Science.gov

Sample records for comparativa das taxas

  1. Rotação do jato em DG tau próximo à região de sua formação: análise comparativa das velocidades radiais simuladas e observadas

    NASA Astrophysics Data System (ADS)

    Cerqueira, A. H.; de Gouveia dal Pino, E. M.

    2003-08-01

    Os modelos magneto-centrífugos utilizados para explicar a formação dos jatos Herbig-Haro assumem a presença de um disco de acresção em rotação kepleriana na base de lançamento do jato. Neste cenário, o jato transmite a informação da rotação do disco para regiões distantes da fonte central, além da superfície de Alfvén, na região de colimação inicial do jato. Recentemente, Bacciotti et al. (2002, ApJ, 537, L49) obtiveram pela primeira vez uma evidência observacional de rotação em um jato HH, o jato em DG Tau, em regiões próximas da fonte central, compatível (qualitativa e quantitativamente) com o esperado a partir dos modelos magneto-centrífugos para a produção e colimação inicial de jatos HH. No presente trabalho, apresentamos mapas de velocidade radial, obtidos através de simulações numéricas tri-dimensionais SPH, para um jato com características semelhantes ao jato em DG Tau, objetivando uma comparação com os mapas de velocidade radiais obtidos por Bacciotti et al.. Nossos resultados, embora preliminares, indicam que a inclusão de efeitos como a precessão, evidenciada em DG Tau (Dougados et al. 2000, A&A, 357, L61) devem ser levadas em consideração na análise da presença de rotação não só em DG Tau mas em qualquer sistema, com o uso das velocidades radias observadas. A ausência de um grau elevado de simetria axial (quebrada, por exemplo, pela precessão do eixo do jato; ou pela presença de uma superfície interna de trabalho, ou seja, um bow shock interno), implica também em uma maior complexidade nos mapas, com conseqüências relevantes para suas interpretações.

  2. Environmental distribution of prokaryotic taxa

    PubMed Central

    2010-01-01

    Background The increasing availability of gene sequences of prokaryotic species in samples extracted from all kind of locations allows addressing the study of the influence of environmental patterns in prokaryotic biodiversity. We present a comprehensive study to address the potential existence of environmental preferences of prokaryotic taxa and the commonness of the specialist and generalist strategies. We also assessed the most significant environmental factors shaping the environmental distribution of taxa. Results We used 16S rDNA sequences from 3,502 sampling experiments in natural and artificial sources. These sequences were taxonomically assigned, and the corresponding samples were also classified into a hierarchical classification of environments. We used several statistical methods to analyze the environmental distribution of taxa. Our results indicate that environmental specificity is not very common at the higher taxonomic levels (phylum to family), but emerges at lower taxonomic levels (genus and species). The most selective environmental characteristics are those of animal tissues and thermal locations. Salinity is another very important factor for constraining prokaryotic diversity. On the other hand, soil and freshwater habitats are the less restrictive environments, harboring the largest number of prokaryotic taxa. All information on taxa, samples and environments is provided at the envDB online database, http://metagenomics.uv.es/envDB. Conclusions This is, as far as we know, the most comprehensive assessment of the distribution and diversity of prokaryotic taxa and their associations with different environments. Our data indicate that we are still far from characterizing prokaryotic diversity in any environment, except, perhaps, for human tissues such as the oral cavity and the vagina. PMID:20307274

  3. Environmental distribution of prokaryotic taxa.

    PubMed

    Tamames, Javier; Abellán, Juan José; Pignatelli, Miguel; Camacho, Antonio; Moya, Andrés

    2010-03-22

    The increasing availability of gene sequences of prokaryotic species in samples extracted from all kind of locations allows addressing the study of the influence of environmental patterns in prokaryotic biodiversity. We present a comprehensive study to address the potential existence of environmental preferences of prokaryotic taxa and the commonness of the specialist and generalist strategies. We also assessed the most significant environmental factors shaping the environmental distribution of taxa. We used 16S rDNA sequences from 3,502 sampling experiments in natural and artificial sources. These sequences were taxonomically assigned, and the corresponding samples were also classified into a hierarchical classification of environments. We used several statistical methods to analyze the environmental distribution of taxa. Our results indicate that environmental specificity is not very common at the higher taxonomic levels (phylum to family), but emerges at lower taxonomic levels (genus and species). The most selective environmental characteristics are those of animal tissues and thermal locations. Salinity is another very important factor for constraining prokaryotic diversity. On the other hand, soil and freshwater habitats are the less restrictive environments, harboring the largest number of prokaryotic taxa. All information on taxa, samples and environments is provided at the envDB online database, http://metagenomics.uv.es/envDB. This is, as far as we know, the most comprehensive assessment of the distribution and diversity of prokaryotic taxa and their associations with different environments. Our data indicate that we are still far from characterizing prokaryotic diversity in any environment, except, perhaps, for human tissues such as the oral cavity and the vagina.

  4. The ontology of biological taxa

    PubMed Central

    Schulz, Stefan; Stenzhorn, Holger; Boeker, Martin

    2008-01-01

    Motivation: The classification of biological entities in terms of species and taxa is an important endeavor in biology. Although a large amount of statements encoded in current biomedical ontologies is taxon-dependent there is no obvious or standard way for introducing taxon information into an integrative ontology architecture, supposedly because of ongoing controversies about the ontological nature of species and taxa. Results: In this article, we discuss different approaches on how to represent biological taxa using existing standards for biomedical ontologies such as the description logic OWL DL and the Open Biomedical Ontologies Relation Ontology. We demonstrate how hidden ambiguities of the species concept can be dealt with and existing controversies can be overcome. A novel approach is to envisage taxon information as qualities that inhere in biological organisms, organism parts and populations. Availability: The presented methodology has been implemented in the domain top-level ontology BioTop, openly accessible at http://purl.org/biotop. BioTop may help to improve the logical and ontological rigor of biomedical ontologies and further provides a clear architectural principle to deal with biological taxa information. Contact: stschulz@uni-freiburg.de PMID:18586729

  5. Corridor use by diverse taxa.

    SciTech Connect

    Haddad, Nick, M.; Browne, David, R.; Cunningham, Alan; Danielson, Brent, J.; Levey, Douglas, J.; Sargent, Sarah; Spira, Tim

    2003-01-01

    Haddad, N.M., D.R. Browne, A. Cunningham, B.J. Danielson, D.J. Levey, S. Sargent, and T. Spira. 2003. Corridor use by diverse taxa. Ecology, 84(3):609-615. One of the most popular approaches for maintaining populations and conserving biodiversity in fragmented landscapes is to retain or create corridors that connect otherwise isolated habitat patches. Working in large-scale, experimental landscapes in which open-habitat patches and corridors were created by harvesting pine forest, we showed that corridors direct movements of different types of species, including butterflies, small mammals, and bird dispersed plants, causing higher movement between connected than between unconnected patches. Corridors directed the movement of all 10 species studied, with all corridor effect sizes >68%. However, this corridor effect was significant for five species, not significant for one species, and inconclusive for four species because of small sample sizes. Although we found no evidence that corridors increase emigration from a patch, our results show that movements of disparate taxa with broadly different life histories and functional roles are directed by corridors.

  6. Predictors of elevational biodiversity gradients change from single taxa to the multi-taxa community level

    PubMed Central

    Peters, Marcell K.; Hemp, Andreas; Appelhans, Tim; Behler, Christina; Classen, Alice; Detsch, Florian; Ensslin, Andreas; Ferger, Stefan W.; Frederiksen, Sara B.; Gebert, Friederike; Haas, Michael; Helbig-Bonitz, Maria; Hemp, Claudia; Kindeketa, William J.; Mwangomo, Ephraim; Ngereza, Christine; Otte, Insa; Röder, Juliane; Rutten, Gemma; Schellenberger Costa, David; Tardanico, Joseph; Zancolli, Giulia; Deckert, Jürgen; Eardley, Connal D.; Peters, Ralph S.; Rödel, Mark-Oliver; Schleuning, Matthias; Ssymank, Axel; Kakengi, Victor; Zhang, Jie; Böhning-Gaese, Katrin; Brandl, Roland; Kalko, Elisabeth K.V.; Kleyer, Michael; Nauss, Thomas; Tschapka, Marco; Fischer, Markus; Steffan-Dewenter, Ingolf

    2016-01-01

    The factors determining gradients of biodiversity are a fundamental yet unresolved topic in ecology. While diversity gradients have been analysed for numerous single taxa, progress towards general explanatory models has been hampered by limitations in the phylogenetic coverage of past studies. By parallel sampling of 25 major plant and animal taxa along a 3.7 km elevational gradient on Mt. Kilimanjaro, we quantify cross-taxon consensus in diversity gradients and evaluate predictors of diversity from single taxa to a multi-taxa community level. While single taxa show complex distribution patterns and respond to different environmental factors, scaling up diversity to the community level leads to an unambiguous support for temperature as the main predictor of species richness in both plants and animals. Our findings illuminate the influence of taxonomic coverage for models of diversity gradients and point to the importance of temperature for diversification and species coexistence in plant and animal communities. PMID:28004657

  7. Predictors of elevational biodiversity gradients change from single taxa to the multi-taxa community level.

    PubMed

    Peters, Marcell K; Hemp, Andreas; Appelhans, Tim; Behler, Christina; Classen, Alice; Detsch, Florian; Ensslin, Andreas; Ferger, Stefan W; Frederiksen, Sara B; Gebert, Friederike; Haas, Michael; Helbig-Bonitz, Maria; Hemp, Claudia; Kindeketa, William J; Mwangomo, Ephraim; Ngereza, Christine; Otte, Insa; Röder, Juliane; Rutten, Gemma; Schellenberger Costa, David; Tardanico, Joseph; Zancolli, Giulia; Deckert, Jürgen; Eardley, Connal D; Peters, Ralph S; Rödel, Mark-Oliver; Schleuning, Matthias; Ssymank, Axel; Kakengi, Victor; Zhang, Jie; Böhning-Gaese, Katrin; Brandl, Roland; Kalko, Elisabeth K V; Kleyer, Michael; Nauss, Thomas; Tschapka, Marco; Fischer, Markus; Steffan-Dewenter, Ingolf

    2016-12-22

    The factors determining gradients of biodiversity are a fundamental yet unresolved topic in ecology. While diversity gradients have been analysed for numerous single taxa, progress towards general explanatory models has been hampered by limitations in the phylogenetic coverage of past studies. By parallel sampling of 25 major plant and animal taxa along a 3.7 km elevational gradient on Mt. Kilimanjaro, we quantify cross-taxon consensus in diversity gradients and evaluate predictors of diversity from single taxa to a multi-taxa community level. While single taxa show complex distribution patterns and respond to different environmental factors, scaling up diversity to the community level leads to an unambiguous support for temperature as the main predictor of species richness in both plants and animals. Our findings illuminate the influence of taxonomic coverage for models of diversity gradients and point to the importance of temperature for diversification and species coexistence in plant and animal communities.

  8. Wildlife Species/Family Taxa Selection | Interspecies ...

    EPA Pesticide Factsheets

    2016-02-22

    Web-ICE estimates acute toxicity (LC50/LD50) of a chemical to a species, genus, or family from the known toxicity of the chemical to a surrogate species. Wildlife species and family taxa selection page. Page provides access to the ICE calculators

  9. New taxa of Euglenophyta from China

    NASA Astrophysics Data System (ADS)

    Shi, Zhi-Xin

    1995-12-01

    Eight new taxa of Euglenophyta are described in this paper. They were collected from several provinces in China and respectively named Euglena allorgei var. exsulcata, E. pisciformis var. globosa, E. tortilis. Lepocinclis glabra var. papillata, Phacus pisiformis, Ph. strombuliformis, Ph. trimarginatus var. truncatus and Astasia angusta.

  10. DAS performance analysis

    SciTech Connect

    Bates, G.; Bodine, S.; Carroll, T.; Keller, M.

    1984-02-01

    This report begins with an overview of the Data Acquisition System (DAS), which supports several of PPPL's experimental devices. Performance measurements which were taken on DAS and the tools used to make them are then described.

  11. Marine taxa track local climate velocities.

    PubMed

    Pinsky, Malin L; Worm, Boris; Fogarty, Michael J; Sarmiento, Jorge L; Levin, Simon A

    2013-09-13

    Organisms are expected to adapt or move in response to climate change, but observed distribution shifts span a wide range of directions and rates. Explanations often emphasize biological distinctions among species, but general mechanisms have been elusive. We tested an alternative hypothesis: that differences in climate velocity-the rate and direction that climate shifts across the landscape-can explain observed species shifts. We compiled a database of coastal surveys around North America from 1968 to 2011, sampling 128 million individuals across 360 marine taxa. Climate velocity explained the magnitude and direction of shifts in latitude and depth much more effectively than did species characteristics. Our results demonstrate that marine species shift at different rates and directions because they closely track the complex mosaic of local climate velocities.

  12. Foundational issues concerning taxa and taxon names.

    PubMed

    Ereshefsky, Marc

    2007-04-01

    In a series of articles, Rieppel (2005, Biol. Philos. 20:465-487; 2006a, Cladistics 22:186-197; 2006b, Systematist 26:5-9), Keller et al. (2003, Bot. Rev. 69:93-110), and Nixon and Carpenter (2000, Cladistics 16:298-318) criticize the philosophical foundations of the PhyloCode. They argue that species and higher taxa are not individuals, and they reject the view that taxon names are rigid designators. Furthermore, they charge supporters of the individuality thesis and rigid designator theory with assuming essentialism, committing logical inconsistencies, and offering proposals that render taxonomy untestable. These charges are unsound. Such charges turn on confusions over rigid designator theory and the distinction between kinds and individuals. In addition, Rieppel's, Keller et al.'s, and Nixon and Carpenter's proposed alternatives are no better and have their own problems. The individuality thesis and rigid designator theory should not be quickly abandoned.

  13. Hot spots, indicator taxa, complementarity and optimal networks of taiga.

    PubMed Central

    Virolainen, K M; Ahlroth, P; Hyvärinen, E; Korkeamäki, E; Mattila, J; Päiivinen, J; Rintala, T; Suomi, T; Suhonen, J

    2000-01-01

    If hot spots for different taxa coincide, priority-setting surveys in a region could be carried out more cheaply by focusing on indicator taxa. Several previous studies show that hot spots of different taxa rarely coincide. However, in tropical areas indicator taxa may be used in selecting complementary networks to represent biodiversity as a whole. We studied beetles (Coleoptera), Heteroptera, polypores or bracket fungi (Polyporaceae) and vascular plants of old growth boreal taiga forests. Optimal networks for Heteroptera maximized the high overall species richness of beetles and vascular plants, but these networks were least favourable options for polypores. Polypores are an important group indicating the conservation value of old growth taiga forests. Random selection provided a better option. Thus, certain groups may function as good indicators for maximizing the overall species richness of some taxonomic groups, but all taxa should be examined separately. PMID:10885520

  14. Quantifying the responses of biological indices to rare macroinvertebrate taxa exclusion: Does excluding more rare taxa cause more error?

    PubMed

    Yu, Zhengda; Wang, Hui; Meng, Jiao; Miao, Mingsheng; Kong, Qiang; Wang, Renqing; Liu, Jian

    2017-03-01

    Including or excluding rare taxa in bioassessment is a controversial topic, which essentially affects the reliability and accuracy of the result. In the present paper, we hypothesize that biological indices such as Shannon-Wiener index, Simpson's index, Margalef index, evenness, BMWP (biological monitoring working party), and ASPT (Average Score Per Taxon) respond differently to rare taxa exclusion. To test this hypothesis, a benthic macroinvertebrate data set based on recent fifteen-year studies in China was built for suppositional plot analyses. A field research was conducted in the Nansi Lake to perform related analyses. The results of suppositional plot simulations showed that Simpson's index placed more weight on common taxa than any other studied indices, followed by Shannon-Wiener index which remained a high value with the exclusion of rare taxa. The results indicated that there was not much of effect on Simpson's index and Shannon-Wiener index when rare taxa were excluded. Rare taxa played an important role in Margalef index and BMWP than in other indices. Evenness showed an increase trend, while ASPT varied inconsistently with the exclusion of rare taxa. Results of the field study also indicated that rare taxa had few impacts on the Shannon-Wiener index. By examining the relationships between the rare taxa and biological indices in our study, it is suggested that including the rare taxa when using BMWP and excluding them in the proposed way (e.g., fixed-count subsampling) to calculate Shannon-Wiener index and Simpson's index could raise the efficiency and reduce the biases in the bioassessment of freshwater ecosystems.

  15. Numerical experiments with model monophyletic and paraphyletic taxa

    NASA Technical Reports Server (NTRS)

    Sepkoski, J. J. Jr; Kendrick, D. C.; Sepkoski JJ, J. r. (Principal Investigator)

    1993-01-01

    The problem of how accurately paraphyletic taxa versus monophyletic (i.e., holophyletic) groups (clades) capture underlying species patterns of diversity and extinction is explored with Monte Carlo simulations. Phylogenies are modeled as stochastic trees. Paraphyletic taxa are defined in an arbitrary manner by randomly choosing progenitors and clustering all descendants not belonging to other taxa. These taxa are then examined to determine which are clades, and the remaining paraphyletic groups are dissected to discover monophyletic subgroups. Comparisons of diversity patterns and extinction rates between modeled taxa and lineages indicate that paraphyletic groups can adequately capture lineage information under a variety of conditions of diversification and mass extinction. This suggests that these groups constitute more than mere "taxonomic noise" in this context. But, strictly monophyletic groups perform somewhat better, especially with regard to mass extinctions. However, when low levels of paleontologic sampling are simulated, the veracity of clades deteriorates, especially with respect to diversity, and modeled paraphyletic taxa often capture more information about underlying lineages. Thus, for studies of diversity and taxic evolution in the fossil record, traditional paleontologic genera and families need not be rejected in favor of cladistically-defined taxa.

  16. Numerical experiments with model monophyletic and paraphyletic taxa

    NASA Technical Reports Server (NTRS)

    Sepkoski, J. J. Jr; Kendrick, D. C.; Sepkoski JJ, J. r. (Principal Investigator)

    1993-01-01

    The problem of how accurately paraphyletic taxa versus monophyletic (i.e., holophyletic) groups (clades) capture underlying species patterns of diversity and extinction is explored with Monte Carlo simulations. Phylogenies are modeled as stochastic trees. Paraphyletic taxa are defined in an arbitrary manner by randomly choosing progenitors and clustering all descendants not belonging to other taxa. These taxa are then examined to determine which are clades, and the remaining paraphyletic groups are dissected to discover monophyletic subgroups. Comparisons of diversity patterns and extinction rates between modeled taxa and lineages indicate that paraphyletic groups can adequately capture lineage information under a variety of conditions of diversification and mass extinction. This suggests that these groups constitute more than mere "taxonomic noise" in this context. But, strictly monophyletic groups perform somewhat better, especially with regard to mass extinctions. However, when low levels of paleontologic sampling are simulated, the veracity of clades deteriorates, especially with respect to diversity, and modeled paraphyletic taxa often capture more information about underlying lineages. Thus, for studies of diversity and taxic evolution in the fossil record, traditional paleontologic genera and families need not be rejected in favor of cladistically-defined taxa.

  17. Symbiont acquisition as neoseme: origin of species and higher taxa

    NASA Technical Reports Server (NTRS)

    Bermudes, D.; Margulis, L.

    1987-01-01

    We examine the hypothesis that, in the origin of species and higher taxa of eukaryotes, symbiont acquisition followed by partner integration has been equivalent to neoseme appearance leading to speciation. The formation of stable symbiotic associations involves partner-surface recognition, behavioral and metabolic interaction, and, in some cases, gene product (RNA, protein) and genic (RNA, DNA) integration. This analysis is applied here to examples of neosemes that define specific taxa and to neosemes in plants, fungi, and animals that involve the appearance of new types of tissue. If this hypothesis is correct--if the origin of major genetic variation leading to speciation and even higher taxa may occur through symbiont acquisition and integration--then the analysis of "origins of species and higher taxa" becomes analogous to the study of microbial community ecology.

  18. Symbiont acquisition as neoseme: origin of species and higher taxa

    NASA Technical Reports Server (NTRS)

    Bermudes, D.; Margulis, L.

    1987-01-01

    We examine the hypothesis that, in the origin of species and higher taxa of eukaryotes, symbiont acquisition followed by partner integration has been equivalent to neoseme appearance leading to speciation. The formation of stable symbiotic associations involves partner-surface recognition, behavioral and metabolic interaction, and, in some cases, gene product (RNA, protein) and genic (RNA, DNA) integration. This analysis is applied here to examples of neosemes that define specific taxa and to neosemes in plants, fungi, and animals that involve the appearance of new types of tissue. If this hypothesis is correct--if the origin of major genetic variation leading to speciation and even higher taxa may occur through symbiont acquisition and integration--then the analysis of "origins of species and higher taxa" becomes analogous to the study of microbial community ecology.

  19. Zulma Ageitos de Castellanos: Publications and status of described taxa.

    PubMed

    Signorelli, Javier H; Urteaga, Diego; Teso, Valeria

    2015-10-28

    Zulma Ageitos de Castellanos was an Argentinian malacologist working in the "Facultad de Ciencias Naturales y Museo" at La Plata University where she taught invertebrate zoology between 1947 and 1990. Her scientific publications are listed in chronological order. Described genus-group and species-group taxa are listed. Information about the type locality and type material, and taxonomic remarks are also provided. Finally, type material of all described taxa was requested and, when located, illustrated.

  20. New and rare taxa in Agaricus section Bivelares (Duploannulati).

    PubMed

    Kerrigan, Richard W; Callac, Philippe; Parra, Luis A

    2008-01-01

    Ongoing field and laboratory studies have led to our recognition of new taxa in Agaricus section Bivelares, a recent combination and now the earliest synonym and correct name of section Duploannulati. Agaricus cupressophilus and A. tlaxcalensis, in the new Agaricus subsection Cupressorum, and A. agrinferus, A. devoniensis subsp. bridghamii, and A. subsubensis in Agaricus subsection Hortenses, are described. Agaricus subfloccosus is lectotypified. Phylogeny reconstruction methods with ITS1+2 DNA sequences were used to determine appropriate placements of the new taxa. Collectively these new taxa and phylogenetic associations represent a substantial augmentation and clarification of our knowledge of section Bivelares; described, sequenced species-level taxa in the northern hemisphere are increased from six to 10, a distinct subsectional lineage is revealed and infraspecific resolution within A. devoniensis is improved. An anomalous ITS1+2 sequence is documented in one collection of A. subsubensis. Preliminary data on another novel member of Bivelares from France also are provided. Several of these taxa are rare, highlighting opportunities and challenges for documenting biodiversity in this group. Additional comments on related taxa treated in recent publications are also provided.

  1. DAS User Manual

    NASA Astrophysics Data System (ADS)

    Østensen, Roy

    2008-10-01

    The HELAS Database for AsteroSeismology (DAS) is one of the deliverables of the Work Package NA5: Asteroseismology of the European Coordination Action in Helio- and Asteroseismology (HELAS). The DAS aims to provide easy access to publicly available asteroseismological timeseries data, both photometric and spectroscopic. In particular, the DAS and the HELAS software package FAMIAS are ideally suited to train Master and PhD students in asteroseismic data analysis and to build longterm datasets. The number of stars in the system is still limited and reflects the willingness of data owners to provide their data after publication. Work continues to populate the database with contributions from the community, and at present the number of stars in the database is 82

  2. The effectiveness of surrogate taxa for the representation of biodiversity.

    PubMed

    Lewandowski, Adam S; Noss, Reed F; Parsons, David R

    2010-10-01

    Biodiversity is too complex to measure directly, so conservation planning must rely on surrogates to estimate the biodiversity of sites. The species richness of selected taxa is often used as a surrogate for the richness of other taxa. Surrogacy values of taxa have been evaluated in diverse contexts, yet broad trends in their effectiveness remain unclear. We reviewed published studies testing the ability of species richness of surrogate taxa to capture the richness of other (target) taxa. We stratified studies into two groups based on whether a complementarity approach (surrogates used to select a combination of sites that together maximize total species richness for the taxon) or a richness-hotspot approach (surrogates used to select sites containing the highest species richness for the taxon) was used. For each comparison of one surrogate taxon with one target, we used the following predictor variables: biome, spatial extent of study area, surrogate taxon, and target taxon. We developed a binary response variable based on whether the surrogate taxon provided better than random representation of the target taxon. For studies that used an evaluation approach that was not based on better than random representation of target taxa, we based the response variable on the interpretation of results in the original study. We performed a categorical regression to elucidate trends in the effectiveness of surrogate taxa with regard to each of the predictor variables. A surrogate was 25% more likely to be effective with a complementarity approach than with a hotspot approach. For hotspot-based approaches, biome, extent of study, surrogate taxon, and target taxon significantly influenced effectiveness of the surrogate. For complementarity-based approaches, biome, extent, and surrogate taxon significantly influenced effectiveness of the surrogate. For all surrogate evaluations, biome explained the greatest amount of variation in surrogate effectiveness. From most to least

  3. Classification and quantification of bacteriophage taxa in human gut metagenomes

    PubMed Central

    Waller, Alison S; Yamada, Takuji; Kristensen, David M; Kultima, Jens Roat; Sunagawa, Shinichi; Koonin, Eugene V; Bork, Peer

    2014-01-01

    Bacteriophages have key roles in microbial communities, to a large extent shaping the taxonomic and functional composition of the microbiome, but data on the connections between phage diversity and the composition of communities are scarce. Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. On average, five phage taxa were identified in each sample, with up to three of these being highly abundant. The abundances of most phage taxa vary by up to four orders of magnitude between the samples, and several taxa that are highly abundant in some samples are absent in others. Significant correlations exist between the abundances of some phage taxa and human host metadata: for example, ‘Group 936 lactococcal phages' are more prevalent and abundant in Danish samples than in samples from Spain or the United States of America. Quantification of phages that exist as integrated prophages revealed that the abundance profiles of prophages are highly individual-specific and remain unique to an individual over a 1-year time period, and prediction of prophage lysis across the samples identified hundreds of prophages that are apparently active in the gut and vary across the samples, in terms of presence and lytic state. Finally, a prophage–host network of the human gut was established and includes numerous novel host–phage associations. PMID:24621522

  4. Benefits of organic farming to biodiversity vary among taxa.

    PubMed

    Fuller, R J; Norton, L R; Feber, R E; Johnson, P J; Chamberlain, D E; Joys, A C; Mathews, F; Stuart, R C; Townsend, M C; Manley, W J; Wolfe, M S; Macdonald, D W; Firbank, L G

    2005-12-22

    Habitat and biodiversity differences between matched pairs of organic and non-organic farms containing cereal crops in lowland England were assessed by a large-scale study of plants, invertebrates, birds and bats. Habitat extent, composition and management on organic farms was likely to favour higher levels of biodiversity and indeed organic farms tended to support higher numbers of species and overall abundance across most taxa. However, the magnitude of the response varied; plants showed larger and more consistent responses than other taxa. Variation in response across taxa may be partly a consequence of the small size and isolated context of many organic farms. Extension of organic farming could contribute to the restoration of biodiversity in agricultural landscapes.

  5. Benefits of organic farming to biodiversity vary among taxa

    PubMed Central

    Fuller, R.J; Norton, L.R; Feber, R.E; Johnson, P.J; Chamberlain, D.E; Joys, A.C; Mathews, F; Stuart, R.C; Townsend, M.C; Manley, W.J; Wolfe, M.S; Macdonald, D.W; Firbank, L.G

    2005-01-01

    Habitat and biodiversity differences between matched pairs of organic and non-organic farms containing cereal crops in lowland England were assessed by a large-scale study of plants, invertebrates, birds and bats. Habitat extent, composition and management on organic farms was likely to favour higher levels of biodiversity and indeed organic farms tended to support higher numbers of species and overall abundance across most taxa. However, the magnitude of the response varied; plants showed larger and more consistent responses than other taxa. Variation in response across taxa may be partly a consequence of the small size and isolated context of many organic farms. Extension of organic farming could contribute to the restoration of biodiversity in agricultural landscapes. PMID:17148225

  6. New taxa, notes and new synonymy in Neoibidionini (Cerambycidae, Coleoptera).

    PubMed

    Martins, Ubirajara R; Galileo, Maria Helena M

    2014-04-11

    New taxa, notes, and new synonymy in Neoibidionini (Cerambycidae, Coleoptera) are given. New taxa are described from Ecuador: Compsibidion inflatum sp. nov., Bezarkia gen. nov. and B. suturalis sp. nov., Corimbion antennatum sp. nov. and Neocompsa muira sp. nov.; from México: Neocompsa chiapensis sp. nov., and from French Guyana: Kunaibidion giesberti sp. nov. Pygmodeon maculatum Martins & Galileo, 2012 is considered a new synonym of Heterachthes xyleus Martins, 1974 which is transferred to the genus Pygmodeon as a new combination. Notes on variability and new records of Asynapteron equatorianum (Martins, 1960) are presented.

  7. Das DNA-Puzzle

    NASA Astrophysics Data System (ADS)

    Kirchner, Stefan

    Im Jahre 1953 wurde von James Watson und Francis Crick erstmalig der strukturelle Aufbau der sogenannten DNA (Desoxyribonukleinsäure) beschrieben, welche das Erbgut jedes Lebewesens enthält. Der wesentliche Teil des Erbguts wird dabei durch eine sehr lange Folge der vier Basen Adenin (A), Cytosin (C), Guanin (G) und Thymin (T) codiert. Seit einigen Jahren ist es möglich, die Folge der vier Basen zu einer gegebenen DNA zu bestimmen. Biologen bezeichnen diesen Vorgang als Sequenzierung.

  8. The hominin fossil record: taxa, grades and clades.

    PubMed

    Wood, Bernard; Lonergan, Nicholas

    2008-04-01

    This paper begins by reviewing the fossil evidence for human evolution. It presents summaries of each of the taxa recognized in a relatively speciose hominin taxonomy. These taxa are grouped in grades, namely possible and probable hominins, archaic hominins, megadont archaic hominins, transitional hominins, pre-modern Homo and anatomically modern Homo. The second part of this contribution considers some of the controversies that surround hominin taxonomy and systematics. The first is the vexed question of how you tell an early hominin from an early panin, or from taxa belonging to an extinct clade closely related to the Pan-Homo clade. Secondly, we consider how many species should be recognized within the hominin fossil record, and review the philosophies and methods used to identify taxa within the hominin fossil record. Thirdly, we examine how relationships within the hominin clade are investigated, including descriptions of the methods used to break down an integrated structure into tractable analytical units, and then how cladograms are generated and compared. We then review the internal structure of the hominin clade, including the problem of how many subclades should be recognized within the hominin clade, and we examine the reliability of hominin cladistic hypotheses. The last part of the paper reviews the concepts of a genus, including the criteria that should be used for recognizing genera within the hominin clade.

  9. The hominin fossil record: taxa, grades and clades

    PubMed Central

    Wood, Bernard; Lonergan, Nicholas

    2008-01-01

    This paper begins by reviewing the fossil evidence for human evolution. It presents summaries of each of the taxa recognized in a relatively speciose hominin taxonomy. These taxa are grouped in grades, namely possible and probable hominins, archaic hominins, megadont archaic hominins, transitional hominins, pre-modern Homo and anatomically modern Homo. The second part of this contribution considers some of the controversies that surround hominin taxonomy and systematics. The first is the vexed question of how you tell an early hominin from an early panin, or from taxa belonging to an extinct clade closely related to the Pan-Homo clade. Secondly, we consider how many species should be recognized within the hominin fossil record, and review the philosophies and methods used to identify taxa within the hominin fossil record. Thirdly, we examine how relationships within the hominin clade are investigated, including descriptions of the methods used to break down an integrated structure into tractable analytical units, and then how cladograms are generated and compared. We then review the internal structure of the hominin clade, including the problem of how many subclades should be recognized within the hominin clade, and we examine the reliability of hominin cladistic hypotheses. The last part of the paper reviews the concepts of a genus, including the criteria that should be used for recognizing genera within the hominin clade. PMID:18380861

  10. Eliciting the Functional Taxonomy from protein annotations and taxa.

    PubMed

    Falda, Marco; Lavezzo, Enrico; Fontana, Paolo; Bianco, Luca; Berselli, Michele; Formentin, Elide; Toppo, Stefano

    2016-08-18

    The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules.

  11. Taxa-area relationship of aquatic fungi on deciduous leaves

    PubMed Central

    Cássio, Fernanda; Pascoal, Cláudia; Bärlocher, Felix

    2017-01-01

    One of the fundamental patterns in macroecology is the increase in the number of observed taxa with size of sampled area. For microbes, the shape of this relationship remains less clear. The current study assessed the diversity of aquatic fungi, by the traditional approach based on conidial morphology (captures reproducing aquatic hyphomycetes) and next generation sequencing (NGS; captures other fungi as well), on graded sizes of alder leaves (0.6 to 13.6 cm2). Leaves were submerged in two streams in geographically distant locations: the Oliveira Stream in Portugal and the Boss Brook in Canada. Decay rates of alder leaves and fungal sporulation rates did not differ between streams. Fungal biomass was higher in Boss Brook than in Oliveira Stream, and in both streams almost 100% of the reads belonged to active fungal taxa. In general, larger leaf areas tended to harbour more fungi, but these findings were not consistent between techniques. Morphospecies-based diversity increased with leaf area in Boss Brook, but not in Oliveira Stream; metabarcoding data showed an opposite trend. The higher resolution of metabarcoding resulted in steeper taxa-accumulation curves than morphospecies-based assessments (fungal conidia morphology). Fungal communities assessed by metabarcoding were spatially structured by leaf area in both streams. Metabarcoding promises greater resolution to assess biodiversity patterns in aquatic fungi and may be more accurate for assessing taxa-area relationships and local to global diversity ratios. PMID:28719634

  12. Dendrothele griseocana (Corticiaceae) and related taxa with hyphal pegs

    Treesearch

    Karen K. Nakasone

    2006-01-01

    Four Dendrothele (Corticiaceae, Polyporales) species with hyphal pegs are described and illustrated. Type specimens of Corticium griseocanum and Dendrothele papillosa were examined and found to be conspecific. Two new taxa, D. americana and D. tanzaniana, are described and illustrated, and the new combination, Dendrothele andina, is proposed. A key to D. griseocana and...

  13. Eliciting the Functional Taxonomy from protein annotations and taxa

    PubMed Central

    Falda, Marco; Lavezzo, Enrico; Fontana, Paolo; Bianco, Luca; Berselli, Michele; Formentin, Elide; Toppo, Stefano

    2016-01-01

    The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules. PMID:27534507

  14. STORAGE BEHAVIOR OF SEEDS FROM NATIVE HAWAIIAN TAXA

    USDA-ARS?s Scientific Manuscript database

    Ex situ conservation is required to preserve genetic diversity of the 956 species native to Hawai’i (89% endemism, 30% federally-listed as endangered or threatened). Optimizing storage procedures to maximize seed longevity is critical to the effort. Storage behavior of seeds from about 280 taxa was ...

  15. Taxa-area relationship of aquatic fungi on deciduous leaves.

    PubMed

    Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia; Bärlocher, Felix

    2017-01-01

    One of the fundamental patterns in macroecology is the increase in the number of observed taxa with size of sampled area. For microbes, the shape of this relationship remains less clear. The current study assessed the diversity of aquatic fungi, by the traditional approach based on conidial morphology (captures reproducing aquatic hyphomycetes) and next generation sequencing (NGS; captures other fungi as well), on graded sizes of alder leaves (0.6 to 13.6 cm2). Leaves were submerged in two streams in geographically distant locations: the Oliveira Stream in Portugal and the Boss Brook in Canada. Decay rates of alder leaves and fungal sporulation rates did not differ between streams. Fungal biomass was higher in Boss Brook than in Oliveira Stream, and in both streams almost 100% of the reads belonged to active fungal taxa. In general, larger leaf areas tended to harbour more fungi, but these findings were not consistent between techniques. Morphospecies-based diversity increased with leaf area in Boss Brook, but not in Oliveira Stream; metabarcoding data showed an opposite trend. The higher resolution of metabarcoding resulted in steeper taxa-accumulation curves than morphospecies-based assessments (fungal conidia morphology). Fungal communities assessed by metabarcoding were spatially structured by leaf area in both streams. Metabarcoding promises greater resolution to assess biodiversity patterns in aquatic fungi and may be more accurate for assessing taxa-area relationships and local to global diversity ratios.

  16. Das Zwillingsparadoxon: Gedankenexperimente

    NASA Astrophysics Data System (ADS)

    Genz, Henning

    2002-09-01

    Das vermeintliche Zwillingsparadoxon ist ein Gedankenexperiment mit einem Zwillingspaar: Ein Zwilling reist mit hoher Geschwindigkeit von der Erde weg und kehrt nach einiger Zeit zurück, sein Partner bleibt auf der Erde. Dabei altert der Reisende langsamer als der Ruhende - warum nicht umgekehrt? Ein Vergleich von Uhren, die sich mit konstanter Geschwindigkeit bewegen, zeigt: Der Effekt hängt nur von Geschwindigkeiten und nicht von Beschleunigungen ab. Er beruht also allein auf der Speziellen Relativitätstheorie. Tauschen die Zwillinge in regelmäßigen Abständen Lichtsignale aus, können sie ihr asymmetrisches Altern sogar in Zeitschritten mitprotokollieren.

  17. Das Allgemeine Statistische Archiv

    NASA Astrophysics Data System (ADS)

    Rinne, Horst

    Das Allgemeine Statistische Archiv1, nachfolgend kurz Archiv genannt, ist die älteste, ausschließlich der Statistik gewidmete deutschsprachige wissenschaftliche Fachzeitschrift. Sie ist gut zwanzig Jahre älter als die Deutsche Statistische Gesellschaft, zu deren Publikationsorgan sie mit der Gründung der Gesellschaft im Jahre 1911 wurde. Zeitschrift und Gesellschaft blicken auf eine sehr wechselvolle, aber erfolgreiche gemeinsame Geschichte zurück. Die wissenschaftliche Arbeit der Gesellschaft ist im Archiv und seinen Sonderheften für nachfolgende Generationen dokumentiert.

  18. Agaricus section Xanthodermatei: a phylogenetic reconstruction with commentary on taxa.

    PubMed

    Kerrigan, Richard W; Callac, Philippe; Guinberteau, Jacques; Challen, Michael P; Parra, Luis A

    2005-01-01

    Agaricus section Xanthodermatei comprises a group of species allied to A. xanthodermus and generally characterized by basidiomata having phenolic odors, transiently yellowing discolorations in some parts of the basidiome, Schaeffer's reaction negative, and mild to substantial toxicity. The section has a global distribution, while most included species have distributions restricted to regions of single continents. Using specimens and cultures from Europe, North America, and Hawaii, we analyzed DNA sequences from the ITS1+2 region of the nuclear rDNA to identify and characterize phylogenetically distinct entities and to construct a hypothesis of relationships, both among members of the section and with representative taxa from other sections of the genus. 61 sequences from affiliated taxa, plus 20 from six (or seven) other sections of Agaricus, and one Micropsalliota sequence, were evaluated under distance, maximum parsimony and maximum likelihood methods. We recognized 21 discrete entities in Xanthodermatei, including 14 established species and 7 new ones, three of which are described elsewhere. Four species from California, New Mexico, and France deserve further study before they are described. Type studies of American taxa are particularly emphasized, and a lectotype is designated for A. californicus. Section Xanthodermatei formed a single clade in most analyses, indicating that the traditional sectional characters noted above are good unifying characters that appear to have arisen only once within Agaricus. Deep divisions within the sequence-derived structure of the section could be interpreted as subsections in Xanthodermatei; however, various considerations led us to refrain from proposing new supraspecific taxa. The nearest neighbors of section Xanthodermatei are putatively in section Duploannulati.

  19. Deciphering The Role of Plankton Taxa in Particle Flux

    NASA Astrophysics Data System (ADS)

    Neuer, Susanne; Amacher, Jessica; DeMartini, Francesca; Wilson, Stephanie

    2015-04-01

    The sinking of phytoplankton derived particulate organic matter to the deep ocean constitutes an important removal process of atmospheric CO2 and is termed the biological carbon pump. Understanding the taxon specific connection between phytoplankton communities in the euphotic zone and their contribution to particle flux is a high priority in current oceanographic research and provides a basis to evaluate how carbon export might change in a future ocean. Here we present results from DNA-based molecular studies that investigate the taxonomic composition of cyanobacterial and protist communities retrieved from shallow particle traps in comparison to those living in the euphotic zone. This research has been mainly carried out in the Sargasso Sea at the Bermuda Atlantic Time-series Study site (BATS). Trap material collected at this oligotrophic ocean site reveals a surprisingly high diversity of small, non-mineral ballasted taxa, some of which are over-represented compared to the euphotic zone communities. But the majority of clones in the traps belong to mostly heterotrophic protist taxa. By analyzing the fingerprints of prey DNA in guts and fecal pellets of dominant zooplankton grazers we find that there is a close link between prey utilization and the recovery of those taxa in the traps, showing the importance of fecal pellets in packaging and mediating their flux out of the euphotic zone.

  20. Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time.

    PubMed

    O'Connor, Anne; Wills, Matthew A

    2016-09-01

    The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpinned claims about temporal and taxonomic patterns of completeness in the fossil record. The most widely used stratigraphic congruence indices are the stratigraphic consistency index (SCI), the modified Manhattan stratigraphic measure (MSM*), and the gap excess ratio (GER) (plus its derivatives; the topological GER and the modified GER). Many factors are believed to variously bias these indices, with several empirical and simulation studies addressing some subset of the putative interactions. This study combines both approaches to quantify the effects (on all five indices) of eight variables reasoned to constrain the distribution of possible values (the number of taxa, tree balance, tree resolution, range of first occurrence (FO) dates, center of gravity of FO dates, the variability of FO dates, percentage of extant taxa, and percentage of taxa with no fossil record). Our empirical data set comprised 647 published animal and plant cladograms spanning the entire Phanerozoic, and for these data we also modeled the effects of mean age of FOs (as a proxy for clade age), the taxonomic rank of the clade, and the higher taxonomic group to which it belonged. The center of gravity of FO dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in our empirical study (top-heavy clades had better congruence). The modified GER was the index least susceptible to bias. We found significant differences across higher taxa for all indices; arthropods had lower congruence and tetrapods higher congruence. Stratigraphic congruence-however measured-also varied throughout the Phanerozoic, reflecting

  1. Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time

    PubMed Central

    O'Connor, Anne; Wills, Matthew A.

    2016-01-01

    The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpinned claims about temporal and taxonomic patterns of completeness in the fossil record. The most widely used stratigraphic congruence indices are the stratigraphic consistency index (SCI), the modified Manhattan stratigraphic measure (MSM*), and the gap excess ratio (GER) (plus its derivatives; the topological GER and the modified GER). Many factors are believed to variously bias these indices, with several empirical and simulation studies addressing some subset of the putative interactions. This study combines both approaches to quantify the effects (on all five indices) of eight variables reasoned to constrain the distribution of possible values (the number of taxa, tree balance, tree resolution, range of first occurrence (FO) dates, center of gravity of FO dates, the variability of FO dates, percentage of extant taxa, and percentage of taxa with no fossil record). Our empirical data set comprised 647 published animal and plant cladograms spanning the entire Phanerozoic, and for these data we also modeled the effects of mean age of FOs (as a proxy for clade age), the taxonomic rank of the clade, and the higher taxonomic group to which it belonged. The center of gravity of FO dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in our empirical study (top-heavy clades had better congruence). The modified GER was the index least susceptible to bias. We found significant differences across higher taxa for all indices; arthropods had lower congruence and tetrapods higher congruence. Stratigraphic congruence—however measured—also varied throughout the Phanerozoic

  2. Connecting the Dots in DAS

    ERIC Educational Resources Information Center

    Ford, Tracy

    2012-01-01

    Many institutions implement a distributed antenna system (DAS) as part of a holistic approach to providing better wireless coverage and capacity on campus. A DAS provides wireless service within a particular area or structure via a network of separate antenna nodes that are connected to a common source through fiber or coaxial cable. Because DAS…

  3. Connecting the Dots in DAS

    ERIC Educational Resources Information Center

    Ford, Tracy

    2012-01-01

    Many institutions implement a distributed antenna system (DAS) as part of a holistic approach to providing better wireless coverage and capacity on campus. A DAS provides wireless service within a particular area or structure via a network of separate antenna nodes that are connected to a common source through fiber or coaxial cable. Because DAS…

  4. The evolutionary reality of higher taxa in mammals.

    PubMed

    Humphreys, Aelys M; Barraclough, Timothy G

    2014-05-22

    Species are generally regarded as a fundamental unit of biodiversity. By contrast, higher taxa such as genera and families, while widely used as biodiversity metrics and for classification and communication, are generally not believed to be shaped by shared evolutionary processes in the same way as species. We use simulations to show that processes which are important for emergence of evolutionarily significant units (ESUs) at the species level, namely geographical isolation and ecological divergence, can generate evolutionary independence above the species level and thereby lead to emergence of discrete phylogenetic clusters (higher ESUs). Extending phylogenetic approaches for delimiting evolutionarily significant species to broader phylogenetic scales, we find evidence for the existence of higher ESUs in mammals. In carnivores, euungulates and lagomorphs the hierarchical level of units detected correspond, on average, to the level of family or genus in traditional taxonomy. The units in euungulates are associated with divergent patterns of body mass, consistent with occupation of distinct ecological zones. Our findings demonstrate a new framework for studying biodiversity that unifies approaches at species and higher levels, thus potentially restoring higher taxa to their historical status as natural entities.

  5. A microarray for assessing transcription from pelagic marine microbial taxa

    PubMed Central

    Shilova, Irina N; Robidart, Julie C; James Tripp, H; Turk-Kubo, Kendra; Wawrik, Boris; Post, Anton F; Thompson, Anne W; Ward, Bess; Hollibaugh, James T; Millard, Andy; Ostrowski, Martin; J Scanlan, David; Paerl, Ryan W; Stuart, Rhona; Zehr, Jonathan P

    2014-01-01

    Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions. PMID:24477198

  6. A microarray for assessing transcription from pelagic marine microbial taxa.

    PubMed

    Shilova, Irina N; Robidart, Julie C; James Tripp, H; Turk-Kubo, Kendra; Wawrik, Boris; Post, Anton F; Thompson, Anne W; Ward, Bess; Hollibaugh, James T; Millard, Andy; Ostrowski, Martin; Scanlan, David J; Paerl, Ryan W; Stuart, Rhona; Zehr, Jonathan P

    2014-07-01

    Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.

  7. Unsegmented annelids? Possible origins of four lophotrochozoan worm taxa.

    PubMed

    Halanych, Kenneth M; Dahlgren, Thomas G; McHugh, Damhnait

    2002-07-01

    In traditional classification schemes, the Annelida consists of the Polychaeta and the Clitellata (the latter including the Oligochaeta and Hirudinida). However, recent analyses suggest that annelids are much more diverse than traditionally believed, and that polychaetes are paraphyletic. Specifically, some lesser-known taxa (previously regarded as separate phyla) appear to fall within the annelid radiation. Abundant molecular, developmental, and morphological data show that the Siboglinidae, which includes the formerly recognized Pogonophora and Vestimentifera, are derived annelids; recent data from the Elongation Factor-1α (EF-1α) gene also suggest that echiurids are of annelid ancestry. Further, the phylogenetic origins of two other lesser-known groups of marine worms, the Myzostomida and Sipuncula, have recently been called into question. Whereas some authors advocate annelid affinities, others argue that these taxa do not fall within the annelid radiation. With advances in our understanding of annelid phylogeny, our perceptions of body plan evolution within the Metazoa are changing. The evolution of segmentation probably is more plastic than traditionally believed. However, as our understanding of organismal evolution is being revised, we are also forced to reconsider the specific characters being examined. Should segmentation be considered a developmental process or an ontological endpoint?

  8. The evolutionary reality of higher taxa in mammals

    PubMed Central

    Humphreys, Aelys M.; Barraclough, Timothy G.

    2014-01-01

    Species are generally regarded as a fundamental unit of biodiversity. By contrast, higher taxa such as genera and families, while widely used as biodiversity metrics and for classification and communication, are generally not believed to be shaped by shared evolutionary processes in the same way as species. We use simulations to show that processes which are important for emergence of evolutionarily significant units (ESUs) at the species level, namely geographical isolation and ecological divergence, can generate evolutionary independence above the species level and thereby lead to emergence of discrete phylogenetic clusters (higher ESUs). Extending phylogenetic approaches for delimiting evolutionarily significant species to broader phylogenetic scales, we find evidence for the existence of higher ESUs in mammals. In carnivores, euungulates and lagomorphs the hierarchical level of units detected correspond, on average, to the level of family or genus in traditional taxonomy. The units in euungulates are associated with divergent patterns of body mass, consistent with occupation of distinct ecological zones. Our findings demonstrate a new framework for studying biodiversity that unifies approaches at species and higher levels, thus potentially restoring higher taxa to their historical status as natural entities. PMID:24695424

  9. Sensitivities of extant animal taxa to ocean acidification

    NASA Astrophysics Data System (ADS)

    Wittmann, Astrid C.; Pörtner, Hans-O.

    2013-11-01

    Anthropogenic CO2 emitted to the atmosphere is absorbed by the oceans, causing a progressive increase in ocean inorganic carbon concentrations and resulting in decreased water pH and calcium carbonate saturation. This phenomenon, called ocean acidification, is in addition to the warming effects of CO2 emissions. Ocean acidification has been reported to affect ocean biota, but the severity of this threat to ocean ecosystems (and humans depending on these ecosystems) is poorly understood. Here we evaluate the scale of this threat in the context of widely used representative concentration pathways (RCPs) by analysing the sensitivities of five animal taxa (corals, echinoderms, molluscs, crustaceans and fishes) to a wide range of CO2 concentrations. Corals, echinoderms and molluscs are more sensitive to RCP8.5 (936 ppm in 2100) than are crustaceans. Larval fishes may be even more sensitive than the lower invertebrates, but taxon sensitivity on evolutionary timescales remains obscure. The variety of responses within and between taxa, together with observations in mesocosms and palaeo-analogues, suggest that ocean acidification is a driver for substantial change in ocean ecosystems this century, potentially leading to long-term shifts in species composition.

  10. The impact of rare taxa on a fish index of biotic integrity

    USGS Publications Warehouse

    Wan, H.; Chizinski, C.J.; Dolph, C.L.; Vondracek, B.; Wilson, B.N.

    2010-01-01

    The index of biotic integrity (IBI) is a commonly used bioassessment tool that integrates abundance and richness measures to assess water quality. In developing IBIs that are both responsive to human disturbance and resistant to natural variability and sampling error, water managers must decide how to weigh information about rare and abundant taxa, which in turn requires an understanding of the sensitivity of indices to rare taxa. Herein, we investigated the influence of rare fish taxa (within the lower 5% of rank abundance curves) on IBI metric and total scores for stream sites in two of Minnesota's major river basins, the St. Croix (n = 293 site visits) and Upper Mississippi (n = 210 site visits). We artificially removed rare taxa from biological samples by (1) separately excluding each individual taxon that fell within the lower 5% of rank abundance curves; (2) simultaneously excluding all taxa that had an abundance of one (singletons) or two (doubletons); and (3) simultaneously excluding all taxa that fell within the lower 5% of rank abundance curves. We then compared IBI metric and total scores before and after removal of rare taxa using the normalized root mean square error (nRMSE) and regression analysis. The difference in IBI metric and total scores increased as more taxa were removed. Moreover, when multiple rare taxa were removed, the nRMSE was related to sample abundance and to total taxa richness, with greater nRMSE observed in samples with a larger number of taxa or sample abundance. Metrics based on relative abundance of fish taxa were less sensitive to the loss of rare taxa, whereas those based on taxa richness were more sensitive, because taxa richness metrics give more weight to rare taxa compared to the relative abundance metrics. ?? 2010 Elsevier Ltd.

  11. Fungal Taxa Target Different Carbon Substrates in Harvard Forest Soils

    NASA Astrophysics Data System (ADS)

    Hanson, C. A.; Allison, S. D.; Wallenstein, M. D.; Mellilo, J. M.; Treseder, K. K.

    2006-12-01

    The mineralization of soil organic carbon is a major component of the global carbon cycle and is largely controlled by soil microbial communities. However, little is known about the functional roles of soil microbes or whether different microbial taxa target different carbon substrates under natural conditions. To examine this possibility, we assessed the community composition of active fungi by using a novel nucleotide analog technique in soils from the Harvard Forest. We hypothesized that fungal community composition would shift in response to the addition of different substrates and that specific fungal taxa would respond differentially to particular carbon sources. To test this hypothesis, we added a nucleotide analog probe directly to soils in conjunction with one of five carbon compounds of increasing recalcitrance: glycine, sucrose, cellulose, tannin-protein complex, and lignin. During 48 hour incubations, the nucleotide analog was incorporated into newly replicated DNA of soil organisms that proliferated following the addition of the substrates. In this way, we labeled the DNA of microbes that respond to a particular carbon source. Labeled DNA was isolated and fungal Internal Transcribed Spacer (ITS) regions of ribosomal DNA (rDNA) were sequenced and analyzed to identify active fungi to near-species resolution. Diversity analyses at the ≥97% sequence similarity level indicated that taxonomic richness was greater under cellulose (Shannon Index: 3.23 ± 0.11 with ± 95% CI) and lignin (2.87 ± 0.15) additions than the other treatments (2.34 ± 0.16 to 2.64 ± 0.13). In addition, community composition of active fungi shifted under glycine, sucrose, and cellulose additions. Specifically, the community under glycine was significantly different from communities under control, cellulose, and tannin-protein (P<0.05). Additionally, the sucrose and cellulose communities were marginally different from the control community (P = 0.059 and 0.054, respectively) and

  12. Fossil preservation and the stratigraphic ranges of taxa

    NASA Technical Reports Server (NTRS)

    Foote, M.; Raup, D. M.

    1996-01-01

    The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of

  13. Parallel phylogeographic structure in ecologically similar sympatric sister taxa.

    PubMed

    Dawson, Michael N

    2012-02-01

    Present-day phylogeographic patterns have been shaped by the dual histories of lineages and places, producing a diversity of relationships that may challenge discovery of general rules. For example, the predicted positive correlation between dispersal ability and gene flow has been supported inconsistently, suggesting unaccounted complexity in theory or the comparative framework. Here, I extend the sympatric sister-species approach, in which variance between lineages and places is minimized, to sister clades and test a fundamental assumption of comparative genetic studies of dispersal: that taxa which evolved at the same time and in the same place will, if they have similar life histories and ecologies, have essentially the same phylogeographic structure. Phylogenetic analyses of 197 Stigmatopora pipefishes using two nuclear (creatine kinase intron 6, α-tropomyosin) and two mitochondrial (16S, noncoding region) loci revealed largely synchronous parallel diversification of sister clades that are codistributed from Western Australia to New Zealand, supporting the null hypothesis. Only one comparison, however, yielded a sympatric sister-species pair (the two stem species), so I also explored the potential for extant species sharing a substantial proportion of their evolutionary histories in sympatry to substitute for sister taxon comparisons. In eastern Australia, where strong environmental structure is lacking, phylogeographic differences between species that have been codistributed for ~85% of their evolutionary histories were consistent with tendencies favoured by their modest life-history differences, that is the larger, rarer species had lower genetic diversity. In contrast, in New Zealand, two species codistributed for ~70% of their evolutionary histories were both structured similarly by a strong biogeographic filter despite differences in life history. Rigorously quantifying the influence of intrinsic and extrinsic factors on phylogeographic structure may

  14. Fossil preservation and the stratigraphic ranges of taxa

    NASA Technical Reports Server (NTRS)

    Foote, M.; Raup, D. M.

    1996-01-01

    The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of

  15. Identifying sighting clusters of endangered taxa with historical records.

    PubMed

    Duffy, Karl J

    2011-04-01

    The probability and time of extinction of taxa is often inferred from statistical analyses of historical records. Many of these analyses require the exclusion of multiple records within a unit of time (i.e., a month or a year). Nevertheless, spatially explicit, temporally aggregated data may be useful for identifying clusters of sightings (i.e., sighting clusters) in space and time. Identification of sighting clusters highlights changes in the historical recording of endangered taxa. I used two methods to identify sighting clusters in historical records: the Ederer-Myers-Mantel (EMM) test and the space-time permutation scan (STPS). I applied these methods to the spatially explicit sighting records of three species of orchids that are listed as endangered in the Republic of Ireland under the Wildlife Act (1976): Cephalanthera longifolia, Hammarbya paludosa, and Pseudorchis albida. Results with the EMM test were strongly affected by the choice of the time interval, and thus the number of temporal samples, used to examine the records. For example, sightings of P. albida clustered when the records were partitioned into 20-year temporal samples, but not when they were partitioned into 22-year temporal samples. Because the statistical power of EMM was low, it will not be useful when data are sparse. Nevertheless, the STPS identified regions that contained sighting clusters because it uses a flexible scanning window (defined by cylinders of varying size that move over the study area and evaluate the likelihood of clustering) to detect them, and it identified regions with high and regions with low rates of orchid sightings. The STPS analyses can be used to detect sighting clusters of endangered species that may be related to regions of extirpation and may assist in the categorization of threat status.

  16. Pollinator sharing and gene flow among closely related sympatric dioecious fig taxa.

    PubMed

    Wang, Gang; Cannon, Charles H; Chen, Jin

    2016-04-13

    Hybridization and insect pollination are widely believed to increase rates of plant diversification. The extreme diversity of figs (Ficus) and their obligate pollinators, fig wasps (Agaonidae), provides an opportunity to examine the possible role of pollinator-mediated hybridization in plant diversification. Increasing evidence suggests that pollinator sharing and hybridization occurs among fig taxa, despite relatively strict coevolution with the pollinating wasp. Using five sympatric dioecious fig taxa and their pollinators, we examine the degree of pollinator sharing and inter-taxa gene flow. We experimentally test pollinator preference for floral volatiles, the main host recognition signal, from different figs. All five fig taxa shared pollinators with other taxa, and gene flow occurred between fig taxa within and between sections. Floral volatiles of each taxon attracted more than one pollinator species. Floral volatiles were more similar between closely related figs, which experienced higher levels of pollinator sharing and inter-taxa gene flow. This study demonstrates that pollinator sharing and inter-taxa gene flow occurs among closely related sympatric dioecious fig taxa and that pollinators choose the floral volatiles of multiple fig taxa. The implications of pollinator sharing and inter-taxa gene flow on diversification, occurring even in this highly specialized obligate pollination system, require further study.

  17. Pollinator sharing and gene flow among closely related sympatric dioecious fig taxa

    PubMed Central

    Cannon, Charles H.

    2016-01-01

    Hybridization and insect pollination are widely believed to increase rates of plant diversification. The extreme diversity of figs (Ficus) and their obligate pollinators, fig wasps (Agaonidae), provides an opportunity to examine the possible role of pollinator-mediated hybridization in plant diversification. Increasing evidence suggests that pollinator sharing and hybridization occurs among fig taxa, despite relatively strict coevolution with the pollinating wasp. Using five sympatric dioecious fig taxa and their pollinators, we examine the degree of pollinator sharing and inter-taxa gene flow. We experimentally test pollinator preference for floral volatiles, the main host recognition signal, from different figs. All five fig taxa shared pollinators with other taxa, and gene flow occurred between fig taxa within and between sections. Floral volatiles of each taxon attracted more than one pollinator species. Floral volatiles were more similar between closely related figs, which experienced higher levels of pollinator sharing and inter-taxa gene flow. This study demonstrates that pollinator sharing and inter-taxa gene flow occurs among closely related sympatric dioecious fig taxa and that pollinators choose the floral volatiles of multiple fig taxa. The implications of pollinator sharing and inter-taxa gene flow on diversification, occurring even in this highly specialized obligate pollination system, require further study. PMID:27075252

  18. THE POTENTIAL INDICATOR VALUE OF RARE TAXA RICHNESS IN DIATOM-BASED STREAM BIOASSESSMENT(1).

    PubMed

    Gillett, Nadezhda D; Pan, Yangdong; Manoylov, Kalina M; Stancheva, Rosalina; Weilhoefer, Christine L

    2011-06-01

    Despite their recognized contribution to species richness, the importance of rare taxa richness in bioassessment is unclear. This study aimed to characterize the environmental factors affecting the number of rare diatom taxa in western U.S. streams and rivers, and to evaluate whether this number can be used to differentiate streams with contrasting human disturbance. Three different categories of rare taxa were used: satellite (taxa with low occurrence and low abundance), rural (taxa with high occurrence and low abundance), and urban (taxa with low occurrence and high abundance). Common taxa were included as a separate category of core taxa (taxa with high occurrence and high abundance). We analyzed 987 diatom samples collected over the period of 5 years (2000-2004) for the U.S. Environmental Protection Agency's (EPA) Western Environmental Monitoring and Assessment Program (WEMAP). The results showed that rural taxa richness (number of rural taxa per site) increased along a longitudinal gradient from mountainous, fast-flowing oligotrophic streams with fewer fine substrates to large, slow-moving, nutrient-rich rivers with abundance of fine substrates. Rural taxa richness was the only rarity metric that distinguished least disturbed (reference) sites from the most disturbed (impacted) sites, but it was significantly different only in the mountains ecoregion. Core taxa richness distinguished reference from impacted sites in the West and in each one of the three ecoregions (mountains, plains, and xeric). Our findings revealed that rural taxa richness can be used as an indicator of human disturbance in streams/rivers, especially in the mountains ecoregion, and that rarity definition is important in bioassessment. © 2011 Phycological Society of America.

  19. Nested taxa-area curves for eastern United States floras

    USGS Publications Warehouse

    Bennett, J.P.

    1997-01-01

    The slopes of log-log species-area curves have been studied extensively and found to be influenced by the range of areas under study. Two such studies of eastern United States floras have yielded species-area curve slopes which differ by more than 100%: 0.251 and 0.113. The first slope may be too steep because the flora of the world was included, and both may be too steep because noncontiguous areas were used. These two hypotheses were tested using a set of nested floras centered in Ohio and continuing up to the flora of the world. The results suggest that this set of eastern United States floras produces a log-log species-area curve with a slope of approximately 0.20 with the flora of the world excluded, and regardless of whether or not the floras are from nested areas. Genera- and family-area curves are less steep than species-area curves and show similar patterns. Taxa ratio curves also increase with area, with the species/family ratio showing the steepest slope.

  20. Comparing mechanisms of host manipulation across host and parasite taxa

    USGS Publications Warehouse

    Lafferty, Kevin D.; Shaw, Jenny C.

    2013-01-01

    Parasites affect host behavior in several ways. They can alter activity, microhabitats or both. For trophically transmitted parasites (the focus of our study), decreased activity might impair the ability of hosts to respond to final-host predators, and increased activity and altered microhabitat choice might increase contact rates between hosts and final-host predators. In an analysis of trophically transmitted parasites, more parasite groups altered activity than altered microhabitat choice. Parasites that infected vertebrates were more likely to impair the host’s reaction to predators, whereas parasites that infected invertebrates were more likely to increase the host’s contact with predators. The site of infection might affect how parasites manipulate their hosts. For instance, parasites in the central nervous system seem particularly suited to manipulating host behavior. Manipulative parasites commonly occupy the body cavity, muscles and central nervous systems of their hosts. Acanthocephalans in the data set differed from other taxa in that they occurred exclusively in the body cavity of invertebrates. In addition, they were more likely to alter microhabitat choice than activity. Parasites in the body cavity (across parasite types) were more likely to be associated with increased host contact with predators. Parasites can manipulate the host through energetic drain, but most parasites use more sophisticated means. For instance, parasites target four physiological systems that shape behavior in both invertebrates and vertebrates: neural, endocrine, neuromodulatory and immunomodulatory. The interconnections between these systems make it difficult to isolate specific mechanisms of host behavioral manipulation.

  1. DNA barcoding and taxonomy: dark taxa and dark texts.

    PubMed

    Page, Roderic D M

    2016-09-05

    Both classical taxonomy and DNA barcoding are engaged in the task of digitizing the living world. Much of the taxonomic literature remains undigitized. The rise of open access publishing this century and the freeing of older literature from the shackles of copyright have greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid- to late-twentieth century remains offline ('dark texts'). DNA barcoding is generating a wealth of computable data that in many ways are much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These 'dark taxa' hamper the classical method of integrating biodiversity data, using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global 'digital dashboard' to assess the extent to which biodiversity data are available online.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

  2. MyDas, an extensible Java DAS server.

    PubMed

    Salazar, Gustavo A; García, Leyla J; Jones, Philip; Jimenez, Rafael C; Quinn, Antony F; Jenkinson, Andrew M; Mulder, Nicola; Martin, Maria; Hunter, Sarah; Hermjakob, Henning

    2012-01-01

    A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users.We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details.

  3. Sustaining salmonid populations: A caring understanding of naturalness of taxa

    USGS Publications Warehouse

    Nielsen, Jennifer L.; Regier, Henry A.; Knudsen, E. Eric

    2004-01-01

    Species of the family of Salmonidae occur naturally in Northern Hemisphere waters that remain clear and cool to cold in summer. For purposes of reproduction, salmonids generally behaviorally respond to the currents of streams and lakes in recently glaciated areas. For feeding and maturation, many larger species migrate into existing systems of large lakes, seas, and oceans. The subfamilies include Salmoninae, Coregoninae, and Thymallinae. In many locales and regions of the hemisphere, numerous species of these subfamilies evolved and self-organized into species flocks or taxocenes of bewildering complexity. For example, any individual species may play different or unique ecological roles in different taxocenes. The northern Pacific and Atlantic Ocean ecosystems, with their seas and tributaries, each contained a metacomplex of such taxocenes that, in their natural state some centuries ago, resembled each other but differed in many ways. Humans have valued all species of this family for subsistence, ceremonial, naturalist, gustatory, angling, and commercial reasons for centuries. Modern progressive humans (MPHs), whose industrial and commercial enterprises have gradually spread over this hemisphere in recent time, now affect aquatic ecosystems at all scales from local to global. These human effects mingle in complex ways that together induce uniquely natural salmonid taxocenes to disintegrate with the loss of species, including those groups least tolerant to human manipulations, but extending more recently to those taxa more adapted to anthropogenic change. As we leave the modern era, dominated by MPHs, will we find ways to live sustainably with salmonid taxocenes that still exhibit self-organizational integrity, or will only individual, isolated populations of salmonid species, derived from those most tolerant of MPHs, survive? To achieve future sustainability of salmonids, we suggest implementation of a search for intuitive knowledge based on faith in the wisdom of

  4. Proteorhodopsin genes are distributed among divergent marine bacterial taxa

    PubMed Central

    de la Torre, José R.; Christianson, Lynne M.; Béjà, Oded; Suzuki, Marcelino T.; Karl, David M.; Heidelberg, John; DeLong, Edward F.

    2003-01-01

    Proteorhodopsin (PR) is a retinal-binding bacterial integral membrane protein that functions as a light-driven proton pump. The gene encoding this photoprotein was originally discovered on a large genome fragment derived from an uncultured marine γ-proteobacterium of the SAR86 group. Subsequently, many variants of the PR gene have been detected in marine plankton, via PCR-based gene surveys. It has not been clear, however, whether these different PR genes are widely distributed among different bacterial groups, or whether they have a restricted taxonomic distribution. We report here comparative analyses of PR-bearing genomic fragments recovered directly from planktonic bacteria inhabiting the California coast, the central Pacific Ocean, and waters offshore the Antarctica Peninsula. Sequence analysis of an Antarctic genome fragment harboring PR (ANT32C12) revealed moderate conservation in gene order and identity, compared with a previously reported PR-containing genome fragment from a Monterey Bay γ-proteobacterium (EBAC31A08). Outside the limited region of synteny shared between these clones, however, no significant DNA or protein identity was evident. Analysis of a third PR-containing genome fragment (HOT2C01) from the North Pacific subtropical gyre showed even more divergence from the γ-proteobacterial PR-flanking region. Subsequent phylogenetic and comparative genomic analyses revealed that the Central North Pacific PR-containing genome fragment (HOT2C01) originated from a planktonic α-proteobacterium. These data indicate that PR genes are distributed among a variety of divergent marine bacterial taxa, including both α- and γ-proteobacteria. Our analyses also demonstrate the utility of cultivation-independent comparative genomic approaches for assessing gene content and distribution in naturally occurring microbes. PMID:14566056

  5. DNA barcode data accurately assign higher spider taxa.

    PubMed

    Coddington, Jonathan A; Agnarsson, Ingi; Cheng, Ren-Chung; Čandek, Klemen; Driskell, Amy; Frick, Holger; Gregorič, Matjaž; Kostanjšek, Rok; Kropf, Christian; Kweskin, Matthew; Lokovšek, Tjaša; Pipan, Miha; Vidergar, Nina; Kuntner, Matjaž

    2016-01-01

    The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios "barcodes" (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families-taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75-100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the

  6. DNA barcode data accurately assign higher spider taxa

    PubMed Central

    Coddington, Jonathan A.; Agnarsson, Ingi; Cheng, Ren-Chung; Čandek, Klemen; Driskell, Amy; Frick, Holger; Gregorič, Matjaž; Kostanjšek, Rok; Kropf, Christian; Kweskin, Matthew; Lokovšek, Tjaša; Pipan, Miha; Vidergar, Nina

    2016-01-01

    The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of

  7. Distribution of high bacterial taxa across the chronosequence of two alpine glacier forelands.

    PubMed

    Philippot, Laurent; Tscherko, Dagmar; Bru, David; Kandeler, Ellen

    2011-02-01

    Little is known about the changes in abundance of microbial taxa in relation to the chronosequence of receding glaciers. This study investigated how the abundances of ten bacterial phyla or classes varied along successional gradients in two glaciers, Ödenwinkelkees and Rotmoosferner, in the central Alps. Quantitative PCR was used to estimate the abundance of the different bacterial taxa in extended glacier chronosequences, including 10- to 160-year-old successional stages, the surface of the glacier, and a fully established soil. Actinobacteria (15-30%) was the dominant group within the chronosequences. Several taxa showed significant differences in the number of taxa-specific 16S rRNA gene copies per nanogram of DNA and/or in the ratio of taxa-specific to the total bacterial 16S rRNA gene copies (i.e., the relative abundance of the different taxa within the bacterial community) between the established soils or the glacier surface and the 10- to 160-year-old successional stages. A significantly higher proportion of Βetaproteobacteria (20%) was observed on the surface of both glaciers. However, no differences were observed between the 10- to 160-year-old successional stages in the number of taxa-specific 16S rRNA gene copies per nanogram of DNA or in the ratio of taxa-specific to the total bacterial 16S rRNA gene copies for the different taxa. Nevertheless, when the relative abundance data from all the studied taxa were combined and analyzed altogether, most of the sites could be distinguished from one other. This indicates that the overall composition of the bacterial community was more affected than the abundance of the targeted taxa by changes in environmental conditions along the chronosequences.

  8. State-of-Science Approaches to Determine Sensitive Taxa for Water Quality Criteria Derivation

    EPA Science Inventory

    Current Ambient Water Quality Criteria (AWQC) guidelines specify pre-defined taxa diversity requirements, which has limited chemical-specific criteria development in the U.S. to less than 100 chemicals. A priori knowledge of sensitive taxa to toxicologically similar groups of che...

  9. Triterpenes of toxic and non-toxic taxa of Lantana camara.

    PubMed

    Hart, N K; Lamberton, J A; Sioumis, A A; Suares, H; Seawright, A A

    1976-04-15

    The taxa of Lantana camara toxic to animals contain lantadene A lantadene B, whereas in two non-toxic taxa other triterpenes predominate. Several new triterpenes have been characterized. Contrary to earlier claims, lantadene A and to a lesser extent lantadene B are toxic when administered intraruminally to sheep.

  10. State-of-Science Approaches to Determine Sensitive Taxa for Water Quality Criteria Derivation

    EPA Science Inventory

    Current Ambient Water Quality Criteria (AWQC) guidelines specify pre-defined taxa diversity requirements, which has limited chemical-specific criteria development in the U.S. to less than 100 chemicals. A priori knowledge of sensitive taxa to toxicologically similar groups of che...

  11. EXCLUSION OF RARE TAXA AFFECTS PERFORMANCE OF THE O/E INDEX IN BIOASSESSMENTS

    EPA Science Inventory

    The contribution of rare taxa to bioassessments based on multispecies assemblages is the subject of continued debate. As a result, users of predictive models such as River InVertebrate Prediction and Classification System (RIVPACS) disagree on whether to exclude locally rare taxa...

  12. Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

    PubMed Central

    2016-01-01

    Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies. PMID:27146442

  13. Comparison of the DAS28-CRP and DAS28-ESR in patients with rheumatoid arthritis.

    PubMed

    Sengul, Ilker; Akcay-Yalbuzdag, Seniz; Ince, Bugra; Goksel-Karatepe, Altinay; Kaya, Taciser

    2015-07-01

    To compare the Disease Activity Score with 28 joint (DAS28) using erythrocyte sedimentation rate (ESR) (DAS28-ESR) and DAS28 using C-reactive protein (CRP) (DAS28-CRP) with thresholds validated for DAS28-ESR in Turkish patients with rheumatoid arthritis. The DAS28 data of 112 patients with rheumatoid arthritis followed in a local outpatient clinic were used. First, the correlation between DAS28-CRP and DAS28-ESR and the correlation between their unique components ([0.36 × In (CRP + 1) + 0.96] and [0.70 × In (ESR)]) were analyzed. Second, a Bland-Altman plot was constructed for the evaluation of the level of agreement between DAS28-CRP and DAS28-ESR. Lastly, the agreement between these two methods was analyzed by κ coefficient. Although there was a strong correlation between DAS28-CRP and DAS28-ESR, the correlation between their unique components was fair. Although more than 95% of the point data fall between the upper and lower bounds of the limit of agreement, the percentage error (46%) was higher than the acceptable proportion of 30%. The κ coefficient of agreement between DAS28- ESR and DAS28-CRP with validated thresholds for DAS28-ESR was 0.42, which was close to the lower boundary for moderate agreement. The results of this study demonstrated that there is discordance between DAS28-ESR and DAS28-CRP with the validated thresholds for DAS28-ESR. Using the DAS28-CRP with threshold values validated for DAS28-ESR may lead to errors in the determination of disease activity and therefore may lead to errors in the management of patients with rheumatoid arthritis. © 2015 Asia Pacific League of Associations for Rheumatology and Wiley Publishing Asia Pty Ltd.

  14. High level of bacterial diversity and novel taxa in continental shelf sediment.

    PubMed

    Hong, Jin-Kyung; Cho, Jae-Chang

    2012-06-01

    The bacterial diversity of the continental shelf sediment in the Yellow Sea was investigated by the cloning and sequencing of PCR-amplified 16S rRNA genes. The majority of the cloned sequences were distinct phylotypes that were novel at the species level. The richness estimator indicated that the sediment sample might harbor up to 32 phylum-level taxa. A large number of low-abundance, phylum-level taxa accounted for most of the observed phylogenetic diversity at our study site, suggesting that these low-abundance taxa might play crucial roles in the shelf sediment ecosystem.

  15. [The role of heterochrony in the establishment of archetype in higher Echinoderm taxa].

    PubMed

    Rozhnov, S V

    2009-01-01

    The analysis based on paleontological data shows that the body plans of higher echinoderm taxa were established through the combination of previously developed characters. These combinations appeared due to various heterochronies and resulted in more or less complete filling of the morphological space of logical capabilities. The maximum rank of new taxa decreased with time. New body plans of higher taxa did not replace the old plans but rather overlay them, extending the hierarchy of body plans and the respective hierarchy of taxa. The macroevolution of echinoderms and other metazoans progressed from the formation of an archetype (a general body plan) to individual details, the development of structural plans of lower levels. Heterochrony resulted in mosaic evolution and obscurity of intermediate forms.

  16. Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin

    PubMed Central

    Fortunato, Caroline S; Eiler, Alexander; Herfort, Lydie; Needoba, Joseph A; Peterson, Tawnya D; Crump, Byron C

    2013-01-01

    Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (ρ=−0.664) and residence time (ρ=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments. PMID:23719153

  17. A nomenclator of extant and fossil taxa of the Valvatidae (Gastropoda, Ectobranchia)

    PubMed Central

    Haszprunar, Gerhard

    2014-01-01

    Abstract A compilation of all supra- and (infra-) specific taxa of extant and fossil Valvatidae, a group of freshwater operculate snails, is provided, including taxa initially described in this family and subsequently classified in other families, as well as names containing errors or misspellings. The extensive reference list is directly linked to the available electronic source (digital view or pdf-download) of the respective papers. PMID:24578604

  18. Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin.

    PubMed

    Fortunato, Caroline S; Eiler, Alexander; Herfort, Lydie; Needoba, Joseph A; Peterson, Tawnya D; Crump, Byron C

    2013-10-01

    Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (ρ=-0.664) and residence time (ρ=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments.

  19. Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia.

    PubMed

    Pyron, R Alexander

    2011-07-01

    Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological data sets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and some studies have merged morphological and molecular data to estimate combined evidence phylogenies containing both extinct and extant taxa. However, few, if any, studies have attempted to estimate divergence times using phylogenies containing both fossil and living taxa sampled for both molecular and morphological data. Here, I infer both the phylogeny and the time of origin for Lissamphibia and a number of stem tetrapods using Bayesian methods based on a data set containing morphological data for extinct taxa, molecular data for extant taxa, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post hoc age constraints on internal nodes and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined evidence analyses whenever possible. © The Author(s) 2011. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.

  20. How oxymonads lost their groove: an ultrastructural comparison of Monocercomonoides and excavate taxa.

    PubMed

    Simpson, Alastair G B; Radek, Renate; Dacks, Joel B; O'Kelly, Charles J

    2002-01-01

    Despite being amongst the more familiar groups of heterotrophic flagellates, the evolutionary affinities of oxymonads remain poorly understood. A re-interpretation of the cytoskeleton of the oxymonad Monocercomonoides hausmanni suggests that this organism has a similar ultrastructural organisation to members of the informal assemblage 'excavate taxa'. The preaxostyle, 'R1' root, and 'R2' root of M. hausmanni are proposed to be homologous to the right, left, and anterior roots respectively of excavate taxa. The 'paracrystalline' portion of the preaxostyle, previously treated as unique to oxymonads, is proposed to be homologous to the I fibre of excavate taxa. Other non-microtubular fibres are identified that have both positional and substructural similarity to the distinctive B and C fibres of excavate taxa. A homologue to the 'singlet root', otherwise distinctive for excavate taxa, is also proposed. The preaxostyle and C fibre homologue in Monocercomonoides are most similar to the homologous structures in Trimastix. suggesting a particularly close relationship. This supports and extends recent molecular phylogenetic findings that Trimastix and oxymonads form a clade. We conclude that oxymonads have an excavate ancestry, and that the 'excavate taxa' sensu stricto form a paraphyletic assemblage.

  1. A swainsonine survey of North American Astragalus and Oxytropis taxa implicated as locoweeds.

    PubMed

    Cook, Daniel; Gardner, Dale R; Lee, Stephen T; Pfister, James A; Stonecipher, Clinton A; Welsh, Stanley L

    2016-08-01

    Swainsonine, an indolizidine alkaloid with significant physiological activity, is an α-mannosidase and mannosidase II inhibitor that causes lysosomal storage disease and alters glycoprotein processing. Swainsonine is found in a number of plant species worldwide, and causes severe toxicosis in livestock grazing these plants, leading to a chronic wasting disease characterized by weight loss, depression, altered behavior, decreased libido, infertility, and death. Swainsonine has been detected in 19 Astragalus and 2 Oxytropis species in North America by thin layer chromatography, gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry and a jack bean α-mannosidase inhibition assay. In addition, 5 species in North America are presumed to contain swainsonine based upon reports from field cases. Many of these plant species have not been analyzed for swainsonine using modern instrumentation such as gas or liquid chromatography coupled with mass spectrometry. To provide clarification, 22 Astragalus species representing 93 taxa and 4 Oxytropis species representing 18 taxa were screened for swainsonine using both liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. Swainsonine was detected in 48 Astragalus taxa representing 13 species and 5 Oxytropis taxa representing 4 species. Forty of the fifty-three swainsonine-positive taxa had not been determined to contain swainsonine previously using liquid or gas chromatography coupled with mass spectrometry. The list of swainsonine-containing taxa reported here will serve as a reference for risk assessment and diagnostic purposes. Published by Elsevier Ltd.

  2. MiDAS: the field guide to the microbes of activated sludge

    PubMed Central

    McIlroy, Simon Jon; Saunders, Aaron Marc; Albertsen, Mads; Nierychlo, Marta; McIlroy, Bianca; Hansen, Aviaja Anna; Karst, Søren Michael; Nielsen, Jeppe Lund; Nielsen, Per Halkjær

    2015-01-01

    The Microbial Database for Activated Sludge (MiDAS) field guide is a freely available online resource linking the identity of abundant and process critical microorganisms in activated sludge wastewater treatment systems to available data related to their functional importance. Phenotypic properties of some of these genera are described, but most are known only from sequence data. The MiDAS taxonomy is a manual curation of the SILVA taxonomy that proposes a name for all genus-level taxa observed to be abundant by large-scale 16 S rRNA gene amplicon sequencing of full-scale activated sludge communities. The taxonomy can be used to classify unknown sequences, and the online MiDAS field guide links the identity to the available information about their morphology, diversity, physiology and distribution. The use of a common taxonomy across the field will provide a solid foundation for the study of microbial ecology of the activated sludge process and related treatment processes. The online MiDAS field guide is a collaborative workspace intended to facilitate a better understanding of the ecology of activated sludge and related treatment processes—knowledge that will be an invaluable resource for the optimal design and operation of these systems. Database URL: http://www.midasfieldguide.org PMID:26120139

  3. MiDAS: the field guide to the microbes of activated sludge.

    PubMed

    McIlroy, Simon Jon; Saunders, Aaron Marc; Albertsen, Mads; Nierychlo, Marta; McIlroy, Bianca; Hansen, Aviaja Anna; Karst, Søren Michael; Nielsen, Jeppe Lund; Nielsen, Per Halkjær

    2015-01-01

    The Microbial Database for Activated Sludge (MiDAS) field guide is a freely available online resource linking the identity of abundant and process critical microorganisms in activated sludge wastewater treatment systems to available data related to their functional importance. Phenotypic properties of some of these genera are described, but most are known only from sequence data. The MiDAS taxonomy is a manual curation of the SILVA taxonomy that proposes a name for all genus-level taxa observed to be abundant by large-scale 16 S rRNA gene amplicon sequencing of full-scale activated sludge communities. The taxonomy can be used to classify unknown sequences, and the online MiDAS field guide links the identity to the available information about their morphology, diversity, physiology and distribution. The use of a common taxonomy across the field will provide a solid foundation for the study of microbial ecology of the activated sludge process and related treatment processes. The online MiDAS field guide is a collaborative workspace intended to facilitate a better understanding of the ecology of activated sludge and related treatment processes--knowledge that will be an invaluable resource for the optimal design and operation of these systems. © The Author(s) 2015. Published by Oxford University Press.

  4. Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.

    PubMed

    Carr, Rogan; Shen-Orr, Shai S; Borenstein, Elhanan

    2013-01-01

    Metagenomics has transformed our understanding of the microbial world, allowing researchers to bypass the need to isolate and culture individual taxa and to directly characterize both the taxonomic and gene compositions of environmental samples. However, associating the genes found in a metagenomic sample with the specific taxa of origin remains a critical challenge. Existing binning methods, based on nucleotide composition or alignment to reference genomes allow only a coarse-grained classification and rely heavily on the availability of sequenced genomes from closely related taxa. Here, we introduce a novel computational framework, integrating variation in gene abundances across multiple samples with taxonomic abundance data to deconvolve metagenomic samples into taxa-specific gene profiles and to reconstruct the genomic content of community members. This assembly-free method is not bounded by various factors limiting previously described methods of metagenomic binning or metagenomic assembly and represents a fundamentally different approach to metagenomic-based genome reconstruction. An implementation of this framework is available at http://elbo.gs.washington.edu/software.html. We first describe the mathematical foundations of our framework and discuss considerations for implementing its various components. We demonstrate the ability of this framework to accurately deconvolve a set of metagenomic samples and to recover the gene content of individual taxa using synthetic metagenomic samples. We specifically characterize determinants of prediction accuracy and examine the impact of annotation errors on the reconstructed genomes. We finally apply metagenomic deconvolution to samples from the Human Microbiome Project, successfully reconstructing genus-level genomic content of various microbial genera, based solely on variation in gene count. These reconstructed genera are shown to correctly capture genus-specific properties. With the accumulation of metagenomic

  5. Fossils impact as hard as living taxa in parsimony analyses of morphology.

    PubMed

    Cobbett, Andrea; Wilkinson, Mark; Wills, Matthew A

    2007-10-01

    Systematists disagree whether data from fossils should be included in parsimony analyses. In a handful of well-documented cases, the addition of fossil data radically overturns a hypothesis of relationships based on extant taxa alone. Fossils can break up long branches and preserve character combinations closer in time to deep splitting events. However, fossils usually require more interpretation than extant taxa, introducing greater potential for spurious codings. Moreover, because fossils often have more "missing" codings, they are frequently accused of increasing numbers of MPTs, frustrating resolution and reducing support. Despite the controversy, remarkably little is known about the effects of fossils more generally. Here we provide the first systematic study, investigating empirically the behavior of fossil and extant taxa in 45 published morphological data sets. First-order jackknifing is used to determine the effects that each terminal has on inferred relationships, on the number of MPTs, and on CI' and RI as measures of homoplasy. Bootstrap leaf stabilities provide a proxy for the contribution of individual taxa to the branch support in the rest of the tree. There is no significant difference in the impact of fossil versus extant taxa on relationships, numbers of MPTs, and CI' or RI. However, adding individual fossil taxa is more likely to reduce the total branch support of the tree than adding extant taxa. This must be weighed against the superior taxon sampling afforded by including judiciously coded fossils, providing data from otherwise unsampled regions of the tree. We therefore recommend that investigators should include fossils, in the absence of compelling and case specific reasons for their exclusion.

  6. Molecular Systematics, GISH and the Origin of Hybrid Taxa in Nicotiana (Solanaceae)

    PubMed Central

    CHASE, MARK W.; KNAPP, SANDRA; COX, ANTONY V.; CLARKSON, JAMES J.; BUTSKO, YELENA; JOSEPH, JEFFREY; SAVOLAINEN, VINCENT; PAROKONNY, ALEX S.

    2003-01-01

    Phylogenetic relationships in the genus Nicotiana were investigated using parsimony analyses of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrDNA). In addition, origins of some amphidiploid taxa in Nicotiana were investigated using the techniques of genomic in situ hybridization (GISH), and the results of both sets of analyses were used to evaluate previous hypotheses about the origins of these taxa. Phylogenetic analyses of the ITS nrDNA data were performed on the entire genus (66 of 77 naturally occurring species, plus three artificial hybrids), comprising both diploid and polyploid taxa, and on the diploid taxa only (35 species) to examine the effects of amphidiploids on estimates of relationships. All taxa, regardless of ploidy, produced clean, single copies of the ITS region, even though some taxa are hybrids. Results are compared with a published plastid (matK) phylogeny using fewer, but many of the same, taxa. The patterns of relationships in Nicotiana, as seen in both analyses, are largely congruent with each other and previous evolutionary ideas based on morphology and cytology, but some important differences are apparent. None of the currently recognized subgenera of Nicotiana is monophyletic and, although most of the currently recognized sections are coherent, others are clearly polyphyletic. Relying solely upon ITS nrDNA analysis to reveal phylogenetic patterns in a complex genus such as Nicotiana is insufficient, and it is clear that conventional analysis of single data sets, such as ITS, is likely to be misleading in at least some respects about evolutionary history. ITS sequences of natural and well‐documented amphidiploids are similar or identical to one of their two parents—usually, but not always, the maternal parent—and are not in any sense themselves ‘hybrid’. Knowing how ITS evolves in artificial amphidiploids gives insight into what ITS analysis might reveal about naturally occurring amphidiploids of

  7. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity.

    PubMed

    Shade, Ashley; Jones, Stuart E; Caporaso, J Gregory; Handelsman, Jo; Knight, Rob; Fierer, Noah; Gilbert, Jack A

    2014-07-15

    Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial "rare biosphere" to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified "one-hit wonder" CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. This observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time. Importance: Microbial communities and their processes are the foundations of ecosystems. The ecological roles of rare microorganisms are largely unknown, but it is thought that they contribute to community stability by acting as a reservoir that can rapidly respond to environmental changes. We investigated the occurrence of typically rare taxa that very occasionally become more prominent in their communities ("conditionally rare"). We quantified conditionally rare

  8. Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

    DOE PAGES

    Shade, Ashley; Jones, Stuart E.; Caporaso, J. Gregory; ...

    2014-07-15

    Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT mademore » up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. In conclusion, this observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time.« less

  9. Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

    SciTech Connect

    Shade, Ashley; Jones, Stuart E.; Caporaso, J. Gregory; Handelsman, Jo; Knight, Rob; Fierer, Noah; Gilbert, Jack A.

    2014-07-15

    Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. In conclusion, this observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time.

  10. Differences among Major Taxa in the Extent of Ecological Knowledge across Four Major Ecosystems

    PubMed Central

    Fisher, Rebecca; Knowlton, Nancy; Brainard, Russell E.; Caley, M. Julian

    2011-01-01

    Existing knowledge shapes our understanding of ecosystems and is critical for ecosystem-based management of the world's natural resources. Typically this knowledge is biased among taxa, with some taxa far better studied than others, but the extent of this bias is poorly known. In conjunction with the publically available World Registry of Marine Species database (WoRMS) and one of the world's premier electronic scientific literature databases (Web of Science®), a text mining approach is used to examine the distribution of existing ecological knowledge among taxa in coral reef, mangrove, seagrass and kelp bed ecosystems. We found that for each of these ecosystems, most research has been limited to a few groups of organisms. While this bias clearly reflects the perceived importance of some taxa as commercially or ecologically valuable, the relative lack of research of other taxonomic groups highlights the problem that some key taxa and associated ecosystem processes they affect may be poorly understood or completely ignored. The approach outlined here could be applied to any type of ecosystem for analyzing previous research effort and identifying knowledge gaps in order to improve ecosystem-based conservation and management. PMID:22073172

  11. Signals of speciation: volatile organic compounds resolve closely related sagebrush taxa, suggesting their importance in evolution.

    PubMed

    Jaeger, Deidre M; Runyon, Justin B; Richardson, Bryce A

    2016-09-01

    Volatile organic compounds (VOCs) play important roles in the environmental adaptation and fitness of plants. Comparison of the qualitative and quantitative differences in VOCs among closely related taxa and assessing the effects of environment on their emissions are important steps to deducing VOC function and evolutionary importance. Headspace VOCs from five taxa of sagebrush (Artemisia, subgenus Tridentatae) growing in two common gardens were collected and analyzed using GC-MS. Of the 74 total VOCs emitted, only 15 were needed to segregate sagebrush taxa using Random Forest analysis with a low error of 4%. All but one of these 15 VOCs showed qualitative differences among taxa. Ordination of results showed strong clustering that reflects taxonomic classification. Random Forest identified five VOCs that classify based on environment (2% error), which do not overlap with the 15 VOCs that segregated taxa. We show that VOCs can discriminate closely related species and subspecies of Artemisia, which are difficult to define using molecular markers or morphology. Thus, it appears that changes in VOCs either lead the way or follow closely behind speciation in this group. Future research should explore the functions of VOCs, which could provide further insights into the evolution of sagebrushes.

  12. Differences among major taxa in the extent of ecological knowledge across four major ecosystems.

    PubMed

    Fisher, Rebecca; Knowlton, Nancy; Brainard, Russell E; Caley, M Julian

    2011-01-01

    Existing knowledge shapes our understanding of ecosystems and is critical for ecosystem-based management of the world's natural resources. Typically this knowledge is biased among taxa, with some taxa far better studied than others, but the extent of this bias is poorly known. In conjunction with the publically available World Registry of Marine Species database (WoRMS) and one of the world's premier electronic scientific literature databases (Web of Science®), a text mining approach is used to examine the distribution of existing ecological knowledge among taxa in coral reef, mangrove, seagrass and kelp bed ecosystems. We found that for each of these ecosystems, most research has been limited to a few groups of organisms. While this bias clearly reflects the perceived importance of some taxa as commercially or ecologically valuable, the relative lack of research of other taxonomic groups highlights the problem that some key taxa and associated ecosystem processes they affect may be poorly understood or completely ignored. The approach outlined here could be applied to any type of ecosystem for analyzing previous research effort and identifying knowledge gaps in order to improve ecosystem-based conservation and management.

  13. Time linkages between pollination onsets of different taxa in Perugia, Central Italy--an update.

    PubMed

    Frenguelli, Giuseppe; Ghitarrini, Sofia; Tedeschini, Emma

    2016-01-01

    In the last decades, increasing attention has been paid to pollinosis. Numerous studies have been carried out concerning the pollination timing of allergenic plant species and the possibility to forecast its beginning and intensity using several statistical methods and models. This study proposes a simple and fast method to identify in advance the time lapse in which the pollination of some allergenic taxa should start. The times of pollination of 14 taxa were recorded in the area of Perugia (Central Italy) by means of a 7-volumetric Hirst-Type pollen trap. For a 30-year period (1984-2013), annual starting dates were calculated for each taxa, using the 5% method (Lejoly-Gabriel). The time linkages between these starting dates were then estimated, considering them in pairs and calculating linear regression coefficients. For the significantly linked species, forecasting models were obtained by means of linear regression analysis. To apply these models to the ongoing pollen season, pollination beginning of the earlier species has to be calculated using a sum-based method. From this date, through the obtained equations, it is possible to predict the approximate period in which the pollination of the second linked taxa should start. The possibility to predict the start of the pollen season of these taxa could be of great importance from the allergological point of view. In fact, an early or delayed flowering can have considerable effects in the prophylaxis programming and efficacy.

  14. Roles of epi-anecic taxa of earthworms in the organic matter recycling

    NASA Astrophysics Data System (ADS)

    Hoeffner, Kevin; Monard, Cécile; Santonja, Mathieu; Pérès, Guénola; Cluzeau, Daniel

    2017-04-01

    Given their impact on soil functioning and their interactions with soil organisms, earthworms contribute to the recycling of organic matter and participate significantly in the numerous ecosystem services provided by soils. Most studies on the role of earthworms in organic matter recycling were conducted at the level of the four functional groups (epigeic, epi-anecic, anecic strict and endogeic), but their effects at taxa level remain largely unknown. Still, within a functional group, anatomic and physiologic earthworm taxa traits are different, which should impact organic matter recycling. This study aims at determining, under controlled conditions, epi-anecic taxa differences in (i) leaf litter mass loss, (ii) assimilation and (iii) impact on microorganisms communities implied in organic matter degradation. In seperate microcosms, we chose 4 epi anecic taxa (Lumbricus rubellus, Lumbricus festivus, Lumbricus centralis and Lumbricus terrestris). Each taxon was exposed separately to leaves of three different plants (Holcus lanatus, Lolium perenne and Corylus avellana). In the same microcosm, leaves of each plant was both placed on the surface and buried 10cm deep. The experiment lasted 10 days for half of the samples and 20 days for the second half. Microorganisms communities were analysed using TRFLP in each earthworm taxon burrow walls at 20 days. We observed differences between epi-anecic taxa depending on species of plant and the duration of the experiment. Results are discussed taking into account physical and chemical properties of these 3 trophic resources (e.g. C/N ratio, phenolic compounds, percentage of lignin and cellulose...).

  15. Differentiating Iconella from Surirella (Bacillariophyceae): typifying four Ehrenberg names and a preliminary checklist of the African taxa

    PubMed Central

    Jahn, Regine; Kusber, Wolf-Henning; Cocquyt, Christine

    2017-01-01

    Abstract To comply with the new phylogeny within the Surirellales as supported by molecular and morphological data, re-evaluations and re-combinations of taxa from and within the genera Surirella, Cymatopleura, and Stenopterobia and with the re-established genus Iconella are necessary. Since the African diatom flora is rich with taxa from these genera, especially Iconella, and the authors have studied these taxa recently, describing also new taxa, a preliminary checklist of African Iconella and Surirella is here presented. 94 names are contained on this list. 57 taxa have been transferred to Iconella; 55 taxa were formerly ranked within Surirella and two taxa within Stenopterobia. 10 taxa have stayed within Surirella and six taxa have been transferred from Cymatopleura to Surirella. 20 Surirella and 1 Stenopterobia names are listed which are either unrevised or unrevisable since morphological data is missing. Four names and taxa described by Ehrenberg are here typified. Two had been transferred to Iconella already: Iconella bifrons (Ehrenb.) Ruck & Nakov and Iconella splendida (Ehrenb.) Ruck & Nakov. Two are re-transferred from Cymatopleura to Surirella: Surirella librile (Ehrenb.) Ehrenb. and Surirella undulata (Ehrenb.) Ehrenb.; both taxa are currently known by their younger synonyms: Cymatopleura solea (Bréb.) W. Smith and Cymatopleura elliptica (Bréb. ex Kützing) W. Smith. Lectotypes for Iconella bifrons, I. splendida, Surirella librile, and S. undulata were designated. PMID:28794683

  16. Data Acquisition System(DAS) Sustaining Engineering

    NASA Technical Reports Server (NTRS)

    1998-01-01

    This paper presents general information describing the Data Acquisition System contract, a summary of objectives, tasks performed and completed. The hardware deliverables which are comprised of: 1) Two ground DAS units; 2) Two flight DAS units; 3) Logistic spares; and 4) Shipping containers are described. Also included are the data requirements and scope of the contract.

  17. New records for Albania based on taxa from the Prespa National Park

    PubMed Central

    2013-01-01

    Abstract Twelve taxa are enumerated as new and three taxa confirmed for the flora of Albania. They were collected between 2007 and 2012 in the Prespa National Park of Albania which is part of the Prespa International Park, a biological protected area at the borders with F.Y.R. Macedonia and Greece. Four taxa, viz., Centaurea galicicae, Festuca galicicae, Laserpitium ochridanum and Micromeria cristata subsp. kosaninii are restricted to Dry and Galičica Mountains. Centaurea decora, a recently described species, is treated as a synonym of Centaurea soskae thus extending the known localities of the latter to the southeast. Detailed information on distribution, occurrence and habitats in Albania are provided for each taxon. PMID:24723753

  18. Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape

    PubMed Central

    Constancias, Florentin; Saby, Nicolas P A; Terrat, Sébastien; Dequiedt, Samuel; Horrigue, Wallid; Nowak, Virginie; Guillemin, Jean-Philippe; Biju-Duval, Luc; Chemidlin Prévost-Bouré, Nicolas; Ranjard, Lionel

    2015-01-01

    Even though recent studies have clarified the influence and hierarchy of environmental filters on bacterial community structure, those constraining bacterial populations variations remain unclear. In consequence, our ability to understand to ecological attributes of soil bacteria and to predict microbial community response to environmental stress is therefore limited. Here, we characterized the bacterial community composition and the various bacterial taxonomic groups constituting the community across an agricultural landscape of 12 km2, by using a 215 × 215 m systematic grid representing 278 sites to precisely decipher their spatial distribution and drivers at this scale. The bacterial and Archaeal community composition was characterized by applying 16S rRNA gene pyrosequencing directly to soil DNA from samples. Geostatistics tools were used to reveal the heterogeneous distribution of bacterial composition at this scale. Soil physical parameters and land management explained a significant amount of variation, suggesting that environmental selection is the major process shaping bacterial composition. All taxa systematically displayed also a heterogeneous and particular distribution patterns. Different relative influences of soil characteristics, land use and space were observed, depending on the taxa, implying that selection and spatial processes might be differentially but not exclusively involved for each bacterial phylum. Soil pH was a major factor determining the distribution of most of the bacterial taxa and especially the most important factor explaining the spatial patterns of α-Proteobacteria and Planctomycetes. Soil texture, organic carbon content and quality were more specific to a few number of taxa (e.g., β-Proteobacteria and Chlorobi). Land management also influenced the distribution of bacterial taxa across the landscape and revealed different type of response to cropping intensity (positive, negative, neutral or hump-backed relationships

  19. Benefits to poorly studied taxa of conservation of bird and mammal diversity on islands.

    PubMed

    Aslan, Clare; Holmes, Nick; Tershy, Bernie; Spatz, Dena; Croll, Donald A

    2015-02-01

    Protected area delineation and conservation action are urgently needed on marine islands, but the potential biodiversity benefits of these activities can be difficult to assess due to lack of species diversity information for lesser known taxa. We used linear mixed effects modeling and simple spatial analyses to investigate whether conservation activities based on the diversity of well-known insular taxa (birds and mammals) are likely to also capture the diversity of lesser known taxa (reptiles, amphibians, vascular land plants, ants, land snails, butterflies, and tenebrionid beetles). We assembled total, threatened, and endemic diversity data for both well-known and lesser known taxa and combined these with physical island biogeography characteristics for 1190 islands from 109 archipelagos. Among physical island biogeography factors, island area was the best indicator of diversity of both well-known and little-known taxa. Among taxonomic factors, total mammal species richness was the best indicator of total diversity of lesser known taxa, and the combination of threatened mammal and threatened bird diversity was the best indicator of lesser known endemic richness. The results of other intertaxon diversity comparisons were highly variable, however. Based on our results, we suggest that protecting islands above a certain minimum threshold area may be the most efficient use of conservation resources. For example, using our island database, if the threshold were set at 10 km(2) and the smallest 10% of islands greater than this threshold were protected, 119 islands would be protected. The islands would range in size from 10 to 29 km(2) and would include 268 lesser known species endemic to a single island, along with 11 bird and mammal species endemic to a single island. Our results suggest that for islands of equivalent size, prioritization based on total or threatened bird and mammal diversity may also capture opportunities to protect lesser known species endemic to

  20. Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities

    PubMed Central

    van der Gast, Christopher J; Walker, Alan W; Stressmann, Franziska A; Rogers, Geraint B; Scott, Paul; Daniels, Thomas W; Carroll, Mary P; Parkhill, Julian; Bruce, Kenneth D

    2011-01-01

    Cystic fibrosis (CF) patients suffer from chronic bacterial lung infections that lead to death in the majority of cases. The need to maintain lung function in these patients means that characterising these infections is vital. Increasingly, culture-independent analyses are expanding the number of bacterial species associated with CF respiratory samples; however, the potential significance of these species is not known. Here, we applied ecological statistical tools to such culture-independent data, in a novel manner, to partition taxa within the metacommunity into core and satellite species. Sputa and clinical data were obtained from 14 clinically stable adult CF patients. Fourteen rRNA gene libraries were constructed with 35 genera and 82 taxa, identified in 2139 bacterial clones. Shannon–Wiener and taxa-richness analyses confirmed no undersampling of bacterial diversity. By decomposing the distribution using the ratio of variance to the mean taxon abundance, we partitioned objectively the species abundance distribution into core and satellite species. The satellite group comprised 67 bacterial taxa from 33 genera and the core group, 15 taxa from 7 genera (including Pseudomonas (1 taxon), Streptococcus (2), Neisseria (2), Catonella (1), Porphyromonas (1), Prevotella (5) and Veillonella (3)], the last four being anaerobes). The core group was dominated by Pseudomonas aeruginosa. Other recognised CF pathogens were rare. Mantel and partial Mantel tests assessed which clinical factors influenced the composition observed. CF transmembrane conductance regulator genotype and antibiotic treatment correlated with all core taxa. Lung function correlated with richness. The clinical significance of these core and satellite species findings in the CF lung is discussed. PMID:21151003

  1. Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities.

    PubMed

    van der Gast, Christopher J; Walker, Alan W; Stressmann, Franziska A; Rogers, Geraint B; Scott, Paul; Daniels, Thomas W; Carroll, Mary P; Parkhill, Julian; Bruce, Kenneth D

    2011-05-01

    Cystic fibrosis (CF) patients suffer from chronic bacterial lung infections that lead to death in the majority of cases. The need to maintain lung function in these patients means that characterising these infections is vital. Increasingly, culture-independent analyses are expanding the number of bacterial species associated with CF respiratory samples; however, the potential significance of these species is not known. Here, we applied ecological statistical tools to such culture-independent data, in a novel manner, to partition taxa within the metacommunity into core and satellite species. Sputa and clinical data were obtained from 14 clinically stable adult CF patients. Fourteen rRNA gene libraries were constructed with 35 genera and 82 taxa, identified in 2139 bacterial clones. Shannon-Wiener and taxa-richness analyses confirmed no undersampling of bacterial diversity. By decomposing the distribution using the ratio of variance to the mean taxon abundance, we partitioned objectively the species abundance distribution into core and satellite species. The satellite group comprised 67 bacterial taxa from 33 genera and the core group, 15 taxa from 7 genera (including Pseudomonas (1 taxon), Streptococcus (2), Neisseria (2), Catonella (1), Porphyromonas (1), Prevotella (5) and Veillonella (3)], the last four being anaerobes). The core group was dominated by Pseudomonas aeruginosa. Other recognised CF pathogens were rare. Mantel and partial Mantel tests assessed which clinical factors influenced the composition observed. CF transmembrane conductance regulator genotype and antibiotic treatment correlated with all core taxa. Lung function correlated with richness. The clinical significance of these core and satellite species findings in the CF lung is discussed. GenBank accession numbers: FM995625–FM997761

  2. Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape.

    PubMed

    Constancias, Florentin; Saby, Nicolas P A; Terrat, Sébastien; Dequiedt, Samuel; Horrigue, Wallid; Nowak, Virginie; Guillemin, Jean-Philippe; Biju-Duval, Luc; Chemidlin Prévost-Bouré, Nicolas; Ranjard, Lionel

    2015-06-01

    Even though recent studies have clarified the influence and hierarchy of environmental filters on bacterial community structure, those constraining bacterial populations variations remain unclear. In consequence, our ability to understand to ecological attributes of soil bacteria and to predict microbial community response to environmental stress is therefore limited. Here, we characterized the bacterial community composition and the various bacterial taxonomic groups constituting the community across an agricultural landscape of 12 km(2) , by using a 215 × 215 m systematic grid representing 278 sites to precisely decipher their spatial distribution and drivers at this scale. The bacterial and Archaeal community composition was characterized by applying 16S rRNA gene pyrosequencing directly to soil DNA from samples. Geostatistics tools were used to reveal the heterogeneous distribution of bacterial composition at this scale. Soil physical parameters and land management explained a significant amount of variation, suggesting that environmental selection is the major process shaping bacterial composition. All taxa systematically displayed also a heterogeneous and particular distribution patterns. Different relative influences of soil characteristics, land use and space were observed, depending on the taxa, implying that selection and spatial processes might be differentially but not exclusively involved for each bacterial phylum. Soil pH was a major factor determining the distribution of most of the bacterial taxa and especially the most important factor explaining the spatial patterns of α-Proteobacteria and Planctomycetes. Soil texture, organic carbon content and quality were more specific to a few number of taxa (e.g., β-Proteobacteria and Chlorobi). Land management also influenced the distribution of bacterial taxa across the landscape and revealed different type of response to cropping intensity (positive, negative, neutral or hump-backed relationships

  3. Short-Term Protein Stable Isotope Probing of Microbial Communities to Associate Functions with Taxa (Invited)

    NASA Astrophysics Data System (ADS)

    Lipton, M. S.; Slysz, G. W.; Steinke, L. A.; Ward, D. M.; Klatt, C. G.; Clauss, T. R.; Purvine, S. O.; Anderson, G. A.; Payne, S. H.; Bryant, D. A.

    2013-12-01

    Determining which taxa in a community perform which functions is essential for understanding metabolite fluxes and metabolic interactions among community members. Specific taxa will alter their metabolism in order to acclimate to changing environmental factors such as light through the diel cycle, changing temperature and other factors. Monitoring which proteins are being expressed, and the quantitative protein expression patterns in the individual taxa as a response to external stimuli is key to understanding these mechanisms. Protein stable isotope probing (Pro-SIP) has strong potential for revealing key metabolizing taxa in complex microbial communities. In Pro-SIP studies, label incorporation is determined by the extent of the change in the isotopic profile of peptides when measured by mass spectrometry. While most Pro-SIP work to date has been performed under controlled laboratory conditions to allow extensive isotope labeling of the target organism(s), these techniques have not been applied to short term in situ studies due to the small degree of partial labeling of the proteins. We have applied Pro-SIP to study the assimilation of a labeled substrate into proteins to determine which taxa are responsible for sequestration of dissolved inorganic carbon in microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park. This community is fueled by sunlight as it transitions from dark to light; the aim was to understand the light-dependent pathway of inorganic carbon incorporation into different taxa during the early morning hours when the mat was in low light and anoxic. Each mat sample was incubated with 13C-bicarbonate for 3 h. Substrate assimilation was determined through standard proteomic techniques along with the use of SIPPER, a collection of algorithms that sensitively measure small changes in peptide isotopic patterns, allowing the determination of which taxa assimilated the substrate during this period. For the

  4. Morpho-colorimetric characterisation of Malva alliance taxa by seed image analysis.

    PubMed

    Lo Bianco, M; Grillo, O; Escobar Garcia, P; Mascia, F; Venora, G; Bacchetta, G

    2017-01-01

    Seed morphometric and -colorimetric features describing shape, size and textural seed traits of 28 taxa belonging to the genera Lavatera L. and Malva L., were recorded by means of computer vision techniques. The data were statistically analysed to contribute to the taxonomical treatment of the Malva alliance and to assess some doubtful systematic positions. A clear differentiation between taxa traditionally attributed to Lavatera or Malva was highlighted. Furthermore, the identification system proposed here was able to discriminate among the Lavatera sections, confirming the taxonomic organization of this genus. The results obtained for Malva, both at the species level and among sections, supported this analytical tool as diagnostic for systematic purposes.

  5. Dominant plant taxa predict plant productivity responses to CO2 enrichment across precipitation and soil gradients

    USDA-ARS?s Scientific Manuscript database

    The responses of water-limited ecosystems to rising atmospheric CO2 concentration (eCO2) depend on the supply and availability of soil moisture and on change in abundance of dominant plant taxa. Soil moisture supply and availability depends primarily on precipitation amount and soil texture. Respo...

  6. Gene Flow Among Different Teosinte Taxa and Into the Domesticated Maize Gene Pool

    USDA-ARS?s Scientific Manuscript database

    Maize (Zea mays ssp. mays) was domesticated from one wild species ancestor, the Balsas teosinte (Zea mays ssp. parviglumis) about 9000 years ago. Higher levels of gene diversity are found in teosinte taxa compared to maize following domestication and selection bottlenecks. Diversity in maize can b...

  7. Signals of speciation: Volatile organic compounds resolve closely related sagebrush taxa, suggesting their importance in evolution

    Treesearch

    Deidre M. Jaeger; Justin B. Runyon; Bryce A. Richardson

    2016-01-01

    Volatile organic compounds (VOCs) play important roles in the environmental adaptation and fitness of plants. Comparison of the qualitative and quantitative differences in VOCs among closely related taxa and assessing the effects of environment on their emissions are important steps to deducing VOC function and evolutionary importance.

  8. Covariance in species diversity and facilitation among non-interactive parasite taxa: all against the host.

    PubMed

    Krasnov, B R; Mouillot, D; Khokhlova, I S; Shenbrot, G I; Poulin, R

    2005-10-01

    Different parasite taxa exploit different host resources and are often unlikely to interact directly. It is unclear, however, whether the diversity of any given parasite taxon is indirectly influenced by that of other parasite taxa on the same host. Some components of host immune defences may operate simultaneously against all kinds of parasites, whereas investment by the host in specific defences against one type of parasite may come at the expense of defence against other parasites. We investigated the relationships between the species diversity of 4 higher taxa of ectoparasites (fleas, sucking lice, mesostigmatid mites, and ixodid ticks), and between the species richness of ectoparasites and endoparasitic helminths, across different species of rodent hosts. Our analyses used 2 measures of species diversity, species richness and taxonomic distinctness, and controlled for the potentially confounding effects of sampling effort and phylogenetic relationships among host species. We found positive pairwise correlations between the species richness of fleas, mites and ticks; however, there was no association between species richness of any of these 3 groups and that of lice. We also found a strong positive relationship between the taxonomic distinctness of ecto- and endoparasite assemblages across host species. These results suggest the existence of a process of apparent facilitation among unrelated taxa in the organization of parasite communities. We propose explanations based on host immune responses, involving acquired cross-resistance to infection and interspecific variation in immunocompetence among hosts, to account for these patterns.

  9. Preliminary assessment of biogeographic affinities of selected insect taxa of the state of Sonora, Mexico

    Treesearch

    Robert W. Jones; Alejandro Obregon-Zuniga; Sandra Guzman-Rodriguez

    2013-01-01

    The biogeographic affinites of butterflies (Lepidoptera: Papilionoidea and Hesperidae), damsel and dragonflies (Odonata), and ants (Hymenoptera: Formicidae) reported from the State of Sonora, Mexico were analyzed using published species lists. The combined distribution of these taxa was proportionally greater (47.4%) for those species within the Mega-Mexico3...

  10. Bacterial taxa-area and distance-decay relationships in marine environments.

    PubMed

    Zinger, L; Boetius, A; Ramette, A

    2014-02-01

    The taxa-area relationship (TAR) and the distance-decay relationship (DDR) both describe spatial turnover of taxa and are central patterns of biodiversity. Here, we compared TAR and DDR of bacterial communities across different marine realms and ecosystems at the global scale. To obtain reliable global estimates for both relationships, we quantified the poorly assessed effects of sequencing depth, rare taxa removal and number of sampling sites. Slope coefficients of bacterial TARs were within the range of those of plants and animals, whereas slope coefficients of bacterial DDR were much lower. Slope coefficients were mostly affected by removing rare taxa and by the number of sampling sites considered in the calculations. TAR and DDR slope coefficients were overestimated at sequencing depth <4000 sequences per sample. Noticeably, bacterial TAR and DDR patterns did not correlate with each other both within and across ecosystem types, suggesting that (i) TAR cannot be directly derived from DDR and (ii) TAR and DDR may be influenced by different ecological factors. Nevertheless, we found marine bacterial TAR and DDR to be steeper in ecosystems associated with high environmental heterogeneity or spatial isolation, namely marine sediments and coastal environments compared with pelagic ecosystems. Hence, our study provides information on macroecological patterns of marine bacteria, as well as methodological and conceptual insights, at a time when biodiversity surveys increasingly make use of high-throughput sequencing technologies.

  11. Twelve invasive plant taxa in U.S. western riparian ecosystems

    EPA Science Inventory

    Assessments of stream ecosystems often include an evaluation of riparian condition; a key stressor in riparian ecosystems is the presence of invasive plants. We analyzed the distribution of 12 invasive taxa (common burdock [Arctium minus], giant reed [Arundo donax], cheatgrass [B...

  12. [Conditionally neutral phylogenetic markers of major taxa: a new aspect of the evolution of macromolecules].

    PubMed

    Petrov, N B; Aleshin, V V

    2002-08-01

    The current phase of molecular phylogenetics can be named the 18S rRNA gene era, which is now approaching the end. To date, almost all phyla of metazoans and many taxa of protists are represented in databases of 18S rRNA gene sequences. The elements of the phylogenetic tree of Metazoa inferred from 18S rRNA genes are characterized by unequal validity: some of them seem to be well grounded; others are not adequately supported, and probably will be revised later. The validity of phylogenetic reconstruction is influenced by two main factors: (1) erroneous grouping of long branches that occur because of abnormally high evolution rate; (2) deficit of phylogenetically informative characters. A method for overcoming these difficulties is suggested in addition to known tools: using phylogenetic markers that are stable within individual taxa and evolve by punctuated equilibrium. These markers are least influenced by the convergence caused by a high evolution rate of the entire gene. The nature of these markers of ancient taxa, paradoxical from the perspective of neutral evolution, is discussed, as well as their importance for establishing monophyly of both new large-scale taxonomic groups of invertebrates (Bilateria + Rhombozoa + Orthonectida + Myxozoa + Cnidaria + Placozoa and Echinodermata + Hemichordata) and some major taxa of Nematoda.

  13. New records of truffle taxa in Tuber and Terfezia from Turkey

    Treesearch

    Michael Angelo Castellano; Aziz. Turkoglu

    2012-01-01

    Turkey has one of the richest floras in the northern hemisphere as it is located at the convergence of 3 phytogeographical regions: Euro-Siberian, Mediterranean, and Irano-Turanian. This is reflected in the high number of plant taxa, particularly plant families that have truffles associated with them. The forests of these regions are dominated by ectomycorrhizal...

  14. Twelve invasive plant taxa in U.S. western riparian ecosystems

    EPA Science Inventory

    Assessments of stream ecosystems often include an evaluation of riparian condition; a key stressor in riparian ecosystems is the presence of invasive plants. We analyzed the distribution of 12 invasive taxa (common burdock [Arctium minus], giant reed [Arundo donax], cheatgrass [B...

  15. Anaerobic trophic interactions of contrasting methane-emitting mire soils: processes versus taxa.

    PubMed

    Hunger, Sindy; Gößner, Anita S; Drake, Harold L

    2015-05-01

    Natural wetlands such as mires contribute up to 33% to the global emission of methane. The emission of methane is driven by trophic interactions of anaerobes that collectively degrade biopolymers. The hypothesis of this study was that these interactions in contrasting methane-emitting mire soils are functionally similar but linked to dissimilar taxa. This hypothesis was addressed by evaluating anaerobic processes and microbial taxa of eutrophic, mesotrophic and oligotrophic mire soils. Glucose was fermented to various products (e.g. H2, CO2, butyrate, acetate). Acetoclastic methanogenesis occurred, and acetogenesis and methanogenesis transformed H2-CO2 to acetate and methane, respectively. Although product profiles, cultivable cell numbers and gene copy numbers [mcrA (encodes alpha-subunit of methyl-CoM reductase) and 16S rRNA genes] were similar for all mire soils, only approximately 15% of detected family-level bacteria and species-level methanogens were shared by all mire soils. Approximately, 40% of the detected family-level taxa of each mire soil have no cultured isolates. Acidic conditions appeared to restrict the number of dominant phylotypes. The results indicated (a) that microbial processes which drive methanogenesis are similar but facilitated by dissimilar microbial communities in contrasting mire soils and (b) that mire soils harbor a large number of taxa with no cultured isolates.

  16. Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams.

    PubMed

    Wilhelm, Linda; Besemer, Katharina; Fasching, Christina; Urich, Tim; Singer, Gabriel A; Quince, Christopher; Battin, Tom J

    2014-08-01

    Glaciers harbour diverse microorganisms, which upon ice melt can be released downstream. In glacier-fed streams microorganisms can attach to stones or sediments to form benthic biofilms. We used 454-pyrosequencing to explore the bulk (16S rDNA) and putatively active (16S rRNA) microbial communities of stone and sediment biofilms across 26 glacier-fed streams. We found differences in community composition between bulk and active communities among streams and a stronger congruence between biofilm types. Relative abundances of rRNA and rDNA were positively correlated across different taxa and taxonomic levels, but at lower taxonomic levels, the higher abundance in either the active or the bulk communities became more apparent. Here, environmental variables played a minor role in structuring active communities. However, we found a large number of rare taxa with higher relative abundances in rRNA compared with rDNA. This suggests that rare taxa contribute disproportionately to microbial community dynamics in glacier-fed streams. Our findings propose that high community turnover, where taxa repeatedly enter and leave the 'seed bank', contributes to the maintenance of microbial biodiversity in harsh ecosystems with continuous environmental perturbations, such as glacier-fed streams. © 2014 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  17. Quaternary disappearance of tree taxa from Southern Europe: Timing and trends

    NASA Astrophysics Data System (ADS)

    Magri, Donatella; Di Rita, Federico; Aranbarri, Josu; Fletcher, William; González-Sampériz, Penélope

    2017-05-01

    A hundred pollen and plant macrofossil records from the Iberian Peninsula, Southern France, the Italian Peninsula, Greece and the Aegean, and the southwestern Black Sea area formed the basis for a review of the Quaternary distribution and extirpation of tree populations from Southern Europe. Following a discussion of the caveats/challenges about using pollen data, the Quaternary history of tree taxa has been reconstructed with attention to Taxodium/Glyptostrobus, Sciadopitys, Cathaya, Cedrus, Tsuga, Eucommia, Engelhardia, Carya, Pterocarya, Parrotia, Liquidambar, and Zelkova. The timing of extinction, distributed over the whole Quaternary, appears very diverse from one region to the other, in agreement with current biodiversity in Southern Europe. The geographical patterns of persistence/disappearance of taxa show unexpected trends and rule out a simple North to South and/or West to East trend in extirpations. In particular, it is possible to detect disjunct populations (Engelhardia), long-term persistence of taxa in restricted regions (Sciadopitys), distinct populations/species/genera in different geographical areas (Taxodium type). Some taxa that are still widespread in Europe have undergone extirpation in Mediterranean areas in the lateglacial period and Holocene (Buxus, Carpinus betulus, Picea); they provide an indication of the modes of disappearance of tree populations that may be useful to evaluate correctly the vulnerability of modern fragmented plant populations. The demographic histories of tree taxa obtained by combined palaeobotanical and genetic studies is a most challenging field of research needed not only to assess species/population differentiation, but also to reach a better understanding of extinction processes, an essential task in the current global change scenario.

  18. Trait-based diversification shifts reflect differential extinction among fossil taxa.

    PubMed

    Wagner, Peter J; Estabrook, George F

    2014-11-18

    Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models.

  19. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance

    SciTech Connect

    Goldfarb, K.C.; Karaoz, U.; Hanson, C.A.; Santee, C.A.; Bradford, M.A.; Treseder, K.K.; Wallenstein, M.D.; Brodie, E.L.

    2011-04-18

    Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.

  20. Climate sensitivity of allergenic taxa in Central Europe associated with new climate change related forces.

    PubMed

    Deák, Aron József; Makra, László; Matyasovszky, István; Csépe, Zoltán; Muladi, Beáta

    2013-01-01

    The aim of the study was to analyse trends of the pollen season with its duration, start and end dates, as well as trends of the annual total pollen count and annual peak pollen concentration for the Szeged agglomeration in Southern Hungary. The data set covered an 11-year period (1997-2007) that included eight taxa and seven daily climate variables. Trend analysis was performed on both annual and daily bases. Trend analysis on a daily basis is a new approach that provides information on the annual cycles of the trends. To quantify the strength of the relationship between the annual cycle of the slope of a pollen concentration trend and the annual cycles of the slopes of the climate variable trends, an association measure and a multiple association measure are introduced. Individual taxa were sorted into three categories according to their climate sensitivities. These were compared with two novel climate change-related forces, namely risk potential and expansion potential due to the climate change. The total annual pollen counts indicated significant trends for 4 taxa and 3 of these 4 trends increased on a daily basis. At the same time, significant changes were detected for the pollen season characteristics of three taxa. The association measures performed well when compared to the climate change-related forces. Significant changes in pollen season characteristics were also in accordance with the risk potential and expansion potential due to the climate change. A novel procedure was applied to separate the effects of the past and current weather conditions that influence the current Ambrosia pollen concentrations. The potential effect of land use changes on pollen release of the given taxa was also discussed using the CORINE Land Cover Database.

  1. Trait-based diversification shifts reflect differential extinction among fossil taxa

    NASA Astrophysics Data System (ADS)

    Wagner, Peter J.; Estabrook, George F.

    2014-11-01

    Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models.

  2. Floral traits driving reproductive isolation of two co-flowering taxa that share vertebrate pollinators

    PubMed Central

    Queiroz, Joel A.; Quirino, Zelma G. M.; Machado, Isabel C.

    2015-01-01

    Floral attributes evolve in response to frequent and efficient pollinators, which are potentially important drivers of floral diversification and reproductive isolation. In this context, we asked, how do flowers evolve in a bat–hummingbird pollination system? Hence, we investigated the pollination ecology of two co-flowering Ipomoea taxa (I. marcellia and I. aff. marcellia) pollinated by bats and hummingbirds, and factors favouring reproductive isolation and pollinator sharing in these plants. To identify the most important drivers of reproductive isolation, we compared the flowers of the two Ipomoea taxa in terms of morphometry, anthesis and nectar production. Pollinator services were assessed using frequency of visits, fruit set and the number of seeds per fruit after visits. The studied Ipomoea taxa differed in corolla size and width, beginning and duration of anthesis, and nectar attributes. However, they shared the same diurnal and nocturnal visitors. The hummingbird Heliomaster squamosus was more frequent in I. marcellia (1.90 visits h−1) than in I. aff. marcellia (0.57 visits h−1), whereas glossophagine bats showed similar visit rates in both taxa (I. marcellia: 0.57 visits h−1 and I. aff. marcellia: 0.64 visits h−1). Bat pollination was more efficient in I. aff. marcellia, whereas pollination by hummingbirds was more efficient in I. marcellia. Differences in floral attributes between Ipomoea taxa, especially related to the anthesis period, length of floral parts and floral arrangement in the inflorescence, favour reproductive isolation from congeners through differential pollen placement on pollinators. This bat–hummingbird pollination system seems to be advantageous in the study area, where the availability of pollinators and floral resources changes considerably throughout the year, mainly as a result of rainfall seasonality. This interaction is beneficial for both sides, as it maximizes the number of potential pollen vectors for plants and

  3. Frankia populations in soil and root nodules of sympatrically grown Alnus taxa.

    PubMed

    Pokharel, Anita; Mirza, Babur S; Dawson, Jeffrey O; Hahn, Dittmar

    2011-01-01

    The genetic diversity of Frankia populations in soil and in root nodules of sympatrically grown Alnus taxa was evaluated by rep-polymerase chain reaction (PCR) and nifH gene sequence analyses. Rep-PCR analyses of uncultured Frankia populations in root nodules of 12 Alnus taxa (n=10 nodules each) growing sympatrically in the Morton Arboretum near Chicago revealed identical patterns for nodules from each Alnus taxon, including replicate trees of the same host taxon, and low diversity overall with only three profiles retrieved. One profile was retrieved from all nodules of nine taxa (Alnus incana subsp. incana, Alnus japonica, Alnus glutinosa, Alnus incana subsp. tenuifolia, Alnus incana subsp. rugosa, Alnus rhombifolia, Alnus mandshurica, Alnus maritima, and Alnus serrulata), the second was found in all nodules of two plant taxa (A. incana subsp. hirsuta and A. glutinosa var. pyramidalis), and the third was unique for all Frankia populations in nodules of A. incana subsp. rugosa var. americana. Comparative sequence analyses of nifH gene fragments in nodules representing these three profiles assigned these frankiae to different subgroups within the Alnus host infection group. None of these sequences, however, represented frankiae detectable in soil as determined by sequence analysis of 73 clones from a Frankia-specific nifH gene clone library. Additional analyses of nodule populations from selected alders growing on different soils demonstrated the presence of different Frankia populations in nodules for each soil, with populations showing identical sequences in nodules from the same soil, but differences between plant taxa. These results suggest that soil environmental conditions and host plant genotype both have a role in the selection of Frankia strains by a host plant for root nodule formation, and that this selection is not merely a function of the abundance of a Frankia strain in soil.

  4. Trait-based diversification shifts reflect differential extinction among fossil taxa

    PubMed Central

    Wagner, Peter J.; Estabrook, George F.

    2014-01-01

    Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models. PMID:25331898

  5. Comparative ITS and AFLP Analysis of Diploid Cardamine (Brassicaceae) Taxa from Closely Related Polyploid Complexes

    PubMed Central

    MARHOLD, KAROL; LIHOVÁ, JUDITA; PERNÝ, MARIÁN; BLEEKER, WALTER

    2004-01-01

    • Background and Aims Diploid representatives from the related polyploid complexes of Cardamine amara, C. pratensis and C. raphanifolia (Brassicaceae), were studied to elucidate phylogenetic relationships among the complexes and among the individual taxa included. • Methods Two independent molecular data sets were used: nucleotide sequences from the internal transcribed spacers (ITS) of nrDNA, and amplified fragment length polymorphism (AFLP) markers. Seventeen diploid taxa from the studied groups were sampled. • Key Results Both ITS and AFLP analyses provided congruent results in inferred relationships, and revealed two main lineages. While the C. amara group, consisting of C. wiedemanniana and four subspecies of C. amara, was resolved as a well‐supported monophyletic group, taxa from the C. pratensis and C. tenera groups (the latter representing diploid taxa of the complex of C. raphanifolia) all appeared together in a single clade/cluster with no support for the recognition of either of the groups. Intra‐individual polymorphisms and patterns of nucleotide variation in the ITS region in C. uliginosa and C. tenera, together with the distribution of AFLP bands, indicate ancient hybridization and introgression among these Caucasian diploids. • Conclusions The lack of supported hierarchical structure suggests that extensive reticulate evolution between these groups, even at the diploid level, has occurred (although an alternative explanation, namely ancestral polymorphism in ITS data, cannot be completely excluded). Several implications for the investigation of the polyploid complexes of concern are drawn. When tracing origins of polyploid taxa, a much more complex scenario should be expected, taking into account all relatives as potential parents, irrespective of the group in which they are classified. PMID:15037449

  6. Floral traits driving reproductive isolation of two co-flowering taxa that share vertebrate pollinators.

    PubMed

    Queiroz, Joel A; Quirino, Zelma G M; Machado, Isabel C

    2015-11-10

    Floral attributes evolve in response to frequent and efficient pollinators, which are potentially important drivers of floral diversification and reproductive isolation. In this context, we asked, how do flowers evolve in a bat-hummingbird pollination system? Hence, we investigated the pollination ecology of two co-flowering Ipomoea taxa (I. marcellia and I. aff. marcellia) pollinated by bats and hummingbirds, and factors favouring reproductive isolation and pollinator sharing in these plants. To identify the most important drivers of reproductive isolation, we compared the flowers of the two Ipomoea taxa in terms of morphometry, anthesis and nectar production. Pollinator services were assessed using frequency of visits, fruit set and the number of seeds per fruit after visits. The studied Ipomoea taxa differed in corolla size and width, beginning and duration of anthesis, and nectar attributes. However, they shared the same diurnal and nocturnal visitors. The hummingbird Heliomaster squamosus was more frequent in I. marcellia (1.90 visits h(-1)) than in I. aff. marcellia (0.57 visits h(-1)), whereas glossophagine bats showed similar visit rates in both taxa (I. marcellia: 0.57 visits h(-1) and I. aff. marcellia: 0.64 visits h(-1)). Bat pollination was more efficient in I. aff. marcellia, whereas pollination by hummingbirds was more efficient in I. marcellia. Differences in floral attributes between Ipomoea taxa, especially related to the anthesis period, length of floral parts and floral arrangement in the inflorescence, favour reproductive isolation from congeners through differential pollen placement on pollinators. This bat-hummingbird pollination system seems to be advantageous in the study area, where the availability of pollinators and floral resources changes considerably throughout the year, mainly as a result of rainfall seasonality. This interaction is beneficial for both sides, as it maximizes the number of potential pollen vectors for plants and

  7. DAS28-CRP and DAS28-ESR cut-offs for high disease activity in rheumatoid arthritis are not interchangeable

    PubMed Central

    Fleischmann, Roy M; van der Heijde, Désirée; Gardiner, Philip V; Szumski, Annette; Marshall, Lisa; Bananis, Eustratios

    2017-01-01

    Background In most patients with rheumatoid arthritis (RA), Disease Activity Score 28-joint count C reactive protein (DAS28-CRP) is lower than DAS28 erythrocyte sedimentation rate (DAS28-ESR), suggesting that use of the DAS28-ESR cut-off to assess high disease activity (HDA) with DAS28-CRP may underestimate the number of patients with HDA. We determined the DAS28-CRP value corresponding to the validated DAS28-ESR cut-off for HDA. Methods Baseline data were pooled from 2 clinical studies evaluating etanercept (ETN) plus methotrexate (MTX) or MTX in early RA; DAS28-CRP and DAS28-ESR were obtained, allowing the determination of the DAS28-CRP HDA value best corresponding to the DAS28-ESR cut-off of >5.1. Results At baseline, as expected, fewer patients had HDA by DAS28-CRP than DAS28-ESR; DAS28-CRP>5.1 and DAS28-ESR>5.1 had only modest agreement (κ coefficients 0.45–0.54). Mean DAS28-CRP and DAS28-ESR were 5.7 and 6.2, respectively, in the ETN+MTX group (n=571), and 6.0 and 6.5 in the MTX group (n=262). A DAS28-CRP cut-off of 4.6 corresponded to a DAS28-ESR cut-off of 5.1. Conclusions We have shown that a DAS28-CRP of 4.6 corresponds to 5.1 for DAS28-ESR. Since this is substantially lower than the DAS28-ESR cut-off of 5.1, using 5.1 as the cut-off for DAS28-CRP underestimates disease activity in RA. Trial registration number NCT00195494; NCT00913458. PMID:28255449

  8. Estimating vertebrate, benthic macroinvertebrate, and diatom taxa richness in raftable Pacific Northwest rivers for bioassessment purposes.

    PubMed

    Hughes, Robert M; Herlihy, Alan T; Gerth, William J; Pan, Yangdong

    2012-05-01

    The number of sites sampled must be considered when determining the effort necessary for adequately assessing taxa richness in an ecosystem for bioassessment purposes; however, there have been few studies concerning the number of sites necessary for bioassessment of large rivers. We evaluated the effect of sample size (i.e., number of sites) necessary to collect vertebrate (fish and aquatic amphibians), macroinvertebrate, and diatom taxa from seven large rivers in Oregon and Washington, USA during the summers of 2006-2008. We used Monte Carlo simulation to determine the number of sites needed to collect 90-95% of the taxa 75-95% of the time from 20 randomly located sites on each river. The river wetted widths varied from 27.8 to 126.0 m, mean substrate size varied from 1 to 10 cm, and mainstem distances sampled varied from 87 to 254 km. We sampled vertebrates at each site (i.e., 50 times the mean wetted channel width) by nearshore-raft electrofishing. We sampled benthic macroinvertebrates nearshore through the use of a 500-μm mesh kick net at 11 systematic stations. From each site composite sample, we identified a target of 500 macroinvertebrate individuals to the lowest possible taxon, usually genus. We sampled benthic diatoms nearshore at the same 11 stations from a 12-cm(2) area. At each station, we sucked diatoms from soft substrate into a 60-ml syringe or brushed them off a rock and rinsed them with river water into the same jar. We counted a minimum of 600 valves at 1,000× magnification for each site. We collected 120-211 diatom taxa, 98-128 macroinvertebrate taxa, and 14-33 vertebrate species per river. To collect 90-95% of the taxa 75-95% of the time that were collected at 20 sites, it was necessary to sample 11-16 randomly distributed sites for vertebrates, 13-17 sites for macroinvertebrates, and 16-18 sites for diatoms. We conclude that 12-16 randomly distributed sites are needed for cost-efficient sampling of vertebrate richness in the main stems of

  9. Ambiguous taxa: Effects on the characterization and interpretation of invertebrate assemblages

    USGS Publications Warehouse

    Cuffney, T.F.; Bilger, M.D.; Haigler, A.M.

    2007-01-01

    Damaged and immature specimens often result in macroinvertebrate data that contain ambiguous parent-child pairs (i.e., abundances associated with multiple related levels of the taxonomic hierarchy such as Baetis pluto and the associated ambiguous parent Baetis sp.). The choice of method used to resolve ambiguous parent-child pairs may have a very large effect on the characterization of invertebrate assemblages and the interpretation of responses to environmental change because very large proportions of taxa richness (73-78%) and abundance (79-91%) can be associated with ambiguous parents. To address this issue, we examined 16 variations of 4 basic methods for resolving ambiguous taxa: RPKC (remove parent, keep child), MCWP (merge child with parent), RPMC (remove parent or merge child with parent depending on their abundances), and DPAC (distribute parents among children). The choice of method strongly affected assemblage structure, assemblage characteristics (e.g., metrics), and the ability to detect responses along environmental (urbanization) gradients. All methods except MCWP produced acceptable results when used consistently within a study. However, the assemblage characteristics (e.g., values of assemblage metrics) differed widely depending on the method used, and data should not be combined unless the methods used to resolve ambiguous taxa are well documented and are known to be comparable. The suitability of the methods was evaluated and compared on the basis of 13 criteria that considered conservation of taxa richness and abundance, consistency among samples, methods, and studies, and effects on the interpretation of the data. Methods RPMC and DPAC had the highest suitability scores regardless of whether ambiguous taxa were resolved for each sample separately or for a group of samples. Method MCWP gave consistently poor results. Methods MCWP and DPAC approximate the use of family-level identifications and operational taxonomic units (OTU), respectively. Our

  10. Nicotiana Roots Recruit Rare Rhizosphere Taxa as Major Root-Inhabiting Microbes.

    PubMed

    Saleem, Muhammad; Law, Audrey D; Moe, Luke A

    2016-02-01

    Root-associated microbes have a profound impact on plant health, yet little is known about the distribution of root-associated microbes among different root morphologies or between rhizosphere and root environments. We explore these issues here with two commercial varieties of burley tobacco (Nicotiana tabacum) using 16S rRNA gene amplicon sequencing from rhizosphere soil, as well as from primary, secondary, and fine roots. While rhizosphere soils exhibited a fairly rich and even distribution, root samples were dominated by Proteobacteria. A comparison of abundant operational taxonomic units (OTUs) between rhizosphere and root samples indicated that Nicotiana roots select for rare taxa (predominantly Proteobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, and Acidobacteria) from their corresponding rhizosphere environments. The majority of root-inhabiting OTUs (~80 %) exhibited habitat generalism across the different root morphological habitats, although habitat specialists were noted. These results suggest a specific process whereby roots select rare taxa from a larger community.

  11. A nomenclator of extant and fossil taxa of the Melanopsidae (Gastropoda, Cerithioidea)

    PubMed Central

    Neubauer, Thomas A.

    2016-01-01

    Abstract This nomenclator provides details on all published names in the family-, genus-, and species-group, as well as for a few infrasubspecific names introduced for, or attributed to, the family Melanopsidae. It includes nomenclaturally valid names, as well as junior homonyms, junior objective synonyms, nomina nuda, common incorrect subsequent spellings, and as far as possible discussion on the current status in taxonomy. The catalogue encompasses three family-group names, 79 genus-group names, and 1381 species-group names. All of them are given in their original combination and spelling (except mandatory corrections requested by the Code), along with their original source. For each family- and genus-group name, the original classification and the type genus and type species, respectively, are given. Data provided for species-group taxa are type locality, type horizon (for fossil taxa), and type specimens, as far as available. PMID:27551193

  12. A nomenclator of extant and fossil taxa of the Melanopsidae (Gastropoda, Cerithioidea).

    PubMed

    Neubauer, Thomas A

    2016-01-01

    This nomenclator provides details on all published names in the family-, genus-, and species-group, as well as for a few infrasubspecific names introduced for, or attributed to, the family Melanopsidae. It includes nomenclaturally valid names, as well as junior homonyms, junior objective synonyms, nomina nuda, common incorrect subsequent spellings, and as far as possible discussion on the current status in taxonomy. The catalogue encompasses three family-group names, 79 genus-group names, and 1381 species-group names. All of them are given in their original combination and spelling (except mandatory corrections requested by the Code), along with their original source. For each family- and genus-group name, the original classification and the type genus and type species, respectively, are given. Data provided for species-group taxa are type locality, type horizon (for fossil taxa), and type specimens, as far as available.

  13. Synopsis of valid species-group taxa for freshwater Gastropoda recorded from the European Neogene

    PubMed Central

    Neubauer, Thomas A.; Kroh, Andreas; Harzhauser, Mathias; Georgopoulou, Elisavet; Mandic, Oleg

    2014-01-01

    Abstract Here we present a complete list of all valid species-group taxa of freshwater gastropods reported from Miocene and Pliocene deposits in Europe. The last comparable work dates back to the 1920s and covered about 1,600 names. The extensive literature research underlying the present work revealed considerable changes in the taxonomic and systematic frameworks of Neogene freshwater gastropods and yielded a total number of 2,156 accepted taxa. Each taxon is accompanied by a full citation of its first description; where the information is available, page number and illustration reference are provided. First descriptions available as open-access full-text sources on the web were linked via hyperlink to the first page of the publication. PMID:25152683

  14. Dominant plant taxa predict plant productivity responses to CO2 enrichment across precipitation and soil gradients

    DOE PAGES

    Fay, Philip A.; Newingham, Beth A.; Polley, H. Wayne; ...

    2015-03-30

    The Earth’s atmosphere will continue to be enriched with carbon dioxide (CO2) over the coming century. Carbon dioxide enrichment often reduces leaf transpiration, which in water-limited ecosystems may increase soil water content, change species abundances and increase the productivity of plant communities. The effect of increased soil water on community productivity and community change may be greater in ecosystems with lower precipitation, or on coarser-textured soils, but responses are likely absent in deserts. We tested correlations among yearly increases in soil water content, community change and community plant productivity responses to CO2 enrichment in experiments in a mesic grassland withmore » fine- to coarse-textured soils, a semi-arid grassland and a xeric shrubland. We found no correlation between CO2-caused changes in soil water content and changes in biomass of dominant plant taxa or total community aboveground biomass in either grassland type or on any soil in the mesic grassland (P > 0.60). Instead, increases in dominant taxa biomass explained up to 85% of the increases in total community biomass under CO2 enrichment. The effect of community change on community productivity was stronger in the semi-arid grassland than in the mesic grassland,where community biomass change on one soil was not correlated with the change in either the soil water content or the dominant taxa. No sustained increases in soil water content or community productivity and no change in dominant plant taxa occurred in the xeric shrubland. Thus, community change was a crucial driver of community productivity responses to CO2 enrichment in the grasslands, but effects of soil water change on productivity were not evident in yearly responses to CO2 enrichment. In conclusion, future research is necessary to isolate and clarify the mechanisms controlling the temporal and spatial variations in the linkages among soil water, community change and plant productivity responses to CO2

  15. A comparison of molecular markers and morphology for Neidium taxa (Bacillariophyta) from eastern North America.

    PubMed

    Lefebvre, Keely E; Hamilton, Paul B; Pick, Frances R

    2017-06-01

    Historically, a morphological species concept has applied shape subjectively in the delimitation of diatom species. This has led to confusion between taxa within the benthic diatom genus Neidium. Samples from Ontario, Quebec, Nova Scotia, Newfoundland (Canada) and New York (USA) were examined for Neidium taxa under LM and SEM. Fourier shape analysis showed that shape as a taxonomic character was not able to discern all species. Isolated individuals from the samples were amplified and sequenced for three chloroplast molecular markers (rbcL, psbC, and psbA) and one nuclear ribosomal molecular marker (18S). Phylogenetic reconstructions were completed with the concatenated chloroplast and 18S dataset using Maximum Likelihood and Bayesian analyses. The concatenated chloroplast dataset exhibited a species-level resolution phylogeny of Neidium taxa. The 18S dataset had a lower level of sequence divergence and was unable to differentiate between Neidium taxa. We present emended species descriptions and sequence data for four previously described species: Neidium sacoense, N. longiceps, N. fossum, and N. affine. We describe three novel species (Neidium lowei, N. promontorium, and N. potapovae) and identify two forms with unique molecular signatures. The distinguishing features of N. lowei are its size, valve shape, and longitudinal canal structure. Distinguishing features of N. promontorium are its valve shape, longitudinal canal and apex formation, and surface depression along the axial area. Neidium potapovae is distinguished by its size, formation of valve and apices and single longitudinal canal. This paper demonstrates how future phylogenetic treatments using single cell multigene sequencing can help resolve taxonomic confusion within diatoms. © 2017 Phycological Society of America.

  16. Crisis of Japanese Vascular Flora Shown By Quantifying Extinction Risks for 1618 Taxa

    PubMed Central

    Kadoya, Taku; Takenaka, Akio; Ishihama, Fumiko; Fujita, Taku; Ogawa, Makoto; Katsuyama, Teruo; Kadono, Yasuro; Kawakubo, Nobumitsu; Serizawa, Shunsuke; Takahashi, Hideki; Takamiya, Masayuki; Fujii, Shinji; Matsuda, Hiroyuki; Muneda, Kazuo; Yokota, Masatsugu; Yonekura, Koji; Yahara, Tetsukazu

    2014-01-01

    Although many people have expressed alarm that we are witnessing a mass extinction, few projections have been quantified, owing to limited availability of time-series data on threatened organisms, especially plants. To quantify the risk of extinction, we need to monitor changes in population size over time for as many species as possible. Here, we present the world's first quantitative projection of plant species loss at a national level, with stochastic simulations based on the results of population censuses of 1618 threatened plant taxa in 3574 map cells of ca. 100 km2. More than 500 lay botanists helped monitor those taxa in 1994–1995 and in 2003–2004. We projected that between 370 and 561 vascular plant taxa will go extinct in Japan during the next century if past trends of population decline continue. This extinction rate is approximately two to three times the global rate. Using time-series data, we show that existing national protected areas (PAs) covering ca. 7% of Japan will not adequately prevent population declines: even core PAs can protect at best <60% of local populations from decline. Thus, the Aichi Biodiversity Target to expand PAs to 17% of land (and inland water) areas, as committed to by many national governments, is not enough: only 29.2% of currently threatened species will become non-threatened under the assumption that probability of protection success by PAs is 0.5, which our assessment shows is realistic. In countries where volunteers can be organized to monitor threatened taxa, censuses using our method should be able to quantify how fast we are losing species and to assess how effective current conservation measures such as PAs are in preventing species extinction. PMID:24922311

  17. Lectotypification of names of Himalayan Brassicaceae taxa currently placed in the genus Cardamine.

    PubMed

    Marhold, Karol; Kempa, Matúš; Al-Shehbaz, Ihsan A

    2015-01-01

    Lectotypes of twenty-eight names of taxa currently recognized or synonymized in Cardamine are designated as part of the work on the account of the genus for the Pan-Himalayan Flora. Among them, the previous first-step lectotypification of the name Cardaminecalthifolia is finalized. In cases when specimen images are available online, stable identifiers for specimens, other permanent links, or links via JSTOR Global Plants are provided.

  18. Temporal consistency in background mortality of four dominant coral taxa along Australia's Great Barrier Reef

    NASA Astrophysics Data System (ADS)

    Pisapia, C.; Anderson, K. D.; Pratchett, M. S.

    2016-09-01

    Studies on the population and community dynamics of scleractinian corals typically focus on catastrophic mortality associated with acute disturbances (e.g., coral bleaching and outbreaks of crown-of-thorns starfish), though corals are subject to high levels of background mortality and injuries caused by routine and chronic processes. This study quantified prevalence (proportion of colonies with injuries) and severity (areal extent of injuries on individual colonies) of background mortality and injuries for four common coral taxa (massive Porites, encrusting Montipora, Acropora hyacinthus and branching Pocillopora) on the Great Barrier Reef, Australia. Sampling was conducted over three consecutive years during which there were no major acute disturbances. A total of 2276 adult colonies were surveyed across 27 sites, within nine reefs and three distinct latitudinal sectors. The prevalence of injuries was very high (>83%) across all four taxa, but highest for Porites (91%) and Montipora (85%). For these taxa ( Montipora and Pocillopora), there was also significant temporal and spatial variation in prevalence of partial mortality. The severity of injuries ranged from 3% to more than 80% and varied among coral taxa, but was fairly constant spatially and temporally. This shows that some injuries have considerable longevity and that corals may invest relatively little in regenerating tissue over sites of previous injuries. Inter-colony variation in the severity of injury also had no apparent effect on the realized growth of individual colonies, suggesting that energy diverted to regeneration has a limited bearing on overall energetic allocation, or impacts on other life-history processes (e.g., reproduction) rather than growth. Establishing background levels of injury and regeneration is important for understanding energy investment and life-history consequences for reef-building corals as well as for predicting susceptibility to, and capacity to recover from, acute

  19. Immunological change in a parasite-impoverished environment: divergent signals from four island taxa.

    PubMed

    Beadell, Jon S; Atkins, Colm; Cashion, Erin; Jonker, Michelle; Fleischer, Robert C

    2007-09-19

    Dramatic declines of native Hawaiian avifauna due to the human-mediated emergence of avian malaria and pox prompted an examination of whether island taxa share a common altered immunological signature, potentially driven by reduced genetic diversity and reduced exposure to parasites. We tested this hypothesis by characterizing parasite prevalence, genetic diversity and three measures of immune response in two recently-introduced species (Neochmia temporalis and Zosterops lateralis) and two island endemics (Acrocephalus aequinoctialis and A. rimitarae) and then comparing the results to those observed in closely-related mainland counterparts. The prevalence of blood parasites was significantly lower in 3 of 4 island taxa, due in part to the absence of certain parasite lineages represented in mainland populations. Indices of genetic diversity were unchanged in the island population of N. temporalis; however, allelic richness was significantly lower in the island population of Z. lateralis while both allelic richness and heterozygosity were significantly reduced in the two island-endemic species examined. Although parasite prevalence and genetic diversity generally conformed to expectations for an island system, we did not find evidence for a pattern of uniformly altered immune responses in island taxa, even amongst endemic taxa with the longest residence times. The island population of Z. lateralis exhibited a significantly reduced inflammatory cell-mediated response while levels of natural antibodies remained unchanged for this and the other recently introduced island taxon. In contrast, the island endemic A. rimitarae exhibited a significantly increased inflammatory response as well as higher levels of natural antibodies and complement. These measures were unchanged or lower in A. aequinoctialis. We suggest that small differences in the pathogenic landscape and the stochastic history of mutation and genetic drift are likely to be important in shaping the unique

  20. Bias and sensitivity in the placement of fossil taxa resulting from interpretations of missing data.

    PubMed

    Sansom, Robert S

    2015-03-01

    The utility of fossils in evolutionary contexts is dependent on their accurate placement in phylogenetic frameworks, yet intrinsic and widespread missing data make this problematic. The complex taphonomic processes occurring during fossilization can make it difficult to distinguish absence from non-preservation, especially in the case of exceptionally preserved soft-tissue fossils: is a particular morphological character (e.g., appendage, tentacle, or nerve) missing from a fossil because it was never there (phylogenetic absence), or just happened to not be preserved (taphonomic loss)? Missing data have not been tested in the context of interpretation of non-present anatomy nor in the context of directional shifts and biases in affinity. Here, complete taxa, both simulated and empirical, are subjected to data loss through the replacement of present entries (1s) with either missing (?s) or absent (0s) entries. Both cause taxa to drift down trees, from their original position, toward the root. Absolute thresholds at which downshift is significant are extremely low for introduced absences (two entries replaced, 6% of present characters). The opposite threshold in empirical fossil taxa is also found to be low; two absent entries replaced with presences causes fossil taxa to drift up trees. As such, only a few instances of non-preserved characters interpreted as absences will cause fossil organisms to be erroneously interpreted as more primitive than they were in life. This observed sensitivity to coding non-present morphology presents a problem for all evolutionary studies that attempt to use fossils to reconstruct rates of evolution or unlock sequences of morphological change. Stem-ward slippage, whereby fossilization processes cause organisms to appear artificially primitive, appears to be a ubiquitous and problematic phenomenon inherent to missing data, even when no decay biases exist. Absent characters therefore require explicit justification and taphonomic

  1. Immunological Change in a Parasite-Impoverished Environment: Divergent Signals from Four Island Taxa

    PubMed Central

    Beadell, Jon S.; Atkins, Colm; Cashion, Erin; Jonker, Michelle; Fleischer, Robert C.

    2007-01-01

    Dramatic declines of native Hawaiian avifauna due to the human-mediated emergence of avian malaria and pox prompted an examination of whether island taxa share a common altered immunological signature, potentially driven by reduced genetic diversity and reduced exposure to parasites. We tested this hypothesis by characterizing parasite prevalence, genetic diversity and three measures of immune response in two recently-introduced species (Neochmia temporalis and Zosterops lateralis) and two island endemics (Acrocephalus aequinoctialis and A. rimitarae) and then comparing the results to those observed in closely-related mainland counterparts. The prevalence of blood parasites was significantly lower in 3 of 4 island taxa, due in part to the absence of certain parasite lineages represented in mainland populations. Indices of genetic diversity were unchanged in the island population of N. temporalis; however, allelic richness was significantly lower in the island population of Z. lateralis while both allelic richness and heterozygosity were significantly reduced in the two island-endemic species examined. Although parasite prevalence and genetic diversity generally conformed to expectations for an island system, we did not find evidence for a pattern of uniformly altered immune responses in island taxa, even amongst endemic taxa with the longest residence times. The island population of Z. lateralis exhibited a significantly reduced inflammatory cell-mediated response while levels of natural antibodies remained unchanged for this and the other recently introduced island taxon. In contrast, the island endemic A. rimitarae exhibited a significantly increased inflammatory response as well as higher levels of natural antibodies and complement. These measures were unchanged or lower in A. aequinoctialis. We suggest that small differences in the pathogenic landscape and the stochastic history of mutation and genetic drift are likely to be important in shaping the unique

  2. Dominant plant taxa predict plant productivity responses to CO2 enrichment across precipitation and soil gradients

    PubMed Central

    Fay, Philip A.; Newingham, Beth A.; Polley, H. Wayne; Morgan, Jack A.; LeCain, Daniel R.; Nowak, Robert S.; Smith, Stanley D.

    2015-01-01

    The Earth's atmosphere will continue to be enriched with carbon dioxide (CO2) over the coming century. Carbon dioxide enrichment often reduces leaf transpiration, which in water-limited ecosystems may increase soil water content, change species abundances and increase the productivity of plant communities. The effect of increased soil water on community productivity and community change may be greater in ecosystems with lower precipitation, or on coarser-textured soils, but responses are likely absent in deserts. We tested correlations among yearly increases in soil water content, community change and community plant productivity responses to CO2 enrichment in experiments in a mesic grassland with fine- to coarse-textured soils, a semi-arid grassland and a xeric shrubland. We found no correlation between CO2-caused changes in soil water content and changes in biomass of dominant plant taxa or total community aboveground biomass in either grassland type or on any soil in the mesic grassland (P > 0.60). Instead, increases in dominant taxa biomass explained up to 85 % of the increases in total community biomass under CO2 enrichment. The effect of community change on community productivity was stronger in the semi-arid grassland than in the mesic grassland, where community biomass change on one soil was not correlated with the change in either the soil water content or the dominant taxa. No sustained increases in soil water content or community productivity and no change in dominant plant taxa occurred in the xeric shrubland. Thus, community change was a crucial driver of community productivity responses to CO2 enrichment in the grasslands, but effects of soil water change on productivity were not evident in yearly responses to CO2 enrichment. Future research is necessary to isolate and clarify the mechanisms controlling the temporal and spatial variations in the linkages among soil water, community change and plant productivity responses to CO2 enrichment. PMID

  3. Nine endangered taxa, one recovering ecosystem: Identifying common ground for recovery on Santa Cruz Island, California

    USGS Publications Warehouse

    McEachern, A. Kathryn; Wilken, Dieter H.

    2011-01-01

    It is not uncommon to have several rare and listed taxa occupying habitats in one landscape or management area where conservation amounts to defense against the possibility of further loss. It is uncommon and extremely exciting, however, to have several listed taxa occupying one island that is managed cooperatively for conservation and recovery. On Santa Cruz Island, the largest of the northern California island group in the Santa Barbara Channel, we have a golden opportunity to marry ecological knowledge and institutional "good will" in a field test of holistic rare plant conservation. Here, the last feral livestock have been removed, active weed control is underway, and management is focused on understanding and demonstrating system response to conservation management. Yet funding limitations still exist and we need to plan the most fiscally conservative and marketable approach to rare plant restoration. We still experience the tension between desirable quick results and the ecological pace of system recovery. Therefore, our research has focused on identifying fundamental constraints on species recovery at individual, demographic, habitat, and ecosystem levels, and then developing suites of actions that might be taken across taxa and landscapes. At the same time, we seek a performance middle ground that balances an institutional need for quick demonstration of hands-on positive results with a contrasting approach that allows ecosystem recovery to facilitate species recovery in the long term. We find that constraints vary across breeding systems, life-histories, and island locations. We take a hybrid approach in which we identify several actions that we can take now to enhance population size or habitat occupancy for some taxa by active restoration, while allowing others to recover at the pace of ecosystem change. We make our recommendations on the basis of data we have collected over the last decade, so that management is firmly grounded in ecological observation.

  4. Crisis of Japanese vascular flora shown by quantifying extinction risks for 1618 taxa.

    PubMed

    Kadoya, Taku; Takenaka, Akio; Ishihama, Fumiko; Fujita, Taku; Ogawa, Makoto; Katsuyama, Teruo; Kadono, Yasuro; Kawakubo, Nobumitsu; Serizawa, Shunsuke; Takahashi, Hideki; Takamiya, Masayuki; Fujii, Shinji; Matsuda, Hiroyuki; Muneda, Kazuo; Yokota, Masatsugu; Yonekura, Koji; Yahara, Tetsukazu

    2014-01-01

    Although many people have expressed alarm that we are witnessing a mass extinction, few projections have been quantified, owing to limited availability of time-series data on threatened organisms, especially plants. To quantify the risk of extinction, we need to monitor changes in population size over time for as many species as possible. Here, we present the world's first quantitative projection of plant species loss at a national level, with stochastic simulations based on the results of population censuses of 1618 threatened plant taxa in 3574 map cells of ca. 100 km2. More than 500 lay botanists helped monitor those taxa in 1994-1995 and in 2003-2004. We projected that between 370 and 561 vascular plant taxa will go extinct in Japan during the next century if past trends of population decline continue. This extinction rate is approximately two to three times the global rate. Using time-series data, we show that existing national protected areas (PAs) covering ca. 7% of Japan will not adequately prevent population declines: even core PAs can protect at best <60% of local populations from decline. Thus, the Aichi Biodiversity Target to expand PAs to 17% of land (and inland water) areas, as committed to by many national governments, is not enough: only 29.2% of currently threatened species will become non-threatened under the assumption that probability of protection success by PAs is 0.5, which our assessment shows is realistic. In countries where volunteers can be organized to monitor threatened taxa, censuses using our method should be able to quantify how fast we are losing species and to assess how effective current conservation measures such as PAs are in preventing species extinction.

  5. Bias and Sensitivity in the Placement of Fossil Taxa Resulting from Interpretations of Missing Data

    PubMed Central

    Sansom, Robert S.

    2015-01-01

    The utility of fossils in evolutionary contexts is dependent on their accurate placement in phylogenetic frameworks, yet intrinsic and widespread missing data make this problematic. The complex taphonomic processes occurring during fossilization can make it difficult to distinguish absence from non-preservation, especially in the case of exceptionally preserved soft-tissue fossils: is a particular morphological character (e.g., appendage, tentacle, or nerve) missing from a fossil because it was never there (phylogenetic absence), or just happened to not be preserved (taphonomic loss)? Missing data have not been tested in the context of interpretation of non-present anatomy nor in the context of directional shifts and biases in affinity. Here, complete taxa, both simulated and empirical, are subjected to data loss through the replacement of present entries (1s) with either missing (?s) or absent (0s) entries. Both cause taxa to drift down trees, from their original position, toward the root. Absolute thresholds at which downshift is significant are extremely low for introduced absences (two entries replaced, 6% of present characters). The opposite threshold in empirical fossil taxa is also found to be low; two absent entries replaced with presences causes fossil taxa to drift up trees. As such, only a few instances of non-preserved characters interpreted as absences will cause fossil organisms to be erroneously interpreted as more primitive than they were in life. This observed sensitivity to coding non-present morphology presents a problem for all evolutionary studies that attempt to use fossils to reconstruct rates of evolution or unlock sequences of morphological change. Stem-ward slippage, whereby fossilization processes cause organisms to appear artificially primitive, appears to be a ubiquitous and problematic phenomenon inherent to missing data, even when no decay biases exist. Absent characters therefore require explicit justification and taphonomic

  6. Lectotypification of names of Himalayan Brassicaceae taxa currently placed in the genus Cardamine

    PubMed Central

    Marhold, Karol; Kempa, Matúš; Al-Shehbaz, Ihsan A.

    2015-01-01

    Abstract Lectotypes of twenty-eight names of taxa currently recognized or synonymized in Cardamine are designated as part of the work on the account of the genus for the Pan-Himalayan Flora. Among them, the previous first-step lectotypification of the name Cardamine calthifolia is finalized. In cases when specimen images are available online, stable identifiers for specimens, other permanent links, or links via JSTOR Global Plants are provided. PMID:26140016

  7. [Fleas from the Neuguén Province (Argentina); description of 4 new taxa (Insecta, Siphonaptera)].

    PubMed

    Beaucournu, J C; Alcover, J A

    1989-01-01

    The collect of 973 Fleas on various small terrestrial mammals, from December 1987 till May 1988, in the Neuquén Province (Argentina), has given 20 taxa. Hectopsylla pascuali n. sp., Plocopsylla consobrina n. sp., Agastopsylla boxi gibbosa n. ssp., Chiliopsylla allophyla tonnii n. ssp. are described. Plocopsylla diana Beaucournu, Gallardo and Launay, 1986, Ctenoparia inopinata Rothschild, 1909, Neotyphloceras crassispina chilensis Jordan, 1936, Tetrapsyllus satyrus Beaucournu and Torrés-Mura, 1986, Ectinorus martini Lewis, 1976, are new from Argentina.

  8. Applying a biomedical top-level ontology to encode biological taxa.

    PubMed

    Boeker, Martin; Stenzhorn, Holger; Schulz, Stefan

    2008-11-06

    Classifying biological entities in terms of species and taxa is an important endeavor in biology. But even though many statements within current biomedical ontologies are indeed taxon-dependent, no standard way exists to properly introduce taxon or species information into current ontological architectures. Therefore we discuss various practices to represent such information by applying a biomedical top-level ontology combined with other standard approaches like description logics or the OBO Foundry.

  9. Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: molecular data change the placement of fossil taxa.

    PubMed

    Wiens, John J; Kuczynski, Caitlin A; Townsend, Ted; Reeder, Tod W; Mulcahy, Daniel G; Sites, Jack W

    2010-12-01

    Molecular data offer great potential to resolve the phylogeny of living taxa but can molecular data improve our understanding of relationships of fossil taxa? Simulations suggest that this is possible, but few empirical examples have demonstrated the ability of molecular data to change the placement of fossil taxa. We offer such an example here. We analyze the placement of snakes among squamate reptiles, combining published morphological data (363 characters) and new DNA sequence data (15,794 characters, 22 nuclear loci) for 45 living and 19 fossil taxa. We find several intriguing results. First, some fossil taxa undergo major changes in their phylogenetic position when molecular data are added. Second, most fossil taxa are placed with strong support in the expected clades by the combined data Bayesian analyses, despite each having >98% missing cells and despite recent suggestions that extensive missing data are problematic for Bayesian phylogenetics. Third, morphological data can change the placement of living taxa in combined analyses, even when there is an overwhelming majority of molecular characters. Finally, we find strong but apparently misleading signal in the morphological data, seemingly associated with a burrowing lifestyle in snakes, amphisbaenians, and dibamids. Overall, our results suggest promise for an integrated and comprehensive Tree of Life by combining molecular and morphological data for living and fossil taxa.

  10. Evidence of Taxa-, Clone-, and Kin-discrimination in Protists: Ecological and Evolutionary Implications

    PubMed Central

    Espinosa, Avelina; Paz-y-Miño-C, Guillermo

    2014-01-01

    Unicellular eukaryotes, or protists, are among the most ancient organisms on Earth. Protists belong to multiple taxonomic groups; they are widely distributed geographically and in all environments. Their ability to discriminate among con- and heterospecifics has been documented during the past decade. Here we discuss exemplar cases of taxa-, clone-, and possible kin-discrimination in five major lineages: Mycetozoa (Dictyostelium, Polysphondylium), Dikarya (Saccharomyces), Ciliophora (Tetrahymena), Apicomplexa (Plasmodium) and Archamoebae (Entamoeba). We summarize the proposed genetic mechanisms involved in discrimination-mediated aggregation (self versus different), including the csA, FLO and trg (formerly lag) genes, and the Proliferation Activation Factors (PAFs), which facilitate clustering in some protistan taxa. We caution about the experimental challenges intrinsic to studying recognition in protists, and highlight the opportunities for exploring the ecology and evolution of complex forms of cell-cell communication, including social behavior, in a polyphyletic, still superficially understood group of organisms. Because unicellular eukaryotes are the evolutionary precursors of multicellular life, we infer that their mechanisms of taxa-, clone-, and possible kin-discrimination gave origin to the complex diversification and sophistication of traits associated with species and kin recognition in plants, fungi, invertebrates and vertebrates. PMID:25400313

  11. Biomechanical modeling and sensitivity analysis of bipedal running ability. II. Extinct taxa.

    PubMed

    Hutchinson, John R

    2004-10-01

    Using an inverse dynamics biomechanical analysis that was previously validated for extant bipeds, I calculated the minimum amount of actively contracting hindlimb extensor muscle that would have been needed for rapid bipedal running in several extinct dinosaur taxa. I analyzed models of nine theropod dinosaurs (including birds) covering over five orders of magnitude in size. My results uphold previous findings that large theropods such as Tyrannosaurus could not run very quickly, whereas smaller theropods (including some extinct birds) were adept runners. Furthermore, my results strengthen the contention that many nonavian theropods, especially larger individuals, used fairly upright limb orientations, which would have reduced required muscular force, and hence muscle mass. Additional sensitivity analysis of muscle fascicle lengths, moment arms, and limb orientation supports these conclusions and points out directions for future research on the musculoskeletal limits on running ability. Although ankle extensor muscle support is shown to have been important for all taxa, the ability of hip extensor muscles to support the body appears to be a crucial limit for running capacity in larger taxa. I discuss what speeds were possible for different theropod dinosaurs, and how running ability evolved in an inverse relationship to body size in archosaurs.

  12. Nomenclatural stability does not justify recognition of paraphyletic taxa: A response to Scherz et al. (2016).

    PubMed

    Peloso, Pedro L V; Raxworthy, Christopher J; Wheeler, Ward C; Frost, Darrel R

    2017-06-01

    Peloso et al. (2015: PELOSO) published a comprehensive phylogenetic study of the frog family Microhylidae, which resulted in the discovery that several taxa were not monophyletic. To remedy this, a series of nomenclatural changes were proposed (several generic synonymies and two new subfamilies named). A recent study published in this journal by Scherz et al. (2016: SCHERZ), provided a novel phylogeny for the Malagasy subfamily Cophylinae. SCHERZ dispute the analyses and taxonomic conclusions of PELOSO. Their study is, however, based on substantial reduction of data from the PELOSO study, limited addition of new data, and different analytical methods. In spite of the fact that their own results are consistent with the taxonomy of PELOSO, SCHERZ reject that conservative taxonomy and suggest the revalidation of Platypelis (from the synonymy of Cophyla), the revalidation of Stumpffia (from the synonymies of Rhombophryne), and the creation of at least two new genera (only one named therein). In doing so, SCHERZ accept the recognition of likely paraphyletic taxa, with Stumpffia paraphyletic in their parsimony analysis. Herein, we provide a response to several points raised in SCHERZ: (1) we discuss issues with their interpretation (and selective use) of available phylogenetic and phenotypic evidence; (2) and provide a new phylogenetic analysis of all the data in PELOSO and SCHERZ combined. In the new analysis Stumpffia is paraphyletic with respect to Rhombophryne, whereas Cophyla and Platypelis are both monophyletic and sister taxa. We provide a case for the use of the taxonomy suggested in PELOSO. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Using computational fluid dynamics to test functional and ecological hypotheses in fossil taxa

    NASA Astrophysics Data System (ADS)

    Rahman, Imran

    2016-04-01

    Reconstructing how ancient organisms moved and fed is a major focus of study in palaeontology. Traditionally, this has been hampered by a lack of objective data on the functional morphology of extinct species, especially those without a clear modern analogue. However, cutting-edge techniques for characterizing specimens digitally and in three dimensions, coupled with state-of-the-art computer models, now provide a robust framework for testing functional and ecological hypotheses even in problematic fossil taxa. One such approach is computational fluid dynamics (CFD), a method for simulating fluid flows around objects that has primarily been applied to complex engineering-design problems. Here, I will present three case studies of CFD applied to fossil taxa, spanning a range of specimen sizes, taxonomic groups and geological ages. First, I will show how CFD enabled a rigorous test of hypothesized feeding modes in an enigmatic Ediacaran organism with three-fold symmetry, revealing previously unappreciated complexity of pre-Cambrian ecosystems. Second, I will show how CFD was used to evaluate hydrodynamic performance and feeding in Cambrian stem-group echinoderms, shedding light on the probable feeding strategy of the latest common ancestor of all deuterostomes. Third, I will show how CFD allowed us to explore the link between form and function in Mesozoic ichthyosaurs. These case studies serve to demonstrate the enormous potential of CFD for addressing long-standing hypotheses for a variety of fossil taxa, opening up an exciting new avenue in palaeontological studies of functional morphology.

  14. Darwin's diagram of divergence of taxa as a causal model for the origin of species.

    PubMed

    Bouzat, Juan L

    2014-03-01

    On the basis that Darwin's theory of evolution encompasses two logically independent processes (common descent and natural selection), the only figure in On the Origin of Species (the Diagram of Divergence of Taxa) is often interpreted as illustrative of only one of these processes: the branching patterns representing common ancestry. Here, I argue that Darwin's Diagram of Divergence of Taxa represents a broad conceptual model of Darwin's theory, illustrating the causal efficacy of natural selection in producing well-defined varieties and ultimately species. The Tree Diagram encompasses the idea that natural selection explains common descent and the origin of organic diversity, thus representing a comprehensive model of Darwin's theory on the origin of species. I describe Darwin's Tree Diagram in relation to his argumentative strategy under the vera causa principle, and suggest that the testing of his theory based on the evidence from the geological record, the geographical distribution of organisms, and the mutual affinities of organic beings can be framed under the hypothetico-deductive method. Darwin's Diagram of Divergence of Taxa therefore represents a broad conceptual model that helps understanding the causal construction of Darwin's theory of evolution, the structure of his argumentative strategy, and the nature of his scientific methodology.

  15. Diatoms from Brazil: the taxa recorded by Christian Gottfried Ehrenberg

    PubMed Central

    da Silva, Weliton José; Jahn, Regine; Menezes, Mariângela

    2012-01-01

    Abstract The flora of diatoms from Brazil has been studied by several authors from the beginning of the 19th up to now. Some of the old lists and descriptions are unknown or have been ignored by Brazilian researchers and the situation of the names cited was not assessed. Here we compiled a list of 101 taxa of diatoms from Brazil registered by Christian Gottfried Ehrenberg during the 19th century. We checked the current nomenclatural status of those taxa and lectotypified species from Brazil described by this author. For this, we accessed the Ehrenberg collection in the Museum für Naturkunde, Berlin, Germany, where 11 samples from Brazil studied by Ehrenberg are housed and published in different papers. Using these samples, we found 101 taxa (specific and infraspecific) published by Ehrenberg from Brazil. Five species (Eunotia bidens Ehrenb., Eunotia depressa Ehrenb., Eunotia elephas Ehrenb., Pinnularia microstauron Ehrenb., and Terpsinoe brasiliensis Ehrenb.) were new descriptions and were lectotypified here. The other species cited for Brazil were described initially from other places. However, 23 names were invalid and one illegitimate. PMID:23730191

  16. Functional gains of including non-commercial epibenthic taxa in coastal beam trawl surveys: A note

    NASA Astrophysics Data System (ADS)

    Brind'Amour, Anik; Rouyer, Armelle; Martin, Jocelyne

    2009-05-01

    The development of ecosystem-based indicators requires the broadening of a view of the community, from fish species to all the species (macrobenthic and fish) correctly captured by a given sampling gear. Many scientific surveys already have such integrated databases. The present note aims to demonstrate that existing databases, herein from dedicated coastal nursery surveys, are actually underexploited. Such databases contain information on non-commercial taxa, which could greatly improve our knowledge on the organisation and functioning of coastal ecosystems. Using two datasets, a "complete" dataset composed of commercial and not-commercial epibenthic trawled species (fish and invertebrate) and a "subset" dataset characterized by commercial and routinely surveyed species (mainly fish and cephalopods), different measures of functional diversity are compared to identify the functional gains of including epibenthic species. The results show that, when included in the analyses, epibenthic taxa provide gains of functional information, associated mainly with the community feeding traits, i.e. organisms composing the primary and secondary consumer levels of the coastal nursery food web. Failure to include some of the primary (zooplanktivores and suspension feeders) and secondary consumers (detritivores-scavengers) in coastal survey analyses may, for instance, hamper our understanding of energy flux between the benthic and water column compartments of these ecosystems. The results also suggest that the exclusion of some taxa associated with these two food web compartments, may lead to the underestimation of the functional redundancy in coastal ecosystems.

  17. Evidence of Taxa-, Clone-, and Kin-discrimination in Protists: Ecological and Evolutionary Implications.

    PubMed

    Espinosa, Avelina; Paz-Y-Miño-C, Guillermo

    2014-11-01

    Unicellular eukaryotes, or protists, are among the most ancient organisms on Earth. Protists belong to multiple taxonomic groups; they are widely distributed geographically and in all environments. Their ability to discriminate among con- and heterospecifics has been documented during the past decade. Here we discuss exemplar cases of taxa-, clone-, and possible kin-discrimination in five major lineages: Mycetozoa (Dictyostelium, Polysphondylium), Dikarya (Saccharomyces), Ciliophora (Tetrahymena), Apicomplexa (Plasmodium) and Archamoebae (Entamoeba). We summarize the proposed genetic mechanisms involved in discrimination-mediated aggregation (self versus different), including the csA, FLO and trg (formerly lag) genes, and the Proliferation Activation Factors (PAFs), which facilitate clustering in some protistan taxa. We caution about the experimental challenges intrinsic to studying recognition in protists, and highlight the opportunities for exploring the ecology and evolution of complex forms of cell-cell communication, including social behavior, in a polyphyletic, still superficially understood group of organisms. Because unicellular eukaryotes are the evolutionary precursors of multicellular life, we infer that their mechanisms of taxa-, clone-, and possible kin-discrimination gave origin to the complex diversification and sophistication of traits associated with species and kin recognition in plants, fungi, invertebrates and vertebrates.

  18. Spatial Scaling of Microbial Diversity across Various Functional and Phylogenetic Taxa

    SciTech Connect

    Schadt, Christopher Warren; Garten Jr, Charles T; Kang, S.; Zhou, Jizhong

    2008-01-01

    Understanding the spatial patterns of organisms and the underlying mechanisms shaping biotic communities is a central goal in community ecology. One of the most well documented spatial patterns in plant and animal communities is the positive-power law relationship between species (or taxa) richness and area. Such a taxa-area relationships (TARs) are one of the principal generalizations in ecology, and are fundamental to our understanding of the distribution of global biodiversity. However, TARs remain elusive and controversial in microbial communities, especially in soil habitats, due to inadequate sampling methodologies. Here, we describe TARs, at a whole-community level, across various microbial functional and phylogenetic groups in a forest soil using a comprehensive functional gene array (FGA) with > 24,000 probes. Our analysis indicated that the forest soil microbial community exhibited a relatively flat taxa-area relationship (slope z = 0.0624), but the z values varied considerably across different functional and phylogenetic groups (z = 0.0475-0.0959), which are several times lower than those commonly observed in higher plants and animals. These results suggest that the turnover in space of microorganisms may be, in general, lower than that of plants and animals.

  19. Surrogate taxa and fossils as reliable proxies of spatial biodiversity patterns in marine benthic communities.

    PubMed

    Tyler, Carrie L; Kowalewski, Michał

    2017-03-15

    Rigorous documentation of spatial heterogeneity (β-diversity) in present-day and preindustrial ecosystems is required to assess how marine communities respond to environmental and anthropogenic drivers. However, the overwhelming majority of contemporary and palaeontological assessments have centred on single higher taxa. To evaluate the validity of single taxa as community surrogates and palaeontological proxies, we compared macrobenthic communities and sympatric death assemblages at 52 localities in Onslow Bay (NC, USA). Compositional heterogeneity did not differ significantly across datasets based on live molluscs, live non-molluscs, and all live organisms. Death assemblages were less heterogeneous spatially, likely reflecting homogenization by time-averaging. Nevertheless, live and dead datasets were greater than 80% congruent in pairwise comparisons to the literature estimates of β-diversity in other marine ecosystems, yielded concordant bathymetric gradients, and produced nearly identical ordinations consistently delineating habitats. Congruent estimates from molluscs and non-molluscs suggest that single groups can serve as reliable community proxies. High spatial fidelity of death assemblages supports the emerging paradigm of Conservation Palaeobiology. Integrated analyses of ecological and palaeontological data based on surrogate taxa can quantify anthropogenic changes in marine ecosystems and advance our understanding of spatial and temporal aspects of biodiversity.

  20. Contribution to the phylogeny and taxonomy of the genus Taeniolella, with a focus on lichenicolous taxa.

    PubMed

    Ertz, Damien; Heuchert, Bettina; Braun, Uwe; Freebury, Colin E; Common, Ralph S; Diederich, Paul

    2016-11-01

    Taeniolella is a genus of asexual ascomycetes with saprophytic, endophytic, and lichenicolous life styles. A phylogeny of representative species is presented, with a focus on lichenicolous taxa. We obtained mtSSU and nuLSU sequence data from culture isolates of Taeniolella and from freshly collected specimens of other taxa. Taeniolella is recovered as strongly polyphyletic. The type species, Taeniolella exilis, is placed in Kirschsteiniotheliaceae within Dothideomycetes. Other saprophytic/endophytic Taeniolella species previously assigned to Sordariomycetes based on sequences were found to represent either contaminants or species that cannot be assigned to Taeniolella for morphological reasons. Lichenicolous species are restricted to Asterotexiales (Dothideomycetes) where the sequenced species of Taeniolella do not form a monophyletic group, but are related to species of Buelliella s. lat., Karschia, Labrocarpon, Melaspilea s. lat., and Stictographa. Molecular data are, however, not sufficient to reallocate the lichenicolous Taeniolella species to other genera so far. Anamorph-teleomorph relationships between these taxa and lichenicolous Taeniolella are discussed but could not be demonstrated. The type of Buelliella is placed in Asterotexiales, and the genus recovered as polyphyletic. Three new lichenicolous Taeniolella species are described, Taeniolella hawksworthiana, Taeniolella pyrenulae and Taeniolella toruloides. Taeniolella rudis is transferred to Sterigmatobotrys. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  1. Dasty3, a WEB framework for DAS

    PubMed Central

    Villaveces, Jose M.; Jimenez, Rafael C.; Garcia, Leyla J.; Salazar, Gustavo A.; Gel, Bernat; Mulder, Nicola; Martin, Maria; Garcia, Alexander; Hermjakob, Henning

    2011-01-01

    Motivation: Dasty3 is a highly interactive and extensible Web-based framework. It provides a rich Application Programming Interface upon which it is possible to develop specialized clients capable of retrieving information from DAS sources as well as from data providers not using the DAS protocol. Dasty3 provides significant improvements on previous Web-based frameworks and is implemented using the 1.6 DAS specification. Availability: Dasty3 is an open-source tool freely available at http://www.ebi.ac.uk/dasty/ under the terms of the GNU General public license. Source and documentation can be found at http://code.google.com/p/dasty/. Contact: hhe@ebi.ac.uk PMID:21798964

  2. Distinguishing terminal monophyletic groups from reticulate taxa: performance of phenetic, tree-based, and network procedures.

    PubMed

    Reeves, Patrick A; Richards, Christopher M

    2007-04-01

    Hybridization is a well-documented, natural phenomenon that is common at low taxonomic levels in the higher plants and other groups. In spite of the obvious potential for gene flow via hybridization to cause reticulation in an evolutionary tree, analytical methods based on a strictly bifurcating model of evolution have frequently been applied to data sets containing taxa known to hybridize in nature. Using simulated data, we evaluated the relative performance of phenetic, tree-based, and network approaches for distinguishing between taxa with known reticulate history and taxa that were true terminal monophyletic groups. In all methods examined, type I error (the erroneous rejection of the null hypothesis that a taxon of interest is not monophyletic) was likely during the early stages of introgressive hybridization. We used the gradual erosion of type I error with continued gene flow as a metric for assessing relative performance. Bifurcating tree-based methods performed poorly, with highly supported, incorrect topologies appearing during some phases of the simulation. Based on our model, we estimate that many thousands of gene flow events may be required in natural systems before reticulate taxa will be reliably detected using tree-based methods of phylogeny reconstruction. We conclude that the use of standard bifurcating tree-based methods to identify terminal monophyletic groups for the purposes of defining or delimiting phylogenetic species, or for prioritizing populations for conservation purposes, is difficult to justify when gene flow between sampled taxa is possible. As an alternative, we explored the use of two network methods. Minimum spanning networks performed worse than most tree-based methods and did not yield topologies that were easily interpretable as phylogenies. The performance of NeighborNet was comparable to parsimony bootstrap analysis. NeighborNet and reverse successive weighting were capable of identifying an ephemeral signature of reticulate

  3. GHRSST-14 DAS-TAG Report

    NASA Technical Reports Server (NTRS)

    Armstrong, Edward; Piolle, Jean Francois

    2013-01-01

    The DAS-TAG provides the informatics and data management expertise in emerging information technologies for the GHRSST community. It provides expertise in data and metadata formats and standards, fosters improvements for GHRSST data curation, experiments with new data processing paradigms, and evaluates services and tools for data usage. It provides a forum for producer and distributor data management issues and coordination.

  4. Physik gestern und heute Das Eiskalorimeter

    NASA Astrophysics Data System (ADS)

    Heering, P.

    2003-07-01

    Kalorimetrische Messungen gehören heute zum experimentellen Standardrepertoire im Bereich der Thermodynamik und der physikalischen Chemie. Das erste Gerät für derartige Messungen entwickelten Ende des 18. Jahrhunderts die französischen Wissenschaftler Antoine Laurent Lavoisier und Pierre Simon de Laplace.

  5. GHRSST-14 DAS-TAG Report

    NASA Technical Reports Server (NTRS)

    Armstrong, Edward; Piolle, Jean Francois

    2013-01-01

    The DAS-TAG provides the informatics and data management expertise in emerging information technologies for the GHRSST community. It provides expertise in data and metadata formats and standards, fosters improvements for GHRSST data curation, experiments with new data processing paradigms, and evaluates services and tools for data usage. It provides a forum for producer and distributor data management issues and coordination.

  6. Higher Thermal Acclimation Potential of Respiration but Not Photosynthesis in Two Alpine Picea Taxa in Contrast to Two Lowland Congeners

    PubMed Central

    Zhang, Xiao Wei; Wang, Jing Ru; Ji, Ming Fei; Milne, Richard Ian; Wang, Ming Hao; Liu, Jian-Quan; Shi, Sheng; Yang, Shu-Li; Zhao, Chang-Ming

    2015-01-01

    The members of the genus Picea form a dominant component in many alpine and boreal forests which are the major sink for atmospheric CO2. However, little is known about the growth response and acclimation of CO2 exchange characteristics to high temperature stress in Picea taxa from different altitudes. Gas exchange parameters and growth characteristics were recorded from four year old seedlings of two alpine (Picea likiangensis vars. rubescens and linzhiensis) and two lowland (P. koraiensis and P. meyeri) taxa. Seedlings were grown at moderate (25°C/15°C) and high (35°C/25°C) day/night temperatures, for four months. The approximated biomass increment (ΔD2H) for all taxa decreased under high temperature stress, associated with decreased photosynthesis and increased respiration. However, the two alpine taxa exhibited lower photosynthetic acclimation and higher respiratory acclimation than either lowland taxon. Moreover, higher leaf dry mass per unit area (LMA) and leaf nitrogen content per unit area (Narea), and a smaller change in the nitrogen use efficiency of photosynthesis (PNUE) for lowland taxa indicated that these maintained higher homeostasis of photosynthesis than alpine taxa. The higher respiration rates produced more energy for repair and maintenance biomass, especially for higher photosynthetic activity for lowland taxa, which causes lower respiratory acclimation. Thus, the changes of ΔD2H for alpine spruces were larger than that for lowland spruces. These results indicate that long term heat stress negatively impact on the growth of Picea seedlings, and alpine taxa are more affected than low altitude ones by high temperature stress. Hence the altitude ranges of Picea taxa should be taken into account when predicting changes to carbon fluxes in warmer conditions. PMID:25874631

  7. Higher thermal acclimation potential of respiration but not photosynthesis in two alpine Picea taxa in contrast to two lowland congeners.

    PubMed

    Zhang, Xiao Wei; Wang, Jing Ru; Ji, Ming Fei; Milne, Richard Ian; Wang, Ming Hao; Liu, Jian-Quan; Shi, Sheng; Yang, Shu-Li; Zhao, Chang-Ming

    2015-01-01

    The members of the genus Picea form a dominant component in many alpine and boreal forests which are the major sink for atmospheric CO2. However, little is known about the growth response and acclimation of CO2 exchange characteristics to high temperature stress in Picea taxa from different altitudes. Gas exchange parameters and growth characteristics were recorded from four year old seedlings of two alpine (Picea likiangensis vars. rubescens and linzhiensis) and two lowland (P. koraiensis and P. meyeri) taxa. Seedlings were grown at moderate (25°C/15°C) and high (35°C/25°C) day/night temperatures, for four months. The approximated biomass increment (ΔD2H) for all taxa decreased under high temperature stress, associated with decreased photosynthesis and increased respiration. However, the two alpine taxa exhibited lower photosynthetic acclimation and higher respiratory acclimation than either lowland taxon. Moreover, higher leaf dry mass per unit area (LMA) and leaf nitrogen content per unit area (Narea), and a smaller change in the nitrogen use efficiency of photosynthesis (PNUE) for lowland taxa indicated that these maintained higher homeostasis of photosynthesis than alpine taxa. The higher respiration rates produced more energy for repair and maintenance biomass, especially for higher photosynthetic activity for lowland taxa, which causes lower respiratory acclimation. Thus, the changes of ΔD2H for alpine spruces were larger than that for lowland spruces. These results indicate that long term heat stress negatively impact on the growth of Picea seedlings, and alpine taxa are more affected than low altitude ones by high temperature stress. Hence the altitude ranges of Picea taxa should be taken into account when predicting changes to carbon fluxes in warmer conditions.

  8. The structure of cystoliths in selected taxa of the genus Ficus L. (Moraceae) in Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Ummu-Hani, B.; Noraini, T.

    2013-11-01

    A study was undertaken on mature leaves of 15 taxa of the genus Ficus in Peninsular Malaysia. The main objectives of this study are to determine the morphology and distribution of cystoliths in the epidermal layers of the leaf lamina in selected taxa of Ficus. The morphology of cystoliths is classified based on its size, shape, colour, and the presence of stalk cystolith. There are seven types of cystolith morphology observed in this study. Most of the cystoliths are either solitary, elongated, narrow or broad, and pointed or blunt at one or both ends. However, double- and rarely triple-cystoliths are also present in some species. The size of the cystoliths varies even within the same species. Based on the position of cystoliths, all the 15 taxa studied can be generally classified into three groups: Group 1 - with cystoliths adjacent to the adaxial epidermis layer (F. annulata, F. benghalensis and F. superba), Group 2 - with cystoliths adjacent to the abaxial epidermis layer (F. aurantiacea, F. lepicarpa, F. hispida, F. obscura var. borneensis, F. religiosa, F. schwarzii, F. ucinata and F. vasculosa), and Group 3 - with cystoliths present in both adaxial and abaxial epidermis layers (F. benjamina, F. depressa, F. microcarpa and F. tinctoria). Based on the occurrence of cystoliths, the types of lithocysts were related to the number of epidermal layers, i.e. hair-like lithocysts in uniseriate epidermis is present in all species studied. However, the characteristics of the cystoliths may not suitably be used as a taxonomic marker but it can be useful as additional character for group identification in Ficusper.

  9. Post-zygotic Reproductive Isolation Between Sympatric Taxa in the Chamaecrista desvauxii Complex (Leguminosae–Caesalpinioideae)

    PubMed Central

    Costa, Cristiana Barros Nascimento; Lambert, Sabrina Mota; Borba, Eduardo Leite; de Queiroz, Luciano Paganucci

    2007-01-01

    Background and Aims Differences in the mating systems and the mechanisms of reproductive isolation between Chamaecrista desvauxii var. graminea and C. desvauxii var. latistipula were examined in the Chapada Diamantina, Brazil. These taxa occur sympatrically, and their populations demonstrate marked morphological differences. The objective of the present work was to determine if reproductive isolation mechanisms exist between these two populations of C. desvauxii, and to determine the influence of these putative mechanisms on their genetic differentiation. Methods Field observations were made of floral biology, phenology and floral visitation, and experiments on intra- and interpopulation pollination and germination rates of the resultant seeds were performed. A genetic examination of the populations was undertaken using four allozyme loci. Key Results The varieties examined demonstrated overlapping of flowering periods during the months of June to September. The main pollinator for both varieties was the bee Bombus brevivillus. Both varieties are self-compatible, and a large number of fruits are formed in cross-pollinations with high seed germination rates. Inter-taxa pollinations result in high levels of fruit production, but no seeds are formed. Two of the four loci examined were diagnostic for the varieties, and exclusive high-frequency alleles were encountered at the other loci, leading to a high genetic distance between the two populations (0·495). Conclusions Pre-zygotic barriers were not found between the two varieties, and these remain isolated due to post-zygotic events. The two varieties demonstrate marked differences in their morphology, floral biology, phenology and genetic make-up, all of which indicate that they should be treated as two distinct species. A complete revision involving the other varieties of the C. desvauxii complex will be necessary in order to define these two taxa formally. PMID:17331960

  10. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation

    PubMed Central

    2013-01-01

    Background The lung microbiome of healthy individuals frequently harbors oral organisms. Despite evidence that microaspiration is commonly associated with smoking-related lung diseases, the effects of lung microbiome enrichment with upper airway taxa on inflammation has not been studied. We hypothesize that the presence of oral microorganisms in the lung microbiome is associated with enhanced pulmonary inflammation. To test this, we sampled bronchoalveolar lavage (BAL) from the lower airways of 29 asymptomatic subjects (nine never-smokers, 14 former-smokers, and six current-smokers). We quantified, amplified, and sequenced 16S rRNA genes from BAL samples by qPCR and 454 sequencing. Pulmonary inflammation was assessed by exhaled nitric oxide (eNO), BAL lymphocytes, and neutrophils. Results BAL had lower total 16S than supraglottic samples and higher than saline background. Bacterial communities in the lower airway clustered in two distinct groups that we designated as pneumotypes. The rRNA gene concentration and microbial community of the first pneumotype was similar to that of the saline background. The second pneumotype had higher rRNA gene concentration and higher relative abundance of supraglottic-characteristic taxa (SCT), such as Veillonella and Prevotella, and we called it pneumotypeSCT. Smoking had no effect on pneumotype allocation, α, or β diversity. PneumotypeSCT was associated with higher BAL lymphocyte-count (P= 0.007), BAL neutrophil-count (P= 0.034), and eNO (P= 0.022). Conclusion A pneumotype with high relative abundance of supraglottic-characteristic taxa is associated with enhanced subclinical lung inflammation. PMID:24450871

  11. Brachyceran Diptera (Insecta) in Cretaceous ambers, Part IV, Significant New Orthorrhaphous Taxa

    PubMed Central

    Grimaldi, David A.; Arillo, Antonio; Cumming, Jeffrey M.; Hauser, Martin

    2011-01-01

    Abstract Thirteen species of basal Brachycera (11 described as new) are reported, belonging to nine families and three infraorders. They are preserved in amber from the Early Cretaceous (Neocomian) of Lebanon, Albian of northern Spain, upper Albian to lower Cenomanian of northern Myanmar, and Late Cretaceous of New Jersey USA (Turonian) and Alberta, Canada (Campanian). Taxa are as follows, with significance as noted: In Stratiomyomorpha: Stratiomyidae (Cretaceogaster pygmaeus Teskey [2 new specimens in Canadian amber], Lysistrata emerita Grimaldi & Arillo, gen. et sp. n. [stem-group species of the family in Spanish amber]), and Xylomyidae (Cretoxyla azari Grimaldi & Cumming, gen. et sp. n. [in Lebanese amber], and an undescribed species from Spain). In Tabanomorpha: Tabanidae (Cratotabanus newjerseyensis Grimaldi, sp. n., in New Jersey amber). In Muscomorpha: Acroceridae (Schlingeromyia minuta Grimaldi & Hauser, gen. et sp. n. and Burmacyrtus rusmithi Grimaldi & Hauser gen. et sp. n., in Burmese amber, the only definitive species of the family from the Cretaceous); Mythicomyiidae (Microburmyia analvena Grimaldi & Cumming gen. et sp. n. and Microburmyia veanalvena Grimaldi & Cumming, sp. n., stem-group species of the family, both in Burmese amber); Apsilocephalidae or near (therevoid family-group) (Kumaromyia burmitica Grimaldi & Hauser, gen. et sp. n. [in Burmese amber]); Apystomyiidae (Hilarimorphites burmanica Grimaldi & Cumming, sp. n. [in Burmese amber], whose closest relatives are from the Late Jurassic of Kazachstan, the Late Cretaceous of New Jersey, and Recent of California). Lastly, two species belonging to families incertae sedis, both in Burmese amber: Tethepomyiidae (Tethepomyia zigrasi Grimaldi & Arillo sp. n., the aculeate oviscapt of which indicates this family was probably parasitoidal and related to Eremochaetidae); and unplaced to family is Myanmyia asteiformia Grimaldi, gen. et sp. n., a minute fly with highly reduced venation. These new taxa

  12. Larger ejaculate volumes are associated with a lower degree of polyandry across bushcricket taxa

    PubMed Central

    Vahed, Karim

    2006-01-01

    In numerous insects, including bushcrickets (Tettigoniidae), males are known to transfer substances in the ejaculate that inhibit the receptivity of females to further matings, but it has not yet been established whether these substances reduce the lifetime degree of polyandry of the female. The aim of this study was to test the hypothesis that larger ejaculate volumes should be associated with a lower degree of polyandry across tettigoniid taxa, controlling for male body mass and phylogeny. Data on ejaculate mass, sperm number, nuptial gift mass and male mass were taken primarily from the literature. The degree of polyandry for 14 species of European bushcrickets was estimated by counting the number of spermatodoses within the spermathecae of field-caught females towards the end of their adult lifespans. Data for four further species were obtained from the literature. Data were analysed by using both species regression and independent contrasts to control for phylogeny. Multiple regression analysis revealed that, as predicted, there was a significant negative association between the degree of polyandry and ejaculate mass, relative to male body mass, across bushcricket taxa. Nuptial gift size and sperm number, however, did not contribute further to interspecific variation in the degree of polyandry. A positive relationship was found, across bushcricket taxa, between relative nuptial gift size and relative ejaculate mass, indicating that larger nuptial gifts allow the male to overcome female resistance to accepting large ejaculates. This appears to be the first comparative evidence that males can manipulate the lifetime degree of polyandry of their mates through the transfer of large ejaculates. PMID:16928643

  13. Larger ejaculate volumes are associated with a lower degree of polyandry across bushcricket taxa.

    PubMed

    Vahed, Karim

    2006-09-22

    In numerous insects, including bushcrickets (Tettigoniidae), males are known to transfer substances in the ejaculate that inhibit the receptivity of females to further matings, but it has not yet been established whether these substances reduce the lifetime degree of polyandry of the female. The aim of this study was to test the hypothesis that larger ejaculate volumes should be associated with a lower degree of polyandry across tettigoniid taxa, controlling for male body mass and phylogeny. Data on ejaculate mass, sperm number, nuptial gift mass and male mass were taken primarily from the literature. The degree of polyandry for 14 species of European bushcrickets was estimated by counting the number of spermatodoses within the spermathecae of field-caught females towards the end of their adult lifespans. Data for four further species were obtained from the literature. Data were analysed by using both species regression and independent contrasts to control for phylogeny. Multiple regression analysis revealed that, as predicted, there was a significant negative association between the degree of polyandry and ejaculate mass, relative to male body mass, across bushcricket taxa. Nuptial gift size and sperm number, however, did not contribute further to interspecific variation in the degree of polyandry. A positive relationship was found, across bushcricket taxa, between relative nuptial gift size and relative ejaculate mass, indicating that larger nuptial gifts allow the male to overcome female resistance to accepting large ejaculates. This appears to be the first comparative evidence that males can manipulate the lifetime degree of polyandry of their mates through the transfer of large ejaculates.

  14. Brachyceran Diptera (Insecta) in Cretaceous ambers, Part IV, Significant New Orthorrhaphous Taxa.

    PubMed

    Grimaldi, David A; Arillo, Antonio; Cumming, Jeffrey M; Hauser, Martin

    2011-01-01

    Thirteen species of basal Brachycera (11 described as new) are reported, belonging to nine families and three infraorders. They are preserved in amber from the Early Cretaceous (Neocomian) of Lebanon, Albian of northern Spain, upper Albian to lower Cenomanian of northern Myanmar, and Late Cretaceous of New Jersey USA (Turonian) and Alberta, Canada (Campanian). Taxa are as follows, with significance as noted: In Stratiomyomorpha: Stratiomyidae (Cretaceogaster pygmaeus Teskey [2 new specimens in Canadian amber], Lysistrata emerita Grimaldi & Arillo, gen. et sp. n. [stem-group species of the family in Spanish amber]), and Xylomyidae (Cretoxyla azari Grimaldi & Cumming, gen. et sp. n. [in Lebanese amber], and an undescribed species from Spain). In Tabanomorpha: Tabanidae (Cratotabanus newjerseyensis Grimaldi, sp. n., in New Jersey amber). In Muscomorpha: Acroceridae (Schlingeromyia minuta Grimaldi & Hauser, gen. et sp. n. and Burmacyrtus rusmithi Grimaldi & Hauser gen. etsp. n., in Burmese amber, the only definitive species of the family from the Cretaceous); Mythicomyiidae (Microburmyia analvena Grimaldi & Cumming gen. et sp. n. and Microburmyia veanalvena Grimaldi & Cumming, sp. n., stem-group species of the family, both in Burmese amber); Apsilocephalidae or near (therevoid family-group) (Kumaromyia burmitica Grimaldi & Hauser, gen. et sp. n. [in Burmese amber]); Apystomyiidae (Hilarimorphites burmanica Grimaldi & Cumming, sp. n. [in Burmese amber], whose closest relatives are from the Late Jurassic of Kazachstan, the Late Cretaceous of New Jersey, and Recent of California). Lastly, two species belonging to families incertae sedis, both in Burmese amber: Tethepomyiidae (Tethepomyia zigrasi Grimaldi & Arillo sp. n., the aculeate oviscapt of which indicates this family was probably parasitoidal and related to Eremochaetidae); and unplaced to family is Myanmyia asteiformia Grimaldi, gen. et sp. n., a minute fly with highly reduced venation. These new taxa significantly

  15. Phylogenetic relationships among higher Nemertean (Nemertea) Taxa inferred from 18S rDNA sequences.

    PubMed

    Sundberg, P; Turbeville, J M; Lindh, S

    2001-09-01

    We estimated the phylogenetic relationships of 15 nemertean (phylum Nemertea) species from the four subclasses Hoplo-, Hetero-, Palaeo-, and Bdellonemertea with 18S rDNA sequence data. Three outgroup taxa were used for rooting: Annelida, Platyhelminthes, and Mollusca. Parsimony and maximum-likelihood analyses supported the monophyletic status of the Heteronemertea and a taxon consisting of hoplonemerteans and Bdellonemertea, while indicating that Palaeonemertea is paraphyletic. The monophyletic status of the two nemertean classes Anopla and Enopla is not supported by the data. The unambiguous clades are well supported, as assessed by a randomization test (bootstrapping) and branch support values. Copyright 2001 Academic Press.

  16. Typification of names of South American taxa related to Woodsia montevidensis (Woodsiaceae)

    PubMed Central

    Arana, Marcelo D.; Mynssen, Claudine M.; Zimmer, Brigitte; Ponce, M. Monica

    2016-01-01

    Abstract A revision of the nomenclature of six South American taxa related to Woodsia is presented, as a part of a taxonomic revision of the genus in South America. Lectotypes are selected for Cheilanthes crenata, Woodsia crenata var. pallidipes, Woodsia incisa, Woodsia montevidensis var. fuscipes and the second step lectotypification for Dicksonia montevidensis and Woodsia peruviana, based on the analysis of their protologues and original herbarium material. All names are currently synonyms of Woodsia montevidensis. Physematium incisum (Gillies ex Hook. & Grev.) Kunze constitutes an illegitimate name and Physematium cumingianum is considered as nomen inquirendum. PMID:27489474

  17. On the chemical composition and nutritional value of pleurotus taxa growing on umbelliferous plants (apiaceae).

    PubMed

    La Guardia, Maurizio; Venturella, Giuseppe; Venturella, Fabio

    2005-07-27

    Unpublished data on the chemical composition and nutritional value of Pleurotus mushrooms, growing on Umbelliferous plants (Apiaceae), are here reported. Cultivated basidiomata of four different Pleurotus taxa were analyzed in order to evaluate the composition in lipids, sugars, nitrogen, water, vitamins, ashes, and energetic values. The results showed that Pleurotus mushrooms are suitable in every type of diet thanks to their low caloric content, gastronomic value, vitamins, and mineral salt contents. The presence of a high content of vitamin B(12) and riboflavin in Pleurotus nebrodensis is noteworthy.

  18. New taxa of the family Syringophilidae (Acari: Prostigmata) from African barbets and woodpeckers (Piciformes: Lybiidae, Picidae).

    PubMed

    Skorack, Maciej; Klimovičová, Miroslava; Muchai, Muchane; Hromada, Martin

    2014-02-25

    New taxa of quill mites (Acari: Syringophilidae) are described from African barbets and woodpeckers in the Ethiopian region. A new monotypic genus Picineoaulonastus gen. nov. is established for a new species Picineoaulonastus pogoniulus sp. nov., parasitising 2 lybiid species, Pogoniulus bilineatus (Sundevall) (type host) in Kenya and Tanzania and P. pusillus (Dumont) (Piciformes: Lybiidae) in Ethiopia. Additionally, 2 more new syringophilid species are described: Neosyringophilopsis lybidus sp. nov. from P. bilineatus in Kenya, and Syringophiloidus picidus sp. nov. from Dendropicos fuscescens (Vieillot) (Piciformes: Picidae) in Kenya, Uganda, and Tanzania.

  19. Suprageneric taxa derived from Amblycoryphini sensu lato (Orthoptera: Tettigonioidea: Phaneropteridae: Phaneropterinae).

    PubMed

    Cadena-Castañeda, Oscar J

    2015-01-07

    Based on the current description of the tribe Amblycoryphini some related genera have been excluded. These genera comprise two new tribes (Vossiini n. trib. and Plangiopsiini n. trib.) and a new generic group (Plangiae n. group). The main differences between the taxa described and the tribe Amblycoryphini are discussed, to understand the new proposed classification. Plangiopsis aedeps is placed in the genus Plangiola. This paper contributes to the knowledge of the tettigonid fauna from Africa and understanding of the taxonomy of neotropical Phaneropterinae. 

  20. Bacterial community dynamics and taxa-time relationships within two activated sludge bioreactors.

    PubMed

    Hai, Reti; Wang, Yulin; Wang, Xiaohui; Li, Yuan; Du, Zhize

    2014-01-01

    Biological activated sludge process must be functionally stable to continuously remove contaminants while relying upon the activity of complex microbial communities. However the dynamics of these communities are as yet poorly understood. A macroecology metric used to quantify community dynamic is the taxa-time relationship (TTR). Although the TTR of animal and plant species has been well documented, knowledge is still lacking in regard to TTR of microbial communities in activated sludge bioreactors. 1) To characterize the temporal dynamics of bacterial taxa in activated sludge from two bioreactors of different scale and investigate factors affecting such dynamics; 2) to evaluate the TTRs of activated sludge microbial communities in two bioreactors of different scale. Temporal variation of bacterial taxa in activated sludge collected from a full- and lab-scale activated sludge bioreactor was monitored over a one-year period using pyrosequencing of 16S rRNA genes. TTR was employed to quantify the bacterial taxa shifts based on the power law equation S = cTw. The power law exponent w for the full-scale bioreactor was 0.43 (R2 = 0.970), which is lower than that of the lab-scale bioreactor (w = 0.55, R2 = 0.971). The exponents for the dominant phyla were generally higher than that of the rare phyla. Canonical correspondence analysis (CCA) result showed that the bacterial community variance was significantly associated with water temperature, influent (biochemical oxygen demand) BOD, bioreactor scale and dissolved oxygen (DO). Variance partitioning analyses suggested that wastewater characteristics had the greatest contribution to the bacterial community variance, explaining 20.3% of the variance of bacterial communities independently, followed by operational parameters (19.9%) and bioreactor scale (3.6%). Results of this study suggest bacterial community dynamics were likely driven partly by wastewater and operational parameters and provide evidence that

  1. Bacterial Community Dynamics and Taxa-Time Relationships within Two Activated Sludge Bioreactors

    PubMed Central

    Hai, Reti; Wang, Yulin; Wang, Xiaohui; Li, Yuan; Du, Zhize

    2014-01-01

    Background Biological activated sludge process must be functionally stable to continuously remove contaminants while relying upon the activity of complex microbial communities. However the dynamics of these communities are as yet poorly understood. A macroecology metric used to quantify community dynamic is the taxa-time relationship (TTR). Although the TTR of animal and plant species has been well documented, knowledge is still lacking in regard to TTR of microbial communities in activated sludge bioreactors. Aims 1) To characterize the temporal dynamics of bacterial taxa in activated sludge from two bioreactors of different scale and investigate factors affecting such dynamics; 2) to evaluate the TTRs of activated sludge microbial communities in two bioreactors of different scale. Methods Temporal variation of bacterial taxa in activated sludge collected from a full- and lab-scale activated sludge bioreactor was monitored over a one-year period using pyrosequencing of 16S rRNA genes. TTR was employed to quantify the bacterial taxa shifts based on the power law equation S = cTw. Results The power law exponent w for the full-scale bioreactor was 0.43 (R2 = 0.970), which is lower than that of the lab-scale bioreactor (w = 0.55, R2 = 0.971). The exponents for the dominant phyla were generally higher than that of the rare phyla. Canonical correspondence analysis (CCA) result showed that the bacterial community variance was significantly associated with water temperature, influent (biochemical oxygen demand) BOD, bioreactor scale and dissolved oxygen (DO). Variance partitioning analyses suggested that wastewater characteristics had the greatest contribution to the bacterial community variance, explaining 20.3% of the variance of bacterial communities independently, followed by operational parameters (19.9%) and bioreactor scale (3.6%). Conclusions Results of this study suggest bacterial community dynamics were likely driven partly by wastewater and

  2. Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors.

    PubMed

    van der Gast, Christopher J; Ager, Duane; Lilley, Andrew K

    2008-06-01

    Microorganisms operate at a range of spatial and temporal scales acting as key drivers of ecosystem properties. Therefore, many key questions in microbial ecology require the consideration of both spatial and temporal scales. Spatial scaling, in particular the species-area relationship (SAR), has a long history in ecology and has recently been addressed in microbial ecology. However, the temporal analogue of the SAR, the species-time relationship, has received far less attention even in the science of general ecology. Here we focus upon the role of temporal scaling in microbial ecological patterns by coupling molecular characterization of bacterial communities in discrete island (bioreactor) systems with a macroecological approach. Our findings showed that the temporal scaling exponent (slope), and therefore taxa turnover of the bacterial taxa-time relationship decreased as selective pressure (industrial wastewater concentration) increased. Also, as the concentration of industrial wastewater increased across the bioreactors, we observed a gradual switch from stochastic community assembly to more deterministic (niche)-based considerations. The identification of broad-scale statistical patterns is particularly relevant to microbial ecology, as it is frequently difficult to identify individual species or their functions. In this study, we identify wide-reaching statistical patterns of diversity and show that they are shaped by the prevalent underlying ecological factors.

  3. Climate-driven C4 plant distributions in China: divergence in C4 taxa

    PubMed Central

    Wang, Renzhong; Ma, Linna

    2016-01-01

    There have been debates on the driving factors of C4 plant expansion, such as PCO2 decline in the late Micocene and warmer climate and precipitation at large-scale modern ecosystems. These disputes are mainly due to the lack of direct evidence and extensive data analysis. Here we use mass flora data to explore the driving factors of C4 distribution and divergent patterns for different C4 taxa at continental scale in China. The results display that it is mean annual climate variables driving C4 distribution at present-day vegetation. Mean annual temperature is the critical restriction of total C4 plants and the precipitation gradients seem to have much less impact. Grass and sedge C4 plants are largely restricted to mean annual temperature and precipitation respectively, while Chenopod C4 plants are strongly restricted by aridity in China. Separate regression analysis can succeed to detect divergences of climate distribution patterns of C4 taxa at global scale. PMID:27302686

  4. Quantitative analysis of total flavonoids and total phenolic acids in thirty Hypericum taxa.

    PubMed

    Pilepić, Kroata Hazler; Males, Zeljan; Crkvencić, Maja

    2013-03-01

    The content of total flavonoids and total phenolic acids in the aerial parts of thirty Hypericum taxa collected over two consecutive seasons was investigated by spectrophotometric methods. All taxa examined contained flavonoids and phenolic acids in different quantities, although the differences between species and year's harvest were not found to be significant. The quantity of total flavonoids ranged from 0.1 to 1.6%. The highest content of flavonoids was found in the samples of H. japonicum (1.6%) and H. perforatum (1.5%), while the samples of H. androsaemum and H. balearicum comprised the lowest flavonoid amount (0.13%). The content of total phenolic acids in the investigated samples was found to be between 1.1-10.4%. The samples of H. perforatum were found to contain the highest quantity of phenolic acids (10.4% and 10.2%), whereas the sample ofH. linarifolium showed the lowest amount of phenolic acids (1.1%).

  5. Fission and fusion in island taxa--serendipity, or something to be expected?

    PubMed

    Emerson, Brent C; Faria, Christiana M A

    2014-11-01

    A well-used metaphor for oceanic islands is that they act as 'natural laboratories' for the study of evolution. But how can islands or archipelagos be considered analogues of laboratories for understanding the evolutionary process itself? It is not necessarily the case that just because two or more related species occur on an island or archipelago, somehow, this can help us understand more about their evolutionary history. But in some cases, it can. In this issue of Molecular Ecology, Garrick et al. () use population-level sampling within closely related taxa of Galapagos giant tortoises to reveal a complex demographic history of the species Chelonoidis becki - a species endemic to Isabela Island, and geographically restricted to Wolf Volcano. Using microsatellite genotyping and mitochondrial DNA sequencing, they provide a strong case for C. becki being derived from C. darwini from the neighbouring island of Santiago. But the interest here is that colonization did not happen only once. Garrick et al. () reveal C. becki to be the product of a double colonization event, and their data reveal these two founding lineages to be now fusing back into one. Their results are compelling and add to a limited literature describing the evolutionary consequences of double colonization events. Here, we look at the broader implications of the findings of Garrick et al. () and suggest genomic admixture among multiple founding populations may be a characteristic feature within insular taxa.

  6. Possible effects of global environmental changes on Antarctic benthos: a synthesis across five major taxa

    PubMed Central

    Ingels, Jeroen; Vanreusel, Ann; Brandt, Angelika; Catarino, Ana I; David, Bruno; De Ridder, Chantal; Dubois, Philippe; Gooday, Andrew J; Martin, Patrick; Pasotti, Francesca; Robert, Henri

    2012-01-01

    Because of the unique conditions that exist around the Antarctic continent, Southern Ocean (SO) ecosystems are very susceptible to the growing impact of global climate change and other anthropogenic influences. Consequently, there is an urgent need to understand how SO marine life will cope with expected future changes in the environment. Studies of Antarctic organisms have shown that individual species and higher taxa display different degrees of sensitivity to environmental shifts, making it difficult to predict overall community or ecosystem responses. This emphasizes the need for an improved understanding of the Antarctic benthic ecosystem response to global climate change using a multitaxon approach with consideration of different levels of biological organization. Here, we provide a synthesis of the ability of five important Antarctic benthic taxa (Foraminifera, Nematoda, Amphipoda, Isopoda, and Echinoidea) to cope with changes in the environment (temperature, pH, ice cover, ice scouring, food quantity, and quality) that are linked to climatic changes. Responses from individual to the taxon-specific community level to these drivers will vary with taxon but will include local species extinctions, invasions of warmer-water species, shifts in diversity, dominance, and trophic group composition, all with likely consequences for ecosystem functioning. Limitations in our current knowledge and understanding of climate change effects on the different levels are discussed. PMID:22423336

  7. Distance decay relationships in foliar fungal endophytes are driven by rare taxa.

    PubMed

    Oono, Ryoko; Rasmussen, Anna; Lefèvre, Emilie

    2017-07-01

    Foliar fungal endophytes represent a diverse and species-rich plant microbiome. Their biogeography provides essential clues to their cryptic relationship with hosts and the environment in which they disperse. We present species composition, diversity, and dispersal patterns of endophytic fungi associated with needles of Pinus taeda trees across regional scales in the absence of strong environmental gradients as well as within individual trees. An empirical designation of rare and abundant taxa enlightens us on the structure of endophyte communities. We report multiple distance-decay patterns consistent with effects of dispersal limitation, largely driven by community changes in rare taxa, those taxonomic units that made up less than 0.31% of reads per sample on average. Distance-decay rates and community structure also depended on specific classes of fungi and were predominantly influenced by rare members of Dothideomycetes. Communities separated by urban areas also revealed stronger effects of distance on community similarity, confirming that host density and diversity plays an important role in symbiont biogeography, which may ultimately lead to a mosaic of functional diversity as well as rare species diversity across landscapes. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  8. Iteration expansion and regional evolution: phylogeography of Dendrobium officinale and four related taxa in southern China

    PubMed Central

    Hou, Beiwei; Luo, Jing; Zhang, Yusi; Niu, Zhitao; Xue, Qingyun; Ding, Xiaoyu

    2017-01-01

    The genus Dendrobium was used as a case study to elucidate the evolutionary history of Orchidaceae in the Sino-Japanese Floristic Region (SJFR) and Southeast Asia region. These evolutionary histories remain largely unknown, including the temporal and spatial distribution of the evolutionary events. The present study used nuclear and plastid DNA to determine the phylogeography of Dendrobium officinale and four closely related taxa. Plastid DNA haplotype and nuclear data were shown to be discordant, suggesting reticulate evolution drove the species’ diversification. Rapid radiation and genetic drift appeared to drive the evolution of D. tosaense and D. flexicaule, whereas introgression or hybridization might have been involved in the evolution of D. scoriarum and D. shixingense. The phylogeographical structure of D. officinale revealed that core natural distribution regions might have served as its glacial refuges. In recent years, human disturbances caused its artificial migration and population extinction. The five taxa may have originated from the Nanling Mountains and the Yungui Plateau and then migrated northward or eastward. After the initial iteration expansion, D. officinale populations appeared to experience the regional evolutionary patterns in different regions and follow the sequential or rapid decline in gene exchange. PMID:28262789

  9. Nuclear DNA content and base composition in 28 taxa of Musa.

    PubMed

    Kamaté, K; Brown, S; Durand, P; Bureau, J M; De Nay, D; Trinh, T H

    2001-08-01

    The nuclear DNA content of 28 taxa of Musa was assessed by flow cytometry, using line PxPC6 of Petunia hybrida as an internal standard. The 2C DNA value of Musa balbisiana (BB genome) was 1.16 pg, whereas Musa acuminata (AA genome) had an average 2C DNA value of 1.27 pg, with a difference of 11% between its subspecies. The two haploid (IC) genomes, A and B, comprising most of the edible bananas, are therefore of similar size, 0.63 pg (610 million bp) and 0.58 pg (560 million bp), respectively. The genome of diploid Musa is thus threefold that of Arabidopsis thaliana. The genome sizes in a set of triploid Musa cultivars or clones were quite different, with 2C DNA values ranging from 1.61 to 2.23 pg. Likewise, the genome sizes of tetraploid cultivars ranged from 1.94 to 2.37 pg (2C). Apparently, tetraploids (for instance, accession I.C.2) can have a genome size that falls within the range of triploid genome sizes, and vice versa (as in the case of accession Simili Radjah). The 2C values estimated for organs such as leaf, leaf sheath, rhizome, and flower were consistent, whereas root material gave atypical results, owing to browning. The genomic base composition of these Musa taxa had a median value of 40.8% GC (SD = 0.43%).

  10. Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa

    PubMed Central

    Reeder, Tod W.; Townsend, Ted M.; Mulcahy, Daniel G.; Noonan, Brice P.; Wood, Perry L.; Sites, Jack W.; Wiens, John J.

    2015-01-01

    Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement. PMID:25803280

  11. Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa.

    PubMed

    Reeder, Tod W; Townsend, Ted M; Mulcahy, Daniel G; Noonan, Brice P; Wood, Perry L; Sites, Jack W; Wiens, John J

    2015-01-01

    Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.

  12. Climate-driven C4 plant distributions in China: divergence in C4 taxa

    NASA Astrophysics Data System (ADS)

    Wang, Renzhong; Ma, Linna

    2016-06-01

    There have been debates on the driving factors of C4 plant expansion, such as PCO2 decline in the late Micocene and warmer climate and precipitation at large-scale modern ecosystems. These disputes are mainly due to the lack of direct evidence and extensive data analysis. Here we use mass flora data to explore the driving factors of C4 distribution and divergent patterns for different C4 taxa at continental scale in China. The results display that it is mean annual climate variables driving C4 distribution at present-day vegetation. Mean annual temperature is the critical restriction of total C4 plants and the precipitation gradients seem to have much less impact. Grass and sedge C4 plants are largely restricted to mean annual temperature and precipitation respectively, while Chenopod C4 plants are strongly restricted by aridity in China. Separate regression analysis can succeed to detect divergences of climate distribution patterns of C4 taxa at global scale.

  13. Unraveling Trichoderma species in the attine ant environment: description of three new taxa.

    PubMed

    Montoya, Quimi Vidaurre; Meirelles, Lucas Andrade; Chaverri, Priscila; Rodrigues, Andre

    2016-05-01

    Fungus-growing "attine" ants forage diverse substrates to grow fungi for food. In addition to the mutualistic fungal partner, the colonies of these insects harbor a rich microbiome composed of bacteria, filamentous fungi and yeasts. Previous work reported some Trichoderma species in the fungus gardens of leafcutter ants. However, no studies systematically addressed the putative association of Trichoderma with attine ants, especially in non-leafcutter ants. Here, a total of 62 strains of Trichoderma were analyzed using three molecular markers (ITS, tef1 and rpb2). In addition, 30 out of 62 strains were also morphologically examined. The strains studied correspond to the largest sampling carried out so far for Trichoderma in the attine ant environment. Our results revealed the richness of Trichoderma in this environment, since we found 20 Trichoderma species, including three new taxa described in the present work (Trichoderma attinorum, Trichoderma texanum and Trichoderma longifialidicum spp. nov.) as well as a new phylogenetic taxon (LESF 545). Moreover, we show that all 62 strains grouped within different clades across the Trichoderma phylogeny, which are identical or closely related to strains derived from several other environments. This evidence supports the transient nature of the genus Trichoderma in the attine ant colonies. The discovery of three new species suggests that the dynamic foraging behavior of these insects might be responsible for accumulation of transient fungi into their colonies, which might hold additional fungal taxa still unknown to science.

  14. Possible effects of global environmental changes on Antarctic benthos: a synthesis across five major taxa.

    PubMed

    Ingels, Jeroen; Vanreusel, Ann; Brandt, Angelika; Catarino, Ana I; David, Bruno; De Ridder, Chantal; Dubois, Philippe; Gooday, Andrew J; Martin, Patrick; Pasotti, Francesca; Robert, Henri

    2012-02-01

    Because of the unique conditions that exist around the Antarctic continent, Southern Ocean (SO) ecosystems are very susceptible to the growing impact of global climate change and other anthropogenic influences. Consequently, there is an urgent need to understand how SO marine life will cope with expected future changes in the environment. Studies of Antarctic organisms have shown that individual species and higher taxa display different degrees of sensitivity to environmental shifts, making it difficult to predict overall community or ecosystem responses. This emphasizes the need for an improved understanding of the Antarctic benthic ecosystem response to global climate change using a multitaxon approach with consideration of different levels of biological organization. Here, we provide a synthesis of the ability of five important Antarctic benthic taxa (Foraminifera, Nematoda, Amphipoda, Isopoda, and Echinoidea) to cope with changes in the environment (temperature, pH, ice cover, ice scouring, food quantity, and quality) that are linked to climatic changes. Responses from individual to the taxon-specific community level to these drivers will vary with taxon but will include local species extinctions, invasions of warmer-water species, shifts in diversity, dominance, and trophic group composition, all with likely consequences for ecosystem functioning. Limitations in our current knowledge and understanding of climate change effects on the different levels are discussed.

  15. Essential oils of three taxa of the Nepeta argolica aggregate from Greece.

    PubMed

    Hanlidou, Effie; Karousou, Regina; Lazari, Diamanto

    2012-08-01

    The essential-oil composition of three not previously studied taxa belonging to the Nepeta argolica aggregate was examined. The oils of N. argolica ssp. malacotrichos and N. argolica ssp. vourinensis (both Greek endemics) are rich in 1,8-cineole (30.9-55.6% of the total oil composition), while those of the Balkan endemic N. spruneri are rich in either sesquiterpenes (mainly caryophyllene oxide, 14.6-19.8%) or in 4aα,7α,7aβ- and 4aα,7α,7aα-nepetalactones (total content 17.5-40.5%), accompanied by caryophyllene oxide (11.5-11.7%) and 1,8-cineole (up to 16.5%). The comparison of our results with published information concerning the related taxa of the N. argolica aggregate showed that while oils with as main components nepetalactones or 1,8-cineole are common, sesquiterpene-rich oils are reported for the first time within the aggregate. Copyright © 2012 Verlag Helvetica Chimica Acta AG, Zürich.

  16. Development, characterisation, and across-taxa utility of oil palm (Elaeis guineensis Jacq.) microsatellite markers.

    PubMed

    Billotte, N; Risterucci, A M; Barcelos, E; Noyer, J L; Amblard, P; Baurens, F C

    2001-06-01

    The results of the development of oil palm (Elaeis guineensis Jacq.) microsatellite markers are given step by step, from the screening of libraries enriched in (GA)n, (GT)n, and (CCG)n simple-sequence repeats (SSRs) to the final characterisation of 21 SSR loci. Also published are primer sequences, estimates of allele size range, and expected heterozygosity in E. guineensis and in the closely related species E. oleifera, in which an optimal utility of the SSR markers was observed. Multivariate data analyses showed the ability of SSR markers to efficiently reveal the genetic-diversity structure of the genus Elaeis in accordance with known geographical origins and with measured genetic relationships based on previous molecular studies. High levels of allelic variability indicated that E. guineensis SSRs will be a powerful tool for genetic studies of the genus Elaeis, including variety identification and intra- or inter-specific genetic mapping. PCR amplification tests on a subset of 16 other palm species and allele-sequence data showed that E. guineensis SSRs are putative transferable markers across palm taxa. In addition, phenetic information based on SSR flanking region sequences makes E. guineensis SSR markers a potentially useful molecular resource for any researcher studying the phylogeny of palm taxa.

  17. Taxonomic and nomenclatural aspects of Hypoxylon taxa from southern South America proposed by Spegazzini.

    PubMed

    Hladki, Adriana I; Romero, Andrea I

    2009-01-01

    The holotypes and isotypes of 20 Hypoxylon taxa described by Spegazzini have been examined and their taxonomic positions and nomenclatural problems are discussed. Two new combinations, Annulohypoxylon apiahynum comb. nov. and A. subeffusum comb. nov., are proposed. H. goliath is considered a synonym of Rosellinia bunodes. H. albostigmatosum and H. guarapiense are synonyms of H. anthochroum, H. anthracoderma of H. monticulosum, H. mbaiense of H. notatum, H. paulistanum of H. diatrypeoides, H. plumbeum and H. rubiginosum var. microcarpum of H. perforatum. H. porteri and H. intermedium belong in Biscogniauxia capnodes, H. puiggarii in Annulophypoxylon subeffusum, H. subvinosum. in H. lenormandii, H. turbinatum var. guaraniticum in Phylacia turbinata and H. valsarioides in Creosphaeria sassafras. H. leptascum is transferred to A. leptascum, H. circostomum to Nemania circostoma and H. latissimum to N. latissima. The holotype of H. albostigmatosum has been recovered, thus the lectotypification by Shear no longer is needed. H. subnigricans and H. umbilicatum are confirmed as good taxa. H. anthochroum and H. lenormandii are reported as first records from Argentina (Tucumán).

  18. Invasion dynamics of two alien Carpobrotus (Aizoaceae) taxa on a Mediterranean island: II. Reproductive strategies.

    PubMed

    Suehs, C M; Affre, L; Médail, F

    2004-06-01

    This study compares sexually and asexually produced fruit set, seed production, biomass, germination, and seedling size in Carpobrotus acinaciformis and C. edulis following controlled pollination experiments in order to evaluate the potential role of reproductive traits with respect to the invasive potential of these taxa. C. edulis is slightly agamospermic, completely self-fertile, slightly preferentially self-compatible, experiences no inbreeding depression, and has low hybrid vigour. In contrast, C. acinaciformis does not have reliable agamospermy, is only slightly self-fertile and self-compatible, experiences a slight inbreeding depression, and has a strong hybrid vigour. Both taxa have relatively low, although significantly different germination frequencies, and insignificantly different seedling sizes. Owing to the high performance in hybridisation as compared to all other controlled pollinations in C. acinaciformis, as well as a large amount of previously demonstrated introgression, we refer to the population studied on the island of Bagaud (France) as C. affine acinaciformis. We conclude that both C. edulis and C. affine acinaciformis should be considered as harmful invasive plants in the Mediterranean Basin, the former because of the flexibility of its mating system and high seed production, and the latter because of its strong clonality, high hybrid vigour, and potential for continued introgression from C. edulis genes. These differences require different control strategies, while the avoidance of sympatry is a distinct priority.

  19. Taxonomic significance of leaf micromorphology in some selected taxa of Acanthaceae (Peninsular Malaysia)

    NASA Astrophysics Data System (ADS)

    Nurul-Aini, C. A. C.; Noraini, T.; Latiff, A.; Amirul-Aiman, A. J.; Ruzi, A. R.; Idris, S.

    2014-09-01

    Comparative leaf micromorphology study was conducted in eight taxa of Acanthaceae from Peninsular Malaysia. Eight chosen taxa were Acanthus ebracteatus Vahl, A. ilicifolius L., A. volubilis Wall, A. montanus T. Anderson, Andrographis paniculata (Burm.f.) Wall. ex Nees, Asystasia gangetica subsp. micrantha (Nees) Ensermu, Chroesthes longifolia (Wight) B. Hansen and Peristrophe roxburghiana (Schult.) Bremek. The objective of this study was to identify the leaf micromorphological characteristics that can be used in species identification and also as supportive data in classification. The procedures involved such as dehydration, critical point drying, gold coated and examination under scanning electron microscope. Findings in this study have demonstrated the similarities and variations in leaf micromorphological characteristics such as in type of epicuticular waxes, cuticular ornamentations, stomata characteristics and in the presence of trichomes. Six types of epicuticular waxes and five types of trichomes were observed. Variations in cuticular ornamentations and stomata structure can be used to differentiate species. One diagnostic character was found and proven to be very useful to identify Acanthus via the presence of simple trichomes (short-conicle like). In conclusion, the results of this study have shown that leaf micromorphological characteristics have taxonomic significance that can be useful in classifications and identification especially at species level.

  20. Molecular phylogenetic evidence for ancient divergence of lizard taxa on either side of Wallace's Line.

    PubMed Central

    Schulte, James A; Melville, Jane; Larson, Allan

    2003-01-01

    Wallace's Line, separating the terrestrial faunas of South East Asia from the Australia-New Guinea region, is the most prominent and well-studied biogeographical division in the world. Phylogenetically distinct subgroups of major animal and plant groups have been documented on either side of Wallace's Line since it was first proposed in 1859. Despite its importance, the temporal history of fragmentation across this line is virtually unknown and the geological foundation has rarely been discussed. Using molecular phylogenetics and dating techniques, we show that the split between taxa in the South East Asian and the Australian-New Guinean geological regions occurred during the Late Jurassic to Early Cretaceous in two independent lizard clades. This estimate is compatible with the hypothesis of rifting Gondwanan continental fragments during the Mesozoic and strongly rejects the hypothetical origin of various members of the Australian-New Guinean herpetofauna as relatively recent invasions from South East Asia. Our finding suggests an ancient fragmentation of lizard taxa on either side of Wallace's Line and provides further evidence that the composition of modern global communities has been significantly affected by rifting and accretion of Gondwanan continental plates during the Middle to Late Mesozoic. PMID:12769459

  1. Iteration expansion and regional evolution: phylogeography of Dendrobium officinale and four related taxa in southern China.

    PubMed

    Hou, Beiwei; Luo, Jing; Zhang, Yusi; Niu, Zhitao; Xue, Qingyun; Ding, Xiaoyu

    2017-03-06

    The genus Dendrobium was used as a case study to elucidate the evolutionary history of Orchidaceae in the Sino-Japanese Floristic Region (SJFR) and Southeast Asia region. These evolutionary histories remain largely unknown, including the temporal and spatial distribution of the evolutionary events. The present study used nuclear and plastid DNA to determine the phylogeography of Dendrobium officinale and four closely related taxa. Plastid DNA haplotype and nuclear data were shown to be discordant, suggesting reticulate evolution drove the species' diversification. Rapid radiation and genetic drift appeared to drive the evolution of D. tosaense and D. flexicaule, whereas introgression or hybridization might have been involved in the evolution of D. scoriarum and D. shixingense. The phylogeographical structure of D. officinale revealed that core natural distribution regions might have served as its glacial refuges. In recent years, human disturbances caused its artificial migration and population extinction. The five taxa may have originated from the Nanling Mountains and the Yungui Plateau and then migrated northward or eastward. After the initial iteration expansion, D. officinale populations appeared to experience the regional evolutionary patterns in different regions and follow the sequential or rapid decline in gene exchange.

  2. Selection of nontarget arthropod taxa for field research on transgenic insecticidal crops: using empirical data and statistical power.

    PubMed

    Prasifka, J R; Hellmich, R L; Dively, G P; Higgins, L S; Dixon, P M; Duan, J J

    2008-02-01

    One of the possible adverse effects of transgenic insecticidal crops is the unintended decline in the abundance of nontarget arthropods. Field trials designed to evaluate potential nontarget effects can be more complex than expected because decisions to conduct field trials and the selection of taxa to include are not always guided by the results of laboratory tests. Also, recent studies emphasize the potential for indirect effects (adverse impacts to nontarget arthropods without feeding directly on plant tissues), which are difficult to predict because of interactions among nontarget arthropods, target pests, and transgenic crops. As a consequence, field studies may attempt to monitor expansive lists of arthropod taxa, making the design of such broad studies more difficult and reducing the likelihood of detecting any negative effects that might be present. To improve the taxonomic focus and statistical rigor of future studies, existing field data and corresponding power analysis may provide useful guidance. Analysis of control data from several nontarget field trials using repeated-measures designs suggests that while detection of small effects may require considerable increases in replication, there are taxa from different ecological roles that are sampled effectively using standard methods. The use of statistical power to guide selection of taxa for nontarget trials reflects scientists' inability to predict the complex interactions among arthropod taxa, particularly when laboratory trials fail to provide guidance on which groups are more likely to be affected. However, scientists still may exercise judgment, including taxa that are not included in or supported by power analyses.

  3. Moisture Forecast Bias Correction in GEOS DAS

    NASA Technical Reports Server (NTRS)

    Dee, D.

    1999-01-01

    Data assimilation methods rely on numerous assumptions about the errors involved in measuring and forecasting atmospheric fields. One of the more disturbing of these is that short-term model forecasts are assumed to be unbiased. In case of atmospheric moisture, for example, observational evidence shows that the systematic component of errors in forecasts and analyses is often of the same order of magnitude as the random component. we have implemented a sequential algorithm for estimating forecast moisture bias from rawinsonde data in the Goddard Earth Observing System Data Assimilation System (GEOS DAS). The algorithm is designed to remove the systematic component of analysis errors and can be easily incorporated in an existing statistical data assimilation system. We will present results of initial experiments that show a significant reduction of bias in the GEOS DAS moisture analyses.

  4. Complex interactions between regional dispersal of native taxa and an invasive species.

    PubMed

    Strecker, Angela L; Arnott, Shelley E

    2010-04-01

    In the event of an environmental disturbance, dispersal of native taxa may provide species and genetic diversity to ecosystems, increasing the likelihood that there will be species and genotypes present that are less vulnerable to the disturbance. This may allow communities to maintain functioning during a disturbance and may be particularly important when the perturbation is novel to the system, such as the establishment of an invasive species. We examined how dispersal of native species may influence crustacean zooplankton communities in freshwater lakes invaded by the invertebrate predator, Bythotrephes longimanus. Using large enclosures, we experimentally tested the effect of dispersal on zooplankton community abundance, richness, and composition in (1) a community invaded by Bythotrephes, (2) the same community with the invader removed, and (3) a community that was never invaded. Dispersal increased zooplankton community abundance and richness; however, these effects were usually only significant in the invader-removed treatment. Dispersal tended to make the invader-removed communities more similar to never-invaded communities in abundance, richness, and composition. Dispersal had little effect on zooplankton abundance in the invaded community; however, richness significantly increased, and the community composition changed to resemble a never-invaded community by the end of the experiment. Our results have implications for understanding the role of dispersal during transitory states in communities. Dispersal of native taxa may be particularly important during the period between the arrival and broad-scale establishment of Bythotrephes, as dispersal through space or time (i.e., from resting eggs) may rapidly increase zooplankton abundance when the invader is absent or in low abundances. Overall, our results suggest that communities with strong local predatory and competitive interactions may be closed to immigration from colonists, but that invasive species

  5. Rare taxa maintain microbial diversity and contribute to terrestrial community dynamics throughout bark beetle infestation.

    PubMed

    Mikkelson, Kristin M; Bokman, Chelsea; Sharp, Jonathan O

    2016-09-16

    A global phenomenon of increasing bark beetle-induced tree mortality has heightened concern regarding ecosystem response and biogeochemical implications. Here we explore microbial dynamics under lodgepole pines through the analysis of bulk (16S rDNA) and potentially active (16S rRNA) communities to understand terrestrial ecosystem responses associated with this form of large-scale tree morality. We found that the relative abundance of bulk and potentially active taxa was correlated across taxonomic levels, but at lower levels cladal differences became more apparent. Despite this correlation, there was a strong differentiation of community composition between bulk and potentially active taxa, with further clustering in association with stages of tree mortality. Surprisingly, community clustering as a function of tree phase had limited correlation to soil water content and total nitrogen concentrations, which were the only two measured edaphic parameters to differ in association with tree phase. Bacterial clustering is more readily explained by the observed decrease in abundance of active, rare microorganisms after tree death in conjunction with stable alpha diversity measurements. This enables the rare fraction of the terrestrial microbial community to maintain metabolic diversity by transitioning between metabolically active and dormant states during this ecosystem disturbance and contributes disproportionately to community dynamics and archived metabolic capabilities. These results suggest that analyzing the bulk and potentially active communities after beetle infestation might be a more sensitive indicator of disruption than measuring local edaphic parameters. Forests around the world are experiencing unprecedented mortality due to insect infestations fueled in part by a changing climate. While above-ground processes have been explored, changes at the terrestrial interface relevant to microbial biogeochemical cycling remain largely unknown. In this study, we

  6. Bioprospecting: evolutionary implications from a post-olmec pharmacopoeia and the relevance of widespread taxa.

    PubMed

    Leonti, Marco; Cabras, Stefano; Castellanos, Maria Eugenia; Challenger, Antony; Gertsch, Jürg; Casu, Laura

    2013-05-02

    depend on phylogeny, biogeography, ecology and ultimately allelopathy, and on culture-specific perception of organoleptic properties. The comparison of the 67 drug-productive Viridiplantae families with the ethnopharmacopoeia of the Popoluca and the APG database, shows that "traditional" pharmacopoeias and plant-derived drugs are obtained from widespread and species-rich taxa. This is not a function of family size alone. We put forward the theory that as a function of evolution, widespread taxa contain a broader range of accumulated ecological information and response encoded in their genes relative to locally occurring taxa. This information is expressed through the synthesis of allelochemicals with a wide ecological radius, showing broad-spectrum biota-specific interactions, including the targeting of proteins of mammals and primates. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  7. Coralsnake Venomics: Analyses of Venom Gland Transcriptomes and Proteomes of Six Brazilian Taxa

    PubMed Central

    Aird, Steven D.; da Silva, Nelson Jorge; Qiu, Lijun; Villar-Briones, Alejandro; Saddi, Vera Aparecida; Pires de Campos Telles, Mariana; Grau, Miguel L.; Mikheyev, Alexander S.

    2017-01-01

    Venom gland transcriptomes and proteomes of six Micrurus taxa (M. corallinus, M. lemniscatus carvalhoi, M. lemniscatus lemniscatus, M. paraensis, M. spixii spixii, and M. surinamensis) were investigated, providing the most comprehensive, quantitative data on Micrurus venom composition to date, and more than tripling the number of Micrurus venom protein sequences previously available. The six venomes differ dramatically. All are dominated by 2–6 toxin classes that account for 91–99% of the toxin transcripts. The M. s. spixii venome is compositionally the simplest. In it, three-finger toxins (3FTxs) and phospholipases A2 (PLA2s) comprise >99% of the toxin transcripts, which include only four additional toxin families at levels ≥0.1%. Micrurus l. lemniscatus venom is the most complex, with at least 17 toxin families. However, in each venome, multiple structural subclasses of 3FTXs and PLA2s are present. These almost certainly differ in pharmacology as well. All venoms also contain phospholipase B and vascular endothelial growth factors. Minor components (0.1–2.0%) are found in all venoms except that of M. s. spixii. Other toxin families are present in all six venoms at trace levels (<0.005%). Minor and trace venom components differ in each venom. Numerous novel toxin chemistries include 3FTxs with previously unknown 8- and 10-cysteine arrangements, resulting in new 3D structures and target specificities. 9-cysteine toxins raise the possibility of covalent, homodimeric 3FTxs or heterodimeric toxins with unknown pharmacologies. Probable muscarinic sequences may be reptile-specific homologs that promote hypotension via vascular mAChRs. The first complete sequences are presented for 3FTxs putatively responsible for liberating glutamate from rat brain synaptosomes. Micrurus C-type lectin-like proteins may have 6–9 cysteine residues and may be monomers, or homo- or heterodimers of unknown pharmacology. Novel KSPIs, 3× longer than any seen previously, appear to

  8. Análise da cinemática interna das regiões HII gigantes e das galáxias HII

    NASA Astrophysics Data System (ADS)

    Plana, H.; Telles, E.; Maíz-Apellániz, J.

    2003-08-01

    Neste trabalho nós mostramos os primeiros resultados de um estudo sobre a cinemática das Regiões HII Gigantes (GHIIRs) em galáxias próximas. Essas regiões HII têm um diâmetro médio entre 100 pc e 1000 pc e uma taxa de formação estelar de 106 M¤ / ano sendo equivalente à observada em galáxias de tipo tardio correspondendo a uma taxa de formação estelar por unidade de volume uma ordem de magnitude maior que a observada em regiões HII normais. Usando espectros de fenda longas em várias posições, nós construímos mapas de velocidades, de dispersão e de intensidade para várias linhas de emissão como Ha, Hb, [NII]6584 Å, [OIII]5007 Å e o doublet de [SII], para cinco regiões gigantes: NGC 2403 II e IV, NGC 595, NGC 5461, NGC 5471, NGC 5455. O estudo da cinemática (mapas de velocidades e da dispersão) mostrou, por exemplo, a presença de cascas em expansão em NGC 595 ou perfis de emissão com várias componentes em NGC 5461. Os perfis de emissão também mostram velocidades supersônicas. Os resultados são discutidos em comparação com os de estudos anteriores realizados.

  9. Allometry and growth of eight tree taxa in United Kingdom woodlands

    PubMed Central

    Evans, Matthew R; Moustakas, Aristides; Carey, Gregory; Malhi, Yadvinder; Butt, Nathalie; Benham, Sue; Pallett, Denise; Schäfer, Stefanie

    2015-01-01

    As part of a project to develop predictive ecosystem models of United Kingdom woodlands we have collated data from two United Kingdom woodlands - Wytham Woods and Alice Holt. Here we present data from 582 individual trees of eight taxa in the form of summary variables relating to the allometric relationships between trunk diameter, height, crown height, crown radius and trunk radial growth rate to the tree’s light environment and diameter at breast height. In addition the raw data files containing the variables from which the summary data were obtained. Large sample sizes with longitudinal data spanning 22 years make these datasets useful for future studies concerned with the way trees change in size and shape over their life-span. PMID:25977813

  10. Galactinol synthase across evolutionary diverse taxa: functional preference for higher plants?

    PubMed

    Sengupta, Sonali; Mukherjee, Sritama; Parween, Sabiha; Majumder, Arun Lahiri

    2012-05-21

    Galactinol synthase (GolS), a GT8 family glycosyltransferase, synthesizes galactinol and raffinose series of oligosaccharides (RFOs). Identification and analysis of conserved domains in GTs among evolutionarily diverse taxa, structure prediction by homology modeling and determination of substrate binding pocket followed by phylogenetic analysis of GolS sequences establish presence of functional GolS predominantly in higher plants, fungi having the closest possible ancestral sequences. Evolutionary preference for a functional GolS expression in higher plants might have arisen in response to the need for galactinol and RFO synthesis to combat abiotic stress, in contrast to other organisms lacking functional GolS for such functions. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  11. Characterization of Two New Records of Zygomycete Species Belonging to Undiscovered Taxa in Korea

    PubMed Central

    Nguyen, Thi Thuong Thuong; Lee, Seo Hee; Bae, Sarah; Jeon, Sun Jeong; Mun, Hye Yeon

    2016-01-01

    During a biodiversity survey of undiscovered taxa in Korea, two zygomycetous fungal strains were isolated. The first strain, EML-FSDY6-1 was isolated from a soil sample collected at Dokdo Island in the East Sea of Korea in 2013, and the second strain, EML-DG-NH3-1 was isolated from a rat dung sample collected at Chonnam National University garden, Gwangju, Korea in 2014. Based on the morphological characteristics and phylogenetic analysis of the internal transcribed spacer, 18S and 28S rDNA, actin and translation elongation factor-1α genes. EML-FSDY6-1 and EML-DG-NH3-1 isolates were confirmed as zygomycete species, Absidia pseudocylindrospora and Absidia glauca, respectively. Neither species has previously been described in Korea. PMID:27103852

  12. Influence of aeration implements, phosphorus fertilizers, and soil taxa on phosphorus losses from grasslands.

    PubMed

    Franklin, D H; Butler, D M; Cabrera, M L; Calvert, V H; West, L T; Rema, J A

    2011-01-01

    Attenuation of rainfall within the solum may help to move contaminants and nutrients into the soil to be better sequestered or utilized by crops. Surface application of phosphorus (P) amendments to grasslands may lead to elevated concentrations of P in surface runoff and eutrophication of surface waters. Aeration of grasslands has been proposed as a treatment to reduce losses of applied P. Here, results from two small-plot aeration studies and two field-scale, paired-watershed studies are supplemented with previously unpublished soil P data and synthesized. The overall objective of these studies was to determine the impact of aeration on soil P, runoff volume, and runoff P losses from mixed tall fescue [Lolium arundinaceum (Schreb.) Darbysh.]-bermudagrass (Cynodon dactylon L.) grasslands fertilized with P. Small-scale rainfall simulations were conducted on two soil taxa using three types of aeration implements: spikes, disks, and cores. The-field scale study was conducted on four soil taxa with slit and knife aeration. Small-plot studies showed that core aeration reduced loads of total P and dissolved reactive P (DRP) in runoff from plots fertilized with broiler litter and that aeration was effective in reducing P export when it increased soil P in the upper 5 cm. In the field-scale study, slit aeration reduced DRP losses by 35% in fields with well-drained soils but not in poorly drained soils. Flow-weighted concentrations of DRP in aerated fields were related to water-soluble P applied in amendments and soil test P in the upper 5 cm. These studies show that the overall effectiveness of mechanical soil aeration on runoff volume and P losses is controlled by the interaction of soil characteristics such as internal drainage and compaction, soil P, type of surface-applied manure, and type of aeration implement.

  13. Spatial patterns of parrotfish corallivory in the Caribbean: the importance of coral taxa, density and size.

    PubMed

    Roff, George; Ledlie, Mary H; Ortiz, Juan C; Mumby, Peter J

    2011-01-01

    The past few decades have seen an increase in the frequency and intensity of disturbance on coral reefs, resulting in shifts in size and composition of coral populations. These changes have lead to a renewed focus on processes that influence demographic rates in corals, such as corallivory. While previous research indicates selective corallivory among coral taxa, the importance of coral size and the density of coral colonies in influencing corallivory are unknown. We surveyed the size, taxonomy and number of bites by parrotfish per colony of corals and the abundance of three main corallivorous parrotfish (Sparisoma viride, Sparisoma aurofrenatum, Scarus vetula) at multiple spatial scales (reefs within islands: 1-100 km, and between islands: >100 km) within the Bahamas Archipelago. We used a linear mixed model to determine the influence of coral taxa, colony size, colony density, and parrotfish abundance on the intensity of corallivory (bites per m(2) of coral tissue). While the effect of colony density was significant in determining the intensity of corallivory, we found no significant influence of colony size or parrotfish abundance (density, biomass or community structure). Parrotfish bites were most frequently observed on the dominant species of reef building corals (Montastraea annularis, Montastraea faveolata and Porites astreoides), yet our results indicate that when the confounding effects of colony density and size were removed, selective corallivory existed only for the less dominant Porites porites. As changes in disturbance regimes result in the decline of dominant frame-work building corals such as Montastraea spp., the projected success of P. porites on Caribbean reefs through high reproductive output, resistance to disease and rapid growth rates may be attenuated through selective corallivory by parrotfish.

  14. Taxas de eventos para as fontes astrofísicas do detector Mario Schenberg

    NASA Astrophysics Data System (ADS)

    Castro, C. S.; Araujo, J. C. N.; Miranda, O. D.; Aguiar, O. D.

    2003-08-01

    O detector de ondas gravitacionais Mario Schenberg será sensível a sinais que cheguem à Terra com amplitude h~10-21 e dentro da faixa em frequências que varia de 3,0 a 3,4 kHz. As principais fontes astrofísicas em condições de gerar um sinal detectável pela antena Schenberg são: colapsos estelares que produzam eventos do tipo supernova; instabilidades hidrodinâmicas em estrelas de nêutrons; excitação dos modos fluído (modos f) de estrelas de nêutrons; excitação dos primeiros modos quadrupolares de buracos negros com massa ~ 3,8 M¤; coalescências de estrelas de nêutrons e buracos negros em sistemas binários e, ainda, espiralações de mini-buracos negros. Neste trabalho nós determinamos as taxas de eventos para o Schenberg associadas a dois tipos de fontes: através da de-excitação dos modos f de estrelas de nêutrons e através da coalescência de mini-buracos negros de 0,5 M¤ (que atualmente têm sido colocados como possíveis candidatos a objetos massivos do halo Galáctico). Nós mostramos que esses tipos de fontes poderão produzir sinais em ondas gravitacionais com uma taxa em torno de um evento por ano dentro da banda do Schenberg.

  15. Spatial Patterns of Parrotfish Corallivory in the Caribbean: The Importance of Coral Taxa, Density and Size

    PubMed Central

    Roff, George; Ledlie, Mary H.; Ortiz, Juan C.; Mumby, Peter J.

    2011-01-01

    The past few decades have seen an increase in the frequency and intensity of disturbance on coral reefs, resulting in shifts in size and composition of coral populations. These changes have lead to a renewed focus on processes that influence demographic rates in corals, such as corallivory. While previous research indicates selective corallivory among coral taxa, the importance of coral size and the density of coral colonies in influencing corallivory are unknown. We surveyed the size, taxonomy and number of bites by parrotfish per colony of corals and the abundance of three main corallivorous parrotfish (Sparisoma viride, Sparisoma aurofrenatum, Scarus vetula) at multiple spatial scales (reefs within islands: 1–100 km, and between islands: >100 km) within the Bahamas Archipelago. We used a linear mixed model to determine the influence of coral taxa, colony size, colony density, and parrotfish abundance on the intensity of corallivory (bites per m2 of coral tissue). While the effect of colony density was significant in determining the intensity of corallivory, we found no significant influence of colony size or parrotfish abundance (density, biomass or community structure). Parrotfish bites were most frequently observed on the dominant species of reef building corals (Montastraea annularis, Montastraea faveolata and Porites astreoides), yet our results indicate that when the confounding effects of colony density and size were removed, selective corallivory existed only for the less dominant Porites porites. As changes in disturbance regimes result in the decline of dominant frame-work building corals such as Montastraea spp., the projected success of P. porites on Caribbean reefs through high reproductive output, resistance to disease and rapid growth rates may be attenuated through selective corallivory by parrotfish. PMID:22216184

  16. New reports of nuclear DNA content for 407 vascular plant taxa from the United States

    PubMed Central

    Bai, Chengke; Alverson, William S.; Follansbee, Aaron; Waller, Donald M.

    2012-01-01

    Background and Aims The amount of DNA in an unreplicated haploid nuclear genome (C-value) ranges over several orders of magnitude among plant species and represents a key metric for comparing plant genomes. To extend previously published datasets on plant nuclear content and to characterize the DNA content of many species present in one region of North America, flow cytometry was used to estimate C-values of woody and herbaceous species collected in Wisconsin and the Upper Peninsula of Michigan, USA. Methods A total of 674 samples and vouchers were collected from locations across Wisconsin and Michigan, USA. From these, C-value estimates were obtained for 514 species, subspecies and varieties of vascular plants. Nuclei were extracted from samples of these species in one of two buffers, stained with the fluorochrome propidium iodide, and an Accuri C-6 flow cytometer was used to measure fluorescence peaks relative to those of an internal standard. Replicate extractions, coefficients of variation and comparisons to published C-values in the same and related species were used to confirm the accuracy and reliability of our results. Key Results and Conclusions Prime C-values for 407 taxa are provided for which no published data exist, including 390 angiosperms, two gymnosperms, ten monilophytes and five lycophytes. Non-prime reports for 107 additional taxa are also provided. The prime values represent new reports for 129 genera and five families (of 303 genera and 97 families sampled). New family C-value maxima or minima are reported for Betulaceae, Ericaceae, Ranunculaceae and Sapindaceae. These data provide the basis for phylogenetic analyses of C-value variation and future analyses of how C-values covary with other functional traits. PMID:23100602

  17. Is catchment productivity a useful predictor of taxa richness in lake plankton communities?

    PubMed

    Soininen, Janne; Luoto, Miska

    2012-03-01

    The influence of catchment variables on lake organisms is understudied. The terrestrial zone in the vicinity of lakes is, however, probably highly important for biota due to the effects on water chemistry and to various processes operating across ecosystem boundaries. We examined the relative importance of lake and catchment variables, as well as large-scale geographical factors, on the taxa richness of phyto- and zooplankton in 100 small lakes in Finland. In variation partitioning, the variability of phytoplankton richness was most strongly related to the effects of lake variables, the joint effects of lake and catchment variables, and the joint effects of all three groups of variables. Zooplankton richness, in turn, was most strongly related to the effects of lake and catchment variables and the joint effect of lake and catchment variables. The exact results of the variation partitioning depended on the catchment sizes considered in the regression models. Among lake variables, planktonic richness was strongly related to variables indicating productivity. Among catchment variables, the normalized difference vegetation index (NDVI), indicating catchment productivity, showed a relatively strong association with planktonic richness. These results provide evidence that catchment variables such as the NDVI may be efficient predictors of planktonic richness in small lakes. It is possible that individual lakes embedded in a highly productive landscape have higher taxa richness than solitary, potentially productive lakes because of the high influx of dispersing propagules from the regional pool. We also suggest that catchment variables may respond to environmental changes at different scales than the lake variables, and explicit consideration of catchment productivity would therefore be useful when planning research and monitoring programs for freshwater organisms.

  18. Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters

    PubMed Central

    Gülay, Arda; Musovic, Sanin; Albrechtsen, Hans-Jørgen; Al-Soud, Waleed Abu; Sørensen, Søren J; Smets, Barth F

    2016-01-01

    Here, we document microbial communities in rapid gravity filtration units, specifically serial rapid sand filters (RSFs), termed prefilters (PFs) and after- filters (AFs), fed with anoxic groundwaters low in organic carbon to prepare potable waters. A comprehensive 16S rRNA-based amplicon sequencing survey revealed a core RSF microbiome comprising few bacterial taxa (29–30 genera) dominated by Nitrospirae, Proteobacteria and Acidobacteria, with a strikingly high abundance (75–87±18%) across five examined waterworks in Denmark. Lineages within the Nitrospira genus consistently comprised the second most and most abundant fraction in PFs (27±23%) and AFs (45.2±23%), respectively, and were far more abundant than typical proteobacterial ammonium-oxidizing bacteria, suggesting a physiology beyond nitrite oxidation for Nitrospira. Within the core taxa, sequences closely related to types with ability to oxidize ammonium, nitrite, iron, manganese and methane as primary growth substrate were identified and dominated in both PFs (73.6±6%) and AFs (61.4±21%), suggesting their functional importance. Surprisingly, operational taxonomic unit richness correlated strongly and positively with sampling location in the drinking water treatment plant (from PFs to AFs), and a weaker negative correlation held for evenness. Significant spatial heterogeneity in microbial community composition was detected in both PFs and AFs, and was higher in the AFs. This is the first comprehensive documentation of microbial community diversity in RSFs treating oligotrophic groundwaters. We have identified patterns of local spatial heterogeneity and dispersal, documented surprising energy–diversity relationships, observed a large and diverse Nitrospira fraction and established a core RSF microbiome. PMID:26953601

  19. Regional Differences in Seasonal Timing of Rainfall Discriminate between Genetically Distinct East African Giraffe Taxa

    PubMed Central

    Thomassen, Henri A.; Freedman, Adam H.; Brown, David M.; Buermann, Wolfgang; Jacobs, David K.

    2013-01-01

    Masai (Giraffa tippelskirchi), Reticulated (G. reticulata) and Rothschild's (G. camelopardalis) giraffe lineages in East Africa are morphologically and genetically distinct, yet in Kenya their ranges abut. This raises the question of how divergence is maintained among populations of a large mammal capable of long-distance travel, and which readily hybridize in zoos. Here we test four hypotheses concerning the maintenance of the phylogeographic boundaries among the three taxa: 1) isolation-by-distance; 2) physical barriers to dispersal; 3) general habitat differences resulting in habitat segregation; or 4) regional differences in the seasonal timing of rainfall, and resultant timing of browse availability. We used satellite remotely sensed and climate data to characterize the environment at the locations of genotyped giraffes. Canonical variate analysis, random forest algorithms, and generalized dissimilarity modelling were employed in a landscape genetics framework to identify the predictor variables that best explained giraffes' genetic divergence. We found that regional differences in the timing of precipitation, and resulting green-up associated with the abundance of browse, effectively discriminate between taxa. Local habitat conditions, topographic and human-induced barriers, and geographic distance did not aid in discriminating among lineages. Our results suggest that selection associated with regional timing of events in the annual climatic cycle may help maintain genetic and phenotypic divergence in giraffes. We discuss potential mechanisms of maintaining divergence, and suggest that synchronization of reproduction with seasonal rainfall cycles that are geographically distinct may contribute to reproductive isolation. Coordination of weaning with green-up cycles could minimize the costs of lactation and predation on the young. Our findings are consistent with theory and empirical results demonstrating the efficacy of seasonal or phenologically dictated

  20. Regional differences in seasonal timing of rainfall discriminate between genetically distinct East African giraffe taxa.

    PubMed

    Thomassen, Henri A; Freedman, Adam H; Brown, David M; Buermann, Wolfgang; Jacobs, David K

    2013-01-01

    Masai (Giraffa tippelskirchi), Reticulated (G. reticulata) and Rothschild's (G. camelopardalis) giraffe lineages in East Africa are morphologically and genetically distinct, yet in Kenya their ranges abut. This raises the question of how divergence is maintained among populations of a large mammal capable of long-distance travel, and which readily hybridize in zoos. Here we test four hypotheses concerning the maintenance of the phylogeographic boundaries among the three taxa: 1) isolation-by-distance; 2) physical barriers to dispersal; 3) general habitat differences resulting in habitat segregation; or 4) regional differences in the seasonal timing of rainfall, and resultant timing of browse availability. We used satellite remotely sensed and climate data to characterize the environment at the locations of genotyped giraffes. Canonical variate analysis, random forest algorithms, and generalized dissimilarity modelling were employed in a landscape genetics framework to identify the predictor variables that best explained giraffes' genetic divergence. We found that regional differences in the timing of precipitation, and resulting green-up associated with the abundance of browse, effectively discriminate between taxa. Local habitat conditions, topographic and human-induced barriers, and geographic distance did not aid in discriminating among lineages. Our results suggest that selection associated with regional timing of events in the annual climatic cycle may help maintain genetic and phenotypic divergence in giraffes. We discuss potential mechanisms of maintaining divergence, and suggest that synchronization of reproduction with seasonal rainfall cycles that are geographically distinct may contribute to reproductive isolation. Coordination of weaning with green-up cycles could minimize the costs of lactation and predation on the young. Our findings are consistent with theory and empirical results demonstrating the efficacy of seasonal or phenologically dictated

  1. An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa.

    PubMed

    Meldal, Birgit H M; Debenham, Nicola J; De Ley, Paul; De Ley, Irma Tandingan; Vanfleteren, Jacques R; Vierstraete, Andy R; Bert, Wim; Borgonie, Gaetan; Moens, Tom; Tyler, Paul A; Austen, Melanie C; Blaxter, Mark L; Rogers, Alex D; Lambshead, P J D

    2007-03-01

    Phylogenetic reconstructions of relations within the phylum Nematoda are inherently difficult but have been advanced with the introduction of large-scale molecular-based techniques. However, the most recent revisions were heavily biased towards terrestrial and parasitic species and greater representation of clades containing marine species (e.g. Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, Enoplida, and Monhysterida) is needed for accurate coverage of known taxonomic diversity. We now add small subunit ribosomal DNA (SSU rDNA) sequences for 100 previously un-sequenced species of nematodes, including 46 marine taxa. SSU rDNA sequences for >200 taxa have been analysed based on Bayesian inference and LogDet-transformed distances. The resulting phylogenies provide support for (i) the re-classification of the Secernentea as the order Rhabditida that derived from a common ancestor of chromadorean orders Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, and Monhysterida and (ii) the position of Bunonema close to the Diplogasteroidea in the Rhabditina. Other, previously controversial relationships can now be resolved more clearly: (a) Alaimus, Campydora, and Trischistoma belong in the Enoplida, (b) Isolaimium is placed basally to a big clade containing the Axonolaimidae, Plectidae, and Rhabditida, (c) Xyzzors belongs in the Desmodoridae, (d) Comesomatidae and Cyartonema belongs in the Monhysterida, (e) Globodera belongs in the Hoplolaimidae and (f) Paratylenchus dianeae belongs in the Criconematoidea. However, the SSU gene did not provide significant support for the class Chromadoria or clear evidence for the relationship between the three classes, Enoplia, Dorylaimia, and Chromadoria. Furthermore, across the whole phylum, the phylogenetically informative characters of the SSU gene are not informative in a parsimony analysis, highlighting the short-comings of the parsimony method for large-scale phylogenetic modelling.

  2. Cellular differentiation and individuality in the “minor” multicellular taxa

    PubMed Central

    Herron, Matthew D.; Rashidi, Armin; Shelton, Deborah E.; Driscoll, William W.

    2014-01-01

    Biology needs a concept of individuality in order to distinguish organisms from parts of organisms and from groups of organisms, to count individuals and compare traits across taxa, and to distinguish growth from reproduction. Most of the proposed criteria for individuality were designed for ‘unitary’ or ‘paradigm’ organisms: contiguous, functionally and physiologically integrated, obligately sexually reproducing multicellular organisms with a germ line sequestered early in development. However, the vast majority of the diversity of life on Earth does not conform to all of these criteria. We consider the issue of individuality in the ‘minor’ multicellular taxa, which collectively span a large portion of the eukaryotic tree of life, reviewing their general features and focusing on a model species for each group. When the criteria designed for unitary organisms are applied to other groups, they often give conflicting answers or no answer at all to the question of whether or not a given unit is an individual. Complex life cycles, intimate bacterial symbioses, aggregative development, and strange genetic features complicate the picture. The great age of some of the groups considered shows that ‘intermediate’ forms, those with some but not all of the traits traditionally associated with individuality, cannot reasonably be considered ephemeral or assumed transitional. We discuss a handful of recent attempts to reconcile the many proposed criteria for individuality and to provide criteria that can be applied across all the domains of life. Finally, we argue that individuality should be defined without reference to any particular taxon and that understanding the emergence of new kinds of individuals requires recognizing individuality as a matter of degree. PMID:23448295

  3. Host-specificity among abundant and rare taxa in the sponge microbiome.

    PubMed

    Reveillaud, Julie; Maignien, Loïs; Murat Eren, A; Huber, Julie A; Apprill, Amy; Sogin, Mitchell L; Vanreusel, Ann

    2014-06-01

    Microbial communities have a key role in the physiology of the sponge host, and it is therefore essential to understand the stability and specificity of sponge-symbiont associations. Host-specific bacterial associations spanning large geographic distance are widely acknowledged in sponges. However, the full spectrum of specificity remains unclear. In particular, it is not known whether closely related sponges host similar or very different microbiota over wide bathymetric and geographic gradients, and whether specific associations extend to the rare members of the sponge microbiome. Using the ultra-deep Illumina sequencing technology, we conducted a comparison of sponge bacterial communities in seven closely related Hexadella species with a well-resolved host phylogeny, as well as of a distantly related sponge Mycale. These samples spanned unprecedentedly large bathymetric (15-960 m) gradients and varying European locations. In addition, this study included a bacterial community analysis of the local background seawater for both Mycale and the widespread deep-sea taxa Hexadella cf. dedritifera. We observed a striking diversity of microbes associated with the sponges, spanning 47 bacterial phyla. The data did not reveal any Hexadella microbiota co-speciation pattern, but confirmed sponge-specific and species-specific host-bacteria associations, even within extremely low abundant taxa. Oligotyping analysis also revealed differential enrichment preferences of closely related Nitrospira members in closely related sponges species. Overall, these results demonstrate highly diverse, remarkably specific and stable sponge-bacteria associations that extend to members of the rare biosphere at a very fine phylogenetic scale, over significant geographic and bathymetric gradients.

  4. Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume

    PubMed Central

    Kleindienst, Sara; Grim, Sharon; Sogin, Mitchell; Bracco, Annalisa; Crespo-Medina, Melitza; Joye, Samantha B

    2016-01-01

    The Deepwater Horizon (DWH) oil well blowout generated an enormous plume of dispersed hydrocarbons that substantially altered the Gulf of Mexico's deep-sea microbial community. A significant enrichment of distinct microbial populations was observed, yet, little is known about the abundance and richness of specific microbial ecotypes involved in gas, oil and dispersant biodegradation in the wake of oil spills. Here, we document a previously unrecognized diversity of closely related taxa affiliating with Cycloclasticus, Colwellia and Oceanospirillaceae and describe their spatio-temporal distribution in the Gulf's deepwater, in close proximity to the discharge site and at increasing distance from it, before, during and after the discharge. A highly sensitive, computational method (oligotyping) applied to a data set generated from 454-tag pyrosequencing of bacterial 16S ribosomal RNA gene V4–V6 regions, enabled the detection of population dynamics at the sub-operational taxonomic unit level (0.2% sequence similarity). The biogeochemical signature of the deep-sea samples was assessed via total cell counts, concentrations of short-chain alkanes (C1–C5), nutrients, (colored) dissolved organic and inorganic carbon, as well as methane oxidation rates. Statistical analysis elucidated environmental factors that shaped ecologically relevant dynamics of oligotypes, which likely represent distinct ecotypes. Major hydrocarbon degraders, adapted to the slow-diffusive natural hydrocarbon seepage in the Gulf of Mexico, appeared unable to cope with the conditions encountered during the DWH spill or were outcompeted. In contrast, diverse, rare taxa increased rapidly in abundance, underscoring the importance of specialized sub-populations and potential ecotypes during massive deep-sea oil discharges and perhaps other large-scale perturbations. PMID:26230048

  5. Biodiversity conservation across taxa and landscapes requires many small as well as single large habitat fragments.

    PubMed

    Rösch, Verena; Tscharntke, Teja; Scherber, Christoph; Batáry, Péter

    2015-09-01

    Agricultural intensification has been shown to reduce biodiversity through processes such as habitat degradation and fragmentation. We tested whether several small or single large habitat fragments (re-visiting the 'single large or several small' debate) support more species across a wide range of taxonomic groups (plants, leafhoppers, true bugs, snails). Our study comprised 14 small (<1 ha) and 14 large (1.5-8 ha) fragments of calcareous grassland in Central Germany along orthogonal gradients of landscape complexity and habitat connectivity. Each taxon was sampled on six plots per fragment. Across taxa, species richness did not differ between large and small fragments, whereas species-area accumulation curves showed that both overall and specialist species richness was much higher on several small fragments of calcareous grassland than on few large fragments. On average, 85% of the overall species richness was recorded on all small fragments taken together (4.6 ha), whereas the two largest ones (15.1 ha) only accounted for 37% of the species. This could be due to the greater geographic extent covered by many small fragments. However, community composition differed strongly between large and small fragments, and some of the rarest specialist species appeared to be confined to large fragments. The surrounding landscape did not show any consistent effects on species richness and community composition. Our results show that both single large and many small fragments are needed to promote landscape-wide biodiversity across taxa. We therefore question the focus on large fragments only and call for a new diversified habitat fragmentation strategy for biodiversity conservation.

  6. Physiological and ecological performance differs in four coral taxa at a volcanic carbon dioxide seep.

    PubMed

    Strahl, J; Stolz, I; Uthicke, S; Vogel, N; Noonan, S H C; Fabricius, K E

    2015-06-01

    Around volcanic carbon dioxide (CO2) seeps in Papua New Guinea, partial pressures of CO2 (pCO2) approximate those as predicted for the end of this century, and coral communities have low diversity and low structural complexity. To assess the mechanisms for such community shifts in response to ocean acidification, we examined the physiological performance of two hard corals that occur with increased or unaltered abundance at a seep site (mean pHTotal=7.8, pCO2=862 μatm) compared to a control site (mean pHTotal=8.1, pCO2=323 μatm), namely massive Porites spp. and Pocillopora damicornis, and two species with reduced abundance, Acropora millepora and Seriatopora hystrix. Oxygen fluxes, calcification, and skeletal densities were analyzed in corals originating from the seep and control site. Net photosynthesis rates increased considerably in Porites spp. and A. millepora and slightly in P. damicornis at increased pCO2, but remained unaltered in S. hystrix. Dark respiration rates remained constant in all corals investigated from both sites. Rates of light calcification declined in S. hystrix at high pCO2, but were unaffected by pCO2 in the other three coral taxa. Dark and net calcification rates remained unchanged in massive Porites and P. damicornis, but were drastically reduced at high pCO2 in A. millepora and S. hystrix. However, skeletal densities were similar at both seep and control sites in all coral taxa investigated. Our data suggest that the pCO2-tolerant corals were characterized by an increased ability to acclimatize to ocean acidification, e.g. by maintaining net calcification. Thus, robust corals, such as Porites spp. and P. damicornis, are more likely to persist for longer in a future high pCO2 world than those unable to acclimatize.

  7. Molecular evolutionary patterns of NAD+/Sirtuin aging signaling pathway across taxa

    PubMed Central

    Gao, Yue; Lian, Ting; Sun, Boyuan; Yang, Deying; Fan, Xiaolan

    2017-01-01

    A deeper understanding of the conserved molecular mechanisms in different taxa have been made possible only because of the evolutionary conservation of crucial signaling pathways. In the present study, we explored the molecular evolutionary pattern of selection signatures in 51 species for 10 genes which are important components of NAD+/Sirtuin pathway and have already been directly linked to lifespan extension in worms and mice. Selection pressure analysis using PAML program revealed that MRPS5 and PPARGC1A were under significant constraints because of their functional significance. FOXO3a also displayed strong purifying selection. All three sirtuins, which were SIRT1, SIRT2 and SIRT6, displayed a great degree of conservation between taxa, which is consistent with the previous report. A significant evolutionary constraint is seen on the anti-oxidant gene, SOD3. As expected, TP53 gene was under significant selection pressure in mammals, owing to its major role in tumor progression. Poly-ADP-ribose polymerase (PARP) genes displayed the most sites under positive selection. Further 3D structural analysis of PARP1 and PARP2 protein revealed that some of these positively selected sites caused a change in the electrostatic potential of the protein structure, which may allow a change in its interaction with other proteins and molecules ultimately leading to difference in the function. Although the functional significance of the positively selected sites could not be established in the variants databases, yet it will be interesting to see if these sites actually affect the function of PARP1 and PARP2. PMID:28767699

  8. Comparative analysis of essential oils of six Anthemis taxa from Serbia and Montenegro.

    PubMed

    Pavlović, Milica; Lakusić, Dmitar; Kovacević, Nada; Tzakou, Olga; Couladis, Maria

    2010-05-01

    The essential-oil composition of six Anthemis taxa from several populations in Serbia and Montenegro, Anthemis triumfetti (L.) DC., A. tinctoria L., A. austriaca Jacq., A. ruthenica Bieb., A. cotula L., and A. cretica ssp. carpatica (Willd.) Grierson were analyzed by GC and GC/MS. The main constituents have been identified as follows: camphor (13.8-15.4%), alpha-pinene (5.2-9.3%), beta-pinene (4.9-7.8%), and (E)-caryophyllene (7.3-9.8%) in three populations, and cis-chrysanthenol (27.0%) and 1,8-cineole (8.4%) in one population of A. triumfetti; 1,8-cineole (9.0-25.8%) in the oils of five populations, and borneol (16.0%) and spatulenol (16.0%) in the oil of one population of A. tinctoria; cis-chrysanthenyl acetate (17.5-22.0%), beta-pinene (8.6-13.2%), and 1,8-cineole (7.2-10.4%) in the oils of A. austriaca; germacrene D (8.3-11.3%) and terpinen-4-ol (6.3-7.3%) in A. ruthenica oils; beta-cedrene (10.3-19.0%), (E)-beta-farnesene (7.8-13.5%), and germacrene D (5.2-9.1%) in the oils of A. cotula; cis-thujone (39.0%), trans-thujone (13.5%), and yomogi alcohol (7.1%) in the oil of A. cretica ssp. carpatica. The essential oil of A. austriaca was studied for the first time. A cluster analysis based on the relative percentages of all components of the essential oils was used to determine the distances between taxa and populations.

  9. Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters.

    PubMed

    Gülay, Arda; Musovic, Sanin; Albrechtsen, Hans-Jørgen; Al-Soud, Waleed Abu; Sørensen, Søren J; Smets, Barth F

    2016-09-01

    Here, we document microbial communities in rapid gravity filtration units, specifically serial rapid sand filters (RSFs), termed prefilters (PFs) and after- filters (AFs), fed with anoxic groundwaters low in organic carbon to prepare potable waters. A comprehensive 16S rRNA-based amplicon sequencing survey revealed a core RSF microbiome comprising few bacterial taxa (29-30 genera) dominated by Nitrospirae, Proteobacteria and Acidobacteria, with a strikingly high abundance (75-87±18%) across five examined waterworks in Denmark. Lineages within the Nitrospira genus consistently comprised the second most and most abundant fraction in PFs (27±23%) and AFs (45.2±23%), respectively, and were far more abundant than typical proteobacterial ammonium-oxidizing bacteria, suggesting a physiology beyond nitrite oxidation for Nitrospira. Within the core taxa, sequences closely related to types with ability to oxidize ammonium, nitrite, iron, manganese and methane as primary growth substrate were identified and dominated in both PFs (73.6±6%) and AFs (61.4±21%), suggesting their functional importance. Surprisingly, operational taxonomic unit richness correlated strongly and positively with sampling location in the drinking water treatment plant (from PFs to AFs), and a weaker negative correlation held for evenness. Significant spatial heterogeneity in microbial community composition was detected in both PFs and AFs, and was higher in the AFs. This is the first comprehensive documentation of microbial community diversity in RSFs treating oligotrophic groundwaters. We have identified patterns of local spatial heterogeneity and dispersal, documented surprising energy-diversity relationships, observed a large and diverse Nitrospira fraction and established a core RSF microbiome.

  10. Host-specificity among abundant and rare taxa in the sponge microbiome

    PubMed Central

    Reveillaud, Julie; Maignien, Loïs; Eren, Murat A; Huber, Julie A; Apprill, Amy; Sogin, Mitchell L; Vanreusel, Ann

    2014-01-01

    Microbial communities have a key role in the physiology of the sponge host, and it is therefore essential to understand the stability and specificity of sponge–symbiont associations. Host-specific bacterial associations spanning large geographic distance are widely acknowledged in sponges. However, the full spectrum of specificity remains unclear. In particular, it is not known whether closely related sponges host similar or very different microbiota over wide bathymetric and geographic gradients, and whether specific associations extend to the rare members of the sponge microbiome. Using the ultra-deep Illumina sequencing technology, we conducted a comparison of sponge bacterial communities in seven closely related Hexadella species with a well-resolved host phylogeny, as well as of a distantly related sponge Mycale. These samples spanned unprecedentedly large bathymetric (15–960 m) gradients and varying European locations. In addition, this study included a bacterial community analysis of the local background seawater for both Mycale and the widespread deep-sea taxa Hexadella cf. dedritifera. We observed a striking diversity of microbes associated with the sponges, spanning 47 bacterial phyla. The data did not reveal any Hexadella microbiota co-speciation pattern, but confirmed sponge-specific and species-specific host–bacteria associations, even within extremely low abundant taxa. Oligotyping analysis also revealed differential enrichment preferences of closely related Nitrospira members in closely related sponges species. Overall, these results demonstrate highly diverse, remarkably specific and stable sponge–bacteria associations that extend to members of the rare biosphere at a very fine phylogenetic scale, over significant geographic and bathymetric gradients. PMID:24401862

  11. Explaining Spatial Variation in the Recording Effort of Citizen Science Data across Multiple Taxa

    PubMed Central

    Mair, Louise; Ruete, Alejandro

    2016-01-01

    The collation of citizen science data in open-access biodiversity databases makes temporally and spatially extensive species’ observation data available to a wide range of users. Such data are an invaluable resource but contain inherent limitations, such as sampling bias in favour of recorder distribution, lack of survey effort assessment, and lack of coverage of the distribution of all organisms. Any technical assessment, monitoring program or scientific research applying citizen science data should therefore include an evaluation of the uncertainty of its results. We use ‘ignorance’ scores, i.e. spatially explicit indices of sampling bias across a study region, to further understand spatial patterns of observation behaviour for 13 reference taxonomic groups. The data is based on voluntary observations made in Sweden between 2000 and 2014. We compared the effect of six geographical variables (elevation, steepness, population density, log population density, road density and footpath density) on the ignorance scores of each group. We found substantial variation among taxonomic groups in the relative importance of different geographic variables for explaining ignorance scores. In general, road access and logged population density were consistently important variables explaining bias in sampling effort, indicating that access at a landscape-scale facilitates voluntary reporting by citizen scientists. Also, small increases in population density can produce a substantial reduction in ignorance score. However the between-taxa variation in the importance of geographic variables for explaining ignorance scores demonstrated that different taxa suffer from different spatial biases. We suggest that conservationists and researchers should use ignorance scores to acknowledge uncertainty in their analyses and conclusions, because they may simultaneously include many correlated variables that are difficult to disentangle. PMID:26820846

  12. Explaining Spatial Variation in the Recording Effort of Citizen Science Data across Multiple Taxa.

    PubMed

    Mair, Louise; Ruete, Alejandro

    2016-01-01

    The collation of citizen science data in open-access biodiversity databases makes temporally and spatially extensive species' observation data available to a wide range of users. Such data are an invaluable resource but contain inherent limitations, such as sampling bias in favour of recorder distribution, lack of survey effort assessment, and lack of coverage of the distribution of all organisms. Any technical assessment, monitoring program or scientific research applying citizen science data should therefore include an evaluation of the uncertainty of its results. We use 'ignorance' scores, i.e. spatially explicit indices of sampling bias across a study region, to further understand spatial patterns of observation behaviour for 13 reference taxonomic groups. The data is based on voluntary observations made in Sweden between 2000 and 2014. We compared the effect of six geographical variables (elevation, steepness, population density, log population density, road density and footpath density) on the ignorance scores of each group. We found substantial variation among taxonomic groups in the relative importance of different geographic variables for explaining ignorance scores. In general, road access and logged population density were consistently important variables explaining bias in sampling effort, indicating that access at a landscape-scale facilitates voluntary reporting by citizen scientists. Also, small increases in population density can produce a substantial reduction in ignorance score. However the between-taxa variation in the importance of geographic variables for explaining ignorance scores demonstrated that different taxa suffer from different spatial biases. We suggest that conservationists and researchers should use ignorance scores to acknowledge uncertainty in their analyses and conclusions, because they may simultaneously include many correlated variables that are difficult to disentangle.

  13. Systematics of the family Plectopylidae in Vietnam with additional information on Chinese taxa (Gastropoda, Pulmonata, Stylommatophora)

    PubMed Central

    Páll-Gergely, Barna; Hunyadi, András; Ablett, Jonathan; Lương, Hào Văn; Fred Naggs; Asami, Takahiro

    2015-01-01

    Abstract Vietnamese species from the family Plectopylidae are revised based on the type specimens of all known taxa, more than 600 historical non-type museum lots, and almost 200 newly-collected samples. Altogether more than 7000 specimens were investigated. The revision has revealed that species diversity of the Vietnamese Plectopylidae was previously overestimated. Overall, thirteen species names (anterides Gude, 1909, bavayi Gude, 1901, congesta Gude, 1898, fallax Gude, 1909, gouldingi Gude, 1909, hirsuta Möllendorff, 1901, jovia Mabille, 1887, moellendorffi Gude, 1901, persimilis Gude, 1901, pilsbryana Gude, 1901, soror Gude, 1908, tenuis Gude, 1901, verecunda Gude, 1909) were synonymised with other species. In addition to these, Gudeodiscus hemmeni sp. n. and Gudeodiscus messageri raheemi ssp. n. are described from north-western Vietnam. Sixteen species and two subspecies are recognized from Vietnam. The reproductive anatomy of eight taxa is described. Based on anatomical information, Halongella gen. n. is erected to include Plectopylis schlumbergeri and Plectopylis fruhstorferi. Additionally, the genus Gudeodiscus is subdivided into two subgenera (Gudeodiscus and Veludiscus subgen. n.) on the basis of the morphology of the reproductive anatomy and the radula. The Chinese Gudeodiscus phlyarius werneri Páll-Gergely, 2013 is moved to synonymy of Gudeodiscus phlyarius. A spermatophore was found in the organ situated next to the gametolytic sac in one specimen. This suggests that this organ in the Plectopylidae is a diverticulum. Statistically significant evidence is presented for the presence of calcareous hook-like granules inside the penis being associated with the absence of embryos in the uterus in four genera. This suggests that these probably play a role in mating periods before disappearing when embryos develop. Sicradiscus mansuyi is reported from China for the first time. PMID:25632253

  14. Determining Clostridium difficile intra-taxa diversity by mining multilocus sequence typing databases.

    PubMed

    Muñoz, Marina; Ríos-Chaparro, Dora Inés; Patarroyo, Manuel Alfonso; Ramírez, Juan David

    2017-03-14

    Multilocus sequence typing (MLST) is a highly discriminatory typing strategy; it is reproducible and scalable. There is a MLST scheme for Clostridium difficile (CD), a gram positive bacillus causing different pathologies of the gastrointestinal tract. This work was aimed at describing the frequency of sequence types (STs) and Clades (C) reported and evalute the intra-taxa diversity in the CD MLST database (CD-MLST-db) using an MLSA approach. Analysis of 1778 available isolates showed that clade 1 (C1) was the most frequent worldwide (57.7%), followed by C2 (29.1%). Regarding sequence types (STs), it was found that ST-1, belonging to C2, was the most frequent. The isolates analysed came from 17 countries, mostly from the United Kingdom (UK) (1541 STs, 87.0%). The diversity of the seven housekeeping genes in the MLST scheme was evaluated, and alleles from the profiles (STs), for identifying CD population structure. It was found that adk and atpA are conserved genes allowing a limited amount of clusters to be discriminated; however, different genes such as drx, glyA and particularly sodA showed high diversity indexes and grouped CD populations in many clusters, suggesting that these genes' contribution to CD typing should be revised. It was identified that CD STs reported to date have a mostly clonal population structure with foreseen events of recombination; however, one group of STs was not assigned to a clade being highly different containing at least nine well-supported clusters, suggesting a greater amount of clades for CD. This study shows the usefulness of CD-MLST-db as a tool for studying CD distribution and population structure, identifying the need for reviewing the usefulness of sodA as housekeeping gene within the MLST scheme and suggesting the existence of a greater amount of CD clades. The study also shows the plausible exchange of genetic material between STs, contributing towards intra-taxa genetic diversity.

  15. The Implications of Stratigraphic Compatibility for Character Integration among Fossil Taxa.

    PubMed

    Wagner, Peter J; Estabrook, George F

    2015-09-01

    Two characters are stratigraphically compatible if some phylogenies indicate that their combinations (state-pairs) evolved without homoplasy and in an order consistent with the fossil record. Simulations assuming independent character change indicate that we expect approximately 95% of compatible character pairs to also be stratigraphically compatible over a wide range of sampling regimes and general evolutionary models. However, two general models of rate heterogeneity elevate expected stratigraphic incompatibility: "early burst" models, where rates of change are higher among early members of a clade than among later members of that clade, and "integration" models, where the evolution of characters is correlated in some manner. Both models have important theoretical and methodological implications. Therefore, we examine 259 metazoan clades for deviations from expected stratigraphic compatibility. We do so first assuming independent change with equal rates of character change through time. We then repeat the analysis assuming independent change with separate "early" and "late" rates (with "early" = the first third of taxa in a clade), with the early and late rates chosen to maximize the probability of the observed compatibility among the early taxa and then the whole clade. We single out Cambrian trilobites as a possible "control" group because morphometric studies suggest that integration patterns are not conserved among closely related species. Even allowing for early bursts, we see excess stratigraphic incompatibility (i.e., negative deviations) in significantly more clades than expected at 0.50, 0.25, and 0.05 [Formula: see text] values. This pattern is particularly strong in chordates, echinoderms, and arthropods. However, stratigraphic compatibility among Cambrian trilobites matches the expectations of integration studies, as they (unlike post-Cambrian trilobites) do not deviate from the expectations of independent change with no early bursts. Thus, these

  16. Molecular evidence indicates that subarctic willow communities in Scotland support a diversity of host-associated Melampsora rust taxa.

    PubMed

    Milne, Jeremy M; Helfer, Stephan; Kirk, Calum; Hollingsworth, Peter M; Ennos, Richard A

    2012-05-01

    Rare and threatened subarctic willow scrub communities in the UK are the subject of ongoing conservation programmes, yet little is known about the diversity of fungal taxa that they support. Isolates of the rust genus Melampsora were sampled from 112 leaves of eight subarctic willow (Salix) taxa and their hybrids from twelve sites in the UK. In order to determine the number of Melampsora taxa present in the samples, isolates were sequenced for the Internal Transcribed Spacer (ITS) region of rDNA and data were subject to phylogenetic analysis. Maximum likelihood and Bayesian analysis indicated that the isolates fell into three strongly supported host-associated clades. Clade I contained only isolates from Salix herbacea and was distinguished morphologically by dense urediniospore echinulation and thin cell walls. Clade II contained isolates from Salix arbuscula and Salix reticulata only. These could not be distinguished morphologically from isolates in Clade III which were found on Salix lapponum, Salix myrsinites, Salix myrsinifolia, Salix aurita, Salix lanata, and their hybrids. Clade II was most distinct in ITS sequence, differing by 50 bases from Clades I and III, while the latter clades differed in sequence by only 24 bases on average. Clades I and III are likely to represent the previously recognised taxa Melampsora alpina Juel 1894 and Melampsora epitea Thüm. 1879 respectively, but Clade II has not apparently been described before. Significant differences in the intensity of infection by isolates of Clade III were found among different Salix species at a single site, suggesting either differences in resistance among Salix taxa, or the presence of further cryptic taxa within Clade III. The study illustrates the power of molecular phylogenetic analysis to reveal cryptic biodiversity within Melampsora, and suggests that conserving Salix host diversity within subarctic willow communities will ensure that a diversity of associated Melampsora taxa is maintained.

  17. PoroTomo: DAS Vibroseis Data

    DOE Data Explorer

    Kurt Feigl

    2016-03-25

    The submitted data correspond to the monitored vibrations caused by a vibroseis seismically exciting the ground in the vertical direction and captured by the DAS horizontal and vertical arrays during the PoroTomo Experiment. The data also include a file with the acceleration record at the Vibroseis. Vibroseis Sweep Details: Sweep on location T84 Stage 4 (Mode P 60 s long record ) Time: 2016-03-25 14:01:15 (UTC) Location: 39.80476089N, -119.0027625W Elevation: 1272.0M (on ground surface at the site) Sweep length: 20 seconds Frequencies: 5 Hz to 20 Hz

  18. Das CARNOTsche Paradigma und seine erkenntnistheoretischen Implikationen

    NASA Astrophysics Data System (ADS)

    Schöpf, Hans-Georg

    Der vorliegende historisch-kritische Essay führt die Eigentümlichkeiten der klassischen phänomenologischen Thermodynamik auf das von CARNOT geschaffene Paradigma zurück und greift einige damit zusammenhängende Fragen auf.Translated AbstractCARNOT's Paradigm and its Epistemological ImplicationsThe present historic-critical essay traces the pecularities of classical phenomenological thermodynamics back to the paradigm, created by CARNOT, and takes up some questions to which this paradigm gives rise.

  19. Histochemistry of Centroorhynchus falconis (Das, 1950).

    PubMed

    Rengaraju, V; Das, E N

    1976-01-01

    With a view to augment the understanding of the animal mucosubstances in general and Acanthocephalan mucosubstances in particular, Acanthocephalan worms of (Centrorhynchus falconis, Das, 1950) were investigated histochemically by employing recent techniques. Variations in the intensity of histochemical reactions in different tissues revealed a heterogenous distribution of mucosubstances. The cuticle contained a mixture of periodate reactive neutral mucosubstances and sulfomucins, whereas the subcuticle contained only glycogen. Retractor muscles contained glycogen together with some acidic mucosubstances which exhibited alcianophilia only at high pH. Cement glands elaborated a mixture of glycogen and galactogen. Histochemical methods revealed two types of acanthors: Some contained only glycogen, whereas others contained glycogen and galactogen.

  20. PoroTomo Project - Subatask 6.2: Deploy and Operate DAS and DTS arrays - DAS Earthquake Data

    DOE Data Explorer

    Kurt Feigl

    2016-03-21

    The submitted data correspond to the vibration caused by a 3.4 M earthquake and captured by the DAS horizontal and vertical arrays during the PoroTomo Experiment. Earthquake information : M 4.3 - 23km ESE of Hawthorne, Nevada Time: 2016-03-21 07:37:10 (UTC) Location: 38.479°N 118.366°W Depth: 9.9 km Files for horizontal DAS array (each file is 30 s long and contain 8700 channels): PoroTomo_iDAS16043_160321073721.sgy PoroTomo_iDAS16043_160321073751.sgy Files for vertical DAS Array (each file is 30 s long and contain 380 channels): PoroTomo_iDAS025_160321073717.sgy PoroTomo_iDAS025_160321073747.sgy

  1. Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa.

    PubMed

    Strait, David S; Grine, Frederick E

    2004-12-01

    Recent discoveries of new fossil hominid species have been accompanied by several phylogenetic hypotheses. All of these hypotheses are based on a consideration of hominid craniodental morphology. However, Collard and Wood (2000) suggested that cladograms derived from craniodental data are inconsistent with the prevailing hypothesis of ape phylogeny based on molecular data. The implication of their study is that craniodental characters are unreliable indicators of phylogeny in hominoids and fossil hominids but, notably, their analysis did not include extinct species. We report here on a cladistic analysis designed to test whether the inclusion of fossil taxa affects the ability of morphological characters to recover the molecular ape phylogeny. In the process of doing so, the study tests both Collard and Wood's (2000) hypothesis of character reliability, and the several recently proposed hypotheses of early hominid phylogeny. One hundred and ninety-eight craniodental characters were examined, including 109 traits that traditionally have been of interest in prior studies of hominoid and early hominid phylogeny, and 89 craniometric traits that represent size-corrected linear dimensions measured between standard cranial landmarks. The characters were partitioned into two data sets. One set contained all of the characters, and the other omitted the craniometric characters. Six parsimony analyses were performed; each data set was analyzed three times, once using an ingroup that consisted only of extant hominoids, a second time using an ingroup of extant hominoids and extinct early hominids, and a third time excluding Kenyanthropus platyops. Results suggest that the inclusion of fossil taxa can play a significant role in phylogenetic analysis. Analyses that examined only extant taxa produced most parsimonious cladograms that were inconsistent with the ape molecular tree. In contrast, analyses that included fossil hominids were consistent with that tree. This consistency

  2. Life history profiles for 27 strepsirrhine primate taxa generated using captive data from the Duke Lemur Center.

    PubMed

    Zehr, Sarah M; Roach, Richard G; Haring, David; Taylor, Julie; Cameron, Freda H; Yoder, Anne D

    2014-01-01

    Since its establishment in 1966, the Duke Lemur Center (DLC) has accumulated detailed records for nearly 4,200 individuals from over 40 strepsirrhine primate taxa-the lemurs, lorises, and galagos. Here we present verified data for 3,627 individuals of 27 taxa in the form of a life history table containing summarized species values for variables relating to ancestry, reproduction, longevity, and body mass, as well as the two raw data files containing direct and calculated variables from which this summary table is built. Large sample sizes, longitudinal data that in many cases span an animal's entire life, exact dates of events, and large numbers of individuals from closely related yet biologically diverse primate taxa make these datasets unique. This single source for verified raw data and systematically compiled species values, particularly in combination with the availability of associated biological samples and the current live colony for research, will support future studies from an enormous spectrum of disciplines.

  3. A Multi-Proxy Investigation into the Biomineralization Pathways of Benthic Invertebrate Taxa

    NASA Astrophysics Data System (ADS)

    DeCorte, I. A.; Liu, Y. W.; Doss, W. C.; Ries, J. B.; Eagle, R.

    2016-12-01

    Ocean acidification is the result of surface ocean absorption of anthropogenic carbon dioxide emissions and endangers many marine organisms. Decreases in pH and a coupled reduction in CaCO3 saturation state have been shown to disrupt the process of biomineralization within many species of marine calcifiers. Recent studies, however, demonstrate that calcifying organisms respond in diverse ways to changes in pH and CaCO3 saturation state. We examine element ratios (including Sr/Ca, Mg/Ca, Li/Ca, and B/Ca) and boron isotope ratios (δ11B) in 7 macro-invertebrate species (blue crab, shrimp, coralline red algae, pencil urchin, purple urchin, temperate coral, and serpulid worm) and compare results to net calcification rates and experimental seawater carbonate system parameters. Correlations between seawater carbonate chemistry and the elemental compositions of biogenic calcite and aragonite vary widely and are highly taxon-specific, ranging from strongly correlated to no significant response—a finding that is consistent with mounting evidence that many marine calcifying organisms regulate the chemistry of the fluid at their site of calcification. A Rayleigh framework is used to interpret the elemental data. We then analyze δ11B of the same samples as a proxy for pH at their site of calcification. Preliminary results suggest that coralline red algae, shrimp, urchin, serpulid worm and temperate coral taxa elevate pH at the site of calcification relative to the organism's ambient seawater. We plan to utilize a multi-proxy approach to examine the biomineralization pathways that influence elemental and boron isotope fractionation during calcification and precipitation of biogenic aragonite and calcite. A better understanding of these biomineralization pathways will help us to predict the responses of benthic invertebrate taxa to ocean acidification, as well as provide insights into drivers of so-called vital effects on elemental and stable boron isotope fractionation

  4. Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility.

    PubMed

    Raji, Adebola Aj; Anderson, James V; Kolade, Olufisayo A; Ugwu, Chike D; Dixon, Alfred Go; Ingelbrecht, Ivan L

    2009-09-11

    Cassava (Manihot esculenta Crantz), a starchy root crop grown in tropical and subtropical climates, is the sixth most important crop in the world after wheat, rice, maize, potato and barley. The repertoire of simple sequence repeat (SSR) markers for cassava is limited and warrants a need for a larger number of polymorphic SSRs for germplasm characterization and breeding applications. A total of 846 putative microsatellites were identified in silico from an 8,577 cassava unigene set with an average density of one SSR every 7 kb. One hundred and ninety-two candidate SSRs were screened for polymorphism among a panel of cassava cultivars from Africa, Latin America and Asia, four wild Manihot species as well as two other important taxa in the Euphorbiaceae, leafy spurge (Euphorbia esula) and castor bean (Ricinus communis). Of 168 markers with clean amplification products, 124 (73.8%) displayed polymorphism based on high resolution agarose gels. Of 85 EST-SSR markers screened, 80 (94.1%) amplified alleles from one or more wild species (M epruinosa, M glaziovii, M brachyandra, M tripartita) whereas 13 (15.3%) amplified alleles from castor bean and 9 (10.6%) amplified alleles from leafy spurge; hence nearly all markers were transferable to wild relatives of M esculenta while only a fraction was transferable to the more distantly related taxa. In a subset of 20 EST-SSRs assessed by fluorescence-based genotyping the number of alleles per locus ranged from 2 to 10 with an average of 4.55 per locus. These markers had a polymorphism information content (PIC) from 0.19 to 0.75 with an average value of 0.55 and showed genetic relationships consistent with existing information on these genotypes. A set of 124 new, unique polymorphic EST-SSRs was developed and characterized which extends the repertoire of SSR markers for cultivated cassava and its wild relatives. The markers show high PIC values and therefore will be useful for cultivar identification, taxonomic studies, and

  5. Reliability and refinement of the higher taxa approach for bee richness and composition assessments.

    PubMed

    Rijn, Itai Van; Neeson, Thomas M; Mandelik, Yael

    2015-01-01

    Limited resources and taxonomic expertise in biodiversity surveys often lead to the application of the higher taxa approach (HTA),i.e., the identification of specimens to genus or higher taxonomic levels rather than to species. The reliability of the HTA varies significantly among studies, yet the factors underlying this variability have rarely been investigated. Bees are an ideal model taxon for testing the HTA because they are highly diverse, challenging to identify, and there is widespread interest in their role as native pollinators, driving demand for efficient diversity assessment tools. Using extensive bee data sets collected across three biomes and various habitats, we assessed the performance of the HTA in reflecting bee species richness and composition patterns at local scales, factors affecting this performance, and ways to improve it. The performance of the HTA varied considerably among biomes, taxonomic levels (genera and subfamilies), and diversity measures (species richness and composition); genus and subfamily richness accounted for 55-77% and 32-61% of the variation in species richness, respectively; genus and subfamily composition accounted for 28-87% and 26-80% of the variation in species composition, respectively. The number of species per higher taxon was a main factor influencing this performance (accounting for 63% of the variation), while the co-occurrence of taxonomically related species had no significant influence on the performance of the HTA. Further subdividing genera by body size contributed to the performance of the HTA and increased its accuracy in representation of compositional patterns by ~16%. Our results have several practical implications. The considerable variability found in the performance of the HTA in representing local-scale richness and composition patterns of bee species dictates caution in implementing this tool in bee surveys. When possible, an a priori evaluation of the expected performance of the HTA should be done

  6. Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility

    PubMed Central

    Raji, Adebola AJ; Anderson, James V; Kolade, Olufisayo A; Ugwu, Chike D; Dixon, Alfred GO; Ingelbrecht, Ivan L

    2009-01-01

    Background Cassava (Manihot esculenta Crantz), a starchy root crop grown in tropical and subtropical climates, is the sixth most important crop in the world after wheat, rice, maize, potato and barley. The repertoire of simple sequence repeat (SSR) markers for cassava is limited and warrants a need for a larger number of polymorphic SSRs for germplasm characterization and breeding applications. Results A total of 846 putative microsatellites were identified in silico from an 8,577 cassava unigene set with an average density of one SSR every 7 kb. One hundred and ninety-two candidate SSRs were screened for polymorphism among a panel of cassava cultivars from Africa, Latin America and Asia, four wild Manihot species as well as two other important taxa in the Euphorbiaceae, leafy spurge (Euphorbia esula) and castor bean (Ricinus communis). Of 168 markers with clean amplification products, 124 (73.8%) displayed polymorphism based on high resolution agarose gels. Of 85 EST-SSR markers screened, 80 (94.1%) amplified alleles from one or more wild species (M epruinosa, M glaziovii, M brachyandra, M tripartita) whereas 13 (15.3%) amplified alleles from castor bean and 9 (10.6%) amplified alleles from leafy spurge; hence nearly all markers were transferable to wild relatives of M esculenta while only a fraction was transferable to the more distantly related taxa. In a subset of 20 EST-SSRs assessed by fluorescence-based genotyping the number of alleles per locus ranged from 2 to 10 with an average of 4.55 per locus. These markers had a polymorphism information content (PIC) from 0.19 to 0.75 with an average value of 0.55 and showed genetic relationships consistent with existing information on these genotypes. Conclusion A set of 124 new, unique polymorphic EST-SSRs was developed and characterized which extends the repertoire of SSR markers for cultivated cassava and its wild relatives. The markers show high PIC values and therefore will be useful for cultivar identification

  7. Venom of the Brown Treesnake, Boiga irregularis: ontogenetic shifts and taxa-specific toxicity.

    PubMed

    Mackessy, Stephen P; Sixberry, Nicole M; Heyborne, William H; Fritts, Thomas

    2006-04-01

    The Brown Treesnake (Boiga irregularis), a rear-fanged member of the polyphyletic family Colubridae, is an introduced predator on Guam which has been responsible for numerous human envenomations. Because little is known about this species' venom, we characterized venom proteins from B. irregularis using enzyme assays, one and 2D electrophoresis, Western blot analysis, mass spectrometry, HPLC and toxicity assays. Venom yields and protein content varied significantly with snake size, and large adult specimens averaged over 500 microl venom (19.2 mg, protein content approximately 90%). Only two enzymes, azocaseinolytic metalloprotease and acetylcholinesterase, were detected in venoms, and both activities increased with snake size/age. Western blot analysis demonstrated a 25 kDa CRiSP homolog in venoms from both neonate and adult snakes. 2D electrophoresis showed variation between venoms from neonate and adult snakes, especially with respect to metalloprotease and acetylcholinesterase. Analysis by MALDI-TOF mass spectrometry revealed the presence of numerous proteins with molecular masses of approximately 8.5-11 kDa. Adult B. irregularis venom was quite toxic to domestic chickens (Gallus domesticus; 1.75 microg/g) and lizards (Hemidactylus geckos: 2.5 microg/g and Carlia skinks: 4.5 microg/g), and intoxication was characterized by rapid paralysis of all species and neck droop in chickens. Toxicity of venom from neonates toward geckos was 1.1 microg/g, consistent with the presence of a greater diversity of 8-11 kDa proteins (suspected neurotoxins) in these venoms. All of these values were notably lower than murine LD50 values (neonate: 18 microg/g; adult: 31 microg/g). Like venoms of several front-fanged species, B. irregularis venom showed an ontogenetic shift in enzyme activities and toxicity, and neonate snakes produced more toxic venoms with lower protease and acetylcholinesterase activities. High toxicity toward non-mammalian prey demonstrated the presence of taxa

  8. S1 satellite DNA repetitive units display identical structure and overall variability in all Anatolian brown frog taxa.

    PubMed

    Picariello, Orfeo; Feliciello, Isidoro; Chinali, Gianni

    2016-02-01

    S1 satellite DNA from Palearctic brown frogs has a species-specific structure in all European species. We characterized S1 satellite DNA from the Anatolian brown frogs Rana macrocnemis, R. camerani, and R. holtzi in order to define their taxonomic rank and the structure of this satellite in this frog lineage. Southern blots of genomic DNA digested with KpnI, EcoRV, NdeI, NheI, or StuI produced the same pattern of satellite DNA bands. Moreover, quantitative dot blots showed that this satellite DNA accounts for 0.1 % of the genome in all taxa. Analysis of the overall genomic variability of the S1a repeat sequence in specimens from various populations demonstrated that this repetitive unit also has the same size (476 bp), the same most common sequence (MCS) and the same overall variability in all three taxa, and also in R. macrocnemis tavasensis. The S1a repetitive unit presents three deletions of 9, 8 and 1 bp compared to the 494-bp S1a repeat from European frogs. The S1a MCS has three variable positions (sequence WWTK in positions 183-186), due to the presence of two repeat subpopulations with motifs AATG and WWTT in all taxa. Unlike previously analyzed mitochondrial and nuclear sequences that show considerable variations among these taxa, no difference could be detected in the structure and variability of the S1 satellite repetitive units. This suggests that these taxa should belong to a single species. Our results indicate that this satellite DNA variety probably formed when the Anatolian lineage radiated from common ancestor about 4 mya, and since then has maintained its structure in all four taxa examined.

  9. TaXA21-A1 on chromosome 5AL is associated with resistance to multiple pests in wheat.

    PubMed

    Liu, Meiyan; Lei, Lei; Powers, Carol; Liu, Zhiyong; Campbell, Kimberly G; Chen, Xianming; Bowden, Robert L; Carver, Brett F; Yan, Liuling

    2016-02-01

    The wheat ortholog of the rice gene OsXA21 against bacterial leaf blight showed resistance to multiple pests in bread wheat but different interacting proteins. A quantitative trait locus QYr.osu-5A on the long arm of chromosome 5A in bread wheat (Triticum aestivum L., 2n = 6x = 42; AABBDD) was previously reported to confer consistent resistance in adult plants to predominant stripe rust races, but the gene causing the quantitative trait locus (QTL) is not known. Single-nucleotide polymorphism (SNP) markers were used to saturate the QTL region. Comparative and syntenic regions between wheat and rice (Oryza sativa) were applied to identify candidate genes for QYr.osu-5A. TaXA21-A1, which is referred to as a wheat ortholog of OsXA21-like gene on chromosome 9 in rice, was mapped under the peak of the QYr.osu-5A. TaXA21-A1 not only explained the phenotypic variation in reaction to different stripe rust races but also showed significant effects on resistance to powdery mildew and Hessian fly biotype BP. The natural allelic variation resulted in the alternations of four amino acids in deduced TaXA21-A1 proteins. The interacting proteins of TaXA21-A1 were different from those identified by OsXA21 on rice chromosome 11 against bacterial leaf blight. TaXA21-A1 confers unique resistance against multiple pests in wheat but might not have common protein interactors or thus overlapping functions with OsXA21 in rice. XA21 function has diverged during evolution of cereal crops. The molecular marker developed for TaXA21-A1 would accelerate its application of the candidate gene at the QYr.osu-5A locus in wheat breeding programs.

  10. A taxa summary for the Simulium damnosum complex, with special reference to distribution outside the control areas of West Africa.

    PubMed

    Crosskey, R W

    1987-04-01

    A synoptic list is provided of currently recognized taxa in the Simulium damnosum complex, with an indication of their geographical distributions. Outline maps are given for the distribution of S. damnosum sensu lato, and for the West African cytospecies of the complex. Short reports on the identities and distributions of member taxa are given for countries other than those of the Onchocerciasis Control Programme in the Volta River Basin (OCP) and its Senegambia Extension; these are mainly based on collation of published and unpublished data for the post-1976 period (since the last WHO Expert Committee Report on Onchocerciasis).

  11. [Evolutional relationships of endemic green algae Draparnaldioides simplex from Lake Baikal with nonbaicalian taxa of family Chaetoforaceae (Chlorophyta)].

    PubMed

    Mincheva, E V; Peretolchina, T E; Izhboldina, L A; Kravtsova, L S; Shcherbakov, D Iu

    2013-01-01

    Phylogenetic relationships between the endemic baicalian green algae Draparnaldioides simplex C. meyer et Skabitsch, 1976 and holarctic taxa of green algae were studied using the fragment of 18S rDNA and internal transcribed spacers ITS1 and ITS2 of nuclear DNA. We showed that the baicalian genus Draparnaldioides is a separate taxon. The genetic difference between Draparnaldioides and nonbaicalian taxa of the sister groups of the green algae are small enough to indicate relative youth of the genus Draparnaldioides and its recent radiation from a common ancestor with Draparnaldia and Chaetophora.

  12. On core jakobids and excavate taxa: the ultrastructure of Jakoba incarcerata.

    PubMed

    Simpson, A G; Patterson, D J

    2001-01-01

    The cellular organisation of the 'excavate' flagellate Jakoba incarcerata Bernard, Simpson and Patterson 2000 is described. Cells have one nucleus and dictyosome. The putative mitochondria lack cristae. Two flagella (anterior and posterior) insert anterior to the feeding groove. The posterior flagellum bears a dorsal vane. An 'anterior' microtubular root arises against the anterior basal body. Two main microtubular roots, left and right, and a singlet 'root' arise around the posterior basal body and support the groove. Non-microtubular fibres termed 'A', 'B', 'I', and 'composite' associate with the right root. A multilaminar 'C' fibre associates with the left root. The cytoskeleton of J. incarcerata indicates a common ancestry with other excavate taxa (i.e. diplomonads, retortamonads, heteroloboseids, 'core jakobids', Malawimonas, Carpediemonas, and Trimastix). Overall, J. incarcerata is most similar to (other) core jakobids, namely Jakoba libera, Reclinomonas, and Histiona. We regard J. incarcerata as a core jakobid and identify the group by the synapomorphy 'vanes restricted to dorsal side of the posterior flagellum'. The anterior root and position of the B fibre (and presence of dense inclusions in the cartwheels and a conscpicuous singlet root-associated fibre) in J. incarcerata are novel for core jakobids and argue for close relationships with Trimastix and/or Heterolobosea. The C fibre is similar in substructure to the costal fibre of parabasalids and it is possible that the structures are homologous.

  13. I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation

    PubMed Central

    Mooers, Arne Ø.; Caccone, Adalgisa; Russello, Michael A.

    2016-01-01

    In the midst of the current biodiversity crisis, conservation efforts might profitably be directed towards ensuring that extinctions do not result in inordinate losses of evolutionary history. Numerous methods have been developed to evaluate the importance of species based on their contribution to total phylogenetic diversity on trees and networks, but existing methods fail to take complementarity into account, and thus cannot identify the best order or subset of taxa to protect. Here, we develop a novel iterative calculation of the heightened evolutionary distinctiveness and globally endangered metric (I-HEDGE) that produces the optimal ranked list for conservation prioritization, taking into account complementarity and based on both phylogenetic diversity and extinction probability. We applied this metric to a phylogenetic network based on mitochondrial control region data from extant and recently extinct giant Galápagos tortoises, a highly endangered group of closely related species. We found that the restoration of two extinct species (a project currently underway) will contribute the greatest gain in phylogenetic diversity, and present an ordered list of rankings that is the optimum complementarity set for conservation prioritization. PMID:27635324

  14. Studies on Leaf Venation in Selected Taxa of the Genus Ficus L. (Moraceae) in Peninsular Malaysia.

    PubMed

    Badron, Ummu Hani; Talip, Noraini; Mohamad, Abdul Latiff; Affenddi, Affina Eliya Aznal; Juhari, Amirul Aiman Ahmad

    2014-12-01

    A study on the variation of leaf venation patterns was conducted on 21 taxa of the genus Ficus in Peninsular Malaysia. The results showed the existence of eight leaf venation patterns based on veinlets, the ultimate marginal and areolar venation. The majority of species, such as F. annulata, F. benghalensis, F. benjamina, F. deltoidea var. angustifolia, F. deltoidea var. kunstleri, F. depressa, F. elastica, F. hispida, F. microcarpa, F. religiosa, F. tinctoria, F. ucinata and F. vasculosa, show tri-veinlets. The others exhibit the following: bi-veinlets in F. aurata and F. heteropleura; uni-veinlets in F. lepicarpa, F. schwarzii and F. superba; and simple veinlets in F. aurantiacea and F. fulva. F. sagittata presents no veinlets for areolar venation. The presence of tracheid or swollen veins at the centre of the lamina and the presence of cystolith cells and trichomes are common anatomical characteristics that could assist in group classification of the studied species. Variations in leaf venation patterns are not only valuable in identifying a taxon group, but can also be used to differentiate between species in the genus Ficus.

  15. Studies on Leaf Venation in Selected Taxa of the Genus Ficus L. (Moraceae) in Peninsular Malaysia

    PubMed Central

    Badron, Ummu Hani; Talip, Noraini; Mohamad, Abdul Latiff; Affenddi, Affina Eliya Aznal; Juhari, Amirul Aiman Ahmad

    2014-01-01

    A study on the variation of leaf venation patterns was conducted on 21 taxa of the genus Ficus in Peninsular Malaysia. The results showed the existence of eight leaf venation patterns based on veinlets, the ultimate marginal and areolar venation. The majority of species, such as F. annulata, F. benghalensis, F. benjamina, F. deltoidea var. angustifolia, F. deltoidea var. kunstleri, F. depressa, F. elastica, F. hispida, F. microcarpa, F. religiosa, F. tinctoria, F. ucinata and F. vasculosa, show tri-veinlets. The others exhibit the following: bi-veinlets in F. aurata and F. heteropleura; uni-veinlets in F. lepicarpa, F. schwarzii and F. superba; and simple veinlets in F. aurantiacea and F. fulva. F. sagittata presents no veinlets for areolar venation. The presence of tracheid or swollen veins at the centre of the lamina and the presence of cystolith cells and trichomes are common anatomical characteristics that could assist in group classification of the studied species. Variations in leaf venation patterns are not only valuable in identifying a taxon group, but can also be used to differentiate between species in the genus Ficus. PMID:27073603

  16. Distribution of Mytilus taxa in European coastal areas as inferred from molecular markers

    NASA Astrophysics Data System (ADS)

    Kijewski, T.; Śmietanka, B.; Zbawicka, M.; Gosling, E.; Hummel, H.; Wenne, R.

    2011-02-01

    The genetic constitution of mussels ( Mytilus spp.) was studied by means of three nuclear (Me 15/16, EF-bis, ITS) and one mtDNA (ND2-COIII) marker on a large European scale. In addition to a sharp cline between Atlantic and Mediterranean M. galloprovincialis, we observed a clear genetic distinction between the Black Sea and Mediterranean populations and a higher incidence of M. trossulus than reported so far in northern European populations. The frequency of M. galloprovincialis nuclear alleles was high along the Iberian Peninsula and decreased abruptly along the French coasts with a high frequency of M. edulis alleles in the Bay of Biscay, The Netherlands, Germany, Iceland, Barents and White Seas, and with little evidence of introgression between the two taxa. M. trossulus alleles were observed in the Baltic Sea and Danish Straits as expected. In addition, occurrence of M. trossulus alleles in cold waters of Iceland, Barents Sea and White Sea is reported for the first time.

  17. Multi-taxa integrated landscape genetics for zoonotic infectious diseases: deciphering variables influencing disease emergence.

    PubMed

    Leo, Sarah S T; Gonzalez, Andrew; Millien, Virginie

    2016-05-01

    Zoonotic disease transmission systems involve sets of species interacting with each other and their environment. This complexity impedes development of disease monitoring and control programs that require reliable identification of spatial and biotic variables and mechanisms facilitating disease emergence. To overcome this difficulty, we propose a framework that simultaneously examines all species involved in disease emergence by integrating concepts and methods from population genetics, landscape ecology, and spatial statistics. Multi-taxa integrated landscape genetics (MTILG) can reveal how interspecific interactions and landscape variables influence disease emergence patterns. We test the potential of our MTILG-based framework by modelling the emergence of a disease system across multiple species dispersal, interspecific interaction, and landscape scenarios. Our simulations showed that both interspecific-dependent dispersal patterns and landscape characteristics significantly influenced disease spread. Using our framework, we were able to detect statistically similar inter-population genetic differences and highly correlated spatial genetic patterns that imply species-dependent dispersal. Additionally, species that were assigned coupled-dispersal patterns were affected to the same degree by similar landscape variables. This study underlines the importance of an integrated approach to investigating emergence of disease systems. MTILG is a robust approach for such studies and can identify potential avenues for targeted disease management strategies.

  18. Understanding lichenicolous heterobasidiomycetes: new taxa and reproductive innovations in Tremella s.l.

    PubMed

    Zamora, Juan Carlos; Millanes, Ana María; Wedin, Mats; Rico, Víctor J; Pérez-Ortega, Sergio

    2016-01-01

    Four new lichenicolous Tremella species are described and characterized morphologically and molecularly. Tremella celata grows on Ramalina fraxinea, inducing the formation of inconspicuous galls, and having hyphae with incomplete clamps. Tremella endosporogena develops intrahymenially in the apothecia of Lecanora carpinea, having single-celled basidia and clampless hyphae. Tremella diederichiana is the name proposed for a species micromorphologically close to T. christiansenii but inducing the formation of small, pale galls on the thallus and apothecia of Lecidea aff. erythrophaea Tremella variae grows on Lecanora varia thallus, instead of on the apothecia, as do the other known Tremella species parasitizing Lecanora s.l. Phylogenetic relationships and host specificity of these species are investigated and compared with other taxa that show morphological resemblances, phylogenetic affinities or similar hosts. The formation of mitotic conidia inside old basidia (endospores), which is a poorly known reproductive strategy in the Basidiomycota, is also a distinctive character of Tremella endosporogena A discussion on the reproductive role and systematic implications of endospores is included.

  19. Brachiopod taxa and shell portions reliably recording past ocean environments: Toward establishing a robust paleoceanographic proxy

    NASA Astrophysics Data System (ADS)

    Yamamoto, Kazuyuki; Asami, Ryuji; Iryu, Yasufumi

    2011-07-01

    Fossils of rhynchonelliform brachiopods (marine invertebrates) constitute ˜70% of the samples used for delineating a well-known Phanerozoic trend in oxygen isotope composition (δ18O) of low-Mg calcite shells. The trend represents secular variations in temperature and/or δ18O of ancient seawater. However, the use of brachiopods as a paleoceanographic proxy is based on the presupposition that the shell calcite is precipitated in isotopic equilibrium with ambient seawater. Here, we show that high-resolution time series of the shell δ18O values along the maximum growth axes of two long-lived cool-water brachiopods are identical to, greater than, or less than those of calcite precipitated in isotopic equilibrium with ambient seawater, depending on the difference in shell growth rates. Coupled with δ18O data from subtropical and warm-temperate brachiopod species examined in our previous studies, we provide a sound framework illustrating which taxa and shell portions reliably recorded past ocean environments.

  20. Comparative lophotrochozoan neurogenesis and larval neuroanatomy: recent advances from previously neglected taxa.

    PubMed

    Wanninger, A

    2008-01-01

    Recently, a number of neurodevelopmental studies of hitherto neglected taxa have become available, contributing to questions relating to the evolution of the nervous system of Lophotrochozoa (Spiralia + Lophophorata). As an example, neurogenesis of echiurans showed that these worm-shaped spiralians, which as adults do not exhibit any signs of segmentation, do show such traits during ontogeny, e.g. by segmentally arranged perikarya and commissures. Similarly, sipunculan worms, which have a single ventral nerve cord in the adult stage, develop this nerve cord by gradual fusion of a paired larval nerve during metamorphosis, and show transitional stages of segmentation. These findings indicate that echiurans, annelids and sipunculans stem from a segmented ancestor. By contrast, no traces of body segmentation are present during neurogenesis of basal molluscs. However, a tetraneurous condition (i.e. one pair of ventral and one pair of lateral nerve cords), as is typical for Mollusca, and a serotonergic larval apical organ that matches the complexity of polyplacophoran apical organs, were found in larval entoprocts, thus strongly supporting a mollusc-entoproct clade. Within the Lophophorata (Ectoprocta + Phoronida + Brachiopoda), data on nervous system development for any of the 3 lophophorate phyla are as of yet too scarce for profound phylogenetic inferences. Taking into account the most recent advances in molecular phylogenetics and developmental neurobiology, a scenario emerges that proposes a clade comprising Sipuncula + Annelida (including Echiura) on the one hand and a monophyletic assemblage of Entoprocta + Mollusca on the other.

  1. Root isoflavonoids and hairy root transformation influence key bacterial taxa in the soybean rhizosphere.

    PubMed

    White, Laura J; Ge, Xijin; Brözel, Volker S; Subramanian, Senthil

    2017-04-01

    Rhizodeposits play a key role in shaping rhizosphere microbial communities. In soybean, isoflavonoids are a key rhizodeposit component that aid in plant defense and enable symbiotic associations with rhizobia. However, it is uncertain if and how they influence rhizosphere microbial communities. Isoflavonoid biosynthesis was silenced via RNA interference of isoflavone synthase in soybean hairy root composite plants. Rhizosphere soil fractions tightly associated with roots were isolated, and PCR amplicons from 16S rRNA gene variable regions V1-V3 and V3-V5 from these fractions were sequenced using 454. The resulting data was resolved using MOTHUR and vegan to identify bacterial taxa and evaluate changes in rhizosphere bacterial communities. The soybean rhizosphere was enriched in Proteobacteria and Bacteroidetes, and had relatively lower levels of Actinobacteria and Acidobacteria compared with bulk soil. Isoflavonoids had a small effect on bacterial community structure, and in particular on the abundance of Xanthomonads and Comamonads. The effect of hairy root transformation on rhizosphere bacterial communities was largely similar to untransformed plant roots with approximately 74% of the bacterial families displaying similar colonization underscoring the suitability of this technique to evaluate the influence of plant roots on rhizosphere bacterial communities. However, hairy root transformation had notable influence on Sphingomonads and Acidobacteria. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  2. TaxaGloss - A Glossary and Translation Tool for Biodiversity Studies.

    PubMed

    Collin, Rachel; Fredericq, Suzanne; Freshwater, D Wilson; Gilbert, Edward; Madrid, Maycol; Maslakova, Svetlana; Miglietta, Maria Pia; Rocha, Rosana M; Rodríguez, Estefanía; Thacker, Robert W

    2016-01-01

    Correctly identifying organisms is key to most biological research, and is especially critical in areas of biodiversity and conservation. Yet it remains one of the greatest challenges when studying all but the few well-established model systems. The challenge is in part due to the fact that most species have yet to be described, vanishing taxonomic expertise and the relative inaccessibility of taxonomic information. Furthermore, identification keys and other taxonomic resources are based on complex, taxon-specific vocabularies used to describe important morphological characters. Using these resources is made difficult by the fact that taxonomic documentation of the world's biodiversity is an international endeavour, and keys and field guides are not always available in the practitioner's native language. To address this challenge, we have developed a publicly available on-line illustrated multilingual glossary and translation tool for technical taxonomic terms using the Symbiota Software Project biodiversity platform. Illustrations, photographs and translations have been sourced from the global community of taxonomists working with marine invertebrates and seaweeds. These can be used as single-language illustrated glossaries or to make customized translation tables. The glossary has been launched with terms and illustrations of seaweeds, tunicates, sponges, hydrozoans, sea anemones, and nemerteans, and already includes translations into seven languages for some groups. Additional translations and development of terms for more taxa are underway, but the ultimate utility of this tool depends on active participation of the international taxonomic community.

  3. Comparative Phylogeography in Fijian Coral Reef Fishes: A Multi-Taxa Approach towards Marine Reserve Design

    PubMed Central

    Drew, Joshua A.; Barber, Paul H.

    2012-01-01

    Delineating barriers to connectivity is important in marine reserve design as they describe the strength and number of connections among a reserve's constituent parts, and ultimately help characterize the resilience of the system to perturbations at each node. Here we demonstrate the utility of multi-taxa phylogeography in the design of a system of marine protected areas within Fiji. Gathering mtDNA control region data from five species of coral reef fish in five genera and two families, we find a range of population structure patterns, from those experiencing little (Chrysiptera talboti, Halichoeres hortulanus, and Pomacentrus maafu), to moderate (Amphiprion barberi, Φst = 0.14 and Amblyglyphidodon orbicularis Φst = 0.05) barriers to dispersal. Furthermore estimates of gene flow over ecological time scales suggest species-specific, asymmetric migration among the regions within Fiji. The diversity among species-specific results underscores the limitations of generalizing from single-taxon studies, including the inability to differentiate between a species-specific result and a replication of concordant phylogeographic patterns, and suggests that greater taxonomic coverage results in greater resolution of community dynamics within Fiji. Our results indicate that the Fijian reefs should not be managed as a single unit, and that closely related species can express dramatically different levels of population connectivity. PMID:23118892

  4. Firmicutes dominate the bacterial taxa within sugar-cane processing plants

    PubMed Central

    Sharmin, Farhana; Wakelin, Steve; Huygens, Flavia; Hargreaves, Megan

    2013-01-01

    Sugar cane processing sites are characterised by high sugar/hemicellulose levels, available moisture and warm conditions, and are relatively unexplored unique microbial environments. The PhyloChip microarray was used to investigate bacterial diversity and community composition in three Australian sugar cane processing plants. These ecosystems were highly complex and dominated by four main Phyla, Firmicutes (the most dominant), followed by Proteobacteria, Bacteroidetes, and Chloroflexi. Significant variation (p < 0.05) in community structure occurred between samples collected from ‘floor dump sediment’, ‘cooling tower water’, and ‘bagasse leachate’. Many bacterial Classes contributed to these differences, however most were of low numerical abundance. Separation in community composition was also linked to Classes of Firmicutes, particularly Bacillales, Lactobacillales and Clostridiales, whose dominance is likely to be linked to their physiology as ‘lactic acid bacteria’, capable of fermenting the sugars present. This process may help displace other bacterial taxa, providing a competitive advantage for Firmicutes bacteria. PMID:24177592

  5. The Effects of Increasing the Number of Taxa on Inferences of Molecular Convergence

    PubMed Central

    Hahn, Matthew W.; Hahn, Yoonsoo

    2017-01-01

    Convergent evolution provides insight into the link between phenotype and genotype. Recently, large-scale comparative studies of convergent evolution have become possible, but researchers are still trying to determine the best way to design these types of analyses. One aspect of molecular convergence studies that has not yet been investigated is how taxonomic sample size affects inferences of molecular convergence. Here we show that increased sample size decreases the amount of inferred molecular convergence associated with the three convergent transitions to a marine environment in mammals. The sampling of more taxa—both with and without the convergent phenotype—reveals that alleles associated only with marine mammals in small datasets are actually more widespread, or are not shared by all marine species. The sampling of more taxa also allows finer resolution of ancestral substitutions, revealing that they are not in fact on lineages leading to solely marine species. We revisit a previous study on marine mammals and find that only 7 of the reported 43 genes with convergent substitutions still show signs of convergence with a larger number of background species. However, four of those seven genes also showed signs of positive selection in the original analysis and may still be good candidates for adaptive convergence. Though our study is framed around the convergence of marine mammals, we expect our conclusions on taxonomic sampling are generalizable to any study of molecular convergence. PMID:28057728

  6. Taxa-area Relationship (TAR) of Microbial Functional Genes with Long-TGerm Fertilization

    SciTech Connect

    Liang, Yuting; Wu, Liyou; Clark, Ian; Xue, Kai; Van Nostrand, Joy D.; Deng, Ye; He, Zhili; Hirsch, Penny; Mcgrath, Steve; Zhou, Jizhong

    2010-05-17

    Diversity and spatial patterns in plant and animal communities are well documented as a positive-power law of a taxa-area relationship (TAR). At present little is known whether this also applies to soil microbial communities and whether long-term fertilization has an influence on the underlying microbial diversity. To test the effects of long-term fertilization on above-ground botanical diversity and below-ground microbial diversity, a nested sampling approach on Park Grass plots (12d& 11/2c) of Rothamsted Reseach in United Kingdom, both at ~;; pH 5 but with plant diversities of between 42 and 13 respectively were used. GeoChip 3.0, covering approximately 57, 000 gene sequences of 292 gene families involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation, was used to determine the gene area relationships for both functional and phylogenetic groups and the relationship to plant diversity. Our analysis indicated that the microbial communities were separated by different plant diversity based on DCA. The soil microbial diversity was in accord with plant diversity. Soil microbial community exhibited different z value with different plant diversity, z = 0.0449 with higher plant diversity and z = 0.0583 with lower plant diversity (P< 0.0001). These results suggest that the turnover in space of microorganisms may be higher with long-term fertilization.

  7. Comments on Triassic pterosaurs with discussion about ontogeny and description of new taxa.

    PubMed

    Kellner, Alexander W A

    2015-01-01

    Eudimorphodon ranzii was the first Triassic pterosaur to be described and several specimens have been referred to this taxon mainly based on the presence of multicuspid teeth. Since this dental feature has been observed in several other pterosaurs, the revision of some specimens assigned to Eudimorphodon shows that they represent new taxa as follows: Arcticodactylus cromptonellus (comb. nov.), Austriadraco dallavecchiai (gen. et sp. nov.) and Bergamodactylus wildi (gen. et sp. nov.). A preliminary analysis of pterosaur ontogeny resulted in the recognition of six distinct ontogenetic stages (OS1-6). According to this classification, the holotype of Arcticodactylus cromptonellus has reached OS2, and although being ontogenetically much younger than others, the conspicuous anatomical differences lead to its exclusion from Eudimorphodon. The holotypes of Austriadraco dallavecchiai, Bergamodactylus wildi and Carniadactylus rosenfeldi have reached at least OS5, which demonstrates that the anatomical differences among them cannot be explained by ontogeny. Moreover, Bergamodactylus wildi reaches about 60% of the maximized wingspan of Carniadactylus rosenfeldi and further concurs that these specimens collected in distinct Triassic Islands of Europe are not conspecific. The present study increases the diversity of Triassic flying reptiles and further pushes the origins of this clade back to at least the Middle Triassic.

  8. AMS Radiocarbon Dating Individual Taxa and Individual Specimens: Implications for Small Mammal Paleoecology.

    NASA Astrophysics Data System (ADS)

    Graham, Russell; Stafford, Thomas, Jr.; Semken, Holmes, Jr.

    2010-05-01

    Advances in AMS physics and organic geochemistry have revolutionized our ability to establish absolute chronologies on vertebrate fossils. Highly purified collagen, which provides extremely accurate 14C ages, can be extracted from single bones and teeth as small as 50 mg. Combined with measurement precisions of ±15 to 25 years for ages of < 20,000 yr, the direct AMS 14C technique enables fossil deposits to be chronologically dissected at the level of single animals. Analysis of data from a variety of sites in the United States indicates that most excavation levels (analysis units) as small as 10 cm can be time averaged by several thousand years at a minimum, even with the greatest care in excavation and processing of sediments. Time averaging of this magnitude has important implications for fine-scale paleoecological analysis of faunas, especially when compared to high-resolution climate records like those derived from speleothems, ice cores, or marine cores. To this end, we propose saturation dating of indicative taxa and plotting dates of individual specimens against high-resolution climate records rather than analysis of complete faunas or faunules. This technique provides even higher resolution of paleoenvironments than pollen spectra.

  9. Wolbachia distribution in selected beetle taxa characterized by PCR screens and MLST data.

    PubMed

    Sontowski, Rebekka; Bernhard, Detlef; Bleidorn, Christoph; Schlegel, Martin; Gerth, Michael

    2015-10-01

    Wolbachia (Alphaproteobacteria) is an inherited endosymbiont of arthropods and filarial nematodes and was reported to be widespread across insect taxa. While Wolbachia's effects on host biology are not understood from most of these hosts, known Wolbachia-induced phenotypes cover a spectrum from obligate beneficial mutualism to reproductive manipulations and pathogenicity. Interestingly, data on Wolbachia within the most species-rich order of arthropods, the Coleoptera (beetles), are scarce. Therefore, we screened 128 species from seven beetle families (Buprestidae, Hydraenidae, Dytiscidae, Hydrophilidae, Gyrinidae, Haliplidae, and Noteridae) for the presence of Wolbachia. Our data show that, contrary to previous estimations, Wolbachia frequencies in beetles (31% overall) are comparable to the ones in other insects. In addition, we used Wolbachia MLST data and host phylogeny to explore the evolutionary history of Wolbachia strains from Hydraenidae, an aquatic lineage of beetles. Our data suggest that Wolbachia from Hydraenidae might be largely host genus specific and that Wolbachia strain phylogeny is not independent to that of its hosts. As this contrasts with most terrestrial Wolbachia-arthropod systems, one potential conclusion is that aquatic lifestyle of hosts may result in Wolbachia distribution patterns distinct from those of terrestrial hosts. Our data thus provide both insights into Wolbachia distribution among beetles in general and a first glimpse of Wolbachia distribution patterns among aquatic host lineages.

  10. Metagenomic identification of bacterioplankton taxa and pathways involved in microcystin degradation in lake erie.

    PubMed

    Mou, Xiaozhen; Lu, Xinxin; Jacob, Jisha; Sun, Shulei; Heath, Robert

    2013-01-01

    Cyanobacterial harmful blooms (CyanoHABs) that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera) and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax) of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr) were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems.

  11. Comparative phylogeography in Fijian coral reef fishes: a multi-taxa approach towards marine reserve design.

    PubMed

    Drew, Joshua A; Barber, Paul H

    2012-01-01

    Delineating barriers to connectivity is important in marine reserve design as they describe the strength and number of connections among a reserve's constituent parts, and ultimately help characterize the resilience of the system to perturbations at each node. Here we demonstrate the utility of multi-taxa phylogeography in the design of a system of marine protected areas within Fiji. Gathering mtDNA control region data from five species of coral reef fish in five genera and two families, we find a range of population structure patterns, from those experiencing little (Chrysiptera talboti, Halichoeres hortulanus, and Pomacentrus maafu), to moderate (Amphiprion barberi, Φ(st) = 0.14 and Amblyglyphidodon orbicularis Φ(st) = 0.05) barriers to dispersal. Furthermore estimates of gene flow over ecological time scales suggest species-specific, asymmetric migration among the regions within Fiji. The diversity among species-specific results underscores the limitations of generalizing from single-taxon studies, including the inability to differentiate between a species-specific result and a replication of concordant phylogeographic patterns, and suggests that greater taxonomic coverage results in greater resolution of community dynamics within Fiji. Our results indicate that the Fijian reefs should not be managed as a single unit, and that closely related species can express dramatically different levels of population connectivity.

  12. Impacts of invasive plants on resident animals across ecosystems, taxa, and feeding types: a global assessment.

    PubMed

    Schirmel, Jens; Bundschuh, Mirco; Entling, Martin H; Kowarik, Ingo; Buchholz, Sascha

    2016-02-01

    As drivers of global change, biological invasions have fundamental ecological consequences. However, it remains unclear how invasive plant effects on resident animals vary across ecosystems, animal classes, and functional groups. We performed a comprehensive meta-analysis covering 198 field and laboratory studies reporting a total of 3624 observations of invasive plant effects on animals. Invasive plants had reducing (56%) or neutral (44%) effects on animal abundance, diversity, fitness, and ecosystem function across different ecosystems, animal classes, and feeding types while we could not find any increasing effect. Most importantly, we found that invasive plants reduced overall animal abundance, diversity and fitness. However, this significant overall effect was contingent on ecosystems, taxa, and feeding types of animals. Decreasing effects of invasive plants were most evident in riparian ecosystems, possibly because frequent disturbance facilitates more intense plant invasions compared to other ecosystem types. In accordance with their immediate reliance on plants for food, invasive plant effects were strongest on herbivores. Regarding taxonomic groups, birds and insects were most strongly affected. In insects, this may be explained by their high frequency of herbivory, while birds demonstrate that invasive plant effects can also cascade up to secondary consumers. Since data on impacts of invasive plants are rather limited for many animal groups in most ecosystems, we argue for overcoming gaps in knowledge and for a more differentiated discussion on effects of invasive plant on native fauna. © 2015 John Wiley & Sons Ltd.

  13. When decisions on homologous structures cause ambiguous taxa relationships: the Neomorphinae (Aves, Cuculidae) example.

    PubMed

    Posso, S R; Donatelli, R J

    2010-02-01

    The anatomy of Neomorphinae is poorly understood and the systematics of this sub-family is also the most controversial of the cuckoo taxa, mainly with regard to the systematic position of Tapera and Dromococcyx. In this study, morphological similarities of the Neomorphinae are discussed after a comprehensive description of the cranial osteology was conducted in seven species, embracing all the Neomorphinae genera. This description is followed by comparisons with other cuckoos in order to contribute to the anatomy and systematics of this sub-family. In this way, we provide illustrations that enable the osteological descriptions and the proposed primary homologies to be visualised and compared. Even though Neomorphinae species share many cranial osteological characteristics, there are some anatomical divergences that allowed us to divide them into two distinct groups: (Dromococcyx/Tapera) and (Morococcyx(Neomorphus/Geococcyx)). After comparisons among all cuckoos this study suggests that Neomorphinae are more similar to Crotophaginae and Couinae than to other sub-families of cuckoos. Our results contrast with a recent phylogenetic study based on morphological features, mainly because alternative interpretations to the primary osteological homologies in this study grouped Tapera and Dromococcyx with Cuculinae. Although morphological studies can be used in phylogenetic analysis, we demonstrated here that decisions in the interpretation of the homologies can provide ambiguous results.

  14. The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach.

    PubMed

    Sun, Keping; Meiklejohn, Kelly A; Faircloth, Brant C; Glenn, Travis C; Braun, Edward L; Kimball, Rebecca T

    2014-09-07

    The most striking feature of peafowl (Pavo) is the males' elaborate train, which exhibits ocelli (ornamental eyespots) that are under sexual selection. Two additional genera within the Phasianidae (Polyplectron and Argusianus) exhibit ocelli, but the appearance and location of these ornamental eyespots exhibit substantial variation among these genera, raising the question of whether ocelli are homologous. Within Polyplectron, ocelli are ancestral, suggesting ocelli may have evolved even earlier, prior to the divergence among genera. However, it remains unclear whether Pavo, Polyplectron and Argusianus form a monophyletic clade in which ocelli evolved once. We estimated the phylogeny of the ocellated species using sequences from 1966 ultraconserved elements (UCEs) and three mitochondrial regions. The three ocellated genera did form a strongly supported clade, but each ocellated genus was sister to at least one genus without ocelli. Indeed, Polyplectron and Galloperdix, a genus not previously suggested to be related to any ocellated taxon, were sister genera. The close relationship between taxa with and without ocelli suggests multiple gains or losses. Independent gains, possibly reflecting a pre-existing bias for eye-like structures among females and/or the existence of a simple mutational pathway for the origin of ocelli, appears to be the most likely explanation.

  15. The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach

    PubMed Central

    Sun, Keping; Meiklejohn, Kelly A.; Faircloth, Brant C.; Glenn, Travis C.; Braun, Edward L.; Kimball, Rebecca T.

    2014-01-01

    The most striking feature of peafowl (Pavo) is the males' elaborate train, which exhibits ocelli (ornamental eyespots) that are under sexual selection. Two additional genera within the Phasianidae (Polyplectron and Argusianus) exhibit ocelli, but the appearance and location of these ornamental eyespots exhibit substantial variation among these genera, raising the question of whether ocelli are homologous. Within Polyplectron, ocelli are ancestral, suggesting ocelli may have evolved even earlier, prior to the divergence among genera. However, it remains unclear whether Pavo, Polyplectron and Argusianus form a monophyletic clade in which ocelli evolved once. We estimated the phylogeny of the ocellated species using sequences from 1966 ultraconserved elements (UCEs) and three mitochondrial regions. The three ocellated genera did form a strongly supported clade, but each ocellated genus was sister to at least one genus without ocelli. Indeed, Polyplectron and Galloperdix, a genus not previously suggested to be related to any ocellated taxon, were sister genera. The close relationship between taxa with and without ocelli suggests multiple gains or losses. Independent gains, possibly reflecting a pre-existing bias for eye-like structures among females and/or the existence of a simple mutational pathway for the origin of ocelli, appears to be the most likely explanation. PMID:25030982

  16. Selective feeding by shredders on leaf-colonizing stream fungi: comparison of macroinvertebrate taxa.

    PubMed

    Arsuffi, T L; Suberkropp, K

    1989-04-01

    Laboratory experiments were conducted to examine the effects of fungal species composition of leaf detritus on the feeding of distantly related macroinvertebrate shredders. Preferences of shredders representing three orders of insects (Diptera: Tipulidae; Plecoptera: Pteronarcidae; Trichoptera: Limnephilidae and Calamatoceridae) and one each of gastropods (Basommatophora: Planorbidae) and crustaceans (Amphipoda: Gammaridae) were compared. Shredder preferences were based on consumption of leaves separately colonized by one of eight species of aquatic hyphomycetes. The feeding patterns of the invertebrates ranged from lack of feeding to heavy consumption of fungal-colonized leaves. Where consumption occurred, rank orders of preference and degree of selectivity differed among invertebrate shredders. Differences in preferences together with relationships between degree of selectivity and the relative mobility and digestive specializations exhibited by shredders suggest that the exploitation of fungal-colonized leaf detritus by different taxa is affected by phylogenetic constraints. Our results suggest that fungal species composition affects the feeding of a variety of shredders and that fungal species composition may be as important as degree of conditioning in determining food selection by shredders.

  17. TaxaGloss - A Glossary and Translation Tool for Biodiversity Studies

    PubMed Central

    Fredericq, Suzanne; Freshwater, D. Wilson; Gilbert, Edward; Madrid, Maycol; Maslakova, Svetlana; Miglietta, Maria Pia; Rocha, Rosana M.; Rodríguez, Estefanía; Thacker, Robert W.

    2016-01-01

    Abstract Background Correctly identifying organisms is key to most biological research, and is especially critical in areas of biodiversity and conservation. Yet it remains one of the greatest challenges when studying all but the few well-established model systems. The challenge is in part due to the fact that most species have yet to be described, vanishing taxonomic expertise and the relative inaccessibility of taxonomic information. Furthermore, identification keys and other taxonomic resources are based on complex, taxon-specific vocabularies used to describe important morphological characters. Using these resources is made difficult by the fact that taxonomic documentation of the world's biodiversity is an international endeavour, and keys and field guides are not always available in the practitioner's native language. New information To address this challenge, we have developed a publicly available on-line illustrated multilingual glossary and translation tool for technical taxonomic terms using the Symbiota Software Project biodiversity platform. Illustrations, photographs and translations have been sourced from the global community of taxonomists working with marine invertebrates and seaweeds. These can be used as single-language illustrated glossaries or to make customized translation tables. The glossary has been launched with terms and illustrations of seaweeds, tunicates, sponges, hydrozoans, sea anemones, and nemerteans, and already includes translations into seven languages for some groups. Additional translations and development of terms for more taxa are underway, but the ultimate utility of this tool depends on active participation of the international taxonomic community. PMID:28174506

  18. [Subordination of the taxa of gram-negative bacteria determined by numerical analysis methods].

    PubMed

    Romanovskaia, V A; Sadovnikov, Iu S; Malashenko, Iu R; el-Said, M

    1986-01-01

    Various numerical methods were used to estimate the coordination of taxa of gram-negative aerobic and facultative anaerobic organoheterotrophic and chemolithotrophic bacteria. Stable phena were found to be formed by cultures belonging to the families Rhizobiaceae, Halobacteriaceae, Enterobacteriaceae, Nitrobacteriaceae (except the genus Nitrobacter), and Methylomonadaceae (except the genus Methylococcus). The unstable position was found in the genera Thermus, Zoogloea, Xanthomonas, Sulfolobus, Methylococcus, Alcaligenes, Brucella, and Acetobacter. The greatest scatter among the objects being analysed was detected among genera belonging to the family Pseudomonadaceae. The taxonomic position of these genera must be defined more precisely. The family Methylomonadaceae is related to such physiologically unique groups of microorganisms as nitrifying, sulfate-reducing, extreme thermophilic and halophilic forms. All in all, the data reported in this work show that numerical analysis can be used to specify the classification structure of bacteria. In a number of cases, the results are consistent with those changes which are performed in the Bergey Manual 9 using logical analysis (for instance, concerning the position of the genera Gluconobacter, Acetobacter, Beijerinckia, and Derxia).

  19. Phylogenetic overview of the genus Genea (Pezizales, Ascomycota) with an emphasis on European taxa.

    PubMed

    Alvarado, Pablo; Cabero, Julio; Moreno, Gabriel; Bratek, Zoltán; van Vooren, Nicolas; Kaounas, Vasileios; Konstantinidis, Giorgos; Agnello, Carlo; Merényi, Zsolt; Smith, Matthew E; Vizzini, Alfredo; Trappe, James M

    2016-01-01

    We constructed a comprehensive phylogeny of the genus Genea, with new molecular data from samples collected in several countries in temperate and Mediterranean Europe, as well as North America. Type specimens and authentic material of most species were examined to support identifications. The molecular identity of the most common species in Genea was compared with nuc rDNA internal transcribed spacer (ITS), D1-D2 domains of 28S nuc rDNA (28S rDNA) and translation elongation factor 1-α ene (TEF1) profiles of 10 recently proposed taxa, G. brunneocarpa, G. compressa, G. dentata, G. fageticola, G. lobulata, G. oxygala, G. pinicola, G. pseudobalsleyi, G. pseudoverrucosa and G. tuberculata, supporting their status as distinct species. Genea mexicana and G. thaxteri on the one hand and G. sphaerica and G. lespiaultii on the other are closely related. Multiple lineages were recorded for G. verrucosa and G. fragrans, but we found no morphological traits to discriminate among them, so we tentatively interpreted them as cryptic species. A key to species of the genus Genea is provided to facilitate identification. We provide macroscopic images of fresh specimens and of representative spores of most species. Finally, we conducted a molecular analysis of the divergence time for Genea and discuss the implications of our results.

  20. Needle longevity, photosynthetic rate and nitrogen concentration of eight spruce taxa planted in northern Japan.

    PubMed

    Kayama, Masazumi; Kitaoka, Satoshi; Wang, Wenjie; Choi, Dongsu; Koike, Takayoshi

    2007-11-01

    Growth characteristics of Picea glehnii Masters, P. jezoensis (Sieb. et Zucc) Carr., P. jezoensis var. hondoensis (Mayr) Rehder and P. shirasawae Hayashi from Japan, P. abies (L.) Karst. from Europe and P. glauca Voss, P. mariana Britt., Sterns and Pogg. and P. rubens Sarg. from North America were compared. The trees were grown in similar conditions at the Tomakomai Experimental Forest of Hokkaido University in northern Japan. Tree growth, needle biomass, longevity, photosynthetic rate, nitrogen concentration and specific leaf area (SLA) were measured, and photosynthetic nitrogen-use efficiency was calculated. Picea jezoensis, P. jezoensis var. hondoensis, P. abies and P. glauca had high growth rates, high photosynthetic rates in young needles, high needle nitrogen concentrations and short needle life spans. In contrast, P. glehnii, P. shirasawae, P. mariana and P. rubens had low growth and photosynthetic rates, low needle nitrogen concentrations, long needle life spans and maintained a high photosynthetic nitrogen-use efficiency in older needles. Examination of relationships between several growth parameters of the eight taxa revealed positive correlations between SLA and mass-based photosynthetic rate and between SLA and mass-based nitrogen concentration, whereas mass-based photosynthetic rate and mass-based nitrogen concentration were negatively correlated with needle longevity. The species differed greatly in growth characteristics despite being grown in similar conditions.

  1. Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial scales.

    PubMed

    Stein, Anke; Gerstner, Katharina; Kreft, Holger

    2014-07-01

    Environmental heterogeneity is regarded as one of the most important factors governing species richness gradients. An increase in available niche space, provision of refuges and opportunities for isolation and divergent adaptation are thought to enhance species coexistence, persistence and diversification. However, the extent and generality of positive heterogeneity-richness relationships are still debated. Apart from widespread evidence supporting positive relationships, negative and hump-shaped relationships have also been reported. In a meta-analysis of 1148 data points from 192 studies worldwide, we examine the strength and direction of the relationship between spatial environmental heterogeneity and species richness of terrestrial plants and animals. We find that separate effects of heterogeneity in land cover, vegetation, climate, soil and topography are significantly positive, with vegetation and topographic heterogeneity showing particularly strong associations with species richness. The use of equal-area study units, spatial grain and spatial extent emerge as key factors influencing the strength of heterogeneity-richness relationships, highlighting the pervasive influence of spatial scale in heterogeneity-richness studies. We provide the first quantitative support for the generality of positive heterogeneity-richness relationships across heterogeneity components, habitat types, taxa and spatial scales from landscape to global extents, and identify specific needs for future comparative heterogeneity-richness research.

  2. Temporal and Spatial Variations in Transcriptional Patterns among Closely Related Marine Microbial Taxa

    NASA Astrophysics Data System (ADS)

    Shilova, I. N.; Robidart, J.; DeLong, E.; Zehr, J. P.

    2016-02-01

    Marine microbial communities are complex, and even closely related marine microbial populations are genetically and physiologically diverse. Despite such great diversity, conserved and highly synchronized rhythmic transcriptional patterns have been observed in microbial communities worldwide. The current widely used approaches analyzing high-throughput sequence data from microbiomes are not designed to differentiate transcription at strain or ecotype level. We used a novel MicroArray-inspired Gene-Centric (MAGC) bioinformatics approach to discern daily transcription by individual strains in previously analyzed metatranscriptomes from two oceanic regions, California Current System and central North Pacific. The results demonstrated that marine microbial taxa (within cyanobacteria Prochlorococcus and Synechococcus, Alphaproteobacterium Pelagibacter and picoeukaryote Ostreococcus) have unique transcription patterns and respond differentially to variability in space and time in the ocean. For example, the timing of maximum transcription for the photosynthesis and pigments genes varied among Synechococcus strains in the California Current study, likely for optimizing light utilization based on their differences in genetics and physiology. While several Prochlorococcus genotypes were present in the North Pacific study, transcription of the phosphate transporter gene, pstS, in specific genotypes was negatively correlated with phosphate concentrations. These individual transcriptional patterns underlie whole microbial community responses and may be sensitive indicators of environmental conditions, including those associated with long-term environmental change. The MAGC applied here to ocean ecosystems is a promising complementary approach that can enhance the ability to analyze metatranscriptomic data from a variety of environmental microbiomes.

  3. Do the rich get richer? Varying effects of tree species identity and diversity on the richness of understory taxa

    USGS Publications Warehouse

    Champagne, Juilette; Paine, C. E. Timothy; Schoolmaster, Donald; Stejskal, Robert; Volařík, Daniel; Šebesta, Jan; Trnka, Filip; Koutecký, Tomáš; Švarc, Petr; Svátek, Martin; Hector, Andy; Matula, Radim

    2016-01-01

    Understory herbs and soil invertebrates play key roles in soil formation and nutrient cycling in forests. Studies suggest that diversity in the canopy and in the understory are positively associated, but these studies often confound the effects of tree species diversity with those of tree species identity and abiotic conditions. We combined extensive field sampling with structural equation modeling to evaluate the simultaneous effects of tree diversity on the species diversity of understory herbs, beetles, and earthworms. The diversity of earthworms and saproxylic beetles was directly and positively associated with tree diversity, presumably because species of both these taxa specialize on certain species of trees. Tree identity also strongly affected diversity in the understory, especially for herbs, likely as a result of interspecific differences in canopy light transmittance or litter decomposition rates. Our results suggest that changes in forest management will disproportionately affect certain understory taxa. For instance, changes in canopy diversity will affect the diversity of earthworms and saproxylic beetles more than changes in tree species composition, whereas the converse would be expected for understory herbs and detritivorous beetles. We conclude that the effects of tree diversity on understory taxa can vary from positive to negative and may affect biogeochemical cycling in temperate forests. Thus, maintaining high diversity in temperate forests can promote the diversity of multiple taxa in the understory.

  4. Nine-year performance of a variety of Populus taxa on an upland site in western Kentucky

    Treesearch

    Randall J. Rousseau; Joshua P. Adams; David W. Wilkerson

    2013-01-01

    A variety of hybrid poplars have been planted on upland sites throughout the Midwest and Midsouth regions of the United States. Very few of these clones have proven to be worthwhile due to susceptibility to a variety of diseases. Five different Populus taxa were planted on an upland site in western Kentucky as a means of assessing resistance to local...

  5. The roles of Lazarus taxa and refugia through the Ordovician-Silurian transition: data from the Brachiopoda

    NASA Astrophysics Data System (ADS)

    Rong, J.-Y.; Boucot, A. J.; Harper, D. A.; Zhan, R.-B.; Neuman, R. B.

    2003-04-01

    Global analyses of nearly 90 families and 275 genera of brachiopods from the middle Ashgill through the Hirnantian (Ordovician) to the lower-middle Rhuddanian (Silurian) suggest that about 60% and 40% of the total number of genera were eliminated at the first and second phases of the end Ordovician extinction event, respectively. Among the 85 surviving genera, about 50 with declining and 10 with proliferating abundances are known from the Hirnantian together with about 20 provisional Lazarus taxa. The Lazarus taxa are essentially survivors and form the extremity of the declining genera. The distributions of declining genera and relicts during the crisis interval shows a random and sporadic pattern, suggesting there was no single, common refugium for end Ordovician brachiopods. In addition to their biological attributes, a markedly decreased population size together with taphonomic failure and poor preservation, and collecting bias have contributed towards the distributional trends apparent during the event. The development of declining genera during the extinction may be linked to their palaeogeographical setting, the phylogenetic history of the taxa, and the ambient environmental conditions. This new global database has significantly reduced the number of Lazarus taxa and minimizes the number of possible locations for collective refugia during the end Ordovician crisis. Nevertheless, the atrypids, athyridids, pentamerids, and spiriferids had more limited distributions during the crisis interval but formed the locus for a Silurian diversification of the phylum into carbonate environments possibly around the Rhuddanian-Aeronian boundary.

  6. Do the rich get richer? Varying effects of tree species identity and diversity on the richness of understory taxa.

    PubMed

    Chamagne, Juliette; Paine, C E Timothy; Schoolmaster, Donald R; Stejskal, Robert; Volarřík, Daniel; Šebesta, Jan; Trnka, Filip; Koutecký, Tomáš; Švarc, Petr; Svátek, Martin; Hector, Andy; Matula, Radim

    2016-09-01

    Understory herbs and soil invertebrates play key roles in soil formation and nutrient cycling in forests. Studies suggest that diversity in the canopy and in the understory are positively associated, but these studies often confound the effects of tree species diversity with those of tree species identity and abiotic conditions. We combined extensive field sampling with structural equation modeling to evaluate the simultaneous effects of tree diversity on the species diversity of understory herbs, beetles, and earthworms. The diversity of earthworms and saproxylic beetles was directly and positively associated with tree diversity, presumably because species of both these taxa specialize on certain species of trees. Tree identity also strongly affected diversity in the understory, especially for herbs, likely as a result of interspecific differences in canopy light transmittance or litter decomposition rates. Our results suggest that changes in forest management will disproportionately affect certain understory taxa. For instance, changes in canopy diversity will affect the diversity of earthworms and saproxylic beetles more than changes in tree species composition, whereas the converse would be expected for understory herbs and detritivorous beetles. We conclude that the effects of tree diversity on understory taxa can vary from positive to negative and may affect biogeochemical cycling in temperate forests. Thus, maintaining high diversity in temperate forests can promote the diversity of multiple taxa in the understory. © 2016 by the Ecological Society of America.

  7. Taxa-area relationship and neutral dynamics influence the diversity of fungal communities on senesced tree leaves.

    PubMed

    Feinstein, Larry M; Blackwood, Christopher B

    2012-06-01

    This study utilized individual senesced sugar maple and beech leaves as natural sampling units within which to quantify saprotrophic fungal diversity. Quantifying communities in individual leaves allowed us to determine if fungi display a classic taxa-area relationship (species richness increasing with area). We found a significant taxa-area relationship for sugar maple leaves, but not beech leaves, consistent with Wright's species-energy theory. This suggests that energy availability as affected plant biochemistry is a key factor regulating the scaling relationships of fungal diversity. We also compared taxa rank abundance distributions to models associated with niche or neutral theories of community assembly, and tested the influence of leaf type as an environmental niche factor controlling fungal community composition. Among rank abundance distribution models, the zero-sum model derived from neutral theory showed the best fit to our data. Leaf type explained only 5% of the variability in community composition. Habitat (vernal pool, upland or riparian forest floor) and site of collection explained > 40%, but could be attributed to either niche or neutral processes. Hence, although niche dynamics may regulate fungal communities at the habitat scale, our evidence points towards neutral assembly of saprotrophic fungi on individual leaves, with energy availability constraining the taxa-area relationship. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  8. Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock.

    PubMed

    Takahashi, Tetsumi; Nagata, Nobuaki; Sota, Teiji

    2014-11-01

    Restriction site-associated DNA (RAD) sequences from entire genomes can be used to resolve complex phylogenetic problems. However, the processed data matrix varies depending on the strategies used to determine orthologous loci and to filter loci according to the number of taxa with sequence data for the loci, and often contains plenty of missing data. To explore the utility of RAD sequences for elucidating the phylogenetics of variously related species, we conducted RAD sequencing for the Ohomopterus ground beetles and attempted maximum-likelihood phylogenetic analyses using 42 data matrices ranging from 1.6×10(4) to 8.1×10(6) base pairs, with 11-72% missing data. We demonstrate that robust phylogenetic trees, in terms of bootstrap values, do not necessarily result from larger data matrices, as previously suggested. Robust trees for distantly related and closely related taxa resulted from different data matrices, and topologically different robust trees for distantly related taxa resulted from various data matrices. For closely related taxa, moderately large data matrices strongly supported a topology that is incompatible with morphological evidence, possibly due to the effect of introgressive hybridization. Practically, exploring variously prepared data matrices is an effective way to propose important alternative phylogenetic hypotheses for this study group.

  9. Leonard A. Kelton, 1923-2011: Biographical sketch, list of publications, described taxa, and patronyms names in his honor

    USDA-ARS?s Scientific Manuscript database

    A biographical sketch of the late heteropterist, Leonard Alexander Kelton (1923-2011), a former systematist at the Canadian National Collection in Ottawa, Canada, is presented. Also provided are lists of his 71 scientific publications, the new taxa he described, and the patronyms named in his honor....

  10. 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.

  11. SSR markers reveal the genetic diversity of Asian Cercis taxa at the U.S. National Arboretum

    USDA-ARS?s Scientific Manuscript database

    The redbud (Cercis L. species) is a popular landscape plant grown widely in the United States. There are more than twenty cultivars of eastern redbud (Cercis canadensis L.) and at least three cultivars of Asian taxa (primarily C. chinensis Bunge) in the trade. The U.S. National Arboretum (USNA) has ...

  12. Phytophthora taxa associated with cultivated Agathosma, with emphasis on the P. citricola complex and P. capensis sp. nov.

    Treesearch

    C.M. Bezuidenhout; S. Denman; S.A. Kirk; W.J. Botha; L. Mostert; A. McLeod

    2010-01-01

    Agathosma species, which are indigenous to South Africa, are also cultivated for commercial use. Recently growers experienced severe plant loss, and symptoms shown by affected plants suggested that a soilborne disease could be the cause of death. A number of Phytophthora taxa were isolated from diseased plants, and this paper...

  13. Phytophthora taxa associated with cultivated Agothosmo, with emphasis on the P. citricola complex and P. capensis sp. nov.

    Treesearch

    C.M. Bezuidenhout; S. Deman; S.A. Kirk; W.J. Botha; L. Mostert; A. McLeod

    2010-01-01

    Agathosma species, which are indigenous to South Africa, are also cultivated for commercial use. Recently growers experienced severe plant loss, and symptoms shown by affected plants suggested that a soilborne disease could be the cause of death. A number of Phytophthora taxa were isolated from diseased plants, and this paper reports...

  14. On the generic placement and taxonomic status of some Miltochrista taxa described by Franz Daniel (Lepidoptera, Erebidae, Arctiinae).

    PubMed

    Volynkin, Anton V

    2016-10-31

    Three Miltochrista Hübner, [1819] taxa described by Daniel, Miltochrista tibeta Daniel, 1951, M. tibeta clara Daniel, 1951 and M. gilva Daniel, 1951 are transferred to the genus Lyclene Moore, [1860]. M. tibeta clara is upgraded to the species level. Adults, male and female genitalia are illustrated.

  15. Chemical and principal-component analyses of the essential oils of Apioideae taxa (Apiaceae) from central Balkan.

    PubMed

    Kapetanos, Chrysostomos; Karioti, Anastasia; Bojović, Srdjan; Marin, Petar; Veljić, Milan; Skaltsa, Helen

    2008-01-01

    The volatile constituents of the essential oils of 23 taxa belonging to the Apioideae subfamily were studied in detail. The investigated taxa were Pimpinella serbica (Vis.) Bentham & Hooker, Libanotis montana Cr., Cnidium silaifolium (Jacq.) Simk. ssp. orientale (Boiss.) Tutin, Bupleurum praealtum L., B. sibthorpianum S. S. var. diversifolium (Roch.) Hay, Aegopodium podagraria L., Torilis anthriscus (L.) Gmel., Orlaya grandiflora (L.) Hoffm., Laserpitium siler L., Laser trilobum (L.) Brokh., Chaerophyllum aureum L., C. hirsutum L., C. temulum L., Pastinaca sativa L., P. hirsuta Pancic., Tordylium maximum L., Physospermum cornubiense (L.) DC., Peucedanum alsaticum L., P. oreoselinum (L.) Moench, P. cervaria (L.) Cuss., P. austriacum (Jacq.) Koch, P. longifolium W. et K., and P. officinale L. All of these species grow wild in the central part of the Balkan Peninsula. The essential oils were found to be complex mixtures of various compounds, more than 100 constituents being in each taxon, with contributions of main products never exceeding 25% of the total content. Sesquiterpene hydrocarbons were found to be the main group of constituents of all taxa, except for Peucedanum species, where monoterpene hydrocarbons were identified as the main components. The chemotaxonomic value of the essential-oil composition is discussed according to results of principal-component analysis (PCA). The essential-oil composition mainly reflects current taxonomic relationships between the investigated taxa.

  16. A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

    PubMed

    Miadlikowska, Jolanta; Kauff, Frank; Högnabba, Filip; Oliver, Jeffrey C; Molnár, Katalin; Fraker, Emily; Gaya, Ester; Hafellner, Josef; Hofstetter, Valérie; Gueidan, Cécile; Otálora, Mónica A G; Hodkinson, Brendan; Kukwa, Martin; Lücking, Robert; Björk, Curtis; Sipman, Harrie J M; Burgaz, Ana Rosa; Thell, Arne; Passo, Alfredo; Myllys, Leena; Goward, Trevor; Fernández-Brime, Samantha; Hestmark, Geir; Lendemer, James; Lumbsch, H Thorsten; Schmull, Michaela; Schoch, Conrad L; Sérusiaux, Emmanuël; Maddison, David R; Arnold, A Elizabeth; Lutzoni, François; Stenroos, Soili

    2014-10-01

    The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed

  17. A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families

    PubMed Central

    Miadlikowska, Jolanta; Kauff, Frank; Högnabba, Filip; Oliver, Jeffrey C.; Molnár, Katalin; Fraker, Emily; Gaya, Ester; Hafellner, Josef; Hofstetter, Valérie; Gueidan, Cécile; Otálora, Mónica A.G.; Hodkinson, Brendan; Kukwa, Martin; Lücking, Robert; Björk, Curtis; Sipman, Harrie J.M.; Burgaz, Ana Rosa; Thell, Arne; Passo, Alfredo; Myllys, Leena; Goward, Trevor; Fernández-Brime, Samantha; Hestmark, Geir; Lendemer, James; Lumbsch, H. Thorsten; Schmull, Michaela; Schoch, Conrad; Sérusiaux, Emmanuël; Maddison, David R.; Arnold, A. Elizabeth; Lutzoni, François; Stenroos, Soili

    2014-01-01

    The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, ‘Candelariomycetidae’). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed

  18. Evaluating green infrastructure in urban environments using a multi-taxa and functional diversity approach.

    PubMed

    Pinho, Pedro; Correia, Otília; Lecoq, Miguel; Munzi, Silvana; Vasconcelos, Sasha; Gonçalves, Paula; Rebelo, Rui; Antunes, Cristina; Silva, Patrícia; Freitas, Catarina; Lopes, Nuno; Santos-Reis, Margarida; Branquinho, Cristina

    2016-05-01

    Forested areas within cities host a large number of species, responsible for many ecosystem services in urban areas. The biodiversity in these areas is influenced by human disturbances such as atmospheric pollution and urban heat island effect. To ameliorate the effects of these factors, an increase in urban green areas is often considered sufficient. However, this approach assumes that all types of green cover have the same importance for species. Our aim was to show that not all forested green areas are equal in importance for species, but that based on a multi-taxa and functional diversity approach it is possible to value green infrastructure in urban environments. After evaluating the diversity of lichens, butterflies and other-arthropods, birds and mammals in 31 Mediterranean urban forests in south-west Europe (Almada, Portugal), bird and lichen functional groups responsive to urbanization were found. A community shift (tolerant species replacing sensitive ones) along the urbanization gradient was found, and this must be considered when using these groups as indicators of the effect of urbanization. Bird and lichen functional groups were then analyzed together with the characteristics of the forests and their surroundings. Our results showed that, contrary to previous assumptions, vegetation density and more importantly the amount of urban areas around the forest (matrix), are more important for biodiversity than forest quantity alone. This indicated that not all types of forested green areas have the same importance for biodiversity. An index of forest functional diversity was then calculated for all sampled forests of the area. This could help decision-makers to improve the management of urban green infrastructures with the goal of increasing functionality and ultimately ecosystem services in urban areas.

  19. A Metagenomic Assembly-Based Approach to Decoding Taxa in the Dead Zone

    NASA Astrophysics Data System (ADS)

    Thrash, C.; Baker, B.; Seitz, K.; Gillies, L.; Temperton, B.; Rabalais, N. N.; Mason, O. U.

    2016-02-01

    Coastal regions of eutrophication-driven oxygen depletion are widespread and increasing in number. Also known as dead zones, these regions take their name from the deleterious effects of hypoxia (dissolved oxygen less than 2 mg/L) on shrimp, demersal fish, and other animal life. Dead zones result from nutrient enrichment of primary production, concomitant consumption by chemoorganotrophic aerobic microorganisms, and strong stratification that prevents ventilation of bottom water. One of the largest dead zones in the world occurs seasonally in the northern Gulf of Mexico (nGOM), where hypoxia can reach up to 22,000 square kilometers. To explore the underlying genomic variation and metabolic potential of microorganisms in hypoxia, we performed metagenomic and metatranscriptomic sequencing on six samples from the 2013 nGOM dead zone from both hypoxic and oxic bottom waters. Over 217 Mb of sequence was assembled into contigs of at least 3 kb with IDBA-UD, with 72 greater than 100 kb, and the largest 495 kb in length. Annotation by IMG recovered over 224 thousand genes in these contigs. Binning with tetra-ESOM and quality filtering based on relative coverage of sample-specific reads led to the recovery of 83 partial to near complete (31 over 70%) high-quality genomes. These metagenomes represent key microbial taxa previously determined to be numerically abundant from 16S rRNA data, such as Thaumarcheaota, Marine Group II Euryarchaeota, SAR406, Synechococcus spp., Actinobacteria, and Planctomycetes. Ongoing work includes the recruitment of metatranscriptomic data to binned contigs for evaluation of relative gene expression, metabolic reconstruction, and comparative genomics with related organisms elsewhere in the global oceans. These data will provide us with detailed information regarding the metabolic potential and activity of many of the key players in the nGOM dead zone.

  20. Reproductive biology and species geographical distribution in the Melastomataceae: a survey based on New World taxa

    PubMed Central

    dos Santos, Ana Paula Milla; Fracasso, Carla Magioni; Luciene dos Santos, Mirley; Romero, Rosana; Sazima, Marlies; Oliveira, Paulo Eugênio

    2012-01-01

    Background and Aims Apomictic plants are less dependent on pollinator services and able to occupy more diverse habitats than sexual species. However, such assumptions are based on temperate species, and comparable evaluation for species-rich Neotropical taxa is lacking. In this context, the Melastomataceae is a predominantly Neotropical angiosperm family with many apomictic species, which is common in the Campos Rupestres, endemism-rich vegetation on rocky outcrops in central Brazil. In this study, the breeding system of some Campo Rupestre Melastomataceae was evaluated, and breeding system studies for New World species were surveyed to test the hypothesis that apomixis is associated with wide distributions, whilst sexual species have more restricted areas. Methods The breeding systems of 20 Campo Rupestre Melastomataceae were studied using hand pollinations and pollen-tube growth analysis. In addition, breeding system information was compiled for 124 New World species of Melastomataceae with either wide (>1000 km) or restricted distributions. Key Results Most (80 %) of the Campo Rupestre species studied were self-compatible. Self-incompatibility in Microlicia viminalis was associated with pollen-tube arrest in the style, as described for other Melastomataceae, but most self-incompatible species analysed showed pollen-tube growth to the ovary irrespective of pollination treatment. Apomictic species showed lower pollen viability and were less frequent among the Campo Rupestre plants. Among the New World species compiled, 43 were apomictic and 77 sexual (24 self-incompatible and 53 self-compatible). Most apomictic (86 %) and self-incompatible species (71 %) presented wide distributions, whilst restricted distributions predominate only among the self-compatible ones (53 %). Conclusions Self-compatibility and dependence on biotic pollination were characteristic of Campo Rupestre and narrowly distributed New World Melastomataceae species, whilst apomictics are widely

  1. A study on the genetic relationships of Avena taxa and the origins of hexaploid oat.

    PubMed

    Chew, Paul; Meade, Kendra; Hayes, Alec; Harjes, Carlos; Bao, Yong; Beattie, Aaron D; Puddephat, Ian; Gusmini, Gabe; Tanksley, Steven D

    2016-07-01

    Using next-generation DNA sequencing, it was possible to clarify the genetic relationships of Avena species and deduce the likely pathway from which hexaploid oat was formed by sequential polyploidization events. A sequence-based diversity study was conducted on a representative sample of accessions from species in the genus Avena using genotyping-by-sequencing technology. The results show that all Avena taxa can be assigned to one of four major genetic clusters: Cluster 1 = all hexaploids including cultivated oat, Cluster 2 = AC genome tetraploids, Cluster 3 = C genome diploids, Cluster 4 = A genome diploid and tetraploids. No evidence was found for the existence of discrete B or D genomes. Through a series of experiments involving the creation of in silico polyploids, it was possible to deduce that hexaploid oat likely formed by the fusion of an ancestral diploid species from Cluster 3 (A. clauda, A. eriantha) with an ancestral diploid species from Cluster 4D (A. longiglumis, A. canariensis, A. wiestii) to create the ancestral tetraploid from Cluster 2 (A. magna, A. murphyi, A. insularis). Subsequently, that ancestral tetraploid fused again with another ancestral diploid from Cluster 4D to create hexaploid oat. Based on the geographic distribution of these species, it is hypothesized that both the tetraploidization and hexaploidization events may have occurred in the region of northwest Africa, followed by radiation of hexaploid oat to its current worldwide distribution. The results from this study shed light not only on the origins of this important grain crop, but also have implications for germplasm collection and utilization in oat breeding.

  2. DNA taxonomy in morphologically plastic taxa: algorithmic species delimitation in the Boodlea complex (Chlorophyta: Cladophorales).

    PubMed

    Leliaert, Frederik; Verbruggen, Heroen; Wysor, Brian; De Clerck, Olivier

    2009-10-01

    DNA-based taxonomy provides a convenient and reliable tool for species delimitation, especially in organisms in which morphological discrimination is difficult or impossible, such as many algal taxa. A group with a long history of confusing species circumscriptions is the morphologically plastic Boodlea complex, comprising the marine green algal genera Boodlea, Cladophoropsis, Phyllodictyon and Struveopsis. In this study, we elucidate species boundaries in the Boodlea complex by analysing nrDNA internal transcribed spacer sequences from 175 specimens collected from a wide geographical range. Algorithmic methods of sequence-based species delineation were applied, including statistical parsimony network analysis, and a maximum likelihood approach that uses a mixed Yule-coalescent model and detects species boundaries based on differences in branching rates at the level of species and populations. Sequence analyses resulted in the recognition of 13 phylogenetic species, although we failed to detect sharp species boundaries, possibly as a result of incomplete reproductive isolation. We found considerable conflict between traditional and phylogenetic species definitions. Identical morphological forms were distributed in different clades (cryptic diversity), and at the same time most of the phylogenetic species contained a mixture of different morphologies (indicating intraspecific morphological variation). Sampling outside the morphological range of the Boodlea complex revealed that the enigmatic, sponge-associated Cladophoropsis (Spongocladia) vaucheriiformis, also falls within the Boodlea complex. Given the observed evolutionary complexity and nomenclatural problems associated with establishing a Linnaean taxonomy for this group, we propose to discard provisionally the misleading morphospecies and genus names, and refer to clade numbers within a single genus, Boodlea.

  3. Two Distinct Triatoma dimidiata (Latreille, 1811) Taxa Are Found in Sympatry in Guatemala and Mexico

    PubMed Central

    Moguel, Barbara; Solorzano, Elizabeth; Dumonteil, Eric; Rodas, Antonieta; de la Rua, Nick; Garnica, Roberto; Monroy, Carlota

    2009-01-01

    Approximately 10 million people are infected with Trypanosoma cruzi, the causative agent of Chagas disease, which remains the most serious parasitic disease in the Americas. Most people are infected via triatomine vectors. Transmission has been largely halted in South America in areas with predominantly domestic vectors. However, one of the main Chagas vectors in Mesoamerica, Triatoma dimidiata, poses special challenges to control due to its diversity across its large geographic range (from Mexico into northern South America), and peridomestic and sylvatic populations that repopulate houses following pesticide treatment. Recent evidence suggests T. dimidiata may be a complex of species, perhaps including cryptic species; taxonomic ambiguity which confounds control. The nuclear sequence of the internal transcribed spacer 2 (ITS2) of the ribosomal DNA and the mitochondrial cytochrome b (mt cyt b) gene were used to analyze the taxonomy of T. dimidiata from southern Mexico throughout Central America. ITS2 sequence divides T. dimidiata into four taxa. The first three are found mostly localized to specific geographic regions with some overlap: (1) southern Mexico and Guatemala (Group 2); (2) Guatemala, Honduras, El Salvador, Nicaragua, and Costa Rica (Group 1A); (3) and Panama (Group 1B). We extend ITS2 Group 1A south into Costa Rica, Group 2 into southern Guatemala and show the first information on isolates in Belize, identifying Groups 2 and 3 in that country. The fourth group (Group 3), a potential cryptic species, is dispersed across parts of Mexico, Guatemala, and Belize. We show it exists in sympatry with other groups in Peten, Guatemala, and Yucatan, Mexico. Mitochondrial cyt b data supports this putative cryptic species in sympatry with others. However, unlike the clear distinction of the remaining groups by ITS2, the remaining groups are not separated by mt cyt b. This work contributes to an understanding of the taxonomy and population subdivision of T

  4. How territoriality and host-tree taxa determine the structure of ant mosaics

    NASA Astrophysics Data System (ADS)

    Dejean, Alain; Ryder, Suzanne; Bolton, Barry; Compin, Arthur; Leponce, Maurice; Azémar, Frédéric; Céréghino, Régis; Orivel, Jérôme; Corbara, Bruno

    2015-06-01

    Very large colonies of territorially dominant arboreal ants (TDAAs), whose territories are distributed in a mosaic pattern in the canopies of many tropical rainforests and tree crop plantations, have a generally positive impact on their host trees. We studied the canopy of an old Gabonese rainforest (ca 4.25 ha sampled, corresponding to 206 "large" trees) at a stage just preceding forest maturity (the Caesalpinioideae dominated; the Burseraceae were abundant). The tree crowns sheltered colonies from 13 TDAAs plus a co-dominant species out of the 25 ant species recorded. By mapping the TDAAs' territories and using a null model co-occurrence analysis, we confirmed the existence of an ant mosaic. Thanks to a large sampling set and the use of the self-organizing map algorithm (SOM), we show that the distribution of the trees influences the structure of the ant mosaic, suggesting that each tree taxon attracts certain TDAA species rather than others. The SOM also improved our knowledge of the TDAAs' ecological niches, showing that these ant species are ecologically distinct from each other based on their relationships with their supporting trees. Therefore, TDAAs should not systematically be placed in the same functional group even when they belong to the same genus. We conclude by reiterating that, in addition to the role played by TDAAs' territorial competition, host trees contribute to structuring ant mosaics through multiple factors, including host-plant selection by TDAAs, the age of the trees, the presence of extrafloral nectaries, and the taxa of the associated hemipterans.

  5. The Ophiostoma clavatum species complex: a newly defined group in the Ophiostomatales including three novel taxa.

    PubMed

    Linnakoski, Riikka; Jankowiak, Robert; Villari, Caterina; Kirisits, Thomas; Solheim, Halvor; de Beer, Z Wilhelm; Wingfield, Michael J

    2016-07-01

    Two species of blue-stain fungi with similar morphologies, Ophiostoma brunneo-ciliatum and Ophiostoma clavatum, are associates of bark beetles infesting Pinus spp. in Europe. This has raised questions whether they represent distinct taxa. Absence of herbarium specimens and contaminated or mistakenly identified cultures of O. brunneo-ciliatum and O. clavatum have accentuated the uncertainty regarding their correct identification. The aim of this study was to reconsider the identity of European isolates reported as O. brunneo-ciliatum and O. clavatum by applying DNA-based identification methods, and to provide appropriate type specimens for them. Phylogenetic analyses of the ITS, βT, TEF-1α and CAL gene sequences revealed that the investigated isolates represent a complex of seven cryptic species. The study confirmed that ITS data is insufficient to delineate species in some Ophiostoma species clusters. Lectotypes and epitypes were designated for O. clavatum and O. brunneo-ciliatum, and three new species, Ophiostoma brunneolum, Ophiostoma macroclavatum and Ophiostoma pseudocatenulatum, are described in the newly defined O. clavatum-complex. The other two species included in the complex are Ophiostoma ainoae and Ophiostoma tapionis. The results suggest co-evolution of these fungi in association with specific bark beetles. The results also confirm the identity of the fungus associated with the pine bark beetle Ips acuminatus as O. clavatum, while O. brunneo-ciliatum appears to be mainly associated with another pine bark beetle, Ips sexdentatus.

  6. Supporting biodiversity by prescribed burning in grasslands - A multi-taxa approach.

    PubMed

    Valkó, Orsolya; Deák, Balázs; Magura, Tibor; Török, Péter; Kelemen, András; Tóth, Katalin; Horváth, Roland; Nagy, Dávid D; Debnár, Zsuzsanna; Zsigrai, György; Kapocsi, István; Tóthmérész, Béla

    2016-12-01

    There are contrasting opinions on the use of prescribed burning management in European grasslands. On the one hand, prescribed burning can be effectively used for the management of open landscapes, controlling dominant species, reducing accumulated litter or decreasing wildfire risk. On the other hand burning can have a detrimental impact on grassland biodiversity by supporting competitor grasses and by threatening several rare and endangered species, especially arthropods. We studied the effects of prescribed burning in alkaline grasslands of high conservation interest. Our aim was to test whether dormant-season prescribed burning can be an alternative conservation measure in these grasslands. We selected six sites in East-Hungary: in three sites, a prescribed fire was applied in November 2011, while three sites remained unburnt. We studied the effects of burning on soil characteristics, plant biomass and on the composition of vegetation and arthropod assemblages (isopods, spiders, ground beetles and rove beetles). Soil pH, organic matter, potassium and phosphorous did not change, but soluble salt content increased significantly in the burnt sites. Prescribed burning had several positive effects from the nature conservation viewpoint. Shannon diversity and the number of flowering shoots were higher, and the cover of the dominant grass Festuca pseudovina was lower in the burnt sites. Graminoid biomass was lower, while total, green and forb biomass were higher in the burnt plots compared to the control. The key finding of our study was that prescribed burning did not decrease the abundance and diversity of arthropod taxa. Species-level analyses showed that out of the most abundant invertebrate species, 10 were not affected, 1 was negatively and 1 was positively affected by burning. Moreover, our results suggest that prescribed burning leaving unburnt patches can be a viable management tool in open landscapes, because it supports plant diversity and does not threaten

  7. A review of the leafhopper tribe Hyalojassini (Hemiptera: Cicadellidae: Iassinae) with description of new taxa.

    PubMed

    Dai, Wu; Dietrich, Christopher H; Zhang, Yalin

    2015-01-16

    The morphologically diverse leafhopper tribe Hyalojassini is reinstated from synonymy under Iassini based on distinctive features of the male genitalia and a key to the Oriental genera is given. The previously monotypic genera Hyalojassus Evans and Coriojassus Evans are revised and redescribed based on study of the type species. The following new genera and species are described from Thailand and China and placed in Hyalojassini: Kanchanaburiassus maculatus gen. nov. & sp. nov. from Kanchanaburi, Thailand; Lamelliassus chaingmaiensis gen. & sp. nov. from Chaingmai, Thailand; Siamiassus constanti gen. & sp. nov. from Loei, Thailand ; Decliviassus gen nov. with D. bipunctatus sp. nov., D. maculatus sp. nov., and D. nudus sp. nov., from Thailand; Trocniassus gen. nov. with T. shaanxiensis and T. henanensis sp. nov.; Hyalojassus elongatus sp. nov. and H. punctulatus sp. nov. from Thailand and H. yunnanensis sp. nov. from China; Coriojassus loeiensis sp. nov. from Thailand, C. yunnanensis sp. nov. and C. zhejiangensis sp. nov. from Yunnan and Zhejiang, China, respectively, the latter representing the first records of the genus from China. Sinojassus Dai et al. 2010 (nec Zhang 1985) is a junior homonym, thus a new replacement name, Siniassus nom. nov., is proposed, the genus is transferred to Hyalojassini, and the following new combinations are made: Siniassus loberus (Dai, Zhang & Zhang, 2010), Siniassus aspinus (Dai, Zhang & Zhang, 2010), Siniassus compressus (Dai, Zhang & Zhang, 2010) and Siniassus webbi (Dai & Dietrich, 2010). Detailed morphological descriptions and illustrations for all new taxa are provided. The following New World genera share the diagnostic morphological features of Hyalojassini and are newly placed in this tribe: Absheta Blocker, Aztrania Blocker, Baldriga Blocker, Bertawolia Blocker, Betawala Blocker, Comanopa Blocker, Daveyoungana Blocker & Webb, Derakandra Blocker, Donleva Blocker, Gargaropsis Fowler, Garlica Blocker, Gehundra Blocker

  8. Biological diversity of Salix taxa in Cu, Pb and Zn phytoextraction from soil.

    PubMed

    Mleczek, Mirosław; Rutkowski, Paweł; Goliński, Piotr; Kaczmarek, Zygmunt; Szentner, Kinga; Waliszewska, Bogusława; Stolarski, Mariusz; Szczukowski, Stefan

    2017-02-01

    The aim of the study was to estimate the efficiency of copper (Cu), lead (Pb) and zinc (Zn) phytoextraction by 145 Salix taxa cultivated in an area affected by industrial activity. Survivability and biomass of plants were also analyzed. The highest Cu, Pb and Zn content in shoots was 33.38 ± 2.91 (S. purpurea × viminalis 8), 24.64 ± 1.97 (S. fragilis 1) and 58.99 ± 4.30 (S. eriocephala 7) mg kg(-1) dry weight, respectively. In the case of unwashed leaves, the highest content of these metals was 135.06 ± 8.14 (S. purpurea 26), 67.98 ± 5.27 (S. purpurea 45) and 142.56 ± 12.69 (S. alba × triandra 2) mg kg(-1) dw, while in washed leaves it was 106.02 ± 11.12 (S. purpurea 45), 55.06 ± 5.75 (S. purpurea 45) and 122.87 ± 12.33 (S. alba × triandra 2) mg kg(-1) dw, respectively. The differences between the highest and lowest values for Cu, Pb and Zn were 545%, 20500% and 535% in shoots; 2692%, 2560% and 7500% in unwashed leaves; and 3286%, 2221% and 6950% in washed leaves, respectively. S. acutifolia was able to effectively accumulate all three metals jointly, producing shoots that were well developed in both length and diameter when compared with the other tested willows-an ability that would suggest its high suitability for practical application.

  9. Impacts of major predators on tropical agroforest arthropods: comparisons within and across taxa.

    PubMed

    Philpott, Stacy M; Greenberg, Russell; Bichier, Peter; Perfecto, Ivette

    2004-06-01

    In food web studies, taxonomically unrelated predators are often grouped into trophic levels regardless of their relative importance on prey assemblages, multiple predator effects, or interactions such as omnivory. Ants and birds are important predators likely to differentially shape arthropod assemblages, but no studies have compared their effects on a shared prey base. In two separate studies, we excluded birds and ants from branches of a canopy tree ( Inga micheliana) in a coffee farm in Mexico for 2 months in the dry and wet seasons of 2002. We investigated changes in arthropod densities with and without predation pressure from (1) birds and (2) ant assemblages dominated by one of two ant species ( Azteca instabilis and Camponotus senex). We first analyzed individual effects of each predator (birds, Azteca instabilis, and C. senex) then used a per day effect metric to compare differences in effects across (birds vs ants) and within predator taxa (the two ant species). Individually, birds reduced densities of total and large arthropods and some arthropod orders (e.g., spiders, beetles, roaches) in both seasons. Azteca instabilis did not significantly affect arthropods (total, small, large or specific orders). Camponotus senex, however, tended to remove arthropods (total, small), especially in the dry season, and affected arthropod densities of some orders both positively and negatively. Predators greatly differed in their effects on Inga arthropods (for all, small, large, and individual orders of arthropods) both in sign (+/-) and magnitudes of effects. Birds had stronger negative effects on arthropods than ants and the two dominant ant species had stronger effects on arthropods in different seasons. Our results show that aggregating taxonomically related and unrelated predators into trophic levels without prior experimental data quantifying the sign and strengths of effects may lead to a misrepresentation of food web interactions.

  10. Genetic and phenotypic differentiation between invasive and native Rhododendron (Ericaceae) taxa and the role of hybridization

    PubMed Central

    Erfmeier, Alexandra; Tsaliki, Marina; Roß, Christel A; Bruelheide, Helge

    2011-01-01

    Hybridization has been repeatedly put forward to explain the invasiveness of Rhododendron ponticum L. in the British Isles. The present study investigates the pattern of ecotypic differentiation and hybridization among native North American R. catawbiense and R. maximum, native R. ponticum from Georgia and Spain, and invasive R. ponticum from Ireland and aims to assess the contribution of hybridization for Rhododendron invasion in the British Isles. Six populations per taxon were analyzed with AFLP markers for genetic dissimilarity, subjected to germination and growth experiments, and tested for frost hardiness. We assessed variation in morphological and ecological characteristics to identify traits displaying evidence of hybridization, thus, promoting invasiveness. Molecular marker analyses revealed a clear distinction between North American R. catawbiense and R. maximum on the one hand, and all R. ponticum populations on the other hand, displaying a complete intermixture of native Spanish and invasive Irish populations. Multivariate analyses of traits revealed leaf length–width ratio, relative growth rates (RGRs) in leaf length, root biomass, and shoot–root ratio to significantly discriminate between the different taxa and unequivocally assigned invasive Irish R. ponticum to the Spanish phenotypes. While the Irish R. ponticum had similar growth traits as conspecific native R. ponticum provenances, germination and biomass allocation were more similar to North American R. catawbiense and R. maximum. Hybridization did not contribute to explaining invasiveness of R. ponticum in Ireland. The similarity in germination and biomass allocation of invasive Irish R. ponticum and North American species has evolved independently and can more probably be attributed to an independent shift within the Ponticum cluster in Ireland. PMID:22393509

  11. Two distinct Triatoma dimidiata (Latreille, 1811) taxa are found in sympatry in Guatemala and Mexico.

    PubMed

    Dorn, Patricia L; Calderon, Claudia; Melgar, Sergio; Moguel, Barbara; Solorzano, Elizabeth; Dumonteil, Eric; Rodas, Antonieta; de la Rua, Nick; Garnica, Roberto; Monroy, Carlota

    2009-01-01

    Approximately 10 million people are infected with Trypanosoma cruzi, the causative agent of Chagas disease, which remains the most serious parasitic disease in the Americas. Most people are infected via triatomine vectors. Transmission has been largely halted in South America in areas with predominantly domestic vectors. However, one of the main Chagas vectors in Mesoamerica, Triatoma dimidiata, poses special challenges to control due to its diversity across its large geographic range (from Mexico into northern South America), and peridomestic and sylvatic populations that repopulate houses following pesticide treatment. Recent evidence suggests T. dimidiata may be a complex of species, perhaps including cryptic species; taxonomic ambiguity which confounds control. The nuclear sequence of the internal transcribed spacer 2 (ITS2) of the ribosomal DNA and the mitochondrial cytochrome b (mt cyt b) gene were used to analyze the taxonomy of T. dimidiata from southern Mexico throughout Central America. ITS2 sequence divides T. dimidiata into four taxa. The first three are found mostly localized to specific geographic regions with some overlap: (1) southern Mexico and Guatemala (Group 2); (2) Guatemala, Honduras, El Salvador, Nicaragua, and Costa Rica (Group 1A); (3) and Panama (Group 1B). We extend ITS2 Group 1A south into Costa Rica, Group 2 into southern Guatemala and show the first information on isolates in Belize, identifying Groups 2 and 3 in that country. The fourth group (Group 3), a potential cryptic species, is dispersed across parts of Mexico, Guatemala, and Belize. We show it exists in sympatry with other groups in Peten, Guatemala, and Yucatan, Mexico. Mitochondrial cyt b data supports this putative cryptic species in sympatry with others. However, unlike the clear distinction of the remaining groups by ITS2, the remaining groups are not separated by mt cyt b. This work contributes to an understanding of the taxonomy and population subdivision of T

  12. Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data

    PubMed Central

    Ungerer, Mark C; Strakosh, Suzanne C; Stimpson, Kaitlin M

    2009-01-01

    Background Long terminal repeat (LTR) retrotransposons are a class of mobile genetic element capable of autonomous transposition via an RNA intermediate. Their large size and proliferative ability make them important contributors to genome size evolution, especially in plants, where they can reach exceptionally high copy numbers and contribute substantially to variation in genome size even among closely related taxa. Using a phylogenetic approach, we characterize dynamics of proliferation events of Ty3/gypsy-like LTR retrotransposons that led to massive genomic expansion in three Helianthus (sunflower) species of ancient hybrid origin. The three hybrid species are independently derived from the same two parental species, offering a unique opportunity to explore patterns of retrotransposon proliferation in light of reticulate evolutionary events in this species group. Results We demonstrate that Ty3/gypsy-like retrotransposons exist as multiple well supported sublineages in both the parental and hybrid derivative species and that the same element sublineage served as the source lineage of proliferation in each hybrid species' genome. This inference is based on patterns of species-specific element numerical abundance within different phylogenetic sublineages as well as through signals of proliferation events present in the distributions of element divergence values. Employing methods to date paralogous sequences within a genome, proliferation events in the hybrid species' genomes are estimated to have occurred approximately 0.5 to 1 million years ago. Conclusion Proliferation of the same retrotransposon major sublineage in each hybrid species indicates that similar dynamics of element derepression and amplification likely occurred in each hybrid taxon during their formation. Temporal estimates of these proliferation events suggest an earlier origin for these hybrid species than previously supposed. PMID:19594956

  13. Near-future ocean acidification causes differences in microbial associations within diverse coral reef taxa.

    PubMed

    Webster, N S; Negri, A P; Flores, F; Humphrey, C; Soo, R; Botté, E S; Vogel, N; Uthicke, S

    2013-04-01

    Microorganisms form symbiotic partnerships with a diverse range of marine organisms and can be critical to the health and survival of their hosts. Despite the importance of these relationships, the sensitivity of symbiotic microbes to ocean acidification (OA) is largely unknown and this needs to be redressed to adequately predict marine ecosystem resilience in a changing climate. We adopted a profiling approach to explore the sensitivity of microbes associated with coral reef biofilms and representatives of three ecologically important calcifying invertebrate phyla [corals, foraminifera and crustose coralline algae (CCA)] to OA. The experimental design for this study comprised four pHs consistent with current IPCC predictions for the next few centuries (pHNIST 8.1, 7.9, 7.7, 7.5); these pH/pCO₂ conditions were produced in flow-through aquaria using CO₂ bubbling. All reduced pH/increased pCO₂ treatments caused clear differences in the microbial communities associated with coral, foraminifera, CCA and reef biofilms over 6 weeks, while no visible signs of host stress were detected over this period. The microbial communities of coral, foraminifera, CCA and biofilms were significantly different between pH 8.1 (pCO₂ = 464 μatm) and pH 7.9 (pCO₂ = 822 μatm), a concentration likely to be exceeded by the end of the present century. This trend continued at lower pHs/higher pCO₂. 16S rRNA gene sequencing revealed variable and species-specific changes in the microbial communities with no microbial taxa consistently present or absent from specific pH treatments. The high sensitivity of coral, foraminifera, CCA and biofilm microbes to OA conditions projected to occur by 2100 is a concern for reef ecosystems and highlights the need for urgent research to assess the implications of microbial shifts for host health and coral reef processes.

  14. A comparative study on the antinociceptive and anti-inflammatory activities of five Juniperus taxa.

    PubMed

    Akkol, Esra Küpeli; Güvenç, Ayşegül; Yesilada, Erdem

    2009-09-07

    Juniperus L. (Cupressaceae) species have been used to various inflammatory and infectious diseases such as bronchitis, colds, cough, fungal infections, hemorrhoids, gynecological diseases, and wounds in Turkish folk medicine. To evaluate this traditional information, anti-inflammatory and antinociceptive activities of the methanolic and aqueous extracts prepared from different parts (stem, fruit and leaves) of the five Turkish taxa under Juniperus section of the gender; J. drupacea, J. communis var. communis, J. communis var. saxatilis, J. oxycedrus subsp. oxycedrus, and J. oxycedrus subsp. macrocarpa growing were investigated. For the anti-inflammatory activity, carrageenan-induced and PGE(2)-induced hind paw edema models, and for the antinociceptive activity p-benzoquinone-induced writhing and hot plate tests in mice were employed. The methanolic extracts of fruit and leaves from J. oxycedrus subsp. oxycedrus and J. communis var. saxatilis exhibited notable inhibition in carrageenan-induced edema model at a dose of 100mg/kg. The same extracts also displayed significant activity against PGE(2)-induced edema model. While, the remaining extracts were found inactive against these edema models. A similar activity pattern was observed against p-benzoquinone-induced abdominal constriction test without inducing any gastric damage or apparent acute toxicity, whereas all extracts were inactive in hot plate test. The experimental data demonstrated that J. oxycedrus subsp. oxycedrus and J. communis var. saxatilis displayed remarkable anti-inflammatory and antinociceptive activities; however, further studies are warranted to define and isolate the active anti-inflammatory and antinociceptive components from these active species which may yield safe and effective agents to be used in the treatment of inflammatory disorders.

  15. A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping.

    PubMed

    Koh, Hyunwook; Blaser, Martin J; Li, Huilin

    2017-04-24

    The role of the microbiota in human health and disease has been increasingly studied, gathering momentum through the use of high-throughput technologies. Further identification of the roles of specific microbes is necessary to better understand the mechanisms involved in diseases related to microbiome perturbations. Here, we introduce a new microbiome-based group association testing method, optimal microbiome-based association test (OMiAT). OMiAT is a data-driven testing method which takes an optimal test throughout different tests from the sum of powered score tests (SPU) and microbiome regression-based kernel association test (MiRKAT). We illustrate that OMiAT efficiently discovers significant association signals arising from varying microbial abundances and different relative contributions from microbial abundance and phylogenetic information. We also propose a way to apply it to fine-mapping of diverse upper-level taxa at different taxonomic ranks (e.g., phylum, class, order, family, and genus), as well as the entire microbial community, within a newly introduced microbial taxa discovery framework, microbiome comprehensive association mapping (MiCAM). Our extensive simulations demonstrate that OMiAT is highly robust and powerful compared with other existing methods, while correctly controlling type I error rates. Our real data analyses also confirm that MiCAM is especially efficient for the assessment of upper-level taxa by integrating OMiAT as a group analytic method. OMiAT is attractive in practice due to the high complexity of microbiome data and the unknown true nature of the state. MiCAM also provides a hierarchical association map for numerous microbial taxa and can also be used as a guideline for further investigation on the roles of discovered taxa in human health and disease.

  16. Detecting reticulate relationships among diploid Leucanthemum Mill. (Compositae, Anthemideae) taxa using multilocus species tree reconstruction methods and AFLP fingerprinting.

    PubMed

    Konowalik, Kamil; Wagner, Florian; Tomasello, Salvatore; Vogt, Robert; Oberprieler, Christoph

    2015-11-01

    We examined the evolutionary history of the diploid representatives of the genus Leucanthemum Mill. (Compositae, Anthemideae), which constitutes an extensive polyploid complex comprising around 41 species with ploidy levels ranging from 2x to 22x. The inference of phylogenetic relationships even on the diploid level is complicated in this genus due to the overlay of hybridisation and incomplete lineage sorting processes leading to incongruence among gene trees based on nuclear and plastid sequence information. Species tree and network reconstructions were based on gene trees from nine low-copy nuclear markers and the concatenated sequence information for five intergenic spacer regions of the chloroplast genome, either sequenced by Roche 454 pyrosequencing techniques or traditional Sanger sequencing techniques. Additional phylogenetic information came from multi-locus AFLP-fingerprinting of representative individuals of all diploid taxa under study and the subsequent analysis of AFLP patterns with Bayesian clustering and network reconstruction methods. To distinguish between hybridisation and incomplete lineage sorting, we developed and utilized a new 'hybrid index' calculation for individual taxa of the data set, which was compared to a simulated null-distribution assuming the occurrence of incomplete lineage sorting alone for pinpointing taxa with a significant hybrid signal. As a result, two species groups with contrasting patterns of gene flow and/or hybrid speciation signals could be identified in the diploids of Leucanthemum: (a) an early-diverging stock of allopatrically distributed diploid species with a lack of evidence for recent hybridisation events among its members and (b) a more recently radiated taxon assemblage with morphologically less clearly circumscribed taxa and a pronounced signal of gene flow among lineages and several candidate taxa, for which a homoploid hybrid origin may be considered.

  17. "Das Konkrete ist das Abstrakte, an das man sich schließlich gewöhnt hat." (Laurent Schwartz) Über den Ablauf des mathematischen Verstehens

    NASA Astrophysics Data System (ADS)

    Lowsky, Martin

    Die im Titel genannte Aussage findet sich in den Lebenserinnerungen von Laurent Schwartz (1915-2002), einem der fruchtbarsten Mathematiker, Mitglied der Gruppe Bourbaki. Im Original lautet die Aussage: "un objet concret est un objet abstrait auquel on a fini par s'habituer." Schwartz erläutert sie am Beispiel des Integrals über {e^{-1/2{x^2}}} , das den Wert Wurzel aus 2π hat und in dem sich also die Zahlen e und π verknüpfen. Was Schwartz aber vor allem ausdrücken will, ist dies: Das mathematische Verständnisd geht langsam vor sich und es bedarf der Anstrengung. "Es ist eine Frage der Zeit und der Energie", sagt Schwartz, und gerade dies mache es so schwer, die höhere Mathematik unter das Volk zu bringen. Das Lernen und Lehren von Mathematik laufe eben mühevoll und langsam ab.

  18. Pedagogical Basis of DAS Formalism in Engineering Education

    ERIC Educational Resources Information Center

    Hiltunen, J.; Heikkinen, E.-P.; Jaako, J.; Ahola, J.

    2011-01-01

    The paper presents a new approach for a bachelor-level curriculum structure in engineering. The approach is called DAS formalism according to its three phases: description, analysis and synthesis. Although developed specifically for process and environmental engineering, DAS formalism has a generic nature and it could also be used in other…

  19. Evidence of Motor Programming Deficits in Children Diagnosed with DAS.

    ERIC Educational Resources Information Center

    Nijland, Lian; Maassen, Ben; van der Meulen, Sjoeke

    2003-01-01

    Five children with developmental apraxia of speech (DAS), 5 controls (ages 5-6), and 6 adults produced utterances in a normal condition and in a bite-block condition in which the mandible was in a fixed position. In children with DAS, the bite-block had large effects on coarticulatory patterns and vowel quality. (Contains references.) (Author/CR)

  20. Pedagogical Basis of DAS Formalism in Engineering Education

    ERIC Educational Resources Information Center

    Hiltunen, J.; Heikkinen, E.-P.; Jaako, J.; Ahola, J.

    2011-01-01

    The paper presents a new approach for a bachelor-level curriculum structure in engineering. The approach is called DAS formalism according to its three phases: description, analysis and synthesis. Although developed specifically for process and environmental engineering, DAS formalism has a generic nature and it could also be used in other…

  1. How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards.

    PubMed

    Streicher, Jeffrey W; Schulte, James A; Wiens, John J

    2016-01-01

    Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolved) question is whether sampling should be designed to maximize sampling of taxa or genes, or to minimize the inclusion of missing data cells. Here, we explore this question for an ancient, rapid radiation of lizards, the pleurodont iguanians. Pleurodonts include many well-known clades (e.g., anoles, basilisks, iguanas, and spiny lizards) but relationships among families have proven difficult to resolve strongly and consistently using traditional sequencing approaches. We generated up to 4921 ultraconserved elements with sampling strategies including 16, 29, and 44 taxa, from 1179 to approximately 2.4 million characters per matrix and approximately 30% to 60% total missing data. We then compared mean branch support for interfamilial relationships under these 15 different sampling strategies for both concatenated (maximum likelihood) and species tree (NJst) approaches (after showing that mean branch support appears to be related to accuracy). We found that both approaches had the highest support when including loci with up to 50% missing taxa (matrices with ~40-55% missing data overall). Thus, our results show that simply excluding all missing data may be highly problematic as the primary guiding principle for the inclusion or exclusion of taxa and genes. The optimal strategy was somewhat different for each approach, a pattern that has not been shown previously. For concatenated analyses, branch support was maximized when including many taxa (44) but fewer characters (1.1 million). For species-tree analyses, branch support was maximized with minimal taxon sampling (16) but many loci (4789 of 4921). We also show that the choice of these sampling

  2. Biomechanical modeling and sensitivity analysis of bipedal running ability. I. Extant taxa.

    PubMed

    Hutchinson, John R

    2004-10-01

    I used a simple mathematical model of the inverse dynamics of locomotion to estimate the minimum muscle masses required to maintain quasi-static equilibrium about the four main limb joints at mid-stance of fast running. Models of 10 extant taxa (a human, a kangaroo, two lizards, an alligator, and five birds) were analyzed in various bipedal poses to examine how anatomy, size, limb orientation, and other model parameters influence running ability. I examined how the muscle masses required for fast running compare to the muscle masses that are actually able to exert moments about the hip, knee, ankle, and toe joints, to see how support ability varies across the limb. I discuss the assumptions and limitations of the models, using sensitivity analysis to see how widely the results differed with feasible parameter input values. Even with a wide range of input values, the models validated the analysis procedure. Animals that are known to run bipedally were calculated as able to preserve quasi-static equilibrium about their hindlimb joints at mid-stance, whereas non-bipedal runners (iguanas and alligators) were recognized as having too little muscle mass to run quickly in bipedal poses. Thus, this modeling approach should be reliable for reconstructing running ability in extinct bipeds such as nonavian dinosaurs. The models also elucidated how key features are important for bipedal running capacity, such as limb orientation, muscle moment arms, muscle fascicle lengths, and body size. None of the animals modeled had extensor muscle masses acting about any one joint that were 7% or more of their body mass, which provides a reasonable limit for how much muscle mass is normally apportioned within a limb to act about a particular joint. The models consistently showed that a key biomechanical limit on running ability is the capacity of ankle extensors to generate sufficiently large joint moments. Additionally, the analysis reveals how large ratite birds remain excellent runners

  3. The Evolution of Diapsid Reproductive Strategy with Inferences about Extinct Taxa

    PubMed Central

    Varricchio, David J.

    2016-01-01

    Diapsids show an extremely wide range of reproductive strategies. Offspring may receive no parental care, care from only one sex, care from both parents, or care under more complex regimes. Young may vary from independent, super-precocial hatchlings to altricial neonates needing much care before leaving the nest. Parents can invest heavily in a few young, or less so in a larger number. Here we examine the evolution of these traits across a composite phylogeny spanning the extant diapsids and including the limited number of extinct taxa for which reproductive strategies can be well constrained. Generalized estimating equation(GEE)-based phylogenetic comparative methods demonstrate the influences of body mass, parental care strategy and hatchling maturity on clutch volume across the diapsids. The influence of polygamous reproduction is not important despite a large sample size. Applying the results of these models to the dinosaurs supports the hypothesis of paternal care (male only) in derived non-avian theropods, previously suggested based on simpler analyses. These data also suggest that sauropodomorphs did not care for their young. The evolution of parental-care occurs in an almost linear series of transitions. Paternal care rarely gives rise to other care strategies. Where hatchling condition changes, diapsids show an almost unidirectional tendency of evolution towards increased altriciality. Transitions to social monogamy from the ancestral state in diapsids, where both sexes are polygamous, are common. In contrast, once evolved, polygyny and polyandry are very evolutionarily stable. Polygyny and maternal care correlate, as do polyandry and paternal care. Ancestral-character estimation (ACE) of these care strategies with the character transition likelihoods estimated from the original data gives good confidence at most important nodes. These analyses suggest that the basalmost diapsids had no parental care. Crocodilians independently evolved maternal care

  4. Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

    PubMed Central

    Agler, Matthew T.; Ruhe, Jonas; Kroll, Samuel; Morhenn, Constanze; Kim, Sang-Tae; Weigel, Detlef; Kemen, Eric M.

    2016-01-01

    Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe–microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe–microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial “hubs,” are strongly interconnected and have a severe effect on communities. By documenting these microbe–microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on “hub” microbes, which, via microbe–microbe interactions, transmit the effects to the microbial community. We analyzed two “hub” microbes (the

  5. New fossil taxa and notes on the Mesozoic evolution of Liadytidae and Dytiscidae (Coleoptera).

    PubMed

    Prokin, Alexander A; Petrov, Pyotr N; Wang, Bo; Ponomarenko, Alexander G

    2013-01-01

    The diagnoses of Liadytidae Ponomarenko, 1977, Liadytiscinae Prokin & Ren, 2010, Liadytiscus Prokin & Ren, 2010 and Mesoderus Prokin & Ren, 2010 (Dytiscidae) are modified, and the following new taxa are described from Mesozoic fossils: Liadytes aspidytoides sp. n. (Liadytidae); Mesoderini trib. n., Liadyxianus kirejtshuki gen. n. et sp. n., Mesoderus punctatus sp. n., Mesoderus ovatus sp. n., Mesodytes rhantoides gen. n. et sp. n., Palaeodytes baissiensis sp. n. and Cretodytes incertus sp. n. (Dytiscidae). A summarized checklist of all Mesozoic Liadytidae and Dytiscidae known from adults is given, and an identification key to the genera of Mesozoic Dytiscidae known from adults is provided for the first time. Palaeodytes incompletus Ponomarenko, Coram & Jarzembowski, 2005 (the suffix of the specific epithet is emended from the original incomnpleta) is found to belong not to this genus, but to another one, which remains to be described. The fossil larva Angaragabus jurassicus Ponomarenko, 1963 from the Lower Jurassic of Irkutsk Oblast, Russia, probably belonging to Liadytidae, is re-examined. If this larva actually belongs to Liadytidae, then its morphological characters provide additional confirmation of the conclusion, based on the characters of adult liadytids, that the family is quite separate from the recent family Aspidytidae, and the similarity between the adults of both families results from parallel processes in the evolution of the superfamily Dytiscoidea. We show that the principal trends of morphological changes of Liadytidae and Dytiscidae during the Upper Jurassic and Lower Cretaceous included a consistent increase in the area of the metacoxal plates at the expense of decreasing area of the lateral lobes of the metaventrite ("wings"), flattening and loss of the lateral border of the elevated median area of the metaventrite, and shortening and dilation of the metafemur and metatibia. These changes were probably associated with an increased load of

  6. The Evolution of Diapsid Reproductive Strategy with Inferences about Extinct Taxa.

    PubMed

    Moore, Jason R; Varricchio, David J

    2016-01-01

    Diapsids show an extremely wide range of reproductive strategies. Offspring may receive no parental care, care from only one sex, care from both parents, or care under more complex regimes. Young may vary from independent, super-precocial hatchlings to altricial neonates needing much care before leaving the nest. Parents can invest heavily in a few young, or less so in a larger number. Here we examine the evolution of these traits across a composite phylogeny spanning the extant diapsids and including the limited number of extinct taxa for which reproductive strategies can be well constrained. Generalized estimating equation(GEE)-based phylogenetic comparative methods demonstrate the influences of body mass, parental care strategy and hatchling maturity on clutch volume across the diapsids. The influence of polygamous reproduction is not important despite a large sample size. Applying the results of these models to the dinosaurs supports the hypothesis of paternal care (male only) in derived non-avian theropods, previously suggested based on simpler analyses. These data also suggest that sauropodomorphs did not care for their young. The evolution of parental-care occurs in an almost linear series of transitions. Paternal care rarely gives rise to other care strategies. Where hatchling condition changes, diapsids show an almost unidirectional tendency of evolution towards increased altriciality. Transitions to social monogamy from the ancestral state in diapsids, where both sexes are polygamous, are common. In contrast, once evolved, polygyny and polyandry are very evolutionarily stable. Polygyny and maternal care correlate, as do polyandry and paternal care. Ancestral-character estimation (ACE) of these care strategies with the character transition likelihoods estimated from the original data gives good confidence at most important nodes. These analyses suggest that the basalmost diapsids had no parental care. Crocodilians independently evolved maternal care

  7. Diversity of Polychaeta (Annelida) and other worm taxa in mangrove habitats of Darwin Harbour, northern Australia

    NASA Astrophysics Data System (ADS)

    Metcalfe, K. N.; Glasby, C. J.

    2008-02-01

    In this paper data on the diversity, distribution and abundance of polychaetes and other worm taxa in the mangroves of Darwin Harbour, northern Australia, are presented and compared with those of other tropical mangrove areas. Aspects of the feeding guild ecology and the effects of disturbance on mangrove worms are also examined. Data were collected over a period of four years, across four mangrove assemblages. Samples were obtained using three sampling techniques: 1 m × 1 m quadrat searches, epifauna searches and a new infaunal sampling technique, the anoxic mat. A total of 76 species (68 polychaetes, 1 oligochaete, 1 echiuran, 3 sipunculans, 2 nemerteans, 1 turbellarian) were recorded from the four main mangrove assemblages. Of these, 30 species are widespread, occurring in mangrove and non-mangrove habitats throughout the Indo-west Pacific. Only seven species (all polychaetes) appear to be restricted to the mangroves of Darwin Harbour and northern Australia. Polychaetes are predominant, comprising 80-96% of all worms sampled, with three families—Nereididae, Capitellidae and Spionidae—accounting for 46% of all species. The highest diversity and abundance was recorded in the soft, unconsolidated substrates of the seaward assemblage, with diversity and abundance decreasing progressively in the landward assemblages. Most of the worm fauna was infaunal (70%), but the intensive sampling regime revealed a hitherto unknown significant percentage of epifaunal species (18%) and species occurring as both infauna and epifauna (12%). Univariate analyses showed annual and seasonal differences in worm species richness and abundance—presumably associated with the intensity of the monsoon and recruitment success. The worm fauna differed between mangrove assemblages but the proportion of species in each feeding guild was relatively consistent across the four assemblages studied. Herbivores were the most species-rich and abundant, followed by carnivores and sub

  8. The frequency of eubacterium-to-eukaryote lateral gene transfers shows significant cross-taxa variation within amoebozoa.

    PubMed

    Watkins, Russell F; Gray, Michael W

    2006-12-01

    Single-celled bacterivorous eukaryotes offer excellent test cases for evaluation of the frequency of prey-to-predator lateral gene transfer (LGT). Here we use analysis of expressed sequence tag (EST) data sets to quantify the extent of LGT from eubacteria to two amoebae, Acanthamoeba castellanii and Hartmannella vermiformis. Stringent screening for LGT proceeded in several steps intended to enrich for authentic events while at the same time minimizing the incidence of false positives due to factors such as limitations in database coverage and ancient paralogy. The results were compared with data obtained when the same methodology was applied to EST libraries from a number of other eukaryotic taxa. Significant differences in the extent of apparent eubacterium-to-eukaryote LGT were found between taxa. Our results indicate that there may be substantial inter-taxon variation in the number of LGT events that become fixed even between amoebozoan species that have similar feeding modalities.

  9. New Calisto species from Cuba, with insights on the relationships of Cuban and Bahamian taxa (Lepidoptera, Nymphalidae, Satyrinae).

    PubMed

    Núnez Aguila, Rayner; Matos-Maraví, Pável F; Wahlberg, Niklas

    2013-01-01

    Three new species and a new subspecies of Calisto Hübner are described from Cuba, Calisto torrei sp. n. Núñez, Calisto dissimulatum sp. n. Núñez, Calisto aquilum sp. n. Núñez, and Calisto aquilum occidentalis ssp. n. Núñez. The immature stages of C. torrei and C. dissimulatum are also described. Notes on the distribution and biology of the species are given. All Cuban and Bahamian taxa form a monophyletic group which seems to have originated in northeastern Cuba spreading later to the west. DNA sequence data also allowed to recognize both Bahamian taxa, Calisto sibylla and Calisto apollinis stat. n., as distinct species, and to synonymize Calisto herophile parsonsi syn. n. under Calisto herophile.

  10. Taxa-specific eco-sensitivity in relation to phytoplankton bloom stability and ecologically relevant lake state

    NASA Astrophysics Data System (ADS)

    Napiórkowska-Krzebietke, Agnieszka; Dunalska, Julita A.; Zębek, Elżbieta

    2017-05-01

    Phytoplankton (including plant-like, animal-like algae and Cyanobacteria) blooms have recently become a serious global threat to the sustenance of ecosystems, to human and animal health and to economy. This study focused on the composition and stability of blooms as well as their taxa-specific ecological sensitivity to the main causal factors (especially phosphorus and nitrogen) in degraded urban lakes. The analyzed lakes were assessed with respect to the trophic state as well as ecological status. Total phytoplankton biomass (ranging from 1.5 to 181.3 mg dm-3) was typical of blooms of different intensity, which can appear during a whole growing season but are the most severe in early or late summer. Our results suggested that steady-state and non-steady-state bloom assemblages including mono-, bi- and multi-species or heterogeneous blooms may occur in urban lakes. The most intense blooms were formed by the genera of Cyanobacteria: Microcystis, Limnothrix, Pseudanabaena, Planktothrix, Bacillariophyta: Cyclotella and Dinophyta mainly Ceratium and Peridinium. Considering the sensitivity of phytoplankton assemblages, a new eco-sensitivity factor was proposed (E-SF), based on the concept of Phytoplankton Trophic Index composed of trophic scores of phytoplankton taxa along the eutrophication gradient. The E-SF values of 0.5, 1.3, 6.7 and 15.1 were recognized in lakes having a high, good, moderate or poor ecological status, respectively. For lake restoration, each type of bloom should be considered separately because of different sensitivities of taxa and relationships with environmental variables. Proper recognition of the taxa-specific response to abiotic (especially to N and P enrichment) and biotic factors could have significant implications for further water protection and management.

  11. Multi-taxa approach shows consistent shifts in arthropod functional traits along grassland land-use intensity gradient.

    PubMed

    Simons, Nadja K; Weisser, Wolfgang W; Gossner, Martin M

    2016-03-01

    Intensification of land use reduces biodiversity but may also shift the trait composition of communities. Understanding how land use affects single traits and community trait composition, helps to understand why some species are more affected by land use than others. Trait-based analyses are common for plants, but rare for arthropods. We collected literature-based traits for nearly 1000 insect and spider species to test how land- use intensity (including mowing, fertilization, and grazing) across 124 grasslands in three regions of Germany affects community-weighted mean traits across taxa and in single taxa. We additionally measured morphometric traits for more than 150 Heteroptera species and tested whether the weighted mean morphometric traits change with increasing land-use intensity. Community average body size decreased and community average dispersal ability increased from low to high land-use intensity. Furthermore, the relative abundance of herbivores and of specialists among herbivores decreased and the relative abundance of species using the herb layer increased with increasing land-use intensity. Community-weighted means of the morphometric traits in Heteroptera also changed from low to high land-use intensity toward longer and thinner shapes as well as longer appendices (legs, wings, and antenna). While changes in traits with increasing mowing and fertilization intensity were consistent with the combined land-use intensity, community average traits did often not change or with opposite direction under increasing grazing intensity. We conclude that high land-use intensity acts as an environmental filter selecting for on average smaller, more mobile, and less specialized species across taxa. Although trait collection across multiple arthropod taxa is laborious and needs clear trait definitions, it is essential for understanding the functional consequences of biodiversity loss due to land-use intensification.

  12. Consistency of effects of tropical forest disturbance on species composition and richness relative to use of indicator taxa.

    PubMed

    Stork, N E; Srivastava, D S; Eggleton, P; Hodda, M; Lawson, G; Leakey, R R B; Watt, A D

    2016-12-16

    A citation-classic study published almost twenty years ago found that the species richness of eight taxa each responded differently to anthropogenic disturbance in Cameroon forests. Recent developments in conservation biology suggest that net number of species is an insensitive measure of change and that understanding which species are affected by disturbance is more important. In addition, it is recognized that all disturbance types are not equal in their effect on species and that grouping species according to function rather than taxonomy is more informative of responses of biodiversity to change. In a reanalysis of most of the original Cameroon dataset (canopy/ground ants, termites, canopy beetles, nematodes and butterflies) using more a inclusive measure of forest disturbance, which recognised four component drivers of change, we found disturbance effects are always stronger on species composition than on species richness and are mostly concordant between taxa. Further, the magnitude of compositional change relative to reference site was correlated across several taxa. In contrast to findings in the original study, species richness for most groups did not decline with disturbance level, providing additional support to the view that trends in species richness at local scales do not reflect the resilience of ecosystems to disturbance. Although disturbance generally caused changes in composition, the strength of this relationship depended on the disturbance driver and the functional group of organisms considered. This re-analysis suggests consideration of the impact of different forms of disturbance on species composition rather than net numbers of species, and the functional similarity of different taxa are important for conservation management when assessing the impacts of disturbance on biodiversity. This article is protected by copyright. All rights reserved.

  13. DIATOMS (BACILLARIOPHYTA) OF ISOLATED ISLANDS: NEW TAXA IN THE GENUS NAVICULA SENSU STRICTO FROM THE GALáPAGOS ISLANDS(1).

    PubMed

    Seddon, Alistair W R; Froyd, Cynthia A; Witkowski, Andrzej

    2011-08-01

    The diatoms (Bacillariophyta) from a coastal lagoon from the Diablas wetlands (Isla Isabela, the Galápagos Islands) were studied in material from surface samples and a sediment core spanning the past 2,700 years in order to examine evidence of diatom evolution under geographic isolation. The total number of taxa found was ∼100. Ultrastructural variation in valve morphology between members of Galápagos taxa was used to describe 10 species from the genus Navicula sensu stricto, which are new to science. Four taxa: N. isabelensis, N. isabelensoides, N. isabelensiformis, and N. isabelensiminor, shared several key characteristics that may be indicative of a common evolutionary heritage; these species therefore provide possible evidence for the in situ evolution of diatoms in the Galápagos coastal lagoons. Shared morphological characteristics include: (i) stria patterning in the central area, (ii) an elevated and thickened external raphe-sternum, (iii) external central raphe endings that are slightly deflected toward the valve primary side, and (iv) an arched valve surface. To explain these findings, two models were proposed. The first suggested limited lateral diatomaceous transport of Navicula species between the Galápagos and continental South America. Alternatively, these new species may be ecological specialists arising from the unique environmental conditions of the Galápagos coastal lagoons, which restrict the colonization of common diatom taxa and enable the establishment of novel, rare species. The Diablas wetlands are an important site for diatom research, where local-scale environmental changes have combined with global-scale biogeographic processes resulting in unique diatom assemblages.

  14. Ribosomal RNA gene detection and targeted culture of novel nitrogen-responsive fungal taxa from temperate pine forest soil.

    PubMed

    Hesse, Cedar Nelson; Torres-Cruz, Terry; Billingsley Tobias, Terri L; Al-Matruk, Maryam; Porras-Alfaro, Andrea; Kuske, Cheryl R

    2016-09-12

    Soil fungal communities are responsible for carbon and nitrogen (N) cycling. The high complexity of the soil fungal community and the high proportion of taxonomically unidentifiable sequences confound ecological interpretations in field studies because physiological information is lacking for many organisms known only by their rRNA sequences. This situation forces experimental comparisons to be made at broader taxonomic racks where functions become difficult to infer. The objective of this study was to determine OTU (operational taxonomic units) level responses of the soil fungal community to N enrichment in a temperate pine forest experiment and to use the sequencing data to guide culture efforts of novel N-responsive fungal taxa. Replicate samples from four soil horizons (up to 10 cm depth) were obtained from ambient, enriched CO2 and N-fertilization plots. Through a fungal large subunit rRNA gene (LSU) sequencing survey, we identified two novel fungal clades that were abundant in our soil sampling (representing up to 27% of the sequences in some samples) and responsive to changes in soil N. The two N-responsive taxa with no predicted taxonomic association were targeted for isolation and culturing from specific soil samples where their sequences were abundant. Representatives of both OTUs were successfully cultured using a filtration approach. One taxon (OTU6) was most closely related to Saccharomycotina; the second taxon (OTU69) was most closely related to Mucoromycotina. Both taxa likely represent novel species. This study shows how observation of specific OTUs level responses to altered N status in a large rRNA gene field survey provided the impetus to design targeted culture approaches for isolation of novel N-responsive fungal taxa.

  15. Carbon concentration of standing and downed woody detritus: effects of tree taxa, decay class, position, and tissue type

    Treesearch

    Mark E. Harmon; Becky Fasth; Christopher W. Woodall; Jay. Sexton

    2013-01-01

    The degree to which carbon concentration (CC) of woody detritus varies by tree taxa, stage of decay, tissue type (i.e., bark versus wood), and vertical orientation was examined in samples of 60 tree species from the Northern Hemisphere. The mean CC of 257 study samples was 49.3% with a range of 43.4-56.8%. Angiosperms had a significantly lower CC than gymnosperms, with...

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

    PubMed

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

    2014-05-01

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

  17. DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa

    PubMed Central

    Rawlence, Nicolas J.; Wood, Jamie R.; Armstrong, Kyle N.; Cooper, Alan

    2009-01-01

    Feathers are known to contain amplifiable DNA at their base (calamus) and have provided an important genetic source from museum specimens. However, feathers in subfossil deposits generally only preserve the upper shaft and feather ‘vane’ which are thought to be unsuitable for DNA analysis. We analyse subfossil moa feathers from Holocene New Zealand rockshelter sites and demonstrate that both ancient DNA and plumage information can be recovered from their upper portion, allowing species identification and a means to reconstruct the appearance of extinct taxa. These ancient DNA sequences indicate that the distal portions of feathers are an untapped resource for studies of museum, palaeontological and modern specimens. We investigate the potential to reconstruct the plumage of pre-historically extinct avian taxa using subfossil remains, rather than assuming morphological uniformity with closely related extant taxa. To test the notion of colour persistence in subfossil feathers, we perform digital comparisons of feathers of the red-crowned parakeet (Cyanoramphus novaezelandiae novaezelandiae) excavated from the same horizons as the moa feathers, with modern samples. The results suggest that the coloration of the moa feathers is authentic, and computer software is used to perform plumage reconstructions of moa based on subfossil remains. PMID:19570784

  18. Pollen Performance in Clarkia Taxa with Contrasting Mating Systems: Implications for Male Gametophytic Evolution in Selfers and Outcrossers

    PubMed Central

    Hove, Alisa A.; Mazer, Susan J.

    2013-01-01

    We tested three predictions regarding the joint evolution of pollen performance and mating system. First, due to the potential for intense intrasexual competition in outcrossing populations, we predicted that outcrossers would produce faster-growing pollen than their selfing relatives. Second, if elevated competition promotes stronger selection on traits that improve pollen performance, then, among-plant variation in pollen performance would be lower in outcrossers than in selfers. Third, given successive generations of adaptation to the same maternal genotype in selfers, we predicted that, in selfing populations (but not in outcrossing ones), pollen would perform better following self- than cross-pollinations. We tested these predictions in field populations of two pairs of Clarkia (Onagraceae) sister taxa. Consistent with our predictions, one outcrosser (C. unguiculata) exhibited faster pollen germination and less variation in pollen tube growth rate (PTGR) among pollen donors than its selfing sister species, C. exilis. Contrary to our predictions, the selfing C. xantiana ssp. parviflora exhibited faster PTGR than the outcrossing ssp. xantiana, and these taxa showed similar levels of variation in this trait. Pollen performance following self- vs. cross-pollinations did not differ within either selfing or outcrossing taxa. While these findings suggest that mating system and pollen performance may jointly evolve in Clarkia, other factors clearly contribute to pollen performance in natural populations. PMID:27137375

  19. Overview of the transcriptome profiles identified in hagfish, shark, and bichir: current issues arising from some nonmodel vertebrate taxa.

    PubMed

    Takechi, Masaki; Takeuchi, Masaki; Ota, Kinya G; Nishimura, Osamu; Mochii, Makoto; Itomi, Kazu; Adachi, Noritaka; Takahashi, Maiko; Fujimoto, Satoko; Tarui, Hiroshi; Okabe, Masataka; Aizawa, Shinichi; Kuratani, Shigeru

    2011-11-15

    Because of their crucial phylogenetic positions, hagfishes, sharks, and bichirs are recognized as key taxa in our understanding of vertebrate evolution. The expression patterns of the regulatory genes involved in developmental patterning have been analyzed in the context of evolutionary developmental studies. However, in a survey of public sequence databases, we found that the large-scale sequence data for these taxa are still limited. To address this deficit, we used conventional Sanger DNA sequencing and a next-generation sequencing technology based on 454 GS FLX sequencing to obtain expressed sequence tags (ESTs) of the Japanese inshore hagfish (Eptatretus burgeri; 161,482 ESTs), cloudy catshark (Scyliorhinus torazame; 165,819 ESTs), and gray bichir (Polypterus senegalus; 34,336 ESTs). We deposited the ESTs in a newly constructed database, designated the "Vertebrate TimeCapsule." The ESTs include sequences from genes that can be effectively used in evolutionary developmental studies; for instance, several encode cartilaginous extracellular matrix proteins, which are central to an understanding of the ways in which evolutionary processes affected the skeletal elements, whereas others encode regulatory genes involved in craniofacial development and early embryogenesis. Here, we discuss how hagfishes, sharks, and bichirs contribute to our understanding of vertebrate evolution, we review the current status of the publicly available sequence data for these three taxa, and we introduce our EST projects and newly developed database. © 2011 Wiley Periodicals, Inc.

  20. Biogeography of Heterotrophic Flagellate Populations Indicates the Presence of Generalist and Specialist Taxa in the Arctic Ocean

    PubMed Central

    Thaler, Mary

    2015-01-01

    Heterotrophic marine flagellates (HF) are ubiquitous in the world's oceans and represented in nearly all branches of the domain Eukaryota. However, the factors determining distributions of major taxonomic groups are poorly known. The Arctic Ocean is a good model environment for examining the distribution of functionally similar but phylogenetically diverse HF because the physical oceanography and annual ice cycles result in distinct environments that could select for microbial communities or favor specific taxa. We reanalyzed new and previously published high-throughput sequencing data from multiple studies in the Arctic Ocean to identify broad patterns in the distribution of individual taxa. HF accounted for fewer than 2% to over one-half of the reads from the water column and for up to 60% of reads from ice, which was dominated by Cryothecomonas. In the water column, many HF phylotypes belonging to Telonemia and Picozoa, uncultured marine stramenopiles (MAST), and choanoflagellates were geographically widely distributed. However, for two groups in particular, Telonemia and Cryothecomonas, some species level taxa showed more restricted distributions. For example, several phylotypes of Telonemia favored open waters with lower nutrients such as the Canada Basin and offshore of the Mackenzie Shelf. In summary, we found that while some Arctic HF were successful over a range of conditions, others could be specialists that occur under particular conditions. We conclude that tracking species level diversity in HF not only is feasible but also provides a potential tool for understanding the responses of marine microbial ecosystems to rapidly changing ice regimes. PMID:25595764

  1. Fine-scale bacterial community dynamics and the taxa-time relationship within a full-scale activated sludge bioreactor.

    PubMed

    Wells, George F; Park, Hee-Deung; Eggleston, Brad; Francis, Christopher A; Criddle, Craig S

    2011-11-01

    In activated sludge bioreactors, aerobic heterotrophic communities efficiently remove organics, nutrients, toxic substances, and pathogens from wastewater, but the dynamics of these communities are as yet poorly understood. A macroecology metric used to quantify community shifts is the taxa-time relationship, a temporal analog of the species-area curve. To determine whether this metric can be applied to full-scale bioreactors, activated sludge samples were collected weekly over a one-year period at a local municipal wastewater treatment plant. Bacterial community dynamics were evaluated by monitoring 16S rRNA genes using Terminal Restriction Fragment Length Polymorphism (T-RFLP), corroborated by clone libraries. Observed taxa richness increased with time according to a power law model, as predicted by macroecological theory, with a power law exponent of w = 0.209. The results reveal strong long-term temporal dynamics during a period of stable performance (BOD removal and nitrification). Community dynamics followed a gradual succession away from initial conditions rather than periodicity around a mean "equilibrium", with greater within-month then among-month community similarities. Changes in community structure were significantly associated via multivariate statistical analyses with dissolved oxygen, temperature, influent silver, biomass (MLSS), flow rate, and influent nitrite, cadmium and chromium concentrations. Overall, our results suggest patterns of bacterial community dynamics likely regulated in part by operational parameters and provide evidence that the taxa-time relationship may be a fundamental ecological pattern in macro- and microbial systems. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. Cambro-ordovician sea-level fluctuations and sequence boundaries: The missing record and the evolution of new taxa

    USGS Publications Warehouse

    Lehnert, O.; Miller, J.F.; Leslie, Stephen A.; Repetski, J.E.; Ethington, Raymond L.

    2005-01-01

    The evolution of early Palaeozoic conodont faunas shows a clear connection to sea-level changes. One way that this connection manifests itself is that thick successions of carbonates are missing beneath major sequence boundaries due to karstification and erosion. From this observation arises the question of how many taxa have been lost from different conodont lineages in these incomplete successions. Although many taxa suffered extinction due to the environmental stresses associated with falling sea-levels, some must have survived in these extreme conditions. The number of taxa missing in the early Palaeozoic tropics always will be unclear, but it will be even more difficult to evaluate the missing record in detrital successions of higher latitudes. A common pattern in the evolution of Cambrian-Ordovician conodont lineages is appearances of new species at sea-level rises and disappearances at sea-level drops. This simple picture can be complicated by intervals that consistently have no representatives of a particular lineage, even after extensive sampling of the most complete sections. Presumably the lineages survived in undocumented refugia. In this paper, we give examples of evolution in Cambrian-Ordovician shallowmarine conodont faunas and highlight problems of undiscovered or truly missing segments of lineages. ?? The Palaeontological Association.

  3. Phalangopsidae crickets from Tropical Africa (Orthoptera, Grylloidea), with descriptions of new taxa and an identification key for African genera.

    PubMed

    Desutter-Grandcolas, Laure

    2015-04-22

    New Phalangopsidae crickets are described from tropical Africa, including three new genera and ten new species: Afrophaloria Desutter-Grandcolas, n.gen., Afrophaloria amani Desutter-Grandcolas, n. sp., type species, Afrophaloria apiariensis Desutter-Grandcolas, n. sp., Afrophaloria hempae Desutter-Grandcolas, n. sp., Kameruloria gabonensis Desutter-Grandcolas, n. sp., Kameruloria nigricornis Desutter-Grandcolas, n. sp., Kameruloria trimaculata Desutter-Grandcolas, n. sp., Paragryllodes amani Desutter-Grandcolas, n. sp., Phasmagryllus Desutter-Grandcolas, n.gen., Phasmagryllus elegans Desutter-Grandcolas, n. sp., type species, Upupagryllus Desutter-Grandcolas, n.gen., Upupagryllus subalatus Desutter-Grandcolas, n. sp., type species, and Upupagryllus alatus Desutter-Grandcolas, n. sp. All these taxa, except Paragryllodes amani Desutter-Grandcolas, n. sp., belong to the subfamily Phaloriinae. The subfamily is redefined, to take into account their morphological (apterous taxa) and ecological (straminicolous taxa) diversity. A key for phalangopsid African genera is proposed, and the status of Larandeicus Chopard, 1937 briefly discussed.

  4. Deciphering the Ecology of Key Diatom Taxa to Understand Climate-Induced Changes in West Greenland Lakes over the Holocene

    NASA Astrophysics Data System (ADS)

    Saros, J. E.; Northington, R.; Malik, H.; Anderson, N. J.

    2014-12-01

    Paleolimnological records from southwest Greenland reveal that diatom communities have not changed in a similar way to other regions of the Arctic, and in general, do not show synchronous change across this area. There are a number of cases in which lakes in close proximity to each other show opposite community changes over the Holocene. These changes in diatom fossil profiles have been difficult to interpret due to a lack of explicit ecological information for key species. The objective of this project is to decipher the ecology of key diatom species that are abundant across these paleolimnological records. We hypothesize that climate-driven changes in nutrients and water column stability (via its effects on light availability) are key factors shaping diatom community structure in these lakes. We assessed the requirements of particular taxa for nutrients and light through comparative lake sampling and resource bioassays. A whole-lake manipulation in which water column stability was reduced through enhanced water circulation was also conducted to assess the response of key taxa to this change. We found that the relative abundances of key diatom taxa are under complex control by the interactive effects of nutrients and light. We discuss how these results will enhance interpretation of climate-induced changes in Arctic lakes in this region.

  5. Twenty‐eight‐joint counts invalidate the DAS28 remission definition owing to the omission of the lower extremity joints: a comparison with the original DAS remission

    PubMed Central

    Landewé, R; van der Heijde, D; van der Linden, S; Boers, M

    2006-01-01

    Objective To compare 28 joint disease activity score (DAS28) remission with comprehensive joint count DAS remission in rheumatoid arthritis. Methods 620 actually measured paired observations of DAS28 and DAS were analysed in 155 patients. Discordant observations (either DAS or DAS28 below remission cut off level: 1.6 for DAS and 2.6 for DAS28) and concordant observations (both DAS and DAS28 below their remission cut off level) were analysed separately. Results 91 of 620 paired DAS observations (15%) were discordant; 87 (in 53 patients) comprised observations in which the DAS28 remission criterion, but not the DAS remission criterion, was met. The reverse was found in only four observations, which were therefore omitted. With the original DAS as standard, DAS28 sensitivity was 95% and specificity 84%. Probability plots showed a swollen joint count >0 in 75% of discordant pairs v 48% of concordant pairs. The same was found for total joint count (TJC >0 in 90% v 40%; median TJC, 0 v 6) and patient global assessment, but not for ESR. Individual joint analysis showed that 51% of discordant v 18% of concordant observations (p<0.0005) had involvement of lower extremity joints that are not included in the DAS28. Conclusions DAS remission is more conservative than DAS28 remission. Activity (tenderness and swelling) in joints not included in the reduced joint counts (ankles, feet) mainly account for the discrepancy between the two assessments. DAS28 remission at a cut off level of 2.6 has insufficient construct validity and should be used with caution in clinical practice and clinical trials. PMID:16219709

  6. Phylogeny and nomenclature of the genus Talaromyces and taxa accommodated in Penicillium subgenus Biverticillium

    PubMed Central

    Samson, R.A.; Yilmaz, N.; Houbraken, J.; Spierenburg, H.; Seifert, K.A.; Peterson, S.W.; Varga, J.; Frisvad, J.C.

    2011-01-01

    The taxonomic history of anamorphic species attributed to Penicillium subgenus Biverticillium is reviewed, along with evidence supporting their relationship with teleomorphic species classified in Talaromyces. To supplement previous conclusions based on ITS, SSU and/or LSU sequencing that Talaromyces and subgenus Biverticillium comprise a monophyletic group that is distinct from Penicillium at the generic level, the phylogenetic relationships of these two groups with other genera of Trichocomaceae was further studied by sequencing a part of the RPB1 (RNA polymerase II largest subunit) gene. Talaromyces species and most species of Penicillium subgenus Biverticillium sensu Pitt reside in a monophyletic clade distant from species of other subgenera of Penicillium. For detailed phylogenetic analysis of species relationships, the ITS region (incl. 5.8S nrDNA) was sequenced for the available type strains and/or representative isolates of Talaromyces and related biverticillate anamorphic species. Extrolite profiles were compiled for all type strains and many supplementary cultures. All evidence supports our conclusions that Penicillium subgenus Biverticillium is distinct from other subgenera in Penicillium and should be taxonomically unified with the Talaromyces species that reside in the same clade. Following the concepts of nomenclatural priority and single name nomenclature, we transfer all accepted species of Penicillium subgenus Biverticillium to Talaromyces. A holomorphic generic diagnosis for the expanded concept of Talaromyces, including teleomorph and anamorph characters, is provided. A list of accepted Talaromyces names and newly combined Penicillium names is given. Species of biotechnological and medical importance, such as P. funiculosum and P. marneffei, are now combined in Talaromyces. Excluded species and taxa that need further taxonomic study are discussed. An appendix lists other generic names, usually considered synonyms of Penicillium sensu lato that

  7. Hybrid Origins of Carex rostrata var. borealis and C. stenolepis, Two Problematic Taxa in Carex Section Vesicariae (Cyperaceae)

    PubMed Central

    M. Pedersen, A. Tiril; Nowak, Michael D.; Brysting, Anne K.; Elven, Reidar; Bjorå, Charlotte S.

    2016-01-01

    Hybridization is frequent in the large and ecologically significant genus Carex (Cyperaceae). In four important sections of the northern regions (Ceratocystis, Glareosae, Phacocystis and Vesicariae), the frequent occurrence of hybrids often renders the identification of “pure” species and hybrids difficult. In this study we address the origins and taxonomic rank of two taxa of section Vesicariae: Carex rostrata var. borealis and C. stenolepis. The origin and taxonomic status of C. stenolepis has been the subject of substantial debate over the years, whereas C. rostrata var. borealis has received very little attention in the years since its first description in the 19th century. By performing an extensive sampling of relevant taxa from a broad distribution range, and analyzing data from fifteen microsatellite loci developed specifically for our study together with pollen stainability measures, we resolve the hybrid origins of C. rostrata var. borealis and C. stenolepis and provide new insights into this taxonomically challenging group of sedges. Our results are in accordance with previous findings suggesting that C. stenolepis is a hybrid between C. vesicaria and C. saxatilis. They are also in accordance with a previous proposition that C. rostrata var. borealis is a hybrid between C. rostrata and C. rotundata, and furthermore suggest that both hybrids are the result of multiple, recent (i.e., postglacial) hybridization events. We found little evidence for successful sexual reproduction within C. rostrata var. borealis and C. stenolepis, but conclude that the common and recurrent, largely predictable occurrence of these taxa justifies accepting both hybrids as hybrid species with binomial names. There are, however, complications as to types and priority names, and we therefore choose to address these problems in a separate paper. PMID:27780239

  8. Leaf-Associated Bacterial and Fungal Taxa Shifts in Response to Larvae of the Tree Hole Mosquito, Ochlerotatus triseriatus

    PubMed Central

    Kaufman, Michael G.; Chen, Shicheng; Walker, Edward D.

    2014-01-01

    Larvae of the eastern tree hole mosquito, Ochlerotatus triseriatus (Say), and related container-breeding species are known to feed upon substrate-associated microorganisms. Although the importance of these microbial resources to larval growth has been established, almost nothing is known about the taxonomic composition and dynamics of these critical microbial food sources. We examined bacterial and fungal community compositional changes on oak leaves tethered in natural tree hole habitats of O. triseriatus. We eliminated larvae experimentally in a subset of the tree holes and examined 16S rDNA gene sequences for bacteria and ergosterol concentrations and 18S rRNA gene sequences for fungi collected from leaf material subsamples. Leaf ergosterol content varied significantly with time, but not treatment. Principal component analysis (PCA) was used to compare microbial taxonomic patterns found in leaves incubated with or without larvae present, and we found that larval presence affected both bacterial and fungal groups, either from loosely attached or strongly adherent categories. Bacterial communities generally grouped more tightly when larvae were present, and class level taxa proportions changed when larvae were present, suggesting selection by larval feeding or activities for particular taxa such as members of the Bacteroidetes, Alphaproteobacteria, and Betaproteobacteria classes. Fungal taxa composite scores also separated along PC axes related to the presence of larvae and indicated larval feeding effects on several higher taxonomic groups, including Saccharomycetes, Dothideomycetes, and Chytridiomycota. These results support the hypothesis that larval mosquito feeding and activities altered microbial communities associated with substrate surfaces, potentially leading to decreased food value of the resource and affecting decomposition of particulate matter in the system. PMID:17899246

  9. Three-dimensional geometric morphometric analysis of talar morphology in extant gorilla taxa from highland and lowland habitats.

    PubMed

    Knigge, Ryan P; Tocheri, Matthew W; Orr, Caley M; Mcnulty, Kieran P

    2015-01-01

    Western gorillas (Gorilla gorilla) are known to climb significantly more often than eastern gorillas (Gorilla beringei), a behavioral distinction attributable to major differences in their respective habitats (i.e., highland vs. lowland). Genetic evidence suggests that the lineages leading to these taxa began diverging from one another between approximately 1 and 3 million years ago. Thus, gorillas offer a special opportunity to examine the degree to which morphology of recently diverged taxa may be "fine-tuned" to differing ecological requirements. Using three-dimensional (3D) geometric morphometrics, we compared talar morphology in a sample of 87 specimens including western (lowland), mountain (highland), and grauer gorillas (lowland and highland populations). Talar shape was captured with a series of landmarks and semilandmarks superimposed by generalized Procrustes analysis. A between-group principal components analysis of overall talar shape separates gorillas by ecological habitat and by taxon. An analysis of only the trochlea and lateral malleolar facet identifies subtle variations in trochlear shape between western lowland and lowland grauer gorillas, potentially indicative of convergent evolution of arboreal adaptations in the talus. Lastly, talar shape scales differently with centroid size for highland and lowland gorillas, suggesting that ankle morphology may track body-size mediated variation in arboreal behaviors differently depending on ecological setting. Several of the observed shape differences are linked biomechanically to the facilitation of climbing in lowland gorillas and to stability and load-bearing on terrestrial substrates in the highland taxa, providing an important comparative model for studying morphological variation in groups known only from fossils (e.g., early hominins). © 2014 Wiley Periodicals, Inc.

  10. The ontogeny of talo-crural appositional articular morphology among catarrhine taxa: adult shape reflects substrate use.

    PubMed

    Turley, Kevin; Frost, Stephen R

    2014-07-01

    The upper ankle joint forms a single articular plane between organism and the foot and substrate. Singular warp analysis shows that its shape reflects substrate use. This study explores whether the differences in shape are genetic with a developmental trajectory evident during ontogeny or epigenetic and the result of substrate use by the individual. A total of 418 matched distal tibial and proximal talar landmarked surfaces from adult and subadult specimens from 12 diverse catarrhine taxa were studied. Specimens were grouped by molar eruption (M1, M2, and M3) for comparative analysis. Generalized Procrustes analysis, multivariate regression, relative warp analysis, singular warp analysis, and permutation tests were used. Singular warp analysis for the entire cohort was highly significant in the first singular warp, with the adult taxa sorting by substrate use. All 173 subadults clustered with an adult "arboreal" shape profile. Among Hominoidea, adults (M3) sorted by substrate use with Pan paniscus and Hylobatidae assuming an "arboreal" shape separate from Pan troglodytes and the remaining taxa with "terrestrial" shape. Cercopithecoid adults sorted by substrate use as well, with the M3 specimens of Papio hamadryas and Macaca thibetana demonstrating a "terrestrial" shape. Differences in mode of locomotion did not affect the findings in the first singular warp. Results confirmed the convergence of talo-crural shape among superfamilies based on substrate use and divergence in shape within Pan and Macaca, based on substrate use. The shape differences among adults (M3) are consistent with a plastic response to the behavioral stimulus of substrate use.

  11. Biogeography of heterotrophic flagellate populations indicates the presence of generalist and specialist taxa in the Arctic Ocean.

    PubMed

    Thaler, Mary; Lovejoy, Connie

    2015-03-01

    Heterotrophic marine flagellates (HF) are ubiquitous in the world's oceans and represented in nearly all branches of the domain Eukaryota. However, the factors determining distributions of major taxonomic groups are poorly known. The Arctic Ocean is a good model environment for examining the distribution of functionally similar but phylogenetically diverse HF because the physical oceanography and annual ice cycles result in distinct environments that could select for microbial communities or favor specific taxa. We reanalyzed new and previously published high-throughput sequencing data from multiple studies in the Arctic Ocean to identify broad patterns in the distribution of individual taxa. HF accounted for fewer than 2% to over one-half of the reads from the water column and for up to 60% of reads from ice, which was dominated by Cryothecomonas. In the water column, many HF phylotypes belonging to Telonemia and Picozoa, uncultured marine stramenopiles (MAST), and choanoflagellates were geographically widely distributed. However, for two groups in particular, Telonemia and Cryothecomonas, some species level taxa showed more restricted distributions. For example, several phylotypes of Telonemia favored open waters with lower nutrients such as the Canada Basin and offshore of the Mackenzie Shelf. In summary, we found that while some Arctic HF were successful over a range of conditions, others could be specialists that occur under particular conditions. We conclude that tracking species level diversity in HF not only is feasible but also provides a potential tool for understanding the responses of marine microbial ecosystems to rapidly changing ice regimes. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  12. Molecular phylogenetic analysis supports a Gondwanan origin of the Hyriidae (Mollusca: Bivalvia: Unionida) and the paraphyly of Australasian taxa.

    PubMed

    Graf, Daniel L; Jones, Hugh; Geneva, Anthony J; Pfeiffer, John M; Klunzinger, Michael W

    2015-04-01

    The freshwater mussel family Hyriidae (Mollusca: Bivalvia: Unionida) has a disjunct trans-Pacific distribution in Australasia and South America. Previous phylogenetic analyses have estimated the evolutionary relationships of the family and the major infra-familial taxa (Velesunioninae and Hyriinae: Hyridellini in Australia; Hyriinae: Hyriini, Castaliini, and Rhipidodontini in South America), but taxon and character sampling have been too incomplete to support a predictive classification or allow testing of biogeographical hypotheses. We sampled 30 freshwater mussel individuals representing the aforementioned hyriid taxa, as well as outgroup species representing the five other freshwater mussel families and their marine sister group (order Trigoniida). Our ingroup included representatives of all Australian genera. Phylogenetic relationships were estimated from three gene fragments (nuclear 28S, COI and 16S mtDNA) using maximum parsimony, maximum likelihood, and Bayesian inference, and we applied a Bayesian relaxed clock model calibrated with fossil dates to estimate node ages. Our analyses found good support for monophyly of the Hyriidae and the subfamilies and tribes, as well as the paraphyly of the Australasian taxa (Velesunioninae, (Hyridellini, (Rhipidodontini, (Castaliini, Hyriini)))). The Hyriidae was recovered as sister to a clade comprised of all other Recent freshwater mussel families. Our molecular date estimation supported Cretaceous origins of the major hyriid clades, pre-dating the Tertiary isolation of South America from Antarctica/Australia. We hypothesize that early diversification of the Hyriidae was driven by terrestrial barriers on Gondwana rather than marine barriers following disintegration of the super-continent. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Incongruent genetic connectivity patterns for VME indicator taxa: implications for the management of New Zealand's vulnerable marine ecosystems

    NASA Astrophysics Data System (ADS)

    Clark, M. R.; Gardner, J.; Holland, L.; Zeng, C.; Hamilton, J. S.; Rowden, A. A.

    2016-02-01

    In the New Zealand region vulnerable marine ecosystems (VMEs) are at risk from commercial fishing activity and future seabed mining. Understanding connectivity among VMEs is important for the design of effective spatial management strategies, i.e. a network of protected areas. To date however, genetic connectivity in the New Zealand region has rarely been documented. As part of a project developing habitat suitability models and spatial management options for VMEs we used DNA sequence data and microsatellite genotyping to assess genetic connectivity for a range of VME indicator taxa, including the coral Desmophyllum dianthus, and the sponges Poecilastra laminaris and Penares palmatoclada. Overall, patterns of connectivity were inconsistent amonst taxa. Nonetheless, genetic data from each taxon were relevant to inform management at a variety of spatial scales. D. dianthus populations in the Kermadec volcanic arc and the Louisville Seamount Chain were indistinguishable, highlighting the importance of considering source-sink dynamics between populations beyond the EEZ in conservation planning. Poecilastra laminaris populations showed significant divergence across the Chatham Rise, in contrast to P. palmatoclada, which had a uniform haplotypic distribution. However, both sponge species exhibited the highest genetic diversity on the Chatham Rise, suggesting that this area is a genetic hotspot. The spatial heterogeneity of genetic patterns of structure suggest that inclusion of several taxa is necessary to facilitate understanding of regional connectivity patterns, variation in which may be attributed to alternate life history strategies, local hydrodynamic regimes, or in some cases, suboptimal sample sizes. Our findings provide important information for use by environmental managers, including summary maps of genetic diversity and barriers to gene flow, which will be used in spatial management decision-support tools.

  14. Realized climatic niche of North American plant taxa lagged behind climate during the end of the Pleistocene.

    PubMed

    Ordonez, Alejandro

    2013-07-01

    Predicting species responses to climate change has become a dynamic field in global change research. A crucial question in this debate is whether-or-not species have been and will be able to respond quickly enough to keep up with changing climatic conditions. Focusing on fossil pollen records and paleoclimatic simulations, this work assesses the change in realized climatic niches (climatic temporal trajectories) of 20 plant taxa over the last 16000 yr, and whether this tracking has been the same for different climatic niche dimensions. Climatic factors showed a consistent trend toward warmer temperatures and higher precipitation. Although the response types varied across taxa, species' realized climatic niches lagged in response to changes in climatic conditions. Temperature niches responded to late Pleistocene (16000-11000 yr ago) climate change, but did so at slower rates than changes in climatic conditions during the same period. In contrast, precipitation niches were relatively stable from 16000 to 11000 yr ago, but still lagged behind changes in climatic conditions. Changes in temperature and precipitation niches eventually stabilized during the Holocene (11000-1000 yr ago). These results underscore how the climatic niche realized at any one moment represents a subset of the climate conditions in which a taxon can persist, particularly during times of fast climatic change. Variability in the rates of temporal trajectories across evaluated climatic variables showed taxa specific responses to changes in climatic conditions over time and emphasizes the need to incorporate variation, intensity, and duration of lag effects in assessments of the possible effects of climatic change.

  15. Belowground carabid beetle diversity in the western Palaearctic - effects of history and climate on range-restricted taxa (Coleoptera, Carabidae).

    PubMed

    Schuldt, Andreas; Assmann, Thorsten

    2011-01-01

    Broad-scale patterns of subterranean diversity are a fascinating but neglected part of biodiversity research. Carabid beetles adapted to belowground habitats form a particularly species-rich part of the subterranean fauna. We studied large-scale diversity patterns of these belowground carabids across the western Palaearctic and evaluated potential impacts of historical and contemporary environmental conditions on the distribution of these taxa, using available species richness and environmental data at country level. Regression modelling and variation partitioning showed a strong relationship between species richness and range in elevation. Potential effects of climatic variables, mainly those related to ambient energy input, were much weaker. We discuss the implications of this combination of effects, which suggests, concordant with the absence of subterranean carabids in northern and highest richness in southern Europe, a strong prevailing influence of historical processes on current richness distributions of these taxa. Previous studies did not provide clear indications for such an influence. In contrast to more mobile and widespread carabid beetles, dispersal limitation due to high adaptation of belowground carabids to subterranean habitats has probably hindered their re-colonization of former permafrost and glaciated regions. Hotspots of highest belowground diversity are located in regions with an assumed long-term stability of environmental conditions, correlating with patterns of other dispersal-limited taxa such as many endemic plants. Our study provides important new information in the discussion of potential determinants of the distinct geographic patterns of belowground diversity. Moreover, it contributes to a better understanding of range size related differences previously found in the distribution of diversity and environmental dependencies of widespread and range-restricted species within the highly diverse carabid beetles.

  16. The movement of pre-adapted cool taxa in north-central Amazonia during the last glacial

    NASA Astrophysics Data System (ADS)

    D'Apolito, Carlos; Absy, Maria Lúcia; Latrubesse, Edgardo M.

    2017-08-01

    The effects of climate change on the lowland vegetation of Amazonia during the last glacial cycle are partially known for the middle and late Pleniglacial intervals (late MIS 3, 59-24 ka and MIS 2, 24-11 ka), but are still unclear for older stages of the last glacial and during the last interglacial. It is known that a more seasonal dry-wet climate caused marginal forest retraction and together with cooling rearranged forest composition to some extent. This is observed in pollen records across Amazonia depicting presence of taxa at glacial times in localities where they do not live presently. The understanding of taxa migration is hindered by the lack of continuous interglacial-glacial lowland records. We present new data from a known locality in NW Amazonia (Six Lakes Hill), showing a vegetation record that probably started during MIS 5 (130-71 ka) and lasted until the onset of the Holocene. The vegetation record unravels a novel pattern in tree taxa migration: (1) from the beginning of this cycle Podocarpus and Myrsine are recorded and (2) only later do Hedyosmum and Alnus appear. The latter group is largely restricted to montane biomes or more distant locations outside Amazonia, whereas the first is found in lowlands close to the study site on sandy soils. These findings imply that Podocarpus and Myrsine responded to environmental changes equally and this reflects their concomitant niche use in NW Amazonia. Temperature drop is not discarded as a trigger of internal forest composition change, but its effects are clearer later in the Pleniglacial rather than the Early Glacial. Therefore early climatic/environmental changes had a first order effect on vegetation that invoke alternative explanations. We claim last glacial climate-induced modifications on forest composition favoured the expansion of geomorphologic-soil related processes that initiated forest rearrangement.

  17. The International Code of Virus Classification and Nomenclature (ICVCN): proposal for text changes for improved differentiation of viral taxa and viruses.

    PubMed

    Kuhn, Jens H; Radoshitzky, Sheli R; Bavari, Sina; Jahrling, Peter B

    2013-07-01

    The International Committee on Taxonomy of Viruses (ICTV) is responsible for the classification of viruses into taxa. Importantly, the ICTV is currently not responsible for the nomenclature of viruses or their subclassification into strains, lineages, or genotypes. ICTV rules for classification of viruses and nomenclature of taxa are laid out in a code, the International Code of Virus Classification and Nomenclature (ICVCN). The most recent version of the Code makes it difficult for the unfamiliar reader to distinguish between viruses and taxa, thereby often giving the impression that certain Rules apply to viruses. Here, Code text changes are proposed to address this problem.

  18. Dominant plant taxa predict plant productivity responses to CO2 enrichment across precipitation and soil gradients

    SciTech Connect

    Fay, Philip A.; Newingham, Beth A.; Polley, H. Wayne; Morgan, Jack A.; LeCain, Daniel R.; Nowak, Robert S.; Smith, Stanley D.

    2015-03-30

    The Earth’s atmosphere will continue to be enriched with carbon dioxide (CO2) over the coming century. Carbon dioxide enrichment often reduces leaf transpiration, which in water-limited ecosystems may increase soil water content, change species abundances and increase the productivity of plant communities. The effect of increased soil water on community productivity and community change may be greater in ecosystems with lower precipitation, or on coarser-textured soils, but responses are likely absent in deserts. We tested correlations among yearly increases in soil water content, community change and community plant productivity responses to CO2 enrichment in experiments in a mesic grassland with fine- to coarse-textured soils, a semi-arid grassland and a xeric shrubland. We found no correlation between CO2-caused changes in soil water content and changes in biomass of dominant plant taxa or total community aboveground biomass in either grassland type or on any soil in the mesic grassland (P > 0.60). Instead, increases in dominant taxa biomass explained up to 85% of the increases in total community biomass under CO2 enrichment. The effect of community change on community productivity was stronger in the semi-arid grassland than in the mesic grassland,where community biomass change on one soil was not correlated with the change in either the soil water content or the dominant taxa. No sustained increases in soil water content or community productivity and no change in dominant plant taxa occurred in the xeric shrubland. Thus, community change was a crucial driver of community productivity responses to CO2 enrichment in the grasslands, but effects of soil water change on productivity were not evident in yearly responses to CO2 enrichment. In conclusion, future research is necessary to isolate and clarify the mechanisms controlling the temporal and spatial variations in the linkages among soil water

  19. Controlling Harmful Cyanobacteria: Taxa-Specific Responses of Cyanobacteria to Grazing by Large-Bodied Daphnia in a Biomanipulation Scenario

    PubMed Central

    Urrutia-Cordero, Pablo; Ekvall, Mattias K.; Hansson, Lars-Anders

    2016-01-01

    Lake restoration practices based on reducing fish predation and promoting the dominance of large-bodied Daphnia grazers (i.e., biomanipulation) have been the focus of much debate due to inconsistent success in suppressing harmful cyanobacterial blooms. While most studies have explored effects of large-bodied Daphnia on cyanobacterial growth at the community level and/or on few dominant species, predictions of such restoration practices demand further understanding on taxa-specific responses in diverse cyanobacterial communities. In order to address these questions, we conducted three grazing experiments during summer in a eutrophic lake where the natural phytoplankton community was exposed to an increasing gradient in biomass of the large-bodied Daphnia magna. This allowed evaluating taxa-specific responses of cyanobacteria to Daphnia grazing throughout the growing season in a desired biomanipulation scenario with limited fish predation. Total cyanobacterial and phytoplankton biomasses responded negatively to Daphnia grazing both in early and late summer, regardless of different cyanobacterial densities. Large-bodied Daphnia were capable of suppressing the abundance of Aphanizomenon, Dolichospermum, Microcystis and Planktothrix bloom-forming cyanobacteria. However, the growth of the filamentous Dolichospermum crassum was positively affected by grazing during a period when this cyanobacterium dominated the community. The eutrophic lake was subjected to biomanipulation since 2005 and nineteen years of lake monitoring data (1996–2014) revealed that reducing fish predation increased the mean abundance (50%) and body-size (20%) of Daphnia, as well as suppressed the total amount of nutrients and the growth of the dominant cyanobacterial taxa, Microcystis and Planktothrix. Altogether our results suggest that lake restoration practices solely based on grazer control by large-bodied Daphnia can be effective, but may not be sufficient to control the overgrowth of all

  20. New taxa and revisionary systematics of alcyonacean octocorals from the Pacific coast of North America (Cnidaria, Anthozoa)

    PubMed Central

    Williams, Gary C.

    2013-01-01

    Abstract A taxonomic assessment of four species of octocorals from the northeastern Pacific Ocean (British Columbia to California) is provided. Included here are a new species of clavulariid stolonifieran Cryptophyton, a new species of the nephtheid soft coral Gersemia, an undetermined species of soft coral in the genus Alcyonium that has been referred in the literature by several other names, and a new genus is named for a plexaurid sea fan originally described in the Indo-Pacific genus Euplexaura. Discussions are included that compare the species to related taxa, or provide revisionary assessments. PMID:23794840

  1. New taxa and revisionary systematics of alcyonacean octocorals from the Pacific coast of North America (Cnidaria, Anthozoa).

    PubMed

    Williams, Gary C

    2013-01-01

    A taxonomic assessment of four species of octocorals from the northeastern Pacific Ocean (British Columbia to California) is provided. Included here are a new species of clavulariid stolonifieran Cryptophyton, a new species of the nephtheid soft coral Gersemia, an undetermined species of soft coral in the genus Alcyonium that has been referred in the literature by several other names, and a new genus is named for a plexaurid sea fan originally described in the Indo-Pacific genus Euplexaura. Discussions are included that compare the species to related taxa, or provide revisionary assessments.

  2. New Guinean Issidae: description of new taxa in a poorly known island fauna (Hemiptera, Fulgoroidea).

    PubMed

    Gnezdilov, V M; Le Cesne, M; Soulier-Perkins, A; Bourgoin, T

    2015-01-05

    In the framework of the recent expedition results of "Our Planet Reviewed Papua-New-Guinea 2012-2013" we provide here the first Issidae (Hemiptera, Fulgoroidea) fauna review of New Guinea with the description of three new taxa: one new genus Papunega Gnezdilov et Bourgoin gen. nov. with two new species: Papunega magnifacies Gnezdilov et Le Cesne, sp. nov. (type species), Papunega armocula Gnezdilov et Soulier-Perkins, sp. nov. Tetrica fasciatifrons Melichar, 1906 is transferred to the genus Papugena gen. nov. to become Papugena fasciatifrons (Melichar, 1906) comb. nov. New Guinean Issidae fauna now includes 7 genera and 16 species. 

  3. Controlling Harmful Cyanobacteria: Taxa-Specific Responses of Cyanobacteria to Grazing by Large-Bodied Daphnia in a Biomanipulation Scenario.

    PubMed

    Urrutia-Cordero, Pablo; Ekvall, Mattias K; Hansson, Lars-Anders

    2016-01-01

    Lake restoration practices based on reducing fish predation and promoting the dominance of large-bodied Daphnia grazers (i.e., biomanipulation) have been the focus of much debate due to inconsistent success in suppressing harmful cyanobacterial blooms. While most studies have explored effects of large-bodied Daphnia on cyanobacterial growth at the community level and/or on few dominant species, predictions of such restoration practices demand further understanding on taxa-specific responses in diverse cyanobacterial communities. In order to address these questions, we conducted three grazing experiments during summer in a eutrophic lake where the natural phytoplankton community was exposed to an increasing gradient in biomass of the large-bodied Daphnia magna. This allowed evaluating taxa-specific responses of cyanobacteria to Daphnia grazing throughout the growing season in a desired biomanipulation scenario with limited fish predation. Total cyanobacterial and phytoplankton biomasses responded negatively to Daphnia grazing both in early and late summer, regardless of different cyanobacterial densities. Large-bodied Daphnia were capable of suppressing the abundance of Aphanizomenon, Dolichospermum, Microcystis and Planktothrix bloom-forming cyanobacteria. However, the growth of the filamentous Dolichospermum crassum was positively affected by grazing during a period when this cyanobacterium dominated the community. The eutrophic lake was subjected to biomanipulation since 2005 and nineteen years of lake monitoring data (1996-2014) revealed that reducing fish predation increased the mean abundance (50%) and body-size (20%) of Daphnia, as well as suppressed the total amount of nutrients and the growth of the dominant cyanobacterial taxa, Microcystis and Planktothrix. Altogether our results suggest that lake restoration practices solely based on grazer control by large-bodied Daphnia can be effective, but may not be sufficient to control the overgrowth of all

  4. A strategy for designing multi-taxa specific reference gene systems. example of application--ppi phosphofructokinase (ppi-PPF) used for the detection and quantification of three taxa: maize (Zea mays), cotton (Gossypium hirsutum) and rice (Oryza sativa).

    PubMed

    Chaouachi, Maher; Giancola, Sandra; Romaniuk, Marcel; Laval, Valérie; Bertheau, Yves; Brunel, Dominique

    2007-10-03

    In the first part of the paper, we report the description of a new strategy for the development of a plant reference gene system that can be used for genetically modified organism (GMO) analysis. On the basis of in silico research for candidate genes, the design of degenerate primers allowed the obtention of genomic sequences of the selected gene ppi-phosphofructokinase ( ppi-PPF) for nine taxa in which GMOs have been developed. The comparison and the analysis of inter- and intraspecies sequence variability were performed using a large number of species and cultivars. As an example of application following the detection of single nucleotide polymorphism, we designed specific conventional and real-time polymerase chain reaction tests for the detection and quantification of three taxa, namely, maize, cotton, and rice. This system was highly specific and sensitive. The gene copy number conservation among different cultivars was analyzed and confirmed with a sequencing step. This reference gene system is adequate for use in routine assays for the quantification of GMOs. We then explain briefly the constraints faced and propose recommendations when designing a reference gene system depending on the species to be targeted.

  5. DAS: A Data Management System for Instrument Tests and Operations

    NASA Astrophysics Data System (ADS)

    Frailis, M.; Sartor, S.; Zacchei, A.; Lodi, M.; Cirami, R.; Pasian, F.; Trifoglio, M.; Bulgarelli, A.; Gianotti, F.; Franceschi, E.; Nicastro, L.; Conforti, V.; Zoli, A.; Smart, R.; Morbidelli, R.; Dadina, M.

    2014-05-01

    The Data Access System (DAS) is a and data management software system, providing a reusable solution for the storage of data acquired both from telescopes and auxiliary data sources during the instrument development phases and operations. It is part of the Customizable Instrument WorkStation system (CIWS-FW), a framework for the storage, processing and quick-look at the data acquired from scientific instruments. The DAS provides a data access layer mainly targeted to software applications: quick-look displays, pre-processing pipelines and scientific workflows. It is logically organized in three main components: an intuitive and compact Data Definition Language (DAS DDL) in XML format, aimed for user-defined data types; an Application Programming Interface (DAS API), automatically adding classes and methods supporting the DDL data types, and providing an object-oriented query language; a data management component, which maps the metadata of the DDL data types in a relational Data Base Management System (DBMS), and stores the data in a shared (network) file system. With the DAS DDL, developers define the data model for a particular project, specifying for each data type the metadata attributes, the data format and layout (if applicable), and named references to related or aggregated data types. Together with the DDL user-defined data types, the DAS API acts as the only interface to store, query and retrieve the metadata and data in the DAS system, providing both an abstract interface and a data model specific one in C, C++ and Python. The mapping of metadata in the back-end database is automatic and supports several relational DBMSs, including MySQL, Oracle and PostgreSQL.

  6. Unique method of tooth replacement in durophagous placodont marine reptiles, with new data on the dentition of Chinese taxa.

    PubMed

    Neenan, James M; Li, Chun; Rieppel, Olivier; Bernardini, Federico; Tuniz, Claudio; Muscio, Giuseppe; Scheyer, Torsten M

    2014-05-01

    The placodonts of the Triassic period (~252-201 mya) represent one of the earliest and most extreme specialisations to a durophagous diet of any known reptile group. Exceptionally enlarged crushing tooth plates on the maxilla, dentary and palatine cooperated to form functional crushing areas in the buccal cavity. However, the extreme size of these teeth, combined with the unusual way they occluded, constrained how replacement occurred. Using an extensive micro-computed tomographic dataset of 11 specimens that span all geographic regions and placodont morphotypes, tooth replacement patterns were investigated. In addition, the previously undescribed dental morphologies and formulae of Chinese taxa are described for the first time and incorporated into the analysis. Placodonts have a unique tooth replacement pattern and results follow a phylogenetic trend. The plesiomorphic Placodus species show many replacement teeth at various stages of growth, with little or no discernible pattern. On the other hand, the more derived cyamodontoids tend to have fewer replacement teeth growing at any one time, replacing teeth unilaterally and/or in functional units, thus maintaining at least one functional crushing area at all times. The highly derived placochelyids have fewer teeth and, as a result, only have one or two replacement teeth in the upper jaw. This supports previous suggestions that these taxa had an alternative diet to other placodonts. Importantly, all specimens show at least one replacement tooth growing at the most posterior palatine tooth plates, indicating increased wear at this point and thus the most efficient functional crushing area.

  7. Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots.

    PubMed

    Pei, Nancai; Erickson, David L; Chen, Bufeng; Ge, Xuejun; Mi, Xiangcheng; Swenson, Nathan G; Zhang, Jin-Long; Jones, Frank A; Huang, Chun-Lin; Ye, Wanhui; Hao, Zhanqing; Hsieh, Chang-Fu; Lum, Shawn; Bourg, Norman A; Parker, John D; Zimmerman, Jess K; McShea, William J; Lopez, Ida C; Sun, I-Fang; Davies, Stuart J; Ma, Keping; Kress, W John

    2015-10-12

    To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities.

  8. Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues

    PubMed Central

    2011-01-01

    Background BAHD acyltransferases are involved in the synthesis and elaboration of a wide variety of secondary metabolites. Previous research has shown that characterized proteins from this family fall broadly into five major clades and contain two conserved protein motifs. Here, we aimed to expand the understanding of BAHD acyltransferase diversity in plants through genome-wide analysis across five angiosperm taxa. We focus particularly on Populus, a woody perennial known to produce an abundance of secondary metabolites. Results Phylogenetic analysis of putative BAHD acyltransferase sequences from Arabidopsis, Medicago, Oryza, Populus, and Vitis, along with previously characterized proteins, supported a refined grouping of eight major clades for this family. Taxon-specific clustering of many BAHD family members appears pervasive in angiosperms. We identified two new multi-clade motifs and numerous clade-specific motifs, several of which have been implicated in BAHD function by previous structural and mutagenesis research. Gene duplication and expression data for Populus-dominated subclades revealed that several paralogous BAHD members in this genus might have already undergone functional divergence. Conclusions Differential, taxon-specific BAHD family expansion via gene duplication could be an evolutionary process contributing to metabolic diversity across plant taxa. Gene expression divergence among some Populus paralogues highlights possible distinctions between their biochemical and physiological functions. The newly discovered motifs, especially the clade-specific motifs, should facilitate future functional study of substrate and donor specificity among BAHD enzymes. PMID:21569431

  9. Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments.

    PubMed

    Yang, Sizhong; Wen, Xi; Shi, Yulan; Liebner, Susanne; Jin, Huijun; Perfumo, Amedea

    2016-11-25

    Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies.

  10. Size, age and composition: characteristics of plant taxa as diversity predictors of gall-midges (Diptera: Cecidomyiidae).

    PubMed

    Araújo, Walter S

    2011-12-01

    Many hypotheses have been proposed to explain the diversity of gall-midge insects (Diptera: Cecidomyiidae), some of them taking into account plant diversity. This study aims to test the importance of size, age and composition of host plant taxa in the diversity of Cecidomyiidae. For this we used inventories data on the diversity of galling and host plants in Brazil. We found that Asterales, Myrtales and Malpighiales, were the most important orders, with 34, 33 and 25, gall morphotypes, respectively. The most representative host families were Asteraceae (34 morphotypes), Myrtaceae (23) and Fabaceae (22). In general, the order size and the plant family were good predictors of the galling diversity, but not the taxon age. The most diverse host genera for gall-midges were Mikania, Eugenia and Styrax, with 15, 13 and nine galler species, respectively. The size of plant genera showed no significant relationship with the richness of Cecidomyiidae, contrary to the prediction of the plant taxon size hypothesis. The plant genera with the greatest diversity of galling insects are not necessarily those with the greatest number of species. These results indicate that some plant taxa have a high intrinsic richness of galling insects, suggesting that the plant species composition may be equally or more important for the diversity of gall-midges than the size or age of the host taxon.

  11. Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments

    PubMed Central

    Yang, Sizhong; Wen, Xi; Shi, Yulan; Liebner, Susanne; Jin, Huijun; Perfumo, Amedea

    2016-01-01

    Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies. PMID:27886221

  12. From Problem Taxa to Problem Solver: A New Miocene Family, Tranatocetidae, Brings Perspective on Baleen Whale Evolution

    PubMed Central

    Gol’din, Pavel; Steeman, Mette Elstrup

    2015-01-01

    Miocene baleen whales were highly diverse and included tens of genera. However, their taxonomy and phylogeny, as well as relationships with living whales, are still a subject of controversy. Here, “Mesocetus” argillarius, a poorly known specimen from Denmark, is redescribed with a focus on the cranial anatomy. It was found to represent not only a new genus, Tranatocetus gen. nov., but also a new family; Tranatocetidae. The whales of this family have the rostral bones either overriding or dividing the frontals; the rostral bones are contacting the parietals and nasals dividing the maxillae on the vertex; the occipital shield is dorsoventrally bent. The tympanic bulla is particularly characteristic of this family featuring a short, narrow anterior portion with a rounded or squared anterior end and a wider and higher posterior portion that is swollen in the posteroventral area. A phylogenetic analysis including 51 taxa supports a monophyletic group comprising most Neogene and modern whales, with Tranatocetidae being possibly closer related to Balaenopteridae (rorquals) than to Cetotheriidae. Tranatocetidae exhibit a charahteristic bulla shape. In fact, all Neogene and modern mysticete families examined have a unique shape of the tympanic bulla that is diagnostic at family-level. Inclusion of problematic taxa like Tranatocetus argillarius in phylogenies brings new understanding of the distribution and diagnostic value of character traits. This underlines the need for re-examination of earlier described specimens in the light of the wealth of new information published in later years. PMID:26331471

  13. Distance-Decay and Taxa-Area Relationships for Bacteria, Archaea and Methanogenic Archaea in a Tropical Lake Sediment

    PubMed Central

    Barreto, Davi Pedroni; Conrad, Ralf; Klose, Melanie; Claus, Peter; Enrich-Prast, Alex

    2014-01-01

    The study of of the distribution of microorganisms through space (and time) allows evaluation of biogeographic patterns, like the species-area index (z). Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units) we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship. PMID:25330320

  14. Adaptations and Predispositions of Different Middle European Arthropod Taxa (Collembola, Araneae, Chilopoda, Diplopoda) to Flooding and Drought Conditions

    PubMed Central

    Marx, Michael Thomas; Guhmann, Patrick; Decker, Peter

    2012-01-01

    Simple Summary This review summarizes adaptations and predispositions of different arthropod taxa (springtails, web spiders, millipedes and centipedes) to flood and drought conditions. The main focus sis directed to arthropod species, which are living in Middle European floodplain forests and wetlands, because of the fast change of flood and drought conditions in these habitats. Furthermore the effects of the predicted regional climate change like increasing aperiodic summer flooding and decreasing winter and spring floods are also discussed. Abstract Floodplain forests and wetlands are amongst the most diverse and species rich habitats on earth. Arthropods are a key group for the high diversity pattern of these landscapes, due to the fact that the change between flooding and drought causes in different life cycles and in a variety of adaptations in the different taxa. The floodplain forests and wetlands of Central Amazonia are well investigated and over the last 50 years many adaptations of several hexapod, myriapod and arachnid orders were described. In contrast to Amazonia the Middle European floodplains were less investigated concerning the adaptations of arthropods to flood and drought conditions. This review summarizes the adaptations and predispositions of springtails, web spiders, millipedes and centipedes to the changeable flood and drought conditions of Middle European floodplain forests and wetlands. Furthermore the impact of regional climate change predictions like increasing aperiodic summer floods and the decrease of typical winter and spring floods are discussed in this article. PMID:26487164

  15. From Problem Taxa to Problem Solver: A New Miocene Family, Tranatocetidae, Brings Perspective on Baleen Whale Evolution.

    PubMed

    Gol'din, Pavel; Steeman, Mette Elstrup

    2015-01-01

    Miocene baleen whales were highly diverse and included tens of genera. However, their taxonomy and phylogeny, as well as relationships with living whales, are still a subject of controversy. Here, "Mesocetus" argillarius, a poorly known specimen from Denmark, is redescribed with a focus on the cranial anatomy. It was found to represent not only a new genus, Tranatocetus gen. nov., but also a new family; Tranatocetidae. The whales of this family have the rostral bones either overriding or dividing the frontals; the rostral bones are contacting the parietals and nasals dividing the maxillae on the vertex; the occipital shield is dorsoventrally bent. The tympanic bulla is particularly characteristic of this family featuring a short, narrow anterior portion with a rounded or squared anterior end and a wider and higher posterior portion that is swollen in the posteroventral area. A phylogenetic analysis including 51 taxa supports a monophyletic group comprising most Neogene and modern whales, with Tranatocetidae being possibly closer related to Balaenopteridae (rorquals) than to Cetotheriidae. Tranatocetidae exhibit a charahteristic bulla shape. In fact, all Neogene and modern mysticete families examined have a unique shape of the tympanic bulla that is diagnostic at family-level. Inclusion of problematic taxa like Tranatocetus argillarius in phylogenies brings new understanding of the distribution and diagnostic value of character traits. This underlines the need for re-examination of earlier described specimens in the light of the wealth of new information published in later years.

  16. New taxa of angiosperm pollen, miospores and associated palynomorphs from the early Late Cretaceous of Egypt (Maghrabi Formation, Kharga Oasis).

    PubMed

    Schrank; Mahmoud

    2000-10-01

    A palynological investigation of samples from various boreholes in the Maghrabi Formation (Kharga Oasis, southern Egypt) resulted in the recovery of pollen and spore assemblages associated with rare marine palynofossils (dinoflagellates, foraminiferal linings) and freshwater algae (e.g. Botryococcus, Ovoidites parvus, Pediastrum, Scenedesmus). The general composition of the assemblages is largely consistent with the estuarine and tidal flat conditions characteristic of the Maghrabi Formation.The formal descriptions of the following new taxa are given: Cicatricosisporites kedvesii Schrank, sp. nov., Equisetosporites lawalii Schrank, sp. nov., Dettmannaepollenites clavatus Schrank, sp. nov., and Integritetradites porosus Schrank and Mahmoud, gen. nov. and sp. nov. Combined scanning electron microscopic and light microscopic techniques have been applied to hand-picked grains to illustrate the new taxa. The palynological ages assigned to the Maghrabi samples are mainly based on angiosperm pollen and range from undifferentiated Cenomanian for an Integritetradites porosus assemblage without triporates to Late Cenomanian-Early Turonian for another assemblage which has I. porosus associated with rare triporate pollen grains (Proteacidites/'Triorites' spp.).

  17. Invasion dynamics of two alien Carpobrotus (Aizoaceae) taxa on a Mediterranean island: I. Genetic diversity and introgression.

    PubMed

    Suehs, C M; Affre, L; Médail, F

    2004-01-01

    This study, based on morphological and isozyme analysis, clearly discriminates two invasive Carpobrotus taxa, C. edulis and C. acinaciformis, in the Hyères archipelago off the southeastern coast of France. However, three different allelic combinations demonstrate the presence of intermediate individuals resulting from an introgression of part of the C. edulis genome into that of C. acinaciformis. Both taxa have higher than average genetic (C. edulis: P(0.95)=62.5%, A=2.25+/-0.70, H(o)=0.329+/-0.324; C. acinaciformis: P(0.95)=75%, A=2.38+/-0.42, H(o)=0.645+/-0.109) and clonal diversities (C. edulis: IP=0.37; C. acinaciformis: IP=0.48). Furthermore, C. acinaciformis has an excess of heterozygotes (F=-0.585+/-0.217), probably due to introgression. The relationship between the probability of clonal identity for two individuals and distance indicates that C. acinaciformis relies more on clonal reproduction than on sexual recruitment (seed recruitment/vegetative propagation=u/v=0.027), in contrast to C. edulis, whose probability of clonal identity did not vary with distance. The overwhelming clonal growth and high genetic diversities of C. acinaciformis and the previously recorded invasion potential for C. edulis raises concern for intensified invasion via hybridisation.

  18. 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.

  19. 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

  20. Global patterns of marine mammal, seabird, and sea turtle bycatch reveal taxa-specific and cumulative megafauna hotspots.

    PubMed

    Lewison, Rebecca L; Crowder, Larry B; Wallace, Bryan P; Moore, Jeffrey E; Cox, Tara; Zydelis, Ramunas; McDonald, Sara; DiMatteo, Andrew; Dunn, Daniel C; Kot, Connie Y; Bjorkland, Rhema; Kelez, Shaleyla; Soykan, Candan; Stewart, Kelly R; Sims, Michelle; Boustany, Andre; Read, Andrew J; Halpin, Patrick; Nichols, W J; Safina, Carl

    2014-04-08

    Recent research on ocean health has found large predator abundance to be a key element of ocean condition. Fisheries can impact large predator abundance directly through targeted capture and indirectly through incidental capture of nontarget species or bycatch. However, measures of the global nature of bycatch are lacking for air-breathing megafauna. We fill this knowledge gap and present a synoptic global assessment of the distribution and intensity of bycatch of seabirds, marine mammals, and sea turtles based on empirical data from the three most commonly used types of fishing gears worldwide. We identify taxa-specific hotspots of bycatch intensity and find evidence of cumulative impacts across fishing fleets and gears. This global map of bycatch illustrates where data are particularly scarce--in coastal and small-scale fisheries and ocean regions that support developed industrial fisheries and millions of small-scale fishers--and identifies fishing areas where, given the evidence of cumulative hotspots across gear and taxa, traditional species or gear-specific bycatch management and mitigation efforts may be necessary but not sufficient. Given the global distribution of bycatch and the mitigation success achieved by some fleets, the reduction of air-breathing megafauna bycatch is both an urgent and achievable conservation priority.

  1. A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa

    PubMed Central

    Raupach, Michael J.; Hannig, Karsten; Morinière, Jérome; Hendrich, Lars

    2016-01-01

    Abstract As molecular identification method, DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has been proven to be a useful tool for species determination in many insect taxa including ground beetles. In this study we tested the effectiveness of DNA barcodes to discriminate species of the ground beetle genus Bembidion and some closely related taxa of Germany. DNA barcodes were obtained from 819 individuals and 78 species, including sequences from previous studies as well as more than 300 new generated DNA barcodes. We found a 1:1 correspondence between BIN and traditionally recognized species for 69 species (89%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for three species pairs, including two species pairs with haplotype sharing (Bembidion atrocaeruleum/Bembidion varicolor and Bembidion guttula/Bembidion mannerheimii). In contrast to this, deep intraspecific sequence divergences with distinct lineages were revealed for two species (Bembidion geniculatum/Ocys harpaloides). Our study emphasizes the use of DNA barcodes for the identification of the analyzed ground beetles species and represents an important step in building-up a comprehensive barcode library for the Carabidae in Germany and Central Europe as well. PMID:27408547

  2. Development of droplet digital PCR assays for methanogenic taxa and examination of methanogen communities in full-scale anaerobic digesters.

    PubMed

    Kim, Tae Gwan; Jeong, So-Yeon; Cho, Kyung-Suk

    2015-01-01

    Droplet digital PCR (ddPCR) is a new DNA quantification platform without an external DNA calibrator. This study examined methanogen communities in four full-scale anaerobic digesters treating municipal sewage sludge, using ddPCR with taxon-specific primer/TaqMan probe sets (5 orders, 11 families, and 13 genera), many of which were developed in this study. Total methanogen abundance was positively correlated with hydraulic retention time (HRT) and temperature (p < 0.05), though the effect of HRT was stronger (r = 0.864 vs. 0.682, respectively). Moreover, total abundance was strongly correlated with biogas production rate (r = 0.896). HRT was positively correlated with seven methanogenic taxa, while temperature was positively or negatively correlated with 13 taxa (p < 0.05). For instance, the predominant genera Methanosaeta and Methanosarcina were negatively and positively associated, respectively, with temperature only (p < 0.05). Redundancy analysis and principal component analysis using the absolute-abundance dataset indicated that only temperature explained the variability in the methanogen communities at all classification levels. Therefore, HRT was the most important operational factor to influence net methanogen abundance and activity, while temperature governed the composition of the methanogen community. ddPCR enabled absolute quantification of methanogens without the external DNA standards and linked methanogen communities and operational factors, suggesting that it is a promising tool for analyzing the microbial ecology of anaerobic digestion.

  3. Quantitation of Crocins and picrocrocin in saffron by HPLC: application to quality control and phytochemical differentiation from other crocus taxa.

    PubMed

    Koulakiotis, Nikolaos Stavros; Gikas, Evangelos; Iatrou, Gregoris; Lamari, Fotini N; Tsarbopoulos, Anthony

    2015-05-01

    A chromatographic method was developed and fully validated for the determination of the major saffron constituents, i.e., picrocrocin and five major crocins. Dried samples (styles of Crocus sativus and other Crocus taxa) were extracted with MeOH : water (1 : 1, v/v), and chromatographic separation of the analytes was achieved by reversed-phase chromatography using a gradient elution. Full validation was performed using spiked samples with analytes, which were isolated, purified, and characterized by MS due to a lack of commercial standards. The method showed a good fit (r2 > 0.999) for all analytes with limit of quantitation values in the range of 1-15 µg/mL, and demonstrated adequate intra- and inter-precision (< 15 % RSD) and accuracy (< 7 % RE). The method was applied to the analysis of various commercial saffron samples and of indigenous Crocus taxa and allowed for the first time the absolute quantitation of several Crocus components.

  4. New mescaline concentrations from 14 taxa/cultivars of Echinopsis spp. (Cactaceae) ("San Pedro") and their relevance to shamanic practice.

    PubMed

    Ogunbodede, Olabode; McCombs, Douglas; Trout, Keeper; Daley, Paul; Terry, Martin

    2010-09-15

    The aim of the present study is to determine in a procedurally uniform manner the mescaline concentrations in stem tissue of 14 taxa/cultivars of the subgenus Trichocereus of the genus Echinopsis (Cactaceae) and to evaluate the relationship (if any) between mescaline concentration and actual shamanic use of these plants. Columnar cacti of the genus Echinopsis, some of which are used for diagnostic and therapeutic purposes by South American shamans in traditional medicine, were selected for analysis because they were vegetative clones of plants of documented geographic origin and/or because they were known to be used by practitioners of shamanism. Mescaline content of the cortical stem chlorenchyma of each cactus was determined by Soxhlet extraction with methanol, followed by acid-base extraction with water and dichloromethane, and high-pressure liquid chromatography (HPLC). By virtue of the consistent analytical procedures used, comparable alkaloid concentrations were obtained that facilitated the ranking of the various selected species and cultivars of Echinopsis, all of which exhibited positive mescaline contents. The range of mescaline concentrations across the 14 taxa/cultivars spanned two orders of magnitude, from 0.053% to 4.7% by dry weight. The mescaline concentrations reported here largely support the hypothesis that plants with the highest mescaline concentrations - particularly E. pachanoi from Peru - are most associated with documented shamanic use. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.

  5. Life history profiles for 27 strepsirrhine primate taxa generated using captive data from the Duke Lemur Center

    PubMed Central

    Zehr, Sarah M; Roach, Richard G; Haring, David; Taylor, Julie; Cameron, Freda H; Yoder, Anne D

    2014-01-01

    Since its establishment in 1966, the Duke Lemur Center (DLC) has accumulated detailed records for nearly 4,200 individuals from over 40 strepsirrhine primate taxa—the lemurs, lorises, and galagos. Here we present verified data for 3,627 individuals of 27 taxa in the form of a life history table containing summarized species values for variables relating to ancestry, reproduction, longevity, and body mass, as well as the two raw data files containing direct and calculated variables from which this summary table is built. Large sample sizes, longitudinal data that in many cases span an animal’s entire life, exact dates of events, and large numbers of individuals from closely related yet biologically diverse primate taxa make these datasets unique. This single source for verified raw data and systematically compiled species values, particularly in combination with the availability of associated biological samples and the current live colony for research, will support future studies from an enormous spectrum of disciplines. PMID:25977776

  6. Temperature dependence of evolutionary diversification: differences between two contrasting model taxa support the metabolic theory of ecology.

    PubMed

    Machac, A; Zrzavý, J; Smrckova, J; Storch, D

    2012-12-01

    Biodiversity patterns are largely determined by variation of diversification rates across clades and geographic regions. Although there are multiple reasons for this variation, it has been hypothesized that metabolic rate is the crucial driver of diversification of evolutionary lineages. According to the metabolic theory of ecology (MTE), metabolic rate - and consequently speciation - is driven mainly by body size and environmental temperature. As environmental temperature affects metabolic rate in ecto- and endotherms differently, its impact on diversification rate should also differ between the two types of organisms. Employing two independent approaches, we analysed correlates of speciation rates and, ultimately, net diversification rates for two contrasting taxa: plethodontid salamanders and carnivoran mammals. Whereas in the ectothermic plethodontids speciation rates positively correlated with environmental temperature, in the endothermic carnivorans a reverse, negative correlation was detected. These findings comply with predictions of the MTE and suggest that similar geographic patterns of biodiversity across taxa (e.g. ecto- and endotherms) might have been generated by different ecological and evolutionary processes.

  7. Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms

    PubMed Central

    Shiba, Takahiko; Watanabe, Takayasu; Kachi, Hirokazu; Koyanagi, Tatsuro; Maruyama, Noriko; Murase, Kazunori; Takeuchi, Yasuo; Maruyama, Fumito; Izumi, Yuichi; Nakagawa, Ichiro

    2016-01-01

    Polymicrobial diseases, which can be life threatening, are caused by the presence and interactions of multiple microbes. Peri-implantitis and periodontitis are representative polymicrobial diseases that show similar clinical symptoms. To establish a means of differentiating between them, we compared microbial species and functional genes in situ by performing metatranscriptomic analyses of peri-implantitis and periodontitis samples obtained from the same subjects (n = 12 each). Although the two diseases differed in terms of 16S rRNA-based taxonomic profiles, they showed similarities with respect to functional genes and taxonomic and virulence factor mRNA profiles. The latter—defined as microbial virulence types—differed from those of healthy periodontal sites. We also showed that networks based on co-occurrence relationships of taxonomic mRNA abundance (co-occurrence networks) were dissimilar between the two diseases. Remarkably, these networks consisted mainly of taxa with a high relative mRNA-to-rRNA ratio, with some showing significant co-occurrence defined as interacting core taxa, highlighting differences between the two groups. Thus, peri-implantitis and periodontitis have shared as well as distinct microbiological characteristics. Our findings provide insight into microbial interactions in polymicrobial diseases with unknown etiologies. PMID:27499042

  8. Gene fishing: the use of a simple protocol to isolate multiple homeodomain classes from diverse invertebrate taxa.

    PubMed

    Lee, Shannon E; Gates, Ruth D; Jacobs, David K

    2003-04-01

    Comparison of relevant gene sequence and functional data is central to understanding the evolution of metazoan development. The conservation of portions of regulatory genes, such as homeoboxes, allows for the design of PCR-based sequence isolation and amplification strategies. Here we describe a simple protocol that uses a degenerate primer pair to isolate a variety of homeobox-containing genes from diverse metazoan taxa. In a nonexhaustive survey, we have isolated 28 gene sequence fragments from 15 taxa, representing eight invertebrate phyla (Mollusca, Echiura, Annelida, Platyhelminth, Acoela, Ctenophora, Cnidaria, and Porifera). Based on BLAST and parsimony analyses, these gene fragments affiliate with several gene groups (PAIRED-like, HOX, and ParaHOX) and several single genes, including pancreas/duodenum homeoboxes (Pdx), empty spiracles (ems/Emx), gastrulation brain homeoboxes (Gbx), hematopoietically expressed homeoboxes (HEX), brain specific homeobox (bsh/BarH1/BarH2), NK-1 (NK-1/s59/slouch), and ladybird (Lbl/Lbe/Lbx). In several cases, these fragments represent the first reported orthologue for the phylum or superphyletic group (i.e., Lophotrochozoa).

  9. Distance-decay and taxa-area relationships for bacteria, archaea and methanogenic archaea in a tropical lake sediment.

    PubMed

    Barreto, Davi Pedroni; Conrad, Ralf; Klose, Melanie; Claus, Peter; Enrich-Prast, Alex

    2014-01-01

    The study of of the distribution of microorganisms through space (and time) allows evaluation of biogeographic patterns, like the species-area index (z). Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units) we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship.

  10. Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots

    PubMed Central

    Pei, Nancai; Erickson, David L.; Chen, Bufeng; Ge, Xuejun; Mi, Xiangcheng; Swenson, Nathan G.; Zhang, Jin-Long; Jones, Frank A.; Huang, Chun-Lin; Ye, Wanhui; Hao, Zhanqing; Hsieh, Chang-Fu; Lum, Shawn; Bourg, Norman A.; Parker, John D.; Zimmerman, Jess K.; McShea, William J.; Lopez, Ida C.; Sun, I-Fang; Davies, Stuart J.; Ma, Keping; Kress, W. John

    2015-01-01

    To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities. PMID:26456472

  11. Global patterns of marine mammal, seabird, and sea turtle bycatch reveal taxa-specific and cumulative megafauna hotspots

    PubMed Central

    Lewison, Rebecca L.; Crowder, Larry B.; Wallace, Bryan P.; Moore, Jeffrey E.; Cox, Tara; Zydelis, Ramunas; McDonald, Sara; DiMatteo, Andrew; Dunn, Daniel C.; Kot, Connie Y.; Bjorkland, Rhema; Kelez, Shaleyla; Soykan, Candan; Stewart, Kelly R.; Sims, Michelle; Boustany, Andre; Read, Andrew J.; Halpin, Patrick; Nichols, W. J.; Safina, Carl

    2014-01-01

    Recent research on ocean health has found large predator abundance to be a key element of ocean condition. Fisheries can impact large predator abundance directly through targeted capture and indirectly through incidental capture of nontarget species or bycatch. However, measures of the global nature of bycatch are lacking for air-breathing megafauna. We fill this knowledge gap and present a synoptic global assessment of the distribution and intensity of bycatch of seabirds, marine mammals, and sea turtles based on empirical data from the three most commonly used types of fishing gears worldwide. We identify taxa-specific hotspots of bycatch intensity and find evidence of cumulative impacts across fishing fleets and gears. This global map of bycatch illustrates where data are particularly scarce—in coastal and small-scale fisheries and ocean regions that support developed industrial fisheries and millions of small-scale fishers—and identifies fishing areas where, given the evidence of cumulative hotspots across gear and taxa, traditional species or gear-specific bycatch management and mitigation efforts may be necessary but not sufficient. Given the global distribution of bycatch and the mitigation success achieved by some fleets, the reduction of air-breathing megafauna bycatch is both an urgent and achievable conservation priority. PMID:24639512

  12. The concept of correlated progression as the basis of a model for the evolutionary origin of major new taxa

    PubMed Central

    Kemp, T.S

    2007-01-01

    Understanding the evolutionary processes responsible for the long treks through morphospace associated with the origin of new higher taxa is hampered by the lack of a realistic and usable model that accounts for long-term phenotypic evolvability. The systems-related concept of correlated progression, in which all the traits are functionally linked and so constrained to evolve by small increments at a time in parallel with each other, provides the basis for such a model. Implications for the process of evolution at high taxonomic level are that: the evolving traits must be considered together as a system, and the exact sequence of incremental changes in characters is indeterminable; there are no identifiable key innovations; selection acts on the phenotype as a whole rather than on individual traits; and the selection force is therefore multidimensional. Application of the model to the pattern of evolution of traits and trait states as revealed by the fossil record of the stem groups of such taxa as mammals, turtles and tetrapods generates realistic testable hypotheses about how such groups evolved. PMID:17472914

  13. Divergence of brain and retinal anatomy and histology in pelagic antarctic notothenioid fishes of the sister taxa Dissostichus and Pleuragramma.

    PubMed

    Eastman, Joseph T; Lannoo, Michael J

    2011-04-01

    The neutrally buoyant Antarctic fishes of the sister taxa Dissostichus (D. eleginoides and D. mawsoni) and Pleuragramma antarcticum diverged early in the notothenioid radiation and filled different niches in the pelagic realm of the developing Southern Ocean. To assess the influence of phylogenetic and ecological factors in shaping neural morphology in these taxa, we studied the anatomy and histology of the brains and retinae, and determined the proportional weights of brain regions. With the brain of the non-Antarctic sister taxon Eleginops maclovinus as plesiomorphic, statistically significant departures in the brains of the two Antarctic taxa include reduction of the corpus cerebelli and expansion of the mesencephalon and medulla. Compared to Eleginops, both species also have a relatively smaller telencephalon, although this is significant only in Dissostichus. There are a number of apomorphic features in the brain of Pleuragramma including reduced olfactory nerves and bulbs, an extremely small corpus cerebelli and an expanded mesencephalon. Although there is not a significant difference in the relative weights of the medulla in the two taxa, the prominence of the eminentia granularis and bulging cap-like appearance of the crista cerebellaris are distinctive in Pleuragramma. Brain histology of Dissostichus and Pleuragramma reflects typical perciform patterns and the two species of Dissostichus are histologically identical. Lateral compression in Pleuragramma and notable lobation in Dissostichus also contribute to differences between the taxa. Compression in Pleuragramma is attributable to convergence on an anchovy/herring body shape and to the relatively large brain in this small fish. The less prominent pattern of lobation of the telencephalon, inferior lobes and corpus cerebelli in Pleuragramma probably reflects underlying histology, specifically a reduction in cellularity of the neuropil in the nuclei and lobes. The retinal histology of Dissostichus and

  14. Metazoan meiofauna in deep-sea canyons and adjacent open slopes: A large-scale comparison with focus on the rare taxa

    NASA Astrophysics Data System (ADS)

    Bianchelli, S.; Gambi, C.; Zeppilli, D.; Danovaro, R.

    2010-03-01

    Metazoan meiofaunal abundance, total biomass, nematode size and the richness of taxa were investigated along bathymetric gradients (from the shelf break down to ca. 5000-m depth) in six submarine canyons and on five adjacent open slopes of three deep-sea regions. The investigated areas were distributed along >2500 km, on the Portuguese to the Catalan and South Adriatic margins. The Portuguese and Catalan margins displayed the highest abundances, biomass and richness of taxa, while the lowest values were observed in the Central Mediterranean Sea. The comparison between canyons and the nearby open slopes showed the lack of significant differences in terms of meiofaunal abundance and biomass at any sampling depth. In most canyons and on most slopes, meiofaunal variables did not display consistent bathymetric patterns. Conversely, we found that the different topographic features were apparently responsible for significant differences in the abundance and distribution of the rare meiofaunal taxa (i.e. taxa accounting for <1% of total meiofaunal abundance). Several taxa belonging to the temporary meiofauna, such as larvae/juveniles of Priapulida, Holothuroidea, Ascidiacea and Cnidaria, were encountered exclusively on open slopes, while others (including the Tanaidacea and Echinodea larvae) were found exclusively in canyons sediments. Results reported here indicate that, at large spatial scales, differences in deep-sea meiofaunal abundance and biomass are not only controlled by the available food sources, but also by the region or habitat specific topographic features, which apparently play a key role in the distribution of rare benthic taxa.

  15. Pedagogical basis of DAS formalism in engineering education

    NASA Astrophysics Data System (ADS)

    Hiltunen, J.; Heikkinen, E.-P.; Jaako, J.; Ahola, J.

    2011-03-01

    The paper presents a new approach for a bachelor-level curriculum structure in engineering. The approach is called DAS formalism according to its three phases: description, analysis and synthesis. Although developed specifically for process and environmental engineering, DAS formalism has a generic nature and it could also be used in other engineering fields. The motivation for this new curriculum structure originates from the urge to solve the problems that engineering education has faced during the past decades, e.g. student recruitment problems and dissatisfactory learning outcomes. The focus of this paper is on the structure of the curriculum but the content is also discussed when it has an effect on the structure and its implementation. The presented structure, i.e. DAS formalism, builds upon the ideas of some classical pedagogical theories, which have regularly been applied at course level but seldom used to solve curriculum-level issues.

  16. Atlas of relations between climatic parameters and distributions of important trees and shrubs in North America: Revisions for all taxa from the United States and Canada and new taxa from the western United States

    USGS Publications Warehouse

    Thompson, Robert S.; Anderson, Katherine H.; Pelltier, Richard T.; Strickland, Laura E.; Shafer, Sarah L.; Bartlein, Patrick J.; McFadden, Andrew K.

    2015-01-01

    This volume of the atlas provides numerous changes, updates, and enhancements from previous volumes. Its geographic coverage is now restricted to Canada and the continental United States, and the source and time period of the climatic data have changed. New variables were added, including monthly values for temperature and precipitation, and measures of interannual variability. The distribution maps for all previously published species were redigitized, some distribution maps were revised, and 148 new species were added from the arid and semiarid western United States. The graphical displays were expanded to illustrate the new climatic variables, and the data tables were modified to provide more detail on the population distributions of plant taxa relative to climatic variables.

  17. Vallabhaneni Sita Rama Das, 1933-2010: teacher and mentor.

    PubMed

    Elchuri, Sailaja V; Govindjee

    2016-05-01

    We present here the life and research of V. S. Rama Das, a distinguished Indian botanist who specialized in photosynthesis. He was the first to purify chloroplasts that were free of mitochondrial contamination. He then studied C4, C3-C4 intermediate and CAM pathways, as well as their taxonomic distribution in tropical climates. His most valuable legacy is that he, as a philosopher, inspired and guided many students to pursue their research career in India. Also see Narayana and Pullaiah (Eminent Indian Botanists: Past and present: Biographies and contributions, pp 394-401, 2010) and Raghavendra and Reddy (Curr Sci 101:798-799, 2011) for further information on Rama Das.

  18. Seasonality and Paleoecology of the Late Cretaceous Multi-Taxa Vertebrate Assemblage of “Lo Hueco” (Central Eastern Spain)

    PubMed Central

    Domingo, Laura; Barroso-Barcenilla, Fernando; Cambra-Moo, Oscar

    2015-01-01

    Isotopic studies of multi-taxa terrestrial vertebrate assemblages allow determination of paleoclimatic and paleoecological aspects on account of the different information supplied by each taxon. The late Campanian-early Maastrichtian “Lo Hueco” Fossil-Lagerstätte (central eastern Spain), located at a subtropical paleolatitude of ~31°N, constitutes an ideal setting to carry out this task due to its abundant and diverse vertebrate assemblage. Local δ18OPO4 values estimated from δ18OPO4 values of theropods, sauropods, crocodyliforms, and turtles are close to δ18OH2O values observed at modern subtropical latitudes. Theropod δ18OH2O values are lower than those shown by crocodyliforms and turtles, indicating that terrestrial endothermic taxa record δ18OH2O values throughout the year, whereas semiaquatic ectothermic taxa δ18OH2O values represent local meteoric waters over a shorter time period when conditions are favorable for bioapatite synthesis (warm season). Temperatures calculated by combining theropod, crocodyliform, and turtle δ18OH2O values and gar δ18OPO4 have enabled us to estimate seasonal variability as the difference between mean annual temperature (MAT, yielded by theropods) and temperature of the warmest months (TWMs, provided by crocodyliforms and turtles). ΔTWMs-MAT value does not point to a significantly different seasonal thermal variability when compared to modern coastal subtropical meteorological stations and Late Cretaceous rudists from eastern Tethys. Bioapatite and bulk organic matter δ13C values point to a C3 environment in the “Lo Hueco” area. The estimated fractionation between sauropod enamel and diet is ~15‰. While waiting for paleoecological information yielded by the ongoing morphological study of the “Lo Hueco” crocodyliforms, δ13C and δ18OCO3 results point to incorporation of food items with brackish influence, but preferential ingestion of freshwater. “Lo Hueco” turtles showed the lowest δ13C and δ18OCO3

  19. Seasonality and paleoecology of the late Cretaceous multi-taxa vertebrate assemblage of "Lo Hueco" (central eastern Spain).

    PubMed

    Domingo, Laura; Barroso-Barcenilla, Fernando; Cambra-Moo, Oscar

    2015-01-01

    Isotopic studies of multi-taxa terrestrial vertebrate assemblages allow determination of paleoclimatic and paleoecological aspects on account of the different information supplied by each taxon. The late Campanian-early Maastrichtian "Lo Hueco" Fossil-Lagerstätte (central eastern Spain), located at a subtropical paleolatitude of ~31°N, constitutes an ideal setting to carry out this task due to its abundant and diverse vertebrate assemblage. Local δ18OPO4 values estimated from δ18OPO4 values of theropods, sauropods, crocodyliforms, and turtles are close to δ18OH2O values observed at modern subtropical latitudes. Theropod δ18OH2O values are lower than those shown by crocodyliforms and turtles, indicating that terrestrial endothermic taxa record δ18OH2O values throughout the year, whereas semiaquatic ectothermic taxa δ18OH2O values represent local meteoric waters over a shorter time period when conditions are favorable for bioapatite synthesis (warm season). Temperatures calculated by combining theropod, crocodyliform, and turtle δ18OH2O values and gar δ18OPO4 have enabled us to estimate seasonal variability as the difference between mean annual temperature (MAT, yielded by theropods) and temperature of the warmest months (TWMs, provided by crocodyliforms and turtles). ΔTWMs-MAT value does not point to a significantly different seasonal thermal variability when compared to modern coastal subtropical meteorological stations and Late Cretaceous rudists from eastern Tethys. Bioapatite and bulk organic matter δ13C values point to a C3 environment in the "Lo Hueco" area. The estimated fractionation between sauropod enamel and diet is ~15‰. While waiting for paleoecological information yielded by the ongoing morphological study of the "Lo Hueco" crocodyliforms, δ13C and δ18OCO3 results point to incorporation of food items with brackish influence, but preferential ingestion of freshwater. "Lo Hueco" turtles showed the lowest δ13C and δ18OCO3 values of the

  20. New proposals for naming lower-ranked taxa within the frame of the International Code of Zoological Nomenclature.

    PubMed

    Dubois, Alain

    2006-10-01

    The recent multiplication of cladistic hypotheses for many zoological groups poses a challenge to zoological nomenclature following the International Code of Zoological Nomenclature: in order to account for these hypotheses, we will need many more ranks than currently allowed in this system, especially in lower taxonomy (around the ranks genus and species). The current Code allows the use of as many ranks as necessary in the family-series of nomina (except above superfamily), but forbids the use of more than a few ranks in the genus and species-series. It is here argued that this limitation has no theoretical background, does not respect the freedom of taxonomic thoughts or actions, and is harmful to zoological taxonomy in two respects at least: (1) it does not allow to express in detail hypothesized cladistic relationships among taxa at lower taxonomic levels (genus and species); (2) it does not allow to point taxonomically to low-level differentiation between populations of the same species, although this would be useful in some cases for conservation biology purposes. It is here proposed to modify the rules of the Code in order to allow use by taxonomists of an indeterminate number of ranks in all nominal-series. Such an 'expanded nomenclatural system' would be highly flexible and likely to be easily adapted to any new finding or hypothesis regarding cladistic relationships between taxa, at genus and species level and below. This system could be useful for phylogeographic analysis and in conservation biology. In zoological nomenclature, whereas robustness of nomina is necessary, the same does not hold for nomenclatural ranks, as the latter are arbitrary and carry no special biological, evolutionary or other information, except concerning the mutual relationships between taxa in the taxonomic hierarchy. Compared to the Phylocode project, the new system is equally unambiguous within the frame of a given taxonomic frame, but it provides more explicit and

  1. Towards a phylogenetic generic classification of Thelypteridaceae: Additional sampling suggests alterations of neotropical taxa and further study of paleotropical genera.

    PubMed

    Almeida, Thaís Elias; Hennequin, Sabine; Schneider, Harald; Smith, Alan R; Batista, João Aguiar Nogueira; Ramalho, Aline Joseph; Proite, Karina; Salino, Alexandre

    2016-01-01

    Thelypteridaceae is one of the largest fern families, having about 950 species and a cosmopolitan distribution but with most species occurring in tropical and subtropical regions. Its generic classification remains controversial, with different authors recognizing from one up to 32 genera. Phylogenetic relationships within the family have not been exhaustively studied, but previous studies have confirmed the monophyly of the lineage. Thus far, sampling has been inadequate for establishing a robust hypothesis of infrafamilial relationships within the family. In order to understand phylogenetic relationships within Thelypteridaceae and thus to improve generic reclassification, we expand the molecular sampling, including new samples of Old World taxa and, especially, many additional neotropical representatives. We also explore the monophyly of exclusively or mostly neotropical genera Amauropelta, Goniopteris, Meniscium, and Steiropteris. Our sampling includes 68 taxa and 134 newly generated sequences from two plastid genomic regions (rps4-trnS and trnL-trnF), plus 73 rps4 and 72 trnL-trnF sequences from GenBank. These data resulted in a concatenated matrix of 1980 molecular characters for 149 taxa. The combined data set was analyzed using maximum parsimony and bayesian inference of phylogeny. Our results are consistent with the general topological structure found in previous studies, including two main lineages within the family: phegopteroid and thelypteroid. The thelypteroid lineage comprises two clades; one of these included the segregates Metathelypteris, Coryphopteris, and Amauropelta (including part of Parathelypteris), whereas the other comprises all segregates of Cyclosorus s.l., such as Goniopteris, Meniscium, and Steiropteris (including Thelypteris polypodioides, previously incertae sedis). The three mainly neotropical segregates were found to be monophyletic but nested in a broadly defined Cyclosorus. The fourth mainly neotropical segregate, Amauropelta

  2. The development of the disease activity score (DAS) and the disease activity score using 28 joint counts (DAS28).

    PubMed

    van Riel, P L C M

    2014-01-01

    In rheumatoid arthritis, disease activity cannot be measured using a single variable. The Disease Activity Score (DAS) has been developed as a quantitative index to be able to measure, study and manage disease activity in RA in daily clinical practice, clinical trials, and long term observational studies. The DAS is a continuous measure of RA disease activity that combines information from swollen joints, tender joints, acute phase response and patient self-report of general health. Cut points were developed to classify patients in remission, as well as low, moderate, and severe disease activity in the 1990s. DAS-based EULAR response criteria were primarily developed to be used in clinical trials to classify individual patients as non-, moderate, or good responders, depending on the magnitude of change and absolute level of disease activity at the conclusion of the test.

  3. Systematics of some calloporid and lacernid Cheilostomata (Bryozoa) from coastal South Korean waters, with the description of new taxa.

    PubMed

    Min, Bum Sik; Seo, Ji Eun; Grischenko, Andrei V; Lee, Sang-Kyu; Gordon, Dennis P

    2017-01-30

    Six species in two families of Cheilostomata-Calloporidae and Lacernidae-are described from the southern coasts of the Korean Peninsula, resulting in a new distributional record and four new species to the Korean fauna. Further, Woosukia n. gen. is described, based on an existing species. Two species names (Crassimarginatella crassimarginata and Arthropoma cecilii) are deleted from the Korean faunal list owing to previous misidentification, with the net result that the Korean cheilostome fauna is increased to 125 species. The new additions to the fauna are: Crassimarginatella kumatae (Okada), Retevirgula asiana n. sp., Woosukia subhexagona (Ortmann), Arthropoma magniporosum n. sp., Arthropoma minus n. sp., and Phonicosia crena n. sp. The biogeographic relationships of some western Pacific taxa are discussed.

  4. On cockroaches of the subfamily Epilamprinae (Dictyoptera: Blaberidae) from South India and Sri Lanka, with descriptions of new taxa.

    PubMed

    Anisyutkin, Leonid N

    2014-08-08

    The new genus Indoapterolampra, gen. nov. and two new species (I. rugosiuscula sp. nov. and Morphna lucida sp. nov.) are described. Rhabdoblatta praecipua (Walker, 1868) is removed from the synonymy with 'Polyzosteria' terranea Walker, 1868. The latter species is considered Epilamprinae gen. sp. The lectotype of Phoraspis (Thorax) porcellana Saussure, 1862 is designated. A key for the genera of Epilamprinae from South India and Sri Lanka is provided. Detailed morphological descriptions of the studied taxa are given. The structure of the male genitalia of I. rugosiuscula sp. nov., M. lucida sp. nov., M. plana (Brunner von Wattenwyl, 1865), M. decolyi (Bolivar, 1897) and R. praecipua and that of the female genital complex of M. decolyi, P. (T.) porcellana and Phlebonotus anomalus (Saussure, 1863) are described for the first time. Some aspects of the cockroach evolution are briefly discussed. 

  5. Identification of members of the Pasteurellaceae isolated from birds and characterization of two new taxa isolated from psittacine birds.

    PubMed

    Bisgaard, M; Hinz, K H; Petersen, K D; Christensen, J P

    1999-08-01

    A collection of 43 unclassified members of the Pasteurellaceae, most of which were obtained from lesions, were investigated using an extensive battery of phenotypical tests as well as by ribotyping. The isolates had been made from Anser anser forma (f) domestica (d), Agapornis fischer, Amazona spp., Ara macao, Columba livia f.d., Melanopsittacus undulatus, and Psittacus erithacus. Comparison of results with those obtained from reference strains allowed classification of 25 strains. Three strains were identified as Pasteurella dagmatis, P. sp. A, and [P.] aerogenes, respectively. Twenty strains were classified as taxon 3 and two as taxon 14. Eighteen strains, all originating from psittacine species, belonged to two new taxa, tentatively named Bisgaard taxon 33 and taxon 37. Characters obtained with taxon 33 allowed classification within the family Pasteurellaceae, while the final classification of taxon 37 remains to be investigated. The present investigation underlines the problems confronting diagnostic laboratories attempting to identify members of the family Pasteurellaceae isolated from birds.

  6. Development of 14 microsatellite markers in Odontites vernus s.l. (Orobanchaceae) and cross-amplification in related taxa1

    PubMed Central

    Pinto-Carrasco, Daniel; Košnar, Jiří; López-González, Noemí; Koutecký, Petr; Těšitel, Jakub; Rico, Enrique; Martínez-Ortega, M. Montserrat

    2016-01-01

    Premise of the study: Microsatellite primers were developed for the first time in the root hemiparasite herb Odontites vernus (Orobanchaceae). These markers will be useful to investigate the role of polyploidization in the evolution of this diploid-tetraploid complex, as well as the extent of gene flow between different ploidy levels. Methods and Results: Fourteen polymorphic and reproducible loci were identified and optimized from O. vernus using a microsatellite-enriched library and 454 Junior sequencing. The set of primers amplified di- to pentanucleotide repeats and showed two to 13 alleles per locus. Transferability was tested in 30 taxa (19 belonging to Odontites and 11 from eight other genera of Orobanchaceae tribe Rhinantheae). Conclusions: The results indicate the utility of the newly developed microsatellites in O. vernus and several other species, which will be useful for taxon delimitation and conservation genetics studies. PMID:27011897

  7. Unique method of tooth replacement in durophagous placodont marine reptiles, with new data on the dentition of Chinese taxa

    PubMed Central

    Neenan, James M; Li, Chun; Rieppel, Olivier; Bernardini, Federico; Tuniz, Claudio; Muscio, Giuseppe; Scheyer, Torsten M

    2014-01-01

    The placodonts of the Triassic period (˜252–201 mya) represent one of the earliest and most extreme specialisations to a durophagous diet of any known reptile group. Exceptionally enlarged crushing tooth plates on the maxilla, dentary and palatine cooperated to form functional crushing areas in the buccal cavity. However, the extreme size of these teeth, combined with the unusual way they occluded, constrained how replacement occurred. Using an extensive micro-computed tomographic dataset of 11 specimens that span all geographic regions and placodont morphotypes, tooth replacement patterns were investigated. In addition, the previously undescribed dental morphologies and formulae of Chinese taxa are described for the first time and incorporated into the analysis. Placodonts have a unique tooth replacement pattern and results follow a phylogenetic trend. The plesiomorphic Placodus species show many replacement teeth at various stages of growth, with little or no discernible pattern. On the other hand, the more derived cyamodontoids tend to have fewer replacement teeth growing at any one time, replacing teeth unilaterally and/or in functional units, thus maintaining at least one functional crushing area at all times. The highly derived placochelyids have fewer teeth and, as a result, only have one or two replacement teeth in the upper jaw. This supports previous suggestions that these taxa had an alternative diet to other placodonts. Importantly, all specimens show at least one replacement tooth growing at the most posterior palatine tooth plates, indicating increased wear at this point and thus the most efficient functional crushing area. PMID:24517163

  8. Late Neogene and Early Quaternary Paleoenvironmental and Paleoclimatic Conditions in Southwestern Europe: Isotopic Analyses on Mammalian Taxa

    PubMed Central

    Domingo, Laura; Koch, Paul L.; Hernández Fernández, Manuel; Fox, David L.; Domingo, M. Soledad; Alberdi, María Teresa

    2013-01-01

    Climatic and environmental shifts have had profound impacts on faunal and floral assemblages globally since the end of the Miocene. We explore the regional expression of these fluctuations in southwestern Europe by constructing long-term records (from ∼11.1 to 0.8 Ma, late Miocene–middle Pleistocene) of carbon and oxygen isotope variations in tooth enamel of different large herbivorous mammals from Spain. Isotopic differences among taxa illuminate differences in ecological niches. The δ13C values (relative to VPDB, mean −10.3±1.1‰; range −13.0 to −7.4‰) are consistent with consumption of C3 vegetation; C4 plants did not contribute significantly to the diets of the selected taxa. When averaged by time interval to examine secular trends, δ13C values increase at ∼9.5 Ma (MN9–MN10), probably related to the Middle Vallesian Crisis when there was a replacement of vegetation adapted to more humid conditions by vegetation adapted to drier and more seasonal conditions, and resulting in the disappearance of forested mammalian fauna. The mean δ13C value drops significantly at ∼4.2−3.7 Ma (MN14–MN15) during the Pliocene Warm Period, which brought more humid conditions to Europe, and returns to higher δ13C values from ∼2.6 Ma onwards (MN16), most likely reflecting more arid conditions as a consequence of the onset of the Northern Hemisphere glaciation. The most notable feature in oxygen isotope records (and mean annual temperature reconstructed from these records) is a gradual drop between MN13 and the middle Pleistocene (∼6.3−0.8 Ma) most likely due to cooling associated with Northern Hemisphere glaciation. PMID:23717470

  9. Viral coinfection is shaped by host ecology and virus–virus interactions across diverse microbial taxa and environments

    PubMed Central

    2017-01-01

    Abstract Infection of more than one virus in a host, coinfection, is common across taxa and environments. Viral coinfection can enable genetic exchange, alter the dynamics of infections, and change the course of viral evolution. Yet, a systematic test of the factors explaining variation in viral coinfection across different taxa and environments awaits completion. Here I employ three microbial data sets of virus–host interactions covering cross-infectivity, culture coinfection, and single-cell coinfection (total: 6,564 microbial hosts, 13,103 viruses) to provide a broad, comprehensive picture of the ecological and biological factors shaping viral coinfection. I found evidence that ecology and virus–virus interactions are recurrent factors shaping coinfection patterns. Host ecology was a consistent and strong predictor of coinfection across all three data sets: cross-infectivity, culture coinfection, and single-cell coinfection. Host phylogeny or taxonomy was a less consistent predictor, being weak or absent in the cross-infectivity and single-cell coinfection models, yet it was the strongest predictor in the culture coinfection model. Virus–virus interactions strongly affected coinfection. In the largest test of superinfection exclusion to date, prophage sequences reduced culture coinfection by other prophages, with a weaker effect on extrachromosomal virus coinfection. At the single-cell level, prophage sequences eliminated coinfection. Virus–virus interactions also increased culture coinfection with ssDNA–dsDNA coinfections >2× more likely than ssDNA-only coinfections. The presence of CRISPR spacers was associated with a ∼50% reduction in single-cell coinfection in a marine bacteria, despite the absence of exact spacer matches in any active infection. Collectively, these results suggest the environment bacteria inhabit and the interactions among surrounding viruses are two factors consistently shaping viral coinfection patterns. These findings

  10. Habitat structure and body size distributions: Cross-ecosystem comparison for taxa with determinate and indeterminate growth

    USGS Publications Warehouse

    Nash, Kirsty L.; Allen, Craig R.; Barichievy, Chris; Nystrom, Magnus; Sundstrom, Shana M.; Graham, Nicholas A.J.

    2014-01-01

    Habitat structure across multiple spatial and temporal scales has been proposed as a key driver of body size distributions for associated communities. Thus, understanding the relationship between habitat and body size is fundamental to developing predictions regarding the influence of habitat change on animal communities. Much of the work assessing the relationship between habitat structure and body size distributions has focused on terrestrial taxa with determinate growth, and has primarily analysed discontinuities (gaps) in the distribution of species mean sizes (species size relationships or SSRs). The suitability of this approach for taxa with indeterminate growth has yet to be determined. We provide a cross-ecosystem comparison of bird (determinate growth) and fish (indeterminate growth) body mass distributions using four independent data sets. We evaluate three size distribution indices: SSRs, species size–density relationships (SSDRs) and individual size–density relationships (ISDRs), and two types of analysis: looking for either discontinuities or abundance patterns and multi-modality in the distributions. To assess the respective suitability of these three indices and two analytical approaches for understanding habitat–size relationships in different ecosystems, we compare their ability to differentiate bird or fish communities found within contrasting habitat conditions. All three indices of body size distribution are useful for examining the relationship between cross-scale patterns of habitat structure and size for species with determinate growth, such as birds. In contrast, for species with indeterminate growth such as fish, the relationship between habitat structure and body size may be masked when using mean summary metrics, and thus individual-level data (ISDRs) are more useful. Furthermore, ISDRs, which have traditionally been used to study aquatic systems, present a potentially useful common currency for comparing body size distributions

  11. Water deficit induces swainsonine of some locoweed taxa, but with no swainsonine-growth trade-off

    NASA Astrophysics Data System (ADS)

    Vallotton, Amber D.; Murray, Leigh W.; Delaney, Kevin J.; Sterling, Tracy M.

    2012-08-01

    Environmental factors like nutrient availability (e.g., C:N) and water deficit can influence secondary metabolites levels in plants and fungal endophytes. Locoweeds (Astragalus and Oxytropis spp.) contain swainsonine (SWA), an alkaloid that causes chronic vertebrate toxicity. In two greenhouse experiments, we studied field transplants of three Astragalus mollissimus varieties that vary in SWA levels (barely detectable SWA in var. 'thompsonae', intermediate SWA in var. 'bigelovii', and high SWA in var. 'mollissimus'), and intermediate SWA in Oxytropis sericea; our results confirmed these rankings. We tested whether SWA induction after water deficit (three 14d water-deficit periods separated by two 7d water recovery periods) was taxon-specific and whether degree of induction was influenced by taxon average SWA. We also looked for signs of a trade-off between primary physiology (photosynthesis) or growth (biomass, relative growth rate) with fungal endophyte SWA production; and if so, whether water stress magnified such a trade-off. Leaf photosynthetic activity decreased during the experiments and often more in water-deficit than control plants; leaf gs and Ci results suggest that stomatal closure reduced photosynthetic activity from mild water deficit. Yet, water-deficit affected plants in other ways: there were more dropped senesced leaves for all tested taxa; higher water-use efficiency for var. mollissimus, var. thompsonae, and O. sericea; higher root mass ratios for var. bigelovii, var. thompsonae, and O. sericea; and lower relative water content for var. thompsonae. Positive SWA increases of 1.6-fold for var. mollissimus and 4-fold for var. bigelovii occurred, so positive SWA induction was taxon-specific and limited to medium/high SWA A. mollissimus varieties. There was little evidence for a clear SWA trade-off with total (shoot + root) biomass, relative growth rate, or photosynthetic rate. Additional studies will need to test whether water deficit positively

  12. Taxonomic complexity in the halophyte Limonium vulgare and related taxa (Plumbaginaceae): insights from analysis of morphological, reproductive and karyological data

    PubMed Central

    Cortinhas, Ana; Erben, Matthias; Paula Paes, Ana; Espírito Santo, Dalila; Guara-Requena, Miguel; Caperta, Ana D.

    2015-01-01

    Background and Aims Limonium is a well-known example of a group of plants that is taxonomically complex due to certain biological characteristics that hamper species' delineation. The closely related polyploid species Limonium vulgare Mill., L. humile Mill. and L. narbonense Mill. are defined species and can be used for studying patterns of morphological and reproductive variation. The first two taxa are usually found in Atlantic Europe and the third in the Mediterranean region, but a number of intermediate morphological forms may be present alongside typical examples of these species. This study attempts to elucidate morphological, floral and karyological diversity representative of these taxa in the Iberian Peninsula. Methods The extent of morphological differentiation was tested through comparison of 197 specimens from both Portugal and Spain using 17 descriptive morphological characters and 19 diagnostic morphometric characters. Analyses of floral morphisms (heterostyly and pollen–stigma dimorphism) and karyological determinations were also conducted. Key Results and Conclusions Discriminant analysis using morphometric variables reliably assigned individuals in natural populations to their respective groups. In addition, the results provide the first direct evidence that L. narbonense and a new species, Limonium maritimum Caperta, Cortinhas, Paes, Guara, Espírito-Santo and Erben, sp. nov., related to L. vulgare are present on Portuguese coasts. Most of these species are found together in mixed populations, especially L. vulgare and L. narbonense. It is hypothesized that taxonomic biodiversity found in sites where distinct species co-occur facilitates the evolutionary processes of hybridization, introgression and apomixis. This study therefore contributes to the elucidation of the taxonomic diversity in L. vulgare-related species and may also help in implementing future conservation programmes to maintain the evolutionary processes generating biodiversity

  13. Molecular phylogenetics and phylogeography of all the Saimiri taxa (Cebidae, Primates) inferred from mt COI and COII gene sequences.

    PubMed

    Ruiz-García, Manuel; Luengas-Villamil, Kelly; Leguizamon, Norberto; de Thoisy, Benoit; Gálvez, Hugo

    2015-04-01

    Some previous genetic studies have been performed to resolve the molecular phylogenetics of the squirrel monkeys (Saimiri). However, these studies did not show consensus in how many taxa are within this genus and what the relationships among them are. For this reason, we sequenced 2,237 base pairs of the mt COI and COII genes in 218 Saimiri individuals. All, less 12 S. sciureus sciureus from French Guyana, were sampled in the wild. These samples represented all the living Saimiri taxa recognized. There were four main findings of this study. (1) Our analysis detected 17 different Saimiri groups: albigena, cassiquiarensis, five polyphyletic macrodon groups, three polyphyletic ustus groups, sciureus, collinsi, boliviensis, peruviensis, vanzolinii, oerstedii and citrinellus. Four different phylogenetic trees showed the Central American squirrel monkey (S. oerstedii) as the most differentiated taxon. In contrast, albigena was indicated to be the most recent taxon. (2) There was extensive hybridization and/or historical introgression among albigena, different macrodon groups, peruviensis, sciureus and collinsi. (3) Different tests showed that our maximum likelihood tree was consistent with two species of Saimiri: S. oerstedii and S. sciureus. If no cases of hybridization were detected implicating S. vanzolinii, this could be a third recognized species. (4) We also estimated that the first temporal splits within this genus occurred around 1.4-1.6 million years ago, which indicates that the temporal split events within Saimiri were correlated with Pleistocene climatic changes. If the biological species concept is applied because, in this case, it is operative due to observed hybridization in the wild, the number of species within this genus is probably more limited than recently proposed by other authors. The Pleistocene was the fundamental epoch when the mitochondrial Saimiri diversification process occurred.

  14. Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae)

    PubMed Central

    Daïnou, K; Mahy, G; Duminil, J; Dick, C W; Doucet, J-L; Donkpégan, A S L; Pluijgers, M; Sinsin, B; Lejeune, P; Hardy, O J

    2014-01-01

    The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically. PMID:24549110

  15. Relationships among epipelic diatom taxa, bacterial abundances and water quality in a highly polluted stream catchment, bursa -- Turkey.

    PubMed

    Dere, Sükran; Dalkiran, Nurhayat; Karacaoğlu, Didem; Elmaci, Ayşe; Dülger, Başaran; Sentürk, Engin

    2006-01-01

    Nilüfer Stream is an important water source in the industrial and metropolitan city of Bursa, Turkey. The stream catchment has been influenced by high human impact. The downstream receives sewage water from households and industry, whereas the headwater of the stream has a source of high-quality drinkable water. In this paper, abundances of epipelic diatom taxa, faecal coliforms (FC), total coliforms (TC) and total bacteria (TB) were studied in relation to measured environmental variables (T, pH, DO, BOD(5), EC, TDS) for the period July 1997 to June 1998 at six stations in the heavily polluted Nilüfer Stream catchment. It is observed that the physicochemical variables and bacterial abundances varied seasonally at all stations, and the level of pollution reached at its highest point in the summer. The results of Kruskal-Wallis and one-way ANOVA indicated that DO gradually decreased, whereas BOD(5), EC, TDS, TB, FC and TC gradually increased from upstream to downstream. The ordination method of Principal Component Analysis (PCA) was carried out for both biologic and physicochemical variables, and the results were supported by the former statistical procedures. The frequency of occurrence of dominant diatoms was examined in relation to the spatial variations in chemical constituents. Both diatoms and bacteria showed strong correlations with the measured physicochemical variables. In Canonical Correlation Analysis (CANCORR) measures of bacterial abundances also displayed strong correlations with abundances of 11 diatom taxa. The results showed that the stream catchment is polluted gradually from upstream to downstream. In addition, pollution load in the stream catchment has been gradually increased, compared with recent years. Urbanisation and industrialisation of the city have affected increasing pollution in Nilüfer Stream. The results also indicated that diatoms are not affected by environmental variables such as bacteria. Bacteria are more sensitive to organic

  16. A Fossil DNA Based High Resolution Record of Holocene Planktonic Taxa and Environmental Change in the Black Sea

    NASA Astrophysics Data System (ADS)

    Coolen, M. J.; Saenz, J. P.; Trowbridge, N.; Eglinton, T.

    2007-12-01

    A standard approach to study past planktonic taxa which carry information about past environments and climate variability is the microscopic determination and enumeration of microfossils. However, most planktonic taxa are soft-bodied and in cases where microfossils are absent or difficult to identify, chemical fossils (lipid biomarkers) can be used as paleoecological tools. Nevertheless, most lipids are not very specific, multiple sources are possible, or their biological source remains unknown. Recently, we and others have shown that under excellent preservation conditions, the analysis of preserved genetic signatures (fossil DNA) offers great potential to study past planktonic communities, including soft-bodied species, at the unprecedented species- and even strain-level (this work). Given the dramatic shifts in hydrography and the present anoxia that permeates most of the water column which promotes preservation of cellular materials, the Black Sea is an excellent setting to study the ancient species composition based on fossil DNA. We developed a high temporal resolution (50-100 yr) fossil DNA and lipid biomarker based stratigraphic record of planktonic community structure in the Black Sea spanning the complete Holocene development from the first post-glacial input of Mediterranean waters in the paleo-lacustrine Black Sea to the present. Preserved genetic markers for microbial communities dwelling at the surface (algal primary producers and zooplankton), the suboxic layer (marine Crenarchaeota), and the sulfidic chemocline (green sulfur bacteria) were targeted to provide information on past environmental change in the Black Sea. Specifically, we targeted markers that contributed to our understanding of past surface water temperature, salinity and stratification. Where possible, a side-by-side phylogenetic and lipid biomarker analyses was performed in order to carefully assess the validity of utilizing the former as proxies of a given biological input. As the

  17. Plants Assemble Species Specific Bacterial Communities from Common Core Taxa in Three Arcto-Alpine Climate Zones

    PubMed Central

    Kumar, Manoj; Brader, Günter; Sessitsch, Angela; Mäki, Anita; van Elsas, Jan D.; Nissinen, Riitta

    2017-01-01

    Evidence for the pivotal role of plant-associated bacteria to plant health and productivity has accumulated rapidly in the last years. However, key questions related to what drives plant bacteriomes remain unanswered, among which is the impact of climate zones on plant-associated microbiota. This is particularly true for wild plants in arcto-alpine biomes. Here, we hypothesized that the bacterial communities associated with pioneer plants in these regions have major roles in plant health support, and this is reflected in the formation of climate and host plant specific endophytic communities. We thus compared the bacteriomes associated with the native perennial plants Oxyria digyna and Saxifraga oppositifolia in three arcto-alpine regions (alpine, low Arctic and high Arctic) with those in the corresponding bulk soils. As expected, the bulk soil bacterial communities in the three regions were significantly different. The relative abundances of Proteobacteria decreased progressively from the alpine to the high-arctic soils, whereas those of Actinobacteria increased. The candidate division AD3 and Acidobacteria abounded in the low Arctic soils. Furthermore, plant species and geographic region were the major determinants of the structures of the endophere communities. The plants in the alpine region had higher relative abundances of Proteobacteria, while plants from the low- and high-arctic regions were dominated by Firmicutes. A highly-conserved shared set of ubiquitous bacterial taxa (core bacteriome) was found to occur in the two plant species. Burkholderiales, Actinomycetales and Rhizobiales were the main taxa in this core, and they were also the main contributors to the differences in the endosphere bacterial community structures across compartments as well as regions. We postulate that the composition of this core is driven by selection by the two plants. PMID:28174556

  18. Código para imageamento indireto de estrelas em sistemas binarios: simulação de variações elipsoidais e do perfil das linhas

    NASA Astrophysics Data System (ADS)

    Souza, T. R.; Baptista, R.

    2003-08-01

    As estrelas secundárias em variáveis cataclí smicas (VCs) e binárias-x de baixa massa (BXBMs) são cruciais para o entendimento da origem, evolução e comportamento destas binárias interagentes. Elas são estrelas magneticamente ativas submetidas a condições ambientais extremas [e.g., estão muito próximas de uma fonte quente e irradiante; têm rotação extremamente rápida e forma distorcida; estão perdendo massa a taxas de 10-8-10-10 M¤/ano] que contribuem para que suas propriedades sejam distintas das de estrelas de mesma massa na seqüência principal. Por outro lado, o padrão de irradiação na face da secundária fornece informação sobre a geometria das estruturas de acréscimo em torno da estrela primária. Assim, a obtenção de imagens da superfície destas estrelas é de grande interesse astrofísico. A Tomografia Roche usa as variações no perfil das linhas de emissão/absorção da estrela secundária em função da fase orbital para mapear a distribuição de brilho em sua superfície. Neste trabalho apresentamos os resultados iniciais do desenvolvimento de um programa para o mapeamento da distribuição de brilho na superfí cie das estrelas secundárias em VCs e BXBMs com técnicas de astro-tomografia. Presentemente temos em operação um código que simula as variações no perfil das linhas em conseqüência de efeito Doppler resultante da combinação de rotação e translação de uma estrela em forma de lobo de Roche em torno do centro de massa da binária, em função da distribuição de brilho na superfície desta estrela. O código igualmente produz a curva de luz resultante das variações de aspecto da estrela em função da fase orbital (variações elipsoidais).

  19. ProServer: a simple, extensible Perl DAS server.

    PubMed

    Finn, Robert D; Stalker, James W; Jackson, David K; Kulesha, Eugene; Clements, Jody; Pettett, Roger

    2007-06-15

    The increasing size and complexity of biological databases has led to a growing trend to federate rather than duplicate them. In order to share data between federated databases, protocols for the exchange mechanism must be developed. One such data exchange protocol that is widely used is the Distributed Annotation System (DAS). For example, DAS has enabled small experimental groups to integrate their data into the Ensembl genome browser. We have developed ProServer, a simple, lightweight, Perl-based DAS server that does not depend on a separate HTTP server. The ProServer package is easily extensible, allowing data to be served from almost any underlying data model. Recent additions to the DAS protocol have enabled both structure and alignment (sequence and structural) data to be exchanged. ProServer allows both of these data types to be served. ProServer can be downloaded from http://www.sanger.ac.uk/proserver/ or CPAN http://search.cpan.org/~rpettett/. Details on the system requirements and installation of ProServer can be found at http://www.sanger.ac.uk/proserver/.

  20. Metagenomic Analysis of Taxa Associated with Lutzomyia longipalpis, Vector of Visceral Leishmaniasis, Using an Unbiased High-Throughput Approach

    PubMed Central

    McCarthy, Christina B.; Diambra, Luis A.; Rivera Pomar, Rolando V.

    2011-01-01

    Background Leishmaniasis is one of the most diverse and complex of all vector-borne diseases worldwide. It is caused by parasites of the genus Leishmania, obligate intramacrophage protists characterised by diversity and complexity. Its most severe form is visceral leishmaniasis (VL), a systemic disease that is fatal if left untreated. In Latin America VL is caused by Leishmania infantum chagasi and transmitted by Lutzomyia longipalpis. This phlebotomine sandfly is only found in the New World, from Mexico to Argentina. In South America, migration and urbanisation have largely contributed to the increase of VL as a public health problem. Moreover, the first VL outbreak was recently reported in Argentina, which has already caused 7 deaths and 83 reported cases. Methodology/Principal Findings An inventory of the microbiota associated with insect vectors, especially of wild specimens, would aid in the development of novel strategies for controlling insect vectors. Given the recent VL outbreak in Argentina and the compelling need to develop appropriate control strategies, this study focused on wild male and female Lu. longipalpis from an Argentine endemic (Posadas, Misiones) and a Brazilian non-endemic (Lapinha Cave, Minas Gerais) VL location. Previous studies on wild and laboratory reared female Lu. longipalpis have described gut bacteria using standard bacteriological methods. In this study, total RNA was extracted from the insects and submitted to high-throughput pyrosequencing. The analysis revealed the presence of sequences from bacteria, fungi, protist parasites, plants and metazoans. Conclusions/Significance This is the first time an unbiased and comprehensive metagenomic approach has been used to survey taxa associated with an infectious disease vector. The identification of gregarines suggested they are a possible efficient control method under natural conditions. Ongoing studies are determining the significance of the associated taxa found in this study in a

  1. Differentiation in the Trochulus hispidus complex and related taxa (Pulmonata: Hygromiidae): morphology, ecology and their relation to phylogeography

    PubMed Central

    Duda, Michael; Kruckenhauser, Luise; Sattmann, Helmut; Harl, Josef; Jaksch, Katharina; Haring, Elisabeth

    2014-01-01

    In this study we investigated the morphology and ecology of representatives of the taxonomically ambiguous genus Trochulus. The main focus was on the T. hispidus complex, which comprises several genetically highly divergent mitochondrial clades, as determined in a parallel molecular genetic study. We analysed shell morphology and anatomical traits and asked whether the clades are differentiated in these characters. In addition, the related species T. oreinos and T. striolatus were investigated and compared with the T. hispidus complex. Finally, we compared the ecological requirements of the taxa. Among the genetic clades of the T. hispidus complex there was no clear morphological differentiation and geographic populations could not be distinguished based on their morphology. The investigated characters of the genital anatomy did not allow discrimination of any of the T. hispidus clades and were not even diagnostic for the group as a whole. The morphotype of T. sericeus is present in all clades and thus cannot be assigned to a genetic group or any specific population. Thus, our morphological data do not provide evidence that any of the mitochondrial T. hispidus clades represent separate species. Concerning interspecific delimitation, the T. hispidus complex was clearly differentiated from T. striolatus and T. oreinos by shell morphological and anatomical characters, e.g. sculpture of shell surface and details of the penis. Finally, the habitat of T. oreinos is different from those of the other two species. In contrast to the lack of correspondence between genetic and morphological differentiation within the T. hispidus complex, related species display intraspecific morphological differentiation corresponding with mitochondrial clades: within T. striolatus there was a slight morphological differentiation between the subspecies T. s. striolatus, T. s. juvavensis and T. s. danubialis. The two subspecies of T. oreinos could be discriminated by a small but consistent

  2. The USA National Phenology Network's National Phenology Database: a multi-taxa, continental-scale dataset for scientific inquiry

    NASA Astrophysics Data System (ADS)

    Weltzin, J. F.

    2012-12-01

    The USA National Phenology Network (USA-NPN; www.usanpn.org) serves science and society by promoting a broad understanding of plant and animal phenology and the relationships among phenological patterns and all aspects of environmental change. The National Phenology Database, maintained by the USA-NPN, is experiencing steady growth in the number of data records it houses. As of August 2012, participants in the USA-NPN national-scale, multi-taxa phenology observation program Nature's Notebook had contributed over 1.3 million observation records (encompassing four and three years of observations for plants and for animals, respectively). Data are freely available www.usanpn.org/results/data, and include FGDC-compliant metadata, data-use and data-attribution policies, vetted and documented methodologies and protocols, and version control. Quality assurance and quality control, and metadata data associated with field observations (e.g., effort and method reporting, site and organism condition) are also documented. Data are also available for exploration, visualization and preliminary analysis at www.usanpn.org/results/visualizations. Participants in Nature's Notebook, who include both professional and volunteer scientists, follow vetted protocols that employ phenological "status" monitoring rather than "event" monitoring: when sampling, observers indicate the status of each phenophase (e.g., "breaking leaf buds" or "active individuals"). This approach has a number of advantages over event monitoring (including estimation of error, estimation of effort, "negative" or "absence" data, capture of multiple events and phenophase duration) and is especially well-suited for integrated multi-taxa monitoring. Further, protocols and a user interface to facilitate the description of development or abundance data (e.g., tree canopy development, animal abundance) create a robust ecological dataset. We demonstrate several types of questions that can be addressed with this observing

  3. Consumption of a Bifidobacterium bifidum Strain for 4 Weeks Modulates Dominant Intestinal Bacterial Taxa and Fecal Butyrate in Healthy Adults

    PubMed Central

    Gargari, Giorgio; Taverniti, Valentina; Balzaretti, Silvia; Ferrario, Chiara; Gardana, Claudio; Simonetti, Paolo

    2016-01-01

    ABSTRACT Modulation of the intestinal microbial ecosystem (IME) is a useful target to establish probiotic efficacy in a healthy population. We conducted a randomized, double-blind, crossover, and placebo-controlled intervention study to determine the impact of Bifidobacterium bifidum strain Bb on the IME of adult healthy volunteers of both sexes. High-throughput 16S rRNA gene sequencing was used to characterize the fecal microbiota before and after 4 weeks of daily probiotic cell consumption. The intake of approximately one billion live B. bifidum cells affected the relative abundance of dominant taxa in the fecal microbiota and modulated fecal butyrate levels. Specifically, Prevotellaceae (P = 0.041) and Prevotella (P = 0.034) were significantly decreased, whereas Ruminococcaceae (P = 0.039) and Rikenellaceae (P = 0.010) were significantly increased. We also observed that the probiotic intervention modulated the fecal concentrations of butyrate in a manner dependent on the initial levels of short-chain fatty acids (SCFAs). In conclusion, our study demonstrates that a single daily administration of Bifidobacterium bifidum strain Bb can significantly modify the IME in healthy (not diseased) adults. These findings demonstrate the need to reassess the notion that probiotics do not influence the complex and stable IME of a healthy individual. IMPORTANCE Foods and supplements claimed to contain health-promoting probiotic microorganisms are everywhere these days and mainly intended for consumption by healthy people. However, it is still debated what actual effects probiotic products may have on the healthy population. In this study, we report the results of an intervention trial aimed at assessing the modifications induced in the intestinal microbial ecosystem of healthy adults from the consumption of a probiotic product. Our results demonstrate that the introduction of a probiotic product in the dietary habits of healthy people may significantly modify dominant taxa of

  4. Differentiation in the Trochulus hispidus complex and related taxa (Pulmonata: Hygromiidae): morphology, ecology and their relation to phylogeography.

    PubMed

    Duda, Michael; Kruckenhauser, Luise; Sattmann, Helmut; Harl, Josef; Jaksch, Katharina; Haring, Elisabeth

    2014-11-01

    In this study we investigated the morphology and ecology of representatives of the taxonomically ambiguous genus Trochulus. The main focus was on the T. hispidus complex, which comprises several genetically highly divergent mitochondrial clades, as determined in a parallel molecular genetic study. We analysed shell morphology and anatomical traits and asked whether the clades are differentiated in these characters. In addition, the related species T. oreinos and T. striolatus were investigated and compared with the T. hispidus complex. Finally, we compared the ecological requirements of the taxa. Among the genetic clades of the T. hispidus complex there was no clear morphological differentiation and geographic populations could not be distinguished based on their morphology. The investigated characters of the genital anatomy did not allow discrimination of any of the T. hispidus clades and were not even diagnostic for the group as a whole. The morphotype of T. sericeus is present in all clades and thus cannot be assigned to a genetic group or any specific population. Thus, our morphological data do not provide evidence that any of the mitochondrial T. hispidus clades represent separate species. Concerning interspecific delimitation, the T. hispidus complex was clearly differentiated from T. striolatus and T. oreinos by shell morphological and anatomical characters, e.g. sculpture of shell surface and details of the penis. Finally, the habitat of T. oreinos is different from those of the other two species. In contrast to the lack of correspondence between genetic and morphological differentiation within the T. hispidus complex, related species display intraspecific morphological differentiation corresponding with mitochondrial clades: within T. striolatus there was a slight morphological differentiation between the subspecies T. s. striolatus, T. s. juvavensis and T. s. danubialis. The two subspecies of T. oreinos could be discriminated by a small but consistent

  5. Bacterial Community Structure after Long-term Organic and Inorganic Fertilization Reveals Important Associations between Soil Nutrients and Specific Taxa Involved in Nutrient Transformations

    PubMed Central

    Li, Fang; Chen, Lin; Zhang, Jiabao; Yin, Jun; Huang, Shaomin

    2017-01-01

    Fertilization has a large impact on the soil microbial communities, which play pivotal roles in soil biogeochemical cycling and ecological processes. While the effects of changes in nutrient availability due to fertilization on the soil microbial communities have received considerable attention, specific microbial taxa strongly influenced by long-term organic and inorganic fertilization, their potential effects and associations with soil nutrients remain unclear. Here, we use deep 16S amplicon sequencing to investigate bacterial community characteristics in a fluvo-aquic soil treated for 24 years with inorganic fertilizers and organics (manure and straw)-inorganic fertilizers, and uncover potential links between soil nutrient parameters and specific bacterial taxa. Our results showed that combined organic-inorganic fertilization increased soil organic carbon (SOC) and total nitrogen (TN) contents and altered bacterial community composition, while inorganic fertilization had little impact on soil nutrients and bacterial community composition. SOC and TN emerged as the major determinants of community composition. The abundances of specific taxa, especially Arenimonas, Gemmatimonas, and an unclassified member of Xanthomonadaceae, were substantially increased by organic-inorganic amendments rather than inorganic amendments only. A co-occurrence based network analysis demonstrated that SOC and TN had strong positive associations with some taxa (Gemmatimonas and the members of Acidobacteria subgroup 6, Myxococcales, Betaproteobacteria, and Bacteroidetes), and Gemmatimonas, Flavobacterium, and an unclassified member of Verrucomicrobia were identified as the keystone taxa. These specific taxa identified above are implicated in the decomposition of complex organic matters and soil carbon, nitrogen, and phosphorus transformations. The present work strengthens our current understanding of the soil microbial community structure and functions under long-term fertilization

  6. Diel, Seasonal, and Interannual Variability in Abundance of Major Mesozooplankton Taxa in the Sargasso Sea as Related to Changing Environmental Parameters

    NASA Astrophysics Data System (ADS)

    Ivory, J.; Steinberg, D. K.; Latour, R. J.

    2016-02-01

    Temporal changes in mesozooplankton community structure affect planktonic food web interactions and biogeochemical cycling. Epipelagic mesozooplankton biomass in the Sargasso Sea has increased over the last two decades, with a related increase in zooplankton-mediated carbon export. Unknown, however, is what are the patterns and variability at different temporal scales (diel, seasonal, and interannual) in abundance of each major zooplankton taxon, and how do these patterns relate to physical and other environmental changes? We enumerated major taxa of mesozooplankton collected from monthly day and night net tows in the epipelagic zone at the Bermuda Atlantic Time-series Study (BATS) site in the Sargasso Sea from 1999 to 2010. Abundances of each taxon were determined using a ZooScan optical imaging system and microscopy. Generalized Linear Models (GLMs) were used to determine what environmental parameters best explain abundance of major taxa. We used annual averages to consider broader patterns. Zooplankton taxa with the most pronounced diel vertical migration (i.e., night:day ratio, N:D, >>1) included Limacina spp. pteropods (N:D=2.02), euphausiids (1.93), calanoid copepods (1.34), and heteropods (1.34). Taxa with a pronounced spring abundance peak included chaetognaths, larvaceans, and Limacina spp. pteropods, while harpacticoid copepods peaked in late summer, and calanoid copepods in both spring and summer. Environmental variables affecting abundance differed amongst taxa. For example, calanoid copepod density was highly influenced by the abundance of a major predator- chaetognaths. Multi-year densities of calanoid copepods and ostracods both increased with increasing Water Column Stratification Index and the Atlantic Multidecadal Oscillation (AMO) index, indicating warmer sea surface temperatures are favorable for these taxa. We discuss how these temporal patterns at different scales help predict effects of global climate change on the zooplankton community.

  7. Linking autotrophic activity in environmental samples with specific bacterial taxa by detection of 13C-labelled fatty acids.

    PubMed

    Knief, Claudia; Altendorf, Karlheinz; Lipski, André

    2003-11-01

    A method for the detection of physiologically active autotrophic bacteria in complex microbial communities was developed based on labelling with the stable isotope 13C. Labelling of autotrophic nitrifying, sulphur-oxidizing and iron-oxidizing populations was performed in situ by incubation with NaH[13C]O3. Incorporated label into fatty acid methyl esters (FAMEs) was detected and quantified using gas chromatography-mass spectrometry in single ion monitoring mode. Before the analyses of different environmental samples, the protocol was evaluated in pure culture experiments. In different environmental samples a selective labelling of fatty acids demonstrated which microbial taxa were responsible for the respective chemolithoautotrophic activity. The most strongly labelled fatty acids of a sample from a sulphide treating biofilter from an animal rendering plant were cis-7-hexadecenoic acid (16:1 cis7) and 11-methyl hexadecanoic acid (16:0 11methyl), which are as-yet not known for any sulphide-oxidizing autotroph. The fatty acid labelling pattern of an experimental biotrickling filter sample supplied with dimethyl disulphide clearly indicated the presence and activity of sulphide-oxidizing bacteria of the genus Thiobacillus. For a third environmental sample from an acid mining lake sediment, the assignment of autotrophic activity to bacteria of the genus Leptospirillum but not to Acidithiobacillus could be made by this method, as the fatty acid patterns of these bacteria show clear differences.

  8. Genetic evidence for three discrete taxa of Melampsora (Pucciniales) affecting willows (Salix spp.) in New York State.

    PubMed

    Kenaley, Shawn C; Smart, Lawrence B; Hudler, George W

    2014-08-01

    Rust fungi in the genus Melampsora (Pucciniales) are the most important pathogens of shrub willows (Salix spp.) cultivated for biomass in New York State and temperate regions worldwide. The taxonomy and species identification of these fungi historically have been problematic as they are morphologically indistinguishable on willow and often have complex life histories. Melampsora of Salix in North America, therefore, have been circumscribed to the collective species Melampsora epitea Thüm. and further delineated to formae speciales by aecial host. Ribosomal DNA (rDNA) data was obtained from 75 collections/isolates of Melampsora in NY State affecting either native and cultivated Salix spp. or suspected alternate hosts. Maximum likelihood (ML), maximum parsimony (MP), and Bayesian (BI) analyses were conducted on three data partitions (individual and concatenated): complete internal transcribed spacer (ITS) and partial large subunit (LSU) rDNA sequences for all collections. Analyses of the ITS and concatenated ITS-LSU sequences revealed that Melampsora on native and cultivated willows in NY State consisted of three phylogenetically delineable taxa (phylotaxa); monophyly for each phylotaxon was strongly supported by ML, MP, and BI credibility values. Phylotaxa were also delimited phylogenetically by aecial host: Alpine currant (Ribes alpinum), eastern larch (Larix laricina), or balsam fir (Abies balsamea). Copyright © 2014 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  9. Identification of homologous, homoeologous and paralogous sequence variants in an outbreeding allopolyploid species based on comparison with progenitor taxa.

    PubMed

    Hand, Melanie L; Ponting, Rebecca C; Drayton, Michelle C; Lawless, Kahlil A; Cogan, Noel O I; Charles Brummer, E; Sawbridge, Timothy I; Spangenberg, German C; Smith, Kevin F; Forster, John W

    2008-10-01

    The combination of homologous, homoeologous and paralogous classes of sequence variation presents major challenges for SNP discovery in outbreeding allopolyploid species. Previous in vitro gene-associated SNP discovery studies in the allotetraploid forage legume white clover (Trifolium repens L.) were vulnerable to such effects, leading to prohibitive levels of attrition during SNP validation. Identification of T. occidentale and T. pallescens as the putative diploid progenitors of white clover has permitted discrimination of the different sequence variant categories. Amplicons from selected abiotic stress tolerance-related genes were obtained using mapping family parents and individuals from each diploid species. Following cloning, progenitor comparison allowed tentative assignment of individual haplotypes to one or other sub-genome, as well as to gene copies within sub-genomes. A high degree of coincidence and identity between SNPs and HSVs was observed. Close similarity was observed between the genome of T. occidentale and one white clover sub-genome, but the affinity between T. pallescens and the other sub-genome was weaker, suggesting that a currently uncharacterised taxon may be the true second progenitor. Selected validated SNPs were attributed to individual sub-genomes by assignment to and naming of homoeologous linkage groups, providing the basis for improved genetic trait-dissection studies. The approach described in this study is broadly applicable to a range of allopolyploid taxa of equivocal ancestry.

  10. Phylogenomic Dating-A Method of Constraining the Age of Microbial Taxa That Lack a Conventional Fossil Record

    NASA Astrophysics Data System (ADS)

    Blank, Carrine E.

    2009-03-01

    A phylogenomic dating approach was used to identify potential age constraints for multiple archaeal groups, many of which have no fossil, isotopic, or biomarker record. First, well-resolved phylogenetic trees were inferred with the use of multiple gene sequences obtained from whole genome sequences. Next, the ability to use oxygen as a terminal electron acceptor was coded into characters, and ancestral state reconstruction was used to identify clades with taxa that metabolize oxygen and likely had an aerobic ancestor. Next, the habitat of the ancestor was inferred. If the local presence of Cyanobacteria could be excluded from the putative ancestral habitat, then these clades would have originated after the rise in atmospheric oxygen 2.32 Ga. With this method, an upper age of 2.32 Ga (an "oxygen age constraint") is proposed for four major archaeal clades: the Sulfolobales, Thermoplasmatales, Thermoproteus neutrophilus/Pyrobaculum spp., and the Thermoproteales. It was also shown that the halophilic archaea likely had an aerobic common ancestor, yet the possibility of local oxygen oases before oxygenation of the atmosphere could not be formally rejected. Thus, an oxygen age constraint was not assessed for this group. This work suggests that many archaeal groups are not as ancient as many in the research community have previously assumed, and it provides a new method for establishing upper age constraints for major microbial groups that lack a conventional fossil record.

  11. Spatial Genetic Structure of a Symbiotic Beetle-Fungal System: Toward Multi-Taxa Integrated Landscape Genetics

    PubMed Central

    James, Patrick M. A.; Coltman, Dave W.; Murray, Brent W.; Hamelin, Richard C.; Sperling, Felix A. H.

    2011-01-01

    Spatial patterns of genetic variation in interacting species can identify shared features that are important to gene flow and can elucidate co-evolutionary relationships. We assessed concordance in spatial genetic variation between the mountain pine beetle (Dendroctonus ponderosae) and one of its fungal symbionts, Grosmanniaclavigera, in western Canada using neutral genetic markers. We examined how spatial heterogeneity affects genetic variation within beetles and fungi and developed a novel integrated landscape genetics approach to assess reciprocal genetic influences between species using constrained ordination. We also compared landscape genetic models built using Euclidean distances based on allele frequencies to traditional pair-wise Fst. Both beetles and fungi exhibited moderate levels of genetic structure over the total study area, low levels of structure in the south, and more pronounced fungal structure in the north. Beetle genetic variation was associated with geographic location while that of the fungus was not. Pinevolume and climate explained beetle genetic variation in the northern region of recent outbreak expansion. Reciprocal genetic relationships were only detectedin the south where there has been alonger history of beetle infestations. The Euclidean distance and Fst-based analyses resulted in similar models in the north and over the entire study area, but differences between methods in the south suggest that genetic distances measures should be selected based on ecological and evolutionary contexts. The integrated landscape genetics framework we present is powerful, general, and can be applied to other systems to quantify the biotic and abiotic determinants of spatial genetic variation within and among taxa. PMID:21991309

  12. Phylogenetic reappraisal of Allium subgenus Cyathophora (Amaryllidaceae) and related taxa, with a proposal of two new sections.

    PubMed

    Huang, De-Qing; Yang, Jing-Tian; Zhou, Chun-Jing; Zhou, Song-Dong; He, Xing-Jin

    2014-03-01

    The phylogeny of subgenus Cyathophora and representatives of its closely related taxa within Allium were reconstructed based on nrDNA ITS and two plastid fragments (trnL-F and rpl32-trnL). The constructed phylogenies indicated that subgenus Cyathophora was not monophyletic and to be split in three parts positioned in different clusters. Allium kingdonii was unequivocally placed within subgenus Amerallium and formed an immediate sister relationship with New World Amerallium clade, suggesting an unexpected intercontinental disjunct distribution. For another, Allium trifurcatum was firmly nested within subgenus Butomissa next to A. tuberosum and A. ramosum, but it is distinctly different morphologically from the latter by thinly leathery bulb tunics, uniovulate locule and obviously 3-cleft stigma. Based on the geographic features, morphological and molecular evidences, two new sections, Kingdonia X.J.He et D.Q.Huang for A. kingdonii and Trifurcatum X.J.He et D.Q.Huang for A. trifurcatum, were proposed. The remaining three species of subgenus Cyathophora formed a well-defined clade, and the phylogenetic relationships among them recovered were consistent with previous findings. In addition, A. weschniakowii and A. subtilissimum were proven to be a member of subgenera Rhizirideum sensu stricto (s. str.) and Cepa, respectively, rather than subgenera Cepa and Polyprason previously proposed. Section Rhizomatosa represented by A. caespitosum should be subsumed within section Caespitosoprason of subgenus Rhizirideum s. str.

  13. Functional characterization of IgA-targeted bacterial taxa from malnourished Malawian children that produce diet-dependent enteropathy

    PubMed Central

    Kau, Andrew L.; Planer, Joseph D.; Liu, Jie; Rao, Sindhuja; Yatsunenko, Tanya; Trehan, Indi; Manary, Mark J.; Liu, Ta-Chiang; Stappenbeck, Thaddeus S.; Maleta, Kenneth M.; Ashorn, Per; Dewey, Kathryn G.; Houpt, Eric R.; Hsieh, Chyi-Song; Gordon, Jeffrey I.

    2015-01-01

    To gain insights into the interrelationships among childhood undernutrition, the gut microbiota, and gut mucosal immune/barrier function, we purified bacterial strains targeted by IgA from the fecal microbiota of two cohorts of Malawian infants and children. IgA responses to several bacterial taxa, including Enterobacteriaceae, correlated with anthropometric measurements of nutritional status in longitudinal studies. The relationship between IgA responses and growth was further explained by enteropathogen burden. Gnotobiotic mouse recipients of an IgA+-bacterial consortium purified from the gut microbiota of undernourished children exhibited a diet-dependent enteropathy characterized by rapid disruption of the small intestinal and colonic epithelial barrier, weight loss and sepsis that could be prevented by administering two IgA-targeted bacterial species from a healthy microbiota. Dissection of a culture collection of 11 IgA-targeted strains from an undernourished donor, sufficient to transmit these phenotypes, disclosed that Enterobacteriaceae interacted with other consortium members to produce enteropathy. These findings indicate that bacterial targets of IgA responses have etiologic, diagnostic, and therapeutic implications for childhood undernutrition. PMID:25717097

  14. Shared Epizoic Taxa and Differences in Diatom Community Structure Between Green Turtles (Chelonia mydas) from Distant Habitats.

    PubMed

    Majewska, Roksana; de Vijver, Bart Van; Nasrolahi, Ali; Ehsanpour, Maryam; Afkhami, Majid; Bolaños, Federico; Iamunno, Franco; Santoro, Mario; De Stefano, Mario

    2017-05-06

    The first reports of diatoms growing on marine mammals date back to the early 1900s. However, only recently has direct evidence been provided for similar associations between diatoms and sea turtles. We present a comparison of diatom communities inhabiting carapaces of green turtles Chelonia mydas sampled at two remote sites located within the Indian (Iran) and Atlantic (Costa Rica) Ocean basins. Diatom observations and counts were carried out using scanning electron microscopy. Techniques involving critical point drying enabled observations of diatoms and other microepibionts still attached to sea turtle carapace and revealed specific aspects of the epizoic community structure. Species-poor, well-developed diatom communities were found on all examined sea turtles. Significant differences between the two host sea turtle populations were observed in terms of diatom abundance and their community structure (including growth form structure). A total of 12 and 22 diatom taxa were found from sea turtles in Iran and Costa Rica, respectively, and eight of these species belonging to Amphora, Chelonicola, Cocconeis, Navicula, Nitzschia and Poulinea genera were observed in samples from both locations. Potential mechanisms of diatom dispersal and the influence of the external environment, sea turtle behaviour, its life stage, and foraging and breeding habitats, as well as epibiotic bacterial flora on epizoic communities, are discussed.

  15. The Type Series of 'Sinemys' Wuerhoensis, a Problematic Turtlefrom the Lower Cretaceous of China, Includes at Least Three Taxa

    SciTech Connect

    Danilov, Igor G.; Parham, James F.

    2007-03-01

    We re-examine the type series of 'Sinemys' wuerhoensis Yeh(at least 20 specimens, including several shells and skulls on threeslabs of matrix and one isolated skull) from the Early Cretaceous TuguluGroup of China. Our study shows that the type series of 'S.'wuerhoensisis actually a chimera made up of at least three distinct taxa. Theholotype of this taxon should be assigned to the basal eucryptodire genusXinjiangchelys Yeh. As there are no characters that distinguish'S.'wuerhoensis from Xinjiangchelys species, we consider it to be a nomendubium. This new assignment of 'S.'wuerhoensis expands the temporal rangeof Xinjiangchelys from the Late Jurassic into the Early Cretaceous inAsia. The majority of the paratypes of 'S.'wuerhoensis (several shells indorsal and ventral aspect and skulls) are referred to the basaleucryptodire genus Ordosemys Brinkman and Peng. We establish a new namefor these specimens, Ordosemys brinkmania sp. nov. One additionalspecimen in the type series of 'S.'wuerhoensis, a skull, is referred tocf. Pantrionychia Joyce, Parham and Gauthier indet.

  16. Import and export fluxes of macrozooplankton are taxa- and season-dependent at Jiuduansha marsh, Yangtze River estuary

    NASA Astrophysics Data System (ADS)

    Qin, Haiming; Sheng, Qiang; Chu, Tianjiang; Wang, Sikai; Wu, Jihua

    2015-09-01

    Macrozooplankton may play important roles in influencing nutrient exchange between salt marsh and nearby estuarine ecosystems through predator-prey interactions and their transport by tidal flows. In this study, macrozooplankton transport through year-round monthly sampling was investigated in a salt marsh creek of the Yangtze River estuary. Twenty-one orders of macrozooplankton were captured. Calanoida and Decapoda were dominant and numerically comprised 59.59% and 37.59% respectively of the total captured macrozooplankton throughout the year. Decapoda mainly occurred in April, May and June. In other months, the Calanoida contributed over 90% of the total individuals. The annual Ferrari index (I) for total individual number of macrozooplankton was 0.27, which generally supports the viewpoint that salt marshes are sources of zooplankton. The salt marsh was mainly a source for decapods and mysids, possibly because of larval release in their breeding seasons. The marsh was also a source for amphipods, probably because some benthic forms became transient planktonic forms during tidal water flushing. Copepods and fish larvae exhibited net import into the salt marsh, which may result from predation from salt marsh settlers or retention in the salt marsh. Monthly Ferrari index (I) estimations revealed that the role of the salt marsh as a sink or source of macrozooplankton was time-dependent, which is related to the life history of animals. This study showed that whether the salt marsh zooplankton act as energy importers or exporters is group/taxa-dependent and time-dependent.

  17. Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy.

    PubMed

    Kau, Andrew L; Planer, Joseph D; Liu, Jie; Rao, Sindhuja; Yatsunenko, Tanya; Trehan, Indi; Manary, Mark J; Liu, Ta-Chiang; Stappenbeck, Thaddeus S; Maleta, Kenneth M; Ashorn, Per; Dewey, Kathryn G; Houpt, Eric R; Hsieh, Chyi-Song; Gordon, Jeffrey I

    2015-02-25

    To gain insights into the interrelationships among childhood undernutrition, the gut microbiota, and gut mucosal immune/barrier function, we purified bacterial strains targeted by immunoglobulin A (IgA) from the fecal microbiota of two cohorts of Malawian infants and children. IgA responses to several bacterial taxa, including Enterobacteriaceae, correlated with anthropometric measurements of nutritional status in longitudinal studies. The relationship between IgA responses and growth was further explained by enteropathogen burden. Gnotobiotic mouse recipients of an IgA(+) bacterial consortium purified from the gut microbiota of undernourished children exhibited a diet-dependent enteropathy characterized by rapid disruption of the small intestinal and colonic epithelial barrier, weight loss, and sepsis that could be prevented by administering two IgA-targeted bacterial species from a healthy microbiota. Dissection of a culture collection of 11 IgA-targeted strains from an undernourished donor, sufficient to transmit these phenotypes, disclosed that Enterobacteriaceae interacted with other consortium members to produce enteropathy. These findings indicate that bacterial targets of IgA responses have etiologic, diagnostic, and therapeutic implications for childhood undernutrition.

  18. Algal Attributes: An Autecological Classification of Algal Taxa Collected by the National Water-Quality Assessment Program

    USGS Publications Warehouse

    Porter, Stephen D.

    2008-01-01

    Algae are excellent indicators of water-quality conditions, notably nutrient and organic enrichment, and also are indicators of major ion, dissolved oxygen, and pH concentrations and stream microhabitat conditions. The autecology, or physiological optima and tolerance, of algal species for various water-quality contaminants and conditions is relatively well understood for certain groups of freshwater algae, notably diatoms. However, applications of autecological information for water-quality assessments have been limited because of challenges associated with compiling autecological literature from disparate sources, tracking name changes for a large number of algal species, and creating an autecological data base from which algal-indicator metrics can be calculated. A comprehensive summary of algal autecological attributes for North American streams and rivers does not exist. This report describes a large, digital data file containing 28,182 records for 5,939 algal taxa, generally species or variety, collected by the U.S. Geological Survey?s National Water-Quality Assessment (NAWQA) Program. The data file includes 37 algal attributes classified by over 100 algal-indicator codes or metrics that can be calculated easily with readily available software. Algal attributes include qualitative classifications based on European and North American autecological literature, and semi-quantitative, weighted-average regression approaches for estimating optima using regional and national NAWQA data. Applications of algal metrics in water-quality assessments are discussed and national quartile distributions of metric scores are shown for selected indicator metrics.

  19. Typing Candida albicans oral isolates from healthy brazilian schoolchildren using multilocus enzyme electrophoresis reveals two highly polymorphic taxa

    PubMed Central

    Boriollo, Marcelo Fabiano Gomes; Spolidorio, Denise Madalena Palomari; Barros, Letizia Monteiro; Bassi, Rodrigo Carlos; Garcia, José Antonio Dias; Costa, Ana Maria Duarte Dias; Rosa, Edvaldo Antonio Ribeiro; Höfling, José Francisco

    2011-01-01

    The genetic diversity of C. albicans oral isolates from 75 healthy schoolchildren from eight schools located in different geographic areas of Piracicaba city, São Paulo state, Brazil, was established using isoenzymes marker (Multilocus Enzyme Electrophoresis – MLEE) and cluster analysis. Patterns of monoclonal and polyclonal oral colonization by C. albicans within and between groups of schoolchildren were identified. However, significant divergence between the observed and the expected genotypic frequencies (Hardy-Weinberg equilibrium test) was not detected in the geographically adjacent groups, suggesting the hypothesis that populations of healthy schoolchildren do not correspond to the selection factor (differential survival) of strains. Two highly polymorphic and distantly genetically related taxa (A and B) were identified within the total population of yeasts, each contained subgroups (A1, A2, A3, A4, B1 and B2) and clusters of moderately related strains (from I to X), suggesting the existence of strains restricted or not to certain groups of geographically limited, healthy students. However, the coexistence of identical strains in healthy schoolchildren from the same school (geographically related) reinforces the hypothesis of oral transmission, where the sources of propagation could be explored. Furthermore, this could also be used in current and retrospective analyses of C. albicans isolated from immunocompetent and immunocompromised people, in order to detect commensal or potentially pathogenic yeast groups, predominantly in candidiasis, and in the development of strategies to prevent transmission or human propagation. PMID:24031720

  20. Spatial genetic structure of a symbiotic beetle-fungal system: toward multi-taxa integrated landscape genetics.

    PubMed

    James, Patrick M A; Coltman, Dave W; Murray, Brent W; Hamelin, Richard C; Sperling, Felix A H

    2011-01-01

    Spatial patterns of genetic variation in interacting species can identify shared features that are important to gene flow and can elucidate co-evolutionary relationships. We assessed concordance in spatial genetic variation between the mountain pine beetle (Dendroctonus ponderosae) and one of its fungal symbionts, Grosmanniaclavigera, in western Canada using neutral genetic markers. We examined how spatial heterogeneity affects genetic variation within beetles and fungi and developed a novel integrated landscape genetics approach to assess reciprocal genetic influences between species using constrained ordination. We also compared landscape genetic models built using Euclidean distances based on allele frequencies to traditional pair-wise Fst. Both beetles and fungi exhibited moderate levels of genetic structure over the total study area, low levels of structure in the south, and more pronounced fungal structure in the north. Beetle genetic variation was associated with geographic location while that of the fungus was not. Pinevolume and climate explained beetle genetic variation in the northern region of recent outbreak expansion. Reciprocal genetic relationships were only detectedin the south where there has been alonger history of beetle infestations. The Euclidean distance and Fst-based analyses resulted in similar models in the north and over the entire study area, but differences between methods in the south suggest that genetic distances measures should be selected based on ecological and evolutionary contexts. The integrated landscape genetics framework we present is powerful, general, and can be applied to other systems to quantify the biotic and abiotic determinants of spatial genetic variation within and among taxa.

  1. A proteomic approach for studying insect phylogeny: CAPA peptides of ancient insect taxa (Dictyoptera, Blattoptera) as a test case

    PubMed Central

    Roth, Steffen; Fromm, Bastian; Gäde, Gerd; Predel, Reinhard

    2009-01-01

    Background Neuropeptide ligands have to fit exactly into their respective receptors and thus the evolution of the coding regions of their genes is constrained and may be strongly conserved. As such, they may be suitable for the reconstruction of phylogenetic relationships within higher taxa. CAPA peptides of major lineages of cockroaches (Blaberidae, Blattellidae, Blattidae, Polyphagidae, Cryptocercidae) and of the termite Mastotermes darwiniensis were chosen to test the above hypothesis. The phylogenetic relationships within various groups of the taxon Dictyoptera (praying mantids, termites and cockroaches) are still highly disputed. Results Tandem mass spectrometry of neuropeptides from perisympathetic organs was used to obtain sequence data of CAPA peptides from single specimens; the data were analysed by Maximum Parsimony and Bayesian Interference. The resulting cladograms, taking 61 species into account, show a topology which is in general agreement with recent molecular and morphological phylogenetic analyses, including the recent phylogenetic arrangement placing termites within the cockroaches. When sequence data sets from other neuropeptides, viz. adipokinetic hormones and sulfakinins, were included, the general topology of the cladogram did not change but bootstrap values increased considerably. Conclusion This study represents the first comprehensive survey of neuropeptides of insects for solely phylogenetic purposes and concludes that sequences of short neuropeptides are suitable to complement molecular biological and morphological data for the reconstruction of phylogenetic relationships. PMID:19257902

  2. DNA-sequence variation among Schistosoma mekongi populations and related taxa; phylogeography and the current distribution of Asian schistosomiasis.

    PubMed

    Attwood, Stephen W; Fatih, Farrah A; Upatham, E Suchart

    2008-03-19

    Schistosomiasis in humans along the lower Mekong River has proven a persistent public health problem in the region. The causative agent is the parasite Schistosoma mekongi (Trematoda: Digenea). A new transmission focus is reported, as well as the first study of genetic variation among S. mekongi populations. The aim is to confirm the identity of the species involved at each known focus of Mekong schistosomiasis transmission, to examine historical relationships among the populations and related taxa, and to provide data for use (a priori) in further studies of the origins, radiation, and future dispersal capabilities of S. mekongi. DNA sequence data are presented for four populations of S. mekongi from Cambodia and southern Laos, three of which were distinguishable at the COI (cox1) and 12S (rrnS) mitochondrial loci sampled. A phylogeny was estimated for these populations and the other members of the Schistosoma sinensium group. The study provides new DNA sequence data for three new populations and one new locus/population combination. A Bayesian approach is used to estimate divergence dates for events within the S. sinensium group and among the S. mekongi populations. The date estimates are consistent with phylogeographical hypotheses describing a Pliocene radiation of the S. sinensium group and a mid-Pleistocene invasion of Southeast Asia by S. mekongi. The date estimates also provide Bayesian priors for future work on the evolution of S. mekongi. The public health implications of S. mekongi transmission outside the lower Mekong River are also discussed.

  3. Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders.

    PubMed

    Wood, Hannah Marie; Matzke, Nicholas J; Gillespie, Rosemary G; Griswold, Charles E

    2013-03-01

    Incorporation of fossils into biogeographic studies can have a profound effect on the conclusions that result, particularly when fossil ranges are nonoverlapping with extant ranges. This is the case in archaeid spiders, where there are known fossils from the Northern Hemisphere, yet all living members are restricted to the Southern Hemisphere. To better understand the biogeographic patterns of archaeid spiders and their palpimanoid relatives, we estimate a dated phylogeny using a relaxed clock on a combined molecular and morphological data set. Dating information is compared with treating the archaeid fossil taxa as both node calibrations and as noncontemporaneous terminal tips, both with and without additional calibration points. Estimation of ancestral biogeographic ranges is then performed, using likelihood and Bayesian methods to take into account uncertainty in phylogeny and in dating. We find that treating the fossils as terminal tips within a Bayesian framework, as opposed to dating the phylogeny based only on molecular data with the dates coming from node calibrations, removes the subjectivity involved in assigning priors, which has not been possible with previous methods. Our analyses suggest that the diversification of the northern and southern archaeid lineages was congruent with the breakup of Pangaea into Laurasia and Gondwanaland. This analysis provides a rare example, and perhaps the most strongly supported, where a dated phylogeny confirms a biogeographical hypothesis based on vicariance due to the breakup of the ancient continental plates.

  4. Iapetonudus (N. gen.) and Iapetognathus Landing, unusual Earliest Ordovician multielement conodont taxa and their utility for biostratigraphy

    USGS Publications Warehouse

    Nicoll, R.S.; Miller, J.F.; Nowlan, G.S.; Repetski, J.E.; Ethington, Raymond L.

    1999-01-01

    The Early Ordovician (Tremadocian) multielement conodont genus Iapetognathus is one of the oldest denticulate euconodont genera known. The ramiform-ramiform apparatus structure of Iapetognathus is not similar morphologically to other Late Cambrian to Earliest Ordovician denticulate multielement taxa, such as Eodentatus or Cordyloduts, because the major denticulate process has a lateral rather than a posterior orientation as it is in the other two examples. For this reason the genus is believed to have developed from the coniform-coniform apparatus Iapetonudus ibexensis (N.gen., n.sp.) through the development of the denticulate lateral processes. The two genera have a number of morphologic features in common and appear in stratigraphic succession. Iapetognathus aengensis (Lindstro??m) is redefined as a multielement taxon using topotype material and Ig. preaengensis Landing is placed in synonymy with it. Iapetognathus sprakersi, recently described by Landing in Landing and others (1996), is recognized as a multielement species and the new multielement species, Ig. fluctivagus, Ig. jilinensis and Ig. landingi n. spp. are described herein, based on type specimens from Utah (U.S.A.), Jilin (China) and Colorado (U.S.A.) respectively. Iapetonudus and Iapetognathus are important genera in defining the level of the Cambrian-Ordovician boundary. Iapetonudus is currently recognized only from Utah, Texas and Oklahoma, but Iapetognathus is cosmopolitan in its distribution.

  5. Ciliate diversity, community structure, and novel taxa in lakes of the McMurdo Dry Valleys, Antarctica.

    PubMed

    Xu, Yuan; Vick-Majors, Trista; Morgan-Kiss, Rachael; Priscu, John C; Amaral-Zettler, Linda

    2014-10-01

    We report an in-depth survey of next-generation DNA sequencing of ciliate diversity and community structure in two permanently ice-covered McMurdo Dry Valley lakes during the austral summer and autumn (November 2007 and March 2008). We tested hypotheses on the relationship between species richness and environmental conditions including environmental extremes, nutrient status, and day length. On the basis of the unique environment that exists in these high-latitude lakes, we expected that novel taxa would be present. Alpha diversity analyses showed that extreme conditions-that is, high salinity, low oxygen, and extreme changes in day length-did not impact ciliate richness; however, ciliate richness was 30% higher in samples with higher dissolved organic matter. Beta diversity analyses revealed that ciliate communities clustered by dissolved oxygen, depth, and salinity, but not by season (i.e., day length). The permutational analysis of variance test indicated that depth, dissolved oxygen, and salinity had significant influences on the ciliate community for the abundance matrices of resampled data, while lake and season were not significant. This result suggests that the vertical trends in dissolved oxygen concentration and salinity may play a critical role in structuring ciliate communities. A PCR-based strategy capitalizing on divergent eukaryotic V9 hypervariable region ribosomal RNA gene targets unveiled two new genera in these lakes. A novel taxon belonging to an unknown class most closely related to Cryptocaryon irritans was also inferred from separate gene phylogenies.

  6. Identifying Shared Genetic Structure Patterns among Pacific Northwest Forest Taxa: Insights from Use of Visualization Tools and Computer Simulations

    PubMed Central

    Miller, Mark P.; Haig, Susan M.

    2010-01-01

    Background Identifying causal relationships in phylogeographic and landscape genetic investigations is notoriously difficult, but can be facilitated by use of multispecies comparisons. Methodology/Principal Findings We used data visualizations to identify common spatial patterns within single lineages of four taxa inhabiting Pacific Northwest forests (northern spotted owl: Strix occidentalis caurina; red tree vole: Arborimus longicaudus; southern torrent salamander: Rhyacotriton variegatus; and western white pine: Pinus monticola). Visualizations suggested that, despite occupying the same geographical region and habitats, species responded differently to prevailing historical processes. S. o. caurina and P. monticola demonstrated directional patterns of spatial genetic structure where genetic distances and diversity were greater in southern versus northern locales. A. longicaudus and R. variegatus displayed opposite patterns where genetic distances were greater in northern versus southern regions. Statistical analyses of directional patterns subsequently confirmed observations from visualizations. Based upon regional climatological history, we hypothesized that observed latitudinal patterns may have been produced by range expansions. Subsequent computer simulations confirmed that directional patterns can be produced by expansion events. Conclusions/Significance We discuss phylogeographic hypotheses regarding historical processes that may have produced observed patterns. Inferential methods used here may become increasingly powerful as detailed simulations of organisms and historical scenarios become plausible. We further suggest that inter-specific comparisons of historical patterns take place prior to drawing conclusions regarding effects of current anthropogenic change within landscapes. PMID:21060824

  7. Identifying shared genetic structure patterns among Pacific Northwest forest taxa: insights from use of visualization tools and computer simulations.

    PubMed

    Miller, Mark P; Haig, Susan M

    2010-10-29

    Identifying causal relationships in phylogeographic and landscape genetic investigations is notoriously difficult, but can be facilitated by use of multispecies comparisons. We used data visualizations to identify common spatial patterns within single lineages of four taxa inhabiting Pacific Northwest forests (northern spotted owl: Strix occidentalis caurina; red tree vole: Arborimus longicaudus; southern torrent salamander: Rhyacotriton variegatus; and western white pine: Pinus monticola). Visualizations suggested that, despite occupying the same geographical region and habitats, species responded differently to prevailing historical processes. S. o. caurina and P. monticola demonstrated directional patterns of spatial genetic structure where genetic distances and diversity were greater in southern versus northern locales. A. longicaudus and R. variegatus displayed opposite patterns where genetic distances were greater in northern versus southern regions. Statistical analyses of directional patterns subsequently confirmed observations from visualizations. Based upon regional climatological history, we hypothesized that observed latitudinal patterns may have been produced by range expansions. Subsequent computer simulations confirmed that directional patterns can be produced by expansion events. We discuss phylogeographic hypotheses regarding historical processes that may have produced observed patterns. Inferential methods used here may become increasingly powerful as detailed simulations of organisms and historical scenarios become plausible. We further suggest that inter-specific comparisons of historical patterns take place prior to drawing conclusions regarding effects of current anthropogenic change within landscapes.