenotypic traits from taxonomic descriptions for the tree of life using natural language processing.

    PubMed

    Endara, Lorena; Cui, Hong; Burleigh, J Gordon

    2018-03-01

    Phenotypic data sets are necessary to elucidate the genealogy of life, but assembling phenotypic data for taxa across the tree of life can be technically challenging and prohibitively time consuming. We describe a semi-automated protocol to facilitate and expedite the assembly of phenotypic character matrices of plants from formal taxonomic descriptions. This pipeline uses new natural language processing (NLP) techniques and a glossary of over 9000 botanical terms. Our protocol includes the Explorer of Taxon Concepts (ETC), an online application that assembles taxon-by-character matrices from taxonomic descriptions, and MatrixConverter, a Java application that enables users to evaluate and discretize the characters extracted by ETC. We demonstrate this protocol using descriptions from Araucariaceae. The NLP pipeline unlocks the phenotypic data found in taxonomic descriptions and makes them usable for evolutionary analyses.

  10. The identity of three South American “smiliine” treehoppers (Hemiptera, Membracidae) and related taxonomic changes, including description of a new genus in Thuridini

    PubMed Central

    McKamey, Stuart H.

    2017-01-01

    Abstract Based on examination of holotypes or interpretation of original descriptions, four taxonomic changes are proposed for South American species erroneously placed in the tribe Smiliini: Flynnia, gen. n. (Thuridini) and F. fascipennis (Funkhouser), comb. n. from Bolivia; Antianthe atromarginata (Goding), comb. n. from Ecuador; Amastris pilosa (Funkhouser), comb. n. from Peru; and Thelia planeflava Fairmaire from Brazil to Polyglyptini incertae sedis, new placement. PMID:28769696

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

    PubMed

    Goldstein, Paul Z; DeSalle, Rob

    2011-02-01

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

  12. Taxa: An R package implementing data standards and methods for taxonomic data

    PubMed Central

    Foster, Zachary S.L.; Chamberlain, Scott; Grünwald, Niklaus J.

    2018-01-01

    The taxa R package provides a set of tools for defining and manipulating taxonomic data. The recent and widespread application of DNA sequencing to community composition studies is making large data sets with taxonomic information commonplace. However, compared to typical tabular data, this information is encoded in many different ways and the hierarchical nature of taxonomic classifications makes it difficult to work with. There are many R packages that use taxonomic data to varying degrees but there is currently no cross-package standard for how this information is encoded and manipulated. We developed the R package taxa to provide a robust and flexible solution to storing and manipulating taxonomic data in R and any application-specific information associated with it. Taxa provides parsers that can read common sources of taxonomic information (taxon IDs, sequence IDs, taxon names, and classifications) from nearly any format while preserving associated data. Once parsed, the taxonomic data and any associated data can be manipulated using a cohesive set of functions modeled after the popular R package dplyr. These functions take into account the hierarchical nature of taxa and can modify the taxonomy or associated data in such a way that both are kept in sync. Taxa is currently being used by the metacoder and taxize packages, which provide broadly useful functionality that we hope will speed adoption by users and developers. PMID:29707201

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2018-05-01

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

  15. Digitising legacy zoological taxonomic literature: Processes, products and using the output

    PubMed Central

    Lyal, Christopher H. C.

    2016-01-01

    Abstract By digitising legacy taxonomic literature using XML mark-up the contents become accessible to other taxonomic and nomenclatural information systems. Appropriate schemas need to be interoperable with other sectorial schemas, atomise to appropriate content elements and carry appropriate metadata to, for example, enable algorithmic assessment of availability of a name under the Code. Legacy (and new) literature delivered in this fashion will become part of a global taxonomic resource from which users can extract tailored content to meet their particular needs, be they nomenclatural, taxonomic, faunistic or other. To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original – the output of the many efforts has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, the means by which many scientific papers are indexed and located is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising taxonomic names is still relatively poor, people’s ability to use search engines effectively is mixed, and many papers cannot be searched directly. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original papers and extract target content manually. This opens the door to dynamic linking of new content with extant systems: automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its

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

    USGS Publications Warehouse

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

    2015-01-01

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

  17. Analysing taxonomic structures and local ecological processes in temperate forests in North Eastern China.

    PubMed

    Fan, Chunyu; Tan, Lingzhao; Zhang, Chunyu; Zhao, Xiuhai; von Gadow, Klaus

    2017-10-30

    One of the core issues of forest community ecology is the exploration of how ecological processes affect community structure. The relative importance of different processes is still under debate. This study addresses four questions: (1) how is the taxonomic structure of a forest community affected by spatial scale? (2) does the taxonomic structure reveal effects of local processes such as environmental filtering, dispersal limitation or interspecific competition at a local scale? (3) does the effect of local processes on the taxonomic structure vary with the spatial scale? (4) does the analysis based on taxonomic structures provide similar insights when compared with the use of phylogenetic information? Based on the data collected in two large forest observational field studies, the taxonomic structures of the plant communities were analyzed at different sampling scales using taxonomic ratios (number of genera/number of species, number of families/number of species), and the relationship between the number of higher taxa and the number of species. Two random null models were used and the "standardized effect size" (SES) of taxonomic ratios was calculated, to assess possible differences between the observed and simulated taxonomic structures, which may be caused by specific ecological processes. We further applied a phylogeny-based method to compare results with those of the taxonomic approach. As expected, the taxonomic ratios decline with increasing grain size. The quantitative relationship between genera/families and species, described by a linearized power function, showed a good fit. With the exception of the family-species relationship in the Jiaohe study area, the exponents of the genus/family-species relationships did not show any scale dependent effects. The taxonomic ratios of the observed communities had significantly lower values than those of the simulated random community under the test of two null models at almost all scales. Null Model 2 which

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

    PubMed

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

    2017-11-01

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

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

    PubMed

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

    2016-12-01

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

  20. A polyphasic taxonomic approach in isolated strains of Cyanobacteria from thermal springs of Greece.

    PubMed

    Bravakos, Panos; Kotoulas, Georgios; Skaraki, Katerina; Pantazidou, Adriani; Economou-Amilli, Athena

    2016-05-01

    Strains of Cyanobacteria isolated from mats of 9 thermal springs of Greece have been studied for their taxonomic evaluation. A polyphasic taxonomic approach was employed which included: morphological observations by light microscopy and scanning electron microscopy, maximum parsimony, maximum likelihood and Bayesian analysis of 16S rDNA sequences, secondary structural comparisons of 16S-23S rRNA Internal Transcribed Spacer sequences, and finally environmental data. The 17 cyanobacterial isolates formed a diverse group that contained filamentous, coccoid and heterocytous strains. These included representatives of the polyphyletic genera of Synechococcus and Phormidium, and the orders Oscillatoriales, Spirulinales, Chroococcales and Nostocales. After analysis, at least 6 new taxa at the genus level provide new evidence in the taxonomy of Cyanobacteria and highlight the abundant diversity of thermal spring environments with many potential endemic species or ecotypes. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    USGS Publications Warehouse

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

    2017-01-01

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

  2. Taxonomic changes in Solanum section Petota

    USDA-ARS?s Scientific Manuscript database

    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...

  3. 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.

  4. Taxonomic and Thematic Organisation of Proper Name Conceptual Knowledge

    PubMed Central

    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

  5. Macrozooplankton biomass in a warm-core Gulf Stream ring: Time series changes in size structure, taxonomic composition, and vertical distribution

    NASA Astrophysics Data System (ADS)

    Davis, Cabell S.; Wiebe, Peter H.

    1985-01-01

    Macrozooplankton size structure and taxonomic composition in warm-core ring 82B was examined from a time series (March, April, June) of ring center MOCNESS (1 m) samples. Size distributions of 15 major taxonomic groups were determined from length measurements digitized from silhouette photographs of the samples. Silhouette digitization allows rapid quantification of Zooplankton size structure and taxonomic composition. Length/weight regressions, determined for each taxon, were used to partition the biomass (displacement volumes) of each sample among the major taxonomic groups. Zooplankton taxonomic composition and size structure varied with depth and appeared to coincide with the hydrographic structure of the ring. In March and April, within the thermostad region of the ring, smaller herbivorous/omnivorous Zooplankton, including copepods, crustacean larvae, and euphausiids, were dominant, whereas below this region, larger carnivores, such as medusae, ctenophores, fish, and decapods, dominated. Copepods were generally dominant in most samples above 500 m. Total macrozooplankton abundance and biomass increased between March and April, primarily because of increases in herbivorous taxa, including copepods, crustacean larvae, and larvaceans. A marked increase in total macrozooplankton abundance and biomass between April and June was characterized by an equally dramatic shift from smaller herbivores (1.0-3.0 mm) in April to large herbivores (5.0-6.0 mm) and carnivores (>15 mm) in June. Species identifications made directly from the samples suggest that changes in trophic structure resulted from seeding type immigration and subsequent in situ population growth of Slope Water zooplankton species.

  6. Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2017-01-01

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

  8. Genomic characterization reconfirms the taxonomic status of Lactobacillus parakefiri

    PubMed Central

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

    2017-01-01

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

  9. proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

    PubMed

    Mende, Daniel R; Letunic, Ivica; Huerta-Cepas, Jaime; Li, Simone S; Forslund, Kristoffer; Sunagawa, Shinichi; Bork, Peer

    2017-01-04

    The availability of microbial genomes has opened many new avenues of research within microbiology. This has been driven primarily by comparative genomics approaches, which rely on accurate and consistent characterization of genomic sequences. It is nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defined prokaryotic clades. Thus, we developed proGenomes, a resource that provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic clade. These genomes are assigned to 5306 consistent and accurate taxonomic species clusters based on previously established methodology. proGenomes also contains functional information for almost 80 million protein-coding genes, including a comprehensive set of general annotations and more focused annotations for carbohydrate-active enzymes and antibiotic resistance genes. Additionally, broad habitat information is provided for many genomes. All genomes and associated information can be downloaded by user-selected clade or multiple habitat-specific sets of representative genomes. We expect that the availability of high-quality genomes with comprehensive functional annotations will promote advances in clinical microbial genomics, functional evolution and other subfields of microbiology. proGenomes is available at http://progenomes.embl.de. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    NASA Astrophysics Data System (ADS)

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

    2011-05-01

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

  11. AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees

    PubMed Central

    Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

    2014-01-01

    A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php. PMID:24892935

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

    PubMed

    Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

    2014-01-01

    A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php.

  13. 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

  14. 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.

  15. 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

  16. Global taxonomic diversity of living reptiles.

    PubMed

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

    2013-01-01

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

  17. 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.

  18. Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle

    PubMed Central

    Seedorf, Henning; Kittelmann, Sandra

    2014-01-01

    Sequencing and analyses of 16S rRNA gene amplicons were performed to estimate the composition of the rumen methanogen community in 252 samples from eight cohorts of sheep and cattle, separated into 16 different sample groups by diet, and to determine which methanogens are most prominent in the rumens of farmed New Zealand ruminants. Methanobacteriales (relative abundance ± standard deviation, 89.6% ± 9.8%) and Methanomassiliicoccales (10.4% ± 9.8%) were the two major orders and contributed 99.98% (±0.1%) to the rumen methanogen communities in the samples. Sequences from Methanobacteriales were almost entirely from only four different species (or clades of very closely related species). Each was detectable in at least 89% of the samples. These four species or clades were the Methanobrevibacter gottschalkii clade and Methanobrevibacter ruminantium clade with a mean abundance of 42.4% (±19.5% standard deviation) and 32.9% (±18.8%), respectively, and Methanosphaera sp. ISO3-F5 (8.2% ± 6.7%) and Methanosphaera sp. group5 (5.6% ± 5.7%). These four species or clades appeared to be primarily represented by only one or, in one case, two dominant sequence types per species or clade when the sequences were grouped into operational taxonomic units (OTUs) at 99% sequence identity. The mean relative abundance of Methanomassiliicoccales in the samples was relatively low but exceeded 40% in some of the treatment groups. Animal feed affected the apparent methanogen community structure of both orders, as evident from differences in relative abundances of the major OTUs in animals under different feeding regimens. PMID:25416771

  19. Common and scientific names of aquatic invertebrates from the United States and Canada: Mollusks

    USGS Publications Warehouse

    Turgeon, D. D.; Quinn, J.F.; Bogan, A.E.; Coan, E. V.; Hochberg, F.G.; Lyons, W.G.; Mikkelsen, P. M.; Neves, R.J.; Roper, C. F. E.; Rosenberg, G.; Roth, B.; Scheltema, A.; Thompson, F.G.; Vecchione, M.; Williams, J.D.

    1998-01-01

    This edition of Common and Scientific Names of Invertebrates from the United States and Canada: Mollusks represents the efforts of 15 molluscan taxonomic specialists in compiling a comprehensive checklist of the mollusks found in North America and Canada and their vernacular names. Built upon the success of the first edition, the authors have updated the nomenclature to reflect recent phylogenetic analyses and have included more than 300 new species.

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

    PubMed

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

    2009-09-01

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

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

    PubMed

    Woodley, Michael A

    2010-01-01

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

  2. 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

  3. Application of an indicator based on taxonomic relatedness of ciliated protozoan assemblages for marine environmental assessment.

    PubMed

    Xu, Henglong; Jiang, Yong; Al-Rasheid, Khaled A S; Al-Farraj, Saleh A; Song, Weibo

    2011-08-01

    Ciliated protozoa play important roles in aquatic ecosystems especially regarding their functions in micro-food web and have many advantages in environmental assessment compared with most other eukaryotic organisms. The aims of this study were focused on analyzing the application of an indicator based on taxonomic relatedness of ciliated protozoan assemblages for marine environmental assessment. The spatial taxonomic patterns and diversity measures in response to physical-chemical variables were studied based on data from samples collected during 1-year cycle in the semi-enclosed Jiaozhou Bay, northern China. The spatial patterns of ciliate communities were significantly correlated with the changes of environmental status. The taxonomic distinctness (Δ*) and the average taxonomic distinctness (Δ+) were significantly negatively correlated with the changes of nutrients (e.g., nitrate nitrogen and soluble active phosphate; P<0.05). Pairwise indices of Δ+ and the variation in taxonomic distinctness (Λ+) showed a decreasing trend of departure from the expected taxonomic breadth in response to the eutrophication stress and anthropogenic impact. The taxonomic relatedness (especially the pairwise Δ+ and Λ+) indices of ciliate communities are robust as an indicator with scientifically operational value in marine environmental assessment.

  4. A taxonomic guide to the fanworms (Sabellidae, Annelida) of Lizard Island, Great Barrier Reef, Australia, including new species and new records.

    PubMed

    Capa, María; Murray, Anna

    2015-09-18

    This comprehensive taxonomic work is the result of the study of fan worms (Sabellidae, Annelida) collected over the last 40 years from around the Lizard Island Archipelago, Great Barrier Reef, Australia. Some species described herein are commonly found in Lizard Island waters but had not previously been formally reported in the literature. Most species appear to be not particularly abundant, and few specimens have been collected despite the sampling effort in the area over this time period. After this study, the overall sabellid diversity of the archipelago has been greatly increased (by more than 650%). Before this revision, only four sabellid species had been recorded for Lizard Island, and in this paper we report 31 species, 13 of which belong to nominal species, six are formally described as new species (Euchone danieloi n. sp., Euchone glennoi n. sp., Jasmineira gustavoi n. sp., Megalomma jubata n. sp., Myxicola nana n. sp., and Paradialychone ambigua n. sp.), and the identity of 12 species is still unknown (those referred as cf. or sp.). Two species are newly recorded in Australia and two in Queensland. The invasive species Branchiomma bairdi is reported for the first time at Lizard Island. The genus Paradialychone is reported for Australia for the first time. Standardised descriptions, general photographs of live and/or preserved specimens and distribution data are provided for all species. New species descriptions are accompanied by detailed illustrations and exhaustive morphological information. A dichotomous key for sabellid identification is also included.

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

    PubMed

    Quiroz-Martínez, Benjamín; Salgado-Maldonado, Guillermo

    2013-01-01

    In this paper, we analyse the distributional patterns of adult helminth parasites of freshwater fishes with respect to the main hydrological basins of Mexico. We use the taxonomic distinctness and the variation in taxonomic distinctness to explore patterns of parasite diversity and how these patterns change between zoogeographical regions. We address questions about the factors that determine the variation of observed diversity of helminths between basins. We also investigate patterns of richness, taxonomic distinctness and distance decay of similarity amongst basins. Our analyses suggest that the evolution of the fauna of helminth parasites in Mexico is mostly dominated by independent host colonization events and that intra--host speciation could be a minor factor explaining the origin of this diversity. This paper points out a clear separation between the helminth faunas of northern--nearctic and southern--neotropical components in Mexican continental waters, suggesting the availability of two distinct taxonomic pools of parasites in Mexican drainage basins. Data identifies Mexican drainage basins as unities inhabited by freshwater fishes, hosting a mixture of neotropical and nearctic species, in addition, data confirms neotropical and neartic basins/helminth faunas. The neotropical basins of Mexico are host to a richest and more diversified helminth fauna, including more families, genera and species, compared to the less rich and less diverse helminth fauna in the nearctic basins. The present analysis confirms distance--decay as one of the important factors contributing to the patterns of diversity observed. The hypothesis that helminth diversity could be explained by the ichthyological diversity of the basin received no support from present analysis.

  6. Taxonomic Distinctness and Richness of Helminth Parasite Assemblages of Freshwater Fishes in Mexican Hydrological Basins

    PubMed Central

    Quiroz-Martínez, Benjamín; Salgado-Maldonado, Guillermo

    2013-01-01

    In this paper, we analyse the distributional patterns of adult helminth parasites of freshwater fishes with respect to the main hydrological basins of Mexico. We use the taxonomic distinctness and the variation in taxonomic distinctness to explore patterns of parasite diversity and how these patterns change between zoogeographical regions. We address questions about the factors that determine the variation of observed diversity of helminths between basins. We also investigate patterns of richness, taxonomic distinctness and distance decay of similarity amongst basins. Our analyses suggest that the evolution of the fauna of helminth parasites in Mexico is mostly dominated by independent host colonization events and that intra - host speciation could be a minor factor explaining the origin of this diversity. This paper points out a clear separation between the helminth faunas of northern - nearctic and southern - neotropical components in Mexican continental waters, suggesting the availability of two distinct taxonomic pools of parasites in Mexican drainage basins. Data identifies Mexican drainage basins as unities inhabited by freshwater fishes, hosting a mixture of neotropical and nearctic species, in addition, data confirms neotropical and neartic basins/helminth faunas. The neotropical basins of Mexico are host to a richest and more diversified helminth fauna, including more families, genera and species, compared to the less rich and less diverse helminth fauna in the nearctic basins. The present analysis confirms distance - decay as one of the important factors contributing to the patterns of diversity observed. The hypothesis that helminth diversity could be explained by the ichthyological diversity of the basin received no support from present analysis. PMID:24086342

  7. Trends in Taxonomic and Functional Composition of Soil Microbiome Along a Precipitation Gradient in Israel.

    PubMed

    Tripathi, Binu M; Moroenyane, Itumeleng; Sherman, Chen; Lee, Yoo Kyung; Adams, Jonathan M; Steinberger, Yosef

    2017-07-01

    The soil microbiome is important for the functioning of terrestrial ecosystems. However, the impacts of climate on taxonomic and functional diversity of soil microbiome are not well understood. A precipitation gradient along regional scale transects may offer a model setting for understanding the effect of climate on the composition and function of the soil microbiome. Here, we compared taxonomic and functional attributes of soil microorganisms in arid, semiarid, Mediterranean, and humid Mediterranean climatic conditions of Israel using shotgun metagenomic sequencing. We hypothesized that there would be a distinct taxonomic and functional soil community for each precipitation zone, with arid environments having lower taxonomic and functional diversity, greater relative abundance of stress response and sporulation-related genes, and lower relative abundance of genes related to nutrient cycling and degradation of complex organic compounds. As hypothesized, our results showed a distinct taxonomic and functional community in each precipitation zone, revealing differences in soil taxonomic and functional selection in the different climates. Although the taxonomic diversity remained similar across all sites, the functional diversity was-as hypothesized-lower in the arid environments, suggesting that functionality is more constrained in "extreme" environments. Also, with increasing aridity, we found a significant increase in genes related to dormancy/sporulation and a decrease in those related to nutrient cycling (genes related to nitrogen, potassium, and sulfur metabolism), respectively. However, relative abundance of genes related to stress response were lower in arid soils. Overall, these results indicate that climatic conditions play an important role in shaping taxonomic and functional attributes of soil microbiome. These findings have important implications for understanding the impacts of climate change (e.g., precipitation change) on structure and function of the

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

    PubMed

    Alsop, Eric B; Raymond, Jason

    2013-01-01

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

  9. New data on the stem and leaf anatomy of two conifers from the Lower Cretaceous of the Araripe Basin, northeastern Brazil, and their taxonomic and paleoecological implications

    PubMed Central

    Batista, Maria Edenilce Peixoto; Silva, Delmira da Costa; Sales, Marcos A. F.; Sá, Artur A.; Saraiva, Antônio A. F.; Loiola, Maria Iracema Bezerra

    2017-01-01

    Pseudofrenelopsis and Brachyphyllum are two conifers that were part of the Lower Cretaceous (Aptian) taphoflora of the Crato Formation, Araripe Basin, northeastern Brazil. The former genus includes, so far, P. capillata and indeterminate species, whilst the latter is mainly represented by B. obesum, the most common plant megafossil recovered from that stratigraphic unit. Here, the stem and leaf anatomy of Pseudofrenelopsis sp. and B. obesum specimens is revisited, including the first report of some epidermal and vascular traits for both taxa from the Crato Formation. Along with its paleoecological significance, the new data suggest the presence of more than one Pseudofrenelopsis species in the Aptian taphoflora of the Araripe Basin and further support the taxonomic placement of B. obesum within Araucariaceae. PMID:28257466

  10. Two new species of Oobius Trjapitzin (Hymenoptera, Encyrtidae) egg parasitoids of Agrilus spp. (Coleoptera, Buprestidae) from the USA, including a key and taxonomic notes on other congeneric Nearctic taxa

    PubMed Central

    Triapitsyn, Serguei V.; Petrice, Toby R.; Gates, Michael W.; Bauer, Leah S.

    2015-01-01

    Abstract Oobius Trjapitzin (Hymenoptera, Encyrtidae) species are egg parasitoids that are important for the biological control of some Buprestidae and Cerambycidae (Coleoptera). Two species, Oobius agrili Zhang & Huang and Oobius longoi (Siscaro), were introduced into North America for classical biocontrol and have successfully established. Two new native North American species that parasitize eggs of Agrilus spp. (Buprestidae) are described and illustrated from the USA: Oobius minusculus Triapitsyn & Petrice, sp. n. (Michigan), an egg parasitoid of both Agrilus subcinctus Gory on ash (Fraxinus spp.) and Agrilus egenus Gory on black locust (Robinia pseudoacacia L.) trees, and Oobius whiteorum Triapitsyn, sp. n. (Pennsylvania), an egg parasitoid of Agrilus anxius Gory on European white birch (Betula pendula Roth). A taxonomic key and notes on the Nearctic native and introduced Oobius species are also included. PMID:25931963

  11. 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

  12. 76 FR 34271 - Hewlett Packard, Global Parts Supply Chain, Global Product Life Cycles Management Unit, Including...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-13

    ... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-74,671] Hewlett Packard, Global Parts Supply Chain, Global Product Life Cycles Management Unit, Including Teleworkers Reporting to... Supply Chain, Global Product Life Cycles Management Unit, including teleworkers reporting to Houston...

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

    PubMed Central

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

    2012-01-01

    The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic and functional β-diversity among tropical estuarine fish communities, through space and time. We found extremely low functional β-diversity values among fish communities (<1.5%) despite high dissimilarity in species composition and species dominance. Additionally, in contrast to the high α and γ taxonomic diversities, α and γ functional diversities were very close to the minimal value. These patterns were caused by two dominant functional groups which maintained a similar functional structure over space and time, despite the strong dissimilarity in taxonomic structure along environmental gradients. Our findings suggest that taxonomic and functional β-diversity deserve to be quantified simultaneously since these two facets can show contrasting patterns and the differences can in turn shed light on community assembly rules. PMID:22792395

  14. Disentangling the drivers of taxonomic and phylogenetic beta diversities in disturbed and undisturbed subtropical forests

    PubMed Central

    Liu, Jinliang; Qian, Hong; Jin, Yi; Wu, Chuping; Chen, Jianhua; Yu, Shuquan; Wei, Xinliang; Jin, Xiaofeng; Liu, Jiajia; Yu, Mingjian

    2016-01-01

    Understanding the relative importance of dispersal limitation and environmental filtering processes in structuring the beta diversities of subtropical forests in human disturbed landscapes is still limited. Here we used taxonomic (TBD) and phylogenetic (PBD), including terminal PBD (PBDt) and basal PBD (PBDb), beta diversity indices to quantify the taxonomic and phylogenetic turnovers at different depths of evolutionary history in disturbed and undisturbed subtropical forests. Multiple linear regression model and distance-based redundancy analysis were used to disentangle the relative importance of environmental and spatial variables. Environmental variables were significantly correlated with TBD and PBDt metrics. Temperature and precipitation were major environmental drivers of beta diversity patterns, which explained 7–27% of the variance in TBD and PBDt, whereas the spatial variables independently explained less than 1% of the variation for all forests. The relative importance of environmental and spatial variables differed between disturbed and undisturbed forests (e.g., when Bray-Curtis was used as a beta diversity metric, environmental variable had a significant effect on beta diversity for disturbed forests but had no effect on undisturbed forests). We conclude that environmental filtering plays a more important role than geographical limitation and disturbance history in driving taxonomic and terminal phylogenetic beta diversity. PMID:27775021

  15. Disentangling the drivers of taxonomic and phylogenetic beta diversities in disturbed and undisturbed subtropical forests

    NASA Astrophysics Data System (ADS)

    Liu, Jinliang; Qian, Hong; Jin, Yi; Wu, Chuping; Chen, Jianhua; Yu, Shuquan; Wei, Xinliang; Jin, Xiaofeng; Liu, Jiajia; Yu, Mingjian

    2016-10-01

    Understanding the relative importance of dispersal limitation and environmental filtering processes in structuring the beta diversities of subtropical forests in human disturbed landscapes is still limited. Here we used taxonomic (TBD) and phylogenetic (PBD), including terminal PBD (PBDt) and basal PBD (PBDb), beta diversity indices to quantify the taxonomic and phylogenetic turnovers at different depths of evolutionary history in disturbed and undisturbed subtropical forests. Multiple linear regression model and distance-based redundancy analysis were used to disentangle the relative importance of environmental and spatial variables. Environmental variables were significantly correlated with TBD and PBDt metrics. Temperature and precipitation were major environmental drivers of beta diversity patterns, which explained 7-27% of the variance in TBD and PBDt, whereas the spatial variables independently explained less than 1% of the variation for all forests. The relative importance of environmental and spatial variables differed between disturbed and undisturbed forests (e.g., when Bray-Curtis was used as a beta diversity metric, environmental variable had a significant effect on beta diversity for disturbed forests but had no effect on undisturbed forests). We conclude that environmental filtering plays a more important role than geographical limitation and disturbance history in driving taxonomic and terminal phylogenetic beta diversity.

  16. Contrasting responses of functional diversity to major losses in taxonomic diversity.

    PubMed

    Edie, Stewart M; Jablonski, David; Valentine, James W

    2018-01-23

    Taxonomic diversity of benthic marine invertebrate shelf species declines at present by nearly an order of magnitude from the tropics to the poles in each hemisphere along the latitudinal diversity gradient (LDG), most steeply along the western Pacific where shallow-sea diversity is at its tropical maximum. In the Bivalvia, a model system for macroevolution and macroecology, this taxonomic trend is accompanied by a decline in the number of functional groups and an increase in the evenness of taxa distributed among those groups, with maximum functional evenness (FE) in polar waters of both hemispheres. In contrast, analyses of this model system across the two era-defining events of the Phanerozoic, the Permian-Triassic and Cretaceous-Paleogene mass extinctions, show only minor declines in functional richness despite high extinction intensities, resulting in a rise in FE owing to the persistence of functional groups. We hypothesize that the spatial decline of taxonomic diversity and increase in FE along the present-day LDG primarily reflect diversity-dependent factors, whereas retention of almost all functional groups through the two mass extinctions suggests the operation of diversity-independent factors. Comparative analyses of different aspects of biodiversity thus reveal strongly contrasting biological consequences of similarly severe declines in taxonomic diversity and can help predict the consequences for functional diversity among different drivers of past, present, and future biodiversity loss.

  17. 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…

  18. Chinese deaf adolescents' free recall of taxonomic, slot-filler, and thematic categories.

    PubMed

    Li, Degao; Zhang, Jijia

    2009-08-01

    Four experiments were conducted to show that deaf adolescents tended to process information in different ways from hearing adolescents. Memorizing items sequentially shown on computer screens under the control of their articulators' movements, deaf adolescents tended to treat items that cohered as taxonomic, thematic, or slot-filler categories as isolated pieces of information. Having to perceive information by means of sign language, however, their achievements were not worse than those of hearing adolescents anymore, no matter whether the stimuli were presented as words or pictures. They could not only utilize categories relations to help memorize categories exemplars but were relatively better aware of slot-filler or thematic than taxonomic relations as well, suggesting that they had a relatively delayed development of taxonomic category representations in comparison with hearing adolescents.

  19. TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

    PubMed Central

    Diaz, Naryttza N; Krause, Lutz; Goesmann, Alexander; Niehaus, Karsten; Nattkemper, Tim W

    2009-01-01

    Background Metagenomics, or the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment, promises direct access to the "unculturable majority". This emerging field offers the potential to lay solid basis on our understanding of the entire living world. However, the taxonomic classification is an essential task in the analysis of metagenomics data sets that it is still far from being solved. We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning. Results Our novel strategy was extensively evaluated using the leave-one-out cross validation strategy on fragments of variable length (800 bp – 50 Kbp) from 373 completely sequenced genomes. TACOA is able to classify genomic fragments of length 800 bp and 1 Kbp with high accuracy until rank class. For longer fragments ≥ 3 Kbp accurate predictions are made at even deeper taxonomic ranks (order and genus). Remarkably, TACOA also produces reliable results when the taxonomic origin of a fragment is not represented in the reference set, thus classifying such fragments to its known broader taxonomic class or simply as "unknown". We compared the classification accuracy of TACOA with the latest intrinsic classifier PhyloPythia using 63 recently published complete genomes. For fragments of length 800 bp and 1 Kbp the overall accuracy of TACOA is higher than that obtained by PhyloPythia at all taxonomic ranks. For all fragment lengths, both methods achieved comparable high specificity results up to rank class and low false negative rates are also obtained. Conclusion An accurate multi-class taxonomic classifier was developed for environmental genomic fragments. TACOA can predict with high reliability the taxonomic origin of genomic fragments as short as 800 bp. The proposed method is transparent, fast, accurate and the reference

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

    PubMed

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

    2014-11-01

    Studies of insect assemblages are suited to the simultaneous DNA-based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR-amplification bias, as well as sufficient sequence divergence to resolve species. We used in silico PCR to compare the taxonomic coverage and resolution of newly designed insect metabarcodes (targeting 16S) with that of existing markers [16S and cytochrome oxidase c subunit I (COI)] and then compared their efficiency in vitro. Existing metabarcoding primers amplified in silico <75% of insect species with complete mitochondrial genomes available, whereas new primers targeting 16S provided >90% coverage. Furthermore, metabarcodes targeting COI appeared to introduce taxonomic PCR-amplification bias, typically amplifying a greater percentage of Lepidoptera and Diptera species, while failing to amplify certain orders in silico. To test whether bias predicted in silico was observed in vitro, we created an artificial DNA blend containing equal amounts of DNA from 14 species, representing 11 insect orders and one arachnid. We PCR-amplified the blend using five primer sets, targeting either COI or 16S, with high-throughput amplicon sequencing yielding more than 6 million reads. In vitro results typically corresponded to in silico PCR predictions, with newly designed 16S primers detecting 11 insect taxa present, thus providing equivalent or better taxonomic coverage than COI metabarcodes. Our results demonstrate that in silico PCR is a useful tool for predicting taxonomic bias in mixed template PCR and that researchers should be wary of potential bias when selecting metabarcoding markers. © 2014 John Wiley & Sons Ltd.

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

    PubMed Central

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

    2016-01-01

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

  2. 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

  3. 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

  4. Evaluative and Taxonomic Encoding in Children's Memory.

    ERIC Educational Resources Information Center

    Kail, Robert V., Jr.; Schroll, John T.

    Two experiments were conducted to investigate the development of evaluative and taxonomic encoding in children's memory. The task used was a modification of the Wickens short-term memory task in which subjects' recall of words is tested following a distraction task. The first experiment found that 11-year-old children, but not 8-year-old children,…

  5. taxonomic diversity and pest vulnerability in street tree assemblages

    EPA Pesticide Factsheets

    Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to what extent diversity reduces vulnerability to polyphagous (i.e. generalist) pests. Drawing on field data from seven communities in metropolitan Cincinnati, Ohio, USA, we tested the hypothesis that communities with higher diversity would exhibit lower vulnerability to the polyphagous Asian longhorned beetle, which currently threatens the region. Based on street tree compositions and the beetle??s host preferences, Asian longhorned beetle threatened up to 35.6% of individual street trees and 47.5% of the total basal area across the study area, but we did not see clear connections between taxonomic diversity and beetle vulnerability among study communities. For example, the city of Fairfield was among the least diverse communities but had the lowest proportion of trees vulnerable to Asian longhorned beetle, whereas the city of Wyoming exhibited high diversity and high vulnerability. On the other hand, Forest Park aligned with our original hypothesis, as it was characterised by low diversity and high vulnerability. Our results demonstrate that relatively high taxonomic diversity in street tree assemblages does not necessarily lead to reduced vulnerability to a polyphagous pest. Considering the threats posed by polyphagous pests, selecting a set of relatively pest resistant trees known to perform well in ur

  6. Pigment Fluorescence Signatures as an Index to the Taxonomic Structure of Phytoplankton Communities

    DTIC Science & Technology

    2001-09-30

    1 Pigment Fluorescence Signatures as an Index to the Taxonomic Structure of Phytoplankton Communities Dr. Gary Hitchcock Marine Biology and... Fisheries Rosenstiel School of Marine and Atmospheric Science 4600 Rickenbacker Cswy. Miami, FL 3149 phone: (305) 361-4926 fax: (305) 361-4765...ghitchcock.html LONG-TERM GOALS The spatial distribution and taxonomic composition of phytoplankton communities are important determinants of the

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

    PubMed

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

    2013-08-15

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

  8. Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

    PubMed Central

    Dröge, J.; Gregor, I.; McHardy, A. C.

    2015-01-01

    Motivation: Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows identifying the sequenced community members and reconstructing taxonomic bins with sequence data for the individual taxa. For the massive datasets generated by next-generation sequencing technologies, this cannot be performed with de-novo phylogenetic inference methods. We describe an algorithm and the accompanying software, taxator-tk, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities. Results: Taxator-tk was precise in its taxonomic assignment across all ranks and taxa for a range of evolutionary distances and for short as well as for long sequences. In addition to the taxonomic binning of metagenomes, it is well suited for profiling microbial communities from metagenome samples because it identifies bacterial, archaeal and eukaryotic community members without being affected by varying primer binding strengths, as in marker gene amplification, or copy number variations of marker genes across different taxa. Taxator-tk has an efficient, parallelized implementation that allows the assignment of 6 Gb of sequence data per day on a standard multiprocessor system with 10 CPU cores and microbial RefSeq as the genomic reference data. Availability and implementation: Taxator-tk source and binary program files are publicly available at http://algbio.cs.uni-duesseldorf.de/software/. Contact: Alice.McHardy@uni-duesseldorf.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25388150

  9. Sympatry in the Culicoides variipennis complex (Diptera: Ceratopogonidae): a taxonomic reassessment.

    PubMed

    Holbrook, F R; Tabachnick, W J; Schmidtmann, E T; McKinnon, C N; Bobian, R J; Grogan, W L

    2000-01-01

    We report sympatry among larval populations of the Culicoides variipennis complex in widespread and diverse aquatic habitats throughout the United States. Six sites in California, Nevada, New Mexico, and Texas were co-inhabited by C. v. occidentalis and C. v. sonorensis, whereas 8 sites in Florida, Georgia, Louisiana, Maryland, and Texas were co-occupied by C. v. sonorensis and C. v. variipennis. No intermediate forms were identified either electrophoretically or morphologically in adults reared from field-collected larvae and pupae. The absence of intergrades in zones of sympatry represents sufficient evidence to confirm species status for Culicoides variipennis (Coquillett) and Culicoides occidentalis Wirth & Jones, and to elevate Culicoides sonorensis to species rank (NEW STATUS). Culicoides v. albertensis Wirth & Jones is a synonym of C. sonorensis (NEW SYNONYMY); C. v. australis Wirth & Jones also is confirmed as a synonym of C. sonorensis. We also demonstrated a correlation between population taxonomic status as determined by electrophoresis and adult morphology.

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

    PubMed Central

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

    2012-01-01

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

  11. 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

  12. 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…

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

    PubMed

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

    2015-06-01

    The subphylum Ustilaginomycotina (Basidiomycota, Fungi) comprises mainly plant pathogenic fungi (smuts). Some of the lineages possess cultivable unicellular stages that are usually classified as yeast or yeast-like species in a largely artificial taxonomic system which is independent from and largely incompatible with that of the smut fungi. Here we performed phylogenetic analyses based on seven genes including three nuclear ribosomal RNA genes and four protein coding genes to address the molecular phylogeny of the ustilaginomycetous yeast species and their filamentous counterparts. Taxonomic revisions were proposed to reflect this phylogeny and to implement the 'One Fungus = One Name' principle. The results confirmed that the yeast-containing classes Malasseziomycetes, Moniliellomycetes and Ustilaginomycetes are monophyletic, whereas Exobasidiomycetes in the current sense remains paraphyletic. Four new genera, namely Dirkmeia gen. nov., Kalmanozyma gen. nov., Golubevia gen. nov. and Robbauera gen. nov. are proposed to accommodate Pseudozyma and Tilletiopsis species that are distinct from the other smut taxa and belong to clades that are separate from those containing type species of the hitherto described genera. Accordingly, new orders Golubeviales ord. nov. with Golubeviaceae fam. nov. and Robbauerales ord. nov. with Robbaueraceae fam. nov. are proposed to accommodate the sisterhood of Golubevia gen. nov. and Robbauera gen. nov. with other orders of Exobasidiomycetes. The majority of the remaining anamorphic yeast species are transferred to corresponding teleomorphic genera based on strongly supported phylogenetic affinities, resulting in the proposal of 28 new combinations. The taxonomic status of a few Pseudozyma species remains to be determined because of their uncertain phylogenetic positions. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the single-species lineages that are temporarily maintained.

  14. 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

  15. Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

    USGS Publications Warehouse

    Strecker, Angela L.; 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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2017-04-01

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

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

    PubMed Central

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

    2018-01-01

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

  20. Distinct progression of the deterioration of thematic and taxonomic links in natural and manufactured objects in Alzheimer's disease.

    PubMed

    Simoes Loureiro, Isabelle; Lefebvre, Laurent

    2016-10-01

    Taxonomic and thematic relationships are core elements of lexico-semantic networks. However, the weight of both links differs in semantic memory, with distinct support for natural and manufactured objects: natural objects tend to be more taxonomically identified while manufactured objects benefit more from the underlying thematic relationships. Alzheimer's disease (AD) causes early semantic memory impairment characterized by a category-specific deterioration, where natural objects are more sensitive to the disease than manufactured objects. However, relatively few studies have examined the progressive deterioration of specific thematic versus taxonomic relations in both categories of objects in AD. To better understand semantic memory disorganization in AD and analyze the potential interaction effect between the category (natural/manufactured), the condition (thematic/taxonomic) and AD, we will investigate the lexico-semantic network in 82 AD patients (divided into three groups depending on their global cognitive deterioration and their performance in a preliminary semantic knowledge questionnaire (mild (AD1), moderate (AD2) and advanced (AD3) stages of semantic knowledge alteration). The experimental protocol contains two tasks: an implicit semantic priming paradigm and an explicit card-sorting test that uses the same items, equally divided between natural and manufactured objects. Results show a distinct taxonomic and thematic evolution pattern with early taxonomic deterioration. Natural objects are also more vulnerable to the disease. Lastly, there is an interaction effect between the category and the condition in the priming task indicating that natural objects are more taxonomically organized and manufactured objects benefit more from both thematic and taxonomic organizations, reinforcing the idea of the robustness of this category. The theoretical accounts of these observations will be discussed in detail. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. 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)

  2. 76 FR 41525 - Hewlett Packard Global Parts Supply Chain, Global Product Life Cycles Management Unit Including...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-14

    ... Parts Supply Chain, Global Product Life Cycles Management Unit Including Teleworkers Reporting to... workers of Hewlett Packard, Global Parts Supply Chain, Global Product Life Cycles Management Unit...). Since eligible workers of Hewlett Packard, Global Parts Supply Chain, Global Product Life Cycles...

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

    PubMed

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

    2008-07-07

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

  4. Taxonomic re-evaluation of black koji molds.

    PubMed

    Hong, Seung-Beom; Yamada, Osamu; Samson, Robert A

    2014-01-01

    Black koji molds including its albino mutant, the white koji mold, have been widely used for making the distilled spirit shochu in Northeast Asia because they produce citric acid which prevents undesirable contamination from bacteria. Since Inui reported Aspergillus luchuensis from black koji in Okinawa in 1901, many fungal names associated with black koji molds were reported. However, some species are similar and differentiation between species is difficult. Fungal taxonomists tried to arrange a taxonomic system for black koji molds, but the results were not clear. Recently, multi-locus sequence typing has been successfully used to taxonomy of black Aspergillus. According to β-tubulin and calmodulin gene sequences, black koji molds can be subdivided in three species, A. luchuensis, Aspergillus niger, and Aspergillus tubingensis. Aspergillus awamori, Aspergillus kawachii, Aspergillus inuii, Aspergillus nakazawai, and Aspergillus coreanus are synonyms of A. luchuensis, Aspergillus batatae, Aspergillus aureus (or Aspergillus foetidus), Aspergillus miyakoensis, and Aspergillus usamii (including A. usamii mut. shirousamii) are synonyms of A. niger and Aspergillus saitoi and A. saitoi var. kagoshimaensis are synonyms of A. tubingensis. A. luchuensis mut. kawachii was suggested particular names for A. kawachii because of their industrial importance. The history and modern taxonomy of black koji molds is further discussed.

  5. Rotational Study of Ambiguous Taxonomic Classified Asteroids

    NASA Astrophysics Data System (ADS)

    Linder, Tyler R.; Sanchez, Rick; Wuerker, Wolfgang; Clayson, Timothy; Giles, Tucker

    2017-01-01

    The Sloan Digital Sky Survey (SDSS) moving object catalog (MOC4) provided the largest ever catalog of asteroid spectrophotometry observations. Carvano et al. (2010), while analyzing MOC4, discovered that individual observations of asteroids which were observed multiple times did not classify into the same photometric-based taxonomic class. A small subset of those asteroids were classified as having both the presence and absence of a 1um silicate absorption feature. If these variations are linked to differences in surface mineralogy, the prevailing assumption that an asteroid’s surface composition is predominantly homogenous would need to be reexamined. Furthermore, our understanding of the evolution of the asteroid belt, as well as the linkage between certain asteroids and meteorite types may need to be modified.This research is an investigation to determine the rotational rates of these taxonomically ambiguous asteroids. Initial questions to be answered:Do these asteroids have unique or nonstandard rotational rates?Is there any evidence in their light curve to suggest an abnormality?Observations were taken using PROMPT6 a 0.41-m telescope apart of the SKYNET network at Cerro Tololo Inter-American Observatory (CTIO). Observations were calibrated and analyzed using Canopus software. Initial results will be presented at AAS.

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

    PubMed

    Cornman, R Scott; Otto, Clint R V; Iwanowicz, Deborah; Pettis, Jeffery S

    2015-01-01

    Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5' of ITS1 and the 3' of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower "read2" quality, further

  7. 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

  8. 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

  9. Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

    PubMed Central

    Lu, Hsiao-Pei; Yeh, Yi-Chun; Sastri, Akash R; Shiah, Fuh-Kwo; Gong, Gwo-Ching; Hsieh, Chih-hao

    2016-01-01

    We propose a method for detecting evolutionary forces underlying community assembly by quantifying the strength of community–environment relationships hierarchically along taxonomic ranks. This approach explores the potential role of phylogenetic conservatism on habitat preferences: wherein, phylogenetically related taxa are expected to exhibit similar environmental responses. Thus, when niches are conserved, broader taxonomic classification should not diminish the strength of community–environment relationships and may even yield stronger associations by summarizing occurrences and abundances of ecologically equivalent finely resolved taxa. In contrast, broader taxonomic classification should weaken community–environment relationships when niches are under great divergence (that is, by combining finer taxa with distinct environmental responses). Here, we quantified the strength of community–environment relationships using distance-based redundancy analysis, focusing on soil and seawater prokaryotic communities. We considered eight case studies (covering a variety of sampling scales and sequencing strategies) and found that the variation in community composition explained by environmental factors either increased or remained constant with broadening taxonomic resolution from species to order or even phylum level. These results support the niche conservatism hypothesis and indicate that broadening taxonomic resolution may strengthen niche-related signals by removing uncertainty in quantifying spatiotemporal distributions of finely resolved taxa, reinforcing the current notion of ecological coherence in deep prokaryotic branches. PMID:27177191

  10. 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.

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

    PubMed

    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.

  12. 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.

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

    PubMed

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

    2015-10-01

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

  14. A "taxonomic affidavit": Why it is needed?

    PubMed

    Por, Francis Dov

    2007-06-01

    Imprecise and faulty taxonomic identification of the biological objects of many ecological and experimental studies renders these studies irreproducible. Incomplete identification to the species level and excessive use of vernacular species names are additional problems. Good science must be able to be falsified. I recommend that publications and granting agencies use and mention the names of the zoologists or botanists who identified the species. Voucher specimens should be marked and deposited in scientific museums for future checking.

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

    Treesearch

    M. Renee Bellinger; Susan M. Haig; Eric D. Forsmann; Thomas D. Mullins

    2005-01-01

    Taxonomic relationships among red tree voles (Phenacomys longicaudus longicaudus, P. I. 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...

  16. Sea Fog Research in the United Kingdom and United States: A Historical Essay Including Outlook.

    NASA Astrophysics Data System (ADS)

    Lewis, J. M.; Korain, D.; Redmond, K. T.

    2004-03-01

    A historical review of research on sea fog is presented. The period of interest is essentially the twentieth century, beginning with the celebrated work of G. I. Taylor in the aftermath of the Titanic tragedy. It has been argued that relative maxima in fog frequency over the North Atlantic (including the Brit-ish Isles and the Grand Banks of Newfoundland) and the North Pacific (including the U.S. West Coast) has led to major contributions by scientists in England and the United States. The early work (pre World War II) tended to be phenomenological—that is, conceptual with broad inference from statistical summaries. Yet, this early work laid the foundation for the numerical modeling that came with the advent of computers in the postwar period. The subtleties associated with sea fog formation and maintenance are explored by analyzing some of the results from the numerical simulations. The essay ends with a speculative view on our prospects for a more complete understanding of sea fog in light of the earlier contributions.

  17. A case study for effects of operational taxonomic units from intracellular endoparasites and ciliates on the eukaryotic phylogeny: phylogenetic position of the haptophyta in analyses of multiple slowly evolving genes.

    PubMed

    Nozaki, Hisayoshi; Yang, Yi; Maruyama, Shinichiro; Suzaki, Toshinobu

    2012-01-01

    Recent multigene phylogenetic analyses have contributed much to our understanding of eukaryotic phylogeny. However, the phylogenetic positions of various lineages within the eukaryotes have remained unresolved or in conflict between different phylogenetic studies. These phylogenetic ambiguities might have resulted from mixtures or integration from various factors including limited taxon sampling, missing data in the alignment, saturations of rapidly evolving genes, mixed analyses of short- and long-branched operational taxonomic units (OTUs), intracellular endoparasite and ciliate OTUs with unusual substitution etc. In order to evaluate the effects from intracellular endoparasite and ciliate OTUs co-analyzed on the eukaryotic phylogeny and simplify the results, we here used two different sets of data matrices of multiple slowly evolving genes with small amounts of missing data and examined the phylogenetic position of the secondary photosynthetic chromalveolates Haptophyta, one of the most abundant groups of oceanic phytoplankton and significant primary producers. In both sets, a robust sister relationship between Haptophyta and SAR (stramenopiles, alveolates, rhizarians, or SA [stramenopiles and alveolates]) was resolved when intracellular endoparasite/ciliate OTUs were excluded, but not in their presence. Based on comparisons of character optimizations on a fixed tree (with a clade composed of haptophytes and SAR or SA), disruption of the monophyly between haptophytes and SAR (or SA) in the presence of intracellular endoparasite/ciliate OTUs can be considered to be a result of multiple evolutionary reversals of character positions that supported the synapomorphy of the haptophyte and SAR (or SA) clade in the absence of intracellular endoparasite/ciliate OTUs.

  18. Conservation status of freshwater gastropods of Canada and the United States

    USGS Publications Warehouse

    Johnson, Paul D.; Bogan, Arthur E.; Brown, Kenneth M.; Burkhead, Noel M.; Cordeiro, James R.; Garner, Jeffrey T.; Hartfield, Paul D.; Lepitzki, Dwayne A.; Mackie, Gerry L.; Pip, Eva; Tarpley, Thomas A.; Tiemann, Jeremy S.; Whelan, Nathan V.; Strong, Ellen E.

    2013-01-01

    This is the first American Fisheries Society conservation assessment of freshwater gastropods (snails) from Canada and the United States by the Gastropod Subcommittee (Endangered Species Committee). This review covers 703 species representing 16 families and 93 genera, of which 67 species are considered extinct, or possibly extinct, 278 are endangered, 102 are threatened, 73 are vulnerable, 157 are currently stable, and 26 species have uncertain taxonomic status. Of the entire fauna, 74% of gastropods are imperiled (vulnerable, threatened, endangered) or extinct, which exceeds imperilment levels in fishes (39%) and crayfishes (48%) but is similar to that of mussels (72%). Comparison of modern to background extinction rates reveals that gastropods have the highest modern extinction rate yet observed, 9,539 times greater than background rates. Gastropods are highly susceptible to habitat loss and degradation, particularly narrow endemics restricted to a single spring or short stream reaches. Compilation of this review was hampered by a paucity of current distributional information and taxonomic uncertainties. Although research on several fronts including basic biology, physiology, conservation strategies, life history, and ecology are needed, systematics and curation of museum collections and databases coupled with comprehensive status surveys (geographic limits, threat identification) are priorities.

  19. Taxonomic Knowledge of Children with and without Cochlear Implants

    ERIC Educational Resources Information Center

    Lund, Emily; Dinsmoor, Jessica

    2016-01-01

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

  20. 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

  1. A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy.

    PubMed

    Gao, Xiang; Lin, Huaiying; Revanna, Kashi; Dong, Qunfeng

    2017-05-10

    Species-level classification for 16S rRNA gene sequences remains a serious challenge for microbiome researchers, because existing taxonomic classification tools for 16S rRNA gene sequences either do not provide species-level classification, or their classification results are unreliable. The unreliable results are due to the limitations in the existing methods which either lack solid probabilistic-based criteria to evaluate the confidence of their taxonomic assignments, or use nucleotide k-mer frequency as the proxy for sequence similarity measurement. We have developed a method that shows significantly improved species-level classification results over existing methods. Our method calculates true sequence similarity between query sequences and database hits using pairwise sequence alignment. Taxonomic classifications are assigned from the species to the phylum levels based on the lowest common ancestors of multiple database hits for each query sequence, and further classification reliabilities are evaluated by bootstrap confidence scores. The novelty of our method is that the contribution of each database hit to the taxonomic assignment of the query sequence is weighted by a Bayesian posterior probability based upon the degree of sequence similarity of the database hit to the query sequence. Our method does not need any training datasets specific for different taxonomic groups. Instead only a reference database is required for aligning to the query sequences, making our method easily applicable for different regions of the 16S rRNA gene or other phylogenetic marker genes. Reliable species-level classification for 16S rRNA or other phylogenetic marker genes is critical for microbiome research. Our software shows significantly higher classification accuracy than the existing tools and we provide probabilistic-based confidence scores to evaluate the reliability of our taxonomic classification assignments based on multiple database matches to query sequences. Despite

  2. 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.

  3. Biodiversity Analysis of Forest Litter Ant Assemblages in the Wayanad Region of Western Ghats Using Taxonomic and Conventional Diversity Measures

    PubMed Central

    Anu, Anto; Sabu, Thomas K.

    2007-01-01

    The diversity of litter ant assemblages in evergreen, deciduous and Shola evergreen (Shola) forest vegetation types of the Wayanad region of the Western Ghats was assessed employing conventional and taxonomic diversity indices. Non-dependence on quantitative data and the ability to relate the phylogenetic structure of assemblages with ecological conditions of the habitat, and to ascertain priorities for conservation of habitats, makes non-parametric taxonomic diversity measures, such as variation in taxonomic distinctness Λ+ and average taxonomic distinctness Δ+, highly useful tools for assessment of litter ant biodiversity. Although Δ+ values saturated leading to closer values for the 3 litter ant assemblages, Λ+ proved to be a more dependable index. Evenness in taxonomic spread was high in ant assemblages in deciduous forests and low in evergreen forests compared to the regional master list. Low Λ+ of ant assemblage in deciduous forests indicates that among the 3 forest vegetation types, deciduous forests provided the most favorable habitat conditions for litter ants. Low evenness, as is indicated by Λ+ in evergreen forests, was attributed to the presence of a group of taxonomically closely related ant assemblage more adapted to prevail in moist and wet ecological conditions. PMID:20334594

  4. Antifungal bacteria on woodland salamander skin exhibit high taxonomic diversity and geographic variability

    USGS Publications Warehouse

    Muletz-Wolz, Carly R.; DiRenzo, Graziella V.; Yarwood, Stephanie A.; Grant, Evan H. Campbell; Fleischer, Robert C.; Lips, Karen R.

    2017-01-01

    Diverse bacteria inhabit amphibian skin; some of those bacteria inhibit growth of the fungal pathogen Batrachochytrium dendrobatidis. Yet there has been no systematic survey of anti-B. dendrobatidis bacteria across localities, species, and elevations. This is important given geographic and taxonomic variations in amphibian susceptibility to B. dendrobatidis. Our collection sites were at locations within the Appalachian Mountains where previous sampling had indicated low B. dendrobatidis prevalence. We determined the numbers and identities of anti-B. dendrobatidis bacteria on 61 Plethodon salamanders (37 P. cinereus, 15 P. glutinosus, 9 P. cylindraceus) via culturing methods and 16S rRNA gene sequencing. We sampled co-occurring species at three localities and sampled P. cinereus along an elevational gradient (700 to 1,000 meters above sea level [masl]) at one locality. We identified 50 anti-B. dendrobatidis bacterial operational taxonomic units (OTUs) and found that the degree of B. dendrobatidis inhibition was not correlated with relatedness. Five anti-B. dendrobatidis bacterial strains occurred on multiple amphibian species at multiple localities, but none were shared among all species and localities. The prevalence of anti-B. dendrobatidis bacteria was higher at Shenandoah National Park (NP), VA, with 96% (25/26) of salamanders hosting at least one anti-B. dendrobatidis bacterial species compared to 50% (7/14) at Catoctin Mountain Park (MP), MD, and 38% (8/21) at Mt. Rogers National Recreation Area (NRA), VA. At the individual level, salamanders at Shenandoah NP had more anti-B. dendrobatidis bacteria per individual (μ = 3.3) than those at Catoctin MP (μ = 0.8) and at Mt. Rogers NRA (μ = 0.4). All salamanders tested negative for B. dendrobatidis. Anti-B. dendrobatidis bacterial species are diverse in central Appalachian Plethodon salamanders, and their distribution varied geographically. The antifungal bacterial species that we identified may play a protective

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

  6. Distribution of taxonomic classes and the compositional structure of the asteroid belt

    NASA Technical Reports Server (NTRS)

    Gradie, Jonathan C.; Chapman, Clark R.; Tedesco, Edward F.

    1989-01-01

    This paper reviews previous studies on the distribution of the asteroid taxonomic classes and analyzes the techniques, results, and interpretations of these studies, with special attention given to the strong and weak points of these studies and the important caveat for their interpretation. It is concluded that, in spite of the differences in class definition, the rather ordered heliocentric distribution of the composition is real and must be due to either primordial, evolutionary, or dynamical processes, or to a combination of all three. In general, the distribution of asteroid taxonomic classes is characterized by moderate-albedo asteroids dominant in the inner asteroid belt, and low-albedo asteroids prevalent in the outer belt and beyond.

  7. 40 CFR 60.1565 - What subcategories of small municipal waste combustion units must I include in my State plan?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... waste combustion units must I include in my State plan? 60.1565 Section 60.1565 Protection of... NEW STATIONARY SOURCES Emission Guidelines and Compliance Times for Small Municipal Waste Combustion... of small municipal waste combustion units must I include in my State plan? This subpart specifies...

  8. 40 CFR 60.1565 - What subcategories of small municipal waste combustion units must I include in my State plan?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... waste combustion units must I include in my State plan? 60.1565 Section 60.1565 Protection of... NEW STATIONARY SOURCES Emission Guidelines and Compliance Times for Small Municipal Waste Combustion... of small municipal waste combustion units must I include in my State plan? This subpart specifies...

  9. 40 CFR 60.1565 - What subcategories of small municipal waste combustion units must I include in my State plan?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... waste combustion units must I include in my State plan? 60.1565 Section 60.1565 Protection of... NEW STATIONARY SOURCES Emission Guidelines and Compliance Times for Small Municipal Waste Combustion... of small municipal waste combustion units must I include in my State plan? This subpart specifies...

  10. 40 CFR 60.1565 - What subcategories of small municipal waste combustion units must I include in my State plan?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... waste combustion units must I include in my State plan? 60.1565 Section 60.1565 Protection of... NEW STATIONARY SOURCES Emission Guidelines and Compliance Times for Small Municipal Waste Combustion... of small municipal waste combustion units must I include in my State plan? This subpart specifies...

  11. 40 CFR 60.1565 - What subcategories of small municipal waste combustion units must I include in my State plan?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... waste combustion units must I include in my State plan? 60.1565 Section 60.1565 Protection of... NEW STATIONARY SOURCES Emission Guidelines and Compliance Times for Small Municipal Waste Combustion... of small municipal waste combustion units must I include in my State plan? This subpart specifies...

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2018-03-01

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

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

    PubMed Central

    Cornman, R. Scott; Otto, Clint R. V.; Iwanowicz, Deborah; Pettis, Jeffery S.

    2015-01-01

    Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality

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

    USGS Publications Warehouse

    Cornman, Robert S.; Otto, Clint R.; Iwanowicz, Deborah; Pettis, Jeffery S

    2015-01-01

    Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality

  16. Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

    PubMed Central

    Ren, Ze; Wang, Fang; Qu, Xiaodong; Elser, James J.; Liu, Yang; Chu, Limin

    2017-01-01

    Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages. PMID:29213266

  17. Macroinvertebrate Taxonomic and Functional Trait Compositions within Lotic Habitats Affected By River Restoration Practices

    NASA Astrophysics Data System (ADS)

    White, J. C.; Hill, M. J.; Bickerton, M. A.; Wood, P. J.

    2017-09-01

    The widespread degradation of lotic ecosystems has prompted extensive river restoration efforts globally, but many studies have reported modest ecological responses to rehabilitation practices. The functional properties of biotic communities are rarely examined within post-project appraisals, which would provide more ecological information underpinning ecosystem responses to restoration practices and potentially pinpoint project limitations. This study examines macroinvertebrate community responses to three projects which aimed to physically restore channel morphologies. Taxonomic and functional trait compositions supported by widely occurring lotic habitats (biotopes) were examined across paired restored and non-restored (control) reaches. The multivariate location (average community composition) of taxonomic and functional trait compositions differed marginally between control and restored reaches. However, changes in the amount of multivariate dispersion were more robust and indicated greater ecological heterogeneity within restored reaches, particularly when considering functional trait compositions. Organic biotopes (macrophyte stands and macroalgae) occurred widely across all study sites and supported a high alpha (within-habitat) taxonomic diversity compared to mineralogical biotopes (sand and gravel patches), which were characteristic of restored reaches. However, mineralogical biotopes possessed a higher beta (between-habitat) functional diversity, although this was less pronounced for taxonomic compositions. This study demonstrates that examining the functional and structural properties of taxa across distinct biotopes can provide a greater understanding of biotic responses to river restoration works. Such information could be used to better understand the ecological implications of rehabilitation practices and guide more effective management strategies.

  18. Benthic impacts of intertidal oyster culture, with consideration of taxonomic sufficiency.

    PubMed

    Forrest, Barrie M; Creese, Robert G

    2006-01-01

    An investigation of the impacts from elevated intertidal Pacific oyster culture in a New Zealand estuary showed enhanced sedimentation beneath culture racks compared with other sites. Seabed elevation beneath racks was generally lower than between them, suggesting that topographic patterns more likely result from a local effect of rack structures on hydrodynamic processes than from enhanced deposition. Compared with control sites, seabed sediments within the farm had a greater silt/clay and organic content, and a lower redox potential and shear strength. While a marked trend in macrofaunal species richness was not evident, species composition and dominance patterns were consistent with a disturbance gradient, with farm effects not evident 35 m from the perimeter of the racks. Of the environmental variables measured, sediment shear strength was most closely associated with the distribution and density of macrofauna, suggesting that human-induced disturbance from farming operations may have contributed to the biological patterns. To evaluate the taxonomic sufficiency needed to document impacts, aggregation to the family level based on Linnean classification was compared with an aggregation scheme based on ;general groups' identifiable with limited taxonomic expertise. Compared with species-level analyses, spatial patterns of impact were equally discernible at both aggregation levels used, provided density rather than presence/absence data were used. Once baseline conditions are established and the efficacy of taxonomic aggregation demonstrated, a ;general group' scheme provides an appropriate and increasingly relevant tool for routine monitoring.

  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.

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

    PubMed

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

    2016-01-01

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

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

    PubMed

    Foster, Zachary S L; Sharpton, Thomas J; Grünwald, Niklaus J

    2017-02-01

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

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

    PubMed Central

    Foster, Zachary S. L.; Sharpton, Thomas J.

    2017-01-01

    Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual. PMID:28222096

  3. A Guide to Basic Taxonomic Literature for the Genera of North American Chironomidae (Diptera) - Adults, Pupae, and Larvae. Bulletin No. 447.

    ERIC Educational Resources Information Center

    Simpson, Karl W.

    A generic list of North American Chironomidae (Diptera) is presented to help aquatic biologists quickly locate important taxonomic references for the adults, larvae, and pupae of each genus. The list (in chart format) includes literature published through 1981. When recent literature is available, older references are omitted, since the purpose of…

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

    PubMed

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

    2016-01-04

    The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  5. Taxonomic status of Myotis occultus

    USGS Publications Warehouse

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

  6. Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.

    PubMed

    Manor, Ohad; Borenstein, Elhanan

    2017-02-08

    Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases. To date, however, microbiome taxonomy and function have mostly been studied independently and the taxonomic drivers of functional imbalances have not been systematically identified. Here, we present FishTaco, an analytical and computational framework that integrates taxonomic and functional comparative analyses to accurately quantify taxon-level contributions to disease-associated functional shifts. Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbiome's functional capacity can be traced back to specific taxa. Furthermore, the set of taxa driving functional shifts and their contribution levels vary markedly between functions. We additionally find that similar functional imbalances in different diseases are driven by both disease-specific and shared taxa. Such integrated analysis of microbiome ecological and functional dynamics can inform future microbiome-based therapy, pinpointing putative intervention targets for manipulating the microbiome's functional capacity. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. A phylogeny for the pomatiopsidae (Gastropoda: Rissooidea): a resource for taxonomic, parasitological and biodiversity studies.

    PubMed

    Liu, Liang; Huo, Guan-Nan; He, Hong-Bin; Zhou, Benjiang; Attwood, Stephen W

    2014-02-18

    The Pomatiopsidae are reported from northern India into southern China and Southeast Asia, with two sub-families, the Pomatiopsinae (which include freshwater, amphibious, terrestrial and marine species) and the freshwater Triculinae. Both include species acting as intermediate host for species of the blood-fluke Schistosoma which cause a public health problem in East Asia. Also, with around 120 species, triculine biodiversity exceeds that of any other endemic freshwater molluscan fauna. Nevertheless, the origins of the Pomatiopsidae, the factors driving such a diverse radiation and aspects of their co-evolution with Schistosoma are not fully understood. Many taxonomic questions remain; there are problems identifying medically relevant species. The predicted range is mostly unsurveyed and the true biodiversity of the family is underestimated. Consequently, the aim of the study was to collect DNA-sequence data for as many pomatiopsid taxa as possible, as a first step in providing a resource for identification of epidemiologically significant species (by non-malacologists), for use in resolving taxonomic confusion and for testing phylogeographical hypotheses. The evolutionary radiation of the Triculinae was shown to have been rapid and mostly post late Miocene. Molecular dating indicated that the radiation of these snails was driven first by the uplift of the Himalaya and onset of a monsoon system, and then by late-Pliocene global warming. The status of Erhaia as Anmicolidae is supported. The genera Tricula and Neotricula are shown to be non-monophyletic and the tribe Jullieniini may be polyphyletic (based on convergent characters). Triculinae from northern Vietnam could be derived from Gammatricula of Fujian/Yunnan, China. The molecular dates and phylogenetic estimates in this study are consistent with an Australasian origin for the Pomatiopsidae and an East to West radiation via Oligocene Borneo-Philippines island hopping to Japan and then China (Triculinae arising

  8. A phylogeny for the pomatiopsidae (Gastropoda: Rissooidea): a resource for taxonomic, parasitological and biodiversity studies

    PubMed Central

    2014-01-01

    Background The Pomatiopsidae are reported from northern India into southern China and Southeast Asia, with two sub-families, the Pomatiopsinae (which include freshwater, amphibious, terrestrial and marine species) and the freshwater Triculinae. Both include species acting as intermediate host for species of the blood-fluke Schistosoma which cause a public health problem in East Asia. Also, with around 120 species, triculine biodiversity exceeds that of any other endemic freshwater molluscan fauna. Nevertheless, the origins of the Pomatiopsidae, the factors driving such a diverse radiation and aspects of their co-evolution with Schistosoma are not fully understood. Many taxonomic questions remain; there are problems identifying medically relevant species. The predicted range is mostly unsurveyed and the true biodiversity of the family is underestimated. Consequently, the aim of the study was to collect DNA-sequence data for as many pomatiopsid taxa as possible, as a first step in providing a resource for identification of epidemiologically significant species (by non-malacologists), for use in resolving taxonomic confusion and for testing phylogeographical hypotheses. Results The evolutionary radiation of the Triculinae was shown to have been rapid and mostly post late Miocene. Molecular dating indicated that the radiation of these snails was driven first by the uplift of the Himalaya and onset of a monsoon system, and then by late-Pliocene global warming. The status of Erhaia as Anmicolidae is supported. The genera Tricula and Neotricula are shown to be non-monophyletic and the tribe Jullieniini may be polyphyletic (based on convergent characters). Triculinae from northern Vietnam could be derived from Gammatricula of Fujian/Yunnan, China. Conclusions The molecular dates and phylogenetic estimates in this study are consistent with an Australasian origin for the Pomatiopsidae and an East to West radiation via Oligocene Borneo-Philippines island hopping to Japan and

  9. 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

  10. Taxonomic and systematic revisions to the North American Nimravidae (Mammalia, Carnivora)

    PubMed Central

    2016-01-01

    The Nimravidae is a family of extinct carnivores commonly referred to as “false saber-tooth cats.” Since their initial discovery, they have prompted difficulty in taxonomic assignments and number of valid species. Past revisions have only examined a handful of genera, while recent advances in cladistic and morphometric analyses have granted us additional avenues to answering questions regarding our understanding of valid nimravid taxa and their phylogenetic relationships. To resolve issues of specific validity, the phylogenetic species concept (PSC) was utilized to maintain consistency in diagnosing valid species, while simultaneously employing character and linear morphometric analyses for confirming the validity of taxa. Determined valid species and taxonomically informative characters were then employed in two differential cladistic analyses to create competing hypotheses of interspecific relationships. The results suggest the validity of twelve species and six monophyletic genera. The first in depth reviews of Pogonodon and Dinictis returned two valid species (P. platycopis, P. davisi) for the former, while only one for the latter (D. felina). The taxonomic validity of Nanosmilus is upheld. Two main clades with substantial support were returned for all cladistic analyses, the Hoplophoneini and Nimravini, with ambiguous positions relative to these main clades for the European taxa: Eofelis, Dinailurictis bonali, and Quercylurus major; and the North American taxa Dinictis and Pogonodon. Eusmilus is determined to represent a non-valid genus for North American taxa, suggesting non-validity for Old World nimravid species as well. Finally, Hoplophoneus mentalis is found to be a junior synonym of Hoplophoneus primaevus, while the validity of Hoplophoneus oharrai is reinstated. PMID:26893959

  11. 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…

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

    PubMed

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

    2015-01-01

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

  13. Amazon plant diversity revealed by a taxonomically verified species list.

    PubMed

    Cardoso, Domingos; Särkinen, Tiina; Alexander, Sara; Amorim, André M; Bittrich, Volker; Celis, Marcela; Daly, Douglas C; Fiaschi, Pedro; Funk, Vicki A; Giacomin, Leandro L; Goldenberg, Renato; Heiden, Gustavo; Iganci, João; Kelloff, Carol L; Knapp, Sandra; Cavalcante de Lima, Haroldo; Machado, Anderson F P; Dos Santos, Rubens Manoel; Mello-Silva, Renato; Michelangeli, Fabián A; Mitchell, John; Moonlight, Peter; de Moraes, Pedro Luís Rodrigues; Mori, Scott A; Nunes, Teonildes Sacramento; Pennington, Terry D; Pirani, José Rubens; Prance, Ghillean T; de Queiroz, Luciano Paganucci; Rapini, Alessandro; Riina, Ricarda; Rincon, Carlos Alberto Vargas; Roque, Nádia; Shimizu, Gustavo; Sobral, Marcos; Stehmann, João Renato; Stevens, Warren D; Taylor, Charlotte M; Trovó, Marcelo; van den Berg, Cássio; van der Werff, Henk; Viana, Pedro Lage; Zartman, Charles E; Forzza, Rafaela Campostrini

    2017-10-03

    Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.

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

    PubMed

    Hamedi, Javad; Mohammadipanah, Fatemeh

    2015-02-01

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

  15. 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...

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

    PubMed

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

    2013-01-01

    The long-recognized genus Gaura was shown recently to be deeply nested within one of two major clades of Oenothera. New molecular data indicate further taxonomic changes are necessary in Oenothera sect. Gaura. We make these changes here, including three new combinations, in advance of the Onagraceae treatment for the Flora of North America. The new phylogenetic studies show that several pairs of taxa treated as subspecies in the most recent revision by Raven and Gregory (1972) had independent origins within sect. Gaura, and are here elevated to species level (Oenothera nealleyi for Gaura suffulta subsp. nealleyi; Oenothera dodgeniana for Gaura neomexicana subsp. neomexicana; and Oenothera podocarpa for Gaura hexandra subsp. gracilis). Also, a nomenclatural problem in Oenothera sect. Calylophus is corrected by adopting the name Oenothera capillifolia Scheele for the species known previously, and nomenclaturally correct, as Calylophus berlandieri Spach. This problem necessitates a new combination Oenothera capillifolia subsp. berlandieri.

  17. 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

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

    PubMed

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

    2005-07-18

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

  19. 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…

  20. Different influences on lexical priming for integrative, thematic, and taxonomic relations

    PubMed Central

    Jones, Lara L.; Golonka, Sabrina

    2012-01-01

    Word pairs may be integrative (i.e., combination of two concepts into one meaningful entity; e.g., fruit—cake), thematically related (i.e., connected in time and place; e.g., party—cake), and/or taxonomically related (i.e., shared features and category co-members; e.g., muffin—cake). Using participant ratings and computational measures, we demonstrated distinct patterns across measures of similarity and co-occurrence, and familiarity for each relational construct in two different item sets. In a standard lexical decision task (LDT) with various delays between prime and target presentation (SOAs), target RTs and priming magnitudes were consistent across the three relations for both item sets. However, across the SOAs, there were distinct patterns among the three relations on some of the underlying measures influencing target word recognition (LSA, Google, and BEAGLE). These distinct patterns suggest different mechanisms of lexical priming and further demonstrate that integrative relations are distinct from thematic and taxonomic relations. PMID:22798950

  1. Taxonomic revision of Stagmatoptera Burmeister, 1838 (Mantodea: Mantidae, Stagmatopterinae).

    PubMed

    Rodrigues, Henrique Miranda; Cancello, Eliana Marques

    2016-11-01

    Stagmatoptera Burmeister, 1838 includes medium to large-sized (49.8-98.7mm) praying mantises distributed in the Neotropical region. They are characterized for having a central, circular spot on each forewing, and 2-4 carinae in the head's frontal shield. This study is an updated revision of the genus on the basis of type and non-type material deposited in various scientific collections from Europe and the Americas. The following nomenclatural procedures were conducted: Stagmatoptera nova is a new junior synonym of Stagmatoptera pia, Stagmatoptera ignota as the junior synonym of Stagmatoptera femoralis, and Stagmatoptera flavipennis is reinstated as the junior synonym of Stagmatoptera supplicaria. Two new species are described: Stagmatoptera diana Rodrigues sp. n. from Colombia and Venezuela, and Stagmatoptera cerdai Rodrigues sp. n. from Trinidad & Tobago and Venezuela. Stagmatoptera now includes 14 species, two of which (Stagmatoptera abdominalis and Stagmatoptera indicator) are considered as species inquirenda. We provide detailed morphological descriptions of all species, a species-level identification key, in addition to abundant visual material to assist identification. Female genitalia, a structure seldom used for taxonomic purposes, was a useful character system to distinguish among species of the genus. Distribution maps for all species are also provided.

  2. 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.

  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.

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

    PubMed Central

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

    2013-01-01

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

  6. Natural revegetation of a semiarid habitat alters taxonomic and functional diversity of soil microbial communities.

    PubMed

    Guo, Yanqing; Chen, Xiaotian; Wu, Yuanyuan; Zhang, Lu; Cheng, Jimin; Wei, Gehong; Lin, Yanbing

    2018-04-18

    Revegetation of degraded lands has a profound impact on the maintenance and stability of ecosystem processes. However, the impacts of this land use change on functional diversity of soil microbial communities are poorly understood. Here, using 16S rRNA gene amplicon and shotgun metagenomic sequencing, we compared the taxonomic and functional communities of soil microbiome, and analyzed the effects of plant diversity and soil chemical properties, in a chronosequence of restored ex-farmland that had been naturally revegetated to grassland over periods of 5, 15 and 30years with adjacent farmland, on the Loess Plateau, China. We found that microbial taxonomic diversity was positively correlated with plant diversity and was higher in the revegetated sites. Functional diversity increased significantly in the oldest grassland. Actinobacteria, commonly considered a copiotrophic phylum, was more abundant in the revegetated sites, while Acidobacteria, an oligotrophic phylum, was more abundant in farmland. Furthermore, the structure of taxonomic and functional communities was significantly different between revegetated sites and farmland, and organic matter was the best environmental predictor in determining these microbial communities. Compared with the farmland, revegetation increased the proportion of genes associated with energy metabolism, carbohydrate metabolism and xenobiotics biodegradation and metabolism. Notably, the higher proportion of carbohydrate degradation gene subfamilies in the revegetated sites indicated higher levels of soil nutrient cycling. These results elucidate the significant shifts in belowground microbial taxonomic and functional diversity following vegetation restoration and have implications for ecological restoration programs in arid and semi-arid ecosystems. Copyright © 2018. Published by Elsevier B.V.

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

    PubMed Central

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

    2013-01-01

    Abstract The long-recognized genus Gaura was shown recently to be deeply nested within one of two major clades of Oenothera. New molecular data indicate further taxonomic changes are necessary in Oenothera sect. Gaura. We make these changes here, including three new combinations, in advance of the Onagraceae treatment for the Flora of North America. The new phylogenetic studies show that several pairs of taxa treated as subspecies in the most recent revision by Raven and Gregory (1972) had independent origins within sect. Gaura, and are here elevated to species level (Oenothera nealleyi for Gaura suffulta subsp. nealleyi; Oenothera dodgeniana for Gaura neomexicana subsp. neomexicana; and Oenothera podocarpa for Gaura hexandra subsp. gracilis). Also, a nomenclatural problem in Oenothera sect. Calylophus is corrected by adopting the name Oenothera capillifolia Scheele for the species known previously, and nomenclaturally correct, as Calylophus berlandieri Spach. This problem necessitates a new combination Oenothera capillifolia subsp. berlandieri. PMID:24399892

  8. Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil.

    PubMed

    Mendes, Lucas William; Tsai, Siu Mui

    2018-01-01

    Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.

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

    PubMed

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

    2013-09-01

    The developmental taxonomic theory proposes that there are two subtypes of antisocial behaviour. The first is a neurodevelopmental disorder which emerges in early childhood and follows a life-course persistent course, whereas the second emerges in adolescence, remits in early adulthood and reflects peer processes such as mimicry of antisocial peers. The aim of this review was to evaluate the developmental taxonomic theory in the light of recent empirical research. We conducted a comprehensive literature review comparing these subtypes of antisocial behaviour based on searches on PubMed and other scientific databases covering the period from 1993 to 2013. We focused on research encompassing psychiatric epidemiology, personality assessment, neuropsychology, neuroendocrinology, genetics, and structural and functional neuroimaging. Sixty one empirical studies were identified that investigated one of these forms of antisocial behaviour separately or explicitly compared childhood-onset and adolescence-onset forms of antisocial behaviour. Empirical research provides support for the hypothesis that life-course persistent antisocial behaviour is a neurodevelopmental disorder which emerges in the transactions between individual vulnerabilities and environmental adversity. In contrast to the developmental taxonomic theory, however, empirical findings suggest that severe antisocial behaviour that emerges in adolescence frequently has a negative prognosis and is rarely limited to the adolescent period. In addition, both forms of antisocial behaviour are associated with emotion processing deficits, changes in brain structure and function, alterations in cortisol secretion, and atypical personality traits (such as increased callous-unemotional traits). We conclude that the developmental taxonomic theory is in need of revision, as differences between life-course persistent and adolescence-onset forms of antisocial behaviour appear to be quantitative, rather than qualitative, in

  10. Amazon plant diversity revealed by a taxonomically verified species list

    PubMed Central

    Cardoso, Domingos; Särkinen, Tiina; Alexander, Sara; Amorim, André M.; Bittrich, Volker; Celis, Marcela; Daly, Douglas C.; Fiaschi, Pedro; Funk, Vicki A.; Giacomin, Leandro L.; Heiden, Gustavo; Iganci, João; Kelloff, Carol L.; Knapp, Sandra; Cavalcante de Lima, Haroldo; Machado, Anderson F. P.; dos Santos, Rubens Manoel; Mello-Silva, Renato; Michelangeli, Fabián A.; Mitchell, John; Moonlight, Peter; de Moraes, Pedro Luís Rodrigues; Mori, Scott A.; Nunes, Teonildes Sacramento; Pennington, Terry D.; Pirani, José Rubens; Prance, Ghillean T.; de Queiroz, Luciano Paganucci; Rapini, Alessandro; Rincon, Carlos Alberto Vargas; Roque, Nádia; Shimizu, Gustavo; Sobral, Marcos; Stehmann, João Renato; Stevens, Warren D.; Taylor, Charlotte M.; Trovó, Marcelo; van den Berg, Cássio; van der Werff, Henk; Viana, Pedro Lage; Zartman, Charles E.; Forzza, Rafaela Campostrini

    2017-01-01

    Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests. PMID:28923966

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

    PubMed Central

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

    2017-01-01

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

  12. Insights into discriminating environmental quality status using taxonomic distinctness based on a small species pool of ciliated protozoa in marine ecosystems.

    PubMed

    Jiang, Yong; Xu, Henglong; Warren, Alan

    2014-01-15

    The objective of this study was to determine the feasibility of developing a protocol for assessing marine water quality based on taxonomic relatedness within a small pool of planktonic ciliates. An annual dataset was compiled based on samples collected biweekly at five sites, with a gradient of environmental stress, during a 1-year cycle in Jiaozhou Bay, northern China. A total of 60 species, belonging to 17 genera 10 families, 5 orders and 2 classes of the phylum Ciliophora, were identified. Among five orders, Tintinnida showed a low variability mainly at species level whereas the other orders (especially Strombidiida and Choreotrichida, although with the exception of the genus Strombidium) represented a high variability at higher taxonomic ranks (e.g. family or order). Mantel analyses showed that spatial patterns of the ciliate assemblages, with tinitinnids and Strombidium spp. excluded, were significantly correlated with those of the total planktonic ciliate communities in terms of their response to environmental status. The average taxonomic distinctness (Δ(+)) based on the small species pool was significantly negatively correlated with the changes in concentrations of nutrients (P<0.05). Furthermore, the paired indices of Δ(+) and the variation in taxonomic distinctness (Λ(+)) showed a clear departure from the expected taxonomic pattern. These findings suggest that it is possible to assess the status of marine water quality using the taxonomic relatedness within a small pool of planktonic ciliates. © 2013.

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Eldridge, Mark D B; Meek, Paul D; Johnson, Rebecca N

    2014-04-01

    The taxonomic uniqueness of island populations is often uncertain which hinders effective prioritization for conservation. The Christmas Island shrew (Crocidura attenuata trichura) is the only member of the highly speciose eutherian family Soricidae recorded from Australia. It is currently classified as a subspecies of the Asian gray or long-tailed shrew (C. attenuata), although it was originally described as a subspecies of the southeast Asian white-toothed shrew (C. fuliginosa). The Christmas Island shrew is currently listed as endangered and has not been recorded in the wild since 1984-1985, when 2 specimens were collected after an 80-year absence. We aimed to obtain DNA sequence data for cytochrome b (cytb) from Christmas Island shrew museum specimens to determine their taxonomic affinities and to confirm the identity of the 1980s specimens. The Cytb sequences from 5, 1898 specimens and a 1985 specimen were identical. In addition, the Christmas Island shrew cytb sequence was divergent at the species level from all available Crocidura cytb sequences. Rather than a population of a widespread species, current evidence suggests the Christmas Island shrew is a critically endangered endemic species, C. trichura, and a high priority for conservation. As the decisions typically required to save declining species can be delayed or deferred if the taxonomic status of the population in question is uncertain, it is hoped that the history of the Christmas Island shrew will encourage the clarification of taxonomy to be seen as an important first step in initiating informed and effective conservation action. © 2013 Society for Conservation Biology.

  16. 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

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

    PubMed

    Tumanov, Denis V

    2018-03-20

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

  18. Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases.

    PubMed

    De Palma, Adriana; Abrahamczyk, Stefan; Aizen, Marcelo A; Albrecht, Matthias; Basset, Yves; Bates, Adam; Blake, Robin J; Boutin, Céline; Bugter, Rob; Connop, Stuart; Cruz-López, Leopoldo; Cunningham, Saul A; Darvill, Ben; Diekötter, Tim; Dorn, Silvia; Downing, Nicola; Entling, Martin H; Farwig, Nina; Felicioli, Antonio; Fonte, Steven J; Fowler, Robert; Franzén, Markus; Goulson, Dave; Grass, Ingo; Hanley, Mick E; Hendrix, Stephen D; Herrmann, Farina; Herzog, Felix; Holzschuh, Andrea; Jauker, Birgit; Kessler, Michael; Knight, M E; Kruess, Andreas; Lavelle, Patrick; Le Féon, Violette; Lentini, Pia; Malone, Louise A; Marshall, Jon; Pachón, Eliana Martínez; McFrederick, Quinn S; Morales, Carolina L; Mudri-Stojnic, Sonja; Nates-Parra, Guiomar; Nilsson, Sven G; Öckinger, Erik; Osgathorpe, Lynne; Parra-H, Alejandro; Peres, Carlos A; Persson, Anna S; Petanidou, Theodora; Poveda, Katja; Power, Eileen F; Quaranta, Marino; Quintero, Carolina; Rader, Romina; Richards, Miriam H; Roulston, T'ai; Rousseau, Laurent; Sadler, Jonathan P; Samnegård, Ulrika; Schellhorn, Nancy A; Schüepp, Christof; Schweiger, Oliver; Smith-Pardo, Allan H; Steffan-Dewenter, Ingolf; Stout, Jane C; Tonietto, Rebecca K; Tscharntke, Teja; Tylianakis, Jason M; Verboven, Hans A F; Vergara, Carlos H; Verhulst, Jort; Westphal, Catrin; Yoon, Hyung Joo; Purvis, Andy

    2016-08-11

    Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.

  19. 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

  20. 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.

  1. Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands

    PubMed Central

    Barboza, Anthony Diego Muller; Pylro, Victor Satler; Jacques, Rodrigo Josemar Seminot; Gubiani, Paulo Ivonir; de Quadros, Fernando Luiz Ferreira; da Trindade, Júlio Kuhn; Triplett, Eric W.

    2018-01-01

    Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. Our data suggest that grasslands maintained a stable microbial community membership along the year with oscillation in abundance. Apparently soil microbial taxa are more susceptible to natural climatic disturbances while functions are more stable and change with less intensity along the year. Finally, our data allow us to conclude that the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.

  2. The taxonomic name resolution service: an online tool for automated standardization of plant names

    PubMed Central

    2013-01-01

    Background The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. Results The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. Conclusions We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ and as a RESTful web service and application programming interface. Source code is available at https

  3. Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession.

    PubMed

    Ortiz-Álvarez, Rüdiger; Fierer, Noah; de Los Ríos, Asunción; Casamayor, Emilio O; Barberán, Albert

    2018-02-20

    Ecologists have long studied primary succession, the changes that occur in biological communities after initial colonization of an environment. Most of this work has focused on succession in plant communities, laying the conceptual foundation for much of what we currently know about community assembly patterns over time. Because of their prevalence and importance in ecosystems, an increasing number of studies have focused on microbial community dynamics during succession. Here, we conducted a meta-analysis of bacterial primary succession patterns across a range of distinct habitats, including the infant gut, plant surfaces, soil chronosequences, and aquatic environments, to determine whether consistent changes in bacterial diversity, community composition, and functional traits are evident over the course of succession. Although these distinct habitats harbor unique bacterial communities, we were able to identify patterns in community assembly that were shared across habitat types. We found an increase in taxonomic and functional diversity with time while the taxonomic composition and functional profiles of communities became less variable (lower beta diversity) in late successional stages. In addition, we found consistent decreases in the rRNA operon copy number and in the high-efficient phosphate assimilation process (Pst system) suggesting that reductions in resource availability during succession select for taxa adapted to low-resource conditions. Together, these results highlight that, like many plant communities, microbial communities also exhibit predictable patterns during primary succession.

  4. Perceptions of Vocational Agriculture Instructors Regarding Knowledge and Importance of Including Selected Agricultural Mechanics Units in the Vocational Agriculture Program.

    ERIC Educational Resources Information Center

    Heimgartner, Dale C.; Foster, Richard M.

    1981-01-01

    A survey of teachers in five northwestern states revealed that respondents in all states rated the units of arc welding and oxyacetylene welding as the most important units to be included in secondary vocational agriculture programs. (LRA)

  5. A taxonomic review of Korean Liogluta Thomson (Coleoptera, Staphylinidae, Aleocharinae) with descriptions of three new species.

    PubMed

    Lee, Seung-Gyu; Ahn, Kee-Jeong

    2016-11-15

    A taxonomic review of the Liogluta Thomson in Korea is presented. The genus is represented in Korea by eight species including three new species, L. changwhani Lee & Ahn, sp. nov., L. jinilli Lee & Ahn, sp. nov. and L. rufescens Lee & Ahn, sp. nov. Two species [L. distans (Sharp) and L. ursi (Sawada)] are new to the Korean peninsula and L. pyonganica is recorded for the first time in South Korea. A key, descriptions, habitus photographs and illustrations of the diagnostic characters are provided.

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

    PubMed

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

    2013-01-01

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

  7. An intercomparison of the taxonomic and size composition of tropical macrozooplankton and micronekton collected using three sampling gears

    NASA Astrophysics Data System (ADS)

    Kwong, Lian E.; Pakhomov, Evgeny A.; Suntsov, Andrey V.; Seki, Michael P.; Brodeur, Richard D.; Pakhomova, Larisa G.; Domokos, Réka

    2018-05-01

    A micronekton intercalibration experiment was conducted off the southwest coast of Oahu Island, Hawaii in October 2004. Day and night samples were collected in the epipelagic and mesopelagic zones using three micronekton sampling gears: the Cobb Trawl, the Isaacs-Kidd Midwater Trawl (IKMT), and the Hokkaido University Frame Trawl (HUFT). Taxonomic composition and contribution by main size groups to total catch varied among gear types. However, the three gears exhibited similar taxonomic composition for macrozooplankton and micronekton ranging from 20 to 100 mm length (MM20-100). The HUFT and IKMT captured more mesozooplankton and small MM20-100, while the Cobb trawl selected towards larger MM20-100 and nekton. Taxonomic composition was described and inter-compared among gears. The relative efficacy of the three gears was assessed, and size dependent intercalibration coefficients were developed for MM20-100.

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

    PubMed

    Corliss, J O

    1981-01-01

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

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

    PubMed Central

    Smith, B. Eugene; Johnston, Mark K.; Lücking, Robert

    2016-01-01

    Accuracy of taxonomic identifications is crucial to data quality in online repositories of species occurrence data, such as the Global Biodiversity Information Facility (GBIF), which have accumulated several hundred million records over the past 15 years. These data serve as basis for large scale analyses of macroecological and biogeographic patterns and to document environmental changes over time. However, taxonomic identifications are often unreliable, especially for non-vascular plants and fungi including lichens, which may lack critical revisions of voucher specimens. Due to the scale of the problem, restudy of millions of collections is unrealistic and other strategies are needed. Here we propose to use verified, georeferenced occurrence data of a given species to apply predictive niche modeling that can then be used to evaluate unverified occurrences of that species. Selecting the charismatic lichen fungus, Usnea longissima, as a case study, we used georeferenced occurrence records based on sequenced specimens to model its predicted niche. Our results suggest that the target species is largely restricted to a narrow range of boreal and temperate forest in the Northern Hemisphere and that occurrence records in GBIF from tropical regions and the Southern Hemisphere do not represent this taxon, a prediction tested by comparison with taxonomic revisions of Usnea for these regions. As a novel approach, we employed Principal Component Analysis on the environmental grid data used for predictive modeling to visualize potential ecogeographical barriers for the target species; we found that tropical regions conform a strong barrier, explaining why potential niches in the Southern Hemisphere were not colonized by Usnea longissima and instead by morphologically similar species. This approach is an example of how data from two of the most important biodiversity repositories, GenBank and GBIF, can be effectively combined to remotely address the problem of inaccuracy of

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

    PubMed

    Smith, B Eugene; Johnston, Mark K; Lücking, Robert

    2016-01-01

    Accuracy of taxonomic identifications is crucial to data quality in online repositories of species occurrence data, such as the Global Biodiversity Information Facility (GBIF), which have accumulated several hundred million records over the past 15 years. These data serve as basis for large scale analyses of macroecological and biogeographic patterns and to document environmental changes over time. However, taxonomic identifications are often unreliable, especially for non-vascular plants and fungi including lichens, which may lack critical revisions of voucher specimens. Due to the scale of the problem, restudy of millions of collections is unrealistic and other strategies are needed. Here we propose to use verified, georeferenced occurrence data of a given species to apply predictive niche modeling that can then be used to evaluate unverified occurrences of that species. Selecting the charismatic lichen fungus, Usnea longissima, as a case study, we used georeferenced occurrence records based on sequenced specimens to model its predicted niche. Our results suggest that the target species is largely restricted to a narrow range of boreal and temperate forest in the Northern Hemisphere and that occurrence records in GBIF from tropical regions and the Southern Hemisphere do not represent this taxon, a prediction tested by comparison with taxonomic revisions of Usnea for these regions. As a novel approach, we employed Principal Component Analysis on the environmental grid data used for predictive modeling to visualize potential ecogeographical barriers for the target species; we found that tropical regions conform a strong barrier, explaining why potential niches in the Southern Hemisphere were not colonized by Usnea longissima and instead by morphologically similar species. This approach is an example of how data from two of the most important biodiversity repositories, GenBank and GBIF, can be effectively combined to remotely address the problem of inaccuracy of

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

    NASA Astrophysics Data System (ADS)

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

    2007-01-01

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

  12. Molecular phylogeny and taxonomic revision of the genus Wittrockiella (Pithophoraceae, Cladophorales), including the descriptions of W. australis sp. nov. and W. zosterae sp. nov.

    PubMed

    Boedeker, Christian; O'Kelly, Charles J; West, John A; Hanyuda, Takeaki; Neale, Adele; Wakana, Isamu; Wilcox, Mike D; Karsten, Ulf; Zuccarello, Giuseppe C

    2017-06-01

    Wittrockiella is a small genus of filamentous green algae that occurs in habitats with reduced or fluctuating salinities. Many aspects of the basic biology of these algae are still unknown and the phylogenetic relationships within the genus have not been fully explored. We provide a phylogeny based on three ribosomal markers (ITS, LSU, and SSU rDNA) of the genus, including broad intraspecific sampling for W. lyallii and W. salina, recommendations for the use of existing names are made, and highlight aspects of their physiology and life cycle. Molecular data indicate that there are five species of Wittrockiella. Two new species, W. australis and W. zosterae, are described, both are endophytes. Although W. lyallii and W. salina can be identified morphologically, there are no diagnostic morphological characters to distinguish between W. amphibia, W. australis, and W. zosterae. A range of low molecular weight carbohydrates were analyzed but proved to not be taxonomically informative. The distribution range of W. salina is extended to the Northern Hemisphere as this species has been found in brackish lakes in Japan. Furthermore, it is shown that there are no grounds to recognize W. salina var. kraftii, which was described as an endemic variety from a freshwater habitat on Lord Howe Island, Australia. Culture experiments indicate that W. australis has a preference for growth in lower salinities over full seawater. For W. amphibia and W. zosterae, sexual reproduction is documented, and the split of these species is possibly attributable to polyploidization. © 2017 Phycological Society of America.

  13. Deaf and hard of hearing adolescents' processing of pictures and written words for taxonomic categories in a priming task of semantic categorization.

    PubMed

    Li, Degao; Gao, Kejuan; Wu, Xueyun; Chen, Xiaojun; Zhang, Xiaona; Li, Ling; He, Weiwei

    2013-01-01

    Inspired by research by Li, Yi, and Kim (2011), the authors examined Chinese deaf and hard of hearing adolescents' responses to pictures for taxonomic categories of basic level (exemplar pictures) preceded by exemplar pictures, and to written words for taxonomic categories of basic level (exemplar words) preceded by exemplar words or by written words for those of superordinate level (category names), in a priming task of semantic categorization. Stimulus onset asynchrony (SOA) was manipulated. The adolescents were less aware of taxonomic relations and were more likely to show the advantage of pictures over written words than their hearing counterparts. Their processing of exemplar primes steadily deepened as SOA increased, reaching its deepest level when SOA was 237 ms. Their processing of category names seemed immune to changes in SOA, probably because of their fuzzy representations of taxonomic categories of superordinate level.

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

    EPA Science Inventory

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

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

    PubMed

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

    2016-03-16

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

  16. Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks.

    PubMed

    Ibarbalz, Federico M; Figuerola, Eva L M; Erijman, Leonardo

    2013-07-01

    Biological degradation of domestic and industrial wastewater by activated sludge depends on a common process of separation of the diverse self-assembled and self-sustained microbial flocs from the treated wastewater. Previous surveys of bacterial communities indicated the presence of a common core of bacterial phyla in municipal activated sludge, an observation consistent with the concept of ecological coherence of high taxonomic ranks. The aim of this work was to test whether this critical feature brings about a common pattern of abundance distribution of high bacterial taxa in industrial and domestic activated sludge, and to relate the bacterial community structure of industrial activated sludge with relevant operational parameters. We have applied 454 pyrosequencing of 16S rRNA genes to evaluate bacterial communities in full-scale biological wastewater treatment plants sampled at different times, including seven systems treating wastewater from different industries and one plant that treats domestic wastewater, and compared our datasets with the data from municipal wastewater treatment plants obtained by three different laboratories. We observed that each industrial activated sludge system exhibited a unique bacterial community composition, which is clearly distinct from the common profile of bacterial phyla or classes observed in municipal plants. The influence of process parameters on the bacterial community structure was evaluated using constrained analysis of principal coordinates (CAP). Part of the differences in the bacterial community structure between industrial wastewater treatment systems were explained by dissolved oxygen and pH. Despite the ecological relevance of floc formation for the assembly of bacterial communities in activated sludge, the wastewater characteristics are likely to be the major determinant that drives bacterial composition at high taxonomic ranks. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

    PubMed

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

    2014-08-01

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

  18. Variance Component Selection With Applications to Microbiome Taxonomic Data.

    PubMed

    Zhai, Jing; Kim, Juhyun; Knox, Kenneth S; Twigg, Homer L; Zhou, Hua; Zhou, Jin J

    2018-01-01

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

  19. Partitioning of functional and taxonomic diversity in surface-associated microbial communities.

    PubMed

    Roth-Schulze, Alexandra J; Zozaya-Valdés, Enrique; Steinberg, Peter D; Thomas, Torsten

    2016-12-01

    Surfaces, including those submerged in the marine environment, are subjected to constant interactions and colonisation by surrounding microorganisms. The principles that determine the assembly of those epibiotic communities are however poorly understood. In this study, we employed a hierarchical design to assess the functionality and diversity of microbial communities on different types of host surfaces (e.g. macroalgae, seagrasses). We found that taxonomic diversity was unique to each type of host, but that the majority of functions (> 95%) could be found in any given surface community, suggesting a high degree of functional redundancy. However, some community functions were enriched on certain surfaces and were related to host-specific properties (e.g. the degradation of specific polysaccharides). Together these observations support a model, whereby communities on surfaces are assembled from guilds of microorganisms with a functionality that is partitioned into general properties for a surface-associated life-style, but also specific features that mediate host-specificity. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

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

    EPA Science Inventory

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

  1. Climate warming promotes species diversity, but with greater taxonomic redundancy, in complex environments

    PubMed Central

    Thakur, Madhav P.; Tilman, David; Purschke, Oliver; Ciobanu, Marcel; Cowles, Jane; Isbell, Forest; Wragg, Peter D.; Eisenhauer, Nico

    2017-01-01

    Climate warming is predicted to alter species interactions, which could potentially lead to extinction events. However, there is an ongoing debate whether the effects of warming on biodiversity may be moderated by biodiversity itself. We tested warming effects on soil nematodes, one of the most diverse and abundant metazoans in terrestrial ecosystems, along a gradient of environmental complexity created by a gradient of plant species richness. Warming increased nematode species diversity in complex (16-species mixtures) plant communities (by ~36%) but decreased it in simple (monocultures) plant communities (by ~39%) compared to ambient temperature. Further, warming led to higher levels of taxonomic relatedness in nematode communities across all levels of plant species richness. Our results highlight both the need for maintaining species-rich plant communities to help offset detrimental warming effects and the inability of species-rich plant communities to maintain nematode taxonomic distinctness when warming occur. PMID:28740868

  2. 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

  3. Cryptic infection of a broad taxonomic and geographic diversity of tadpoles by Perkinsea protists.

    PubMed

    Chambouvet, Aurélie; Gower, David J; Jirků, Miloslav; Yabsley, Michael J; Davis, Andrew K; Leonard, Guy; Maguire, Finlay; Doherty-Bone, Thomas M; Bittencourt-Silva, Gabriela Bueno; Wilkinson, Mark; Richards, Thomas A

    2015-08-25

    The decline of amphibian populations, particularly frogs, is often cited as an example in support of the claim that Earth is undergoing its sixth mass extinction event. Amphibians seem to be particularly sensitive to emerging diseases (e.g., fungal and viral pathogens), yet the diversity and geographic distribution of infectious agents are only starting to be investigated. Recent work has linked a previously undescribed protist with mass-mortality events in the United States, in which infected frog tadpoles have an abnormally enlarged yellowish liver filled with protist cells of a presumed parasite. Phylogenetic analyses revealed that this infectious agent was affiliated with the Perkinsea: a parasitic group within the alveolates exemplified by Perkinsus sp., a "marine" protist responsible for mass-mortality events in commercial shellfish populations. Using small subunit (SSU) ribosomal DNA (rDNA) sequencing, we developed a targeted PCR protocol for preferentially sampling a clade of the Perkinsea. We tested this protocol on freshwater environmental DNA, revealing a wide diversity of Perkinsea lineages in these environments. Then, we used the same protocol to test for Perkinsea-like lineages in livers of 182 tadpoles from multiple families of frogs. We identified a distinct Perkinsea clade, encompassing a low level of SSU rDNA variation different from the lineage previously associated with tadpole mass-mortality events. Members of this clade were present in 38 tadpoles sampled from 14 distinct genera/phylogroups, from five countries across three continents. These data provide, to our knowledge, the first evidence that Perkinsea-like protists infect tadpoles across a wide taxonomic range of frogs in tropical and temperate environments, including oceanic islands.

  4. Genome-Based Taxonomic Classification of Bacteroidetes

    PubMed Central

    Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina; Mukherjee, Supratim; Huntemann, Marcel; Ivanova, Natalia N.; Woyke, Tanja; Kyrpides, Nikos C.; Klenk, Hans-Peter; Göker, Markus

    2016-01-01

    The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved. PMID:28066339

  5. 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

  6. Functional and taxonomic dynamics of an electricity-consuming methane-producing microbial community.

    PubMed

    Bretschger, Orianna; Carpenter, Kayla; Phan, Tony; Suzuki, Shino; Ishii, Shun'ichi; Grossi-Soyster, Elysse; Flynn, Michael; Hogan, John

    2015-11-01

    The functional and taxonomic microbial dynamics of duplicate electricity-consuming methanogenic communities were observed over a 6 months period to characterize the reproducibility, stability and recovery of electromethanogenic consortia. The highest rate of methanogenesis was 0.72 mg-CH4/L/day, which occurred during the third month of enrichment when multiple methanogenic phylotypes and associated Desulfovibrionaceae phylotypes were present in the electrode-associated microbial community. Results also suggest that electromethanogenic microbial communities are very sensitive to electron donor-limiting open-circuit conditions. A 45 min exposure to open-circuit conditions induced an 87% drop in volumetric methane production rates. Methanogenic performance recovered after 4 months to a maximum value of 0.30 mg-CH4/L/day under set potential operation (-700 mV vs Ag/AgCl); however, current consumption and biomass production was variable over time. Long-term functional and taxonomic analyses from experimental replicates provide new knowledge toward understanding how to enrich electromethanogenic communities and operate bioelectrochemical systems for stable and reproducible performance. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment

    PubMed Central

    Anwar, Nadia; Hunt, Ela

    2009-01-01

    Background TreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory. Results We report on a new wrapper supporting taxon queries on TreeBASE by utilising a Taxonomy and Classification Database (TCl-Db) we created. TCl-Db holds merged and consolidated taxonomic names from multiple data sources and can be used to translate hierarchical, vernacular and synonym queries into specific query terms in TreeBASE. The query expansion supported by TCl-Db shows very significant information retrieval quality improvement. The wrapper can be accessed at the URL The methodology we developed is scalable and can be applied to new data, as those become available in the future. Conclusion Significantly improved data retrieval quality is shown for all queries, and additional flexibility is achieved via user-driven taxonomy selection. PMID:19426482

  8. Insights into assessing water quality using taxonomic distinctness based on a small species pool of biofilm-dwelling ciliate fauna in coastal waters of the Yellow Sea, northern China.

    PubMed

    Zhang, Wei; Liu, Yuanyuan; Warren, Alan; Xu, Henglong

    2014-12-15

    The aim of this study is to determine the feasibility of using a small species pool from a raw dataset of biofilm-dwelling ciliates for bioassessment based on taxonomic diversity. Samples were collected monthly at four stations within a gradient of environmental stress in coastal waters of the Yellow Sea, northern China from August 2011 to July 2012. A 33-species subset was identified from the raw 137-species dataset using a multivariate method. The spatial patterns of this subset were significantly correlated with the changes in the nutrients and chemical oxygen demand. The taxonomic diversity indices were significantly correlated with nutrients. The pair-wise indices of average taxonomic distinctness (Δ(+)) and the taxonomic distinctness (Λ(+)) showed a clear departure from the expected taxonomic pattern. These findings suggest that this small ciliate assemblage might be used as an adequate species pool for discriminating water quality status based on taxonomic distinctness in marine ecosystems. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

    PubMed

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

    2014-07-01

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

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

    ERIC Educational Resources Information Center

    Dunham, Philip; Dunham, Frances

    1995-01-01

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

  11. 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

  12. Identifying designatable units for intraspecific conservation prioritization: a hierarchical approach applied to the lake whitefish species complex (Coregonus spp.)

    PubMed Central

    Mee, Jonathan A; Bernatchez, Louis; Reist, Jim D; Rogers, Sean M; Taylor, Eric B

    2015-01-01

    The concept of the designatable unit (DU) affords a practical approach to identifying diversity below the species level for conservation prioritization. However, its suitability for defining conservation units in ecologically diverse, geographically widespread and taxonomically challenging species complexes has not been broadly evaluated. The lake whitefish species complex (Coregonus spp.) is geographically widespread in the Northern Hemisphere, and it contains a great deal of variability in ecology and evolutionary legacy within and among populations, as well as a great deal of taxonomic ambiguity. Here, we employ a set of hierarchical criteria to identify DUs within the Canadian distribution of the lake whitefish species complex. We identified 36 DUs based on (i) reproductive isolation, (ii) phylogeographic groupings, (iii) local adaptation and (iv) biogeographic regions. The identification of DUs is required for clear discussion regarding the conservation prioritization of lake whitefish populations. We suggest conservation priorities among lake whitefish DUs based on biological consequences of extinction, risk of extinction and distinctiveness. Our results exemplify the need for extensive genetic and biogeographic analyses for any species with broad geographic distributions and the need for detailed evaluation of evolutionary history and adaptive ecological divergence when defining intraspecific conservation units. PMID:26029257

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

    USDA-ARS?s Scientific Manuscript database

    Community composition data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alt...

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

    PubMed Central

    Watson, Linda E; Bates, Paul L; Evans, Timothy M; Unwin, Matthew M; Estes, James R

    2002-01-01

    Background Subtribe Artemisiinae of Tribe Anthemideae (Asteraceae) is composed of 18 largely Asian genera that include the sagebrushes and mugworts. The subtribe includes the large cosmopolitan, wind-pollinated genus Artemisia, as well as several smaller genera and Seriphidium, that altogether comprise the Artemisia-group. Circumscription and taxonomic boundaries of Artemisia and the placements of these small segregate genera is currently unresolved. Results We constructed a molecular phylogeny for the subtribe using the internal transcribed spacers (ITS) of nuclear ribosomal DNA analyzed with parsimony, likelihood, and Bayesian criteria. The resulting tree is comprised of three major clades that correspond to the radiate genera (e.g., Arctanthemum and Dendranthema), and two clades of Artemisia species. All three clades have allied and segregate genera embedded within each. Conclusions The data support a broad concept of Artemisia s.l. that includes Neopallasia, Crossostephium, Filifolium, Seriphidium, and Sphaeromeria. However, the phylogeny excludes Elachanthemum, Kaschgaria, and Stilnolepis from the Artemisia-group. Additionally, the monophyly of the four subgenera of Artemisia is also not supported, with the exception of subg. Dracunculus. Homogamous, discoid capitula appear to have arisen in parallel four to seven times, with the loss of ray florets. Thus capitular morphology is not a reliable taxonomic character, which traditionally has been one of the defining characters. PMID:12350234

  15. Evolutionary dynamics of taxonomic structure

    PubMed Central

    Foote, Michael

    2012-01-01

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

  16. Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species.

    PubMed

    Dahruddin, Hadi; Hutama, Aditya; Busson, Frédéric; Sauri, Sopian; Hanner, Robert; Keith, Philippe; Hadiaty, Renny; Hubert, Nicolas

    2017-03-01

    Among the 899 species of freshwater fishes reported from Sundaland biodiversity hotspot, nearly 50% are endemics. The functional integrity of aquatic ecosystems is currently jeopardized by human activities, and landscape conversion led to the decline of fish populations in several part of Sundaland, particularly in Java. The inventory of the Javanese ichthyofauna has been discontinuous, and the taxonomic knowledge is scattered in the literature. This study provides a DNA barcode reference library for the inland fishes of Java and Bali with the aim to streamline the inventory of fishes in this part of Sundaland. Owing to the lack of available checklist for estimating the taxonomic coverage of this study, a checklist was compiled based on online catalogues. A total of 95 sites were visited, and a library including 1046 DNA barcodes for 159 species was assembled. Nearest neighbour distance was 28-fold higher than maximum intraspecific distance on average, and a DNA barcoding gap was observed. The list of species with DNA barcodes displayed large discrepancies with the checklist compiled here as only 36% (i.e. 77 species) and 60% (i.e. 24 species) of the known species were sampled in Java and Bali, respectively. This result was contrasted by a high number of new occurrences and the ceiling of the accumulation curves for both species and genera. These results highlight the poor taxonomic knowledge of this ichthyofauna, and the apparent discrepancy between present and historical occurrence data is to be attributed to species extirpations, synonymy and misidentifications in previous studies. © 2016 John Wiley & Sons Ltd.

  17. A Guide to the Common Diatoms at Water Pollution Surveillance System Stations.

    ERIC Educational Resources Information Center

    Weber, Cornelius I.

    This guide was developed by the United States Environmental Protection Agency (EPA) as a taxonomic reference for the identification of diatoms. The taxonomic information included consists of a generic key to the common genera of diatoms, a section illustrating 164 diatom species representing 43 common genera found at the Water Pollution…

  18. DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts.

    PubMed

    Lara, Ariagna; Ponce de León, José Luis; Rodríguez, Rodet; Casane, Didier; Côté, Guillaume; Bernatchez, Louis; García-Machado, Erik

    2010-05-01

    Despite ongoing efforts to protect species and ecosystems in Cuba, habitat degradation, overuse and introduction of alien species have posed serious challenges to native freshwater fish species. In spite of the accumulated knowledge on the systematics of this freshwater ichthyofauna, recent results suggested that we are far from having a complete picture of the Cuban freshwater fish diversity. It is estimated that 40% of freshwater Cuban fish are endemic; however, this number may be even higher. Partial sequences (652 bp) of the mitochondrial gene COI (cytochrome c oxidase subunit I) were used to barcode 126 individuals, representing 27 taxonomically recognized species in 17 genera and 10 families. Analysis was based on Kimura 2-parameter genetic distances, and for four genera a character-based analysis (population aggregation analysis) was also used. The mean conspecific, congeneric and confamiliar genetic distances were 0.6%, 9.1% and 20.2% respectively. Molecular species identification was in concordance with current taxonomical classification in 96.4% of cases, and based on the neighbour-joining trees, in all but one instance, members of a given genera clustered within the same clade. Within the genus Gambusia, genetic divergence analysis suggests that there may be at least four cryptic species. In contrast, low genetic divergence and a lack of diagnostic sites suggest that Rivulus insulaepinorum may be conspecific with Rivulus cylindraceus. Distance and character-based analysis were completely concordant, suggesting that they complement species identification. Overall, the results evidenced the usefulness of the DNA barcodes for cataloguing Cuban freshwater fish species and for identifying those groups that deserve further taxonomic attention. © 2009 Blackwell Publishing Ltd.

  19. Revision of the genus Cuvierina Boas, 1886 based on integrative taxonomic data, including the description of a new species from the Pacific Ocean (Gastropoda, Thecosomata)

    PubMed Central

    Burridge, Alice K.; Janssen, Arie W.; Peijnenburg, Katja T.C.A.

    2016-01-01

    Abstract Shelled pteropods (Gastropoda, Thecosomata, Euthecosomata) are a group of holoplanktonic gastropods that occur predominantly in the surface layers of the world’s oceans. Accurate species identifications are essential for tracking changes in species assemblages of planktonic gastropods, because different species are expected to have different sensitivities to ocean changes. The genus Cuvierina has a worldwide warm water distribution pattern between ~36°N and ~39°S. Based on an integrative taxonomic approach combining morphometric, genetic, and biogeographic information, the two subgenera of Cuvierina, Cuvierina s. str. and Urceolarica, are rejected. A new species is introduced: Cuvierina tsudai sp. n., which has to date been considered the same species as Cuvierina pacifica. Cuvierina tsudai sp. n. is endemic to the Pacific Ocean and is characterised by a shell height of 7.2-8.0 mm, a moderately cylindrical shell shape, the absence of micro-ornamentation and a triangular aperture. Cuvierina pacifica is restricted to the centre of the oligotrophic southern Pacific gyre, has a shell height of 6.6-8.5 mm, a more cylindrical shell shape, no micro-ornamentation and a less triangular aperture than Cuvierina tsudai sp. n. PMID:27829786

  20. Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability

    PubMed Central

    Lewin, Gina R.; Johnson, Amanda L.; Soto, Rolando D. Moreira; Perry, Kailene; Book, Adam J.; Horn, Heidi A.; Pinto-Tomás, Adrián A.; Currie, Cameron R.

    2016-01-01

    Deconstruction of the cellulose in plant cell walls is critical for carbon flow through ecosystems and for the production of sustainable cellulosic biofuels. Our understanding of cellulose deconstruction is largely limited to the study of microbes in isolation, but in nature, this process is driven by microbes within complex communities. In Neotropical forests, microbes in leaf-cutter ant refuse dumps are important for carbon turnover. These dumps consist of decaying plant material and a diverse bacterial community, as shown here by electron microscopy. To study the portion of the community capable of cellulose degradation, we performed enrichments on cellulose using material from five Atta colombica refuse dumps. The ability of enriched communities to degrade cellulose varied significantly across refuse dumps. 16S rRNA gene amplicon sequencing of enriched samples identified that the community structure correlated with refuse dump and with degradation ability. Overall, samples were dominated by Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. Half of abundant operational taxonomic units (OTUs) across samples were classified within genera containing known cellulose degraders, including Acidovorax, the most abundant OTU detected across samples, which was positively correlated with cellulolytic ability. A representative Acidovorax strain was isolated, but did not grow on cellulose alone. Phenotypic and compositional analyses of enrichment cultures, such as those presented here, help link community composition with cellulolytic ability and provide insight into the complexity of community-based cellulose degradation. PMID:26999749

  1. Deaf and Hard of Hearing Adolescents' Processing of Pictures and Written Words for Taxonomic Categories in a Priming Task of Semantic Categorization

    ERIC Educational Resources Information Center

    Li, Degao; Gao, Kejuan; Wu, Xueyun; Chen, Xiaojun; Zhang, Xiaona; Li, Ling; He, Weiwei

    2013-01-01

    Inspired by research by Li, Yi, and Kim (2011), the authors examined Chinese deaf and hard of hearing adolescents' responses to pictures for taxonomic categories of basic level (exemplar pictures) preceded by exemplar pictures, and to written words for taxonomic categories of basic level (exemplar words) preceded by exemplar words or by written…

  2. What's in a name: the taxonomic status of human head and body lice.

    PubMed

    Light, Jessica E; Toups, Melissa A; Reed, David L

    2008-06-01

    Human head lice (Anoplura: Pediculidae: Pediculus) are pandemic, parasitizing countless school children worldwide due to the evolution of insecticide resistance, and human body (clothing) lice are responsible for the deaths of millions as a result of vectoring several deadly bacterial pathogens. Despite the obvious impact these lice have had on their human hosts, it is unclear whether head and body lice represent two morphological forms of a single species or two distinct species. To assess the taxonomic status of head and body lice, we provide a synthesis of publicly available molecular data in GenBank, and we compare phylogenetic and population genetic methods using the most diverse geographic and molecular sampling presently available. Our analyses find reticulated networks, gene flow, and a lack of reciprocal monophyly, all of which indicate that head and body lice do not represent genetically distinct evolutionary units. Based on these findings, as well as inconsistencies of morphological, behavioral, and ecological variability between head and body lice, we contend that no known species concept would recognize these louse morphotypes as separate species. We recommend recognizing head and body lice as morphotypes of a single species, Pediculus humanus, until compelling new data and analyses (preferably analyses of fast evolving nuclear markers in a coalescent framework) indicate otherwise.

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

    USGS Publications Warehouse

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

    2014-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  5. Taxonomic revision and phylogenetic analysis of the flightless Mancallinae (Aves, Pan-Alcidae)

    PubMed Central

    Smith, Neil Adam

    2011-01-01

    Abstract Although flightless alcids from the Miocene and Pliocene of the eastern Pacific Ocean have been known for over 100 years, there is no detailed evaluation of diversity and systematic placement of these taxa. This is the first combined analysis of morphological and molecular data to include all extant alcids, the recently extinct Great Auk Pinguinus impennis, the mancalline auks, and a large outgroup sampling of 29 additional non-alcid charadriiforms. Based on the systematic placement of Mancallinae outside of crown clade Alcidae, the clade name Pan-Alcidae is proposed to include all known alcids. An extensive review of the Mancallinae fossil record resulted in taxonomic revision of the clade, and identification of three new species. In addition to positing the first hypothesis of inter-relationships between Mancallinae species, phylogenetic results support placement of Mancallinae as the sister taxon to all other Alcidae, indicating that flightlessness evolved at least twice in the alcid lineage. Convergent osteological characteristics of Mancallinae, the flightless Great Auk, and Spheniscidae are summarized, and implications of Mancallinae diversity, radiation, and extinction in the context of paleoclimatic changes are discussed. PMID:21594108

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

    PubMed Central

    Häser, Annette

    2016-01-01

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

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

    PubMed

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

    2013-12-01

    Species boundaries are traditionally inferred using morphological characters, although morphology sometimes fails to correctly delineate species. To overcome this limitation, researchers have widely taken advantage of alternative methods such as DNA barcoding or analysis of cuticular hydrocarbons (CHs) profiles, but rarely use them simultaneously in an iterative taxonomic approach. Here, we follow such an approach using morphology, DNA barcoding and CHs profiles to precisely discriminate species of soldierless termites, a diversified clade constituting about one-third of the Neotropical termite species richness, but poorly resolved taxonomically due to the paucity of useful characters. We sampled soldierless termites in various forest types of the Nouragues Nature Reserve, French Guiana. Our results show that morphological species determination generally matches DNA barcoding, which only suggests the existence of three cryptic species in the 31 morphological species. Among them, Longustitermes manni is the only species whose splitting is corroborated by ecological data, other widely distributed species being supported by DNA barcoding. On the contrary, although CHs profiles provide a certain taxonomic signal, they often suggest inconsistent groupings which are not supported by other methods. Overall, our data support DNA barcoding and morphology as two efficient methods to distinguish soldierless termite species. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. Clever birds are lousy: co-variation between avian innovation and the taxonomic richness of their amblyceran lice.

    PubMed

    Vas, Zoltán; Lefebvre, Louis; Johnson, Kevin P; Reiczigel, Jeno; Rózsa, Lajos

    2011-10-01

    Lice (Insecta: Phthiraptera) are ectoparasites that reduce host life expectancy and sexual attractiveness. Their taxonomic richness varies considerably among their hosts. Previous studies have already explored some important factors shaping louse diversity. An unexplored potential correlate of louse taxonomic richness is host behavioural flexibility. In this comparative study, we examine the relationship between louse generic richness, innovative capabilities (as a proxy for behavioural flexibility), and brain size while controlling for host species diversity, phylogeny, body size and research effort. Using data for 108 avian families, we found a highly significant positive relationship between host innovative capabilities and the taxonomic richness of amblyceran lice, but a lack of a similar relationship in ischnoceran lice. Host brain size had only a marginal impact on amblyceran diversity and no correlation with ischnoceran diversity. This suggests that the effect in Amblycera is not mediated by metabolic limitations due to the energetic costs of brain size and maintenance, rather directly caused by the ecological differences between hosts with differing cognitive capabilities. We propose four alternative and mutually non-exclusive hypotheses that may explain this phenomenon. Copyright © 2011 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  9. Genome-Based Taxonomic Classification of Bacteroidetes

    DOE PAGES

    Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina; ...

    2016-12-20

    The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogeneticmore » analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.« less

  10. Genome-Based Taxonomic Classification of Bacteroidetes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina

    The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogeneticmore » analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.« less

  11. Effectiveness of protected areas for vertebrates based on taxonomic and phylogenetic diversity.

    PubMed

    Quan, Qing; Che, Xianli; Wu, Yongjie; Wu, Yuchun; Zhang, Qiang; Zhang, Min; Zou, Fasheng

    2018-04-01

    Establishing protected areas is the primary goal and tool for preventing irreversible biodiversity loss. However, the effectiveness of protected areas that target specific species has been questioned for some time because targeting key species for conservation may impair the integral regional pool of species diversity and phylogenetic and functional diversity are seldom considered. We assessed the efficacy of protected areas in China for the conservation of phylogenetic diversity based on the ranges and phylogenies of 2279 terrestrial vertebrates. Phylogenetic and taxonomic diversity were strongly and positively correlated, and only 12.1-43.8% of priority conservation areas are currently protected. However, the patterns and coverage of phylogenetic diversity were affected when weighted by species richness. These results indicated that in China, protected areas targeting high species richness protected phylogenetic diversity well overall but failed to do so in some regions with more unique or threatened communities (e.g., coastal areas of eastern China, where severely threatened avian communities were less protected). Our results suggest that the current distribution of protected areas could be improved, although most protected areas protect both taxonomic and phylogenetic diversity. © 2017 Society for Conservation Biology.

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

    PubMed Central

    Borkenhagen, Kai; Krupp, Friedhelm

    2013-01-01

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

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

    PubMed

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

    2015-10-15

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

  14. Updates on information about free-living marine nematodes in Brazil: new records and comments on problems in taxonomic studies.

    PubMed

    Venekey, Virág

    2017-10-17

    New records of nematode species in Brazil, which appeared after or were not mentioned in the last review, are shown in this paper. All environments were considered, including the continental margin. In addition, all studies on marine nematodes in Brazil, including grey literature, ecological papers and book chapters, are listed. Furthermore, information on genera/species richness, dominant genera, and densities is also presented. A total of 11 orders, 72 families, 372 genera, and 450 species of nematodes were recorded in Brazilian marine environments by April 2017. Following problems are discussed: taxonomic lists available only in grey literature, use of outdated identification keys (leading to incorrect identifications), and identifications mostly to putative species or to the genus level.

  15. Systematics and biogeography of Orconectes, subgenus Trisellescens, in the southeastern United States, a test of morphology-based classification

    Treesearch

    Christopher A. Taylor; Susan B. Adams; Guenter A. Schuster

    2014-01-01

    Diagnosable taxonomic units are fundamental to conservation biology and management of resources and the need for sound science in both fields is more pressing for aquatic ecosystems. Within freshwater crayfishes, the North American genus Orconectes is one of the most diverse in the World. Accurate assessments of species level relationships and species boundaries within...

  16. A Neurocomputational Account of Taxonomic Responding and Fast Mapping in Early Word Learning

    ERIC Educational Resources Information Center

    Mayor, Julien; Plunkett, Kim

    2010-01-01

    We present a neurocomputational model with self-organizing maps that accounts for the emergence of taxonomic responding and fast mapping in early word learning, as well as a rapid increase in the rate of acquisition of words observed in late infancy. The quality and efficiency of generalization of word-object associations is directly related to…

  17. Typification and taxonomic status re-evaluation of 15 taxon names within the species complex Cymbella affinis/tumidula/turgidula (Cymbellaceae, Bacillariophyta)

    PubMed Central

    da Silva, Weliton José; Jahn, Regine; Ludwig, Thelma Alvim Veiga; Hinz, Friedel; Menezes, Mariângela

    2015-01-01

    Abstract Specimens belonging to the Cymbella affinis / Cymbella tumidula / Cymbella turgidula species complex have many taxonomic problems, due to their high morphological variability and lack of type designations. Fifteen taxon names of this complex, distributed in five species, were re-evaluated concerning their taxonomic status, and lectotypified based on original material. In addition to light microscopy, some material was analyzed by electron microscopy. Four new combinations are proposed in order to reposition infraspecific taxa. PMID:26312038

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

    PubMed

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

    2018-02-01

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

  19. Classification of malignant and benign lung nodules using taxonomic diversity index and phylogenetic distance.

    PubMed

    de Sousa Costa, Robherson Wector; da Silva, Giovanni Lucca França; de Carvalho Filho, Antonio Oseas; Silva, Aristófanes Corrêa; de Paiva, Anselmo Cardoso; Gattass, Marcelo

    2018-05-23

    Lung cancer presents the highest cause of death among patients around the world, in addition of being one of the smallest survival rates after diagnosis. Therefore, this study proposes a methodology for diagnosis of lung nodules in benign and malignant tumors based on image processing and pattern recognition techniques. Mean phylogenetic distance (MPD) and taxonomic diversity index (Δ) were used as texture descriptors. Finally, the genetic algorithm in conjunction with the support vector machine were applied to select the best training model. The proposed methodology was tested on computed tomography (CT) images from the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), with the best sensitivity of 93.42%, specificity of 91.21%, accuracy of 91.81%, and area under the ROC curve of 0.94. The results demonstrate the promising performance of texture extraction techniques using mean phylogenetic distance and taxonomic diversity index combined with phylogenetic trees. Graphical Abstract Stages of the proposed methodology.

  20. Geographical and taxonomic biases in invasion ecology.

    PubMed

    Pysek, Petr; Richardson, David M; Pergl, Jan; Jarosík, Vojtech; Sixtová, Zuzana; Weber, Ewald

    2008-05-01

    Invasive alien species come from most taxonomic groups, and invasion biology is searching for robust cross-taxon generalizations and principles. An analysis of 2,670 papers dealing with 892 invasive species showed that all major groups of invaders are well studied, but that most information on the mechanisms of invasion has emerged from work on a limited number of the most harmful invaders. A strong geographical bias, with Africa and Asia understudied, inhibits a balanced understanding of invasion, because we might be lacking knowledge of specific invasion mechanisms from poorly studied, regionally specific habitats. International cooperation is required to achieve a more geographically balanced picture of biological invasions. Invasive species with the greatest impact are best studied, but more studies of species that are naturalized but not (yet) invasive are needed to improve understanding of the mechanisms acting during the naturalization phase of invasions and leading to successful invasion.

  1. PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes.

    PubMed

    Gregor, Ivan; Dröge, Johannes; Schirmer, Melanie; Quince, Christopher; McHardy, Alice C

    2016-01-01

    Background. Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into 'bins' representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trained PhyloPythiaS package, where a human expert decides on the taxa to incorporate in the model and identifies 'training' sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have. Results. We have developed PhyloPythiaS+, a successor to our PhyloPythia(S) software. The new (+) component performs the work previously done by the human expert. PhyloPythiaS+ also includes a new k-mer counting algorithm, which accelerated the simultaneous counting of 4-6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. PhyloPythiaS+ was compared to MEGAN, taxator-tk, Kraken and the generic PhyloPythiaS model. The results showed that PhyloPythiaS+ performs especially well for samples originating from novel environments in comparison to the other methods. Availability. PhyloPythiaS+ in a virtual machine is available for installation under Windows, Unix systems or OS X on: https://github.com/algbioi/ppsp/wiki.

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

    PubMed

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

    2017-08-01

    Several species of marine fish use different coastal systems especially during their early development. However, these habitats are jeopardized by anthropogenic influences threatening the success of fish populations, and urgent measures are needed to priorize areas to protect their sustainability. We applied taxonomic (Δ+) and functional (X+) distinctiveness indices that represent taxonomic composition and functional roles to assess biodiversity of three different costal systems: bays, coastal lagoons and oceanic beaches. We hypothesized that difference in habitat characteristics, especially in the more dynamism and habitat homogeneity of oceanic beaches compared with more habitat diversity and sheltered conditions of bays and coastal lagoons results in differences in fish richness and taxonomic and functional diversity. The main premise is that communities phylogenetically and functionally more distinct have more interest in conservation policies. Significant differences (P < 0.004) were found in the species richness, Δ+ and X+ among the three systems according to PERMANOVA. Fish richness was higher in bays compared with the coastal lagoons and oceanic beaches. Higher Δ+ was found for the coastal lagoons compared with the bays and oceanic beaches, with the bays having some values below the confidence limit. Similar patterns were found for X+, although all values were within the confidence limits for the bays, suggesting that the absence of some taxa does not interfere in functional diversity. The hypothesis that taxonomic and functional structure of fish assemblages differ among the three systems was accepted and we suggest that coastal lagoons should be priorized in conservation programs because they support more taxonomic and functional distinctiveness. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Taxonomic and nontaxonomic responses to ecological changes in an urban lowland stream through the use of Chironomidae (Diptera) larvae.

    PubMed

    Cortelezzi, A; Paggi, A C; Rodríguez, M; Capítulo, A Rodrigues

    2011-03-01

    Biotic descriptors--both taxonomic (diversity indices, species richness, and indicator species) and nontaxonomic (biomass, oxygen consumption/production, and anatomical deformities)--are useful tools for measuring a stream's ecological condition. Nontaxonomic parameters detect critical effects not reflected taxonomically. We analyzed changes in Chironomidae populations as taxonomic parameters and mentum deformities as a nontaxonomic parameter for evaluating a South-American-plains stream (Argentina). We performed samplings seasonally (March, June, September, and December; 2005) and physical and chemical measurements at three sampling sites of the stream (DC1 at river source, through DC3 downstream). The specimens collected in sediment and vegetation were analyzed to investigate mouth deformities in Chironomidae larvae. We identified a total of 9 taxa from Chironomidae and Orthocladiinae subfamilies. Shannon's diversity index for Chironomidae decreased from 1.6 bits ind⁻¹ (DC1) to 0.3 bits ind⁻¹ (DC3). The total density of the Chironomidae exhibited a great increase in abundance at site DC3, especially that of Chironomus calligraphus. Chironomidae taxonomic composition also changed among the three sites despite their spatial proximity: C. calligraphus, Goeldichironomus holoprasinus, Parachironomus longistilus, and Polypedilum were present at all three; Corynoneura and Paratanytarsu at DC1 only; Cricotopus at DC1 and DC3; Apedilum elachistus notably at DC2 and DC3; and Parametriocnemus only at DC2. C. calligraphus individuals from DC1 showed no mentum deformities; only 2 from DC2 exhibited mouth-structure alterations; while specimens from DC3 presented the most abnormalities, especially during autumn and late winter. Type-II deformities (supernumerary teeth and gaps) were the most common. Anatomical deformities are sublethal effects representing an early alert to chemically caused environmental degradation. Mentum deformities in benthic-Chironomidae larvae

  4. Ionizing radiation and taxonomic, functional and evolutionary diversity of bird communities.

    PubMed

    Morelli, Federico; Benedetti, Yanina; Mousseau, Timothy A; Møller, Anders Pape

    2018-08-15

    Ionizing radiation from nuclear accidents at Chernobyl, Fukushima and elsewhere has reduced the abundance, species richness and diversity of ecosystems. Here we analyzed the taxonomic, functional and evolutionary diversity of bird communities in forested areas around Chernobyl. Species richness decreased with increasing radiation, mainly in 2007. Functional richness, but not functional evenness and divergence, decreased with increasing level of ionizing radiation. Evolutionary distinctiveness of bird communities was higher in areas with higher levels of ionizing radiation. Regression tree models revealed that species richness was higher in bird communities in areas with radiation levels lower than 0.7 μSv/h. In contrast, when radiation levels were higher than 16.67 μSv/h, bird species richness reached a minimum. Functional richness was affected by two variables: Forest cover and radiation level. Higher functional richness was found in bird communities in areas with forest cover lower than 50%. In the areas with forest cover higher than 50%, the functional richness was lower when radiation level was higher than 0.91 μSv/h. Finally, the average evolutionary distinctiveness of bird communities was higher in areas with forest cover exceeding 50%. These findings imply that level of ionizing radiation interacted with forest cover to affect species richness and its component parts, i.e. taxonomic, functional, and evolutionary diversity. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.

    PubMed

    Blank, Carrine E; Cui, Hong; Moore, Lisa R; Walls, Ramona L

    2016-01-01

    MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). During the MicroPIE design process, we realized there was a need for a prokaryotic ontology which would capture the evolutionary diversity of phenotypes and metabolic processes across the tree of life, capture the diversity of synonyms and information contained in the taxonomic literature, and relate microbiological entities and processes to terms in a large number of other ontologies, most particularly the Gene Ontology (GO), the Phenotypic Quality Ontology (PATO), and the Chemical Entities of Biological Interest (ChEBI). We thus constructed MicrO to be rich in logical axioms and synonyms gathered from the taxonomic literature. MicrO currently has ~14550 classes (~2550 of which are new, the remainder being microbiologically-relevant classes imported from other ontologies), connected by ~24,130 logical axioms (5,446 of which are new), and is available at (http://purl.obolibrary.org/obo/MicrO.owl) and on the project website at https://github.com/carrineblank/MicrO. MicrO has been integrated into the OBO Foundry Library (http://www.obofoundry.org/ontology/micro.html), so that other ontologies can borrow and re-use classes. Term requests and user feedback can be made using MicrO's Issue Tracker in GitHub. We designed MicrO such that it can support the ongoing and future development of algorithms that can leverage the controlled vocabulary and logical inference power provided by the ontology. By connecting microbial classes with large numbers of chemical entities, material entities, biological processes, molecular functions, and qualities using a dense array of logical axioms, we

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  8. Taxonomic profiling of bacterial community structure from coastal sediment of Alang-Sosiya shipbreaking yard near Bhavnagar, India.

    PubMed

    Patel, Vilas; Munot, Hitendra; Shah, Varun; Shouche, Yogesh S; Madamwar, Datta

    2015-12-30

    The Alang-Sosiya shipbreaking yard (ASSBY) is considered the largest of its kind in the world, and a major source of anthropogenic pollutants. The aim of this study was to investigate the impact of shipbreaking activities on the bacterial community structure with a combination of culture-dependent and culture-independent approaches. In the culture-dependent approach, 200 bacterial cultures were isolated and analyzed by molecular fingerprinting and 16S ribosomal RNA (r-RNA) gene sequencing, as well as being studied for degradation of polycyclic aromatic hydrocarbons (PAHs). In the culture-independent approach, operational taxonomic units (OTUs) were related to eight major phyla, of which Betaproteobacteria (especially Acidovorax) was predominantly found in the polluted sediments of ASSBY and Gammaproteobacteria in the pristine sediment sample. The statistical approaches showed a significant difference in the bacterial community structure between the pristine and polluted sediments. To the best of our knowledge, this is the first study investigating the effect of shipbreaking activity on the bacterial community structure of the coastal sediment at ASSBY. Copyright © 2015. Published by Elsevier Ltd.

  9. Taxonomic position of Chinese voles of the tribe Arvicolini and the description of 2 new species from Xizang, China

    PubMed Central

    Jin, Wei; Liu, Yang; Murphy, Robert W.; Lv, Bin; Hao, Haibang; Liao, Rui; Sun, Zhiyu; Tang, Mingkun; Chen, Weicai; Fu, Jianrong

    2017-01-01

    Abstract China has 26 species in the tribe Arvicolini. The taxonomic status of these voles remains controversial despite much effort. Herein, we evaluate the taxonomic position of 22 species plus 2 unidentified taxa using mitochondrial DNA gene sequences (cytb + CO1). We also evaluate 18 species and 2 unidentified taxa using morphological data. Phylogenetic analyses of cytb resolve monophyly for the genera Alexandromys, Lasiopodomys, Microtus, Neodon, Proedromys, and Volemys with strong support. Stenocranius clusters with Chionomys but with very weak support. Analyses of concatenated cytb + CO1 resolve the same genera with strong support, but the topology of the tree differs from that of cytb in that Chionomys roots at the base of the tree independent of Stenocranius, which forms the sister-group of Lasiopodomys in a more terminal position. The matrilineal genealogy excludes the type species Arvicola amphibius from the rest of the Arvicolini. This species forms the sister-group of Ondatra with high support. Neodon includes N. irene, N. linzhiensis, N. fuscus, N. leucurus, N. sikimensis, Microtus clarkei, and 2 unidentified specimens. Alexandromys includes the former species Microtus oeconomus, M. kikuchii, M. limnophilus, M. fortis, and M. maximowiczii. Finally, Microtus has the subgenera Blanfordimys, Microtus, Mynomes, Pedomys, Pitymys, and Terricola, which includes the Chinese species M. agrestis, M. arvalis, and Blanfordimys juldaschi. General mixed Yule-coalescent species delimitation modeling demarcates 6 currently recognized species and 2 new species of Neodon. A principal component analysis of the morphological data among 7 matrilines shows that all variables have positive loadings of high magnitude on the 1st component. Canonical discriminant analysis for Neodon (including M. clarkei and 2 unidentified species) correctly classifies 93.0% of specimens. Overall, our analyses support the recognition of Alexandromys, Lasiopodomys, Microtus, Neodon, Proedromys

  10. Phylogenetic relationships and taxonomic revision of Paranoplocephala Lühe, 1910 sensu lato (Cestoda, Cyclophyllidea, Anoplocephalidae)

    USDA-ARS?s Scientific Manuscript database

    An extensive phylogenetic analysis and genus-level taxonomic revision of Paranoplocephala Lühe, 1910 -like cestodes (Cyclophyllidea, Anoplocephalidae) are presented. The phylogenetic analysis is based on DNA sequences of two partial mitochondrial genes, i.e. cytochrome c oxidase subunit 1 (cox1) and...

  11. 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

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

    PubMed

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

    2018-04-01

    Monitoring of macroinvertebrate communities is frequently used to define the ecological health status of rivers. Ideally, biomonitoring should also give an indication on the major stressors acting on the macroinvertebrate communities supporting the selection of appropriate management measures. However, most indices are affected by more than one stressor. Biological traits (e.g. size, generation time, reproduction) could potentially lead to more stressor-specific indices. However, such an approach has rarely been tested. In this study we classify 324 macroinvertebrate taxa as vulnerable (decreasing abundances) or tolerant (increasing abundances) along 21 environmental gradients (i.e. nutrients, major ions, oxygen and micropollutants) from 422 monitoring sites in Germany using Threshold Indicator Taxa Analysis (TITAN). Subsequently, we investigate which biological traits and taxonomic groups are associated with taxa classified as vulnerable or tolerant with regard to specific gradients. The response of most taxa towards different gradients was similar and especially high for correlated gradients. Traits associated with vulnerable taxa across most gradients included: larval aquatic life stages, isolated cemented eggs, reproductive cycle per year <1, scrapers, aerial and aquatic active dispersal and plastron respiration. Traits associated with tolerant taxa included: adult aquatic life stages, polyvoltinism, ovoviviparity or egg clutches in vegetation, food preference for dead animals or living microinvertebrates, substrate preference for macrophytes, microphytes, silt or mud and a body size >2-4cm. Our results question whether stressor-specific indices based on macroinvertebrate assemblages can be achieved using single traits, because we observed that similar taxa responded to different gradients and also similar traits were associated with vulnerable and tolerant taxa across a variety of water quality gradients. Future studies should examine whether combinations of

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

    PubMed

    Wu, Shu; Xiong, Jie; Yu, Yuhe

    2015-01-01

    Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.

  14. Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda

    PubMed Central

    Wu, Shu; Xiong, Jie; Yu, Yuhe

    2015-01-01

    Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1–9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy. PMID:26107258

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

    PubMed Central

    2017-01-01

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

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

    PubMed

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

    2017-01-01

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

  17. The complex roles of space and environment in structuring functional, taxonomic and phylogenetic beta diversity of frogs in the Atlantic Forest

    PubMed Central

    Luiz, Amom Mendes; Sawaya, Ricardo J.

    2018-01-01

    Ecological communities are complex entities that can be maintained and structured by niche-based processes such as environmental conditions, and spatial processes such as dispersal. Thus, diversity patterns may be shaped simultaneously at different spatial scales by very distinct processes. Herein we assess whether and how functional, taxonomic, and phylogenetic beta diversities of frog tadpoles are explained by environmental and/or spatial predictors. We implemented a distance–based redundancy analysis to explore variation in components of beta diversity explained by pure environmental and pure spatial predictors, as well as their interactions, at both fine and broad spatial scales. Our results indicated important but complex roles of spatial and environmental predictors in structuring phylogenetic, taxonomic and functional beta diversities. The pure fine-scales spatial fraction was more important in structuring all beta diversity components, especially to functional and taxonomical spatial turnover. Environmental variables such as canopy cover and vegetation structure were important predictors of all components, but especially to functional and taxonomic beta diversity. We emphasize that distinct factors related to environment and space are affecting distinct components of beta diversity in different ways. Although weaker, phylogenetic beta diversity, which is structured more on biogeographical scales, and thus can be represented by spatially structured processes, was more related to broad spatial processes than other components. However, selected fine-scale spatial predictors denoted negative autocorrelation, which may be revealing the existence of differences in unmeasured habitat variables among samples. Although overall important, local environmental-based processes explained better functional and taxonomic beta diversity, as these diversity components carry an important ecological value. We highlight the importance of assessing different components of

  18. Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability

    DOE PAGES

    Lewin, Gina R.; Johnson, Amanda L.; Soto, Rolando D. Moreira; ...

    2016-03-21

    Deconstruction of the cellulose in plant cell walls is critical for carbon flow through ecosystems and for the production of sustainable cellulosic biofuels. Our understanding of cellulose deconstruction is largely limited to the study of microbes in isolation, but in nature, this process is driven by microbes within complex communities. In Neotropical forests, microbes in leaf-cutter ant refuse dumps are important for carbon turnover. These dumps consist of decaying plant material and a diverse bacterial community, as shown here by electron microscopy. To study the portion of the community capable of cellulose degradation, we performed enrichments on cellulose using materialmore » from five Atta colombica refuse dumps. The ability of enriched communities to degrade cellulose varied significantly across refuse dumps. 16S rRNA gene amplicon sequencing of enriched samples identified that the community structure correlated with refuse dump and with degradation ability. Overall, samples were dominated by Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. Half of abundant operational taxonomic units (OTUs) across samples were classified within general containing known cellulose degraders, including Acidovorax, the most abundant OTU detected across samples, which was positively correlated with cellulolytic ability. Lastly, a representative Acidovorax strain was isolated, but did not grow on cellulose alone. Phenotypic and compositional analyses of enrichment cultures, such as those presented here, help link community composition with cellulolytic ability and provide insight into the complexity of community-based cellulose degradation.« less

  19. Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lewin, Gina R.; Johnson, Amanda L.; Soto, Rolando D. Moreira

    Deconstruction of the cellulose in plant cell walls is critical for carbon flow through ecosystems and for the production of sustainable cellulosic biofuels. Our understanding of cellulose deconstruction is largely limited to the study of microbes in isolation, but in nature, this process is driven by microbes within complex communities. In Neotropical forests, microbes in leaf-cutter ant refuse dumps are important for carbon turnover. These dumps consist of decaying plant material and a diverse bacterial community, as shown here by electron microscopy. To study the portion of the community capable of cellulose degradation, we performed enrichments on cellulose using materialmore » from five Atta colombica refuse dumps. The ability of enriched communities to degrade cellulose varied significantly across refuse dumps. 16S rRNA gene amplicon sequencing of enriched samples identified that the community structure correlated with refuse dump and with degradation ability. Overall, samples were dominated by Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. Half of abundant operational taxonomic units (OTUs) across samples were classified within general containing known cellulose degraders, including Acidovorax, the most abundant OTU detected across samples, which was positively correlated with cellulolytic ability. Lastly, a representative Acidovorax strain was isolated, but did not grow on cellulose alone. Phenotypic and compositional analyses of enrichment cultures, such as those presented here, help link community composition with cellulolytic ability and provide insight into the complexity of community-based cellulose degradation.« less

  20. 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

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

    Treesearch

    Mitchell A. Pavao-Zuckerman; David C. Coleman

    2007-01-01

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

  2. Systematic and biogeographic review of the Staphylinini rove beetles of Lord Howe Island with description of new species and taxonomic changes (Coleoptera, Staphylinidae)

    PubMed Central

    Shaw, Josh Jenkins; Solodovnikov, Alexey

    2016-01-01

    Abstract Lord Howe is an oceanic and relatively young island situated in an area of complex geological and therefore biogeographical processes. The island boasts a large number of endemic species, including many beetles, however, few groups are in an adequate state of systematic knowledge for biogeographic investigation. Recent advances in the systematics of the hyper-diverse rove beetle tribe Staphylinini on a global scale enable us to implement taxonomic changes for species from Lord Howe Island. With the improved systematics we are able to make more accurate biogeographic conclusions and set a framework for further more in-depth exploration of this unique island using rove beetles. Two new species are described: Cheilocolpus olliffi sp. n. and Quediopsis howensis sp. n. Taxonomic changes for the tribe are implemented resulting in the following new combinations: Cheilocolpus castaneus (Lea, 1925), comb. n., Cheilocolpus kentiae (Lea, 1925), comb. n., Ctenandropus mirus (Lea, 1925), comb. n., and Hesperus dolichoderes (Lea, 1925), comb. n. With the updated state of knowledge, the Staphylinini fauna of Lord Howe Island appears to be mainly derived from lineages on mainland Australia. PMID:28174494

  3. 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.

  4. Community analysis of pigment patterns from 37 microalgae strains reveals new carotenoids and porphyrins characteristic of distinct strains and taxonomic groups

    PubMed Central

    Bérard, Jean-Baptiste; Kaas, Raymond; Pasquet, Virginie; Picot, Laurent; Cadoret, Jean-Paul

    2017-01-01

    Phytoplankton, with an estimated 30 000 to 1 000 000 species clustered in 12 phyla, presents a high taxonomic and ecophysiological diversity, reflected by the complex distribution of pigments among the different algal classes. High performance liquid chromatography is the gold standard method for qualitative and quantitative analysis of phytoplankton pigments in seawater and culture samples, but only a few pigments can be used as robust chemotaxonomic markers. A major challenge is thus to identify new ones, characteristic of a strain, species, class or taxon that cannot be currently identified on the basis of its pigment signature. Using an optimized extraction process coupled to a HPLC de-replication strategy, we examined the pigment composition of 37 microalgae strains, representative of the broad taxonomic diversity of marine and freshwater species (excluding cyanobacteria). For each species, the major pigments already described were unambiguously identified. We also observed the presence of several minor unidentified pigments in each chromatogram. The global analysis of pigment compositions revealed a total of 124 pigments, including 98 pigments or derivatives unidentified using the standards. Absorption spectra indicated that 35 corresponded to chlorophyll/porphyrin derivatives, 57 to carotenoids and six to derivatives having both spectral signatures. Sixty-one of these unidentified or new carotenoids and porphyrin derivatives were characteristic of particular strains or species, indicating their possible use as highly specific chemotaxonomic markers capable of identifying one strain out of the 37 selected. We developed a graphical analysis using Gephi software to give a clear representation of pigment communities among the various phytoplankton strains, and to reveal strain-characteristic and shared pigments. This made it possible to reconstruct the taxonomic evolution of microalgae classes, on the basis of the conservation, loss, and/or appearance of

  5. Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

    PubMed Central

    Porter, Teresita M; Gibson, Joel F; Shokralla, Shadi; Baird, Donald J; Golding, G Brian; Hajibabaei, Mehrdad

    2014-01-01

    Current methods to identify unknown insect (class Insecta) cytochrome c oxidase (COI barcode) sequences often rely on thresholds of distances that can be difficult to define, sequence similarity cut-offs, or monophyly. Some of the most commonly used metagenomic classification methods do not provide a measure of confidence for the taxonomic assignments they provide. The aim of this study was to use a naïve Bayesian classifier (Wang et al. Applied and Environmental Microbiology, 2007; 73: 5261) to automate taxonomic assignments for large batches of insect COI sequences such as data obtained from high-throughput environmental sequencing. This method provides rank-flexible taxonomic assignments with an associated bootstrap support value, and it is faster than the blast-based methods commonly used in environmental sequence surveys. We have developed and rigorously tested the performance of three different training sets using leave-one-out cross-validation, two field data sets, and targeted testing of Lepidoptera, Diptera and Mantodea sequences obtained from the Barcode of Life Data system. We found that type I error rates, incorrect taxonomic assignments with a high bootstrap support, were already relatively low but could be lowered further by ensuring that all query taxa are actually present in the reference database. Choosing bootstrap support cut-offs according to query length and summarizing taxonomic assignments to more inclusive ranks can also help to reduce error while retaining the maximum number of assignments. Additionally, we highlight gaps in the taxonomic and geographic representation of insects in public sequence databases that will require further work by taxonomists to improve the quality of assignments generated using any method.

  6. Minimal Similarity between Biogeographic Patterns of Morphological Disparity and Taxonomic Richness in Extant Coccolithophores

    NASA Astrophysics Data System (ADS)

    Villarosa Garcia, M.

    2016-02-01

    Morphologic disparity, carries both an ecological and evolutionary signal and, where practical, might bridge ecological processes observed in modern seas with macroevolutionary processes observed in the fossil record, complementing taxonomic diversity studies. I compare the biogeography of morphologic disparity and taxonomic richness in extant coccolithophores to understand the role of environmental conditions in their spatial partitioning. I analyze 112 traits in 125 species and measure geographic extent as the occupation of pelagic biogeographic provinces (sensu Spalding et al. 2012). In the modern ocean, coccolithophorid species richness increases towards the equator, peaking in the subtropics, and certain biomes harbor more species. In contrast, their morphologic disparity does not vary across latitudes and biomes, yielding similar values of variance and mean pair-wise distances. Disparity is weakly correlated to richness across clades and biomes (no clear latitudinal pattern). I also study the morphological breadth of clades in a multivariate morphospace plotted as principal coordinate axes (PCO). Clades have distinct centroids but show some overlap in volume. However, they are completely separate when using canonical variates analysis (CVA) on these PCO axes. The centroids of latitudinal groups are closely spaced, and overlap in morphospace, but again separate with CVA. However biome groups can't be distinguished using PCO or CVA. Although clades with the most species tend to have high disparity, most clades are found in every region yielding similar group disparities. Despite the fact that taxonomic diversity is spatially partitioned on the globe, morphologic disparity has no such organization. Past studies using marine gastropods (Roy et al. 2001; McClain 2005), cuttlefish (Neige 2003), and birds (Jønsson et al. 2015) also find minimal support for a biogeographic structure of disparity, highlighting the profound nature of this differential response.

  7. Taxonomic revision of the tarantula genus Aphonopelma Pocock, 1901 (Araneae, Mygalomorphae, Theraphosidae) within the United States

    PubMed Central

    Hamilton, Chris A.; Hendrixson, Brent E.; Bond, Jason E.

    2016-01-01

    Abstract This systematic study documents the taxonomy, diversity, and distribution of the tarantula spider genus Aphonopelma Pocock, 1901 within the United States. By employing phylogenomic, morphological, and geospatial data, we evaluated all 55 nominal species in the United States to examine the evolutionary history of Aphonopelma and the group’s taxonomy by implementing an integrative approach to species delimitation. Based on our analyses, we now recognize only 29 distinct species in the United States. We propose 33 new synonymies (Aphonopelma apacheum, Aphonopelma minchi, Aphonopelma rothi, Aphonopelma schmidti, Aphonopelma stahnkei = Aphonopelma chalcodes; Aphonopelma arnoldi = Aphonopelma armada; Aphonopelma behlei, Aphonopelma vogelae = Aphonopelma marxi; Aphonopelma breenei = Aphonopelma anax; Aphonopelma chambersi, Aphonopelma clarum, Aphonopelma cryptethum, Aphonopelma sandersoni, Aphonopelma sullivani = Aphonopelma eutylenum; Aphonopelma clarki, Aphonopelma coloradanum, Aphonopelma echinum, Aphonopelma gurleyi, Aphonopelma harlingenum, Aphonopelma odelli, Aphonopelma waconum, Aphonopelma wichitanum = Aphonopelma hentzi; Aphonopelma heterops = Aphonopelma moderatum; Aphonopelma jungi, Aphonopelma punzoi = Aphonopelma vorhiesi; Aphonopelma brunnius, Aphonopelma chamberlini, Aphonopelma iviei, Aphonopelma lithodomum, Aphonopelma smithi, Aphonopelma zionis = Aphonopelma iodius; Aphonopelma phanum, Aphonopelma reversum = Aphonopelma steindachneri), 14 new species (Aphonopelma atomicum sp. n., Aphonopelma catalina sp. n., Aphonopelma chiricahua sp. n., Aphonopelma icenoglei sp. n., Aphonopelma johnnycashi sp. n., Aphonopelma madera sp. n., Aphonopelma mareki sp. n., Aphonopelma moellendorfi sp. n., Aphonopelma parvum sp. n., Aphonopelma peloncillo sp. n., Aphonopelma prenticei sp. n., Aphonopelma saguaro sp. n., Aphonopelma superstitionense sp. n., and Aphonopelma xwalxwal sp. n.), and seven nomina dubia (Aphonopelma baergi, Aphonopelma cratium, Aphonopelma

  8. Comparing efficacy of different taxonomic resolutions and surrogates in detecting changes in soft bottom assemblages due to coastal defence structures.

    PubMed

    Bertasi, Fabio; Colangelo, Marina Antonia; Colosio, Francesco; Gregorio, Gianni; Abbiati, Marco; Ceccherelli, Victor Ugo

    2009-05-01

    Sandy shores on the West coast of the North Adriatic Sea are extensively protected by different types of defence structures to prevent coastal erosion. Coastal defence schemes modify the hydrodynamic regime, the sediment structure and composition thus affecting the benthic assemblages. This study examines the effectiveness in detecting changes in soft bottom assemblages caused by coastal defence structures by using different levels of taxonomic resolution, polychaetes and/or bivalves as surrogates and different data transformations. A synoptic analyses of three datasets of subtidal benthic macrofauna used in studies aimed at assessing the impact of breakwaters along the North Adriatic coast has been done. Analyses of similarities and correlations between distance matrices were done using matrices with different levels of taxonomic resolution, and with polychaetes or bivalves data alone. Lentidium mediterraneum was the most abundant species in all datasets. Its abundance was not consistently related to the presence of defence structures. Moreover, distribution patterns of L. mediterraneum were masking the structure of the whole macrofaunal assemblages. Removal of L. mediterraneum from the datasets allowed the detection of changes in benthic assemblages due to coastal defences. Analyses on different levels of taxonomic resolution showed that the level of family maintained sufficient information to detect the impacts of coastal defence structures on benthic assemblages. Moreover, the outcomes depended on the transformation used. Patterns of distribution of bivalves, used as surrogates, showed low correlations with the patterns of the total macrofaunal species assemblages. Patterns of polychaetes, if identified to the species or genus level showed higher correlations with the whole dataset. However, the identification of polychaetes to species and genus level is as costly as the identification of all macrobenthic taxa at family level. This study provided additional

  9. Taxonomic revision of Israeli snakes belonging to the Platyceps rhodorachis species complex (Reptilia: Squamata: Colubridae).

    PubMed

    Sinaiko, Guy; Magory-Cohen, Tali; Meiri, Shai; Dor, Roi

    2018-02-15

    The Platyceps rhodorachis species complex encompasses a widespread group of morphologically similar colubrid snakes. The number and identities of species from this complex in Israel have recently been debated. Studies from the previous decade concluded that there are two species in Israel and its vicinity (compared with one previously recognized), but their identity remained contested. We estimated the number of species and their taxonomic identity using morphological and molecular data. We found some evidence for clinal variation in many of the characters used to differentiate the species, and a great overlap in traits of putative species. Genetic data revealed very low sequence divergence, with all putative species being paraphyletic. Platyceps rogersi emerged as genetically closer to Platyceps saharicus rather than to its putative conspecific, P. karelini. The phylogenetic and taxonomic results thus indicate that the Israeli populations of the P. rhodorachis complex all belong to a single species, Platyceps saharicus (Schätti McCarthy 2004).

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

    EPA Science Inventory

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

  11. Circumscription and Taxonomic Arrangement of Nigroboletus roseonigrescens Gen. Et Sp. Nov., a New Member of Boletaceae from Tropical South–Eastern China

    PubMed Central

    Gelardi, Matteo; Vizzini, Alfredo; Ercole, Enrico; Horak, Egon; Ming, Zhang; Li, Tai–Hui

    2015-01-01

    Nigroboletus is proposed as a novel genus in family Boletaceae, subfamily Boletoideae, to include N. roseonigrescens, a new boletoid species from tropical environment in south–eastern China. Detailed morphological description, color pictures of both fresh basidiomes in habitat and dried material along with photomicrographs and line drawings of the main anatomical features are provided, supported by a comprehensive phylogeny based on multigene molecular analysis (nrITS, nrLSU, rpb1, rpb2 and tef1-α datasets). Taxonomic placement and evolutionary relationships of Nigroboletus are investigated. PMID:26263180

  12. Taxonomic and Biological Characterization of Steinernema rarum Found in the Southeastern United States

    PubMed Central

    Nguyen, Khuong B.; Shapiro-Ilan, David I.; Fuxa, James R.; Wood, Bruce W.; Bertolotti, Maria A.; Adams, Byron J.

    2006-01-01

    Two Steinernema isolates found in Louisiana and Mississippi were later identified as isolates of S. rarum. DNA sequences of ITS regions of the United States isolates are identical with sequences of Argentinean S. rarum strains Samiento and Noetinger and differ by two bases from the Arroyo Cabral isolate from Córdoba, Argentina. SEM observations revealed several new structures in the isolates from the US: female face views have a hexagonal-star perioral disc and eye-shaped lips; some females do not have cephalic papillae; lateral fields of infective juveniles are variable; there are two openings observed close to the posterior edge of the cloaca. Virulence of the US isolates to Anthonomus grandis, Diaprepes abbreviatus, Solenopsis invicta, Coptotermes formosanus, Agrotis ipsilon, Spodoptera frugiperda, and Trichoplusia ni and reproductive potential were evaluated in comparison with other heterorhabditid and steinernematid nematodes. Results such as particularly high virulence to S. frugiperda indicate that the biocontrol potential of the new S. rarum strains merits further study. PMID:19259427

  13. 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

  14. 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.

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

    PubMed

    Felsõ, B; Rózsa, L

    2006-08-01

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

  16. Contrasting Taxonomic and Phylogenetic Diversity Responses to Forest Modifications: Comparisons of Taxa and Successive Plant Life Stages in South African Scarp Forest

    PubMed Central

    Grass, Ingo; Brandl, Roland; Botzat, Alexandra; Neuschulz, Eike Lena; Farwig, Nina

    2015-01-01

    The degradation of natural forests to modified forests threatens subtropical and tropical biodiversity worldwide. Yet, species responses to forest modification vary considerably. Furthermore, effects of forest modification can differ, whether with respect to diversity components (taxonomic or phylogenetic) or to local (α-diversity) and regional (β-diversity) spatial scales. This real-world complexity has so far hampered our understanding of subtropical and tropical biodiversity patterns in human-modified forest landscapes. In a subtropical South African forest landscape, we studied the responses of three successive plant life stages (adult trees, saplings, seedlings) and of birds to five different types of forest modification distinguished by the degree of within-forest disturbance and forest loss. Responses of the two taxa differed markedly. Thus, the taxonomic α-diversity of birds was negatively correlated with the diversity of all plant life stages and, contrary to plant diversity, increased with forest disturbance. Conversely, forest disturbance reduced the phylogenetic α-diversity of all plant life stages but not that of birds. Forest loss neither affected taxonomic nor phylogenetic diversity of any taxon. On the regional scale, taxonomic but not phylogenetic β-diversity of both taxa was well predicted by variation in forest disturbance and forest loss. In contrast to adult trees, the phylogenetic diversity of saplings and seedlings showed signs of contemporary environmental filtering. In conclusion, forest modification in this subtropical landscape strongly shaped both local and regional biodiversity but with contrasting outcomes. Phylogenetic diversity of plants may be more threatened than that of mobile species such as birds. The reduced phylogenetic diversity of saplings and seedlings suggests losses in biodiversity that are not visible in adult trees, potentially indicating time-lags and contemporary shifts in forest regeneration. The different

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

    EPA Science Inventory

    Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to what extent diversity reduces vulnerability to polyphagous (i.e. generalist) pests. Drawing on field data from seven c...

  18. Pyrosequencing analysis of bacterial diversity in dental unit waterlines.

    PubMed

    Costa, Damien; Mercier, Anne; Gravouil, Kevin; Lesobre, Jérôme; Delafont, Vincent; Bousseau, Anne; Verdon, Julien; Imbert, Christine

    2015-09-15

    Some infections cases due to exposure to output water from dental unit waterlines (DUWL) have been reported in the literature. However, this type of healthcare-associated risk has remained unclear and up until now the overall bacterial composition of DUWL has been poorly documented. In this study, 454 high-throughput pyrosequencing was used to investigate the bacterial community in seven dental offices (N = 7) and to identify potential bacterial pathogenic sequences. Dental unit waters (DUW) were collected from the tap water supplying units (Incoming Water; IW) to the output exposure point of the turbine handpiece (Output water; OW) following a stagnation period (OWS), and immediately after the last patient of the sampling day (OWA). A high bacterial diversity was revealed in DUW with 394 operational taxonomic units detected at the genus level. In addition to the inter-unit variability observed, results showed increased total bacterial cell concentration and shifts in bacterial community composition and abundance at the genus level, mainly within the Gamma- and Alpha-Proteobacteria class, as water circulated in the dental unit (DU). Results showed that 96.7%, 96.8% and 97.4% of the total sequences from IW, OWS and OWA respectively were common to the 3 defined water groups, thereby highlighting a common core microbiome. Results also suggested that stagnation and DU maintenance practices were critical to composition of the bacterial community. The presence of potentially pathogenic genera was detected, including Pseudomonas and Legionella spp. Emerging and opportunistic pathogenic genera such as Mycobacterium, Propionibacterium and Stenotrophomonas were likewise recovered in DUW. For the first time, an exhaustive evaluation of the bacterial communities present in DUW was performed taking into account the circulation of water within the DU. This study highlights an ignored diversity of the DUWL bacterial community. Our findings also contribute to a better

  19. A Study of the Homogeneity of Items Produced From Item Forms Across Different Taxonomic Levels.

    ERIC Educational Resources Information Center

    Weber, Margaret B.; Argo, Jana K.

    This study determined whether item forms ( rules for constructing items related to a domain or set of tasks) would enable naive item writers to generate multiple-choice items at three taxonomic levels--knowledge, comprehension, and application. Students wrote 120 multiple-choice items from 20 item forms, corresponding to educational objectives…

  20. EEG Theta and Alpha Responses Reveal Qualitative Differences in Processing Taxonomic versus Thematic Semantic Relationships

    ERIC Educational Resources Information Center

    Maguire, Mandy J.; Brier, Matthew R.; Ferree, Thomas C.

    2010-01-01

    Despite the importance of semantic relationships to our understanding of semantic knowledge, the nature of the neural processes underlying these abilities are not well understood. In order to investigate these processes, 20 healthy adults listened to thematically related (e.g., leash-dog), taxonomically related (e.g., horse-dog), or unrelated…

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

    ERIC Educational Resources Information Center

    Kuchinke, Lars; van der Meer, Elke; Krueger, Frank

    2009-01-01

    Conceptual knowledge of our world is represented in semantic memory in terms of concepts and semantic relations between concepts. We used functional magnetic resonance imaging (fMRI) to examine the cortical regions underlying the processing of sequential and taxonomic relations. Participants were presented verbal cues and performed three tasks:…

  2. The systematic component of phylogenetic error as a function of taxonomic sampling under parsimony.

    PubMed

    Debry, Ronald W

    2005-06-01

    The effect of taxonomic sampling on phylogenetic accuracy under parsimony is examined by simulating nucleotide sequence evolution. Random error is minimized by using very large numbers of simulated characters. This allows estimation of the consistency behavior of parsimony, even for trees with up to 100 taxa. Data were simulated on 8 distinct 100-taxon model trees and analyzed as stratified subsets containing either 25 or 50 taxa, in addition to the full 100-taxon data set. Overall accuracy decreased in a majority of cases when taxa were added. However, the magnitude of change in the cases in which accuracy increased was larger than the magnitude of change in the cases in which accuracy decreased, so, on average, overall accuracy increased as more taxa were included. A stratified sampling scheme was used to assess accuracy for an initial subsample of 25 taxa. The 25-taxon analyses were compared to 50- and 100-taxon analyses that were pruned to include only the original 25 taxa. On average, accuracy for the 25 taxa was improved by taxon addition, but there was considerable variation in the degree of improvement among the model trees and across different rates of substitution.

  3. CONCORDANCE OF TAXONOMIC COMPOSITION PATTERNS ACROSS MULTIPLE LAKE ASSEMBLAGES: EFFECTS OF SCALE, BODY SIZE, AND LAND USE

    EPA Science Inventory

    We assessed environmental gradients and the extent to which they induced concordant patterns of taxonomic composition among benthic macroinvertebrate, riparian bird, sedimentary diatom, fish, and pelagic zooplankton assemblages in 186 northeastern U.S.A. lakes. Human population ...

  4. Phylogenetic analyses of mtDNA sequences corroborate taxonomic designations based on cuticular hydrocarbons in subterranean termites

    Treesearch

    Kirsten A. Copren; Lori J. Nelson; Edward L. Vargo; Michael I. Haverty

    2005-01-01

    Cuticular hydrocarbons (CHCs) are valuable characters for the analysis of cryptic insect species with few discernible morphological characters. Yet, their use in insect systematics, speciWcally in subterranean termites in the genus Reticulitermes (Isoptera: Rhinotermitidae), remains controversial. In this paper, we show that taxonomic designations...

  5. Taxonomic revision of the long-nosed armadillos, Genus Dasypus Linnaeus, 1758 (Mammalia, Cingulata)

    PubMed Central

    Patterson, Bruce D.; Cordeiro-Estrela, Pedro

    2018-01-01

    Dasypus is the most speciose genus of the order Cingulata, including approximately 40% of known living armadillos. Nine species are currently recognized, although comprehensive analyses of the entire genus have never been done. Our aim is to revise the taxonomy of the long-nosed armadillos and properly define the taxa. We examined 2126 specimens of Dasypus preserved in 39 different museum collections, including 17 type specimens. Three complementary methods were applied to explore morphological datasets both qualitatively and quantitatively. Qualitative morphological variation in discrete characters was assessed by direct observations of specimens. Linear morphometric variation was based on external data and cranial measurements of 887 adult skulls. The shape and size of the skull was abstracted through two-dimensional geometric morphometric analyses of dorsal, lateral and ventral views of respectively 421, 211, and 220 adult specimens. Our results converge on the recognition of eight living species (D. beniensis, D. kappleri, D. mazzai, D. novemcinctus, D. pastasae, D. pilosus, D. sabanicola, and D. septemcinctus), and three subspecies of D. septemcinctus (D. s. septemcinctus, D. s. hybridus, and a new subspecies from Cordoba described here). Information on type material, diagnosis, distribution, and taxonomic comments for each taxon are provided. We designate a lectotype for D. novemcinctus; and a neotype for Loricatus hybridus (= D. septemcinctus hybridus). PMID:29624590

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

    USDA-ARS?s Scientific Manuscript database

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

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

    PubMed

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

    2017-01-01

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

  8. Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse

    PubMed Central

    Tanca, Alessandro; Manghina, Valeria; Fraumene, Cristina; Palomba, Antonio; Abbondio, Marcello; Deligios, Massimo; Silverman, Michael; Uzzau, Sergio

    2017-01-01

    Previous studies on mouse models report that cecal and fecal microbial communities may differ in the taxonomic structure, but little is known about their respective functional activities. Here, we employed a metaproteogenomic approach, including 16S rRNA gene sequencing, shotgun metagenomics and shotgun metaproteomics, to analyze the microbiota of paired mouse cecal contents (CCs) and feces, with the aim of identifying changes in taxon-specific functions. As a result, Gram-positive anaerobes were observed as considerably higher in CCs, while several key enzymes, involved in oxalate degradation, glutamate/glutamine metabolism, and redox homeostasis, and most actively expressed by Bacteroidetes, were clearly more represented in feces. On the whole, taxon and function abundance appeared to vary consistently with environmental changes expected to occur throughout the transit from the cecum to outside the intestine, especially when considering metaproteomic data. The results of this study indicate that functional and metabolic differences exist between CC and stool samples, paving the way to further metaproteogenomic investigations aimed at elucidating the functional dynamics of the intestinal microbiota. PMID:28352255

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

    Treesearch

    A.E. Squillace; Jesse P. Perry

    1992-01-01

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

  10. The taxonomic distinctness of macroinvertebrate communities of Atlantic Forest streams cannot be predicted by landscape and climate variables, but traditional biodiversity indices can.

    PubMed

    Roque, F O; Guimarães, E A; Ribeiro, M C; Escarpinati, S C; Suriano, M T; Siqueira, T

    2014-11-01

    Predicting how anthropogenic activities may influence the various components of biodiversity is essential for finding ways to reduce diversity loss. This challenge involves: a) understanding how environmental factors influence diversity across different spatial scales, and b) developing ways to measure these relationships in a way that is fast, economical, and easy to communicate. In this study, we investigate whether landscape and bioclimatic variables could explain variation in biodiversity indices in macroinvertebrate communities from 39 Atlantic Forest streams. In addition to traditional diversity measures, i.e., species richness, abundance and Shannon index, we used a taxonomic distinctness index that measures the degree of phylogenetic relationship among taxa. The amount of variation in the diversity measures that was explained by environmental and spatial variables was estimated using variation partitioning based on multiple regression. Our study demonstrates that taxonomic distinctness does not respond in the same way as the traditional used in biodiversity studies. We found no evidence that taxonomic distinctness responds predictably to variation in landscape metrics, indicating the need for the incorporation of predictors at multiple scales in this type of study. The lack of congruence between taxonomic distinctness and other indices and its low predictability may be related to the fact that this measure expresses long-term evolutionary adaptation to ecosystem conditions, while the other traditional biodiversity metrics respond to short-term environmental changes.

  11. Snake species of the world: A taxonomic and geographic reference. v. 1

    USGS Publications Warehouse

    McDiarmid, R.W.; Campbell, J.A.; Toure, T.

    1999-01-01

    Given the absence of a current source on snake diversity and nomenclature and the expressed global need to understand better the diversity of our biota, we think that a catalogue of the world snake fauna complete with synonymies at the familial, generic, and specific levels is essential. We provide that here beginning with publication of the first volume. This compendium will facilitate comparative studies on the ecology, genetics, and behavior of snakes and, we hope, contribute to their conservation. At the very least, this work, when completed, will provide a readily available reference to the current taxonomic statuses and geographic distributions of snakes on a global scale. No comprehensive, up-to-date catalogue of snake species exists, and it is obvious that a detailed and inclusive treatment is long overdue. Snake Species of the World provides a comprehensive treatment of 31 families, 450 genera, and more than 2500 species of living snakes. The magnitude of the compilation requires publication in several volumes. This volume, the first of three, covers 682 species. A primary goal of this synthesis is to provide interested readers with a means for tracking scientific names that have been applied to a snake and determining the currently accepted name of that species. A secondary goal is to alert those interested in snakes as research subjects that in general many species are poorly known, that some have limited distributions, and that several are characterized by taxonomic problems.

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

    NASA Astrophysics Data System (ADS)

    Laman, Charlie J. M.; Kho, Angel

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

  13. THE EFFECTS OF MACROINVERTEBRATE TAXONOMIC RESOLUTION IN LARGE LANDSCAPE BIOASSESSMENTS: AN EXAMPLE FROM THE MID-ATLANTIC HIGHLANDS, USA

    EPA Science Inventory

    The macroinvertebrate taxonomic resolution needed for detecting human impacts on stream ecosystems draws continued attention from stream ecologists. During late spring 1993-1995, the U.S. Environmental Protection Agency's Environmental Monitoring and Assessment Program (EMAP) sam...

  14. Ionic liquids, electrolyte solutions including the ionic liquids, and energy storage devices including the ionic liquids

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gering, Kevin L.; Harrup, Mason K.; Rollins, Harry W.

    2015-12-08

    An ionic liquid including a phosphazene compound that has a plurality of phosphorus-nitrogen units and at least one pendant group bonded to each phosphorus atom of the plurality of phosphorus-nitrogen units. One pendant group of the at least one pendant group comprises a positively charged pendant group. Additional embodiments of ionic liquids are disclosed, as are electrolyte solutions and energy storage devices including the embodiments of the ionic liquid.

  15. Taxonomic review of Argentine mackerel Scomber japonicus (Houttuyn, 1782) by phylogenetic analysis

    PubMed Central

    Trucco, María Inés; Buratti, Claudio César

    2017-01-01

    Taxonomically, Argentine mackerels were first considered as Scomber japonicus marplatensis and later as Scomber japonicus Houttuyn 1782, although, in the last years, different studies have suggested that South Atlantic mackerel species belongs to Scomber colias Gmelin 1789. These latter results, incorporated in the main fish databases (FishBase and Catalog of Fishes), promoted a phylogenetic study using cytochrome c oxidase I (COI) gene sequences taken from the Barcode of Life (FISH-BOL) database. Thus, 76 sequences of S. japonicus, S. colias, S. australasicus and S. scombrus from different regions were used; including 3 from Sarda sarda as outgroup. Among S. japonicus selected sequences are those corresponding to the Argentine mackerels collected in 2007. Phylogenetic trees were obtained by neighbor joining and maximum likelihood methods and a network of haplotypes was reconstructed to analyze the relationship between species. The results showed the clear differentiation of S. australasicus, S. scombrus and S. japonicus from the Pacific while S. japonicus from Argentina was included in the S. colias group, with genetic differences corresponding to conspecific populations (0.1%). Four of the five Argentine specimens shared the same haplotype with S. colias, and none were shared with S. japonicus from the Pacific. These results suggest that the current specific name of Argentine mackerel S. japonicus should be changed to S. colias, in agreement with several genetic studies carried out with species of the genus Scomber. PMID:29071283

  16. 20 CFR 408.809 - What happens to your SVB payments if you are removed (including deported) from the United States?

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 20 Employees' Benefits 2 2013-04-01 2013-04-01 false What happens to your SVB payments if you are removed (including deported) from the United States? 408.809 Section 408.809 Employees' Benefits SOCIAL SECURITY ADMINISTRATION SPECIAL BENEFITS FOR CERTAIN WORLD WAR II VETERANS Suspensions and Terminations...

  17. 20 CFR 408.809 - What happens to your SVB payments if you are removed (including deported) from the United States?

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 20 Employees' Benefits 2 2014-04-01 2014-04-01 false What happens to your SVB payments if you are removed (including deported) from the United States? 408.809 Section 408.809 Employees' Benefits SOCIAL SECURITY ADMINISTRATION SPECIAL BENEFITS FOR CERTAIN WORLD WAR II VETERANS Suspensions and Terminations...

  18. 20 CFR 408.809 - What happens to your SVB payments if you are removed (including deported) from the United States?

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 20 Employees' Benefits 2 2012-04-01 2012-04-01 false What happens to your SVB payments if you are removed (including deported) from the United States? 408.809 Section 408.809 Employees' Benefits SOCIAL SECURITY ADMINISTRATION SPECIAL BENEFITS FOR CERTAIN WORLD WAR II VETERANS Suspensions and Terminations...

  19. 20 CFR 408.809 - What happens to your SVB payments if you are removed (including deported) from the United States?

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false What happens to your SVB payments if you are removed (including deported) from the United States? 408.809 Section 408.809 Employees' Benefits SOCIAL SECURITY ADMINISTRATION SPECIAL BENEFITS FOR CERTAIN WORLD WAR II VETERANS Suspensions and Terminations...

  20. 20 CFR 408.809 - What happens to your SVB payments if you are removed (including deported) from the United States?

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 20 Employees' Benefits 2 2011-04-01 2011-04-01 false What happens to your SVB payments if you are removed (including deported) from the United States? 408.809 Section 408.809 Employees' Benefits SOCIAL SECURITY ADMINISTRATION SPECIAL BENEFITS FOR CERTAIN WORLD WAR II VETERANS Suspensions and Terminations...

  1. 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.

  2. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.

    PubMed

    Rodriguez-R, Luis M; Gunturu, Santosh; Harvey, William T; Rosselló-Mora, Ramon; Tiedje, James M; Cole, James R; Konstantinidis, Konstantinos T

    2018-06-14

    The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts. MiGA integrates best practices in sequence quality trimming and assembly and allows input to be raw reads or assemblies from isolate genomes, single-cell sequences, and metagenome-assembled genomes (MAGs). Further, MiGA can take as input hundreds of closely related genomes of the same or closely related species (a so-called 'Clade Project') to assess their gene content diversity and evolutionary relationships, and calculate important clade properties such as the pangenome and core gene sets. Therefore, MiGA is expected to facilitate a range of genome-based taxonomic and diversity studies, and quality assessment across environmental and clinical settings. MiGA is available at http://microbial-genomes.org/.

  3. The importance of taxonomic resolution for additive beta diversity as revealed through DNA barcoding.

    PubMed

    Bringloe, Trevor T; Cottenie, Karl; Martin, Gillian K; Adamowicz, Sarah J

    2016-12-01

    Additive diversity partitioning (α, β, and γ) is commonly used to study the distribution of species-level diversity across spatial scales. Here, we first investigate whether published studies of additive diversity partitioning show signs of difficulty attaining species-level resolution due to inherent limitations with morphological identifications. Second, we present a DNA barcoding approach to delineate specimens of stream caddisfly larvae (order Trichoptera) and consider the importance of taxonomic resolution on classical (additive) measures of beta (β) diversity. Caddisfly larvae were sampled using a hierarchical spatial design in two regions (subarctic Churchill, Manitoba, Canada; temperate Pennsylvania, USA) and then additively partitioned according to Barcode Index Numbers (molecular clusters that serve as a proxy for species), genus, and family levels; diversity components were expressed as proportional species turnover. We screened 114 articles of additive diversity partitioning and found that a third reported difficulties with achieving species-level identifications, with a clear taxonomic tendency towards challenges identifying invertebrate taxa. Regarding our own study, caddisfly BINs appeared to show greater subregional turnover (e.g., proportional additive β) compared to genus or family levels. Diversity component studies failing to achieve species resolution due to morphological identifications may therefore be underestimating diversity turnover at larger spatial scales.

  4. Beyond botany to genetic resource preservation: the S. P. Vander Kloet Vaccinium L. collections

    USDA-ARS?s Scientific Manuscript database

    Dr. S. P. Vander Kloet, botanist, traveled the world examining and obtaining specimens to redefine infrageneric taxonomic units within Vaccinium L., family Ericaceae. Besides his botanical treatises, his legacy includes herbarium voucher specimens and ex situ genetic resource collections including a...

  5. The taxonomic distribution of asteroids from multi-filter all-sky photometric surveys

    NASA Astrophysics Data System (ADS)

    DeMeo, F. E.; Carry, B.

    2013-09-01

    The distribution of asteroids across the main belt has been studied for decades to understand the current compositional distribution and what that tells us about the formation and evolution of our Solar System. All-sky surveys now provide orders of magnitude more data than targeted surveys. We present a method to bias-correct the asteroid population observed in the Sloan Digital Sky Survey (SDSS) according to size, distance, and albedo. We taxonomically classify this dataset consistent with the Bus and Binzel (Bus, S.J., Binzel, R.P. [2002]. Icarus 158, 146-177) and Bus-DeMeo et al. (DeMeo, F.E., Binzel, R.P., Slivan, S.M., Bus, S.J. [2009]. Icarus 202(July), 160-180) systems and present the resulting taxonomic distribution. The dataset includes asteroids as small as 5 km, a factor of three in diameter smaller than in previous work such as by Mothé-Diniz et al. (Mothé-Diniz, T., Carvano, J.M.Á., Lazzaro, D. [2003]. Icarus 162(March), 10-21). Because of the wide range of sizes in our sample, we present the distribution by number, surface area, volume, and mass whereas previous work was exclusively by number. While the distribution by number is a useful quantity and has been used for decades, these additional quantities provide new insights into the distribution of total material. We find evidence for D-types in the inner main belt where they are unexpected according to dynamical models of implantation of bodies from the outer Solar System into the inner Solar System during planetary migration (Levison, H.F., Bottke, W.F., Gounelle, M., Morbidelli, A., Nesvorný, D., Tsiganis, K. [2009]. Nature 460(July), 364-366). We find no evidence of S-types or other unexpected classes among Trojans and Hildas, albeit a bias favoring such a detection. Finally, we estimate for the first time the total amount of material of each class in the inner Solar System. The main belt’s most massive classes are C, B, P, V and S in decreasing order. Excluding the four most massive

  6. Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

    PubMed Central

    Liu, Jiemeng; Wang, Haifeng; Yang, Hongxing; Zhang, Yizhe; Wang, Jinfeng; Zhao, Fangqing; Qi, Ji

    2013-01-01

    Compared with traditional algorithms for long metagenomic sequence classification, characterizing microorganisms’ taxonomic and functional abundance based on tens of millions of very short reads are much more challenging. We describe an efficient composition and phylogeny-based algorithm [Metagenome Composition Vector (MetaCV)] to classify very short metagenomic reads (75–100 bp) into specific taxonomic and functional groups. We applied MetaCV to the Meta-HIT data (371-Gb 75-bp reads of 109 human gut metagenomes), and this single-read-based, instead of assembly-based, classification has a high resolution to characterize the composition and structure of human gut microbiota, especially for low abundance species. Most strikingly, it only took MetaCV 10 days to do all the computation work on a server with five 24-core nodes. To our knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time. PMID:22941634

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

    PubMed

    Jiménez-Mejías, Pedro; Martinetto, Edoardo

    2013-08-01

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

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

    PubMed

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

    1997-12-01

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

  9. A taxonomic review of the centipede genus Scolopendra Linnaeus, 1758 (Scolopendromorpha, Scolopendridae) in mainland Southeast Asia, with description of a new species from Laos

    PubMed Central

    Siriwut, Warut; Edgecombe, Gregory D.; Sutcharit, Chirasak; Tongkerd, Piyoros; Panha, Somsak

    2016-01-01

    Abstract The centipede genus Scolopendra in mainland Southeast Asia is reviewed taxonomically based on morphological characters, informed by a molecular phylogenetic analysis using sequences from three mitochondrial and nuclear genes (COI, 16S rRNA and 28S rRNA). Eight nominal species of Scolopendra, namely Scolopendra morsitans Linnaeus, 1758, Scolopendra subspinipes Leach, 1816, Scolopendra dehaani Brandt, 1840, Scolopendra multidens Newport, 1844, Scolopendra calcarata Porat, 1876, Scolopendra japonica Koch, 1878, Scolopendra pinguis Pocock, 1891, and Scolopendra dawydoffi Kronmüller, 2012, are redescribed together with some revision of type materials. Geographical variation in each species has been compiled with reference to samples that span their distribution ranges in Southeast Asia and some parts of neighbouring areas such as East Asia, the Indian Ocean, and Africa. Comparative study of traditional taxonomic characters from external morphology provides further information to distinguish some closely related species. Scolopendra cataracta Siriwut, Edgecombe & Panha, sp. n., is described from the southern part of Laos, with additional records in Thailand and Vietnam. The phylogenetic framework for Southeast Asian Scolopendra recognizes Scolopendra calcarata + Scolopendra pinguis, Scolopendra morsitans, and a Scolopendra subspinipes group that unites the other six species as the main clades. Within the Scolopendra subspinipes group, two monophyletic groups can be distinguished by having either slender or short, thick ultimate leg prefemora and different numbers of apical spines on the coxopleuron. Scolopendra arborea Lewis, 1982, is placed in subjective synonymy with Scolopendra dehaani. A survey of external morphology of the genital segments confirms its potential for improving species identification in Scolopendra. Some observations on biology and behaviour are recorded based on field surveys in this area. PMID:27408540

  10. Taxonomic discrimination of higher plants by pyrolysis mass spectrometry.

    PubMed

    Kim, S W; Ban, S H; Chung, H J; Choi, D W; Choi, P S; Yoo, O J; Liu, J R

    2004-02-01

    Pyrolysis mass spectrometry (PyMS) is a rapid, simple, high-resolution analytical method based on thermal degradation of complex material in a vacuum and has been widely applied to the discrimination of closely related microbial strains. Leaf samples of six species and one variety of higher plants (Rosa multiflora, R. multiflora var. platyphylla, Sedum kamtschaticum, S. takesimense, S. sarmentosum, Hepatica insularis, and H. asiatica) were subjected to PyMS for spectral fingerprinting. Principal component analysis of PyMS data was not able to discriminate these plants in discrete clusters. However, canonical variate analysis of PyMS data separated these plants from one another. A hierarchical dendrogram based on canonical variate analysis was in agreement with the known taxonomy of the plants at the variety level. These results indicate that PyMS is able to discriminate higher plants based on taxonomic classification at the family, genus, species, and variety level.

  11. 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

    2015-04-28

    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. 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

  13. Distinct Growth and Secretome Strategies for Two Taxonomically Divergent Brown Rot Fungi.

    PubMed

    Presley, Gerald N; Schilling, Jonathan S

    2017-04-01

    Brown rot fungi are wood-degrading fungi that employ both oxidative and hydrolytic mechanisms to degrade wood. Hydroxyl radicals that facilitate the oxidative component are powerful nonselective oxidants and are incompatible with hydrolytic enzymes unless they are spatially segregated in wood. Differential gene expression has been implicated in the segregation of these reactions in Postia placenta , but it is unclear if this two-step mechanism varies in other brown rot fungi with different traits and life history strategies that occupy different niches in nature. We employed proteomics to analyze a progression of wood decay on thin wafers, using brown rot fungi with significant taxonomic and niche distances: Serpula lacrymans (Boletales; "dry rot" lumber decay) and Gloeophyllum trabeum (order Gloeophyllales; slash, downed wood). Both fungi produced greater oxidoreductase diversity upon wood colonization and greater glycoside hydrolase activity later, consistent with a two-step mechanism. The two fungi invested very differently, however, in terms of growth (infrastructure) versus protein secretion (resource capture), with the ergosterol/extracted protein ratio being 7-fold higher with S. lacrymans than with G. trabeum In line with the native substrate associations of these fungi, hemicellulase-specific activities were dominated by mannanase in S. lacrymans and by xylanase in G. trabeum Consistent with previous observations, S. lacrymans did not produce glycoside hydrolase 6 (GH6) cellobiohydrolases (CBHs) in this study, despite taxonomically belonging to the order Boletales, which is distinguished among brown rot fungi by having CBH genes. This work suggests that distantly related brown rot fungi employ staggered mechanisms to degrade wood, but the underlying strategies vary among taxa. IMPORTANCE Wood-degrading fungi are important in forest nutrient cycling and offer promise in biotechnological applications. Brown rot fungi are unique among these fungi in that they

  14. 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

  15. Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.

    PubMed

    Rudney, Joel D; Jagtap, Pratik D; Reilly, Cavan S; Chen, Ruoqiong; Markowski, Todd W; Higgins, LeeAnn; Johnson, James E; Griffin, Timothy J

    2015-12-19

    The etiology of dental caries is multifactorial, but frequent consumption of free sugars, notably sucrose, appears to be a major factor driving the supragingival microbiota in the direction of dysbiosis. Recent 16S rRNA-based studies indicated that caries-associated communities were less diverse than healthy supragingival plaque but still displayed considerable taxonomic diversity between individuals. Metagenomic studies likewise have found that healthy oral sites from different people were broadly similar with respect to gene function, even though there was an extensive individual variation in their taxonomic profiles. That pattern may also extend to dysbiotic communities. In that case, shifts in community-wide protein relative abundance might provide better biomarkers of dysbiosis that can be achieved through taxonomy alone. In this study, we used a paired oral microcosm biofilm model of dental caries to investigate differences in community composition and protein relative abundance in the presence and absence of sucrose. This approach provided large quantities of protein, which facilitated deep metaproteomic analysis. Community composition was evaluated using 16S rRNA sequencing and metaproteomic approaches. Although taxonomic diversity was reduced by sucrose pulsing, considerable inter-subject variation in community composition remained. By contrast, functional analysis using the SEED ontology found that sucrose induced changes in protein relative abundance patterns for pathways involving glycolysis, lactate production, aciduricity, and ammonia/glutamate metabolism that were conserved across taxonomically diverse dysbiotic oral microcosm biofilm communities. Our findings support the concept of using function-based changes in protein relative abundance as indicators of dysbiosis. Our microcosm model cannot replicate all aspects of the oral environment, but the deep level of metaproteomic analysis it allows makes it suitable for discovering which proteins are

  16. Seed traits and taxonomic relationships determine the occurrence of mutualisms versus seed predation in a tropical forest rodent and seed dispersal system.

    PubMed

    Wang, Zhenyu; Cao, Lin; Zhang, Zhibin

    2014-06-01

    Although many studies have been carried out on plant-animal mutualistic assemblages, the roles of functional traits and taxonomy in determining both whether interactions involve mutualisms or predation and the structure of such assemblages are unclear. We used semi-natural enclosures to quantitatively assess the interaction strengths between seeds of 8 sympatric tree species and 4 rodent species in a tropical forest in Xishuangbanna, Yunnan, Southwest China. We found 2 clusters of species in the seed-rodent network represented by 2 genera in the Fagaceae (Castanopsis, Lithocarpus). Compared to seeds of 3 Castanopsis species, seeds with heavy weight, hard coat or caloric content (including 3 Lithocarpus species) were eaten less and more frequently hoarded by rodents. In turn, hoarded seeds showed less predation and more mutualism with rodents. Our results suggest that seed traits significantly affected the hoarding behavior of rodents, and, consequently, the occurrence of mutualisms and predation as well as assemblage structure in the plant-animal seed dispersal system. Taxonomically-related species with similar seed traits as functional groups belong to the same substructures in the assemblage. Our results indicate that both seed traits and taxonomic relationships may simplify thinking about seed dispersal systems by helping to elucidate whether interactions are likely to be dominated by predation or mutualism. © 2013 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

  17. An annotated key to the identification of commonly occurring and dominant genera of algae observed in the phytoplankton of the United States

    USGS Publications Warehouse

    Greeson, Phillip E.

    1982-01-01

    In early 1979, a retrieval was made for all phytoplankton data contained in the computerized data file of the U. S. Geological Survey. The retrieval revealed the analytical results of 17,959 samples collected and processed between October 1973 and October 1978. Of the approximately 500 genera of freshwater algae reported in the United States, the U.S. Geological Survey observed 321 genera in the phytoplankton. Fifty-two genera were considered to be commonly occurring and 42 genera were considered to be community dominants. The report lists, describes, and provides a detailed taxonomic key to the identification of 58 genera of algae considered either commonly occurring or dominant. Also included is a summary of environmental conditions under which each algal genus was observed, as well as a glossary and an extensive list of selected references.

  18. Korean Deaf Adolescents' Awareness of Thematic and Taxonomic Relations among Ordinary Concepts Represented by Pictures and Written Words

    ERIC Educational Resources Information Center

    Yi, Kwangoh; Li, Degao; Park, Woon Seok; Park, Kyung-hee; Shim, Tae-taek; Kwern, Ohgoo; Kim, Jung Yeon

    2011-01-01

    Individuals' relative awareness of thematic and taxonomic relations is influenced by factors such as language and background knowledge. Relatively weak in Korean language skills and also having relatively limited social opportunities, Korean deaf adolescents might be different from hearing adolescents in how they make decisions in taxonomically…

  19. 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

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

    PubMed

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

    2016-04-13

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

  1. 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

  2. Complex depth-related patterns in taxonomic and functional diversity of polychaetes in the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Carvalho, Russell; Wei, Chih-Lin; Rowe, Gilbert; Schulze, Anja

    2013-10-01

    Patterns of taxonomic and functional diversity in polychaete assemblages were examined in the deep northern Gulf of Mexico, including the first analysis of polychaete feeding guild distribution. An analysis of samples from a total of 51 stations located along 7 transects plus additional nearby sites, indicated that density decreased exponentially with depth, with the central locations having higher densities than the eastern and western regions. Alpha diversity was also highest at the central stations associated with the Mississippi trough. The samples can be grouped into three significant clusters based on thirty percent similarity of species composition. BIO-ENV indicated depth, sediment particle size, and export POC were most important variables explaining distributions. The diversity of polychaete feeding guilds was high in the Mississippi trough, upper and mid-slope regions but declined to a few guilds on the Sigsbee abyssal plain. Combining feeding guild analysis with traditional analysis of species diversity contributes to a clearer understanding of trophic diversity in deep-sea benthic assemblages.

  3. RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets.

    PubMed

    Scheuch, Matthias; Höper, Dirk; Beer, Martin

    2015-03-03

    Fuelled by the advent and subsequent development of next generation sequencing technologies, metagenomics became a powerful tool for the analysis of microbial communities both scientifically and diagnostically. The biggest challenge is the extraction of relevant information from the huge sequence datasets generated for metagenomics studies. Although a plethora of tools are available, data analysis is still a bottleneck. To overcome the bottleneck of data analysis, we developed an automated computational workflow called RIEMS - Reliable Information Extraction from Metagenomic Sequence datasets. RIEMS assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications. After completion of the analyses, the results are summarised in a clearly structured result protocol organised taxonomically. The high accuracy and performance of RIEMS analyses were proven in comparison with other tools for metagenomics data analysis using simulated sequencing read datasets. RIEMS has the potential to fill the gap that still exists with regard to data analysis for metagenomics studies. The usefulness and power of RIEMS for the analysis of genuine sequencing datasets was demonstrated with an early version of RIEMS in 2011 when it was used to detect the orthobunyavirus sequences leading to the discovery of Schmallenberg virus.

  4. Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters among taxonomically close Streptomyces strains.

    PubMed

    Komaki, Hisayuki; Sakurai, Kenta; Hosoyama, Akira; Kimura, Akane; Igarashi, Yasuhiro; Tamura, Tomohiko

    2018-05-02

    To identify the species of butyrolactol-producing Streptomyces strain TP-A0882, whole genome-sequencing of three type strains in a close taxonomic relationship was performed. In silico DNA-DNA hybridization using the genome sequences suggested that Streptomyces sp. TP-A0882 is classified as Streptomyces diastaticus subsp. ardesiacus. Strain TP-A0882, S. diastaticus subsp. ardesiacus NBRC 15402 T , Streptomyces coelicoflavus NBRC 15399 T , and Streptomyces rubrogriseus NBRC 15455 T harbor at least 14, 14, 10, and 12 biosynthetic gene clusters (BGCs), respectively, coding for nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). All 14 gene clusters were shared by S. diastaticus subsp. ardesiacus strains TP-A0882 and NBRC 15402 T , while only four gene clusters were shared by the three distinct species. Although BGCs for bacteriocin, ectoine, indole, melanine, siderophores such as deferrioxamine, terpenes such as albaflavenone, hopene, carotenoid and geosmin are shared by the three species, many BGCs for secondary metabolites such as butyrolactone, lantipeptides, oligosaccharide, some terpenes are species-specific. These results indicate the possibility that strains belonging to the same species possess the same set of secondary metabolite-biosynthetic pathways, whereas strains belonging to distinct species have species-specific pathways, in addition to some common pathways, even if the strains are taxonomically close.

  5. A Phylogenetic, Biogeographic, and Taxonomic study of all Extant Species of Anolis (Squamata; Iguanidae).

    PubMed

    Poe, Steven; Nieto-Montes de Oca, Adrián; Torres-Carvajal, Omar; De Queiroz, Kevin; Velasco, Julián A; Truett, Brad; Gray, Levi N; Ryan, Mason J; Köhler, Gunther; Ayala-Varela, Fernando; Latella, Ian

    2017-09-01

    Anolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has been hampered by limited phylogenetic information on this group. Here, we present a phylogenetic analysis of all 379 extant species of Anolis, with new phylogenetic data for 139 species including new DNA data for 101 species. We use the resulting estimates as a basis for defining anole clade names under the principles of phylogenetic nomenclature and to examine the biogeographic history of anoles. Our new taxonomic treatment achieves the supposed advantages of recent subdivisions of anoles that employed ranked Linnaean-based nomenclature while avoiding the pitfalls of those approaches regarding artificial constraints imposed by ranks. Our biogeographic analyses demonstrate complexity in the dispersal history of anoles, including multiple crossings of the Isthmus of Panama, two invasions of the Caribbean, single invasions to Jamaica and Cuba, and a single evolutionary dispersal from the Caribbean to the mainland that resulted in substantial anole diversity. Our comprehensive phylogenetic estimate of anoles should prove useful for rigorous testing of many comparative evolutionary hypotheses. [Anoles; biogeography; lizards; Neotropics; phylogeny; taxonomy]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  6. Bovine Teat Microbiome Analysis Revealed Reduced Alpha Diversity and Significant Changes in Taxonomic Profiles in Quarters with a History of Mastitis

    PubMed Central

    Falentin, Hélène; Rault, Lucie; Nicolas, Aurélie; Bouchard, Damien S.; Lassalas, Jacques; Lamberton, Philippe; Aubry, Jean-Marc; Marnet, Pierre-Guy; Le Loir, Yves; Even, Sergine

    2016-01-01

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

  7. Filling in the GAPS: evaluating completeness and coverage of open-access biodiversity databases in the United States

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Troia, Matthew J.; McManamay, Ryan A.

    Primary biodiversity data constitute observations of particular species at given points in time and space. Open-access electronic databases provide unprecedented access to these data, but their usefulness in characterizing species distributions and patterns in biodiversity depend on how complete species inventories are at a given survey location and how uniformly distributed survey locations are along dimensions of time, space, and environment. Our aim was to compare completeness and coverage among three open-access databases representing ten taxonomic groups (amphibians, birds, freshwater bivalves, crayfish, freshwater fish, fungi, insects, mammals, plants, and reptiles) in the contiguous United States. We compiled occurrence records frommore » the Global Biodiversity Information Facility (GBIF), the North American Breeding Bird Survey (BBS), and federally administered fish surveys (FFS). In this study, we aggregated occurrence records by 0.1° × 0.1° grid cells and computed three completeness metrics to classify each grid cell as well-surveyed or not. Next, we compared frequency distributions of surveyed grid cells to background environmental conditions in a GIS and performed Kolmogorov–Smirnov tests to quantify coverage through time, along two spatial gradients, and along eight environmental gradients. The three databases contributed >13.6 million reliable occurrence records distributed among >190,000 grid cells. The percent of well-surveyed grid cells was substantially lower for GBIF (5.2%) than for systematic surveys (BBS and FFS; 82.5%). Still, the large number of GBIF occurrence records produced at least 250 well-surveyed grid cells for six of nine taxonomic groups. Coverages of systematic surveys were less biased across spatial and environmental dimensions but were more biased in temporal coverage compared to GBIF data. GBIF coverages also varied among taxonomic groups, consistent with commonly recognized geographic, environmental, and institutional

  8. Filling in the GAPS: evaluating completeness and coverage of open-access biodiversity databases in the United States

    DOE PAGES

    Troia, Matthew J.; McManamay, Ryan A.

    2016-06-12

    Primary biodiversity data constitute observations of particular species at given points in time and space. Open-access electronic databases provide unprecedented access to these data, but their usefulness in characterizing species distributions and patterns in biodiversity depend on how complete species inventories are at a given survey location and how uniformly distributed survey locations are along dimensions of time, space, and environment. Our aim was to compare completeness and coverage among three open-access databases representing ten taxonomic groups (amphibians, birds, freshwater bivalves, crayfish, freshwater fish, fungi, insects, mammals, plants, and reptiles) in the contiguous United States. We compiled occurrence records frommore » the Global Biodiversity Information Facility (GBIF), the North American Breeding Bird Survey (BBS), and federally administered fish surveys (FFS). In this study, we aggregated occurrence records by 0.1° × 0.1° grid cells and computed three completeness metrics to classify each grid cell as well-surveyed or not. Next, we compared frequency distributions of surveyed grid cells to background environmental conditions in a GIS and performed Kolmogorov–Smirnov tests to quantify coverage through time, along two spatial gradients, and along eight environmental gradients. The three databases contributed >13.6 million reliable occurrence records distributed among >190,000 grid cells. The percent of well-surveyed grid cells was substantially lower for GBIF (5.2%) than for systematic surveys (BBS and FFS; 82.5%). Still, the large number of GBIF occurrence records produced at least 250 well-surveyed grid cells for six of nine taxonomic groups. Coverages of systematic surveys were less biased across spatial and environmental dimensions but were more biased in temporal coverage compared to GBIF data. GBIF coverages also varied among taxonomic groups, consistent with commonly recognized geographic, environmental, and institutional

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

    PubMed

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

    2015-10-01

    While dixenous trypanosomatids represent one of the most dangerous pathogens for humans and domestic animals, their monoxenous relatives have frequently become model organisms for studies of diversity of parasitic protists and host-parasite associations. Yet, the classification of the family Trypanosomatidae is not finalized and often confusing. Here we attempt to make a blueprint for future studies in this field. We would like to elicit a discussion about an updated procedure, as traditional taxonomy was not primarily designed to be used for protists, nor can molecular phylogenetics solve all the problems alone. The current status, specific cases, and examples of generalized solutions are presented under conditions where practicality is openly favored over rigid taxonomic codes or blind phylogenetic approach. Copyright © 2015 Elsevier Ltd. All rights reserved.

  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. Two new species of Euglossa from South America, with notes on their taxonomic affinities (Hymenoptera, Apidae)

    PubMed Central

    Hinojosa-Díaz, Ismael A.; Nemésio, André; Engel, Michael S.

    2012-01-01

    Abstract Two new species of the genus Euglossa Latreille, subgenus Glossurella Dressler are here presented. Euglossa (Glossurella) embera sp. n., from the Pacific lowlands of Colombia, and Euglossa (Glossurella) adiastola sp. n., from the Atlantic Forest of Brazil. Their taxonomic association and distinction are discussed, as well as the correct understanding of the subgenus Glossurella. PMID:23129981

  12. Annotated bibliography and index map of sulfur and pyrites deposits in the United States and Alaska (including references to July 1, 1951)

    USGS Publications Warehouse

    Espenshade, Gilbert H.; Broedel, Carl H.

    1952-01-01

    Since the end of World War II, the pattern of sulfur production and consumption in the United States and abroad has changed markedly from the pattern that existed before the war. Although production of sulfur in the United States in 1950 was more than double the average annual production for the 1935-39 period, consumption had increased at such a rate that current domestic and foreign demand for U. S. sulfur exceeds the productive capacity of the industry. Production of sulfur (including brimstone, pyrites, and all other forms) in the 1935-39 period and in 1950 are compared in the table below.

  13. Chinese deaf and hard of hearing adolescents' awareness of thematic and taxonomic relations among ordinary concepts represented by pictures and written words.

    PubMed

    Li, Degao; Gao, Kejuan; Zhang, Yue; Wu, Xueyun

    2012-01-01

    Inspired by a previous study of Korean deaf and hard of hearing adolescents, the researchers conducted a priming task of living-nonliving categorization with a sample of Chinese deaf and hard of hearing adolescents. The sample in this study had significantly lower accuracy levels for the thematically related items than for the taxonomically related items and significantly larger differences in reaction times than a group of hearing adolescents when stimuli were changed from pictures to written words. However, they were not significantly different from the hearing adolescents in their performance with the taxonomically related written words. Furthermore, unlike the hearing adolescents, they did not have significantly different reaction times as the result of changes in positions of stimulus presentations.

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

    PubMed

    Lakhujani, Vijay; Badapanda, Chandan

    2017-06-01

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

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

    PubMed Central

    Gomila, Margarita; Busquets, Antonio; Mulet, Magdalena; García-Valdés, Elena; Lalucat, Jorge

    2017-01-01

    The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae, and P. savastanoi are later synonyms of P. amygdali and that “P. coronafaciens” should be revived as a nomenspecies. PMID:29270162

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

    PubMed

    Gomila, Margarita; Busquets, Antonio; Mulet, Magdalena; García-Valdés, Elena; Lalucat, Jorge

    2017-01-01

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

  17. Metabolome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants.

    PubMed

    Hagel, Jillian M; Mandal, Rupasri; Han, Beomsoo; Han, Jun; Dinsmore, Donald R; Borchers, Christoph H; Wishart, David S; Facchini, Peter J

    2015-09-15

    Recent progress toward the elucidation of benzylisoquinoline alkaloid (BIA) metabolism has focused on a small number of model plant species. Current understanding of BIA metabolism in plants such as opium poppy, which accumulates important pharmacological agents such as codeine and morphine, has relied on a combination of genomics and metabolomics to facilitate gene discovery. Metabolomics studies provide important insight into the primary biochemical networks underpinning specialized metabolism, and serve as a key resource for metabolic engineering, gene discovery, and elucidation of governing regulatory mechanisms. Beyond model plants, few broad-scope metabolomics reports are available for the vast number of plant species known to produce an estimated 2500 structurally diverse BIAs, many of which exhibit promising medicinal properties. We applied a multi-platform approach incorporating four different analytical methods to examine 20 non-model, BIA-accumulating plant species. Plants representing four families in the Ranunculales were chosen based on reported BIA content, taxonomic distribution and importance in modern/traditional medicine. One-dimensional (1)H NMR-based profiling quantified 91 metabolites and revealed significant species- and tissue-specific variation in sugar, amino acid and organic acid content. Mono- and disaccharide sugars were generally lower in roots and rhizomes compared with stems, and a variety of metabolites distinguished callus tissue from intact plant organs. Direct flow infusion tandem mass spectrometry provided a broad survey of 110 lipid derivatives including phosphatidylcholines and acylcarnitines, and high-performance liquid chromatography coupled with UV detection quantified 15 phenolic compounds including flavonoids, benzoic acid derivatives and hydroxycinnamic acids. Ultra-performance liquid chromatography coupled with high-resolution Fourier transform mass spectrometry generated extensive mass lists for all species, which were

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

    PubMed

    Serrao, Natasha R; Steinke, Dirk; Hanner, Robert H

    2014-01-01

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

  19. Antifungal Bacteria on Woodland Salamander Skin Exhibit High Taxonomic Diversity and Geographic Variability

    PubMed Central

    DiRenzo, Graziella V.; Yarwood, Stephanie A.; Campbell Grant, Evan H.; Fleischer, Robert C.; Lips, Karen R.

    2017-01-01

    ABSTRACT Diverse bacteria inhabit amphibian skin; some of those bacteria inhibit growth of the fungal pathogen Batrachochytrium dendrobatidis. Yet there has been no systematic survey of anti-B. dendrobatidis bacteria across localities, species, and elevations. This is important given geographic and taxonomic variations in amphibian susceptibility to B. dendrobatidis. Our collection sites were at locations within the Appalachian Mountains where previous sampling had indicated low B. dendrobatidis prevalence. We determined the numbers and identities of anti-B. dendrobatidis bacteria on 61 Plethodon salamanders (37 P. cinereus, 15 P. glutinosus, 9 P. cylindraceus) via culturing methods and 16S rRNA gene sequencing. We sampled co-occurring species at three localities and sampled P. cinereus along an elevational gradient (700 to 1,000 meters above sea level [masl]) at one locality. We identified 50 anti-B. dendrobatidis bacterial operational taxonomic units (OTUs) and found that the degree of B. dendrobatidis inhibition was not correlated with relatedness. Five anti-B. dendrobatidis bacterial strains occurred on multiple amphibian species at multiple localities, but none were shared among all species and localities. The prevalence of anti-B. dendrobatidis bacteria was higher at Shenandoah National Park (NP), VA, with 96% (25/26) of salamanders hosting at least one anti-B. dendrobatidis bacterial species compared to 50% (7/14) at Catoctin Mountain Park (MP), MD, and 38% (8/21) at Mt. Rogers National Recreation Area (NRA), VA. At the individual level, salamanders at Shenandoah NP had more anti-B. dendrobatidis bacteria per individual (μ = 3.3) than those at Catoctin MP (μ = 0.8) and at Mt. Rogers NRA (μ = 0.4). All salamanders tested negative for B. dendrobatidis. Anti-B. dendrobatidis bacterial species are diverse in central Appalachian Plethodon salamanders, and their distribution varied geographically. The antifungal bacterial species that we identified may play a

  20. Antifungal Bacteria on Woodland Salamander Skin Exhibit High Taxonomic Diversity and Geographic Variability.

    PubMed

    Muletz-Wolz, Carly R; DiRenzo, Graziella V; Yarwood, Stephanie A; Campbell Grant, Evan H; Fleischer, Robert C; Lips, Karen R

    2017-05-01

    Diverse bacteria inhabit amphibian skin; some of those bacteria inhibit growth of the fungal pathogen Batrachochytrium dendrobatidis Yet there has been no systematic survey of anti- B. dendrobatidis bacteria across localities, species, and elevations. This is important given geographic and taxonomic variations in amphibian susceptibility to B. dendrobatidis Our collection sites were at locations within the Appalachian Mountains where previous sampling had indicated low B. dendrobatidis prevalence. We determined the numbers and identities of anti- B. dendrobatidis bacteria on 61 Plethodon salamanders (37 P. cinereus , 15 P. glutinosus , 9 P. cylindraceus ) via culturing methods and 16S rRNA gene sequencing. We sampled co-occurring species at three localities and sampled P. cinereus along an elevational gradient (700 to 1,000 meters above sea level [masl]) at one locality. We identified 50 anti- B. dendrobatidis bacterial operational taxonomic units (OTUs) and found that the degree of B. dendrobatidis inhibition was not correlated with relatedness. Five anti- B. dendrobatidis bacterial strains occurred on multiple amphibian species at multiple localities, but none were shared among all species and localities. The prevalence of anti- B. dendrobatidis bacteria was higher at Shenandoah National Park (NP), VA, with 96% (25/26) of salamanders hosting at least one anti- B. dendrobatidis bacterial species compared to 50% (7/14) at Catoctin Mountain Park (MP), MD, and 38% (8/21) at Mt. Rogers National Recreation Area (NRA), VA. At the individual level, salamanders at Shenandoah NP had more anti- B. dendrobatidis bacteria per individual (μ = 3.3) than those at Catoctin MP (μ = 0.8) and at Mt. Rogers NRA (μ = 0.4). All salamanders tested negative for B. dendrobatidis Anti- B. dendrobatidis bacterial species are diverse in central Appalachian Plethodon salamanders, and their distribution varied geographically. The antifungal bacterial species that we identified may play a

  1. On the taxonomic status of Gegeneophis nadkarnii Bhatta & Prashanth, 2004 (Amphibia: Gymnophiona: Indotyphlidae).

    PubMed

    Gower, David J; Giri, Varad; Torsekar, Varun R; Gaikwad, Kshamata

    2013-01-29

    Examination of type material and new collections from Goa, southern Maharashtra and northern Karnataka, leads to the conclusion that Gegeneophis nadkarnii Bhatta & Prashanth, 2004 is a subjective junior synonym of Gegeneophis danieli Giri, Wilkinson & Gower, 2003. The purported differences between these species are very minor and attributable to nor-mal individual variation, except for some features of the dentition that are peculiar to the exceptionally abnormal paratype of G. nadkarnii. This taxonomic revision extends the known geographic range of G. danieli and suggests it could be trans-ferred from Data Deficient to Least Concern status in the IUCN Red List.

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

    PubMed

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

    2017-05-01

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

  3. Weather information network including graphical display

    NASA Technical Reports Server (NTRS)

    Leger, Daniel R. (Inventor); Burdon, David (Inventor); Son, Robert S. (Inventor); Martin, Kevin D. (Inventor); Harrison, John (Inventor); Hughes, Keith R. (Inventor)

    2006-01-01

    An apparatus for providing weather information onboard an aircraft includes a processor unit and a graphical user interface. The processor unit processes weather information after it is received onboard the aircraft from a ground-based source, and the graphical user interface provides a graphical presentation of the weather information to a user onboard the aircraft. Preferably, the graphical user interface includes one or more user-selectable options for graphically displaying at least one of convection information, turbulence information, icing information, weather satellite information, SIGMET information, significant weather prognosis information, and winds aloft information.

  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.

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

    PubMed

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

    2016-08-18

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

  6. 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

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

    PubMed Central

    2013-01-01

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

  8. Taxonomic composition and endemism of the helminth fauna of freshwater fishes of Mexico.

    PubMed

    Salgado-Maldonado, Guillermo; Quiroz-Martínez, Benjamín

    2013-01-01

    We examine the taxonomic composition and endemism of adult helminth parasites of freshwater fishes of Mexico, with regard to the main hydrological basins of the country. A presence-absence matrix, including every species of adult helminth parasites of freshwater fishes from 23 Mexican hydrological basins was compiled and examined in this paper. The helminth fauna of freshwater fishes of Mexico consists of a large group of Central American Neotropical species (S = 119) and another set, less rich of Nearctic species (S = 48), which are distributed along with the families of its fish hosts; insufficient data preclude the assignation of three species. This fauna is composed predominantly by nematodes, trematodes, and monogeneans, which together contributed 86 % of the total species recorded; cestodes and acanthocephalans being the taxa with the least species recorded. Current data suggests a 22 % (37/170) endemism amongst helminths of freshwater fishes of Mexico. Data suggests that the isolation of bodies of water in the Mexican territory, mostly in the Neotropical areas of southeastern Mexico and in the central Altiplano Mexicano (Mexican Highland Plateau), with well delimited basins separated by orographic features, provided peculiar conditions that have been conducive to the diversification of a unique helminth fauna.

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

    PubMed

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

    2013-04-01

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

  10. Using hand proportions to test taxonomic boundaries within the Tupaia glis species complex (Scandentia, Tupaiidae)

    USGS Publications Warehouse

    Sargos, Eric J.; Woodman, Neal; Reese, Aspen T.; Olson, Link E.

    2013-01-01

    Treeshrews (order Scandentia) comprise 2 families of squirrel-sized terrestrial, arboreal, and scansorial mammals distributed throughout much of tropical South and Southeast Asia. The last comprehensive taxonomic revision of treeshrews was published in 1913, and a well-supported phylogeny clarifying relationships among all currently recognized extant species within the order has only recently been published. Within the family Tupaiidae, 2 widely distributed species, the northern treeshrew, Tupaia belangeri (Wagner, 1841), and the common treeshrew, T. glis (Diard, 1820), represent a particularly vexing taxonomic complex. These 2 species are currently distinguished primarily based on their respective distributions north and south of the Isthmus of Kra on the Malay Peninsula and on their different mammae counts. This problematic species complex includes 54 published synonyms, many of which represent putative island endemics. The widespread T. glis and T. belangeri collectively comprise a monophyletic assemblage representing the sister lineage to a clade composed of the golden-bellied treeshrew, T. chrysogaster Miller, 1903 (Mentawai Islands), and the long-footed treeshrew, T. longipes (Thomas, 1893) (Borneo). As part of a morphological investigation of the T. glis–T. belangeri complex, we studied the proportions of hand bones, which have previously been shown to be useful in discriminating species of soricids (true shrews). We measured 38 variables from digital X-ray images of 148 museum study skins representing several subspecies of T. glis, T. belangeri, T. chrysogaster, and T. longipes and analyzed these data using principal components and cluster analyses. Manus proportions among these 4 species readily distinguish them, particularly in the cases of T. chrysogaster and T. longipes. We then tested the distinctiveness of several of the populations comprising T. glis and T. longipes. T. longipes longipes and T. l. salatana Lyon, 1913, are distinguishable from each

  11. 31 CFR 515.321 - United States; continental United States.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 31 Money and Finance:Treasury 3 2013-07-01 2013-07-01 false United States; continental United... General Definitions § 515.321 United States; continental United States. The term United States means the United States and all areas under the jurisdiction or authority thereof, including the Trust Territory of...

  12. 31 CFR 535.321 - United States; continental United States.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 31 Money and Finance:Treasury 3 2011-07-01 2011-07-01 false United States; continental United... General Definitions § 535.321 United States; continental United States. The term United States means the United States and all areas under the jurisdiction or authority thereof including the Trust Territory of...

  13. 31 CFR 535.321 - United States; continental United States.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 31 Money and Finance:Treasury 3 2013-07-01 2013-07-01 false United States; continental United... General Definitions § 535.321 United States; continental United States. The term United States means the United States and all areas under the jurisdiction or authority thereof including the Trust Territory of...

  14. 31 CFR 535.321 - United States; continental United States.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false United States; continental United... General Definitions § 535.321 United States; continental United States. The term United States means the United States and all areas under the jurisdiction or authority thereof including the Trust Territory of...

  15. 31 CFR 515.321 - United States; continental United States.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false United States; continental United... General Definitions § 515.321 United States; continental United States. The term United States means the United States and all areas under the jurisdiction or authority thereof, including the Trust Territory of...

  16. 31 CFR 515.321 - United States; continental United States.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 31 Money and Finance:Treasury 3 2014-07-01 2014-07-01 false United States; continental United... General Definitions § 515.321 United States; continental United States. The term United States means the United States and all areas under the jurisdiction or authority thereof, including the Trust Territory of...

  17. 31 CFR 500.321 - United States; continental United States.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false United States; continental United... General Definitions § 500.321 United States; continental United States. The term United States means the United States and all areas under the jurisdiction or authority thereof, including U.S. trust territories...

  18. 31 CFR 515.321 - United States; continental United States.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 31 Money and Finance:Treasury 3 2011-07-01 2011-07-01 false United States; continental United... General Definitions § 515.321 United States; continental United States. The term United States means the United States and all areas under the jurisdiction or authority thereof, including the Trust Territory of...

  19. 31 CFR 535.321 - United States; continental United States.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 31 Money and Finance:Treasury 3 2012-07-01 2012-07-01 false United States; continental United... General Definitions § 535.321 United States; continental United States. The term United States means the United States and all areas under the jurisdiction or authority thereof including the Trust Territory of...

  20. 31 CFR 535.321 - United States; continental United States.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 31 Money and Finance:Treasury 3 2014-07-01 2014-07-01 false United States; continental United... General Definitions § 535.321 United States; continental United States. The term United States means the United States and all areas under the jurisdiction or authority thereof including the Trust Territory of...

  1. 31 CFR 515.321 - United States; continental United States.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 31 Money and Finance:Treasury 3 2012-07-01 2012-07-01 false United States; continental United... General Definitions § 515.321 United States; continental United States. The term United States means the United States and all areas under the jurisdiction or authority thereof, including the Trust Territory of...

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

    PubMed

    Mayor, Julien; Plunkett, Kim

    2010-01-01

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

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

    PubMed

    Vaníčková, Lucie; Nagy, Radka; Pompeiano, Antonio; Kalinová, Blanka

    2017-01-01

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

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

    PubMed Central

    Vaníčková, Lucie; Nagy, Radka; Pompeiano, Antonio

    2017-01-01

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

  5. Taxonomic review of the genus Indomyrlaea Roesler & Küppers 1979 of China, with descriptions of five new species (Lepidoptera: Pyralidae: Phycitinae).

    PubMed

    Ren, Yingdang; Yang, Linlin; Li, Houhun

    2015-08-24

    The taxonomy of the Chinese species of the genus Indomyrlaea Roesler & Küppers, 1979 is revised. Five new species, namely I. bannensis Ren & Li sp. nov., I. fastigipalpa Ren & Li sp. nov., I. nigra Ren & Li sp. nov., I. proceripalpa Ren & Li sp. nov., and I. sinuapalpa Ren & Li sp. nov., are described. The following taxonomic changes are proposed: Sandrabatis Ragonot, 1893 and its type species Sandrabatis crassiella Ragonot, 1893 are synonymized with Ceroprepes Zeller, 1867 and Ceroprepes ophthalmicella (Christoph, 1881), respectively; Indomyrlaea phaeella (Hampson, 1903) comb. nov. is transferred from Sandrabatis. The original combination Nephopterix eugraphella Ragonot, 1888 is resurrected from its previous affiliation with Indomyrlaea. A checklist and a key to all the known species of the world are included.

  6. Defining operational taxonomic units using DNA barcode data.

    PubMed

    Blaxter, Mark; Mann, Jenna; Chapman, Tom; Thomas, Fran; Whitton, Claire; Floyd, Robin; Abebe, Eyualem

    2005-10-29

    The scale of diversity of life on this planet is a significant challenge for any scientific programme hoping to produce a complete catalogue, whatever means is used. For DNA barcoding studies, this difficulty is compounded by the realization that any chosen barcode sequence is not the gene 'for' speciation and that taxa have evolutionary histories. How are we to disentangle the confounding effects of reticulate population genetic processes? Using the DNA barcode data from meiofaunal surveys, here we discuss the benefits of treating the taxa defined by barcodes without reference to their correspondence to 'species', and suggest that using this non-idealist approach facilitates access to taxon groups that are not accessible to other methods of enumeration and classification. Major issues remain, in particular the methodologies for taxon discrimination in DNA barcode data.

  7. Defining operational taxonomic units using DNA barcode data

    PubMed Central

    Blaxter, Mark; Mann, Jenna; Chapman, Tom; Thomas, Fran; Whitton, Claire; Floyd, Robin; Abebe, Eyualem

    2005-01-01

    Abstract The scale of diversity of life on this planet is a significant challenge for any scientific programme hoping to produce a complete catalogue, whatever means is used. For DNA barcoding studies, this difficulty is compounded by the realization that any chosen barcode sequence is not the gene ‘for’ speciation and that taxa have evolutionary histories. How are we to disentangle the confounding effects of reticulate population genetic processes? Using the DNA barcode data from meiofaunal surveys, here we discuss the benefits of treating the taxa defined by barcodes without reference to their correspondence to ‘species’, and suggest that using this non-idealist approach facilitates access to taxon groups that are not accessible to other methods of enumeration and classification. Major issues remain, in particular the methodologies for taxon discrimination in DNA barcode data. PMID:16214751

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

    PubMed

    Yamamoto, Nao; Yamamoto, Masaru

    2016-11-15

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

  9. Gut microbiota in MS: possible influence of immunomodulators

    PubMed Central

    Cantarel, Brandi L.; Waubant, Emmanuelle; Chehoud, Christel; Kuczynski, Justin; DeSantis, Todd Z.; Warrington, Janet; Venkatesan, Arun; Fraser, Claire M.; Mowry, Ellen M.

    2015-01-01

    Objectives Differences in gut bacteria have been described in several autoimmune disorders. In this exploratory pilot study, we compared gut bacteria in multiple sclerosis patients and healthy controls and evaluated the influence of glatiramer acetate and vitamin D treatment on the microbiota. Methods Subjects were otherwise healthy white women with or without relapsing-remitting multiple sclerosis who were vitamin D insufficient. Multiple sclerosis patients were untreated or were receiving glatiramer acetate. Subjects collected stool at baseline and after 90 days of vitamin D3 (5,000 IU/day) supplementation. The abundance of operational taxonomic units was evaluated by hybridization of 16S rRNA to a DNA microarray. Results While there was overlap of gut bacterial communities, the abundance of some operational taxonomic units, including Faecalibacterium, was lower in multiple sclerosis patients. Glatiramer acetate-treated MS subjects showed differences in community composition compared to untreated subjects, including Bacteroidaceae, Faecalibacterium, Ruminococcus, Lactobacillaceae, Clostridium, and Other Clostridiales. Compared to the other groups, untreated multiple sclerosis subjects had an increase in the Akkermansia, Faecalibacterium, and Coprococcus genera after vitamin D supplementation. Conclusions While overall bacterial communities were similar, specific operational taxonomic units differed between healthy and multiple sclerosis subjects. Glatiramer acetate and vitamin D supplementation were associated with differences or changes in the microbiota. This study was exploratory, and larger studies are needed to confirm these preliminary results. PMID:25775034

  10. Gut microbiota in multiple sclerosis: possible influence of immunomodulators.

    PubMed

    Cantarel, Brandi L; Waubant, Emmanuelle; Chehoud, Christel; Kuczynski, Justin; DeSantis, Todd Z; Warrington, Janet; Venkatesan, Arun; Fraser, Claire M; Mowry, Ellen M

    2015-06-01

    Differences in gut bacteria have been described in several autoimmune disorders. In this exploratory pilot study, we compared gut bacteria in patients with multiple sclerosis and healthy controls and evaluated the influence of glatiramer acetate and vitamin D treatment on the microbiota. Subjects were otherwise healthy white women with or without relapsing-remitting multiple sclerosis who were vitamin D insufficient. Patients with multiple sclerosis were untreated or were receiving glatiramer acetate. Subjects collected stool at baseline and after 90 days of vitamin D3 (5000 IU/d) supplementation. The abundance of operational taxonomic units was evaluated by hybridization of 16S rRNA to a DNA microarray. While there was overlap of gut bacterial communities, the abundance of some operational taxonomic units, including Faecalibacterium, was lower in patients with multiple sclerosis. Glatiramer acetate-treated patients with multiple sclerosis showed differences in community composition compared with untreated subjects, including Bacteroidaceae, Faecalibacterium, Ruminococcus, Lactobacillaceae, Clostridium, and other Clostridiales. Compared with the other groups, untreated patients with multiple sclerosis had an increase in the Akkermansia, Faecalibacterium, and Coprococcus genera after vitamin D supplementation. While overall bacterial communities were similar, specific operational taxonomic units differed between healthy controls and patients with multiple sclerosis. Glatiramer acetate and vitamin D supplementation were associated with differences or changes in the microbiota. This study was exploratory, and larger studies are needed to confirm these preliminary results.

  11. Styrene-spaced copolymers including anthraquinone and β-O-4 lignin model units: synthesis, characterization and reactivity under alkaline pulping conditions.

    PubMed

    Megiatto, Jackson D; Cazeils, Emmanuel; Ham-Pichavant, Frédérique; Grelier, Stéphane; Gardrat, Christian; Castellan, Alain

    2012-05-14

    A series of random copoly(styrene)s has been synthesized via radical polymerization of functionalized anthraquinone (AQ) and β-O-4 lignin model monomers. The copolymers were designed to have a different number of styrene spacer groups between the AQ and β-O-4 lignin side chains aiming at investigating the distance effects on AQ/β-O-4 electron transfer mechanisms. A detailed molecular characterization, including techniques such as size exclusion chromatography, MALDI-TOF mass spectrometry, and (1)H, (13)C, (31)P NMR and UV-vis spectroscopies, afforded quantitative information about the composition of the copolymers as well as the average distribution of the AQ and β-O-4 groups in the macromolecular structures. TGA and DSC thermal analysis have indicated that the copolymers were thermally stable under regular pulping conditions, revealing the inertness of the styrene polymer backbone in the investigation of electron transfer mechanisms. Alkaline pulping experiments showed that close contact between the redox active side chains in the copolymers was fundamental for an efficient degradation of the β-O-4 lignin model units, highlighting the importance of electron transfer reactions in the lignin degradation mechanisms catalyzed by AQ. In the absence of glucose, AQ units oxidized phenolic β-O-4 lignin model parts, mainly by electron transfer leading to vanillin as major product. By contrast, in presence of glucose, anthrahydroquinone units (formed by reduction of AQ) reduced the quinone-methide units (issued by dehydration of phenolic β-O-4 lignin model part) mainly by electron transfer leading to guaiacol as major product. Both processes were distance dependent.

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

    PubMed

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

    2017-08-14

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

  13. Taxonomic challenges in freshwater fishes: a mismatch between morphology and DNA barcoding in fish of the north-eastern part of the Congo basin.

    PubMed

    Decru, Eva; Moelants, Tuur; De Gelas, Koen; Vreven, Emmanuel; Verheyen, Erik; Snoeks, Jos

    2016-01-01

    This study evaluates the utility of DNA barcoding to traditional morphology-based species identifications for the fish fauna of the north-eastern Congo basin. We compared DNA sequences (COI) of 821 samples from 206 morphologically identified species. Best match, best close match and all species barcoding analyses resulted in a rather low identification success of 87.5%, 84.5% and 64.1%, respectively. The ratio 'nearest-neighbour distance/maximum intraspecific divergence' was lower than 1 for 26.1% of the samples, indicating possible taxonomic problems. In ten genera, belonging to six families, the number of species inferred from mtDNA data exceeded the number of species identified using morphological features; and in four cases indications of possible synonymy were detected. Finally, the DNA barcodes confirmed previously known identification problems within certain genera of the Clariidae, Cyprinidae and Mormyridae. Our results underscore the large number of taxonomic problems lingering in the taxonomy of the fish fauna of the Congo basin and illustrate why DNA barcodes will contribute to future efforts to compile a reliable taxonomic inventory of the Congo basin fish fauna. Therefore, the obtained barcodes were deposited in the reference barcode library of the Barcode of Life Initiative. © 2015 John Wiley & Sons Ltd.

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

    PubMed

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

    2004-06-01

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

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

    USGS Publications Warehouse

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

    2005-01-01

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

  16. Taxonomic revision of the species of Parvanachis Radwin, 1968 (Gastropoda: Columbellidae) from the Gulf of Panama.

    PubMed

    de Maintenon, Marta J

    2014-01-07

    Species of Parvanachis Radwin, 1968 collected from the Gulf of Panama are anatomically characterized and taxonomically revised. Six species are reported to occur in the region: P. pygmaea (Sowerby, 1832), P. pardalis (Hinds, 1843), P. diminuta (C.B. Adams, 1852), P. albonodosa (Carpenter, 1857), P. milium (Dall, 1916), and P. dalli Bartsch, 1931. Of these six, three are confirmed as described. P. milium was not found in new collections or the previous survey collection and may be more common further south. P. dalli is a synonym of P. pygmaea; and P. albonodosa (auct.) is renamed, because the type material represents a different species. Two new species are described, P. dichroma and P. adamsi. P. pardalis, based on anatomy and shell and radular morphology, is referred to the genus Anachis, and Costoanachis nigricans (Sowerby, 1844), based on anatomy and shell morphology, is transferred to Parvanachis. The resulting seven species of Parvanachis constitute two groups; one (including the type species) with smaller shells and a simple penis morphology, and a group of four larger species with more complex penis morphology.

  17. Tardigrada of Ireland: a review of records and an updated checklist of species including a new addition to the Irish fauna.

    PubMed

    DeMilio, Erica; Lawton, Colin; Marley, Nigel J

    2016-01-01

    The phylum Tardigrada was not recorded in Ireland until the Clare Island Survey of 1909-1911, with only rare subsequent reports on Irish tardigrade species. In recent decades, significant taxonomic revision has occurred within Tardigrada. This has resulted in the need for a review of all known historical records from Ireland and Northern Ireland in order to produce an updated checklist of valid taxa. The new checklist includes fifty-one tardigrade species and subspecies including a new addition to the Irish fauna reported herein, Echiniscus quadrispinosus quadrispinosus Richters, 1902 from Newtown, Ballyvaughan, Co. Clare.

  18. 43 CFR 3137.50 - What optional terms may I include in a unit agreement?

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... following optional terms for a unit agreement if they promote additional development or enhanced production... modification; or (d) Other terms that BLM determines will promote the greatest economic recovery of oil and gas...

  19. 43 CFR 3137.50 - What optional terms may I include in a unit agreement?

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... following optional terms for a unit agreement if they promote additional development or enhanced production... modification; or (d) Other terms that BLM determines will promote the greatest economic recovery of oil and gas...

  20. Taxonomic revision of Drymoluber Amaral, 1930 (Serpentes: Colubridae).

    PubMed

    Costa, Henrique Caldeira; Moura, Mário Ribeiro; Feio, Renato Neves

    2013-01-01

    The present study is a taxonomic revision of the genus Drymoluber Amaral, 1930, using meristic and morphometric characters, aspects of external hemipenial morphology and body coloration. Sexual dimorphism occurs in D. dichrous and D. brazili but was not detected in D. apurimacensis. Morphological variation within D. dichrous is related to geographic distance between populations. Furthermore, variation in the number of ventrals and subcaudals in D. dichrous and D. brazili follows latitudinal and longitudinal clinal patterns. Drymoluber dichrous is diagnosed by the presence of 15-15-15 smooth dorsal scale rows with two apical pits, and 157-180 ventrals and 86-110 subcaudals; it occurs along the eastern versant of the Andes, in the Amazon forest, on the Guiana Shield, in the Atlantic forest, and its transitional areas with the Caatinga and Cerrado. Drymoluber brazili has 17-17-15 smooth dorsal scale rows with two apical pits, 182-202 ventrals and 109-127 subcaudals, and ranges throughout the Caatinga, Cerrado, Atlantic forest and transitional areas between these last two domains. Drymoluber apurimacensis has 13-13-13 smooth dorsal scale rows without apical pits, 158-182 ventrals and 84-93 subcaudals, and occurs in the Apurimac Valley, south of the Apurimac and Pampas rivers in Peru.

  1. Using open-access taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections.

    PubMed

    McIntyre, K M; Setzkorn, C; Wardeh, M; Hepworth, P J; Radford, A D; Baylis, M

    2014-10-01

    What are all the species of pathogen that affect our livestock? As 6 out of every 10 human pathogens came from animals, with a good number from livestock and pets, it seems likely that the majority that emerge in the future, and which could threaten or devastate human health, will come from animals. Only 10 years ago, the first comprehensive pathogen list was compiled for humans; we still have no equivalent for animals. Here we describe the creation of a novel pathogen database, and present outputs from the database that demonstrate its value. The ENHanCEd Infectious Diseases database (EID2) is open-access and evidence-based, and it describes the pathogens of humans and animals, their host and vector species, and also their global occurrence. The EID2 systematically collates information on pathogens into a single resource using evidence from the NCBI Taxonomy database, the NCBI Nucleotide database, the NCBI MeSH (Medical Subject Headings) library and PubMed. Information about pathogens is assigned using data-mining of meta-data and semi-automated literature searches. Here we focus on 47 mammalian and avian hosts, including humans and animals commonly used in Europe as food or kept as pets. Currently, the EID2 evidence suggests that: • Within these host species, 793 (30.5%) pathogens were bacteria species, 395 (15.2%) fungi, 705 (27.1%) helminths, 372 (14.3%) protozoa and 332 (12.8%) viruses. • The odds of pathogens being emerging compared to not emerging differed by taxonomic division, and increased when pathogens had greater numbers of host species associated with them, and were zoonotic rather than non-zoonotic. • The odds of pathogens being zoonotic compared to non-zoonotic differed by taxonomic division and also increased when associated with greater host numbers. • The pathogens affecting the greatest number of hosts included: Escherichia coli, Giardia intestinalis, Toxoplasma gondii, Anaplasma phagocytophilum, Cryptosporidium parvum, Rabies virus

  2. 45 CFR 400.209 - Claims involving family units which include refugees who have been in the United States more than...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... refugees who have been in the United States more than 36 months. 400.209 Section 400.209 Public Welfare Regulations Relating to Public Welfare OFFICE OF REFUGEE RESETTLEMENT, ADMINISTRATION FOR CHILDREN AND FAMILIES, DEPARTMENT OF HEALTH AND HUMAN SERVICES REFUGEE RESETTLEMENT PROGRAM Federal Funding Federal...

  3. A survey of the praying mantises of Rwanda, including new records (Insecta, Mantodea).

    PubMed

    Tedrow, Riley; Nathan, Kabanguka; Richard, Nasasira; Svenson, Gavin J

    2015-10-01

    We report the results of two surveys targeting praying mantises in four localities in Rwanda, specifically Akagera National Park, Nyungwe National Park, Volcanoes National Park, and the Arboretum de Ruhande at the National University of Rwanda. Using an assortment of collecting techniques, including metal halide light traps, sweep netting vegetation and general searching, we obtained 387 adult and 352 juvenile specimens, representing 41 species. A total of 28 novel species records for Rwanda are added to the 18 previously recorded species for the country, in addition to 20 novel species records for the broader region, including neighbouring Uganda and Burundi. This study provides high resolution images of the dorsal habitus of both sexes of representative species, both pinned and living. Species distribution records are presented and discussed. With a 155% increase in species recorded from Rwanda, this survey illustrates the need for further taxonomic work in the region.

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

    PubMed

    Buckley, Hannah L; Rafat, Arash; Ridden, Johnathon D; Cruickshank, Robert H; Ridgway, Hayley J; Paterson, Adrian M

    2014-01-01

    The role of species' interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran's eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners' genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence

  5. A taxonomic review of Korean species of the AthetaThomsonsubgenusMicrodota Mulsant & Rey, with descriptions of two new species (Coleoptera, Staphylinidae, Aleocharinae).

    PubMed

    Lee, Seung-Gyu; Ahn, Kee-Jeong

    2015-01-01

    A taxonomic review of the AthetaThomsonsubgenusMicrodota Mulsant & Rey in Korea is presented. The subgenus is represented in Korea by 15 species including two new species, Atheta (Microdota) jangtaesanensis Lee & Ahn, sp. n. and Atheta (Microdota) pasniki Lee & Ahn, sp. n. Four species [Atheta (Microdota) kawachiensis Cameron, Atheta (Microdota) muris Sawada, Atheta (Microdota) spiniventris Bernhauer, and Atheta (Microdota) spinula (Sawada)] are new to the Korean Peninsula and two [Atheta (Microdota) formicetorum Bernhauer and Atheta (Microdota) subcrenulata Bernhauer] to South Korea. Two other species [Atheta (Microdota) kobensis Cameron and Atheta (Microdota) scrobicollis (Kraatz)] previously recorded in North Korea had been identified incorrectly. A key, descriptions, habitus photographs and illustrations of the diagnostic features are provided. Species distributions and diversity in East Asia are discussed.

  6. A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

    PubMed

    Bryant, Harold N; Cantino, Philip D

    2002-02-01

    The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.

  7. 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).

  8. Taxonomic revision of the olingos (Bassaricyon), with description of a new species, the Olinguito

    PubMed Central

    Helgen, Kristofer M.; Pinto, C. Miguel; Kays, Roland; Helgen, Lauren E.; Tsuchiya, Mirian T. N.; Quinn, Aleta; Wilson, Don E.; Maldonado, Jesús E.

    2013-01-01

    Abstract We present the first comprehensive taxonomic revision and review the biology of the olingos, the endemic Neotropical procyonid genus Bassaricyon, based on most specimens available in museums, and with data derived from anatomy, morphometrics, mitochondrial and nuclear DNA, field observations, and geographic range modeling. Species of Bassaricyon are primarily forest-living, arboreal, nocturnal, frugivorous, and solitary, and have one young at a time. We demonstrate that four olingo species can be recognized, including a Central American species (Bassaricyon gabbii), lowland species with eastern, cis-Andean (Bassaricyon alleni) and western, trans-Andean (Bassaricyon medius) distributions, and a species endemic to cloud forests in the Andes. The oldest evolutionary divergence in the genus is between this last species, endemic to the Andes of Colombia and Ecuador, and all other species, which occur in lower elevation habitats. Surprisingly, this Andean endemic species, which we call the Olinguito, has never been previously described; it represents a new species in the order Carnivora and is the smallest living member of the family Procyonidae. We report on the biology of this new species based on information from museum specimens, niche modeling, and fieldwork in western Ecuador, and describe four Olinguito subspecies based on morphological distinctions across different regions of the Northern Andes. PMID:24003317

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

    PubMed

    Aira, Manuel; Bybee, Seth; Pérez-Losada, Marcos; Domínguez, Jorge

    2015-11-01

    Earthworms play a key role in nutrient cycling by interacting with microorganisms thus accelerating organic matter turnover in soil systems. As detritivores, some earthworm types ingest and digest a mixture of dead organic matter and microorganisms, like animal manures (i.e. animal gut microbiomes). Here we described the earthworm cast microbiome and the role ingested bacteria play on its composition. We fed Eisenia andrei with cow, horse and pig manures and determined the taxonomic and phylogenetic composition of the these manures before and after passage through the earthworm gut. Earthworm cast microbiomes showed a smaller diversity than the manure they fed on. Manures strongly differed in their taxonomic and phylogenetic composition, but these differences were markedly reduced once transformed into earthworm cast microbiomes after passage through the earthworm gut. The core earthworm cast microbiome comprised 30 OTUs (2.6% of OTUs from cast samples), of which 10 are possibly native to the earthworm gut. Most of the core cast microbiome OTUs belonged to phyla Actinobacteria and Proteobacteria, as opposed to already described animal core gut microbiomes, which are composed mainly of Firmicutes and Bacteroidetes. Our results suggest that earthworms build up their cast microbiome by selecting from the pool of ingested bacteria. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

    PubMed Central

    Alvarez, Fernando

    2017-01-01

    Background and Aims Cryptic peracarids are an important component of the coral reef fauna in terms of diversity and abundance, yet they have been poorly studied. The aim of this study was to evaluate the taxonomic richness and abundance of cryptic peracarids in coral rubble in the Puerto Morelos Reef National Park, Mexico (PMRNP), and their relationship with depth. Methods Three reef sites were selected: (1) Bonanza, (2) Bocana, and (3) Jardines. At each site six kilograms of coral rubble were collected over four sampling periods at three depths: 3 m (back-reef), 6–8 m (fore-reef), and 10–12 m (fore-reef). Results A total of 8,887 peracarid crustaceans belonging to 200 taxa distributed over five orders and 63 families was obtained; 70% of the taxa were identified to species and 25% to genus level. Fifty species of those collected represent new records for the Mexican Caribbean Sea. Isopoda was the most speciose order while Tanaidacea was the most abundant. Discussion Cryptic peracarid taxonomic richness and abundance were related to depth with higher values of both parameters being found in the shallow (3 m) back-reef, possibly due to a higher reef development and a greater accumulation of coral rubble produced during hurricanes. Peracarid data obtained in the present study can be used as a baseline for future monitoring programs in the PMRNP. PMID:28630800

  11. Rates of species accumulation and taxonomic diversification during phototrophic biofilm development are controlled by both nutrient supply and current velocity.

    PubMed

    Larson, Chad A; Passy, Sophia I

    2013-03-01

    The accumulation of new and taxonomically diverse species is a marked feature of community development, but the role of the environment in this process is not well understood. To address this problem, we subjected periphyton in laboratory streams to low (10-cm · s(-1)), high (30-cm · s(-1)), and variable (9- to 32-cm · s(-1)) current velocity and low- versus high-nutrient inputs. We examined how current velocity and resource supply constrained (i) the rates of species accumulation, a measure of temporal beta-diversity, and (ii) the rates of diversification of higher taxonomic categories, defined here as the rate of higher taxon richness increase with the increase of species richness. Temporal biofilm dynamics were controlled by a strong nutrient-current interaction. Nutrients accelerated the rates of accumulation of new species, when flow velocity was not too stressful. Species were more taxonomically diverse under variable than under low-flow conditions, indicating that flow heterogeneity increased the niche diversity in the high-nutrient treatments. Conversely, the lower diversification rates under high- than under low-nutrient conditions at low velocity are explained with finer resource partitioning among species, belonging to a limited number of related genera. The overall low rates of diversification in high-current treatments suggest that the ability to withstand current stress was conserved within closely related species. Temporal heterogeneity of disturbance has been shown to promote species richness, but here we further demonstrate that it also affects two other components of biodiversity, i.e., temporal beta-diversity and diversification rate. Therefore, management efforts for preserving the inherent temporal heterogeneity of natural ecosystems will have detectable positive effects on biodiversity.

  12. Rates of Species Accumulation and Taxonomic Diversification during Phototrophic Biofilm Development Are Controlled by both Nutrient Supply and Current Velocity

    PubMed Central

    2013-01-01

    The accumulation of new and taxonomically diverse species is a marked feature of community development, but the role of the environment in this process is not well understood. To address this problem, we subjected periphyton in laboratory streams to low (10-cm · s−1), high (30-cm · s−1), and variable (9- to 32-cm · s−1) current velocity and low- versus high-nutrient inputs. We examined how current velocity and resource supply constrained (i) the rates of species accumulation, a measure of temporal beta-diversity, and (ii) the rates of diversification of higher taxonomic categories, defined here as the rate of higher taxon richness increase with the increase of species richness. Temporal biofilm dynamics were controlled by a strong nutrient-current interaction. Nutrients accelerated the rates of accumulation of new species, when flow velocity was not too stressful. Species were more taxonomically diverse under variable than under low-flow conditions, indicating that flow heterogeneity increased the niche diversity in the high-nutrient treatments. Conversely, the lower diversification rates under high- than under low-nutrient conditions at low velocity are explained with finer resource partitioning among species, belonging to a limited number of related genera. The overall low rates of diversification in high-current treatments suggest that the ability to withstand current stress was conserved within closely related species. Temporal heterogeneity of disturbance has been shown to promote species richness, but here we further demonstrate that it also affects two other components of biodiversity, i.e., temporal beta-diversity and diversification rate. Therefore, management efforts for preserving the inherent temporal heterogeneity of natural ecosystems will have detectable positive effects on biodiversity. PMID:23335757

  13. Morphology, taxonomic status and distribution of the opisthobranch mollusc Coryphella (s.l.) japonica from the central deep water basin of the Sea of Japan

    NASA Astrophysics Data System (ADS)

    Martynov, Alexander V.

    2013-02-01

    The opisthobranch fauna (Gastropoda: Opisthobranchia) of the deep sea basins of the Sea of Japan is reviewed. A detailed description of the most common deep sea nudibranch species Coryphella japonicaVolodchenko, 1941 is given based on materials from various expeditions (including R/V "Vityaz" cruises and SoJaBio project). Distinct morphological features of C. japonica are discussed and its valid taxonomic status is confirmed. The considerable radular variability of C. japonica for the first time is documented using a scanning electron microscope. Unique features of the bathymetric distribution of C. japonica ranging from shelf to the abyssal depths are discussed in connection with the "pseudabyssal area" concept. C. japonica was compared to its assumed synonym C. salmonacea, and to similar C. athadona. Material from all these species, including types of C. japonica, was examined externally, anatomically via dissection, and SEM. C. salmonacea is restricted to North Atlantic and Arctic only, whereas C. japonica inhabits NE Pacific including deep water basins of the Sea of Japan.

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

    PubMed

    Uher, Jana

    2015-12-01

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

  15. Genus-level taxonomic changes implied by the mitochondrial phylogeny of grey mullets (Teleostei: Mugilidae).

    PubMed

    Durand, Jean-Dominique; Chen, Wei-Jen; Shen, Kang-Ning; Fu, Cuizhang; Borsa, Philippe

    2012-01-01

    , Osteomugil))]. Agonostomus monticola and several species with large distribution ranges (including Moolgarda seheli, Mugil cephalus and M. curema) consist of separate lineages whose geographic distribution suggests they are cryptic species, thus warranting further taxonomic work in the Mugilidae at the infra-generic level. Copyright © 2012 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  16. Taxonomic status and morphological variation of Hydrodynastes bicinctus (Hermann, 1804) (Serpentes: Dipsadidae).

    PubMed

    Murta-Fonseca, Roberta A; Franco, Francisco L; Fernandes, Daniel Silva

    2016-08-26

    Hydrodynastes bicinctus was described with no type material or locality and it has two subspecies currently recognized that are not taxonomically well defined. We tested the validity of the two subspecies through meristic, morphometric, and color pattern characters. Two apparently distinct color patterns of H. bicinctus were noticed, one from the Cerrado open formations and the other from the Amazon rainforest. These aforementioned patterns, however, exhibited a high degree of geographic overlap and many specimens showed a blended pattern. Based on these results we propose synonymizing H. bicinctus schultzi with the nominal taxon. Furthermore, we designate a neotype for the species, present data on geographic distribution, and provide morphological descriptions of the hemipenis, cephalic glands, and skull.

  17. Further elucidation of the taxonomic relationships and geographic distribution of Escobaria sneedii var. sneedii, E. sneedii var. leei, and E. guadalupensis (Cactaceae)

    Treesearch

    Marc A. Baker

    2007-01-01

    Individuals of E. sneedii var. sneedii were found to occur in greater abundance within the Guadalupe Mountains than was previously recorded. No additional populations morphologically intermediate between E. guadalupensis and E. sneedii were found. Taxonomic affiliation and geographic...

  18. Beta-diversity of ectoparasites at two spatial scales: nested hierarchy, geography and habitat type.

    PubMed

    Warburton, Elizabeth M; van der Mescht, Luther; Stanko, Michal; Vinarski, Maxim V; Korallo-Vinarskaya, Natalia P; Khokhlova, Irina S; Krasnov, Boris R

    2017-06-01

    Beta-diversity of biological communities can be decomposed into (a) dissimilarity of communities among units of finer scale within units of broader scale and (b) dissimilarity of communities among units of broader scale. We investigated compositional, phylogenetic/taxonomic and functional beta-diversity of compound communities of fleas and gamasid mites parasitic on small Palearctic mammals in a nested hierarchy at two spatial scales: (a) continental scale (across the Palearctic) and (b) regional scale (across sites within Slovakia). At each scale, we analyzed beta-diversity among smaller units within larger units and among larger units with partitioning based on either geography or ecology. We asked (a) whether compositional, phylogenetic/taxonomic and functional dissimilarities of flea and mite assemblages are scale dependent; (b) how geographical (partitioning of sites according to geographic position) or ecological (partitioning of sites according to habitat type) characteristics affect phylogenetic/taxonomic and functional components of dissimilarity of ectoparasite assemblages and (c) whether assemblages of fleas and gamasid mites differ in their degree of dissimilarity, all else being equal. We found that compositional, phylogenetic/taxonomic, or functional beta-diversity was greater on a continental rather than a regional scale. Compositional and phylogenetic/taxonomic components of beta-diversity were greater among larger units than among smaller units within larger units, whereas functional beta-diversity did not exhibit any consistent trend regarding site partitioning. Geographic partitioning resulted in higher values of beta-diversity of ectoparasites than ecological partitioning. Compositional and phylogenetic components of beta-diversity were higher in fleas than mites but the opposite was true for functional beta-diversity in some, but not all, traits.

  19. A taxonomy of state public health preparedness units: an empirical examination of organizational structure.

    PubMed

    Menachemi, Nir; Yeager, Valerie A; Duncan, W Jack; Katholi, Charles R; Ginter, Peter M

    2012-01-01

    State public health preparedness units (SPHPUs) were developed in response to federal funding to improve response to disasters: a responsibility that had not traditionally been within the purview of public health. The SPHPUs were created within the existing public health organizational structure, and their placement may have implications for how the unit functions, how communication takes place, and ultimately how well the key responsibilities are performed. This study empirically identifies a taxonomy of similarly structured SPHPUs and examines whether this structure is associated with state geographic, demographic, and threat-vulnerability characteristics. Data representing each SPHPU were extracted from publically available sources, including organizational charts and emergency preparedness plans for 2009. A cross-sectional segmentation analysis was conducted of variables representing structural attributes. Fifty state public health departments. Variables representing "span of control" and "hierarchal levels" were extracted from organizational charts. Structural "complexity" and "centralization" were extracted from state emergency preparedness documents and other secondary sources. On average, 6.6 people report to the same manager as the SPHPU director; 2.1 levels separate the SPHPU director from the state health officer; and a mean of 13.5 agencies collaborate with SPHPU during a disaster. Despite considerable variability in how SPHPUs had been structured, results of the cluster and principal component analysis identified 7 similarly structured groups. Neither the taxonomic groups nor the individual variables representing structure were found to be associated with state characteristics, including threat vulnerabilities. Our finding supports the hypothesis that SPHPUs are seemingly inadvertently (eg, not strategically) organized. This taxonomy provides the basis for which future research can examine how SPHPU structure relates to performance measures and

  20. 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.

  1. Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass

    PubMed Central

    Guo, Xue; Zhou, Xishu; Hale, Lauren; Yuan, Mengting; Feng, Jiajie; Ning, Daliang; Shi, Zhou; Qin, Yujia; Liu, Feifei; Wu, Liyou; He, Zhili; Van Nostrand, Joy D.; Liu, Xueduan; Luo, Yiqi; Tiedje, James M.; Zhou, Jizhong

    2018-01-01

    Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010–2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P < 0.05) increased root and microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P < 0.05) changed by clipping. Clipping significantly (P < 0.05) increased the abundances of labile carbon (C) degrading genes. More importantly, the abundances of recalcitrant C degrading genes were consistently and significantly (P < 0.05) increased by clipping in the last 2 years, which could accelerate recalcitrant C degradation and weaken long-term soil carbon stability. Furthermore, genes involved in nutrient-cycling processes including nitrogen cycling and phosphorus utilization were also significantly increased by clipping. The shifts of microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices. PMID:29904372

  2. Aggregate resource availability in the conterminous United States, including suggestions for addressing shortages, quality, and environmental concerns

    USGS Publications Warehouse

    Langer, William H.

    2011-01-01

    Although potential sources of aggregate are widespread throughout the United States, many sources may not meet certain physical property requirements, such as soundness, hardness, strength, porosity, and specific gravity, or they may contain contaminants or deleterious materials that render them unusable. Encroachment by conflicting land uses, permitting considerations, environmental issues, and societal pressures can prevent or limit development of otherwise suitable aggregate. The use of sustainable aggregate resource management can help ensure an economically viable supply of aggregate. Sustainable aggregate resource management techniques that have successfully been used include (1) protecting potential resources from encroachment; (2) using marginal-quality local aggregate for applications that do not demand a high-quality resource; (3) using substitute materials such as clinker, scoria, and recycled asphalt and concrete; and (4) using rail and water to transport aggregates from remote sources.

  3. A taxonomic review of the Korean species of the subgenus Datomicra Mulsant & Rey of the genus Atheta Thomson, with description of a new species (Coleoptera, Staphylinidae, Aleocharinae).

    PubMed

    Lee, Seung-Gyu; Ahn, Kee-Jeong

    2017-05-18

    A taxonomic review of the subgenus Datomicra Mulsant & Rey of the genus Atheta Thomson in Korea is presented. A new synonym is proposed: Datomicra Mulsant & Rey, 1874 = Datostiba Sawada, 1976, syn. nov. The subgenus is represented in Korea by eight species including a new species, Atheta (Datomicra) semidentiventris Lee & Ahn, sp. nov. Two species [A. (D.) dadopora Thomson and A. (D.) dentiventris Bernhauer] are new to the Korean Peninsula and one [A. (D.) celata (Erichson)] to South Korea. A key, descriptions, habitus photographs and illustrations of the diagnostic characters of the new species and two newly recorded species are provided.

  4. Iron-ore resources of the United States including Alaska and Puerto Rico, 1955

    USGS Publications Warehouse

    Carr, Martha S.; Dutton, Carl E.

    1959-01-01

    The importance of iron ore, the basic raw material of steel, as a fundamental mineral, resource is shown by the fact that about 100 million long tons of steel is used annually in the economy of the United States, as compared with a combined total of about 5 million long tons of copper, lead, zinc, and aluminum. Satisfying this annual demand for steel requires about 110 million tons of iron ore and 70 million tons of scrap iron and steel. The average annual consumption of iron ore in the United States from 1951 to 1955, inclusive, was about 110 million long tons, which is about twice the annual average from 1900 to 1930. Production of iron ore in the United States in this 5-year period averaged approximately 100 million long tons annually, divided by regions as follows (in percent): Lake Superior, 84.1; southeastern, 6.7; western, 6.7; northeastern, 1.4; and central and gulf, 1.1. Mining of iron ore began in the American Colonies about 1619, and for 225 years it was limited to eastern United States where fuel and markets were readily available. Production of iron ore from the Lake Superior region began in 1846; the region became the leading domestic source by 1890, and the Mesabi range in Minnesota has been the world's most productive area since 1896. Proximity of raw materials, water transportation, and markets has resulted in centralization of the country's iron and steel industry in the lower Great Lakes area. Increased imports of iron ore being delivered to eastern United States as well as demands for steel in nearby markets have given impetus to expansion in the steel-making capacity in this area. The four chief iron-ore minerals - hematite, liminite, magnetite, and siderite - are widely distributed but only locally form deposits of sufficient tonnage and grade to be commercially valuable at the present time. The iron content of these minerals, of which hematite is the most important, ranges from 48 percent in siderite to 72 percent in magnetite, but as these

  5. Taxonomic position of Hormaphis similibetulae Qiao & Zhang, 2004 (Hemiptera, Aphididae): molecular and biological evidences

    PubMed Central

    Chen, Jing; Jiang, Li-Yun; Qiao, Ge-Xia

    2011-01-01

    Abstract The taxonomic position of Hormaphis similibetulae Qiao & Zhang, 2004 has been reexamined. The phylogenetic position of Hormaphis similibetulae was inferred by maximum parsimony, maximum likelihood and Bayesian analyses on the basis of partial nuclear elongation factor-1α and mitochondrial tRNA leucine/cytochrome oxidase II sequences. The results showed that this species fell into the clade of Hamamelistes species, occupying a basal position, and was clearly distinct from other Hormaphis species. A closer relationship between Hormaphis similibetulae and Hamamelistes species was also revealed by life cycle analysis. Therefore, we conclude that Hormaphis similibetulae should be transferred to the genus Hamamelistes as Hamamelistes similibetulae (Qiao & Zhang), comb. n. PMID:21852935

  6. Levels of genetic diversity and taxonomic status of Epinephelus species in United Arab Emirates fish markets.

    PubMed

    Ketchum, Remi N; Dieng, Mame M; Vaughan, Grace O; Burt, John A; Idaghdour, Youssef

    2016-04-30

    Understanding the patterns of genetic diversity of fish species is essential for marine conservation and management. This is particularly important in the Arabian Gulf where marine life is subject to extreme environmental conditions that could impact genetic diversity. Here we assess genetic diversity of the most commercially important fish in the United Arab Emirates; groupers (Epinephelus spp.). Sequencing of 973 bp mitochondrial DNA from 140 tissue samples collected in four main fish markets revealed 58 haplotypes clustered within three groups. Data analysis revealed the presence of three distinct Epinephelus species being marketed as one species (hammour): Epinephelus coioides, Epinephelus areolatus and Epinephelus bleekeri. We report species-specific genetic markers and demonstrate that all three species exhibit relatively low levels of genetic variation, reflecting the effect of overfishing and environmental pressures. In light of the genetic evidence presented here, conservation and management of groupers in the UAE warrant the implementation of species-specific measures. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Tardigrada of Ireland: a review of records and an updated checklist of species including a new addition to the Irish fauna

    PubMed Central

    DeMilio, Erica; Lawton, Colin; Marley, Nigel J.

    2016-01-01

    Abstract The phylum Tardigrada was not recorded in Ireland until the Clare Island Survey of 1909–1911, with only rare subsequent reports on Irish tardigrade species. In recent decades, significant taxonomic revision has occurred within Tardigrada. This has resulted in the need for a review of all known historical records from Ireland and Northern Ireland in order to produce an updated checklist of valid taxa. The new checklist includes fifty-one tardigrade species and subspecies including a new addition to the Irish fauna reported herein, Echiniscus quadrispinosus quadrispinosus Richters, 1902 from Newtown, Ballyvaughan, Co. Clare. PMID:27667947

  8. The benthic macrofauna from the Lower Maastrichtian chalk of Kronsmoor (northern Germany, Saturn quarry): taxonomic outline and palaeoecologic implications

    NASA Astrophysics Data System (ADS)

    Engelke, Julia; Esser, Klaus J. K.; Linnert, Christian; Mutterlose, Jörg; Wilmsen, Markus

    2016-12-01

    The benthic macroinvertebrates of the Lower Maastrichtian chalk of Saturn quarry at Kronsmoor (northern Germany) have been studied taxonomically based on more than 1,000 specimens. Two successive benthic macrofossil assemblages were recognised: the lower interval in the upper part of the Kronsmoor Formation (Belemnella obtusa Zone) is characterized by low abundances of macroinvertebrates while the upper interval in the uppermost Kronsmoor and lowermost Hemmoor formations (lower to middle Belemnella sumensis Zone) shows a high macroinvertebrate abundance (eight times more than in the B. obtusa Zone) and a conspicuous dominance of brachiopods. The palaeoecological analysis of these two assemblages indicates the presence of eight different guilds, of which epifaunal suspension feeders (fixo-sessile and libero-sessile guilds), comprising approximately half of the trophic nucleus of the lower interval, increased to a dominant 86% in the upper interval, including a considerable proportion of rhynchonelliform brachiopods. It is tempting to relate this shift from the lower to the upper interval to an increase in nutrient supply and/or a shallowing of the depositional environment but further data including geochemical proxies are needed to fully understand the macrofossil distribution patterns in the Lower Maastrichtian of Kronsmoor.

  9. New taxonomic and faunistic data on the Himalayan Lesteva Latreille, 1797 (Coleoptera: Staphylinidae: Omaliinae).

    PubMed

    Shavrin, Alexey V

    2016-12-05

    New taxonomic and faunistc data for seven species of the genus Lesteva Latreille, 1797 of the Himalayas are presented. Two species are redescribed: L. (s.str.) kargilensis Cameron, 1934 and L. (s.str.) steeli Lohse, 1982. The aedeagus of L. (s.str.) steeli is illustrated. One synonym is proposed: L. (s.str.) brevipennis Cameron, 1941 = L. pakistana Coiffait, 1984 syn. n. A lectotype and paralectotypes for L. (s.str.) torrentum Cameron, 1924 are designated. A key to species known from the Himalayan Region is provided.

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

    PubMed

    Cisneros, Laura M; Fagan, Matthew E; Willig, Michael R

    2016-01-01

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

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

    PubMed Central

    Fagan, Matthew E.; Willig, Michael R.

    2016-01-01

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

  12. Two-stage stochastic unit commitment model including non-generation resources with conditional value-at-risk constraints

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Huang, Yuping; Zheng, Qipeng P.; Wang, Jianhui

    2014-11-01

    tThis paper presents a two-stage stochastic unit commitment (UC) model, which integrates non-generation resources such as demand response (DR) and energy storage (ES) while including riskconstraints to balance between cost and system reliability due to the fluctuation of variable genera-tion such as wind and solar power. This paper uses conditional value-at-risk (CVaR) measures to modelrisks associated with the decisions in a stochastic environment. In contrast to chance-constrained modelsrequiring extra binary variables, risk constraints based on CVaR only involve linear constraints and con-tinuous variables, making it more computationally attractive. The proposed models with risk constraintsare able to avoid over-conservative solutions butmore » still ensure system reliability represented by loss ofloads. Then numerical experiments are conducted to study the effects of non-generation resources ongenerator schedules and the difference of total expected generation costs with risk consideration. Sen-sitivity analysis based on reliability parameters is also performed to test the decision preferences ofconfidence levels and load-shedding loss allowances on generation cost reduction.« less

  13. A Taxonomic Update of Small Mammal Plague Reservoirs in South America.

    PubMed

    Bonvicino, Cibele R; Oliveira, João A; Cordeiro-Estrela, Pedro; D'andrea, Paulo S; Almeida, Alzira M P

    2015-10-01

    Plague is a disease of epidemic potential that may emerge with discontinuous outbreaks. In South America, 50 wild rodent species have been identified as plague reservoirs, in addition to one lagomorph and two marsupials. To review the nomenclature of plague reservoirs, we examined specimens collected in plague foci, carried out new surveys in Brazilian plague regions, and re-evaluated the nomenclature of South American reservoirs on the basis of the current literature. Five of the 15 species involved with plague in Argentina, three of 10 species involved with plague in Bolivia, three of the seven species involved with plague in Peru, five of the nine species involved with plague in Ecuador, and six of the nine species involved with plague in Brazil have undergone taxonomic changes. In the last 20 years, plague cases were recorded in Bolivia, Brazil, Ecuador, and Peru. These four countries have a high rodent species richness in plague foci, a fact that may be decisive for the maintenance of plague in the wild.

  14. Taxonomic and functional diversity increase the aesthetic value of coralligenous reefs

    PubMed Central

    Tribot, Anne-Sophie; Mouquet, Nicolas; Villéger, Sébastien; Raymond, Michel; Hoff, Fabrice; Boissery, Pierre; Holon, Florian; Deter, Julie

    2016-01-01

    The aesthetic value of landscapes contributes to human well-being. However, studies which have investigated the link between biodiversity and ecosystem services have not taken aesthetic value into account. In this study we evaluated how the aesthetics of coralligenous reefs, a key marine ecosystem in the Mediterranean, is perceived by the general public and how aesthetic preferences are related to biodiversity facets (taxonomic, phylogenetic and functional diversities). We performed both biodiversity measures and online-surveys of aesthetic perception on photographic quadrats sampled along the French Mediterranean coast. Our results show that species richness and functional richness have a significant positive effect on aesthetic value. Most of the ecological literature, exploring the relationship between biodiversity and ecosystem functioning and service has focused so far on ‘economical’ aspects of biodiversity (provision or regulation). Our results illustrate that cultural facets, such as ‘beauty’, should also be central in our motivations to preserve ecological diversity. PMID:27677850

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

    PubMed Central

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

    2014-01-01

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

  16. Definition of Tenuipalpus sensu stricto (Acari, Tenuipalpidae), with redescription of Tenuipalpus caudatus (Dugès) and description of a new species from Costa Rica

    USDA-ARS?s Scientific Manuscript database

    We discuss the taxonomic history of the genus Tenuipalpus Donnadieu and re-describe Tenuipalpus caudatus (Dugès) (= T. palmatus Donnadieu) based on specimens from Portugal intercepted at the United States ports of entry, and references including photographic records of the neotype of T. caudatus. In...

  17. Teaching the Scientific Method: It's All in the Perspective

    ERIC Educational Resources Information Center

    Ayers, James M.; Ayers, Kathleen M.

    2007-01-01

    A three unit module of inquiry, including morphological comparison, cladogram construction, and data mining has been developed to teach students the nature of experimental science. Students generate angiosperm morphological data, form cladistic hypotheses, then mine taxonomic, bioinformatic and historical data from many sources to replicate and…

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

    NASA Astrophysics Data System (ADS)

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

    2017-11-01

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

  19. Multivariate functions for predicting the sorption of 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitro-1,3,5-tricyclohexane (RDX) among taxonomically distinct soils.

    PubMed

    Katseanes, Chelsea K; Chappell, Mark A; Hopkins, Bryan G; Durham, Brian D; Price, Cynthia L; Porter, Beth E; Miller, Lesley F

    2016-11-01

    After nearly a century of use in numerous munition platforms, TNT and RDX contamination has turned up largely in the environment due to ammunition manufacturing or as part of releases from low-order detonations during training activities. Although the basic knowledge governing the environmental fate of TNT and RDX are known, accurate predictions of TNT and RDX persistence in soil remain elusive, particularly given the universal heterogeneity of pedomorphic soil types. In this work, we proposed a new solution for modeling the sorption and persistence of these munition constituents as multivariate mathematical functions correlating soil attribute data over a variety of taxonomically distinct soil types to contaminant behavior, instead of a single constant or parameter of a specific absolute value. To test this idea, we conducted experiments measuring the sorption of TNT and RDX on taxonomically different soil types that were extensively physical and chemically characterized. Statistical decomposition of the log-transformed, and auto-scaled soil characterization data using the dimension-reduction technique PCA (principal component analysis) revealed a strong latent structure based in the multiple pairwise correlations among the soil properties. TNT and RDX sorption partitioning coefficients (KD-TNT and KD-RDX) were regressed against this latent structure using partial least squares regression (PLSR), generating a 3-factor, multivariate linear functions. Here, PLSR models predicted KD-TNT and KD-RDX values based on attributes contributing to endogenous alkaline/calcareous and soil fertility criteria, respectively, exhibited among the different soil types: We hypothesized that the latent structure arising from the strong covariance of full multivariate geochemical matrix describing taxonomically distinguished soil types may provide the means for potentially predicting complex phenomena in soils. The development of predictive multivariate models tuned to a local soil

  20. Pressure vessel sliding support unit and system using the sliding support unit

    DOEpatents

    Breach, Michael R.; Keck, David J.; Deaver, Gerald A.

    2013-01-15

    Provided is a sliding support and a system using the sliding support unit. The sliding support unit may include a fulcrum capture configured to attach to a support flange, a fulcrum support configured to attach to the fulcrum capture, and a baseplate block configured to support the fulcrum support. The system using the sliding support unit may include a pressure vessel, a pedestal bracket, and a plurality of sliding support units.

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

    PubMed

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

    2018-01-01

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

  2. 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.

  3. 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

  4. Petroleum supply monthly, April 1991. [Glossary included

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Not Available

    1991-04-29

    Data presented in the PSM (Petroleum Supply Monthly) describe the supply and disposition of petroleum products in the United States and major US geographic regions. The data series describe production, imports and exports, inter-Petroleum Administration for Defense (PAD) District movements, and inventories by the primary suppliers of petroleum products in the United States (50 States and the District of Columbia). The reporting universe includes those petroleum sectors in Primary Supply. Included are: petroleum refiners, motor gasoline blenders, operators of natural gas processing plants and fractionators, inter-PAD transporters, importers, and major inventory holders of petroleum products and crude oil. When aggregated,more » the data reported by these sectors approximately represent the consumption of petroleum products in the United States. The tables and figures in the Summary Statistics section of the PSM present a time series of selected petroleum data on a US level. Most time series include preliminary estimates for one month. The Detailed Statistics tables of the PSM present statistics for the most current month available as well as year-to-date. Industry terminology and product definitions are listed alphabetically in the Glossary. 14 figs., 65 tabs.« less

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

    PubMed

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

    2000-10-01

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

  6. 15 CFR 2006.1 - Information to be included in petition.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... property right, or foreign direct investment matter for which the rights of the United States under the... nature of any foreign direct investment proposed by the United States person, including estimates of... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false Information to be included in petition...

  7. Phylogeny and taxonomic revision of the Planistromellaceae including its coelomycetous anamorphs: contributions towards a monograph of the genus Kellermania

    Treesearch

    A.M. Minnis; A.H. Kennedy; D.B. Grenier; M.E. Palm; A.Y. Rossman

    2012-01-01

    The core species of the family Planistromellaceae are included in the teleomorphic genera Planistroma and Planistromella and the connected anamorphic, coelomycetous genera Alpakesa, Kellermania, and Piptarthron. These genera have been defined primarily on the basis of...

  8. Taxonomic status of Parotia berlepschi Kleinschmidt, 1897 based on analysis of external appearance, voice and behavior (Aves: Paradisaeidae).

    PubMed

    Scholes, Edwin; Beehler, Bruce M; Laman, Timothy G

    2017-10-10

    Described from trade-skins of unknown origins, Parotia berlepschi Kleinschmidt, 1897 was the subject of a longstanding ornithological mystery that remained unresolved for well over a century. With few specimens and no known wild population, most taxonomic assessments over the last century have treated P. berlepschi as a subspecies of Parotia carolae Meyer, 1894. Following discovery of its geographical home in 2005, most authorities returned to giving P. berlepschi full species status. However, evidence supporting the delineation of P. berlepschi from P. carolae has not yet been fully articulated in the literature. Here, we assess phenotypic differentiation and the taxonomic status of P. berlepschi relative to P. carolae based on specimens and recordings of wild birds. With regard to external appearance and voice, which are important intersexual signals among polygynous birds-of-paradise, our analysis confirms that P. berlepschi is well-differentiated from P. carolae and should be treated as specifically distinct. Evidence for differentiation in courtship behavior is inconclusive and requires further study.

  9. Phylogeny and taxonomic revision of the Planistromellaceae including its coelomycetous anamorphs: contributions towards a monograph of the genus Kellermania

    USDA-ARS?s Scientific Manuscript database

    The core species of the family Planistromellaceae are included in the teleomorphic genera Planistroma and Planistromella and their anamorphic, coelomycetous genera Alpakesa, Kellermania, and Piptarthron. These genera have been defined primarily on the basis of ascospore septation or number of conidi...

  10. Karyotype description of Pomacea patula catemacensis (Caenogastropoda, Ampullariidae), with an assessment of the taxonomic status of Pomacea patula.

    PubMed

    Diupotex-Chong, María Esther; Cazzaniga, Néstor J; Hernández-Santoyo, Alejandra; Betancourt-Rule, José Miguel

    2004-12-01

    Mitotic chromosomes of the freshwater snail Pomacea patula catemacensis (Baker 1922) were analyzed on gill tissue of specimens from the type locality (Lake Catemaco, Mexico). The diploid number of chromosomes is 2n = 26, including nine metacentric and four submetacentric pairs; therefore, the fundamental number is FN = 52, No sex chromosomes could be identified. The same chromosome number and morphology were already reported for P. flagellata, i.e., the other species of the genus living in Mexico. The basic haploid number for family Ampullariidae was reported to be n = 14 in the literature; so, its reduction to n = 13 is probably an apomorphy of the Mexican Pomacea snails. Lanistes bolteni, from Egypt, also shows n = 13, but its karyotype is much more asymmetrical, and seems to have evolved independently from P. flagellata and P. patula catemacensis. The nominotypical subspecies, P. patula patula (Reeve 1856), is a poorly known taxon, whose original locality is unknown. A taxonomical account is presented here, and a Mexican origin postulated as the most parsimonious hypothesis.

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

    PubMed Central

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

    2015-01-01

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

  12. The role of taxonomy in species conservation.

    PubMed Central

    Mace, Georgina M

    2004-01-01

    Taxonomy and species conservation are often assumed to be completely interdependent activities. However, a shortage of taxonomic information and skills, and confusion over where the limits to 'species' should be set, both cause problems for conservationists. There is no simple solution because species lists used for conservation planning (e.g. threatened species, species richness estimates, species covered by legislation) are often also used to determine which units should be the focus of conservation actions; this despite the fact that the two processes have such different goals and information needs. Species conservation needs two kinds of taxonomic solution: (i) a set of practical rules to standardize the species units included on lists; and (ii) an approach to the units chosen for conservation recovery planning which recognizes the dynamic nature of natural systems and the differences from the units in listing processes that result. These solutions are well within our grasp but require a new kind of collaboration among conservation biologists, taxonomists and legislators, as well as an increased resource of taxonomists with relevant and high-quality skills. PMID:15253356

  13. Brine shrimp bioassay: importance of correct taxonomic identification of Artemia (Anostraca) species.

    PubMed

    Ruebhart, David R; Cock, Ian E; Shaw, Glen R

    2008-08-01

    Despite the common use of the brine shrimp bioassay in toxicology, there is confusion in the literature regarding citation of the correct taxonomic identity of the Artemia species used. The genus Artemia, once thought to be represented by a single species Artemia salina, is now known to be composed of several bisexual species as well as parthenogenetic populations. Artemia franciscana is the best studied of the Artemia species and is considered to represent the vast majority of studies in which Artemia is used as an experimental test organism. We found that in studies referring to the use of A. salina, the zoogeography of the cyst harvest site indicated that the species used was actually A. franciscana. Those performing bioassays with Artemia need to exercise diligence in assigning correct species identification, as the identity of the test organism is an important parameter in assuring the validity of the results of the assay.

  14. A New Fossil of Necrotauliidae (Insecta: Trichoptera) from the Jiulongshan Formation of China and Its Taxonomic Significance

    PubMed Central

    Liu, Yujia; Zhang, Weiting; Yao, Yunzhi; Ren, Dong

    2014-01-01

    Background Acisarcuatus variradius gen. et sp. nov., an extinct new species representing a new genus, is described from the Middle Jurassic Jiulongshan Formation in Daohugou Village, Inner Mongolia, China. Methodology/Principal Findings In this paper, we revised the diagnosis of Necrotauliidae Handlirsch, 1906. One new genus and species of Necrotauliidae is described. An analysis based on the fossil morphological characters clarified the taxonomic status of the new taxa. Conclusions/Significance New fossil evidence supports the viewpoint that the family Necrotauliidae belongs to the Integripalpia. PMID:25494387

  15. Recharacterization of Rhinophis dorsimaculatus Deraniyagala, 1941 (Serpentes: Uropeltidae), including description of new material.

    PubMed

    Gower, David J; Wickramasinghe, L J Mendis

    2016-08-29

    The Sri Lankan uropeltid (shieldtail) snake Rhinophis dorsimaculatus Deraniyagala, 1941 was described originally from two specimens that were subsequently lost. The small amount of previously published data and lack of published colour photographs made this one of South Asia's most poorly known snake species, and this resulted in at least one instance of taxonomic misidentification. An additional 10 specimens from a historical collection from the vicinity of the type locality recently came to light. This material is reviewed and documented and the species recharacterized. An additional locality for the species is reported. The newly reported material helps to corroborate the taxonomic validity and distinctiveness of Rhinophis dorsimaculatus. The species is readily distinguished from congeners by having 227 or more ventral scales; a large, dorsally carinate rostral shield; posterior margins of paired anals that are largely separated by the posteriormost ventral scale; and a distinctive colour pattern with bilaterally asymmetrical dark blotches within a broad, pale middorsal stripe and regularly punctate flanks.

  16. Anampses viridis Valenciennes 1840 (Pisces: Labridae)--a case of taxonomic con- fusion and mistaken extinction.

    PubMed

    Russell, Barry C; Craig, Matthew T

    2013-01-01

    Anampses viridis Valenciennes 1840 is known from only three specimens collected from Mauritius, and despite intensive sampling, the species has not been seen or reported since it was originally described. This apparent failure to 'rediscover' A. viridis at Mauritius has led to speculation that it is extinct, and the species has been widely cited as an example of a marine fish extinction. Far from being extinct, Anampses viridis has been taxonomically confused and actually is the adult male (terminal phase) colour form and a junior synonym of A. caeruleopunctatus Rüppell 1829, a species that is common and widespread throughout the Indo-West Pacific region.

  17. 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

    2016-07-20

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

  18. Standardized terminology and potential taxonomic utility for hadrosaurid skin impressions: a case study for Saurolophus from Canada and Mongolia.

    PubMed

    Bell, Phil R

    2012-01-01

    The characterization of palaeospecies typically relies on hard-tissue anatomy, such as bones or teeth that is more readily fossilized than soft parts. Among dinosaurs, skin impressions are commonly associated with partial and complete hadrosaurid skeletons, and consist of non-imbricating tubercles or scales. Skin impressions from various parts of the body of two species of the hadrosaurine Saurolophus (S. angustirostris from Mongolia and S. osborni from Canada) are described from multiple specimens. These species, recently validated on osteological grounds, can be differentiated based solely on soft-tissue anatomy, namely scale shape and pattern. This study demonstrates for the first time the applicability of soft-tissue (i.e., scale impressions) as a means to differentiate species within the Dinosauria. Differences are most spectacular in the tail, where S. angustirostris is differentiated by the presence of vertical bands of morphologically distinct scales, a grid-like arrangement of circular feature-scales, and tabular scales along the dorsal midline. Preliminary results indicate scale architecture remained consistent throughout ontogeny in S. angustirostris. These results support previous assertions that hadrosaurid scale architecture has a positive phylogenetic signal. As such, future taxonomic descriptions should include, where possible, the standardized description of skin impressions including the position and orientation of these impressions on the body.

  19. Standardized Terminology and Potential Taxonomic Utility for Hadrosaurid Skin Impressions: A Case Study for Saurolophus from Canada and Mongolia

    PubMed Central

    Bell, Phil R.

    2012-01-01

    The characterization of palaeospecies typically relies on hard-tissue anatomy, such as bones or teeth that is more readily fossilized than soft parts. Among dinosaurs, skin impressions are commonly associated with partial and complete hadrosaurid skeletons, and consist of non-imbricating tubercles or scales. Skin impressions from various parts of the body of two species of the hadrosaurine Saurolophus (S. angustirostris from Mongolia and S. osborni from Canada) are described from multiple specimens. These species, recently validated on osteological grounds, can be differentiated based solely on soft-tissue anatomy, namely scale shape and pattern. This study demonstrates for the first time the applicability of soft-tissue (i.e., scale impressions) as a means to differentiate species within the Dinosauria. Differences are most spectacular in the tail, where S. angustirostris is differentiated by the presence of vertical bands of morphologically distinct scales, a grid-like arrangement of circular feature-scales, and tabular scales along the dorsal midline. Preliminary results indicate scale architecture remained consistent throughout ontogeny in S. angustirostris. These results support previous assertions that hadrosaurid scale architecture has a positive phylogenetic signal. As such, future taxonomic descriptions should include, where possible, the standardized description of skin impressions including the position and orientation of these impressions on the body. PMID:22319623

  20. A taxonomic index, with names of descriptive authorities of termite genera and species: An accompaniment to Biology of Termites: A Modern Synthesis (Bignell DE, Roisin Y, Lo N, Editors. 2011. Springer, Dordrecht. 576 pp.)

    PubMed Central

    Bignell, D. E.; Jones, D. T.

    2014-01-01

    Abstract Biology of Termites: A Modern Synthesis (Bignell DE, Roisin Y, Lo N, (Editors), Springer, Dordrecht, 576pp, ISBN 978-90-481-3976-7, e-ISBN 978-90-481-3977-4, DOI 10.1007/978-90-481-3977-4) was published in 2011. With the agreement of the publishers, we give a taxonomic index of the book comprising 494 termite entries, 103 entries of other multicellular animal species mentioned as associates or predators of termites, with 9 fungal, 60 protist, and 64 prokaryote identities, which are listed as termite symbionts ( sensu stricto ). In addition, we add descriptive authorities for living (and some fossil) termite genera and species. Higher taxonomic groupings for termites are indicated by 25 code numbers. Microorganisms (prokaryotes, protists, and fungi) are listed separately, using broad modern taxonomic affiliations from the contemporary literature of bacteriology, protozoology, and mycology. PMID:25368037