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Sample records for related genera inferred

  1. Sphingomonas and Related Genera

    SciTech Connect

    Balkwill, David L.; Fredrickson, Jim K.; Romine, Margaret F.

    2003-12-31

    INTRODUCTION-The genus Sphingomonas was defined by Yabuuchi et al. (1990) as a group of Gram-negative, rod-shaped, chemoheterotrophic, strictly aerobic bacteria that possess ubiquinone 10 as the major respiratory quinone, contain glycosphingolipids (GSLs) instead of lipopolysaccharide in their cell envelopes, and typically produce yellow-pigmented colonies. By 2001, the genus included more than 20 species that were quite diverse in terms of their phylogenetic, ecological, and physiological properties. As a result, Takeuchi et al. (2001) subdivided Sphingomonas into four genera: Sphingomonas, Sphingobium, Novosphingobium and Sphingopyxis...

  2. Multilocus phylogenetic inference in subfamily Chlorogaloideae and related genera of Agavaceae - informing questions in taxonomy at multiple ranks.

    PubMed

    Archibald, Jenny K; Kephart, Susan R; Theiss, Kathryn E; Petrosky, Anna L; Culley, Theresa M

    2015-03-01

    A series of taxonomic questions at the subfamilial, generic, and intrageneric levels have remained within subfamily Chlorogaloideae s.s. (comprising Camassia, Chlorogalum, Hastingsia, and Schoenolirion) and relatives in Agavaceae. We present the first phylogenetic hypotheses focused on Chlorogaloideae that are based on multiple independent loci and include a wide sampling of outgroups across Agavaceae. In addition to chloroplast regions ndhF and trnL-trnF, we used nrDNA ITS for phylogenetic inference. Incomplete concerted evolution of the latter is indicated by intra-individual site polymorphisms for nearly half of the individuals. Comparisons of four coding and analysis methods for these characters indicate that the region remains phylogenetically informative. Our results confirm that Chlorogaloideae s.s. is not monophyletic, due to the close relationship of Schoenolirion with Hesperaloe and Hesperoyucca, as well as the likely sister relationship between Hesperocallis and core Chlorogaloideae (Camassia, Chlorogalum, and Hastingsia). Chlorogalum is also not monophyletic, being divided with strong support into vespertine and diurnal clades. This study produced the first phylogenetic hypotheses across Hesperaloe, allowing initial tests of several taxonomic disagreements within this genus. Our results reveal the lack of cohesion of H. funifera, indicating that H. funifera ssp. funifera may be more closely related to H. campanulata than to H. funifera ssp. chiangii (=H. chiangii). With potential gene flow between many members of Hesperaloe and a possible hybrid origin for H. campanulata, the genetic relationships within this genus appear complex. Further population-level investigation of many of the taxa in Chlorogaloideae s.l. would benefit our understanding of the evolution and taxonomy of these groups; Camassia and Hastingsia are the current focus of ongoing study.

  3. Phylogenetic relationship among genera of Polymorphidae (Acanthocephala), inferred from nuclear and mitochondrial gene sequences.

    PubMed

    García-Varela, Martín; Pérez-Ponce de León, Gerardo; Aznar, Francisco J; Nadler, Steven A

    2013-08-01

    Acanthocephalans of the family Polymorphidae Meyer, 1931 are obligate endoparasites with complex life cycles. These worms use vertebrates (marine mammals, fish-eating birds and waterfowl) as definitive hosts and invertebrates (amphipods, decapods and euphausiids) as intermediate hosts to complete their life cycle. Polymorphidae has a wordwide distribution, containing 12 genera, with approximately 127 species. The family is diagnosed by having a spinose trunk, bulbose proboscis, double-walled proboscis receptacle, and usually four to eight tubular cement glands. To conduct a phylogenetic analysis, in the current study sequences of the small (18S) and large-subunit (28S) ribosomal RNA, and cytochrome c oxidase subunit 1 (cox 1) were generated for 27 taxa representing 10 of 12 genera of Polymorphidae, plus three additional species of acanthocephalans that were used as outgroups. Maximum likelihood (ML), maximum parsimony (MP), and Bayesian analyses were conducted on a combined nuclear rRNA (18S+28S) data set and on a concatenated dataset of nuclear plus one mitochondrial gene (18S+28S+cox 1). Phylogenetic analyses inferred with the concatenated dataset of three genes support the monophyly of nine genera (Andracantha, Corynosoma, Bolbosoma, Profilicollis, Pseudocorynosoma, Southwellina, Arhythmorhynchus, Hexaglandula and Ibirhynchus). However, the four sampled species of Polymorphus were nested within several clades, indicating that these species do not share a common ancestor, requiring further taxonomic revision using phylogenetic systematics, and reexamination of morphological and ecological data. By mapping definitive and intermediate host association onto the resulting cladogram, we observe that aquatic birds were the ancestral definitive hosts for the family with a secondary colonization and diversification to marine mammals. Whereas amphipods were ancestral intermediate hosts and that the association with decapods represent episodes of secondary colonization

  4. New genera of RNA viruses in subtropical seawater, inferred from polymerase gene sequences.

    PubMed

    Culley, Alexander I; Steward, Grieg F

    2007-09-01

    Viruses are an integral component of the marine food web, contributing to the disease and mortality of essentially every type of marine life, yet the diversity of viruses in the sea, especially those with RNA genomes, remains very poorly characterized. Isolates of RNA-containing viruses that infect marine plankton are still rare, and the only cultivation-independent surveys of RNA viral diversity reported so far were conducted for temperate coastal waters of British Columbia. Here, we report on our improvements to a previously used protocol to investigate the diversity of marine picorna-like viruses and our results from applying this protocol in subtropical waters. The original protocol was simplified by using direct filtration, rather than tangential flow filtration, to harvest viruses from seawater, and new degenerate primers were designed to amplify a fragment of the RNA-dependent RNA polymerase gene by reverse transcription-PCR from RNA extracted from the filters. Whereas the original protocol was unsuccessful in a preliminary test, the new protocol resulted in amplification of picorna-like virus sequences in every sample of subtropical and temperate coastal seawater assayed. These polymerase sequences formed a diverse, but monophyletic cluster along with other sequences amplified previously from seawater and sequences from isolates infecting marine protists. Phylogenetic analysis suggested that our sequences represent at least five new genera and 24 new species of RNA viruses. These results contribute to our understanding of RNA virus diversity and suggest that picorna-like viruses are a source of mortality for a wide variety of marine protists.

  5. Quantitative analysis of oxyresveratrol in different plant parts of Morus species and related Genera by HPTLC

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Four aromatic compounds; oxyresveratrol (1), mulberroside A (2), cudraflavone C (3) and kuwanone J (4) were isolated from the stems of Morus rubra L. The quantitative determination of oxyresveratrol from M. rubra L., M. alba L. and related genera by high performance thin layer chromatography (HPTLC)...

  6. Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae.

    PubMed

    Normand, P; Orso, S; Cournoyer, B; Jeannin, P; Chapelon, C; Dawson, J; Evtushenko, L; Misra, A K

    1996-01-01

    The members of the actinomycete genus Frankia are nitrogen-fixing symbionts of may species of woody dicotyledonous plants belonging to eight families. Several strains isolated from diverse actinorhizal plants growing in different geographical areas were used in this study. The phylogenetic relationships of these organisms and uncharacterized microsymbionts that are recalcitrant to isolation in pure culture were determined by comparing complete 16S ribosomal DNA sequences. The resulting phylogenetic tree revealed that there was greater diversity among the Alnus-infective strains than among the strains that infect other host plants. The four main subdivisions of the genus Frankia revealed by this phylogenetic analysis are (i) a very large group comprising Frankia alni and related organisms (including Alnus rugosa Sp+ microsymbionts that are seldom isolated in pure culture), to which Casuarina-infective strains, a Myrica nagi microsymbiont, and other effective Alnus-infective strains are related; (ii) unisolated microsymbionts of Dryas, Coriaria, and Datisca species; (iii) Elaeagnus-infective strains; and (iv) "atypical" strains (a group which includes an Alnus-infective, non-nitrogen-fixing strain). Taxa that are related to this well-defined, coherent Frankia cluster are the genera Geodermatophilus, "Blastococcus," Sporichthya, Acidothermus, and Actinoplanes. However, the two genera whose members have multilocular sporangia (the genera Frankia and Geodermatophilus) did not form a coherent group. For this reason, we propose that the family Frankiaceae should be emended so that the genera Geodermatophilus and "Blastococcus" are excluded and only the genus Frankia is retained. PMID:8573482

  7. A plastid gene phylogeny of the non-photosynthetic parasitic Orobanche (Orobanchaceae) and related genera

    USGS Publications Warehouse

    Park, J.-M.; Manen, J.-F.; Colwell, A.E.; Schneeweiss, G.M.

    2008-01-01

    The phylogenetic relationships of the non-photosynthetic Orobanche sensu lato (Orobanchaceae), which includes some of the economically most important parasitic weeds, remain insufficiently understood and controversial. This concerns both the phylogenetic relationships within the genus, in particular its monophyly or lack thereof, and the relationships to other holoparasitic genera such as Cistanche or Conopholis. Here we present the first comprehensive phylogenetic study of this group based on a region from the plastid genome (rps2 gene). Although substitution rates appear to be elevated compared to the photosynthetic members of Orobanchaceae, relationships among the major lineages Cistanche, Conopholis plus Epifagus, Boschniakia rossica (Cham. & Schltdl.) B. Fedtsch., B. himalaica Hook. f. & Thomson, B. hookeri Walp. plus B. strobilacea A. Gray, and Orobanche s. l. remain unresolved. Resolution within Orobanche, however, is much better. In agreement with morphological, cytological and other molecular phylogenetic evidence, five lineages, corresponding to the four traditionally recognised sections (Gymnocaulis, Myzorrhiza, Orobanche, Trionychon) and O. latisquama Reut. ex Boiss. (of sect. Orobanche), can be distinguished. A combined analysis of plastid rps2 and nuclear ITS sequences of the holoparasitic genera results in more resolved and better supported trees, although the relationships among Orobanche s. l., Cistanche, and the clade including the remaining genera is unresolved. Therefore, rps2 is a marker from the plastid genome that is well-suited to be used in combination with other already established nuclear markers for resolving generic relationships of Orobanche and related genera. ?? 2008 The Botanical Society of Japan and Springer.

  8. Relationships of cucumbers and melons unraveled: molecular phylogenetics of Cucumis and related genera (Benincaseae, Cucurbitaceae).

    PubMed

    Ghebretinsae, Amanuel G; Thulin, Mats; Barber, Janet C

    2007-07-01

    Cucumis (Cucurbitaceae) comprises 33 species of annuals and perennials with a major native center of diversity in tropical and southern Africa. The genus includes some economically important and widely grown vegetables such as cucumbers and melons. Monophyly of the genus has been disputed in previous studies, but with only limited sampling. Relationships within Cucumis are thus poorly understood; moreover, the validity of the closely related genera has not been thoroughly tested. The present study was undertaken to test the monophyly of Cucumis and several closely related genera, to test sectional circumscriptions within Cucumis, and to understand the biogeographical history of the genus. We sequenced the nuclear ITS and plastid trnS-trnG regions for 40 ingroup and three outgroup taxa, representing all recognized subgenera and sections. Parsimony, maximum likelihood, and Bayesian analyses found Cucumella, Oreosyce, Mukia, Myrmecosicyos, and Dicaelospermum nested within Cucumis. The clades recovered within the Cucumis complex in some instances represent the first phylogenetically derived hypothesis of relationships, whereas others correspond to previous subgeneric and sectional classifications. At least four introductions from Africa to Asia, as well as one reintroduction to Africa, are suggested within the Cucumis complex. Cucumis sativus (cucumber) is strongly supported as sister to the eastern Asian C. hystrix, whereas C. melo (melon) is strongly supported as sister to C. sagittatus in southern Africa.

  9. Systematic relations among Philornis Meinert, Passeromyia Rodhain & Villeneuve and allied genera (Diptera, Muscidae).

    PubMed

    Couri, M S; Carvalho, C J

    2003-05-01

    Passeromyia Rodhain & Villeneuve and Philornis Meinert are the only known Muscidae whose larvae are parasites of birds. Passeromyia is known from the Old World and Philornis from the New World. Opinions on the relations between these two genera and their systematic positions among the Muscidae have varied. This survey aims to clear the discussion on the relations of Passeromyia, Philornis, and of some allied genera and give an overview of the classification of the Muscidae based on cladistic methodology. Thirty-two terminal taxa (2 of them outgroups) were analysed based on 54 characters. The cladistic analysis, carried out using Hennig86, resulted in 1 minimal tree (length 373), with a consistency index of 71 and a retention index of 85. Philornis and Passeromyia belong to a monophyletic group, supported by a synapomorphy, the presence of a cocoon, enclosing the pupa. The phylogenetic relationships found in this group are: (Muscina (Philornis (Phaonina ((Fraserella, Passeromyia) (Synthesiomyia (Calliphoroides, Reinwardtia)))))). Other probable monophyletic muscid groups, like Muscinae (with Stomoxyini and Muscini) and Coenosiinae (with Limnophorini and Coenosiini) are also discussed. Phylogenetic patterns within Reinwardtinae and Dichaetomyiinae could be explained by a Gondwana distribution.

  10. Chromosome numbers and karyotype evolution in holoparasitic Orobanche (Orobanchaceae) and related genera

    USGS Publications Warehouse

    Schneeweiss, G.M.; Palomeque, T.; Colwell, A.E.; Weiss-Schneeweiss, H.

    2004-01-01

    Chromosome numbers and karyotypes of species of Orobanche, Cistanche, and Diphelypaea (Orobanchaceae) were investigated, and 108 chromosome counts of 53 taxa, 19 counted for the first time, are presented with a thorough compilation of previously published data. Additionally, karyotypes of representatives of these genera, including Orobanche sects. Orobanche and Trionychon, are reported. Cistanche (x = 20) has large meta- to submetacentric chromosomes, while those of Diphelypaea (x = 19) are medium-sized submeta-to acrocentrics. Within three analyzed sections of Orobanche, sects. Myzorrhiza (x = 24) and Trionychon (x = 12) possess medium-sized submeta- to acrocentrics, while sect. Orobanche (x = 19) has small, mostly meta- to submetacentric, chromosomes. Polyploidy is unevenly distributed in Orobanche and restricted to a few lineages, e.g., O. sect. Myzorrhiza or Orobanche gracilis and its relatives (sect. Orobanche). The distribution of basic chromosome numbers supports the groups found by molecular phylogenetic analyses: Cistanche has x = 20, the Orobanche-group (Orobanche sect. Orobanche, Diphelypaea) has x = 19, and the Phelipanche-group (Orobanche sects. Gymnocaulis, Myzorrhiza, Trionychon) has x = 12, 24. A model of chromosome number evolution in Orobanche and related genera is presented: from two ancestral base numbers, xh = 5 and xh = 6, independent polyploidizations led to x = 20 (Cistanche) and (after dysploidization) x = 19 (Orobanche-group) and to x = 12 and x = 24 (Phelipanche-group), respectively.

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

    PubMed Central

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

    2010-01-01

    Fungal taxonomists routinely encounter problems when dealing with asexual fungal species due to poly- and paraphyletic generic phylogenies, and unclear species boundaries. These problems are aptly illustrated in the genus Phoma. This phytopathologically significant fungal genus is currently subdivided into nine sections which are mainly based on a single or just a few morphological characters. However, this subdivision is ambiguous as several of the section-specific characters can occur within a single species. In addition, many teleomorph genera have been linked to Phoma, three of which are recognised here. In this study it is attempted to delineate generic boundaries, and to come to a generic circumscription which is more correct from an evolutionary point of view by means of multilocus sequence typing. Therefore, multiple analyses were conducted utilising sequences obtained from 28S nrDNA (Large Subunit - LSU), 18S nrDNA (Small Subunit - SSU), the Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS), and part of the β-tubulin (TUB) gene region. A total of 324 strains were included in the analyses of which most belonged to Phoma taxa, whilst 54 to related pleosporalean fungi. In total, 206 taxa were investigated, of which 159 are known to have affinities to Phoma. The phylogenetic analysis revealed that the current Boeremaean subdivision is incorrect from an evolutionary point of view, revealing the genus to be highly polyphyletic. Phoma species are retrieved in six distinct clades within the Pleosporales, and appear to reside in different families. The majority of the species, however, including the generic type, clustered in a recently established family, Didymellaceae. In the second part of this study, the phylogenetic variation of the species and varieties in this clade was further assessed. Next to the genus Didymella, which is considered to be the sole teleomorph of Phoma s. str., we also retrieved taxa belonging to the teleomorph genera

  12. A molecular phylogeny of Acronychia, Euodia, Melicope and relatives (Rutaceae) reveals polyphyletic genera and key innovations for species richness.

    PubMed

    Appelhans, Marc S; Wen, Jun; Wagner, Warren L

    2014-10-01

    We present the first detailed phylogenetic study of the genus Melicope, the largest genus of the Citrus family (Rutaceae). The phylogenetic analysis sampled about 50% of the 235 accepted species of Melicope as well as representatives of 26 related genera, most notably Acronychia and Euodia. The results based on five plastid and nuclear markers have revealed that Acronychia, Euodia and Melicope are each not monophyletic in their current circumscriptions and that several small genera mainly from Australia and New Caledonia need to be merged with one of the three genera to ensure monophyly at the generic level. The phylogenetic position of the drupaceous Acronychia in relation to Melicope, which has capsular or follicular fruits, remains unclear and Acronychia might be a separate genus or a part of Melicope. The seed coats of Melicope, Acronychia and related genera show adaptations to bird-dispersal, which might be regarded as key innovations for species radiations. Euodia and its relatives, which lack these adaptations, include only about 20 species while the Melicope-Acronychia group consists of about 340 species. The drupaceous genera Comptonella, Dutaillyea, Picrella and Sarcomelicope are nested within Melicope and need to be merged with Melicope. The expanded genus is a prime example of the artificial classification system of Engler, who defined Rutaceous subfamilies mainly based on gynoecial and fruit characters. PMID:24971739

  13. Resistance of Citrus and Related Genera to Diaphorina citri Kuwayama (Hemiptera: Liviidae).

    PubMed

    Borgoni, P C; Vendramim, J D; Lourencão, A L; Machado, M A

    2014-10-01

    The present study was developed to evaluate the resistance of the following genotypes of Citrus and related genera to this pest: 'Pera,' 'Natal', and 'Washington Navel' oranges (Citrus sinensis), 'Marsh Seedless' grapefruit (Citrus paradisi), hardy orange 'Rubidoux' (Poncirus trifoliata), kumquat (Fortunella margarita Swingle), citrumelo 'Swingle' (C. paradisi x P. trifoliata), and citrange 'Troyer' (P. trifoliata x C. sinensis). The experiments were performed in greenhouses with plants grafted onto 'Rangpur' lime (Citrus limonia) and placed individually in voile cages. The preference for oviposition in a no-choice test, and the effect of genotype were evaluated. The egg-adult cycle was monitored to determine the effect of genotype on the biology of the insect. Poncirus 'Rubidoux' was the least preferred genotype for oviposition; reduced number of eggs was also found to occur on citrange 'Troyer', and 'Marsh Seedless' was the genotype with the most eggs. No significant variation in the duration of the embryonic period was observed; however, a difference in the viability of eggs was found, with the lowest egg viabilities on 'Swingle.' Kumquat and 'Marsh Seedless' genotypes were correlated with increased durations of the nymphal phase, however, there was no difference in the survival of this phase. Fecundity of females on 'Troyer', 'Swingle', and kumquat was reduced. Considering all of the evaluated parameters, it was concluded that cultivars of sweet orange are the most susceptible genotypes to Diaphorina citri. Regarding oviposition, P. trifoliata 'Rubidoux' showed resistance of the antixenosis type.

  14. Resistance of Citrus and Related Genera to Diaphorina citri Kuwayama (Hemiptera: Liviidae).

    PubMed

    Borgoni, P C; Vendramim, J D; Lourencão, A L; Machado, M A

    2014-10-01

    The present study was developed to evaluate the resistance of the following genotypes of Citrus and related genera to this pest: 'Pera,' 'Natal', and 'Washington Navel' oranges (Citrus sinensis), 'Marsh Seedless' grapefruit (Citrus paradisi), hardy orange 'Rubidoux' (Poncirus trifoliata), kumquat (Fortunella margarita Swingle), citrumelo 'Swingle' (C. paradisi x P. trifoliata), and citrange 'Troyer' (P. trifoliata x C. sinensis). The experiments were performed in greenhouses with plants grafted onto 'Rangpur' lime (Citrus limonia) and placed individually in voile cages. The preference for oviposition in a no-choice test, and the effect of genotype were evaluated. The egg-adult cycle was monitored to determine the effect of genotype on the biology of the insect. Poncirus 'Rubidoux' was the least preferred genotype for oviposition; reduced number of eggs was also found to occur on citrange 'Troyer', and 'Marsh Seedless' was the genotype with the most eggs. No significant variation in the duration of the embryonic period was observed; however, a difference in the viability of eggs was found, with the lowest egg viabilities on 'Swingle.' Kumquat and 'Marsh Seedless' genotypes were correlated with increased durations of the nymphal phase, however, there was no difference in the survival of this phase. Fecundity of females on 'Troyer', 'Swingle', and kumquat was reduced. Considering all of the evaluated parameters, it was concluded that cultivars of sweet orange are the most susceptible genotypes to Diaphorina citri. Regarding oviposition, P. trifoliata 'Rubidoux' showed resistance of the antixenosis type. PMID:27193957

  15. Relationships in Ananas and other related genera using chloroplast DNA restriction site variation.

    PubMed

    Duval, M F; Buso, G S C; Ferreira, F R; Noyer, J L; Coppens d'Eeckenbrugge, G; Hamon, P; Ferreira, M E

    2003-12-01

    Chloroplast DNA (cpDNA) diversity was examined using PCR-RFLP to study phylogenetic relationships in Ananas and related genera. One hundred fifteen accessions representing the seven Ananas species and seven other Bromelioideae including the neighboring monospecific genus Pseudananas, two Pitcairnioideae, and one Tillandsioideae were included in the study. Eight primers designed from cpDNA were used for generating fragments. Restriction by 18 endonucleases generated 255 variable fragments. Dissimilarities were calculated from the resulting matrix using the Sokal and Michener index and the neighbor-joining method was used to reconstruct the diversity tree. Phylogenetic reconstruction was attempted using Wagner parsimony. Phenetic and cladistic analyses gave consistent results. They confirm the basal position of Bromelia in the Bromelioideae. Ananas and Pseudananas form a monophyletic group, with three strongly supported sub-groups, two of which are geographically consistent. The majority of Ananas parguazensis accessions constitute a northern group restricted to the Rio Negro and Orinoco basins in Brazil. The tetraploid Pseudananas sagenarius joins the diploid Ananas fritzmuelleri to constitute a southern group. The third and largest group, which includes all remaining species plus some accessions of A. parguazensis and intermediate phenotypes, is the most widespread and its distribution overlaps those of the northern and southern groups. Ananas ananassoides is dominant in this sub-group and highly variable. Its close relationship to all cultivated species supports the hypothesis that this species is the wild ancestor of the domesticated pineapple. The data indicate that gene flow is common within this group and scarcer with both the first and second groups. Comparison of cpDNA data with published genomic DNA data point to the hybrid origin of Ananas bracteatus and support the autopolyploidy of Pseudananas. The Ananas-Pseudananas group structure and distribution are

  16. Inferring the relative resilience of alternative states

    USGS Publications Warehouse

    Angeler, David G.; Allen, Craig R.; Rojo, Carmen; Alvarez-Cobelas, Miguel; Rodrigo, Maria A.; Sanchez-Carrillo, Salvador

    2013-01-01

    Ecological systems may occur in alternative states that differ in ecological structures, functions and processes. Resilience is the measure of disturbance an ecological system can absorb before changing states. However, how the intrinsic structures and processes of systems that characterize their states affects their resilience remains unclear. We analyzed time series of phytoplankton communities at three sites in a floodplain in central Spain to assess the dominant frequencies or “temporal scales” in community dynamics and compared the patterns between a wet and a dry alternative state. The identified frequencies and cross-scale structures are expected to arise from positive feedbacks that are thought to reinforce processes in alternative states of ecological systems and regulate emergent phenomena such as resilience. Our analyses show a higher species richness and diversity but lower evenness in the dry state. Time series modeling revealed a decrease in the importance of short-term variability in the communities, suggesting that community dynamics slowed down in the dry relative to the wet state. The number of temporal scales at which community dynamics manifested, and the explanatory power of time series models, was lower in the dry state. The higher diversity, reduced number of temporal scales and the lower explanatory power of time series models suggest that species dynamics tended to be more stochastic in the dry state. From a resilience perspective our results highlight a paradox: increasing species richness may not necessarily enhance resilience. The loss of cross-scale structure (i.e. the lower number of temporal scales) in community dynamics across sites suggests that resilience erodes during drought. Phytoplankton communities in the dry state are therefore likely less resilient than in the wet state. Our case study demonstrates the potential of time series modeling to assess attributes that mediate resilience. The approach is useful for assessing

  17. Inferring the relative resilience of alternative states.

    PubMed

    Angeler, David G; Allen, Craig R; Rojo, Carmen; Alvarez-Cobelas, Miguel; Rodrigo, María A; Sánchez-Carrillo, Salvador

    2013-01-01

    Ecological systems may occur in alternative states that differ in ecological structures, functions and processes. Resilience is the measure of disturbance an ecological system can absorb before changing states. However, how the intrinsic structures and processes of systems that characterize their states affects their resilience remains unclear. We analyzed time series of phytoplankton communities at three sites in a floodplain in central Spain to assess the dominant frequencies or "temporal scales" in community dynamics and compared the patterns between a wet and a dry alternative state. The identified frequencies and cross-scale structures are expected to arise from positive feedbacks that are thought to reinforce processes in alternative states of ecological systems and regulate emergent phenomena such as resilience. Our analyses show a higher species richness and diversity but lower evenness in the dry state. Time series modeling revealed a decrease in the importance of short-term variability in the communities, suggesting that community dynamics slowed down in the dry relative to the wet state. The number of temporal scales at which community dynamics manifested, and the explanatory power of time series models, was lower in the dry state. The higher diversity, reduced number of temporal scales and the lower explanatory power of time series models suggest that species dynamics tended to be more stochastic in the dry state. From a resilience perspective our results highlight a paradox: increasing species richness may not necessarily enhance resilience. The loss of cross-scale structure (i.e. the lower number of temporal scales) in community dynamics across sites suggests that resilience erodes during drought. Phytoplankton communities in the dry state are therefore likely less resilient than in the wet state. Our case study demonstrates the potential of time series modeling to assess attributes that mediate resilience. The approach is useful for assessing

  18. Genetic structure, phylogeny, and biogeography of Brazilian eyelid-less lizards of genera Calyptommatus and Nothobachia (Squamata, Gymnophthalmidae) as inferred from mitochondrial DNA sequences.

    PubMed

    Siedchlag, Ana Carolina; Benozzati, Maria Lúcia; Passoni, José Carlos; Rodrigues, Miguel Trefaut

    2010-08-01

    Calyptommatus and Nothobachia genera of gymnophthalmid lizards are restricted to sandy open habitats on São Francisco River margins, northeastern Brazil. Phylogenetic relationships and geographic distribution of the four recognized species of Calyptommatus were analyzed from partial mitochondrial cyt b, 12S, and 16S rRNA genes sequencing, taking allopatric populations of the monotypic Nothobachia ablephara as the outgroup. In Calyptommatus a basal split separated C. sinebrachiatus, a species restricted to the eastern bank of the river, from the three other species. In this clade, C. confusionibus, found on western margin, was recovered as the sister group of the two other species, C. leiolepis and C. nicterus, from opposite margins. According to approximate date estimations, C. sinebrachiatus would have separated from the other congeneric species by 4.4-6.5 my, and C. nicterus, also from eastern bank, would be diverging by 1.8-2.6 my from C. leiolepis, the sister species on the opposite margin. C. confusionibus and C. leiolepis, both from western sandy areas, would be differentiating by 2.8-5.0 my. Divergence times of about 3.0-4.0 my were estimated for allopatric populations of Nothobachia restricted to western margin. Significant differences in 16S rRNA secondary structure relatively to other vertebrates are reported. Distinct evolutionary patterns are proposed for different taxa in those sandy areas, probably related to historical changes in the course of São Francisco River. PMID:20434569

  19. Genetic structure, phylogeny, and biogeography of Brazilian eyelid-less lizards of genera Calyptommatus and Nothobachia (Squamata, Gymnophthalmidae) as inferred from mitochondrial DNA sequences.

    PubMed

    Siedchlag, Ana Carolina; Benozzati, Maria Lúcia; Passoni, José Carlos; Rodrigues, Miguel Trefaut

    2010-08-01

    Calyptommatus and Nothobachia genera of gymnophthalmid lizards are restricted to sandy open habitats on São Francisco River margins, northeastern Brazil. Phylogenetic relationships and geographic distribution of the four recognized species of Calyptommatus were analyzed from partial mitochondrial cyt b, 12S, and 16S rRNA genes sequencing, taking allopatric populations of the monotypic Nothobachia ablephara as the outgroup. In Calyptommatus a basal split separated C. sinebrachiatus, a species restricted to the eastern bank of the river, from the three other species. In this clade, C. confusionibus, found on western margin, was recovered as the sister group of the two other species, C. leiolepis and C. nicterus, from opposite margins. According to approximate date estimations, C. sinebrachiatus would have separated from the other congeneric species by 4.4-6.5 my, and C. nicterus, also from eastern bank, would be diverging by 1.8-2.6 my from C. leiolepis, the sister species on the opposite margin. C. confusionibus and C. leiolepis, both from western sandy areas, would be differentiating by 2.8-5.0 my. Divergence times of about 3.0-4.0 my were estimated for allopatric populations of Nothobachia restricted to western margin. Significant differences in 16S rRNA secondary structure relatively to other vertebrates are reported. Distinct evolutionary patterns are proposed for different taxa in those sandy areas, probably related to historical changes in the course of São Francisco River.

  20. Identification of Elymus (Triticeae, Poaceae) and its related genera genomes by RFLP analysis of PCR-amplified Adh genes.

    PubMed

    Liu, QuanLan; Zhang, NingNing; Li, Lei; Liu, Jie

    2010-10-01

    Elymus L. is the largest genus in Triticeae, containing about 150 species with four recognized genome donors (St, H, P, and W). Traditionally, the genome compound of this genus is identified based on cytological data. Recently, molecular phylogenetic analysis was used to investigate its genomic combination. Here we describe a restriction fragment length polymorphism (RFLP) assay based on digesting alcohol dehydrogenase (Adh) amplicons with two restriction enzyme combinations, EcoRI-HindIII and EcoRI-PstI, which easily can be used to distinguish Elymus and its closely related genera genomes. The method includes only four steps: (1) amplifying nuclear Adh genes with universal primers; (2) purifying and cloning PCR products; (3) digesting plasmids with restriction enzymes that identify a given genome; (4) running the digested products on an agarose gel and identify the sample based on the restriction profiles. Results showed that: (1) PCR products ranged from 1,200 to 2,000 bp; (2) Adh2 gene was amplified from all the tested genomes; Adh1 gene was amplified from almost all of the tested genomes except the W genome; Adh3 gene was amplified only from the St genome; (3) the EcoRI-HindIII combination was effective to distinguish different Adh gene types (Adh1, Adh2, and Adh3); (4) the Adh2-EcoRI-PstI fragments could be used to distinguish Elymus and its closely related genera genomes. Therefore, This RFLP assay provides an inexpensive and simple means of identifying Elymus genomes.

  1. The potential health benefit of polyisoprenylated benzophenones from Garcinia and related genera: ethnobotanical and therapeutic importance.

    PubMed

    Kumar, Satyanshu; Sharma, Shelly; Chattopadhyay, Sunil Kumar

    2013-09-01

    The diversity present in biological activities and the medicinal significance of natural products provide a renewed interest in the use of natural compounds and, more importantly, their role as a basis for drug development. Advancements in the field of natural product chemistry provide valuable information on Garcinia fruits which revealed the presence of biologically important secondary metabolites named as polyisoprenylated benzophenones (PIBs). They are mainly present in the genus Garcinia (Guttiferae) which occupies a prominent position in the history of natural products. Compared to the long history of medicinal uses and widespread research on Garcinia, the study of polyisoprenylated benzophenones was relatively limited. During recent years, these PIBs have been recognized as interesting and valuable biologically active secondary metabolites as many of the isolated polyisoprenylated benzophenones exhibited significant cytotoxic activity in in vitro and in vivo assay. During past decades, some promising advances had been achieved in understanding the chemistry and pharmacology of polyisoprenylated benzophenones. However, there has been not any systematic review on the ethnobotanical importance, chemistry, isolation techniques, structure activity relationships and the biological activities of polyisoprenylated benzophenones. In this review, the biological activity of different structures of polyisoprenylated benzophenones isolated from genus Clusia, Garcinia, Vismia, Allanblackia, Moronobea, Symphonia, Hypericum, Tovomita, Tovomiptosis and Ochrocarpus have been described. Therefore, the goal of this review article would be a valuable reference for the natural product chemists and biologists working on these PIBs. Furthermore, the review article on polyisoprenylated benzophenones would also be useful from the drug discovery point of view as cytotoxic agents in near future. This review focuses our understanding about the specific biological effects of Garcinia

  2. Genera variation of tropical mid-upper montane rainforest inferred from a marine pollen record in southern Philippines during the glacial-interglacial cycle

    NASA Astrophysics Data System (ADS)

    Bian, Y.

    2015-12-01

    Tropical vegetation is the most outstanding and obvious feature of South-East Asia, and it is expected to provide valuable information for the palaeoclmatic conditions. Pollen records from the tropical West Pacific indicate that the tropical vegetation is much sensitive to the environment and climate change, and their good correspondence with palaeocliamte change in glacial/interglacial timescales. It is shown that the range of the tropical montane rainforest was affected by the temperature change during the glacial cycle. But, from some marine core, the genera variation of tropical mid-upper montane pollen record is also distinct during the glacial cycle. In this study, examination of the pollen content of marine core MD06-3075 taken from Davao Gulf in the Southern Philippines reveals a ~116,000 year record of tropical vegetation change as well as the influence of the environment and climate variability on the ecosystem of the tropical area. Chronology was determined by 16 AMS 14C dates and a detailed oxygen isotope record. A high representation of pollen from tropical upper montane rainforest (mainly Podocarpus) (40-60%) during the last glacial period indicates that this forest type extended to lower attitudes. And the genera variations of the tropical mid-upper montane rainforest exist between the Phyllocladus and Podocarpus with the environment and climate changing. The pollen content of Phyllocladus is much high in marine isotope stage (MIS) 5, but Podocarpus is much higher in the glacial period. During the onset of MIS 5a and 5c, the percentage of Phyllocladus pollen declines dramatically. Vegetation investigation in Mindanao, shows that Podocarpus exists in altitude ranging from 1,200-1,700 m, and Phyllocladus appear in altitude range from 1700-2100 m, but is more abundant above the 2,400 m. Thus, Phyllocladus might be more sensitive to the temperature change. Then, in this study, the pollen content of is much high during the interglacial period

  3. Relative changes in krill abundance inferred from Antarctic fur seal.

    PubMed

    Huang, Tao; Sun, Liguang; Stark, John; Wang, Yuhong; Cheng, Zhongqi; Yang, Qichao; Sun, Song

    2011-01-01

    Antarctic krill Euphausia superba is a predominant species in the Southern Ocean, it is very sensitive to climate change, and it supports large stocks of fishes, seabirds, seals and whales in Antarctic marine ecosystems. Modern krill stocks have been estimated directly by net hauls and acoustic surveys; the historical krill density especially the long-term one in the Southern Ocean, however, is unknown. Here we inferred the relative krill population changes along the West Antarctic Peninsula (WAP) over the 20th century from the trophic level change of Antarctic fur seal Arctocephalus gazella using stable carbon (δ(13)C) and nitrogen (δ(15)N) isotopes of archival seal hairs. Since Antarctic fur seals feed preferentially on krill, the variation of δ(15)N in seal hair indicates a change in the proportion of krill in the seal's diets and thus the krill availability in local seawater. For the past century, enriching fur seal δ(15)N values indicated decreasing krill availability. This is agreement with direct observation for the past ∼30 years and suggests that the recently documented decline in krill populations began in the early parts of the 20th century. This novel method makes it possible to infer past krill population changes from ancient tissues of krill predators.

  4. Relative Changes in Krill Abundance Inferred from Antarctic Fur Seal

    PubMed Central

    Huang, Tao; Sun, Liguang; Stark, John; Wang, Yuhong; Cheng, Zhongqi; Yang, Qichao; Sun, Song

    2011-01-01

    Antarctic krill Euphausia superba is a predominant species in the Southern Ocean, it is very sensitive to climate change, and it supports large stocks of fishes, seabirds, seals and whales in Antarctic marine ecosystems. Modern krill stocks have been estimated directly by net hauls and acoustic surveys; the historical krill density especially the long-term one in the Southern Ocean, however, is unknown. Here we inferred the relative krill population changes along the West Antarctic Peninsula (WAP) over the 20th century from the trophic level change of Antarctic fur seal Arctocephalus gazella using stable carbon (δ13C) and nitrogen (δ15N) isotopes of archival seal hairs. Since Antarctic fur seals feed preferentially on krill, the variation of δ15N in seal hair indicates a change in the proportion of krill in the seal's diets and thus the krill availability in local seawater. For the past century, enriching fur seal δ15N values indicated decreasing krill availability. This is agreement with direct observation for the past ∼30 years and suggests that the recently documented decline in krill populations began in the early parts of the 20th century. This novel method makes it possible to infer past krill population changes from ancient tissues of krill predators. PMID:22087294

  5. Bioprospecting of Plant Growth Promoting Bacilli and Related Genera Prevalent in Soils of Pristine Sacred Groves: Biochemical and Molecular Approach

    PubMed Central

    Lyngwi, Nathaniel A.; Nongkhlaw, Macmillan; Kalita, Debajit; Joshi, Santa Ram

    2016-01-01

    Bacillus spp. and related genera native to soils of the pristine sacred groves from Meghalaya, India were characterized using biochemical and 16S rRNA gene analysis which revealed dominance of Bacillus, Paenibacillus, Lysinibacillus and Viridibacillus in the groves. Biochemical estimation was carried out for in vitro testing of plant growth promoting traits present in these isolates. PCR screening were performed for plant growth-promoting related genes involved in the biosynthesis of acid phosphatase (AcPho), indolepyruvate decarboxylase (ipdC), 1-aminocyclopropane-1-carboxylate deaminase (accd) and siderophore biosynthesis protein (asbA). 76% of the sacred grove isolates gave an amplified fragment for AcPho. Three of the isolates gave an amplified fragment for IpdC gene. Apart from 2 isolates, all the other isolates including the reference strains were positive for the amplification of the accd gene indicating their potential to produce ACC deaminase enzyme. 42% of the isolates gave an amplified fragment for asbA gene indicating the potential ability of these isolates to produce the catechol type siderophore, petrobactin. Overall findings indicated multiple PGP genetic traits present in these isolates which suggested that these isolates are capable of expressing multiple PGP traits. Phylogenetic and sequence analysis of accd and asbA genes from the isolates revealed that asbA genes from Paenibacillus taichungiensis SG3 and Paenibacillus tylopili SG24 indicated the occurrence of intergeneric horizontal transfer between Paenibacillus and Bacillus. PMID:27111883

  6. Description and evaluation of the semiautomated 4-hour rapid ID 32 Strep method for identification of streptococci and members of related genera.

    PubMed Central

    Freney, J; Bland, S; Etienne, J; Desmonceaux, M; Boeufgras, J M; Fleurette, J

    1992-01-01

    The rapid ID 32 Strep system (bioMérieux, La Balme les Grottes, France) is a new system which allows the identification in 4 h of most streptococci and members of related genera encountered in medical and veterinary bacteriology. Four hundred thirty-three isolates first identified by conventional methods and belonging to the genera Streptococcus, Lactococcus, Enterococcus, Aerococcus, Gemella, Leuconostoc, Erysipelothrix, Gardnerella, and Listeria were tested. Overall, rapid ID 32 Strep correctly identified 413 (95.3%) of the strains, with 109 (25.1%) requiring extra tests for complete identification. Sixteen strains (3.7%) were not identified, and 4 (1.0%) were misidentified. The rapid ID 32 Strep system is a suitable alternative for rapid identification of members of the genus Streptococcus and of related genera. PMID:1400965

  7. Infants use relative numerical group size to infer social dominance

    PubMed Central

    Pun, Anthea; Birch, Susan A. J.; Baron, Andrew Scott

    2016-01-01

    Detecting dominance relationships, within and across species, provides a clear fitness advantage because this ability helps individuals assess their potential risk of injury before engaging in a competition. Previous research has demonstrated that 10- to 13-mo-old infants can represent the dominance relationship between two agents in terms of their physical size (larger agent = more dominant), whereas younger infants fail to do so. It is unclear whether infants younger than 10 mo fail to represent dominance relationships in general, or whether they lack sensitivity to physical size as a cue to dominance. Two studies explored whether infants, like many species across the animal kingdom, use numerical group size to assess dominance relationships and whether this capacity emerges before their sensitivity to physical size. A third study ruled out an alternative explanation for our findings. Across these studies, we report that infants 6–12 mo of age use numerical group size to infer dominance relationships. Specifically, preverbal infants expect an agent from a numerically larger group to win in a right-of-way competition against an agent from a numerically smaller group. In addition, this is, to our knowledge, the first study to demonstrate that infants 6–9 mo of age are capable of understanding social dominance relations. These results demonstrate that infants’ understanding of social dominance relations may be based on evolutionarily relevant cues and reveal infants’ early sensitivity to an important adaptive function of social groups. PMID:26884199

  8. Infants use relative numerical group size to infer social dominance.

    PubMed

    Pun, Anthea; Birch, Susan A J; Baron, Andrew Scott

    2016-03-01

    Detecting dominance relationships, within and across species, provides a clear fitness advantage because this ability helps individuals assess their potential risk of injury before engaging in a competition. Previous research has demonstrated that 10- to 13-mo-old infants can represent the dominance relationship between two agents in terms of their physical size (larger agent = more dominant), whereas younger infants fail to do so. It is unclear whether infants younger than 10 mo fail to represent dominance relationships in general, or whether they lack sensitivity to physical size as a cue to dominance. Two studies explored whether infants, like many species across the animal kingdom, use numerical group size to assess dominance relationships and whether this capacity emerges before their sensitivity to physical size. A third study ruled out an alternative explanation for our findings. Across these studies, we report that infants 6-12 mo of age use numerical group size to infer dominance relationships. Specifically, preverbal infants expect an agent from a numerically larger group to win in a right-of-way competition against an agent from a numerically smaller group. In addition, this is, to our knowledge, the first study to demonstrate that infants 6-9 mo of age are capable of understanding social dominance relations. These results demonstrate that infants' understanding of social dominance relations may be based on evolutionarily relevant cues and reveal infants' early sensitivity to an important adaptive function of social groups. PMID:26884199

  9. Flexitibia, a new genus of Harpactorinae (Hemiptera: Heteroptera: Reduviidae), with a discussion on the functional morphology of forelegs of the related genera.

    PubMed

    Zhao, Ping; Pham, Minhlan; Truong, Xuan Lam; Cai, Wanzhi

    2014-01-01

    Flexitibia, a new genus, in the division Euagorasaria of the assassin bug subfamily Harpactorinae from Yunnan Province of China is described. The type species, Flexitibia orientalis sp. nov., is described and illustrated. A key to the closely related genera is provided. The type specimens are kept in the Entomological Museum of China Agricultural University, Beijing. PMID:24870499

  10. Redefining Ceratocystis and allied genera.

    PubMed

    de Beer, Z W; Duong, T A; Barnes, I; Wingfield, B D; Wingfield, M J

    2014-09-01

    The genus Ceratocystis was established in 1890 and accommodates many important fungi. These include serious plant pathogens, significant insect symbionts and agents of timber degradation that result in substantial economic losses. Virtually since its type was described from sweet potatoes, the taxonomy of Ceratocystis has been confused and vigorously debated. In recent years, particulary during the last two decades, it has become very obvious that this genus includes a wide diversity of very different fungi. These have been roughly lumped together due to their similar morphological structures that have clearly evolved through convergent evolution linked to an insect-associated ecology. As has been true for many other groups of fungi, the emergence of DNA-based sequence data and associated phylogenetic inferences, have made it possible to robustly support very distinct boundaries defined by morphological characters and ecological differences. In this study, DNA-sequence data for three carefully selected gene regions (60S, LSU, MCM7) were generated for 79 species residing in the aggregate genus Ceratocystis sensu lato and these data were subjected to rigorous phylogenetic analyses. The results made it possible to distinguish seven major groups for which generic names have been chosen and descriptions either provided or emended. The emended genera included Ceratocystis sensu stricto, Chalaropsis, Endoconidiophora, Thielaviopsis, and Ambrosiella, while two new genera, Davidsoniella and Huntiella, were described. In total, 30 new combinations have been made. This major revision of the generic boundaries in the Ceratocystidaceae will simplify future treatments and work with an important group of fungi including distantly related species illogically aggregated under a single name. PMID:25492989

  11. Redefining Ceratocystis and allied genera

    PubMed Central

    de Beer, Z.W.; Duong, T.A.; Barnes, I.; Wingfield, B.D.; Wingfield, M.J.

    2014-01-01

    The genus Ceratocystis was established in 1890 and accommodates many important fungi. These include serious plant pathogens, significant insect symbionts and agents of timber degradation that result in substantial economic losses. Virtually since its type was described from sweet potatoes, the taxonomy of Ceratocystis has been confused and vigorously debated. In recent years, particulary during the last two decades, it has become very obvious that this genus includes a wide diversity of very different fungi. These have been roughly lumped together due to their similar morphological structures that have clearly evolved through convergent evolution linked to an insect-associated ecology. As has been true for many other groups of fungi, the emergence of DNA-based sequence data and associated phylogenetic inferences, have made it possible to robustly support very distinct boundaries defined by morphological characters and ecological differences. In this study, DNA-sequence data for three carefully selected gene regions (60S, LSU, MCM7) were generated for 79 species residing in the aggregate genus Ceratocystis sensu lato and these data were subjected to rigorous phylogenetic analyses. The results made it possible to distinguish seven major groups for which generic names have been chosen and descriptions either provided or emended. The emended genera included Ceratocystis sensu stricto, Chalaropsis, Endoconidiophora, Thielaviopsis, and Ambrosiella, while two new genera, Davidsoniella and Huntiella, were described. In total, 30 new combinations have been made. This major revision of the generic boundaries in the Ceratocystidaceae will simplify future treatments and work with an important group of fungi including distantly related species illogically aggregated under a single name. PMID:25492989

  12. Redefining Ceratocystis and allied genera.

    PubMed

    de Beer, Z W; Duong, T A; Barnes, I; Wingfield, B D; Wingfield, M J

    2014-09-01

    The genus Ceratocystis was established in 1890 and accommodates many important fungi. These include serious plant pathogens, significant insect symbionts and agents of timber degradation that result in substantial economic losses. Virtually since its type was described from sweet potatoes, the taxonomy of Ceratocystis has been confused and vigorously debated. In recent years, particulary during the last two decades, it has become very obvious that this genus includes a wide diversity of very different fungi. These have been roughly lumped together due to their similar morphological structures that have clearly evolved through convergent evolution linked to an insect-associated ecology. As has been true for many other groups of fungi, the emergence of DNA-based sequence data and associated phylogenetic inferences, have made it possible to robustly support very distinct boundaries defined by morphological characters and ecological differences. In this study, DNA-sequence data for three carefully selected gene regions (60S, LSU, MCM7) were generated for 79 species residing in the aggregate genus Ceratocystis sensu lato and these data were subjected to rigorous phylogenetic analyses. The results made it possible to distinguish seven major groups for which generic names have been chosen and descriptions either provided or emended. The emended genera included Ceratocystis sensu stricto, Chalaropsis, Endoconidiophora, Thielaviopsis, and Ambrosiella, while two new genera, Davidsoniella and Huntiella, were described. In total, 30 new combinations have been made. This major revision of the generic boundaries in the Ceratocystidaceae will simplify future treatments and work with an important group of fungi including distantly related species illogically aggregated under a single name.

  13. Inferring coupling strength from event-related dynamics

    NASA Astrophysics Data System (ADS)

    Łęski, Szymon; Wójcik, Daniel K.

    2008-10-01

    We propose an approach for inferring strength of coupling between two systems from their transient dynamics. This is of vital importance in cases where most information is carried by the transients, for instance, in evoked potentials measured commonly in electrophysiology. We show viability of our approach using nonlinear and linear measures of synchronization on a population model of thalamocortical loop and on a system of two coupled Rössler-type oscillators in nonchaotic regime.

  14. Fruit and Seed Anatomy of Chenopodium and Related Genera (Chenopodioideae, Chenopodiaceae/Amaranthaceae): Implications for Evolution and Taxonomy

    PubMed Central

    Sukhorukov, Alexander P.; Zhang, Mingli

    2013-01-01

    A comparative carpological study of 96 species of all clades formerly considered as the tribe Chenopodieae has been conducted for the first time. The results show important differences in the anatomical structure of the pericarp and seed coat between representatives of terminal clades including Chenopodium s.str.+Chenopodiastrum and the recently recognized genera Blitum, Oxybasis and Dysphania. Within Chenopodium the most significant changes in fruit and seed structure are found in members of C. sect. Skottsbergia. The genera Rhagodia and Einadia differ insignificantly from Chenopodium. The evolution of heterospermy in Chenopodium is discussed. Almost all representatives of the tribe Dysphanieae are clearly separated from other Chenopodioideae on the basis of a diverse set of characteristics, including the small dimensions of the fruits (especially in Australian taxa), their subglobose shape (excl. Teloxys and Suckleya), and peculiarities of the pericarp indumentum. The set of fruit and seed characters evolved within the subfamily Chenopodioideae is described. A recent phylogenetic hypothesis is employed to examine the evolution of three (out of a total of 21) characters, namely seed color, testa-cell protoplast characteristics and embryo orientation. PMID:23626750

  15. On the violation of causal, emotional, and locative inferences: An event-related potentials study.

    PubMed

    Rodríguez-Gómez, Pablo; Sánchez-Carmona, Alberto; Smith, Cybelle; Pozo, Miguel A; Hinojosa, José A; Moreno, Eva M

    2016-07-01

    Previous event-related potential studies have demonstrated the online generation of inferences during reading for comprehension tasks. The present study contrasted the brainwave patterns of activity to the fulfilment or violation of various types of inferences (causal, emotional, locative). Relative to inference congruent sentence endings, a typical centro-parietal N400 was elicited for the violation of causal and locative inferences. This N400 effect was initially absent for emotional inferences, most likely due to their lower cloze probability. Between 500 and 750ms, a larger frontal positivity (pN400FP) was elicited by inference incongruent sentence endings in the causal condition. In emotional sentences, both inference congruent and incongruent endings exerted this frontally distributed late positivity. For the violation of locative inferences, the larger positivity was only marginally significant over left posterior scalp locations. Thus, not all inference eliciting sentences evoked a similar pattern of ERP responses. We interpret and discuss our results in line with recent views on what the N400, the P600 and the pN400FP brainwave potentials index.

  16. The genetic diversity of genus Bacillus and the related genera revealed by 16s rRNA gene sequences and ardra analyses isolated from geothermal regions of turkey

    PubMed Central

    Cihan, Arzu Coleri; Tekin, Nilgun; Ozcan, Birgul; Cokmus, Cumhur

    2012-01-01

    Previously isolated 115 endospore-forming bacilli were basically grouped according to their temperature requirements for growth: the thermophiles (74%), the facultative thermophiles (14%) and the mesophiles (12%). These isolates were taken into 16S rRNA gene sequence analyses, and they were clustered among the 7 genera: Anoxybacillus, Aeribacillus, Bacillus, Brevibacillus, Geobacillus, Paenibacillus, and Thermoactinomycetes. Of these bacilli, only the thirty two isolates belonging to genera Bacillus (16), Brevibacillus (13), Paenibacillus (1) and Thermoactinomycetes (2) were selected and presented in this paper. The comparative sequence analyses revealed that the similarity values were ranged as 91.4–100 %, 91.8- 99.2 %, 92.6- 99.8 % and 90.7 - 99.8 % between the isolates and the related type strains from these four genera, respectively. Twenty nine of them were found to be related with the validly published type strains. The most abundant species was B. thermoruber with 9 isolates followed by B. pumilus (6), B. lichenformis (3), B. subtilis (3), B. agri (3), B. smithii (2), T. vulgaris (2) and finally P. barengoltzii (1). In addition, isolates of A391a, B51a and D295 were proposed as novel species as their 16S rRNA gene sequences displayed similarities ≤ 97% to their closely related type strains. The AluI-, HaeIII- and TaqI-ARDRA results were in congruence with the 16S rRNA gene sequence analyses. The ARDRA results allowed us to differentiate these isolates, and their discriminative restriction fragments were able to be determined. Some of their phenotypic characters and their amylase, chitinase and protease production were also studied and biotechnologically valuable enzyme producing isolates were introduced in order to use in further studies. PMID:24031834

  17. Determination of the essential nutrient requirements of wine-related bacteria from the genera Oenococcus and Lactobacillus.

    PubMed

    Terrade, Nicolas; Mira de Orduña, Ramón

    2009-07-31

    Wine lactic acid bacteria (LAB) are responsible for the malolactic fermentation (MLF) in wine production. Wine LAB have fastidious nutrient requirements but their auxotrophies remain little studied. The ability of specific wine nutrients to meet the nutritional requirements of wine LAB, and thus support MLF, remains unclear. This work investigated the essential growth requirements of four strains of wine LAB from the genera Oenococcus and Lactobacillus using the single omission technique with a suitable chemically defined medium. For the determination of auxotrophies, at least 3 (and up to 15) subcultures in deficient media were made, and intra- and extracellular nutrient carry over was reduced by small inoculation rates and washing cells 3 times between transfers. This careful methodology revealed more auxotrophies than those described for wine LAB in the literature. The essential bacterial nutrient requirements were found to be strain specific. 10 compounds were essential for all wine LAB tested, the carbon and phosphate source, manganese, as well as several amino acids (proline, arginine and the branched amino acids valine, leucine and isoleucine) and vitamins (nicotinic acid and pantothenic acids). Nucleotides were not essential for any of the bacteria studied. The two Oenococcus oeni strains revealed a larger number of auxotrophies (18 and 21) and had a higher degree of nutritional similarity (86%) defined as percentage of common requirements per maximum total requirements. The two Lactobacillus strains only had 11 and 14 auxotrophies and the similarity was 79%, but both were auxotroph for riboflavin, which was not needed by the O. oeni strains. Data on the common requirements may be used to further study the ability of wines or commercial nutrients to support MLF and to consider the microbiological stability of finished wines. The results indicate that absence of riboflavin in oenological nutrient preparations may allow to create a specific advantage for

  18. Inferring Facts From Fiction: Reading Correct and Incorrect Information Affects Memory for Related Information

    PubMed Central

    Butler, Andrew C.; Dennis, Nancy A.; Marsh, Elizabeth J.

    2012-01-01

    People can acquire both true and false knowledge about the world from fictional stories (Marsh & Fazio, 2007). The present study explored whether the benefits and costs of learning about the world from fictional stories extend beyond memory for directly stated pieces of information. Of interest was whether readers would use correct and incorrect story references to make deductive inferences about related information in the story, and then integrate those inferences into their knowledge bases. Subjects read stories containing correct, neutral, and misleading references to facts about the world; each reference could be combined with another reference that occurred in a later sentence to make a deductive inference. Later, they answered general knowledge questions that tested for these deductive inferences. The results showed that subjects generated and retained the deductive inferences regardless of whether the inferences were consistent or inconsistent with world knowledge, and irrespective of whether the references were placed consecutively in the text or separated by many sentences. Readers learn more than what is directly stated in stories; they use references to the real world to make both correct and incorrect inferences that are integrated into their knowledge bases. PMID:22640369

  19. Generation of amphidiploids from hybrids of wheat and related species from the genera Aegilops, Secale, Thinopyrum, and Triticum as a source of genetic variation for wheat improvement.

    PubMed

    Nemeth, Csilla; Yang, Cai-yun; Kasprzak, Paul; Hubbart, Stella; Scholefield, Duncan; Mehra, Surbhi; Skipper, Emma; King, Ian; King, Julie

    2015-02-01

    We aim to improve diversity of domesticated wheat by transferring genetic variation for important target traits from related wild and cultivated grass species. The present study describes the development of F1 hybrids between wheat and related species from the genera Aegilops, Secale, Thinopyrum, and Triticum and production of new amphidiploids. Amphidiploid lines were produced from 20 different distant relatives. Both colchicine and caffeine were successfully used to double the chromosome numbers. The genomic constitution of the newly formed amphidiploids derived from seven distant relatives was determined using genomic in situ hybridization (GISH). Altogether, 42 different plants were analysed, 19 using multicolour GISH separating the chromosomes from the A, B, and D genomes of wheat, as well as the distant relative, and 23 using single colour GISH. Restructuring of the allopolyploid genome, both chromosome losses and aneuploidy, was detected in all the genomes contained by the amphidiploids. From the observed chromosome numbers there is an indication that in amphidiploids the B genome of wheat suffers chromosome losses less frequently than the other wheat genomes. Phenotyping to realize the full potential of the wheat-related grass germplasm is underway, linking the analyzed genotypes to agronomically important target traits.

  20. Causal Inference Based on the Analysis of Events of Relations for Non-stationary Variables.

    PubMed

    Yin, Yu; Yao, Dezhong

    2016-01-01

    The main concept behind causality involves both statistical conditions and temporal relations. However, current approaches to causal inference, focusing on the probability vs. conditional probability contrast, are based on model functions or parametric estimation. These approaches are not appropriate when addressing non-stationary variables. In this work, we propose a causal inference approach based on the analysis of Events of Relations (CER). CER focuses on the temporal delay relation between cause and effect, and a binomial test is established to determine whether an "event of relation" with a non-zero delay is significantly different from one with zero delay. Because CER avoids parameter estimation of non-stationary variables per se, the method can be applied to both stationary and non-stationary signals. PMID:27389921

  1. Causal Inference Based on the Analysis of Events of Relations for Non-stationary Variables

    PubMed Central

    Yin, Yu; Yao, Dezhong

    2016-01-01

    The main concept behind causality involves both statistical conditions and temporal relations. However, current approaches to causal inference, focusing on the probability vs. conditional probability contrast, are based on model functions or parametric estimation. These approaches are not appropriate when addressing non-stationary variables. In this work, we propose a causal inference approach based on the analysis of Events of Relations (CER). CER focuses on the temporal delay relation between cause and effect, and a binomial test is established to determine whether an “event of relation” with a non-zero delay is significantly different from one with zero delay. Because CER avoids parameter estimation of non-stationary variables per se, the method can be applied to both stationary and non-stationary signals. PMID:27389921

  2. Event-related functional magnetic resonance imaging: modelling, inference and optimization.

    PubMed Central

    Josephs, O; Henson, R N

    1999-01-01

    Event-related functional magnetic resonance imaging is a recent and popular technique for detecting haemodynamic responses to brief stimuli or events. However, the design of event-related experiments requires careful consideration of numerous issues of measurement, modelling and inference. Here we review these issues, with particular emphasis on the use of basis functions within a general linear modelling framework to model and make inferences about the haemodynamic response. With these models in mind, we then consider how the properties of functional magnetic resonance imaging data determine the optimal experimental design for a specific hypothesis, in terms of stimulus ordering and interstimulus interval. Finally, we illustrate various event-related models with examples from recent studies. PMID:10466147

  3. Nature of polymorphisms in 16S-23S rRNA gene intergenic transcribed spacer fingerprinting of Bacillus and related genera.

    PubMed

    Daffonchio, Daniele; Cherif, Ameur; Brusetti, Lorenzo; Rizzi, Aurora; Mora, Diego; Boudabous, Abdellatif; Borin, Sara

    2003-09-01

    The intergenic transcribed spacers (ITS) between the 16S and 23S rRNA genetic loci are frequently used in PCR fingerprinting to discriminate bacterial strains at the species and intraspecies levels. We investigated the molecular nature of polymorphisms in ITS-PCR fingerprinting of low-G+C-content spore-forming bacteria belonging to the genera Bacillus, Brevibacillus, Geobacillus, and Paenibacillus: We found that besides the polymorphisms in the homoduplex fragments amplified by PCR, heteroduplex products formed during PCR between amplicons from different ribosomal operons, with or without tRNA genes in the ITS, contribute to the interstrain variability in ITS-PCR fingerprinting patterns obtained in polyacrylamide-based gel matrices. The heteroduplex nature of the discriminating bands was demonstrated by fragment separation in denaturing polyacrylamide gels, by capillary electrophoresis, and by cloning, sequencing, and recombination of purified short and tRNA gene-containing long ITS. We also found that heteroduplex product formation is enhanced by increasing the number of PCR cycles. Homoduplex-heteroduplex polymorphisms (HHP) in a conserved region, such as the 16S and 23S rRNA gene ITS, allowed discrimination of closely related strains and species undistinguishable by other methods, indicating that ITS-HHP analysis is an easy and reproducible additional tool for strain typing.

  4. Nature of polymorphisms in 16S-23S rRNA gene intergenic transcribed spacer fingerprinting of Bacillus and related genera.

    PubMed

    Daffonchio, Daniele; Cherif, Ameur; Brusetti, Lorenzo; Rizzi, Aurora; Mora, Diego; Boudabous, Abdellatif; Borin, Sara

    2003-09-01

    The intergenic transcribed spacers (ITS) between the 16S and 23S rRNA genetic loci are frequently used in PCR fingerprinting to discriminate bacterial strains at the species and intraspecies levels. We investigated the molecular nature of polymorphisms in ITS-PCR fingerprinting of low-G+C-content spore-forming bacteria belonging to the genera Bacillus, Brevibacillus, Geobacillus, and Paenibacillus: We found that besides the polymorphisms in the homoduplex fragments amplified by PCR, heteroduplex products formed during PCR between amplicons from different ribosomal operons, with or without tRNA genes in the ITS, contribute to the interstrain variability in ITS-PCR fingerprinting patterns obtained in polyacrylamide-based gel matrices. The heteroduplex nature of the discriminating bands was demonstrated by fragment separation in denaturing polyacrylamide gels, by capillary electrophoresis, and by cloning, sequencing, and recombination of purified short and tRNA gene-containing long ITS. We also found that heteroduplex product formation is enhanced by increasing the number of PCR cycles. Homoduplex-heteroduplex polymorphisms (HHP) in a conserved region, such as the 16S and 23S rRNA gene ITS, allowed discrimination of closely related strains and species undistinguishable by other methods, indicating that ITS-HHP analysis is an easy and reproducible additional tool for strain typing. PMID:12957895

  5. Using Semantic Association to Extend and Infer Literature-Oriented Relativity Between Terms.

    PubMed

    Cheng, Liang; Li, Jie; Hu, Yang; Jiang, Yue; Liu, Yongzhuang; Chu, Yanshuo; Wang, Zhenxing; Wang, Yadong

    2015-01-01

    Relative terms often appear together in the literature. Methods have been presented for weighting relativity of pairwise terms by their co-occurring literature and inferring new relationship. Terms in the literature are also in the directed acyclic graph of ontologies, such as Gene Ontology and Disease Ontology. Therefore, semantic association between terms may help for establishing relativities between terms in literature. However, current methods do not use these associations. In this paper, an adjusted R-scaled score (ARSS) based on information content (ARSSIC) method is introduced to infer new relationship between terms. First, set inclusion relationship between terms of ontology was exploited to extend relationships between these terms and literature. Next, the ARSS method was presented to measure relativity between terms across ontologies according to these extensional relationships. Then, the ARSSIC method using ratios of information shared of term's ancestors was designed to infer new relationship between terms across ontologies. The result of the experiment shows that ARSS identified more pairs of statistically significant terms based on corresponding gene sets than other methods. And the high average area under the receiver operating characteristic curve (0.9293) shows that ARSSIC achieved a high true positive rate and a low false positive rate. Data is available at http://mlg.hit.edu.cn/ARSSIC/.

  6. Using Semantic Association to Extend and Infer Literature-Oriented Relativity Between Terms.

    PubMed

    Cheng, Liang; Li, Jie; Hu, Yang; Jiang, Yue; Liu, Yongzhuang; Chu, Yanshuo; Wang, Zhenxing; Wang, Yadong

    2015-01-01

    Relative terms often appear together in the literature. Methods have been presented for weighting relativity of pairwise terms by their co-occurring literature and inferring new relationship. Terms in the literature are also in the directed acyclic graph of ontologies, such as Gene Ontology and Disease Ontology. Therefore, semantic association between terms may help for establishing relativities between terms in literature. However, current methods do not use these associations. In this paper, an adjusted R-scaled score (ARSS) based on information content (ARSSIC) method is introduced to infer new relationship between terms. First, set inclusion relationship between terms of ontology was exploited to extend relationships between these terms and literature. Next, the ARSS method was presented to measure relativity between terms across ontologies according to these extensional relationships. Then, the ARSSIC method using ratios of information shared of term's ancestors was designed to infer new relationship between terms across ontologies. The result of the experiment shows that ARSS identified more pairs of statistically significant terms based on corresponding gene sets than other methods. And the high average area under the receiver operating characteristic curve (0.9293) shows that ARSSIC achieved a high true positive rate and a low false positive rate. Data is available at http://mlg.hit.edu.cn/ARSSIC/. PMID:26684460

  7. How to infer relative fitness from a sample of genomic sequences.

    PubMed

    Dayarian, Adel; Shraiman, Boris I

    2014-07-01

    Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from those expected under neutral evolution and described statistically by Kingman's coalescent. While differences in the statistical structure of genealogies have long been used as a test for the presence of selection, the full extent of the information that they contain has not been exploited. Here we demonstrate that the shape of the reconstructed genealogical tree for a moderately large number of random genomic samples taken from a fitness diverse, but otherwise unstructured, asexual population can be used to predict the relative fitness of individuals within the sample. To achieve this we define a heuristic algorithm, which we test in silico, using simulations of a Wright-Fisher model for a realistic range of mutation rates and selection strength. Our inferred fitness ranking is based on a linear discriminator that identifies rapidly coalescing lineages in the reconstructed tree. Inferred fitness ranking correlates strongly with actual fitness, with a genome in the top 10% ranked being in the top 20% fittest with false discovery rate of 0.1-0.3, depending on the mutation/selection parameters. The ranking also enables us to predict the genotypes that future populations inherit from the present one. While the inference accuracy increases monotonically with sample size, samples of 200 nearly saturate the performance. We propose that our approach can be used for inferring relative fitness of genomes obtained in single-cell sequencing of tumors and in monitoring viral outbreaks. PMID:24770330

  8. The relative roles of visuospatial and linguistic working memory systems in generating inferences during visual narrative comprehension.

    PubMed

    Magliano, Joseph P; Larson, Adam M; Higgs, Karyn; Loschky, Lester C

    2016-02-01

    This study investigated the relative roles of visuospatial versus linguistic working memory (WM) systems in the online generation of bridging inferences while viewers comprehend visual narratives. We contrasted these relative roles in the visuospatial primacy hypothesis versus the shared (visuospatial & linguistic) systems hypothesis, and tested them in 3 experiments. Participants viewed picture stories containing multiple target episodes consisting of a beginning state, a bridging event, and an end state, respectively, and the presence of the bridging event was manipulated. When absent, viewers had to infer the bridging-event action to comprehend the end-state image. A pilot study showed that after viewing the end-state image, participants' think-aloud protocols contained more inferred actions when the bridging event was absent than when it was present. Likewise, Experiment 1 found longer viewing times for the end-state image when the bridging-event image was absent, consistent with viewing times revealing online inference generation processes. Experiment 2 showed that both linguistic and visuospatial WM loads attenuated the inference viewing time effect, consistent with the shared systems hypothesis. Importantly, however, Experiment 3 found that articulatory suppression did not attenuate the inference viewing time effect, indicating that (sub)vocalization did not support online inference generation during visual narrative comprehension. Thus, the results support a shared-systems hypothesis in which both visuospatial and linguistic WM systems support inference generation in visual narratives, with the linguistic WM system operating at a deeper level than (sub)vocalization.

  9. Inferences on weather extremes and weather-related disasters: a review of statistical methods

    NASA Astrophysics Data System (ADS)

    Visser, H.; Petersen, A. C.

    2012-02-01

    The study of weather extremes and their impacts, such as weather-related disasters, plays an important role in research of climate change. Due to the great societal consequences of extremes - historically, now and in the future - the peer-reviewed literature on this theme has been growing enormously since the 1980s. Data sources have a wide origin, from century-long climate reconstructions from tree rings to relatively short (30 to 60 yr) databases with disaster statistics and human impacts. When scanning peer-reviewed literature on weather extremes and its impacts, it is noticeable that many different methods are used to make inferences. However, discussions on these methods are rare. Such discussions are important since a particular methodological choice might substantially influence the inferences made. A calculation of a return period of once in 500 yr, based on a normal distribution will deviate from that based on a Gumbel distribution. And the particular choice between a linear or a flexible trend model might influence inferences as well. In this article, a concise overview of statistical methods applied in the field of weather extremes and weather-related disasters is given. Methods have been evaluated as to stationarity assumptions, the choice for specific probability density functions (PDFs) and the availability of uncertainty information. As for stationarity assumptions, the outcome was that good testing is essential. Inferences on extremes may be wrong if data are assumed stationary while they are not. The same holds for the block-stationarity assumption. As for PDF choices it was found that often more than one PDF shape fits to the same data. From a simulation study the conclusion can be drawn that both the generalized extreme value (GEV) distribution and the log-normal PDF fit very well to a variety of indicators. The application of the normal and Gumbel distributions is more limited. As for uncertainty, it is advisable to test conclusions on extremes

  10. Inference of Disease-Related Molecular Logic from Systems-Based Microarray Analysis

    PubMed Central

    Varadan, Vinay; Anastassiou, Dimitris

    2006-01-01

    Computational analysis of gene expression data from microarrays has been useful for medical diagnosis and prognosis. The ability to analyze such data at the level of biological modules, rather than individual genes, has been recognized as important for improving our understanding of disease-related pathways. It has proved difficult, however, to infer pathways from microarray data by deriving modules of multiple synergistically interrelated genes, rather than individual genes. Here we propose a systems-based approach called Entropy Minimization and Boolean Parsimony (EMBP) that identifies, directly from gene expression data, modules of genes that are jointly associated with disease. Furthermore, the technique provides insight into the underlying biomolecular logic by inferring a logic function connecting the joint expression levels in a gene module with the outcome of disease. Coupled with biological knowledge, this information can be useful for identifying disease-related pathways, suggesting potential therapeutic approaches for interfering with the functions of such pathways. We present an example providing such gene modules associated with prostate cancer from publicly available gene expression data, and we successfully validate the results on additional independently derived data. Our results indicate a link between prostate cancer and cellular damage from oxidative stress combined with inhibition of apoptotic mechanisms normally triggered by such damage. PMID:16789819

  11. Inferences on weather extremes and weather-related disasters: a review of statistical methods

    NASA Astrophysics Data System (ADS)

    Visser, H.; Petersen, A. C.

    2011-09-01

    The study of weather extremes and their impacts, such as weather-related disasters, plays an important role in climate-change research. Due to the great societal consequences of extremes - historically, now and in the future - the peer-reviewed literature on this theme has been growing enormously since the 1980s. Data sources have a wide origin, from century-long climate reconstructions from tree rings to short databases with disaster statistics and human impacts (30 to 60 yr). In scanning the peer-reviewed literature on weather extremes and impacts thereof we noticed that many different methods are used to make inferences. However, discussions on methods are rare. Such discussions are important since a particular methodological choice might substantially influence the inferences made. A calculation of a return period of once in 500 yr, based on a normal distribution will deviate from that based on a Gumbel distribution. And the particular choice between a linear or a flexible trend model might influence inferences as well. In this article we give a concise overview of statistical methods applied in the field of weather extremes and weather-related disasters. Methods have been evaluated as to stationarity assumptions, the choice for specific probability density functions (PDFs) and the availability of uncertainty information. As for stationarity we found that good testing is essential. Inferences on extremes may be wrong if data are assumed stationary while they are not. The same holds for the block-stationarity assumption. As for PDF choices we found that often more than one PDF shape fits to the same data. From a simulation study we conclude that both the generalized extreme value (GEV) distribution and the log-normal PDF fit very well to a variety of indicators. The application of the normal and Gumbel distributions is more limited. As for uncertainty it is advised to test conclusions on extremes for assumptions underlying the modeling approach. Finally, we

  12. Great apes and children infer causal relations from patterns of variation and covariation.

    PubMed

    Völter, Christoph J; Sentís, Inés; Call, Josep

    2016-10-01

    We investigated whether nonhuman great apes (N=23), 2.5-year-old (N=20), and 3-year-old children (N=40) infer causal relations from patterns of variation and covariation by adapting the blicket detector paradigm for apes. We presented chimpanzees (Pan troglodytes), bonobos (Pan paniscus), orangutans (Pongo abelii), gorillas (Gorilla gorilla), and children (Homo sapiens) with a novel reward dispenser, the blicket detector. The detector was activated by inserting specific (yet randomly determined) objects, the so-called blickets. Once activated a reward was released, accompanied by lights and a short tone. Participants were shown different patterns of variation and covariation between two different objects and the activation of the detector. When subsequently choosing between one of the two objects to activate the detector on their own all species, except gorillas (who failed the training), took these patterns of correlation into account. In particular, apes and 2.5-year-old children ignored objects whose effect on the detector completely depended on the presence of another object. Follow-up experiments explored whether the apes and children were also able to re-evaluate evidence retrospectively. Only children (3-year-olds in particular) were able to make such retrospective inferences about causal structures from observing the effects of the experimenter's actions. Apes succeeded here only when they observed the effects of their own interventions. Together, this study provides evidence that apes, like young children, accurately infer causal structures from patterns of (co)variation and that they use this information to inform their own interventions. PMID:27343481

  13. Reading a suspenseful literary text activates brain areas related to social cognition and predictive inference.

    PubMed

    Lehne, Moritz; Engel, Philipp; Rohrmeier, Martin; Menninghaus, Winfried; Jacobs, Arthur M; Koelsch, Stefan

    2015-01-01

    Stories can elicit powerful emotions. A key emotional response to narrative plots (e.g., novels, movies, etc.) is suspense. Suspense appears to build on basic aspects of human cognition such as processes of expectation, anticipation, and prediction. However, the neural processes underlying emotional experiences of suspense have not been previously investigated. We acquired functional magnetic resonance imaging (fMRI) data while participants read a suspenseful literary text (E.T.A. Hoffmann's "The Sandman") subdivided into short text passages. Individual ratings of experienced suspense obtained after each text passage were found to be related to activation in the medial frontal cortex, bilateral frontal regions (along the inferior frontal sulcus), lateral premotor cortex, as well as posterior temporal and temporo-parietal areas. The results indicate that the emotional experience of suspense depends on brain areas associated with social cognition and predictive inference.

  14. Reading a Suspenseful Literary Text Activates Brain Areas Related to Social Cognition and Predictive Inference

    PubMed Central

    Lehne, Moritz; Engel, Philipp; Rohrmeier, Martin; Menninghaus, Winfried; Jacobs, Arthur M.; Koelsch, Stefan

    2015-01-01

    Stories can elicit powerful emotions. A key emotional response to narrative plots (e.g., novels, movies, etc.) is suspense. Suspense appears to build on basic aspects of human cognition such as processes of expectation, anticipation, and prediction. However, the neural processes underlying emotional experiences of suspense have not been previously investigated. We acquired functional magnetic resonance imaging (fMRI) data while participants read a suspenseful literary text (E.T.A. Hoffmann's “The Sandman”) subdivided into short text passages. Individual ratings of experienced suspense obtained after each text passage were found to be related to activation in the medial frontal cortex, bilateral frontal regions (along the inferior frontal sulcus), lateral premotor cortex, as well as posterior temporal and temporo-parietal areas. The results indicate that the emotional experience of suspense depends on brain areas associated with social cognition and predictive inference. PMID:25946306

  15. Correct names for some of the closest relatives of Carica papaya: A review of the Mexican/Guatemalan genera Jarilla and Horovitzia

    PubMed Central

    Carvalho, Fernanda Antunes; Renner, Susanne S.

    2013-01-01

    Abstract Using molecular data, we recently showed that Carica papaya L. is sister to a Mexican/Guatemalan clade of two genera, Jarilla Rusby with three species and Horovitzia V.M. Badillo with one. These species are herbs or thin-stemmed trees and may be of interest for future genomics-enabled papaya breeding. Here we clarify the correct names of Jarilla heterophylla (Cerv. ex La Llave) Rusby and Jarilla caudata (Brandegee) Standl., which were confused in a recent systematic treatment of Jarilla (McVaugh 2001). We designate epitypes for both, provide weblinks to type specimens, a key to the species of Jarilla and Horovitzia, and notes on their habitats and distribution. PMID:24399895

  16. A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium

    SciTech Connect

    Taylor, Ronald C.; Singhal, Mudita; Weller, Jennifer B.; Khoshnevis, Saeed; Shi, Liang; McDermott, Jason E.

    2009-04-20

    Inference of the structure of mRNA transcriptional regulatory networks, protein regulatory or interaction networks, and protein activation/inactivation-based signal transduction networks are critical tasks in systems biology. In this article we discuss a workflow for the reconstruction of parts of the transcriptional regulatory network of the pathogenic bacterium Salmonella typhimurium based on the information contained in sets of microarray gene expression data now available for that organism, and describe our results obtained by following this workflow. The primary tool is one of the network inference algorithms deployed in the Software Environment for BIological Network Inference (SEBINI). Specifically, we selected the algorithm called Context Likelihood of Relatedness (CLR), which uses the mutual information contained in the gene expression data to infer regulatory connections. The associated analysis pipeline automatically stores the inferred edges from the CLR runs within SEBINI and, upon request, transfers the inferred edges into either Cytoscape or the plug-in Collective Analysis of Biological of Biological Interaction Networks (CABIN) tool for further post-analysis of the inferred regulatory edges. The following article presents the outcome of this workflow, as well as the protocols followed for microarray data collection, data cleansing, and network inference. Our analysis revealed several interesting interactions, functional groups, metabolic pathways, and regulons in S. typhimurium.

  17. Inferring the phylogenetic position of Boa constrictor among the Boinae.

    PubMed

    Burbrink, Frank T

    2005-01-01

    Snakes of the subfamily Boinae are found in Madagascar, the Papuan-Pacific Islands, and the Neotropics. It has been suggested that genera within each of these particular areas do not form monophyletic groups. Further, it was proposed that the New World Boa constrictor is more closely related to boine genera in Madagascar than to boines in the Neotropics. Along with inferring the relationship of all boine genera using data from the cytochrome b gene and morphology, the placement of Boa was also examined. Phylogenetic inferences using maximum likelihood and Bayesian (BI) methods for combined data analyses and separate analyses of DNA sequence and morphological data were conducted. Priors, parametric bootstraps, and the Shimodaira-Hasegawa test were used to examine the previously proposed placement of Boa with Madagascan taxa using these DNA data. DNA data and combined data analyses strongly reject the hypothesis that Boa is more closely related to Old World genera than to other New World genera. Additionally, strong tree support suggests that all species within Madagascar, the Papuan-Pacific Islands, and the Neotropics each form a monophyletic group with respect to their geographic region.

  18. Inference of Distant Genetic Relations in Humans Using “1000 Genomes”

    PubMed Central

    Al-Khudhair, Ahmed; Qiu, Shuhao; Wyse, Meghan; Chowdhury, Shilpi; Cheng, Xi; Bekbolsynov, Dulat; Saha-Mandal, Arnab; Dutta, Rajib; Fedorova, Larisa; Fedorov, Alexei

    2015-01-01

    Nucleotide sequence differences on the whole-genome scale have been computed for 1,092 people from 14 populations publicly available by the 1000 Genomes Project. Total number of differences in genetic variants between 96,464 human pairs has been calculated. The distributions of these differences for individuals within European, Asian, or African origin were characterized by narrow unimodal peaks with mean values of 3.8, 3.5, and 5.1 million, respectively, and standard deviations of 0.1–0.03 million. The total numbers of genomic differences between pairs of all known relatives were found to be significantly lower than their respective population means and in reverse proportion to the distance of their consanguinity. By counting the total number of genomic differences it is possible to infer familial relations for people that share down to 6% of common loci identical-by-descent. Detection of familial relations can be radically improved when only very rare genetic variants are taken into account. Counting of total number of shared very rare single nucleotide polymorphisms (SNPs) from whole-genome sequences allows establishing distant familial relations for persons with eighth and ninth degrees of relationship. Using this analysis we predicted 271 distant familial pairwise relations among 1,092 individuals that have not been declared by 1000 Genomes Project. Particularly, among 89 British and 97 Chinese individuals we found three British–Chinese pairs with distant genetic relationships. Individuals from these pairs share identical-by-descent DNA fragments that represent 0.001%, 0.004%, and 0.01% of their genomes. With affordable whole-genome sequencing techniques, very rare SNPs should become important genetic markers for familial relationships and population stratification. PMID:25573959

  19. The early emergence and puzzling decline of relational reasoning: Effects of knowledge and search on inferring abstract concepts.

    PubMed

    Walker, Caren M; Bridgers, Sophie; Gopnik, Alison

    2016-11-01

    We explore the developmental trajectory and underlying mechanisms of abstract relational reasoning. We describe a surprising developmental pattern: Younger learners are better than older ones at inferring abstract causal relations. Walker and Gopnik (2014) demonstrated that toddlers are able to infer that an effect was caused by a relation between two objects (whether they are the same or different), rather than by individual kinds of objects. While these findings are consistent with evidence that infants recognize same-different relations, they contrast with a large literature suggesting that older children tend to have difficulty inferring these relations. Why might this be? In Experiment 1a, we demonstrate that while younger children (18-30-month-olds) have no difficulty learning these relational concepts, older children (36-48-month-olds) fail to draw this abstract inference. Experiment 1b replicates the finding with 18-30-month-olds using a more demanding intervention task. Experiment 2 tests whether this difference in performance might be because older children have developed the general hypothesis that individual kinds of objects are causal - the high initial probability of this alternative hypothesis might override the data that favors the relational hypothesis. Providing additional information falsifying the alternative hypothesis improves older children's performance. Finally, Experiment 3 demonstrates that prompting for explanations during learning also improves performance, even without any additional information. These findings are discussed in light of recent computational and algorithmic theories of learning.

  20. The early emergence and puzzling decline of relational reasoning: Effects of knowledge and search on inferring abstract concepts.

    PubMed

    Walker, Caren M; Bridgers, Sophie; Gopnik, Alison

    2016-11-01

    We explore the developmental trajectory and underlying mechanisms of abstract relational reasoning. We describe a surprising developmental pattern: Younger learners are better than older ones at inferring abstract causal relations. Walker and Gopnik (2014) demonstrated that toddlers are able to infer that an effect was caused by a relation between two objects (whether they are the same or different), rather than by individual kinds of objects. While these findings are consistent with evidence that infants recognize same-different relations, they contrast with a large literature suggesting that older children tend to have difficulty inferring these relations. Why might this be? In Experiment 1a, we demonstrate that while younger children (18-30-month-olds) have no difficulty learning these relational concepts, older children (36-48-month-olds) fail to draw this abstract inference. Experiment 1b replicates the finding with 18-30-month-olds using a more demanding intervention task. Experiment 2 tests whether this difference in performance might be because older children have developed the general hypothesis that individual kinds of objects are causal - the high initial probability of this alternative hypothesis might override the data that favors the relational hypothesis. Providing additional information falsifying the alternative hypothesis improves older children's performance. Finally, Experiment 3 demonstrates that prompting for explanations during learning also improves performance, even without any additional information. These findings are discussed in light of recent computational and algorithmic theories of learning. PMID:27472036

  1. Two new species of Cylicospirura Vevers, 1922 (Nematoda: Spirocercidae) from carnivores in southern Africa, with validation of the related genera Gastronodus Singh, 1934 and Skrjabinocercina Matschulsky, 1952.

    PubMed

    Junker, Kerstin; Lane, Emily P; McRee, Anna E; Foggin, Chris; van Dyk, D Schalk; Mutafchiev, Yasen

    2013-09-01

    Two new species of Cylicospirura Vevers, 1922 are described from carnivores from southern Africa. Cylicospirura crocutae Junker et Mutafchiev sp. n. from Crocuta crocuta (Erxleben) in Zimbabwe is distinguished from its congeners by combinations of characters, including the presence of four cephalic and four external labial papillae, while internal labial papillae were not distinct, the presence of groups of small accessory teeth between the six large tricuspid teeth, the fifth and the sixth pairs of the caudal papillae being equidistant from the cloaca, and a large ratio of length of the muscular oesophagus to that of the glandular oesophagus. Cylicospirura pardalis Junker et Mutafchiev sp. n. from Panthera pardus (Linnaeus) in the Republic of South Africa is characterized by having tricuspid teeth with large, claw-like, abaxial cusps, four cephalic and six internal labial papillae. Based on the number of caudal papillae and the position of the vulva, the subgenera Gastronodus Singh, 1934 and Skrjabinocercina Matschulsky, 1952 are re-elevated to generic rank. Amended diagnoses are proposed for the genera Cylicospirura, Gastronodus and Skrjabinocercina. Petrowospirura lyncis Matschulsky, 1952 is recognized as valid and, together with P. petrowi Sadykhov, 1957 and P. barusi Arya, 1979, is transferred to Cylicospirura as C. lyncis (Matschulsky, 1952) Junker et Mutafchiev comb. n., C. petrowi (Sadykhov, 1957) Junker et Mutafchiev comb. n. and C. barusi (Arya, 1979) Junker et Mutafchiev comb. n., respectively. PMID:24261135

  2. Two new species of Cylicospirura Vevers, 1922 (Nematoda: Spirocercidae) from carnivores in southern Africa, with validation of the related genera Gastronodus Singh, 1934 and Skrjabinocercina Matschulsky, 1952.

    PubMed

    Junker, Kerstin; Lane, Emily P; McRee, Anna E; Foggin, Chris; van Dyk, D Schalk; Mutafchiev, Yasen

    2013-09-01

    Two new species of Cylicospirura Vevers, 1922 are described from carnivores from southern Africa. Cylicospirura crocutae Junker et Mutafchiev sp. n. from Crocuta crocuta (Erxleben) in Zimbabwe is distinguished from its congeners by combinations of characters, including the presence of four cephalic and four external labial papillae, while internal labial papillae were not distinct, the presence of groups of small accessory teeth between the six large tricuspid teeth, the fifth and the sixth pairs of the caudal papillae being equidistant from the cloaca, and a large ratio of length of the muscular oesophagus to that of the glandular oesophagus. Cylicospirura pardalis Junker et Mutafchiev sp. n. from Panthera pardus (Linnaeus) in the Republic of South Africa is characterized by having tricuspid teeth with large, claw-like, abaxial cusps, four cephalic and six internal labial papillae. Based on the number of caudal papillae and the position of the vulva, the subgenera Gastronodus Singh, 1934 and Skrjabinocercina Matschulsky, 1952 are re-elevated to generic rank. Amended diagnoses are proposed for the genera Cylicospirura, Gastronodus and Skrjabinocercina. Petrowospirura lyncis Matschulsky, 1952 is recognized as valid and, together with P. petrowi Sadykhov, 1957 and P. barusi Arya, 1979, is transferred to Cylicospirura as C. lyncis (Matschulsky, 1952) Junker et Mutafchiev comb. n., C. petrowi (Sadykhov, 1957) Junker et Mutafchiev comb. n. and C. barusi (Arya, 1979) Junker et Mutafchiev comb. n., respectively.

  3. Do people reason rationally about causally related events? Markov violations, weak inferences, and failures of explaining away.

    PubMed

    Rottman, Benjamin M; Hastie, Reid

    2016-06-01

    Making judgments by relying on beliefs about the causal relationships between events is a fundamental capacity of everyday cognition. In the last decade, Causal Bayesian Networks have been proposed as a framework for modeling causal reasoning. Two experiments were conducted to provide comprehensive data sets with which to evaluate a variety of different types of judgments in comparison to the standard Bayesian networks calculations. Participants were introduced to a fictional system of three events and observed a set of learning trials that instantiated the multivariate distribution relating the three variables. We tested inferences on chains X1→Y→X2, common cause structures X1←Y→X2, and common effect structures X1→Y←X2, on binary and numerical variables, and with high and intermediate causal strengths. We tested transitive inferences, inferences when one variable is irrelevant because it is blocked by an intervening variable (Markov Assumption), inferences from two variables to a middle variable, and inferences about the presence of one cause when the alternative cause was known to have occurred (the normative "explaining away" pattern). Compared to the normative account, in general, when the judgments should change, they change in the normative direction. However, we also discuss a few persistent violations of the standard normative model. In addition, we evaluate the relative success of 12 theoretical explanations for these deviations.

  4. Genera of the human lineage

    PubMed Central

    Cela-Conde, Camilo J.; Ayala, Francisco J.

    2003-01-01

    Human fossils dated between 3.5 and nearly 7 million years old discovered during the last 8 years have been assigned to as many as four new genera of the family Hominidae: Ardipithecus, Orrorin, Kenyanthropus, and Sahelanthropus. These specimens are described as having morphological traits that justify placing them in the family Hominidae while creating a new genus for the classification of each. The discovery of these fossils pushed backward by >2 million years the date of the oldest hominids known. Only two or three hominid genera, Australopithecus, Paranthropus, and Homo, had been previously accepted, with Paranthropus considered a subgenus of Australopithecus by some authors. Two questions arise from the classification of the newly discovered fossils: (i) Should each one of these specimens be placed in the family Hominidae? (ii) Are these specimens sufficiently distinct to justify the creation of four new genera? The answers depend, in turn, on the concepts of what is a hominid and how the genus category is defined. These specimens seem to possess a sufficient number of morphological traits to be placed in the Hominidae. However, the nature of the morphological evidence and the adaptation-rooted concept of what a genus is do not justify the establishment of four new genera. We propose a classification that includes four well defined genera: Praeanthropus, Ardipithecus, Australopithecus, and Homo, plus one tentative incertae sedis genus: Sahelanthropus. PMID:12794185

  5. Methods for inferring health-related social networks among coworkers from online communication patterns.

    PubMed

    Matthews, Luke J; DeWan, Peter; Rula, Elizabeth Y

    2013-01-01

    Studies of social networks, mapped using self-reported contacts, have demonstrated the strong influence of social connections on the propensity for individuals to adopt or maintain healthy behaviors and on their likelihood to adopt health risks such as obesity. Social network analysis may prove useful for businesses and organizations that wish to improve the health of their populations by identifying key network positions. Health traits have been shown to correlate across friendship ties, but evaluating network effects in large coworker populations presents the challenge of obtaining sufficiently comprehensive network data. The purpose of this study was to evaluate methods for using online communication data to generate comprehensive network maps that reproduce the health-associated properties of an offline social network. In this study, we examined three techniques for inferring social relationships from email traffic data in an employee population using thresholds based on: (1) the absolute number of emails exchanged, (2) logistic regression probability of an offline relationship, and (3) the highest ranked email exchange partners. As a model of the offline social network in the same population, a network map was created using social ties reported in a survey instrument. The email networks were evaluated based on the proportion of survey ties captured, comparisons of common network metrics, and autocorrelation of body mass index (BMI) across social ties. Results demonstrated that logistic regression predicted the greatest proportion of offline social ties, thresholding on number of emails exchanged produced the best match to offline network metrics, and ranked email partners demonstrated the strongest autocorrelation of BMI. Since each method had unique strengths, researchers should choose a method based on the aspects of offline behavior of interest. Ranked email partners may be particularly useful for purposes related to health traits in a social network.

  6. Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs) : 3. Genome relationships in Brassica and related genera and the origin of B. oleracea and B. rapa (syn. campestns).

    PubMed

    Song, K; Osborn, T C; Williams, P H

    1990-04-01

    RFLPs were used to study genome evolution and phylogeny in Brassica and related genera. Thirtyeight accessions, including 10 accessions of B. rapa (syn. campestris), 9 cultivated types of B. oleracea, 13 nine-chromosome wild brassicas related to B. oleracea, and 6 other species in Brassica and allied genera, were examined with more then 30 random genomic DNA probes, which identified RFLPs mapping to nine different linkage groups of the B. rapa genome. Based on the RFLP data, phylogenetic trees were constructed using the PAUP microcomputer program. Within B. rapa, accessions of pak choi, narinosa, and Chinese cabbage from East Asia constituted a group distinct from turnip and wild European populations, consistent with the hypothesis that B. rapa had two centers of domestication. A wild B. rapa accession from India was positioned in the tree between European types and East Asian types, suggesting an evolutionary pathway from Europe to India, then to South China. Cultivated B. oleracea morphotypes showed monophyletic origin with wild B. oleracea or B. alboglabra as possible ancestors. Various kales constitute a highly diverse group, and represent the primitive morphotypes of cultivated B. oleracea from which cabbage, broccoli, cauliflower, etc. probably have evolved. Cauliflower was found to be closely related to broccoli, whereas cabbage was closely related to leafy kales. A great diversity existed among the 13 collections of nine-chromosome wild brassicas related to B. oleracea, representing various taxonomic states from subspecies to species. Results from these studies suggested that two basic evolutionary pathways exist for the diploid species examined. One pathway gave rise to B. fruticulosa, B. nigra, and Sinapis arvensis, with B. adpressa or a close relative as the initial ancestor. Another pathway gave rise to B. oleracea and B. rapa, with Diplotaxis erucoides or a close relative as the initial ancestor. Raphanus sativus and Eruca sativus represented

  7. Liouville Theory and Elliptic Genera

    NASA Astrophysics Data System (ADS)

    Taormina, A.

    The structure and modular properties of N = 4 superconformal characters are reviewed and exploited, in an attempt to construct elliptic genera-like functions by decompactifying K_3. The construction is tested against expressions obtained in the context of strings propagating in background ALE spaces of type A_{N-1}, using the underlying superconformal theory N = 2 minimal ⊗ N = 2 Liouville.

  8. Relative Contribution of Vocabulary Knowledge and Working Memory Span to Elaborative Inferences in Reading

    ERIC Educational Resources Information Center

    Calvo, Manuel G.

    2005-01-01

    Eye fixations were assessed during the reading of continuation sentences confirming inferences suggested by a preceding context sentence. In multiple regression analysis, individual differences in available prior vocabulary knowledge, working memory span, and speed of access to prior word knowledge served as predictors of eye fixations.…

  9. A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA.

    PubMed

    Yang, Yau-Wen; Tai, Pon-Yean; Chen, Ying; Li, Wen-Hsiung

    2002-05-01

    There are two evolutionary lineages in the genus Brassica: the rapa/oleracea lineage and the nigra lineage. Using nuclear DNA sequences such as the intergenic spacer between 5S rRNA genes and the internal transcribed spacer between 18S and 25S rRNA genes, we and others had previously demonstrated that Raphanus sativus is closely related to the nigra lineage. In the present study, we sequenced the chloroplast noncoding region between trnT and trnF and that between trnD and trnT in seven species and showed that R. sativus is more closely related to the rapa/oleracea lineage than to the nigra lineage. The conflicting results from nuclear DNA and chloroplast DNA support the hypothesis that Raphanus was derived from a hybridization between the rapa/oleracea and the nigra lineages. We estimated the date of this hybridization event to be 60% of the divergence time between the two Brassica lineages. In addition, the pattern and rate of nucleotide substitution were studied. There were more transversions than transitions in these noncoding regions, which have a high AT content. Furthermore, the proportion of transversions among the substitutions at a site increases with increasing A + T content of its two adjacent nucleotides. An influence of immediate 5(') pyrimidine on substitution pattern is also observed when both adjacent bases in the two DNA strands are A or T. The rate of nucleotide substitution in the trnL group I intron is only about one third of the rate in the nearby intergenic spacers in the trnT-trnF fragment. The rate of nucleotide substitution in the rapa/oleracea lineage is at least 1.5 times that in the nigra lineage.

  10. Bergbambos and Oldeania, new genera of African bamboos (Poaceae, Bambusoideae)

    PubMed Central

    Stapleton, Chris M. A.

    2013-01-01

    Abstract Two new monotypic genera, Bergbambos and Oldeania are described for African temperate bamboo species in the tribe Arundinarieae, after a comparison of their morphological characteristics with those of similar species from Asia. Morphological differences are supported by their isolated geographical distributions. Molecular evidence does not support the inclusion of these species in related Asian genera, recognising them instead as distinct lineages. New combinations Bergbambos tessellata and Oldeania alpina are made. PMID:24198715

  11. Australian Marsh Beetles (Coleoptera: Scirtidae). 9. The relations of Australasian Ypsiloncyphon species to their Asian congeners, additions, mainly to Petrocyphon and Prionocyphon, and a key to Australian genera of Scirtinae.

    PubMed

    Zwick, Peter

    2016-03-02

    The endemic Australasian species of Ypsiloncyphon are the sister group of the combined Asian species groups 1, 2, and 4. The description of the type species, Y. chlorizans (Klausnitzer), is supplemented by details of male and female genitalia. New species are described and illustrated in several genera: Austrocyphon scissus n. sp., Leptocyphon abnormis n. sp., Petrocyphon bonang n. sp., P. lacteus n. sp., P. televisionarius n. sp., Prionocyphon bidentatus n. sp., P. cacatua n. sp., P. laurae n. sp., P. neboissi n. sp., P. serratus n. sp., P. uncatus n. sp., and P. urbanus n. sp. Genus Prionocyphon is distinguished from Oriental genera with similar antennal modifications. However, a synapomorphy of Prionocyphon as presently understood is not known. Supplementary information on various species in the aforementioned genera and in Pachycyphon and Calvarium is provided. A key to the genera of adult Australian Scirtidae: Scirtinae is presented.

  12. Late Quaternary paleoclimate of western Alaska inferred from fossil chironomids and its relation to vegetation histories

    USGS Publications Warehouse

    Kurek, Joshua; Cwynar, Les C.; Ager, Thomas A.; Abbott, Mark B.; Edwards, Mary E.

    2009-01-01

    Fossil Chironomidae assemblages (with a few Chaoboridae and Ceratopogonidae) from Zagoskin and Burial Lakes in western Alaska provide quantitative reconstructions of mean July air temperatures for periods of the late-middle Wisconsin (~39,000-34,000 cal yr B.P.) to the present. Inferred temperatures are compared with previously analyzed pollen data from each site summarized here by indirect ordination. Paleotemperature trends reveal substantial differences in the timing of climatic warming following the late Wisconsin at each site, although chronological uncertainty exists. Zagoskin Lake shows early warming beginning at about 21,000 cal yr B.P., whereas warming at Burial Lake begins ~4000 years later. Summer climates during the last glacial maximum (LGM) were on average ~3.5C° below the modern temperatures at each site. Major shifts in vegetation occurred from ~19,000 to 10,000 cal yr B.P. at Zagoskin Lake and from ~17,000 to 10,000 cal yr B.P. at Burial Lake. Vegetation shifts followed climatic warming, when temperatures neared modern values. Both sites provide evidence of an early postglacial thermal maximum at ~12,300 cal yr B.P. These chironomid records, combined with other insect-based climatic reconstructions from Beringia, indicate that during the LGM: (1) greater continentality likely influenced regions adjacent to the Bering Land Bridge and (2) summer climates were, at times, not dominated by severe cold.

  13. Getting a cue before getting a clue: Event-related potentials to inference in visual narrative comprehension.

    PubMed

    Cohn, Neil; Kutas, Marta

    2015-10-01

    Inference has long been emphasized in the comprehension of verbal and visual narratives. Here, we measured event-related brain potentials to visual sequences designed to elicit inferential processing. In Impoverished sequences, an expressionless "onlooker" watches an undepicted event (e.g., person throws a ball for a dog, then watches the dog chase it) just prior to a surprising finale (e.g., someone else returns the ball), which should lead to an inference (i.e., the different person retrieved the ball). Implied sequences alter this narrative structure by adding visual cues to the critical panel such as a surprised facial expression to the onlooker implying they saw an unexpected, albeit undepicted, event. In contrast, Expected sequences show a predictable, but then confounded, event (i.e., dog retrieves ball, then different person returns it), and Explicit sequences depict the unexpected event (i.e., different person retrieves then returns ball). At the critical penultimate panel, sequences representing depicted events (Explicit, Expected) elicited a larger posterior positivity (P600) than the relatively passive events of an onlooker (Impoverished, Implied), though Implied sequences were slightly more positive than Impoverished sequences. At the subsequent and final panel, a posterior positivity (P600) was greater to images in Impoverished sequences than those in Explicit and Implied sequences, which did not differ. In addition, both sequence types requiring inference (Implied, Impoverished) elicited a larger frontal negativity than those explicitly depicting events (Expected, Explicit). These results show that neural processing differs for visual narratives omitting events versus those depicting events, and that the presence of subtle visual cues can modulate such effects presumably by altering narrative structure. PMID:26320706

  14. Getting a cue before getting a clue: Event-related potentials to inference in visual narrative comprehension.

    PubMed

    Cohn, Neil; Kutas, Marta

    2015-10-01

    Inference has long been emphasized in the comprehension of verbal and visual narratives. Here, we measured event-related brain potentials to visual sequences designed to elicit inferential processing. In Impoverished sequences, an expressionless "onlooker" watches an undepicted event (e.g., person throws a ball for a dog, then watches the dog chase it) just prior to a surprising finale (e.g., someone else returns the ball), which should lead to an inference (i.e., the different person retrieved the ball). Implied sequences alter this narrative structure by adding visual cues to the critical panel such as a surprised facial expression to the onlooker implying they saw an unexpected, albeit undepicted, event. In contrast, Expected sequences show a predictable, but then confounded, event (i.e., dog retrieves ball, then different person returns it), and Explicit sequences depict the unexpected event (i.e., different person retrieves then returns ball). At the critical penultimate panel, sequences representing depicted events (Explicit, Expected) elicited a larger posterior positivity (P600) than the relatively passive events of an onlooker (Impoverished, Implied), though Implied sequences were slightly more positive than Impoverished sequences. At the subsequent and final panel, a posterior positivity (P600) was greater to images in Impoverished sequences than those in Explicit and Implied sequences, which did not differ. In addition, both sequence types requiring inference (Implied, Impoverished) elicited a larger frontal negativity than those explicitly depicting events (Expected, Explicit). These results show that neural processing differs for visual narratives omitting events versus those depicting events, and that the presence of subtle visual cues can modulate such effects presumably by altering narrative structure.

  15. Getting a cue before getting a clue: Event-related potentials to inference in visual narrative comprehension

    PubMed Central

    Cohn, Neil; Kutas, Marta

    2015-01-01

    Inference has long been emphasized in the comprehension of verbal and visual narratives. Here, we measured event-related brain potentials to visual sequences designed to elicit inferential processing. In Impoverished sequences, an expressionless “onlooker” watches an undepicted event (e.g., person throws a ball for a dog, then watches the dog chase it) just prior to a surprising finale (e.g., someone else returns the ball), which should lead to an inference (i.e., the different person retrieved the ball). Implied sequences alter this narrative structure by adding visual cues to the critical panel such as a surprised facial expression to the onlooker implying they saw an unexpected, albeit undepicted, event. In contrast, Expected sequences show a predictable, but then confounded, event (i.e., dog retrieves ball, then different person returns it), and Explicit sequences depict the unexpected event (i.e., different person retrieves then returns ball). At the critical penultimate panel, sequences representing depicted events (Explicit, Expected) elicited a larger posterior positivity (P600) than the relatively passive events of an onlooker (Impoverished, Implied), though Implied sequences were slightly more positive than Impoverished sequences. At the subsequent and final panel, a posterior positivity (P600) was greater to images in Impoverished sequences than those in Explicit and Implied sequences, which did not differ. In addition, both sequence types requiring inference (Implied, Impoverished) elicited a larger frontal negativity than those explicitly depicting events (Expected, Explicit). These results show that neural processing differs for visual narratives omitting events versus those depicting events, and that the presence of subtle visual cues can modulate such effects presumably by altering narrative structure. PMID:26320706

  16. A Hybrid Approach to Inferring a Consistent Temporal Relation Set in Natural Language Text

    ERIC Educational Resources Information Center

    Lee, Chong Min

    2013-01-01

    This dissertation investigates the temporal relation identification task. The goal is to construct consistent temporal relations between temporal entities (e.g., events and time expressions) in a narrative. Constructing consistent temporal relations is challenging due to the exponential increase in the number of candidates for temporal relations…

  17. Geographic distribution and dispersal of normapolles genera in North America

    USGS Publications Warehouse

    Tschudy, R.H.

    1981-01-01

    Normapolles pollen have been found in North America in Cretaceous and Lower Tertiary rocks from the eastern Atlantic Seaboard, the Mississippi embayment region and from the states and provinces from western North America as far north as the District of Mackenzie, Northwest Territories. Previous postulates relating to the Normapolles floral province (western Europe-eastern North America) were re-examined in the light of new finds of Normapolles genera in rocks from west of the Cretaceous epeiric seaway which separated the Normapolles province from the western North American Aquilapollenites province. A study of published occurrences of Normapolles genera and U.S. Geological Survey Denver Laboratory Normapolles records revealed that of the approximately 60 Normapolles genera recognized from western Europe, only 26 of these have been recognized from eastern North America. These data suggest that Normapolles-producing plants originated in western Europe and migrated to eastern North America prior to the opening of the north Atlantic seaway. Ten of these 26 genera also have been found in rocks from west of the Cretaceous epeiric seaway, suggesting that these genera were the only ones able to cross this barrier. At least six genera having Normapolles characteristics occur in eastern North America but have not yet been recorded from Europe. Two additional genera with Normapolles characteristics have been reported only from the Aquilapollenites province of western North America. Several discrepancies in the record need resolution, such as the latitudinal restriction of Thomsonipollis and Nudopollis to areas south 40??N latitude, the absence of records of Thomsonipollis east and north of central Georgia, and the absence of records of Kyandopollenites and Choanopollenites west of eastern Texas. These data show that the known boundaries of the Normapolles province are somewhat hazy and that firm conclusions regarding the geographic distribution and history of dispersal of

  18. Neural correlates of inferring speaker sincerity from white lies: an event-related potential source localization study.

    PubMed

    Rigoulot, Simon; Fish, Karyn; Pell, Marc D

    2014-05-27

    During social interactions, listeners weigh the importance of linguistic and extra-linguistic speech cues (prosody) to infer the true intentions of the speaker in reference to what is actually said. In this study, we investigated what brain processes allow listeners to detect when a spoken compliment is meant to be sincere (true compliment) or not ("white lie"). Electroencephalograms of 29 participants were recorded while they listened to Question-Response pairs, where the response was expressed in either a sincere or insincere tone (e.g., "So, what did you think of my presentation?"/"I found it really interesting."). Participants judged whether the response was sincere or not. Behavioral results showed that prosody could be effectively used to discern the intended sincerity of compliments. Analysis of temporal and spatial characteristics of event-related potentials (P200, N400, P600) uncovered significant effects of prosody on P600 amplitudes, which were greater in response to sincere versus insincere compliments. Using low resolution brain electromagnetic tomography (LORETA), we determined that the anatomical sources of this activity were likely located in the (left) insula, consistent with previous reports of insular activity in the perception of lies and concealments. These data extend knowledge of the neurocognitive mechanisms that permit context-appropriate inferences about speaker feelings and intentions during interpersonal communication.

  19. On the transmission of partial information: inferences from movement-related brain potentials

    NASA Technical Reports Server (NTRS)

    Osman, A.; Bashore, T. R.; Coles, M. G.; Donchin, E.; Meyer, D. E.

    1992-01-01

    Results are reported from a new paradigm that uses movement-related brain potentials to detect response preparation based on partial information. The paradigm uses a hybrid choice-reaction go/nogo procedure in which decisions about response hand and whether to respond are based on separate stimulus attributes. A lateral asymmetry in the movement-related brain potential was found on nogo trials without overt movement. The direction of this asymmetry depended primarily on the signaled response hand rather than on properties of the stimulus. When the asymmetry first appeared was influenced by the time required to select the signaled hand, and when it began to differ on go and nogo trials was influenced by the time to decide whether to respond. These findings indicate that both stimulus attributes were processed in parallel and that the asymmetry reflected preparation of the response hand that began before the go/nogo decision was completed.

  20. Distinctions between the snake genera Contia and Eirenis

    USGS Publications Warehouse

    Stickel, W.H.

    1951-01-01

    Summary: Various workers have believed Contia to be related to or congeneric with either or both Sonora and Eirenis, the latter a genus of Western Asia. Study of hemipenes, teeth, and jaws indicates that these genera are not related to one another. The hemipenes of Eirenis modesta and Contia tenuis are described. Eirenis is thought to be a derivative of the racer group. Relationships of Contia are unknown. It is suggested that some North American genera with xenodontine-type hemipenes may not be of the South American faunal element and may have been in North America at least as long as the Old Northerners.

  1. Coping with Trial-to-Trial Variability of Event Related Signals: A Bayesian Inference Approach

    NASA Technical Reports Server (NTRS)

    Ding, Mingzhou; Chen, Youghong; Knuth, Kevin H.; Bressler, Steven L.; Schroeder, Charles E.

    2005-01-01

    In electro-neurophysiology, single-trial brain responses to a sensory stimulus or a motor act are commonly assumed to result from the linear superposition of a stereotypic event-related signal (e.g. the event-related potential or ERP) that is invariant across trials and some ongoing brain activity often referred to as noise. To extract the signal, one performs an ensemble average of the brain responses over many identical trials to attenuate the noise. To date, h s simple signal-plus-noise (SPN) model has been the dominant approach in cognitive neuroscience. Mounting empirical evidence has shown that the assumptions underlying this model may be overly simplistic. More realistic models have been proposed that account for the trial-to-trial variability of the event-related signal as well as the possibility of multiple differentially varying components within a given ERP waveform. The variable-signal-plus-noise (VSPN) model, which has been demonstrated to provide the foundation for separation and characterization of multiple differentially varying components, has the potential to provide a rich source of information for questions related to neural functions that complement the SPN model. Thus, being able to estimate the amplitude and latency of each ERP component on a trial-by-trial basis provides a critical link between the perceived benefits of the VSPN model and its many concrete applications. In this paper we describe a Bayesian approach to deal with this issue and the resulting strategy is referred to as the differentially Variable Component Analysis (dVCA). We compare the performance of dVCA on simulated data with Independent Component Analysis (ICA) and analyze neurobiological recordings from monkeys performing cognitive tasks.

  2. A smaller Macadamia from a more vagile tribe: inference of phylogenetic relationships, divergence times, and diaspore evolution in Macadamia and relatives (tribe Macadamieae; Proteaceae).

    PubMed

    Mast, Austin R; Willis, Crystal L; Jones, Eric H; Downs, Katherine M; Weston, Peter H

    2008-07-01

    Tribe Macadamieae (91 spp., 16 genera; Proteaceae) is widespread across the southern hemisphere on all major fragments of Gondwana except New Zealand and India. Macadamia is cultivated outside its natural range as a "nut" crop (notably in Hawaii, where it is the principal orchard crop). We sampled seven DNA regions and 53 morphological characters from the tribe to infer its phylogeny and address the common assumption that the distribution of the extant diversity of the tribe arose by the rafting of ancestors on Gondwanan fragments. Macadamia proves to be paraphyletic with respect to the African genus Brabejum, the South American genus Panopsis, and the Australian species Orites megacarpus. We erect two new generic names, Nothorites and Lasjia, to produce monophyly at that rank. The earliest disjunctions in the tribe are inferred to be the result of long-distance dispersal out of Australia (with one possible exception), rather than vicariance. Evolution of tardy fruit dehiscence is correlated with these dispersals, and the onset of the Antarctic Circumpolar Current (ACC) precedes them. We suggest that the ancestors of extant diversity arrived on their respective continents via the ACC, and we recognize that this is a mechanism precluded, rather than facilitated, by Gondwana's terrestrial continuity.

  3. A smaller Macadamia from a more vagile tribe: inference of phylogenetic relationships, divergence times, and diaspore evolution in Macadamia and relatives (tribe Macadamieae; Proteaceae).

    PubMed

    Mast, Austin R; Willis, Crystal L; Jones, Eric H; Downs, Katherine M; Weston, Peter H

    2008-07-01

    Tribe Macadamieae (91 spp., 16 genera; Proteaceae) is widespread across the southern hemisphere on all major fragments of Gondwana except New Zealand and India. Macadamia is cultivated outside its natural range as a "nut" crop (notably in Hawaii, where it is the principal orchard crop). We sampled seven DNA regions and 53 morphological characters from the tribe to infer its phylogeny and address the common assumption that the distribution of the extant diversity of the tribe arose by the rafting of ancestors on Gondwanan fragments. Macadamia proves to be paraphyletic with respect to the African genus Brabejum, the South American genus Panopsis, and the Australian species Orites megacarpus. We erect two new generic names, Nothorites and Lasjia, to produce monophyly at that rank. The earliest disjunctions in the tribe are inferred to be the result of long-distance dispersal out of Australia (with one possible exception), rather than vicariance. Evolution of tardy fruit dehiscence is correlated with these dispersals, and the onset of the Antarctic Circumpolar Current (ACC) precedes them. We suggest that the ancestors of extant diversity arrived on their respective continents via the ACC, and we recognize that this is a mechanism precluded, rather than facilitated, by Gondwana's terrestrial continuity. PMID:21632410

  4. High-Level Clouds and Relation to Sea Surface Temperature as Inferred from Japan's GMS Measurements

    NASA Technical Reports Server (NTRS)

    Chou, Ming-Dah; Lindzen, Richard S.; Lee, Kyu-Tae; Einaudi, Franco (Technical Monitor)

    2000-01-01

    High-level clouds have a significant impact on the radiation energy budgets and, hence, the climate of the Earth. Convective cloud systems, which are controlled by large-scale thermal and dynamical conditions, propagate rapidly within days. At this time scale, changes of sea surface temperature (SST) are small. Radiances measured by Japan's Geostationary Meteorological Satellite (GMS) are used to study the relation between high-level clouds and SST in the tropical western and central Pacific (30 S-30 N; 130 E-170 W), where the ocean is warm and deep convection is intensive. Twenty months (January 1998 - August, 1999) of GMS data are used, which cover the second half of the strong 1997-1998 El Nino. Brightness temperature at the 11-micron channel is used to identify high-level clouds. The core of convection is identified based on the difference in the brightness temperatures of the 11- and 12-micron channels. Because of the rapid movement of clouds, there is little correlation between clouds six hours apart. When most of deep convection moves to regions of high SST, the domain averaged high-level cloud amount decreases. A +2C change of SST in cloudy regions results in a relative change of -30% in high-level cloud amount. This large change in cloud amount is due to clouds moving from cool regions to warm regions but not the change in SST itself. A reduction in high-level cloud amount in the equatorial region implies an expanded dry upper troposphere in the off-equatorial region, and the greenhouse warming of high clouds and water vapor is reduced through enhanced longwave cooling to space. The results are important for understanding the physical processes relating SST, convection, and water vapor in the tropics. They are also important for validating climate simulations using global general circulation models.

  5. Humanoid infers Archimedes' principle: understanding physical relations and object affordances through cumulative learning experiences.

    PubMed

    Bhat, Ajaz Ahmad; Mohan, Vishwanathan; Sandini, Giulio; Morasso, Pietro

    2016-07-01

    Emerging studies indicate that several species such as corvids, apes and children solve 'The Crow and the Pitcher' task (from Aesop's Fables) in diverse conditions. Hidden beneath this fascinating paradigm is a fundamental question: by cumulatively interacting with different objects, how can an agent abstract the underlying cause-effect relations to predict and creatively exploit potential affordances of novel objects in the context of sought goals? Re-enacting this Aesop's Fable task on a humanoid within an open-ended 'learning-prediction-abstraction' loop, we address this problem and (i) present a brain-guided neural framework that emulates rapid one-shot encoding of ongoing experiences into a long-term memory and (ii) propose four task-agnostic learning rules (elimination, growth, uncertainty and status quo) that correlate predictions from remembered past experiences with the unfolding present situation to gradually abstract the underlying causal relations. Driven by the proposed architecture, the ensuing robot behaviours illustrated causal learning and anticipation similar to natural agents. Results further demonstrate that by cumulatively interacting with few objects, the predictions of the robot in case of novel objects converge close to the physical law, i.e. the Archimedes principle: this being independent of both the objects explored during learning and the order of their cumulative exploration. PMID:27466440

  6. Humanoid infers Archimedes' principle: understanding physical relations and object affordances through cumulative learning experiences.

    PubMed

    Bhat, Ajaz Ahmad; Mohan, Vishwanathan; Sandini, Giulio; Morasso, Pietro

    2016-07-01

    Emerging studies indicate that several species such as corvids, apes and children solve 'The Crow and the Pitcher' task (from Aesop's Fables) in diverse conditions. Hidden beneath this fascinating paradigm is a fundamental question: by cumulatively interacting with different objects, how can an agent abstract the underlying cause-effect relations to predict and creatively exploit potential affordances of novel objects in the context of sought goals? Re-enacting this Aesop's Fable task on a humanoid within an open-ended 'learning-prediction-abstraction' loop, we address this problem and (i) present a brain-guided neural framework that emulates rapid one-shot encoding of ongoing experiences into a long-term memory and (ii) propose four task-agnostic learning rules (elimination, growth, uncertainty and status quo) that correlate predictions from remembered past experiences with the unfolding present situation to gradually abstract the underlying causal relations. Driven by the proposed architecture, the ensuing robot behaviours illustrated causal learning and anticipation similar to natural agents. Results further demonstrate that by cumulatively interacting with few objects, the predictions of the robot in case of novel objects converge close to the physical law, i.e. the Archimedes principle: this being independent of both the objects explored during learning and the order of their cumulative exploration.

  7. Humanoid infers Archimedes' principle: understanding physical relations and object affordances through cumulative learning experiences

    PubMed Central

    2016-01-01

    Emerging studies indicate that several species such as corvids, apes and children solve ‘The Crow and the Pitcher’ task (from Aesop's Fables) in diverse conditions. Hidden beneath this fascinating paradigm is a fundamental question: by cumulatively interacting with different objects, how can an agent abstract the underlying cause–effect relations to predict and creatively exploit potential affordances of novel objects in the context of sought goals? Re-enacting this Aesop's Fable task on a humanoid within an open-ended ‘learning–prediction–abstraction’ loop, we address this problem and (i) present a brain-guided neural framework that emulates rapid one-shot encoding of ongoing experiences into a long-term memory and (ii) propose four task-agnostic learning rules (elimination, growth, uncertainty and status quo) that correlate predictions from remembered past experiences with the unfolding present situation to gradually abstract the underlying causal relations. Driven by the proposed architecture, the ensuing robot behaviours illustrated causal learning and anticipation similar to natural agents. Results further demonstrate that by cumulatively interacting with few objects, the predictions of the robot in case of novel objects converge close to the physical law, i.e. the Archimedes principle: this being independent of both the objects explored during learning and the order of their cumulative exploration. PMID:27466440

  8. Sex differences in the inference and perception of causal relations within a video game

    PubMed Central

    Young, Michael E.

    2014-01-01

    The learning of immediate causation within a dynamic environment was examined. Participants encountered seven decision points in which they needed to choose, which of three possible candidates was the cause of explosions in the environment. Each candidate was firing a weapon at random every few seconds, but only one of them produced an immediate effect. Some participants showed little learning, but most demonstrated increases in accuracy across time. On average, men showed higher accuracy and shorter latencies that were not explained by differences in self-reported prior video game experience. This result suggests that prior reports of sex differences in causal choice in the game are not specific to situations involving delayed or probabilistic causal relations. PMID:25202293

  9. Processing inferences derived from event-related potential measures in a monitoring task

    NASA Technical Reports Server (NTRS)

    Horst, R. L.; Munson, R. C.; Ruchkin, D. S.

    1985-01-01

    Event-related potentials (ERPs) were recorded from the scalp of subjects as they monitored changing digital readouts for values that went 'out-of-bounds'. Workload was manipulated by varying the number of readouts that were monitored concurrently. The ERPs elicited by changes in the readouts showed long latency positivities that increased in amplitude, not only with the number of readouts monitored, but also with the number of monitored readouts that were 'in danger' of going out-of-bounds. No effects were found due to the number of nonmonitored readouts 'in danger'. This evidence indicates that subjects (1) selectively attended to the monitored readouts and (2) processed the monitored readouts differently as the readouts approached the out-of-bounds levels to which an overt response was required.

  10. Decreasing emissions of NOx relative to CO2 in East Asia inferred from satellite observations

    NASA Astrophysics Data System (ADS)

    Reuter, M.; Buchwitz, M.; Hilboll, A.; Richter, A.; Schneising, O.; Hilker, M.; Heymann, J.; Bovensmann, H.; Burrows, J. P.

    2014-11-01

    At present, global CO2 emission inventories are mainly based on bottom-up estimates that rely, for example, on reported fossil fuel consumptions and fuel types. The associated uncertainties propagate into the CO2-to-NOx emission ratios that are used in pollution prediction and monitoring, as well as into biospheric carbon fluxes derived by inverse models. Here we analyse simultaneous and co-located satellite retrievals from SCIAMACHY (ref. ; SCanning Imaging Absorption SpectroMeter for Atmospheric CHartographY) of the column-average dry-air mole fraction of CO2 (refs , ) and NO2 (refs , , ) for the years 2003-2011 to provide a top-down estimate of trends in emissions and in the ratio between CO2 and NOx emissions. Our analysis shows that the CO2-to-NOx emission ratio has increased by 4.2 +/- 1.7% yr-1 in East Asia. In this region, we find a large positive trend of CO2 emissions (9.8 +/- 1.7% yr-1), which we largely attribute to the growing Chinese economy. This trend exceeds the positive trend of NOx emissions (5.8 +/- 0.9% yr-1). Our findings suggest that the recently installed and renewed technology in East Asia, such as power plants, transportation and so on, is cleaner in terms of NOx emissions than the old infrastructure, and roughly matches relative emission levels in North America and Europe.

  11. Inferring the Relative Quality of Reanalysis Data from a Historical Reforecast Using a Vorticity Equation Model

    NASA Astrophysics Data System (ADS)

    Ballesteros, C. A.; Herrmann, M.; Huang, H.

    2011-12-01

    The improvement of numerical weather prediction models in recent decades has led to a measurable decrease in forecast error, for instance as quantified by the 500-hPa geopotential height anomaly correlation. This improvement can be attributed in part to the refinements in the numerical architecture and the representation of physical processes in the model. It is more difficult to attribute the reduction in forecast error to improvements in the accuracy of the models' initial conditions, not least because of the complexity of the data assimilation process. As a contribution to this problem that will also be pedagogically useful, a reforecast experiment was conducted using a simple regional vorticity equation model for the 500-hPa flow over North America. This model is comparable in complexity to the Charney-Fjörtoft-von Neumann model used for the first numerical weather prediction experiment in 1949. Six-hourly predictions are made out to 36 hours for the period from 1948-2010, using the NCEP Reanalysis dataset for the initial conditions. Because initialization is trivial for this "filtered" model, one can clearly attribute the change in forecast skill to the changing quality of the initial state. The choice of the 500 hPa level is relevant since it will reflect the effect of the significant change in the density of upper-air observations from the mid- to late 20th Century. As an important byproduct of this exercise, a trend of improved forecast over time will imply an improved relative quality of the reanalysis data for the mid-troposphere. Therefore, the experiment serves two purposes of studying the forecast error and checking the quality of the reanalysis. An analysis of selected cases indicates that the predictions made for the 21st century have smaller errors compared to those made for the 1950s. A comprehensive analysis for the whole set of forecast is underway and the outcome will be discussed.

  12. Inferring ultraviolet anatomical exposure patterns while distinguishing the relative contribution of radiation components

    SciTech Connect

    Vuilleumier, Laurent; Milon, Antoine; Vernez, David; Bulliard, Jean-Luc; Moccozet, Laurent

    2013-05-10

    Exposure to solar ultraviolet (UV) radiation is the main causative factor for skin cancer. UV exposure depends on environmental and individual factors, but individual exposure data remain scarce. While ground UV irradiance is monitored via different techniques, it is difficult to translate such observations into human UV exposure or dose because of confounding factors. A multi-disciplinary collaboration developed a model predicting the dose and distribution of UV exposure on the basis of ground irradiation and morphological data. Standard 3D computer graphics techniques were adapted to develop a simulation tool that estimates solar exposure of a virtual manikin depicted as a triangle mesh surface. The amount of solar energy received by various body locations is computed for direct, diffuse and reflected radiation separately. Dosimetric measurements obtained in field conditions were used to assess the model performance. The model predicted exposure to solar UV adequately with a symmetric mean absolute percentage error of 13% and half of the predictions within 17% range of the measurements. Using this tool, solar UV exposure patterns were investigated with respect to the relative contribution of the direct, diffuse and reflected radiation. Exposure doses for various body parts and exposure scenarios of a standing individual were assessed using erythemally-weighted UV ground irradiance data measured in 2009 at Payerne, Switzerland as input. For most anatomical sites, mean daily doses were high (typically 6.2-14.6 Standard Erythemal Dose, SED) and exceeded recommended exposure values. Direct exposure was important during specific periods (e.g. midday during summer), but contributed moderately to the annual dose, ranging from 15 to 24% for vertical and horizontal body parts, respectively. Diffuse irradiation explained about 80% of the cumulative annual exposure dose.

  13. Inferring ultraviolet anatomical exposure patterns while distinguishing the relative contribution of radiation components

    NASA Astrophysics Data System (ADS)

    Vuilleumier, Laurent; Milon, Antoine; Bulliard, Jean-Luc; Moccozet, Laurent; Vernez, David

    2013-05-01

    Exposure to solar ultraviolet (UV) radiation is the main causative factor for skin cancer. UV exposure depends on environmental and individual factors, but individual exposure data remain scarce. While ground UV irradiance is monitored via different techniques, it is difficult to translate such observations into human UV exposure or dose because of confounding factors. A multi-disciplinary collaboration developed a model predicting the dose and distribution of UV exposure on the basis of ground irradiation and morphological data. Standard 3D computer graphics techniques were adapted to develop a simulation tool that estimates solar exposure of a virtual manikin depicted as a triangle mesh surface. The amount of solar energy received by various body locations is computed for direct, diffuse and reflected radiation separately. Dosimetric measurements obtained in field conditions were used to assess the model performance. The model predicted exposure to solar UV adequately with a symmetric mean absolute percentage error of 13% and half of the predictions within 17% range of the measurements. Using this tool, solar UV exposure patterns were investigated with respect to the relative contribution of the direct, diffuse and reflected radiation. Exposure doses for various body parts and exposure scenarios of a standing individual were assessed using erythemally-weighted UV ground irradiance data measured in 2009 at Payerne, Switzerland as input. For most anatomical sites, mean daily doses were high (typically 6.2-14.6 Standard Erythemal Dose, SED) and exceeded recommended exposure values. Direct exposure was important during specific periods (e.g. midday during summer), but contributed moderately to the annual dose, ranging from 15 to 24% for vertical and horizontal body parts, respectively. Diffuse irradiation explained about 80% of the cumulative annual exposure dose.

  14. Indirect effects of pandemic deer overabundance inferred from caterpillar-host relations.

    PubMed

    Wheatall, Laura; Nuttle, Tim; Yerger, Ellen

    2013-10-01

    Externally feeding phytophagous insect larvae (i.e., caterpillars, here, larval Lepidoptera and sawflies, Hymenoptera: Symphyta) are important canopy herbivores and prey resources in temperate deciduous forests. However, composition of forest trees has changed dramatically in the eastern United States since 1900. In particular, browsing by high densities of white-tailed deer (Odocoileus virginianus) has resulted in forests dominated by browse-tolerant species, such as black cherry (Prunus serotina), and greatly reduced relative abundance of other tree species, notably pin cherry (Prunus pensylvanica) and birches (Betula spp.). To quantify effects of these changes on caterpillars, we sampled caterpillars from 960 branch tips of the 8 tree species that comprise 95% of trees in Allegheny hardwood forests: red maple (Acer rubrum), striped maple (Acer pensylvanicum), sugar maple (Acer saccharum), sweet birch (Betula lenta), yellow birch (Betula allegheniensis), American beech (Fagus grandifolia), black cherry, and pin cherry. We collected 547 caterpillar specimens that belonged to 66 Lepidoptera and 10 Hymenoptera species. Caterpillar density, species richness, and community composition differed significantly among tree species sampled. Pin cherry, nearly eliminated at high deer density, had the highest density and diversity of caterpillars. Pin cherry shared a common caterpillar community with black cherry, which was distinct from those of other tree hosts. As high deer density continues to replace diverse forests of cherries, maples, birches, and beech with monodominant stands of black cherry, up to 66% of caterpillar species may be eliminated. Hence, deer-induced changes in forest vegetation are likely to ricochet back up forest food webs and therefore negatively affect species that depend on caterpillars and moths for food and pollination. PMID:23678968

  15. Indirect effects of pandemic deer overabundance inferred from caterpillar-host relations.

    PubMed

    Wheatall, Laura; Nuttle, Tim; Yerger, Ellen

    2013-10-01

    Externally feeding phytophagous insect larvae (i.e., caterpillars, here, larval Lepidoptera and sawflies, Hymenoptera: Symphyta) are important canopy herbivores and prey resources in temperate deciduous forests. However, composition of forest trees has changed dramatically in the eastern United States since 1900. In particular, browsing by high densities of white-tailed deer (Odocoileus virginianus) has resulted in forests dominated by browse-tolerant species, such as black cherry (Prunus serotina), and greatly reduced relative abundance of other tree species, notably pin cherry (Prunus pensylvanica) and birches (Betula spp.). To quantify effects of these changes on caterpillars, we sampled caterpillars from 960 branch tips of the 8 tree species that comprise 95% of trees in Allegheny hardwood forests: red maple (Acer rubrum), striped maple (Acer pensylvanicum), sugar maple (Acer saccharum), sweet birch (Betula lenta), yellow birch (Betula allegheniensis), American beech (Fagus grandifolia), black cherry, and pin cherry. We collected 547 caterpillar specimens that belonged to 66 Lepidoptera and 10 Hymenoptera species. Caterpillar density, species richness, and community composition differed significantly among tree species sampled. Pin cherry, nearly eliminated at high deer density, had the highest density and diversity of caterpillars. Pin cherry shared a common caterpillar community with black cherry, which was distinct from those of other tree hosts. As high deer density continues to replace diverse forests of cherries, maples, birches, and beech with monodominant stands of black cherry, up to 66% of caterpillar species may be eliminated. Hence, deer-induced changes in forest vegetation are likely to ricochet back up forest food webs and therefore negatively affect species that depend on caterpillars and moths for food and pollination.

  16. Affected sib-pair interval mapping and exclusion for complex genetic traits: Inferring identity by descent status from relatives

    SciTech Connect

    Hauser, E.R.; Boehnke, M.; Guo, S.W.

    1994-09-01

    Affected sib-pair (ASP) methods provide a useful approach for the initial genetic mapping of complex diseases for which mode of inheritance is uncertain. Risch described a method for interval mapping and exclusion based on the ratio lambda comparing disease risk in the first degree relatives of affected individuals to disease risk in the general population. He assumed marker identity by descent (IBD) status for the ASP could be deduced from parental genotypes. For late onset diseases such as type 2 diabetes, parents may be dead or otherwise unavailable, so that marker IBD status generally cannot be inferred with certainty. Guo has developed efficient methods for probabilistic determination of marker IBD sharing for two or more loci. We have combined and extended the methods of Risch and Guo to carry out interval mapping and exclusion when parents are missing but other relatives such as additional siblings are available. Our method is based on calculating the likelihood of marker data of the ASP and their relatives conditional on the disease status of the ASP, as a function of lambda and the position of the disease locus within the genetic map. We currently are using this method to compare the information to detect or exclude linkage provided by various types of ASP nuclear families -- zero, one, or two typed parents and zero, one, two, or more additional siblings -- as a function of sample size, marker density and informativity, and risk ratio lambda.

  17. Relation Between Type II Bursts and CMEs Inferred from STEREO Observations

    NASA Technical Reports Server (NTRS)

    Gopalswamy, N.; Thompson, W.; Davila, J.; Kaiser, M.; Yashiro, S.; Maelekae, P.; Michalek, G.; Bougret, J.-L.; Howard, R. A.

    2009-01-01

    The inner coronagraph (COR1) of the Solar Terrestrial Relations Observatory (STEREO) mission has made it possible to observe CMEs in the spatial domain overlapping with that of the metric type II radio bursts. The type II bursts were associated with generally weak flares (mostly B and C class soft X-ray flares), but the CMEs were quite energetic. Using CME data for a set of type II bursts during the declining phase of solar cycle 23, we determine the CME height when the type II bursts start, thus giving an estimate of the heliocentric distance at which CME-driven shocks form. This distance has been determined to be approx. 1.5Rs (solar radii), which coincides with the distance at which the Alfven speed profile has a minimum value.We also use type II radio observations from STEREO/WAVES and Wind/WAVES observations to show that CMEs with moderate speed drive either weak shocks or no shock at all when they attain a height where the Alfven speed peaks (approx. 3Rs - 4Rs). Thus the shocks seem to be most efficient in accelerating electrons in the heliocentric distance range of 1.5Rs to 4Rs. By combining the radial variation of the CME speed in the inner corona (CME speed increase) and interplanetary medium (speed decrease) we were able to correctly account for the deviations from the universal drift-rate spectrum of type II bursts, thus confirming the close physical connection between type II bursts and CMEs. The average height (approx 1.5Rs) of STEREO CMEs at the time of type II bursts is smaller than that (2.2Rs) obtained for SOHO (Solar and Heliospheric Observatory) CMEs. We suggest that this may indicate, at least partly, the density reduction in the corona between the maximum and declining phases, so a given plasma level occurs closer to the Sun in the latter phase. In two cases, there was a diffuse shock-like feature ahead of the main body of the CME, indicating a standoff distance of 1Rs - 2Rs by the time the CME left the LASCO field of view.

  18. Relation Between Type II Bursts and CMEs Inferred from STEREO Observations

    NASA Technical Reports Server (NTRS)

    Gopalswamy, N.; Thompson, W.; Davila, J.; Kaiser, M. L.; Yashiro, S.; Maekelae, P.; Michalek, G.; Bougeret, J.-L.; Hoawrd, R. A.

    2010-01-01

    The inner coronagraph (COR1) of the Solar Terrestrial Relations Observatory (STEREO) mission has made it possible to observe coronal mass ejections (CMEs) a in the spatial domain overlapping with that of the metric type II radio bursts. The type II bursts were associated with generally weak flares (mostly B and C class soft X-ray flares), but the CMEs were quite energetic. Using CME data for a set of type II bursts during the declining phase of solar cycle 23, we determine the CME height when the type II bursts start, thus giving an estimate of the heliocentric distance at which CME-driven shocks form. This distance has been determined to be approximately 1.5Rs (solar radii), which coincides with the distance at which the Alfv?n speed profile has a minimum value. We also use type II radio observations from STEREO/WAVES and Wind/WAVES observations to show that CMEs with moderate speed drive either weak shocks or no shock at all when they attain a height where the Alfv?n speed peaks (?3Rs ? 4Rs). Thus the shocks seem to be most efficient in accelerating electrons in the heliocentric distance range of 1.5Rs to 4Rs. By combining the radial variation of the CME speed in the inner corona (CME speed increase) and interplanetary medium (speed decrease) we were able to correctly account for the deviations from the universal drift-rate spectrum of type II bursts, thus confirming the close physical connection between type II bursts and CMEs. The average height (approximately 1.5 Rs) of STEREO CMEs at the time of type II bursts is smaller than that (2.2 Rs) obtained for SOHO (Solar and Heliospheric Observatory) CMEs. We suggest that this may indicate, at least partly, the density reduction in the corona between the maximum and declining phases, so a given plasma level occurs closer to the Sun in the latter phase. In two cases, there was a diffuse shock-like feature ahead of the main body of the CME, indicating a standoff distance of 1Rs - 2Rs by the time the CME left the LASCO

  19. Global Diversity and Phylogeny of Pelagic Shrimps of the Former Genera Sergestes and Sergia (Crustacea, Dendrobranchiata, Sergestidae), with Definition of Eight New Genera

    PubMed Central

    Vereshchaka, Alexander L.; Olesen, Jørgen; Lunina, Anastasia A.

    2014-01-01

    We revise the global diversity of the former genera Sergia and Sergestes which include 71 valid species. The revision is based on examination of more than 37,000 specimens from collections in the Natural History Museum of Denmark and the Museum of Natural History, Paris. We used 72 morphological characters (61 binary, 11 multistate) and Sicyonella antennata as an outgroup for cladistic analysis. There is no support for the genera Sergia and Sergestes as they have been defined until now. We define and diagnose eight genera of the former genus Sergia (Sergia and new genera Gardinerosergia, Phorcosergia, Prehensilosergia, Robustosergia, Scintillosergia, Challengerosergia, and Lucensosergia) and seven genera of the former genus Sergestes (Sergestes, Deosergestes, Eusergestes, Allosergestes, Parasergestes, Neosergestes, and a new genus Cornutosergestes). An identification key is presented for all genera of the family Sergestidae. The phylogeny of Sergestidae is mainly based on three categories of characters related to: (1) general decapod morphology, (2) male copulatory organs, and (3) photophores. Only simultaneous use of all three character types resulted in a resolved tree with minimal Bootstrap support 75 for each clade. Most genera are interzonal mesopelagic migrants, some are benthopelagic (Scintillosergia, Lucensosergia), bathypelagic (Sergia), or epipelagic (Cornutosergestes). Within each of meso- and benthopelagic genera there is one species with panoceanic distribution, while most species ranges are restricted to a single ocean. The genera demonstrate two different strategies expressed both in morphology and behavior: protective (Eusergestes, Sergestes, Cornutosergestes, Prehensilosergia, Scintillosergia, Lucensosergia, Challengerosergia, Gardinerosergia, Robustosergia, Phorcosergia, Sergia) and offensive (Neosergestes, Parasergestes, Allosergestes, Deosergestes). PMID:25409458

  20. Global diversity and phylogeny of pelagic shrimps of the former genera Sergestes and Sergia (Crustacea, Dendrobranchiata, Sergestidae), with definition of eight new genera.

    PubMed

    Vereshchaka, Alexander L; Olesen, Jørgen; Lunina, Anastasia A

    2014-01-01

    We revise the global diversity of the former genera Sergia and Sergestes which include 71 valid species. The revision is based on examination of more than 37,000 specimens from collections in the Natural History Museum of Denmark and the Museum of Natural History, Paris. We used 72 morphological characters (61 binary, 11 multistate) and Sicyonella antennata as an outgroup for cladistic analysis. There is no support for the genera Sergia and Sergestes as they have been defined until now. We define and diagnose eight genera of the former genus Sergia (Sergia and new genera Gardinerosergia, Phorcosergia, Prehensilosergia, Robustosergia, Scintillosergia, Challengerosergia, and Lucensosergia) and seven genera of the former genus Sergestes (Sergestes, Deosergestes, Eusergestes, Allosergestes, Parasergestes, Neosergestes, and a new genus Cornutosergestes). An identification key is presented for all genera of the family Sergestidae. The phylogeny of Sergestidae is mainly based on three categories of characters related to: (1) general decapod morphology, (2) male copulatory organs, and (3) photophores. Only simultaneous use of all three character types resulted in a resolved tree with minimal Bootstrap support 75 for each clade. Most genera are interzonal mesopelagic migrants, some are benthopelagic (Scintillosergia, Lucensosergia), bathypelagic (Sergia), or epipelagic (Cornutosergestes). Within each of meso- and benthopelagic genera there is one species with panoceanic distribution, while most species ranges are restricted to a single ocean. The genera demonstrate two different strategies expressed both in morphology and behavior: protective (Eusergestes, Sergestes, Cornutosergestes, Prehensilosergia, Scintillosergia, Lucensosergia, Challengerosergia, Gardinerosergia, Robustosergia, Phorcosergia, Sergia) and offensive (Neosergestes, Parasergestes, Allosergestes, Deosergestes). PMID:25409458

  1. Molecular phylogeny of three oxymonad genera: Pyrsonympha, Dinenympha and Oxymonas.

    PubMed

    Moriya, Shigeharu; Dacks, Joel B; Takagi, Aika; Noda, Satoko; Ohkuma, Moriya; Doolittle, W Ford; Kudo, Toshiaki

    2003-01-01

    Oxymonads are a morphologically well-characterized and highly diverse lineage of protists. They are, however, under sampled at a molecular level. It has recently been demonstrated that a genus of oxymonads, Pyrsonympha, is phylogenetically related to the excavate taxon Trimastix. Here, we addressed issues of internal oxymonad evolution. Pyrsonympha and Dinenympha are shown, by fluorescent in situ hybridization and phylogenetic evidence, to be separate genera and not morphotypes of the same organism. We demonstrated that three genera of oxymonads, Dinenympha, Pyrsonympha, and Oxymonas are each monophyletic and together form a clade which excludes other known eukaryotes. We have presented a taxonomic scheme of oxymonads taking into account their sisterhood with Trimastix and speculated on morphological evolution of oxymonads, particularly of their attachment apparatuses. Our biogeographical analysis with Japanese and Canadian Pyrsonympha and Dinenympha suggests that these genera diverged before the separation of termites that inhabit Eastern Asia and Western North America.

  2. PHYLOGENY OF FOUR DINOPHYSIACEAN GENERA (DINOPHYCEAE, DINOPHYSIALES) BASED ON rDNA SEQUENCES FROM SINGLE CELLS AND ENVIRONMENTAL SAMPLES(1).

    PubMed

    Handy, Sara M; Bachvaroff, Tsvetan R; Timme, Ruth E; Wayne Coats, D; Kim, Sunju; Delwiche, Charles F

    2009-10-01

    Dinoflagellates are a highly diverse and environmentally important group of protists with relatively poor resolution of phylogenetic relationships, particularly among heterotrophic species. We examined the phylogeny of several dinophysiacean dinoflagellates using samples collected from four Atlantic sites. As a rule, 3.5 kb of sequence including the nuclear ribosomal genes SSU, 5.8S, LSU, plus their internal transcribed spacer (ITS) 1 and 2 regions were determined for 26 individuals, including representatives of two genera for which molecular data were previously unavailable, Ornithocercus F. Stein and Histioneis F. Stein. In addition, a clone library targeting the dinophysiacean ITS2 and LSU sequences was constructed from bulk environmental DNA from three sites. Three phylogenetic trees were inferred from the data, one using data from this study for cells identified to genus or species (3.5 kb, 28 taxa); another containing dinoflagellate SSU submissions from GenBank and the 12 new dinophysiacean sequences (1.9 kb, 56 taxa) from this study; and the third tree combing data from identified taxa, dinophysiacean GenBank submissions, and the clone libraries from this study (2.1 kb, 136 taxa). All trees were congruent and indicated a distinct division between the genera Phalacroma F. Stein and Dinophysis Ehrenb. The cyanobionts containing genera Histioneis and Ornithocercus were also monophyletic. This was the largest molecular phylogeny of dinophysoid taxa performed to date and was consistent with the view that the genus Phalacroma may not be synonymous with Dinophysis.

  3. New genera of Lachesillidae (Psocodea: 'Psocoptera': Eolachesillinae: Graphocaeciliini) from Valle del Cauca, Colombia.

    PubMed

    García Aldrete, Alfonso N; González Obando, Ranulfo; Carrejo, Nancy S

    2013-01-01

    Two new related Colombian genera of Lachesillidae, including three new species, from the Department of Valle del Cauca, are here described and illustrated. They belong in the tribe Graphocaeciliini (Eolachesillinae). The new genera differ from the other genera in the tribe lacking ocelli, by characters of the male clunium, phallosome, endophallus, paraprocts, and female subgenital plate, gonapophyses and IX sternum. The types are deposited in the Entomological Museum of the Universidad del Valle (MUSENUV), in Santiago de Cali, Colombia.

  4. Clarification of the Phylogenetic Framework of the Tribe Baorini (Lepidoptera: Hesperiidae: Hesperiinae) Inferred from Multiple Gene Sequences.

    PubMed

    Fan, Xiaoling; Chiba, Hideyuki; Huang, Zhenfu; Fei, Wen; Wang, Min; Sáfián, Szabolcs

    2016-01-01

    Members of the skipper tribe Baorini generally resemble each other and are characterized by dark brown wings with hyaline white spots. These shared characteristics have caused difficulties with revealing the relationships among genera and species in the group, and some conflicting taxonomic views remain unresolved. The present study aims to infer a more comprehensive phylogeny of the tribe using molecular data, to test the monophyly of the tribe as well as the genera it includes in order to clarify their taxonomic status, and finally to revise the current classification of the group. In order to reconstruct a phylogenetic tree, the mitochondrial COI-COII and 16S genes as well as the nuclear EF-1α and 28S genes were analyzed using parsimony, maximum likelihood, and Bayesian inference. The analysis included 67 specimens of 41 species, and we confirmed the monophyly of Baorini, and revealed that 14 genera are well supported. The genus Borbo is separated into three clades: Borbo, Pseudoborbo, and Larsenia gen. nov. We confirmed that Polytremis is polyphyletic and separated into three genera: Polytremis, Zinaida, and Zenonoida gen. nov., and also confirmed that the genus Prusiana is a member of the tribe. Relationships among some genera were strongly supported. For example, Zenonia and Zenonoida were found to be sister taxa, closely related to Zinaida and Iton, while Pelopidas and Baoris were also found to cluster together. PMID:27463803

  5. Clarification of the Phylogenetic Framework of the Tribe Baorini (Lepidoptera: Hesperiidae: Hesperiinae) Inferred from Multiple Gene Sequences

    PubMed Central

    Fan, Xiaoling; Chiba, Hideyuki; Huang, Zhenfu; Fei, Wen; Wang, Min; Sáfián, Szabolcs

    2016-01-01

    Members of the skipper tribe Baorini generally resemble each other and are characterized by dark brown wings with hyaline white spots. These shared characteristics have caused difficulties with revealing the relationships among genera and species in the group, and some conflicting taxonomic views remain unresolved. The present study aims to infer a more comprehensive phylogeny of the tribe using molecular data, to test the monophyly of the tribe as well as the genera it includes in order to clarify their taxonomic status, and finally to revise the current classification of the group. In order to reconstruct a phylogenetic tree, the mitochondrial COI-COII and 16S genes as well as the nuclear EF-1α and 28S genes were analyzed using parsimony, maximum likelihood, and Bayesian inference. The analysis included 67 specimens of 41 species, and we confirmed the monophyly of Baorini, and revealed that 14 genera are well supported. The genus Borbo is separated into three clades: Borbo, Pseudoborbo, and Larsenia gen. nov. We confirmed that Polytremis is polyphyletic and separated into three genera: Polytremis, Zinaida, and Zenonoida gen. nov., and also confirmed that the genus Prusiana is a member of the tribe. Relationships among some genera were strongly supported. For example, Zenonia and Zenonoida were found to be sister taxa, closely related to Zinaida and Iton, while Pelopidas and Baoris were also found to cluster together. PMID:27463803

  6. Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways.

    PubMed

    Righetti, Karima; Vu, Joseph Ly; Pelletier, Sandra; Vu, Benoit Ly; Glaab, Enrico; Lalanne, David; Pasha, Asher; Patel, Rohan V; Provart, Nicholas J; Verdier, Jerome; Leprince, Olivier; Buitink, Julia

    2015-10-01

    Seed longevity, the maintenance of viability during storage, is a crucial factor for preservation of genetic resources and ensuring proper seedling establishment and high crop yield. We used a systems biology approach to identify key genes regulating the acquisition of longevity during seed maturation of Medicago truncatula. Using 104 transcriptomes from seed developmental time courses obtained in five growth environments, we generated a robust, stable coexpression network (MatNet), thereby capturing the conserved backbone of maturation. Using a trait-based gene significance measure, a coexpression module related to the acquisition of longevity was inferred from MatNet. Comparative analysis of the maturation processes in M. truncatula and Arabidopsis thaliana seeds and mining Arabidopsis interaction databases revealed conserved connectivity for 87% of longevity module nodes between both species. Arabidopsis mutant screening for longevity and maturation phenotypes demonstrated high predictive power of the longevity cross-species network. Overrepresentation analysis of the network nodes indicated biological functions related to defense, light, and auxin. Characterization of defense-related wrky3 and nf-x1-like1 (nfxl1) transcription factor mutants demonstrated that these genes regulate some of the network nodes and exhibit impaired acquisition of longevity during maturation. These data suggest that seed longevity evolved by co-opting existing genetic pathways regulating the activation of defense against pathogens. PMID:26410298

  7. Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways

    PubMed Central

    Righetti, Karima; Vu, Joseph Ly; Pelletier, Sandra; Vu, Benoit Ly; Glaab, Enrico; Lalanne, David; Pasha, Asher; Patel, Rohan V.; Provart, Nicholas J.; Verdier, Jerome; Leprince, Olivier

    2015-01-01

    Seed longevity, the maintenance of viability during storage, is a crucial factor for preservation of genetic resources and ensuring proper seedling establishment and high crop yield. We used a systems biology approach to identify key genes regulating the acquisition of longevity during seed maturation of Medicago truncatula. Using 104 transcriptomes from seed developmental time courses obtained in five growth environments, we generated a robust, stable coexpression network (MatNet), thereby capturing the conserved backbone of maturation. Using a trait-based gene significance measure, a coexpression module related to the acquisition of longevity was inferred from MatNet. Comparative analysis of the maturation processes in M. truncatula and Arabidopsis thaliana seeds and mining Arabidopsis interaction databases revealed conserved connectivity for 87% of longevity module nodes between both species. Arabidopsis mutant screening for longevity and maturation phenotypes demonstrated high predictive power of the longevity cross-species network. Overrepresentation analysis of the network nodes indicated biological functions related to defense, light, and auxin. Characterization of defense-related wrky3 and nf-x1-like1 (nfxl1) transcription factor mutants demonstrated that these genes regulate some of the network nodes and exhibit impaired acquisition of longevity during maturation. These data suggest that seed longevity evolved by co-opting existing genetic pathways regulating the activation of defense against pathogens. PMID:26410298

  8. The relative timing of Lunar Magma Ocean solidification and the Late Heavy Bombardment inferred from highly degraded impact basin structures

    NASA Astrophysics Data System (ADS)

    Kamata, Shunichi; Sugita, Seiji; Abe, Yutaka; Ishihara, Yoshiaki; Harada, Yuji; Morota, Tomokatsu; Namiki, Noriyuki; Iwata, Takahiro; Hanada, Hideo; Araki, Hiroshi; Matsumoto, Koji; Tajika, Eiichi; Kuramoto, Kiyoshi; Nimmo, Francis

    2015-04-01

    The solidification of the Lunar Magma Ocean (LMO) and formation of impact basins are important events that took place on the early Moon. The relative timing of these events, however, is poorly constrained. The aim of this study is to constrain the formation ages of old impact basins based on inferences of their thermal state. Most proposed basins formed before Pre-Nectarian (PN) 5 stage do not exhibit clear concentric features in either topography or gravity, suggesting substantial viscous lateral flow in the crust. Recent geodetic measurements reveal that the lunar crust is thinner than previously estimated, indicating that an extremely high crustal temperature is required for lateral flow to occur. In this study, we calculate lunar thermal evolution and viscoelastic deformation of basins and investigate the thermal state at the time of basin formation using recent crustal thickness models. We find that a Moho temperature >1300-1400 K at the time of basin formation is required for substantial viscous relaxation of topography to occur; the implied elastic thickness at the time of loading is <30 km. Such a high temperature can be maintained only for a short time (i.e., <50 Myr for most conditions) after solidification of the LMO or after mantle overturn if it took place; relaxed impact basins forming ⩾150 Myr later than LMO solidification are unlikely. This result is in conflict with an intensive Late Heavy Bombardment (LHB) model, which assumes that most impact basins were formed at ∼3.9 Ga, since it requires LMO solidification time much later than previous theoretical estimates. Either the LHB was moderate, or the majority of proposed early PN basins were not in fact formed by impacts.

  9. Inferring social structure and its drivers from refuge use in the desert tortoise, a relatively solitary species

    USGS Publications Warehouse

    Sah, Pratha; Nussear, Kenneth E.; Esque, Todd C.; Aiello, Christina M.; Hudson, Peter J.; Bansal, Shweta

    2016-01-01

    For several species, refuges (such as burrows, dens, roosts, nests) are an essential resource for protection from predators and extreme environmental conditions. Refuges also serve as focal sites for social interactions including mating, courtship and aggression. Knowledge of refuge use patterns can therefore provide information about social structure, mating and foraging success, as well as the robustness and health of wildlife populations, especially for species considered to be relatively solitary. In this study, we construct networks of burrow use to infer social associations in a threatened wildlife species typically considered solitary - the desert tortoise. We show that tortoise social networks are significantly different than null networks of random associations, and have moderate spatial constraints. We next use statistical models to identify major mechanisms behind individual-level variation in tortoise burrow use, popularity of burrows in desert tortoise habitat and test for stressor-driven changes in refuge use patterns. We show that seasonal variation has a strong impact on tortoise burrow switching behavior. On the other hand, burrow age and topographical condition influence the number of tortoises visiting a burrow in desert tortoise habitat. Of three major population stressors affecting this species (translocation, drought, disease), translocation alters tortoise burrow switching behavior, with translocated animals visiting fewer unique burrows than residents. In a species that is not social, our study highlights the importance of leveraging refuge use behavior to study the presence of and mechanisms behind non-random social structure and individual-level variation. Our analysis of the impact of stressors on refuge-based social structure further emphasizes the potential of this method to detect environmental or anthropogenic disturbances.

  10. Inference Based on Transitive Relation in Tree Shrews ("Tupaia belangeri") and Rats ("Rattus norvegicus") on a Spatial Discrimination Task

    ERIC Educational Resources Information Center

    Takahashi, Makoto; Ushitani, Tomokazu; Fujita, Kazuo

    2008-01-01

    Six tree shrews and 8 rats were tested for their ability to infer transitively in a spatial discrimination task. The apparatus was a semicircular radial-arm maze with 8 arms labeled A through H. In Experiment 1, the animals were first trained in sequence on 4 discriminations to enter 1 of the paired adjacent arms, AB, BC, CD, and DE, with right…

  11. Paraholcoglossum and Tsiorchis, Two New Orchid Genera Established by Molecular and Morphological Analyses of the Holcoglossum Alliance

    PubMed Central

    Chen, Sing-Chi; Cai, Jing; Tsai, Wen-Chieh; Hsiao, Yu-Yun; Rao, Wen-Hui; Ma, Xue-Yong; Zhang, Guo-Qiang

    2011-01-01

    Background Holcoglossum is a small orchid genus of 12 species ranging from SW China to Thailand and NE India. Although molecular and morphological analyses have been performed to establish the phylogenetic relationships within this genus, the interspecific relations and its relations with allied genera, such as Rhynchostylis, Aerides and Vanda, remain unclear. Methodology/Principal Findings In addition to morphological analysis, maximum parsimony, maximum likelihood, and Bayesian inference analyses were performed based on fragments of the nuclear ITS and chloroplast trnL-F and matK genes of 31 taxa (15 Holcoglossum, 14 Aeridinae, 2 outgroups) representing all major clades of the Holcoglossum alliance. The results suggest that Holcoglossum is triphyletic, comprising three clades: the Holcoglossum clade, its sister clade, and a distant clade more closely related to Rhynchostylis, Aerides, and Vanda than to the Holcoglossum clade. The Holcoglossum clade is further divided into three subclades; the genetic distances between these three subclades also support this delimitation. The molecular conclusion is consistent with their distinct morphological characters. Conclusions We propose that the latter two clades comprise two new genera, Paraholcoglossum and Tsiorchis, and Holcoglossum clade divides into three sections. In addition, a new section, Holcoglossum sect. Nujiangensia, and a new species, Holcoglossum linearifolium, are proposed. Some new combinations are made, and a new scheme is provided for the classification of all species of Holcoglossum, Paraholcoglossum, and Tsiorchis. PMID:22016762

  12. Reducing bias in population and landscape genetic inferences: the effects of sampling related individuals and multiple life stages.

    PubMed

    Peterman, William; Brocato, Emily R; Semlitsch, Raymond D; Eggert, Lori S

    2016-01-01

    In population or landscape genetics studies, an unbiased sampling scheme is essential for generating accurate results, but logistics may lead to deviations from the sample design. Such deviations may come in the form of sampling multiple life stages. Presently, it is largely unknown what effect sampling different life stages can have on population or landscape genetic inference, or how mixing life stages can affect the parameters being measured. Additionally, the removal of siblings from a data set is considered best-practice, but direct comparisons of inferences made with and without siblings are limited. In this study, we sampled embryos, larvae, and adult Ambystoma maculatum from five ponds in Missouri, and analyzed them at 15 microsatellite loci. We calculated allelic richness, heterozygosity and effective population sizes for each life stage at each pond and tested for genetic differentiation (F ST and D C ) and isolation-by-distance (IBD) among ponds. We tested for differences in each of these measures between life stages, and in a pooled population of all life stages. All calculations were done with and without sibling pairs to assess the effect of sibling removal. We also assessed the effect of reducing the number of microsatellites used to make inference. No statistically significant differences were found among ponds or life stages for any of the population genetic measures, but patterns of IBD differed among life stages. There was significant IBD when using adult samples, but tests using embryos, larvae, or a combination of the three life stages were not significant. We found that increasing the ratio of larval or embryo samples in the analysis of genetic distance weakened the IBD relationship, and when using D C , the IBD was no longer significant when larvae and embryos exceeded 60% of the population sample. Further, power to detect an IBD relationship was reduced when fewer microsatellites were used in the analysis. PMID:26989639

  13. Reducing bias in population and landscape genetic inferences: the effects of sampling related individuals and multiple life stages

    PubMed Central

    Brocato, Emily R.; Semlitsch, Raymond D.; Eggert, Lori S.

    2016-01-01

    In population or landscape genetics studies, an unbiased sampling scheme is essential for generating accurate results, but logistics may lead to deviations from the sample design. Such deviations may come in the form of sampling multiple life stages. Presently, it is largely unknown what effect sampling different life stages can have on population or landscape genetic inference, or how mixing life stages can affect the parameters being measured. Additionally, the removal of siblings from a data set is considered best-practice, but direct comparisons of inferences made with and without siblings are limited. In this study, we sampled embryos, larvae, and adult Ambystoma maculatum from five ponds in Missouri, and analyzed them at 15 microsatellite loci. We calculated allelic richness, heterozygosity and effective population sizes for each life stage at each pond and tested for genetic differentiation (FST and DC) and isolation-by-distance (IBD) among ponds. We tested for differences in each of these measures between life stages, and in a pooled population of all life stages. All calculations were done with and without sibling pairs to assess the effect of sibling removal. We also assessed the effect of reducing the number of microsatellites used to make inference. No statistically significant differences were found among ponds or life stages for any of the population genetic measures, but patterns of IBD differed among life stages. There was significant IBD when using adult samples, but tests using embryos, larvae, or a combination of the three life stages were not significant. We found that increasing the ratio of larval or embryo samples in the analysis of genetic distance weakened the IBD relationship, and when using DC, the IBD was no longer significant when larvae and embryos exceeded 60% of the population sample. Further, power to detect an IBD relationship was reduced when fewer microsatellites were used in the analysis. PMID:26989639

  14. Nine genera of Eucnemidae (Coleoptera) new to Peru, with a key to Peruvian genera

    PubMed Central

    Muona, Jyrki; Linna, Ari; Sääksjärvi, Ilari E.

    2015-01-01

    Abstract Thirteen genera of Eucnemidae containing forty species were collected from the Iquitos region in Peru. Nine of the genera are new to the country: Rhagomicrus Fleutiaux, 1902, Adelorhagus Horn, 1890, Adelothyreus Chevrolat, 1867, Microrhagus Dejean, 1833, Dyscharachthis Blackburn, 1900, Heterotaxis Bonvouloir, 1871, Spinifornax Fleutiaux, 1926, Serrifornax Fleutiaux, 1926 and Maelodrus Fleutiaux, 1928. The previous eucnemid record from Peru contained eleven species in ten genera. Only one of the forty species caught, Entomophthalmus americanus Bonvouloir, was previously known and described from the country. Dyscharachthis, Maelodrus and Adelorhagus are recorded from South America for the first time. Many of the collected species seem to favor white-sand forest as their habitat. Possible reasons for this are discussed. A list of eucnemids from Peru is included, containing taxa already recorded from the country and also taxa that are likely to occur there. A key to the Peruvian genera is included. PMID:25834475

  15. Orbifold genera, product formulas and power operations

    NASA Astrophysics Data System (ADS)

    Ganter, Nora

    2004-07-01

    We generalize the definition of orbifold elliptic genus, and introduce orbifold genera of chromatic level h, using h-tuples rather than pairs of commuting elements. We show that our genera are in fact orbifold invariants, and we prove integrality results for them. If the genus arises from an H-infinity-map into the Morava-Lubin-Tate theory E_h, then we give a formula expressing the orbifold genus of the symmetric powers of a stably almost complex manifold M in terms of the genus of M itself. Our formula is the p-typical analogue of the Dijkgraaf-Moore-Verlinde-Verlinde formula for the orbifold elliptic genus. It depends only on h and not on the genus.

  16. Genome sizes for all genera of Cycadales.

    PubMed

    Zonneveld, B J M

    2012-01-01

    Nuclear DNA content (2C) is reported for all genera of the Cycadales, using flow cytometry with propidium iodide. Nuclear DNA content ranges from 24 to 64 pg in cycads. This implies that the largest genome contains roughly 40 × 10(9) more base pairs than the smallest genome. The narrow range in nuclear DNA content within a genus is remarkable for such an old group. Furthermore, 42 of the 58 plants measured, covering five genera, have 18 chromosomes. They vary from 36.1 to 64.7 pg, covering the whole range of genome sizes (excluding the genome of Cycas). Hence, their does not seem to be a correlation between genome size and the number of chromosomes. PMID:22117644

  17. Differentiation of genera of the coryneform bacteria.

    PubMed

    Golovlev, E L; Baryshnikova, L M

    1979-01-01

    A scheme of the generic structure of the group of coryneform bacteria, including the genera Arthrobacter, Brevibacterium, Cellulomonas, Corynebacterium, and Rhodococcus, is suggested. Morphological, chemotaxonomic (presence and stereochemical form of diaminopimelic acid, lipid A, and L-arabinose), and physiological features were used as diagnostic criteria. The position of Microbacterum and Mycococcus and of coryneforms with a nocardial wall but giving a positive Hugh-Leifson anaerobic test, and also of Arthrobacter pascens, which may be identical with Mycoplana sp., remains uncertain.

  18. The relative influences of climate and volcanic activity on Holocene lake development inferred from a mountain lake in central Kamchatka

    NASA Astrophysics Data System (ADS)

    Self, A. E.; Klimaschewski, A.; Solovieva, N.; Jones, V. J.; Andrén, E.; Andreev, A. A.; Hammarlund, D.; Brooks, S. J.

    2015-11-01

    A sediment sequence was taken from a closed, high altitude lake (informal name Olive-backed Lake) in the central mountain range of Kamchatka, in the Russian Far East. The sequence was dated by radiocarbon and tephrochronology and used for multi-proxy analyses (chironomids, pollen, diatoms). Although the evolution of Beringian climate through the Holocene is primarily driven by global forcing mechanisms, regional controls, such as volcanic activity or vegetation dynamics, lead to a spatial heterogeneous response. This study aims to reconstruct past changes in the aquatic and terrestrial ecosystems and to separate the climate-driven response from a response to regional or localised environmental change. Radiocarbon dates from plant macrophytes gave a basal date of 7800 cal yr BP. Coring terminated in a tephra layer, so sedimentation at the lake started prior to this date, possibly in the early Holocene following local glacier retreat. Initially the catchment vegetation was dominated by Betula and Alnus woodland with a mosaic of open, wet, aquatic and semi-aquatic habitats. Between 7800 and 6000 cal yr BP the diatom-inferred lake water was pH 4.4-5.3 and chironomid and diatom assemblages in the lake were initially dominated by a small number of acidophilic/acid tolerant taxa. The frequency of Pinus pumila (Siberian dwarf pine) pollen increased from 5000 cal yr BP and threshold analysis indicates that P. pumila arrived in the catchment between 4200 and 3000 cal yr BP. Its range expansion was probably mediated by strengthening of the Aleutian Low pressure system and increased winter snowfall. The diatom-inferred pH reconstructions show that after an initial period of low pH, pH gradually increased from 5500 cal yr BP to pH 5.8 at 1500 cal yr BP. This trend of increasing pH through the Holocene is unusual in lake records, but the initially low pH may have resulted directly or indirectly from intense regional volcanic activity during the mid-Holocene. The chironomid-inferred

  19. Techniques for inferring terrain parameters related to ground vehicle mobility using UAV born IFSAR and lidar data

    NASA Astrophysics Data System (ADS)

    Durst, Phillip J.; Baylot, Alex; McKinley, Burney

    2011-05-01

    Predicting ground vehicle performance requires in-depth knowledge, captured as numeric parameters, of the terrain on which the vehicles will be operating. For off-road performance, predictions are based on rough terrain ride comfort, which is described using a parameter entitled root-mean-square (RMS) surface roughness. Likewise, on-road vehicle performance depends heavily on the slopes of the individual road segments. Traditional methods of computing RMS and road slope values call for high-resolution (inch-scale) surface elevation data. At this scale, surface elevation data is both difficult and time consuming to collect. Nevertheless, a current need exists to attribute large geographic areas with RMS and road slope values in order to better support vehicle mobility predictions, and high-resolution surface data is neither available nor collectible for many of these regions. On the other hand, meter scale data can be quickly and easily collected for these areas using unmanned aerial vehicle (UAV) based IFSAR and LIDAR sensors. A statistical technique for inferring RMS values for large areas using a combination of fractal dimension and spectral analysis of five-meter elevation data is presented. Validation of the RMS prediction technique was based on 43 vehicle ride courses with 30-centimeter surface elevation data. Also presented is a model for classifying road slopes for long road sections using five-meter elevation data. The road slope model was validated against one-meter LIDAR surface elevation profiles. These inference algorithms have been successfully implemented for regions of northern Afghanistan, and some initial results are presented.

  20. Liouville field, modular forms and elliptic genera

    NASA Astrophysics Data System (ADS)

    Eguchi, Tohru; Sugawara, Yuji; Taormina, Anne

    2007-03-01

    When we describe non-compact or singular Calabi-Yau manifolds by CFT, continuous as well as discrete representations appear in the theory. These representations mix in an intricate way under the modular transformations. In this article, we propose a method of combining discrete and continuous representations so that the resulting combinations have a simpler modular behavior and can be used as conformal blocks of the theory. We compute elliptic genera of ALE spaces and obtain results which agree with those suggested from the decompactification of K3 surface. Consistency of our approach is assured by some remarkable identity of theta functions whose proof, by D. Zagier, is included in an appendix.

  1. Redefining Microascus, Scopulariopsis and allied genera.

    PubMed

    Sandoval-Denis, M; Gené, J; Sutton, D A; Cano-Lira, J F; de Hoog, G S; Decock, C A; Wiederhold, N P; Guarro, J

    2016-06-01

    The genera Microascus and Scopulariopsis comprise species commonly isolated from soil, decaying plant material and indoor environments. A few species are also recognised as opportunistic pathogens of insects and animals, including humans. In the past, the taxonomy of these fungi has been based on morphology only. With the aim to clarify the taxonomy and phylogeny of these fungi, we studied a large set of clinical and environmental isolates, including the available ex-type strains of numerous species, by means of morphological, physiological and molecular analyses. Species delineation was assessed under the Genealogical Phylogenetic Species Recognition (GCPSR) criterion using DNA sequence data of four loci (ITS region, and fragments of rDNA LSU, translation elongation factor 1-α and β-tubulin). The genera Microascus and Scopulariopsis were found to be separated in two distinct lineages. The genus Pithoascus is reinstated and the new genus Pseudoscopulariopsis is erected, typified by P. schumacheri. Seven new species of Microascus and one of Scopulariopsis are described, namely M. alveolaris, M. brunneosporus, M. campaniformis, M. expansus, M. intricatus, M. restrictus, M. verrucosus and Scopulariopsis cordiae. Microascus trigonosporus var. macrosporus is accepted as a species distinct from M. trigonosporus. Nine new combinations are introduced. Microascus cinereus, M. longirostris, P. schumacheri and S. flava are neotypified. A table summarising the morphological features of the species treated and identification keys for each genus are provided.

  2. Redefining Microascus, Scopulariopsis and allied genera.

    PubMed

    Sandoval-Denis, M; Gené, J; Sutton, D A; Cano-Lira, J F; de Hoog, G S; Decock, C A; Wiederhold, N P; Guarro, J

    2016-06-01

    The genera Microascus and Scopulariopsis comprise species commonly isolated from soil, decaying plant material and indoor environments. A few species are also recognised as opportunistic pathogens of insects and animals, including humans. In the past, the taxonomy of these fungi has been based on morphology only. With the aim to clarify the taxonomy and phylogeny of these fungi, we studied a large set of clinical and environmental isolates, including the available ex-type strains of numerous species, by means of morphological, physiological and molecular analyses. Species delineation was assessed under the Genealogical Phylogenetic Species Recognition (GCPSR) criterion using DNA sequence data of four loci (ITS region, and fragments of rDNA LSU, translation elongation factor 1-α and β-tubulin). The genera Microascus and Scopulariopsis were found to be separated in two distinct lineages. The genus Pithoascus is reinstated and the new genus Pseudoscopulariopsis is erected, typified by P. schumacheri. Seven new species of Microascus and one of Scopulariopsis are described, namely M. alveolaris, M. brunneosporus, M. campaniformis, M. expansus, M. intricatus, M. restrictus, M. verrucosus and Scopulariopsis cordiae. Microascus trigonosporus var. macrosporus is accepted as a species distinct from M. trigonosporus. Nine new combinations are introduced. Microascus cinereus, M. longirostris, P. schumacheri and S. flava are neotypified. A table summarising the morphological features of the species treated and identification keys for each genus are provided. PMID:27616786

  3. Inferring the Phylogeny of Bovidae Using Mitochondrial DNA Sequences: Resolving Power of Individual Genes Relative to Complete Genomes

    PubMed Central

    Arif, Ibrahim A.; Bakir, Mohammad A.; Khan, Haseeb A.

    2012-01-01

    Molecular techniques that assess biodiversity through the analysis of a small segment of mitochondrial genome have been getting wide attention for inferring the mammalian diversity. Due to their highly conserved nature, specific mitochondrial genes offer a promising tool for phylogenetic analysis. However, there is no established criteria for selecting the typical mitochondrial DNA (mtDNA) segments to achieve a greater resolving power. We therefore chose the family Bovidae as a model and compared the tree-topologies resulting from the commonly used and phylogenetically-informative genes including 16S rRNA, 12S rRNA, COI, Cyt b and D-loop with respect to complete mitochondrial genome. The tree topologies from the whole mitochondrial genome of 12 species were not identical albeit similar with those resulting from the five individual genes mentioned above. High bootstrap values were observed for mtDNA compared with that of any single gene. The average pair-wise sequence divergence using different genetic modes was found to be: D-loop (0.229) > Cyt b (0.159) > COI or complete mtDNA (0.143) > 12S rRNA (0.094) > 16S rRNA (0.091). The tree resulting from complete mtDNA clearly separated the 12 taxa of Bovidae into 3 major clusters, one cluster each for subfamily Cervinae and Bovinae and the third cluster comprised the distinctive clades of Caprinae and Antilopinae. However, jumping clades of Antilopinae were observed while using the individual genes. This study showed that Bison bison and Bos Taurus have very close phylogenetic relationship compared to Bubalus bubalis (Bovinae), irrespective of the method used. Our findings suggest that complete mtDNA genome provides most reliable understanding of complex phylogenetic relationships while the reliability of individual gene trees should be verified with high bootstrap support. PMID:22399841

  4. "I think they believe in me": the predictive effects of teammate- and classmate-focused relation-inferred self-efficacy in sport and physical activity settings.

    PubMed

    Jackson, Ben; Gucciardi, Daniel F; Lonsdale, Chris; Whipp, Peter R; Dimmock, James A

    2014-10-01

    Despite the prevalence of group-/team-based enactment within sport and physical activity settings, to this point the study of relation-inferred self-efficacy (RISE) has been focused upon estimations regarding a single target individual (e.g., one's coach). Accordingly, researchers have not yet considered whether individuals may also form RISE estimations regarding the extent to which the others in their group/team as a whole are confident in their ability. We applied structural equation modeling analyses with cross-sectional and prospective data collected from members of interdependent sport teams (Studies 1 and 2) and undergraduate physical activity classes (Studies 3 and 4), with the purpose of exploring these group-focused RISE inferences. Analyses showed that group-focused RISE perceptions (a) predicted individuals' confidence in their own ability, (b) were empirically distinct from conceptually related constructs, and (c) directly and/or indirectly predicted a range of downstream outcomes over and above the effects of other efficacy perceptions. Taken together, these findings provide preliminary evidence that individuals' group-focused RISE appraisals may be important to consider when investigating the network of efficacy perceptions that develops in group-based physical activity contexts. PMID:25356612

  5. Relating the equatorial electrojet strength inferred from multi-satellite magnetic observations to ExB drift and equatorial scintillation measurements

    NASA Astrophysics Data System (ADS)

    Kimbrel, A.; Maus, S.

    2006-12-01

    The dayside eastward electric field drives a strong electric current along the magnetic equator. This equatorial electrojet (EEJ) follows a narrow band in the ionospheric E-region, the Cowling channel. The strength of the EEJ is essentially the product of the eastward electric field with the Cowling conductivity. Observations of the electrojet strength could therefore provide valuable information on the eastward electric field, as well as on ionospheric conductivity. It is already known that the EEJ strength inferred from magnetic observatory measurements correlates well with the ExB drift observed by equatorial radars. Potentially, the EEJ strength could also be an indicator for the occurrence of equatorial plasma instabilities. To investigate these possibilities we use a dataset of 76,000 EEJ strengths, inferred from equator-crossings of the magnetic field measuring satellites CHAMP, Oersted and SAC-C. These EEJ strengths correlate well with the corresponding Julia ExB radar observations. Since the eastward electric field is ultimately responsible for building up the equatorial plasma anomaly, one can go one step further and correlate the EEJ strengths with the occurrence of night-time equatorial scintillations. An initial attempt to directly relate EEJ strength to SCINDA observations did not show any obvious correlation, though. In the next step, we plan to account for variations in the Cowling conductivity in order to obtain cleaner correlations with the ExB radar drifts. Possibly, this will also help to establish a relationship with the SCINDA observations.

  6. Phylogenetic placement of plant pathogenic Sclerotium species among teleomorph genera.

    PubMed

    Xu, Zhihan; Harrington, Thomas C; Gleason, Mark L; Batzer, Jean C

    2010-01-01

    Phylogenetic analyses and morphological characteristics were used to assess the taxonomic placement of eight plant-pathogenic Sclerotium species. Members of this genus produce only sclerotia and no fruiting bodies or spores, so Sclerotium species have been difficult to place taxonomically. Sequences of rDNA large subunit (LSU) and internal transcribed spacer (ITS) regions were determined for isolates of Sclerotium cepivorum, S. coffeicola, S. denigrans, S. hydrophilum, Ceratorhiza oryzae-sativae, S. perniciosum, S. rhizodes, S. rolfsii and S. rolfsii var. delphinii. Parsimony analysis grouped two species previously thought to be in the Basidiomycota, S. denigrans and S. perniciosum, within the Ascomycota; these species were found to have affinities with the teleomorph genera Sclerotinia and Stromatinia and the asexual Sclerotium cepivorum, which was known earlier to be related to Sclerotinia species. The other Sclerotium species were placed in one of two basidiomycetous groups, genera Athelia or Ceratobasidium. Based on rDNA analysis and morphology the basidiomycetous Sclerotium hydrophilum and S. rhizodes were transferred to genus Ceratorhiza, the anamorph of Ceratobasidium species. Sclerotium coffeicola was found to be close to S. rolfsii var. delphinii and S. rolfsii var. rolfsii, which was shown earlier to have an Athelia teleomorph. PMID:20361501

  7. Anthropogenic sedimentation in Pacific Northwest streams inferred from Aquatic Habitat Survey datausing a relative bed stability index

    EPA Science Inventory

    We evaluated anthropogenic sedimentation in U.S. Pacific Northwest coastal streams using an index of relative bed stability (LRBS*) based on low flow survey data collected using the U.S. Environmental Protection Agency’s Environmental Monitoring and Assessment Program (EMAP) fiel...

  8. The Role of Gender-Related Information and Self-Endorsement of Traits in Preadolescents' Inferences and Judgments.

    ERIC Educational Resources Information Center

    Lobel, Thalma E.; And Others

    1993-01-01

    Fifth and sixth graders completed a sex role orientation measure, viewed a film portraying a child playing gender-appropriate games with members of the same sex or gender-inappropriate games with members of the opposite sex, and made judgments about the child. Subjects' judgments were influenced by the child's gender-related behaviors but not by…

  9. Metabonomics and population studies: age-related amino acids excretion and inferring networks through the study of urine samples in two Italian isolated populations.

    PubMed

    D'Adamo, Pio; Ulivi, Sheila; Beneduci, Amerigo; Pontoni, Gabriele; Capasso, Giovambattista; Lanzara, Carmela; Andrighetto, Gilberto; Hladnik, Uros; Nunes, Virginia; Palacin, Manuel; Gasparini, Paolo

    2010-01-01

    The study of two different Italian isolated populations was combined with a metabonomic approach to better understand tubular handling of amino acids. Levels of amino acids and metabolites have been analyzed by Nucleic Magnetic Resonance and expressed as ratio vs urinary creatinine concentration (mmol/mol). For most of the amino acids there is an age-related U shape pattern of excretion, with the peaks during childhood and old age, and a significant reduction in the adult age. Hierarchical cluster analysis has clearly identified three groups clustering the same amino acids: His, Thr and Ala (group one); Gly and Phe (group two) and a third larger one. Results have been further confirmed by factor and regression analysis, and used to confirm and, in some cases, infer new amino acids networks. As a matter of facts, the identification of strong evidences for clustering of urine excretion of several neutral amino acids suggests the predominant impact of relevant and common transporters.

  10. Possible migration front of gas-related fluid inferred from 3D seismic in the eastern Nankai Trough

    NASA Astrophysics Data System (ADS)

    Otsuka, H.; Morita, S.; Tanahashi, M.; Ashi, J.; Nagakubo, S.

    2010-12-01

    High resolution 3D seismic survey, “Tokai-oki to Kumano-nada”, was conducted for methane hydrate exploration in the eastern Nankai Trough by METI in 2002. Our study focuses on a series of accordion-shaped reflectors with horizontal axis of fold back. They are connected to the edge of BSRs and alternate their polarities at every fold back hinge. We call the reflectors “Foldback Reflectors (FBRs)” in this study. Sedimentary horizons are successive across these series of reflectors with no fault displacement as a general rule. FBR generally corresponds to lateral seismic facies boundary between BSR distribution area and outside of the BSR area. The formation beneath the BSR shows dimmed facies characterized by relatively low amplitude and lack of high frequency components in contrast to outside of the BSR area with normal facies. Seismic velocity analysis suggests that FBRs correspond to velocity boundaries, where the dimmed faceis below the BSR coinsides with relatively low velocity. The polarities of FBRs are also consistent with such velocity changes. Such dimmed facies with low velocity and low amplitude anomaly suggests effects of gas components in the pore water. In this area, FBRs are mostly developed in the well-stratified formation but not in the area of frequent fractures and the area of major lateral lithological change. The observed FBRs are clustered in northern slope of the uplifted outer ridge, whereas few FBRs are developed in the southern slope of the outer ridge with frequent compressive and strike-slip deformations related to major fault systems including the Kodaiba faults and the Tokai faults. The estimated strike directions of each FBRs are probably controlled by the dip direction of crossing formation. Another important character of FBRs is that it never crosses major unconformities into lower strata. In addition, high amplitude layers are sometimes recognized at hinges of foldbacks convex to the outside of the BSR area. These high

  11. Skeletal morphology of two controversial Poecilosclerid genera (Porifera, Demospongiae): Discorhabdella and Crambe

    NASA Astrophysics Data System (ADS)

    Maldonado, M.; Uriz, M. J.

    1996-09-01

    The genera Discorhabdella and Crambe are characterized by bearing uncommon spicule types, i.e. pseudoastrose acanthostyles and sphaeroclones, respectively. They have traditionally been considered to be unrelated taxa, but the present reexamination made evident that an important amount of skeletal features are shared by both. Some of these morphological features, such as the ornamentation on the point of the ectosomal subtylostyles, are reported for the first time. The study also revealed that a tuberose nature of the tyles of the main choanosomal megascleres could be a common ancestral condition in both genera. The morphology of the multi-toothed anchorate chelae showed a gradual transition across the species, suggesting that the morphological diversity in chelae was generated in these genera through a “palmate-anchorate-arcuate” evolutionary sequence. However, the forward or backward direction of this sequence remained unclear from the available evidence. Important levels of skeletal variability were found to affect many of the skeletal characters, especially in the genus Crambe. In some cases, this variability transgressed the limits theoretically defining a species, making evident that the traditional procedure just based on comparison of the skeletons becomes unreliable when tackling the taxonomy of these genera. Most of the skeletal variability seemed to correspond to genetic polymorphisms, except in the case of C. acuata. In this taxon, the skeletal variability could be a result of the existence of a cryptic species, originated by a misconceived synonymy between C. acuata and C. chelastra. Besides the skeletal variability, the obscure taxonomic meaning of many skeletal features favored the existence of conflicting taxonomic proposals for the suprageneric location of these genera, depending on the author’s criteria. This study made evident that any subsequent attempt of phylogenetic inference should be based on an unweighted analysis of the available

  12. Sulfuric acid vapor and other cloud-related gases in the Venus atmosphere - Abundances inferred from observed radio opacity

    NASA Technical Reports Server (NTRS)

    Steffes, P. G.; Eshleman, V. R.

    1982-01-01

    It is suggested that the absorbing characteristics of sulfuric acid vapor appear to reconcile what had been thought to be an inconsistency among measurements and deductions regarding the constituents of the Venus atmosphere and radio occultation, radar reflection, and radio emission measurements of its opacity. Laboratory measurements of sulfuric acid, sulfur dioxide, water vapor, and carbon dioxide are used to model relative contributions to opacity as a function of height in a way that is consistent with observations of the constituents and absorbing properties of the atmosphere. It is concluded that sulfuric acid vapor is likely to be the principal microwave absorber in the 30-50 km altitude range of the middle atmosphere of Venus.

  13. Microplanktonic Community Structure in a Coastal System Relative to a Phaeocystis Bloom Inferred from Morphological and Tag Pyrosequencing Methods

    PubMed Central

    Monchy, Sébastien; Grattepanche, Jean-David; Breton, Elsa; Meloni, Dionigia; Sanciu, Giovanna; Chabé, Magali; Delhaes, Laurence; Viscogliosi, Eric; Sime-Ngando, Télesphore; Christaki, Urania

    2012-01-01

    Background Massive phytoplankton blooms, like the recurrent Phaeocystis proliferation observed every year in the Eastern English Channel (EEC), have a significant influence on the overall planktonic community structure and their food web dynamics. As well as being an important area for local fisheries, the EEC is an ideal ecosystem for work on microbial diversity. This is because, although its environmental context is relatively complex, it is reasonably well understood due to several years of monitoring and morphological observations of its planktonic organisms. The objective of our study was to better understand the under-explored microbial eukaryotic diversity relative to the Phaeocystis bloom. Methodology and Principal Findings The community structure of microplankton (diatoms, haptophytes, ciliates and dinoflagellates) was studied through morphological observations and tag pyrosequencing. During the annual Phaeocystis spring bloom, the phytoplankton biomass increased by 34-fold, while the microzooplankton biomass showed a 4-fold increase, representing on average about 4.6% of the biomass of their phytoplankton prey. Tag pyrosequencing unveiled an extensive diversity of Gymnodiniaceae, with G. spirale and G. fusiformis representing the most abundant reads. An extended diversity of Phaeocystales, with partial 18S rDNA genes sequence identity as low as 85% was found, with taxa corresponding to P. globosa, but also to unknown Phaeocystaceae. Conclusions Morphological analyses and pyrosequencing were generally in accordance with capturing frequency shifts of abundant taxa. Tag pyrosequencing allowed highlighting the maintenance of microplankton diversity during the Phaeocystis bloom and the increase of the taxa presenting low number of reads (minor taxa) along with the dominant ones in response to biotic and/or abiotic changing conditions. Although molecular approaches have enhanced our perception on diversity, it has come to light that the challenge of modelling

  14. Phylogeny of Parasitic Parabasalia and Free-Living Relatives Inferred from Conventional Markers vs. Rpb1, a Single-Copy Gene

    PubMed Central

    Malik, Shehre-Banoo; Brochu, Cynthia D.; Bilic, Ivana; Yuan, Jing; Hess, Michael; Logsdon, John M.; Carlton, Jane M.

    2011-01-01

    Background Parabasalia are single-celled eukaryotes (protists) that are mainly comprised of endosymbionts of termites and wood roaches, intestinal commensals, human or veterinary parasites, and free-living species. Phylogenetic comparisons of parabasalids are typically based upon morphological characters and 18S ribosomal RNA gene sequence data (rDNA), while biochemical or molecular studies of parabasalids are limited to a few axenically cultivable parasites. These previous analyses and other studies based on PCR amplification of duplicated protein-coding genes are unable to fully resolve the evolutionary relationships of parabasalids. As a result, genetic studies of Parabasalia lag behind other organisms. Principal Findings Comparing parabasalid EF1α, α-tubulin, enolase and MDH protein-coding genes with information from the Trichomonas vaginalis genome reveals difficulty in resolving the history of species or isolates apart from duplicated genes. A conserved single-copy gene encodes the largest subunit of RNA polymerase II (Rpb1) in T. vaginalis and other eukaryotes. Here we directly sequenced Rpb1 degenerate PCR products from 10 parabasalid genera, including several T. vaginalis isolates and avian isolates, and compared these data by phylogenetic analyses. Rpb1 genes from parabasalids, diplomonads, Parabodo, Diplonema and Percolomonas were all intronless, unlike intron-rich homologs in Naegleria, Jakoba and Malawimonas. Conclusions/Significance The phylogeny of Rpb1 from parasitic and free-living parabasalids, and conserved Rpb1 insertions, support Trichomonadea, Tritrichomonadea, and Hypotrichomonadea as monophyletic groups. These results are consistent with prior analyses of rDNA and GAPDH sequences and ultrastructural data. The Rpb1 phylogenetic tree also resolves species- and isolate-level relationships. These findings, together with the relative ease of Rpb1 isolation, make it an attractive tool for evaluating more extensive relationships within

  15. Congruence of morphologically-defined genera with molecular phylogenies

    PubMed Central

    Jablonski, David; Finarelli, John A.

    2009-01-01

    Morphologically-defined mammalian and molluscan genera (herein “morphogenera”) are significantly more likely to be monophyletic relative to molecular phylogenies than random, under 3 different models of expected monophyly rates: ≈63% of 425 surveyed morphogenera are monophyletic and 19% are polyphyletic, although certain groups appear to be problematic (e.g., nonmarine, unionoid bivalves). Compiled nonmonophyly rates are probably extreme values, because molecular analyses have focused on “problem” taxa, and molecular topologies (treated herein as error-free) contain contradictory groupings across analyses for 10% of molluscan morphogenera and 37% of mammalian morphogenera. Both body size and geographic range, 2 key macroevolutionary and macroecological variables, show significant rank correlations between values for morphogenera and molecularly-defined clades, even when strictly monophyletic morphogenera are excluded from analyses. Thus, although morphogenera can be imperfect reflections of phylogeny, large-scale statistical treatments of diversity dynamics or macroevolutionary variables in time and space are unlikely to be misleading. PMID:19416868

  16. Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach

    PubMed Central

    Veeramah, Krishna R.; Woerner, August E.; Johnstone, Laurel; Gut, Ivo; Gut, Marta; Marques-Bonet, Tomas; Carbone, Lucia; Wall, Jeff D.; Hammer, Michael F.

    2015-01-01

    Gibbons are believed to have diverged from the larger great apes ∼16.8 MYA and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the family Hylobatidae is divided into four genera, Nomascus, Symphalangus, Hoolock, and Hylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mitochondrial DNA (mtDNA), the Y chromosome, and short autosomal sequences have been inconclusive . To examine the relationships among gibbon genera in more depth, we performed second-generation whole genome sequencing (WGS) to a mean of ∼15× coverage in two individuals from each genus. We developed a coalescent-based approximate Bayesian computation (ABC) method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. Although Hoolock and Symphalangus are likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Instead, our results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1 × 10−9/site/year this speciation process occurred ∼5 MYA during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera. PMID:25769979

  17. Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach.

    PubMed

    Veeramah, Krishna R; Woerner, August E; Johnstone, Laurel; Gut, Ivo; Gut, Marta; Marques-Bonet, Tomas; Carbone, Lucia; Wall, Jeff D; Hammer, Michael F

    2015-05-01

    Gibbons are believed to have diverged from the larger great apes ∼16.8 MYA and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the family Hylobatidae is divided into four genera, Nomascus, Symphalangus, Hoolock, and Hylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mitochondrial DNA (mtDNA), the Y chromosome, and short autosomal sequences have been inconclusive . To examine the relationships among gibbon genera in more depth, we performed second-generation whole genome sequencing (WGS) to a mean of ∼15× coverage in two individuals from each genus. We developed a coalescent-based approximate Bayesian computation (ABC) method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. Although Hoolock and Symphalangus are likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Instead, our results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1 × 10(-9)/site/year this speciation process occurred ∼5 MYA during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera.

  18. Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach.

    PubMed

    Veeramah, Krishna R; Woerner, August E; Johnstone, Laurel; Gut, Ivo; Gut, Marta; Marques-Bonet, Tomas; Carbone, Lucia; Wall, Jeff D; Hammer, Michael F

    2015-05-01

    Gibbons are believed to have diverged from the larger great apes ∼16.8 MYA and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the family Hylobatidae is divided into four genera, Nomascus, Symphalangus, Hoolock, and Hylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mitochondrial DNA (mtDNA), the Y chromosome, and short autosomal sequences have been inconclusive . To examine the relationships among gibbon genera in more depth, we performed second-generation whole genome sequencing (WGS) to a mean of ∼15× coverage in two individuals from each genus. We developed a coalescent-based approximate Bayesian computation (ABC) method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. Although Hoolock and Symphalangus are likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Instead, our results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1 × 10(-9)/site/year this speciation process occurred ∼5 MYA during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera. PMID:25769979

  19. Hybridization and massive mtDNA unidirectional introgression between the closely related Neotropical toads Rhinella marina and R. schneideri inferred from mtDNA and nuclear markers

    PubMed Central

    2011-01-01

    Background The classical perspective that interspecific hybridization in animals is rare has been changing due to a growing list of empirical examples showing the occurrence of gene flow between closely related species. Using sequence data from cyt b mitochondrial gene and three intron nuclear genes (RPL9, c-myc, and RPL3) we investigated patterns of nucleotide polymorphism and divergence between two closely related toad species R. marina and R. schneideri. By comparing levels of differentiation at nuclear and mtDNA levels we were able to describe patterns of introgression and infer the history of hybridization between these species. Results All nuclear loci are essentially concordant in revealing two well differentiated groups of haplotypes, corresponding to the morphologically-defined species R. marina and R. schneideri. Mitochondrial DNA analysis also revealed two well-differentiated groups of haplotypes but, in stark contrast with the nuclear genealogies, all R. schneideri sequences are clustered with sequences of R. marina from the right Amazon bank (RAB), while R. marina sequences from the left Amazon bank (LAB) are monophyletic. An Isolation-with-Migration (IM) analysis using nuclear data showed that R. marina and R. schneideri diverged at ≈ 1.69 Myr (early Pleistocene), while R. marina populations from LAB and RAB diverged at ≈ 0.33 Myr (middle Pleistocene). This time of divergence is not consistent with the split between LAB and RAB populations obtained with mtDNA data (≈ 1.59 Myr), which is notably similar to the estimate obtained with nuclear genes between R. marina and R. schneideri. Coalescent simulations of mtDNA phylogeny under the speciation history inferred from nuclear genes rejected the hypothesis of incomplete lineage sorting to explain the conflicting signal between mtDNA and nuclear-based phylogenies. Conclusions The cytonuclear discordance seems to reflect the occurrence of interspecific hybridization between these two closely related

  20. Recommended names for pleomorphic genera in Dothideomycetes.

    PubMed

    Rossman, Amy Y; Crous, Pedro W; Hyde, Kevin D; Hawksworth, David L; Aptroot, André; Bezerra, Jose L; Bhat, Jayarama D; Boehm, Eric; Braun, Uwe; Boonmee, Saranyaphat; Camporesi, Erio; Chomnunti, Putarak; Dai, Dong-Qin; D'souza, Melvina J; Dissanayake, Asha; Gareth Jones, E B; Groenewald, Johannes Z; Hernández-Restrepo, Margarita; Hongsanan, Sinang; Jaklitsch, Walter M; Jayawardena, Ruvishika; Jing, Li Wen; Kirk, Paul M; Lawrey, James D; Mapook, Ausana; McKenzie, Eric H C; Monkai, Jutamart; Phillips, Alan J L; Phookamsak, Rungtiwa; Raja, Huzefa A; Seifert, Keith A; Senanayake, Indunil; Slippers, Bernard; Suetrong, Satinee; Taylor, Joanne E; Thambugala, Kasun M; Tian, Qing; Tibpromma, Saowaluck; Wanasinghe, Dhanushka N; Wijayawardene, Nalin N; Wikee, Saowanee; Woudenberg, Joyce H C; Wu, Hai-Xia; Yan, Jiye; Yang, Tao; Zhang, Ying

    2015-12-01

    This paper provides recommendations of one name for use among pleomorphic genera in Dothideomycetes by the Working Group on Dothideomycetes established under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). A number of these generic names are proposed for protection because they do not have priority and/or the generic name selected for use is asexually typified. These include: Acrogenospora over Farlowiella; Alternaria over Allewia, Lewia, and Crivellia; Botryosphaeria over Fusicoccum; Camarosporula over Anthracostroma; Capnodium over Polychaeton; Cladosporium over Davidiella; Corynespora over Corynesporasca; Curvularia over Pseudocochliobolus; Elsinoë over Sphaceloma; Excipulariopsis over Kentingia; Exosporiella over Anomalemma; Exserohilum over Setosphaeria; Gemmamyces over Megaloseptoria; Kellermania over Planistromella; Kirschsteiniothelia over Dendryphiopsis; Lecanosticta over Eruptio; Paranectriella over Araneomyces; Phaeosphaeria over Phaeoseptoria; Phyllosticta over Guignardia; Podonectria over Tetracrium; Polythrincium over Cymadothea; Prosthemium over Pleomassaria; Ramularia over Mycosphaerella; Sphaerellopsis over Eudarluca; Sphaeropsis over Phaeobotryosphaeria; Stemphylium over Pleospora; Teratosphaeria over Kirramyces and Colletogloeopsis; Tetraploa over Tetraplosphaeria; Venturia over Fusicladium and Pollaccia; and Zeloasperisporium over Neomicrothyrium. Twenty new combinations are made: Acrogenospora carmichaeliana (Berk.) Rossman & Crous, Alternaria scrophulariae (Desm.) Rossman & Crous, Pyrenophora catenaria (Drechsler) Rossman & K.D. Hyde, P. dematioidea (Bubák & Wróbl.) Rossman & K.D. Hyde, P. fugax (Wallr.) Rossman & K.D. Hyde, P. nobleae (McKenzie & D. Matthews) Rossman & K.D. Hyde, P. triseptata (Drechsler) Rossman & K.D. Hyde, Schizothyrium cryptogamum (Batzer & Crous) Crous & Batzer, S. cylindricum (G.Y. Sun et al.) Crous & Batzer, S. emperorae (G.Y. Sun & L. Gao) Crous & Batzer, S. inaequale (G.Y. Sun & L

  1. Molecular systematics of the bubblegum coral genera (Paragorgiidae, Octocorallia) and description of a new deep-sea species.

    PubMed

    Herrera, Santiago; Baco, Amy; Sánchez, Juan A

    2010-04-01

    Bubblegum octocorals (Paragorgia and Sibogagorgia) play an important ecological role in many deep-sea ecosystems. However, these organisms are currently threatened by destructive fishing methods such as bottom trawling. Taxonomic knowledge of conservation targets is necessary for the creation and implementation of efficient conservation strategies. However, for most deep-sea coral groups this knowledge remains incomplete. For instance, despite its similarities with Paragorgia, Sibogagorgia is particular in lacking polyp sclerites, which are present in groups like Paragorgia and the Coralliidae. Although two kinds of sclerites are very similar between Paragorgia and Sibogagorgia, other characters challenge the monophyly of these genera. Here we help to clarify the taxonomy and evolutionary relationships of the bubblegum octocorals and related taxa by examining molecular data. We employed nucleotide sequences of mitochondrial (ND6, ND6-ND3 intergenic spacer, ND3, ND2, COI, msh1 and 16S) and nuclear (28S and ITS2) genomic regions from several taxa to infer molecular phylogenetics and to examine the correspondence of morphological features with the underlying genetic information. Our data strongly supported the monophyly of the genus Paragorgia, the family Coralliidae (precious corals), and a group of undescribed specimens resembling Sibogagorgia. Further morphological observations were congruent regarding the uniqueness of the undescribed specimens, here defined as a new species, Sibogagorgia cauliflora sp. nov., which occurs in both sides of the North American landmass at depths below 1700 m. This new species resembles S. dennisgordoni with branching in one plane but has fairly different radiate sclerites and significantly divergent DNA sequences. The existence of several diagnostic characters of Sibogagorgia in S. cauliflora indicates that they indeed belong to this genus. It is however remarkable that a small number of medullar canals are also found in this species

  2. Geographic comparison of plant genera used in frugivory among the pitheciids Cacajao, Callicebus, Chiropotes, and Pithecia.

    PubMed

    Boyle, Sarah A; Thompson, Cynthia L; Deluycker, Anneke; Alvarez, Silvia J; Alvim, Thiago H G; Aquino, Rolando; Bezerra, Bruna M; Boubli, Jean P; Bowler, Mark; Caselli, Christini Barbosa; Chagas, Renata R D; Ferrari, Stephen F; Fontes, Isadora P; Gregory, Tremaine; Haugaasen, Torbjørn; Heiduck, Stefanie; Hores, Rose; Lehman, Shawn; Melo, Fabiano R de; Moreira, Leandro S; Moura, Viviane S; Nagy-Reis, Mariana B; Palacios, Erwin; Palminteri, Suzanne; Peres, Carlos A; Pinto, Liliam; Port-Carvalho, Marcio; Rodríguez, Adriana; Santos, Ricardo R dos; Setz, Eleonore Z F; Shaffer, Christopher A; Silva, Felipe Ennes; Silva, Rafaela F Soares da; Souza-Alves, João P; Trevelin, Leonardo C; Veiga, Liza M; Vieira, Tatiana M; DuBose, Mary E; Barnett, Adrian A

    2016-05-01

    Pitheciids are known for their frugivorous diets, but there has been no broad-scale comparison of fruit genera used by these primates that range across five geographic regions in South America. We compiled 31 fruit lists from data collected from 18 species (three Cacajao, six Callicebus, five Chiropotes, and four Pithecia) at 26 study sites in six countries. Together, these lists contained 455 plant genera from 96 families. We predicted that 1) closely related Chiropotes and Cacajao would demonstrate the greatest similarity in fruit lists; 2) pitheciids living in closer geographic proximity would have greater similarities in fruit lists; and 3) fruit genus richness would be lower in lists from forest fragments than continuous forests. Fruit genus richness was greatest for the composite Chiropotes list, even though Pithecia had the greatest overall sampling effort. We also found that the Callicebus composite fruit list had lower similarity scores in comparison with the composite food lists of the other three genera (both within and between geographic areas). Chiropotes and Pithecia showed strongest similarities in fruit lists, followed by sister taxa Chiropotes and Cacajao. Overall, pitheciids in closer proximity had more similarities in their fruit list, and this pattern was evident in the fruit lists for both Callicebus and Chiropotes. There was no difference in the number of fruit genera used by pitheciids in habitat fragments and continuous forest. Our findings demonstrate that pitheciids use a variety of fruit genera, but phylogenetic and geographic patterns in fruit use are not consistent across all pitheciid genera. This study represents the most extensive examination of pitheciid fruit consumption to date, but future research is needed to investigate the extent to which the trends in fruit genus richness noted here are attributable to habitat differences among study sites, differences in feeding ecology, or a combination of both.

  3. Circular inferences in schizophrenia.

    PubMed

    Jardri, Renaud; Denève, Sophie

    2013-11-01

    A considerable number of recent experimental and computational studies suggest that subtle impairments of excitatory to inhibitory balance or regulation are involved in many neurological and psychiatric conditions. The current paper aims to relate, specifically and quantitatively, excitatory to inhibitory imbalance with psychotic symptoms in schizophrenia. Considering that the brain constructs hierarchical causal models of the external world, we show that the failure to maintain the excitatory to inhibitory balance results in hallucinations as well as in the formation and subsequent consolidation of delusional beliefs. Indeed, the consequence of excitatory to inhibitory imbalance in a hierarchical neural network is equated to a pathological form of causal inference called 'circular belief propagation'. In circular belief propagation, bottom-up sensory information and top-down predictions are reverberated, i.e. prior beliefs are misinterpreted as sensory observations and vice versa. As a result, these predictions are counted multiple times. Circular inference explains the emergence of erroneous percepts, the patient's overconfidence when facing probabilistic choices, the learning of 'unshakable' causal relationships between unrelated events and a paradoxical immunity to perceptual illusions, which are all known to be associated with schizophrenia. PMID:24065721

  4. Circular inferences in schizophrenia.

    PubMed

    Jardri, Renaud; Denève, Sophie

    2013-11-01

    A considerable number of recent experimental and computational studies suggest that subtle impairments of excitatory to inhibitory balance or regulation are involved in many neurological and psychiatric conditions. The current paper aims to relate, specifically and quantitatively, excitatory to inhibitory imbalance with psychotic symptoms in schizophrenia. Considering that the brain constructs hierarchical causal models of the external world, we show that the failure to maintain the excitatory to inhibitory balance results in hallucinations as well as in the formation and subsequent consolidation of delusional beliefs. Indeed, the consequence of excitatory to inhibitory imbalance in a hierarchical neural network is equated to a pathological form of causal inference called 'circular belief propagation'. In circular belief propagation, bottom-up sensory information and top-down predictions are reverberated, i.e. prior beliefs are misinterpreted as sensory observations and vice versa. As a result, these predictions are counted multiple times. Circular inference explains the emergence of erroneous percepts, the patient's overconfidence when facing probabilistic choices, the learning of 'unshakable' causal relationships between unrelated events and a paradoxical immunity to perceptual illusions, which are all known to be associated with schizophrenia.

  5. In-Situ and Remote-Sensing Data Fusion Using Machine Learning Techniques to Infer Urban and Fire Related Pollution Plumes

    NASA Technical Reports Server (NTRS)

    Russell, P. B.; Segal-Rozenhaimer, M.; Schmid, B.; Redemann, J.; Livingston, J. M.; Flynn, C.J.; Johnson, R. R.; Dunagan, S. E.; Shinozuka, Y.; Kacenelenbogen, M.; Chatfield, R. B.

    2014-01-01

    Airmass type characterization is key in understanding the relative contribution of various emission sources to atmospheric composition and air quality and can be useful in bottom-up model validation and emission inventories. However, classification of pollution plumes from space is often not trivial. Sub-orbital campaigns, such as SEAC4RS (Studies of Emissions, Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys) give us a unique opportunity to study atmospheric composition in detail, by using a vast suite of in-situ instruments for the detection of trace gases and aerosols. These measurements allow identification of spatial and temporal atmospheric composition changes due to various pollution plumes resulting from urban, biogenic and smoke emissions. Nevertheless, to transfer the knowledge gathered from such campaigns into a global spatial and temporal context, there is a need to develop workflow that can be applicable to measurements from space. In this work we rely on sub-orbital in-situ and total column remote sensing measurements of various pollution plumes taken aboard the NASA DC-8 during 2013 SEAC4RS campaign, linking them through a neural-network (NN) algorithm to allow inference of pollution plume types by input of columnar aerosol and trace-gas measurements. In particular, we use the 4STAR (Spectrometer for Sky-Scanning, Sun-Tracking Atmospheric Research) airborne measurements of wavelength dependent aerosol optical depth (AOD), particle size proxies, O3, NO2 and water vapor to classify different pollution plumes. Our method relies on assigning a-priori ground-truth labeling to the various plumes, which include urban pollution, different fire types (i.e. forest and agriculture) and fire stage (i.e. fresh and aged) using cluster analysis of aerosol and trace-gases in-situ and auxiliary (e.g. trajectory) data and the training of a NN scheme to fit the best prediction parameters using 4STAR measurements as input. We explore our

  6. Multi-model inference of adult and childhood leukaemia excess relative risks based on the Japanese A-bomb survivors mortality data (1950-2000).

    PubMed

    Walsh, Linda; Kaiser, Jan Christian

    2011-03-01

    Some relatively new issues that augment the usual practice of ignoring model uncertainty, when making inference about parameters of a specific model, are brought to the attention of the radiation protection community here. Nine recently published leukaemia risk models, developed with the Japanese A-bomb epidemiological mortality data, have been included in a model-averaging procedure so that the main conclusions do not depend on just one type of model or statistical test. The models have been centred here at various adult and young ages at exposure, for some short times since exposure, in order to obtain specially computed childhood Excess Relative Risks (ERR) with uncertainties that account for correlations in the fitted parameters associated with the ERR dose-response. The model-averaged ERR at 1 Sv was not found to be statistically significant for attained ages of 7 and 12 years but was statistically significant for attained ages of 17, 22 and 55 years. Consequently, such risks when applied to other situations, such as children in the vicinity of nuclear installations or in estimates of the proportion of childhood leukaemia incidence attributable to background radiation (i.e. low doses for young ages and short times since exposure), are only of very limited value, with uncertainty ranges that include zero risk. For example, assuming a total radiation dose to a 5-year-old child of 10 mSv and applying the model-averaged risk at 10 mSv for a 7-year-old exposed at 2 years of age would result in an ERR=0.33, 95% CI: -0.51 to 1.22. One model (United Nations scientific committee on the effects of atomic radiation report. Volume 1. Annex A: epidemiological studies of radiation and cancer, United Nations, New York, 2006) weighted model-averaged risks of leukaemia most strongly by half of the total unity weighting and is recommended for application in future leukaemia risk assessments that continue to ignore model uncertainty. However, on the basis of the analysis

  7. Optimal inference with suboptimal models: Addiction and active Bayesian inference

    PubMed Central

    Schwartenbeck, Philipp; FitzGerald, Thomas H.B.; Mathys, Christoph; Dolan, Ray; Wurst, Friedrich; Kronbichler, Martin; Friston, Karl

    2015-01-01

    When casting behaviour as active (Bayesian) inference, optimal inference is defined with respect to an agent’s beliefs – based on its generative model of the world. This contrasts with normative accounts of choice behaviour, in which optimal actions are considered in relation to the true structure of the environment – as opposed to the agent’s beliefs about worldly states (or the task). This distinction shifts an understanding of suboptimal or pathological behaviour away from aberrant inference as such, to understanding the prior beliefs of a subject that cause them to behave less ‘optimally’ than our prior beliefs suggest they should behave. Put simply, suboptimal or pathological behaviour does not speak against understanding behaviour in terms of (Bayes optimal) inference, but rather calls for a more refined understanding of the subject’s generative model upon which their (optimal) Bayesian inference is based. Here, we discuss this fundamental distinction and its implications for understanding optimality, bounded rationality and pathological (choice) behaviour. We illustrate our argument using addictive choice behaviour in a recently described ‘limited offer’ task. Our simulations of pathological choices and addictive behaviour also generate some clear hypotheses, which we hope to pursue in ongoing empirical work. PMID:25561321

  8. Distinguishing centrarchid genera by use of lateral line scales

    USGS Publications Warehouse

    Roberts, N.M.; Rabeni, C.F.; Stanovick, J.S.

    2007-01-01

    Predator-prey relations involving fishes are often evaluated using scales remaining in gut contents or feces. While several reliable keys help identify North American freshwater fish scales to the family level, none attempt to separate the family Centrarchidae to the genus level. Centrarchidae is of particular concern in the midwestern United States because it contains several popular sport fishes, such as smallmouth bass Micropterus dolomieu, largemouth bass M. salmoides, and rock bass Ambloplites rupestris, as well as less-sought-after species of sunfishes Lepomis spp. and crappies Pomoxis spp. Differentiating sport fish from non-sport fish has important management implications. Morphological characteristics of lateral line scales (n = 1,581) from known centrarchid fishes were analyzed. The variability of measurements within and between genera was examined to select variables that were the most useful in further classifying unknown centrarchid scales. A linear discriminant analysis model was developed using 10 variables. Based on this model, 84.4% of Ambloplites scales, 81.2% of Lepomis scales, and 86.6% of Micropterus scales were classified correctly using a jackknife procedure. ?? Copyright by the American Fisheries Society 2007.

  9. Phylogenetic Relationships of Five Asian Schilbid Genera Including Clupisoma (Siluriformes: Schilbeidae).

    PubMed

    Wang, Jing; Lu, Bin; Zan, Ruiguang; Chai, Jing; Ma, Wei; Jin, Wei; Duan, Rongyao; Luo, Jing; Murphy, Robert W; Xiao, Heng; Chen, Ziming

    2016-01-01

    The phylogenetic relationships of Asian schilbid catfishes of the genera Clupisoma, Ailia, Horabagrus, Laides and Pseudeutropius are poorly understood, especially those of Clupisoma. Herein, we reconstruct the phylogeny of 38 species of catfishes belonging to 28 genera and 14 families using the concatenated mitochondrial genes COI, cytb, and 16S rRNA, as well as the nuclear genes RAG1 and RAG2. The resulting phylogenetic trees consistently place Clupisoma as the sister taxon of Laides, and the five representative Asian schilbid genera form two monophyletic groups with the relationships (Ailia (Laides, Clupisoma)) and (Horabagrus, Pseudeutropius). The so-called "Big Asia" lineage relates distantly to African schilbids. Independent analyses of the mitochondrial and nuclear DNA data yield differing trees for the two Asian schilbid groups. Analyses of the mitochondrial gene data support a sister-group relationship for (Ailia (Laides, Clupisoma)) and the Sisoroidea and a sister-taxon association of (Horabagrus, Pseudeutropius) and the Bagridae. In contrast, analyses of the combined nuclear data indicate (Ailia (Laides, Clupisoma)) to be the sister group to (Horabagrus, Pseudeutropius). Our results indicate that the Horabagridae, recognized by some authors as consisting of Horabagrus, Pseudeutropius and Clupisoma does not include the latter genus. We formally erect a new family, Ailiidae fam. nov. for a monophyletic Asian group comprised of the genera Ailia, Laides and Clupisoma. PMID:26751688

  10. Phylogenetic Relationships of Five Asian Schilbid Genera Including Clupisoma (Siluriformes: Schilbeidae)

    PubMed Central

    Zan, Ruiguang; Chai, Jing; Ma, Wei; Jin, Wei; Duan, Rongyao; Luo, Jing; Murphy, Robert W.; Xiao, Heng; Chen, Ziming

    2016-01-01

    The phylogenetic relationships of Asian schilbid catfishes of the genera Clupisoma, Ailia, Horabagrus, Laides and Pseudeutropius are poorly understood, especially those of Clupisoma. Herein, we reconstruct the phylogeny of 38 species of catfishes belonging to 28 genera and 14 families using the concatenated mitochondrial genes COI, cytb, and 16S rRNA, as well as the nuclear genes RAG1 and RAG2. The resulting phylogenetic trees consistently place Clupisoma as the sister taxon of Laides, and the five representative Asian schilbid genera form two monophyletic groups with the relationships (Ailia (Laides, Clupisoma)) and (Horabagrus, Pseudeutropius). The so-called “Big Asia” lineage relates distantly to African schilbids. Independent analyses of the mitochondrial and nuclear DNA data yield differing trees for the two Asian schilbid groups. Analyses of the mitochondrial gene data support a sister-group relationship for (Ailia (Laides, Clupisoma)) and the Sisoroidea and a sister-taxon association of (Horabagrus, Pseudeutropius) and the Bagridae. In contrast, analyses of the combined nuclear data indicate (Ailia (Laides, Clupisoma)) to be the sister group to (Horabagrus, Pseudeutropius). Our results indicate that the Horabagridae, recognized by some authors as consisting of Horabagrus, Pseudeutropius and Clupisoma does not include the latter genus. We formally erect a new family, Ailiidae fam. nov. for a monophyletic Asian group comprised of the genera Ailia, Laides and Clupisoma. PMID:26751688

  11. Inferring Diversity: Life After Shannon

    NASA Astrophysics Data System (ADS)

    Giffin, Adom

    The diversity of a community that cannot be fully counted must be inferred. The two preeminent inference methods are the MaxEnt method, which uses information in the form of constraints and Bayes' rule which uses information in the form of data. It has been shown that these two methods are special cases of the method of Maximum (relative) Entropy (ME). We demonstrate how this method can be used as a measure of diversity that not only reproduces the features of Shannon's index but exceeds them by allowing more types of information to be included in the inference. A specific example is solved in detail. Additionally, the entropy that is found is the same form as the thermodynamic entropy.

  12. Dated Phylogenies of the Sister Genera Macaranga and Mallotus (Euphorbiaceae): Congruence in Historical Biogeographic Patterns?

    PubMed Central

    van Welzen, Peter C.; Strijk, Joeri S.; van Konijnenburg-van Cittert, Johanna H. A.; Nucete, Monica; Merckx, Vincent S. F. T.

    2014-01-01

    Molecular phylogenies and estimates of divergence times within the sister genera Macaranga and Mallotus were estimated using Bayesian relaxed clock analyses of two generic data sets, one per genus. Both data sets were based on different molecular markers and largely different samples. Per genus three calibration points were utilised. The basal calibration point (crown node of all taxa used) was taken from literature and used for both taxa. The other three calibrations were based on fossils of which two were used per genus. We compared patterns of dispersal and diversification in Macaranga and Mallotus using ancestral area reconstruction in RASP (S-DIVA option) and contrasted our results with biogeographical and geological records to assess accuracy of inferred age estimates. A check of the fossil calibration point showed that the Japanese fossil, used for dating the divergence of Mallotus, probably had to be attached to a lower node, the stem node of all pioneer species, but even then the divergence time was still younger than the estimated age of the fossil. The African (only used in the Macaranga data set) and New Zealand fossils (used for both genera) seemed reliably placed. Our results are in line with existing geological data and the presence of stepping stones that provided dispersal pathways from Borneo to New Guinea-Australia, from Borneo to mainland Asia and additionally at least once to Africa and Madagascar via land and back to India via Indian Ocean island chains. The two genera show congruence in dispersal patterns, which corroborate divergence time estimates, although the overall mode and tempo of dispersal and diversification differ significantly as shown by distribution patterns of extant species. PMID:24465660

  13. Incomplete lineage sorting is common in extant gibbon genera.

    PubMed

    Wall, Jeffrey D; Kim, Sung K; Luca, Francesca; Carbone, Lucia; Mootnick, Alan R; de Jong, Pieter J; Di Rienzo, Anna

    2013-01-01

    We sequenced reduced representation libraries by means of Illumina technology to generate over 1.5 Mb of orthologous sequence from a representative of each of the four extant gibbon genera (Nomascus, Hylobates, Symphalangus, and Hoolock). We used these data to assess the evolutionary relationships between the genera by evaluating the likelihoods of all possible bifurcating trees involving the four taxa. Our analyses provide weak support for a tree with Nomascus and Hylobates as sister taxa and with Hoolock and Symphalangus as sister taxa, though bootstrap resampling suggests that other phylogenetic scenarios are also possible. This uncertainty is due to short internal branch lengths and extensive incomplete lineage sorting across taxa. The true phylogenetic relationships among gibbon genera will likely require a more extensive whole-genome sequence analysis.

  14. Age of overwash and rate of relative sea-level rise inferred from detrital heads and microatolls of medieval corals at Anegada, British Virgin Islands

    NASA Astrophysics Data System (ADS)

    Jennifer, W.; Feuillet, N.; Robert, H.; Brian, A.; Ten Brink, U. S.; Deschamps, P.; Tuttle, M. P.; Wei, Y.; Fuentes, Z.

    2012-12-01

    Coral boulders deposited on Anegada, an island 120 km south of the Puerto Rico Trench, record overwash dated to AD 1200-1450 and relative sea-level changes that preceded it. Composed largely of Pleistocene limestone, Anegada is less than 8 m above sea level and is fringed on the north and east by a coral reef where Atlantic Ocean waves break. The lowest parts of the island were washed over from the north in AD 1650-1800, as judged from landforms and deposits reported previously (doi:10.1007/s11069-010-9622-6). The coral boulders indicate overwash of higher elevation and earlier age. The boulders were apparently torn from the adjacent reef by a tsunami of nearby origin, as inferred in companion abstracts on geology and modeling. We found the corals scattered in five areas inland from the north shore. Two of the areas show solitary coral heads 1500 m from the reef. The boulders are more numerous in the three other areas, where they are up to 500-700 m from the reef and up to 4 m above sea level. Some were transported over beach ridges or through breaches cut into them. Others are hundreds of meters inland from a modern storm berm. Most rest on the Pleistocene limestone. Many are overturned. Most are broken but few are whole. The largest measured diameter is 2 m and the greatest measured height is 1 m. Most of the boulders are of the brain coral Diploria strigosa, but smaller Porites asteroides and Montastrea annularis are also present. Some of the D. strigosa retain the rounded shape typical of living heads and are dimpled with holes perhaps left by feather-duster worms. The preservation of these features suggests that many of the boulders came ashore alive. We avoided dating a head that shows field evidence for death before transport; an erosional surface cuts across its youngest growth bands and is covered with the remains of encrusting marine organisms. Among the 18 coral boulders dated, 13 form a young group with ages in the range 890±25 to 1020±25 14C yr BP

  15. Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov.

    PubMed

    Gerritsen, Jacoline; Fuentes, Susana; Grievink, Wieke; van Niftrik, Laura; Tindall, Brian J; Timmerman, Harro M; Rijkers, Ger T; Smidt, Hauke

    2014-05-01

    A Gram-positive staining, rod-shaped, non-motile, spore-forming obligately anaerobic bacterium, designated CRIBT, was isolated from the gastro-intestinal tract of a rat and characterized. The major cellular fatty acids of strain CRIBT were saturated and unsaturated straight-chain C12-C19 fatty acids, with C16:0 being the predominant fatty acid. The polar lipid profile comprised six glycolipids, four phospholipids and one lipid that did not stain with any of the specific spray reagents used. The only quinone was MK-6. The predominating cell-wall sugars were glucose and galactose. The peptidoglycan type of strain CRIBT was A1σ lanthionine-direct. The genomic DNA G+C content of strain CRIBT was 28.1 mol%. On the basis of 16S rRNA gene sequence similarity, strain CRIBT was most closely related to a number of species of the genus Clostridium, including Clostridium lituseburense (97.2%), Clostridium glycolicum (96.2%), Clostridium mayombei (96.2%), Clostridium bartlettii (96.0%) and Clostridium irregulare (95.5%). All these species show very low 16S rRNA gene sequence similarity (<85%) to the type strain of Clostridium butyricum, the type species of the genus Clostridium. DNA-DNA hybridization with closely related reference strains indicated reassociation values below 32%. On the basis of phenotypic and genetic studies, a novel genus, Romboutsia gen. nov., is proposed. The novel isolate CRIBT (=DSM 25109T=NIZO 4048T) is proposed as the type strain of the type species, Romboutsia ilealis gen. nov., sp. nov., of the proposed novel genus. It is proposed that C. lituseburense is transferred to this genus as Romboutsia lituseburensis comb. nov. Furthermore, the reclassification into novel genera is proposed for C. bartlettii, as Intestinibacter bartlettii gen. nov., comb. nov. (type species of the genus), C. glycolicum, as Terrisporobacter glycolicus gen. nov., comb. nov. (type species of the genus), C. mayombei, as Terrisporobacter mayombei gen. nov., comb. nov., and C

  16. Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov.

    PubMed

    Gerritsen, Jacoline; Fuentes, Susana; Grievink, Wieke; van Niftrik, Laura; Tindall, Brian J; Timmerman, Harro M; Rijkers, Ger T; Smidt, Hauke

    2014-05-01

    A Gram-positive staining, rod-shaped, non-motile, spore-forming obligately anaerobic bacterium, designated CRIBT, was isolated from the gastro-intestinal tract of a rat and characterized. The major cellular fatty acids of strain CRIBT were saturated and unsaturated straight-chain C12-C19 fatty acids, with C16:0 being the predominant fatty acid. The polar lipid profile comprised six glycolipids, four phospholipids and one lipid that did not stain with any of the specific spray reagents used. The only quinone was MK-6. The predominating cell-wall sugars were glucose and galactose. The peptidoglycan type of strain CRIBT was A1σ lanthionine-direct. The genomic DNA G+C content of strain CRIBT was 28.1 mol%. On the basis of 16S rRNA gene sequence similarity, strain CRIBT was most closely related to a number of species of the genus Clostridium, including Clostridium lituseburense (97.2%), Clostridium glycolicum (96.2%), Clostridium mayombei (96.2%), Clostridium bartlettii (96.0%) and Clostridium irregulare (95.5%). All these species show very low 16S rRNA gene sequence similarity (<85%) to the type strain of Clostridium butyricum, the type species of the genus Clostridium. DNA-DNA hybridization with closely related reference strains indicated reassociation values below 32%. On the basis of phenotypic and genetic studies, a novel genus, Romboutsia gen. nov., is proposed. The novel isolate CRIBT (=DSM 25109T=NIZO 4048T) is proposed as the type strain of the type species, Romboutsia ilealis gen. nov., sp. nov., of the proposed novel genus. It is proposed that C. lituseburense is transferred to this genus as Romboutsia lituseburensis comb. nov. Furthermore, the reclassification into novel genera is proposed for C. bartlettii, as Intestinibacter bartlettii gen. nov., comb. nov. (type species of the genus), C. glycolicum, as Terrisporobacter glycolicus gen. nov., comb. nov. (type species of the genus), C. mayombei, as Terrisporobacter mayombei gen. nov., comb. nov., and C

  17. Keys to genera of the spider wasps (Hymenoptera: Pompilidae) of Russia and neighbouring countries, with check-list of genera.

    PubMed

    Loktionov, Valery M; Lelej, Arkady S

    2015-10-28

    Keys to 55 genera of spider wasps of Russia and neighbouring countries in females and males are given. Of them 34 genera are distributed in Russia. An annotated list of genera with type species and distribution data within Russia and biogeographical regions is given. The genus Xenaporus Ashmead, 1902 and X. eremocanus Wolf, 1990 are newly recorded from Russia. According to ICZN 1995 (Opinion 1820) new synonymy (valid name first) is proposed for the type species of genus Cryptocheilus Panzer, 1806: Sphex annulata Fabricius, 1798 (=Pompilus alternatus Lepeletier de Saint Fargeau, 1845, syn. nov.; =Pompilus comparatus Smith, 1855, syn. nov.; =Priocnemis culpabilis Costa, 1893, syn. nov.; Salius annulatilis Richards, 1935, syn. nov.).

  18. Inference in `poor` languages

    SciTech Connect

    Petrov, S.

    1996-10-01

    Languages with a solvable implication problem but without complete and consistent systems of inference rules (`poor` languages) are considered. The problem of existence of finite complete and consistent inference rule system for a ``poor`` language is stated independently of the language or rules syntax. Several properties of the problem arc proved. An application of results to the language of join dependencies is given.

  19. Phylogeny and character evolution of the fern genus Tectaria (Tectariaceae) in the Old World inferred from chloroplast DNA sequences.

    PubMed

    Ding, Hui-Hui; Chao, Yi-Shan; Callado, John Rey; Dong, Shi-Yong

    2014-11-01

    In this study we provide a phylogeny for the pantropical fern genus Tectaria, with emphasis on the Old World species, based on sequences of five plastid regions (atpB, ndhF plus ndhF-trnL, rbcL, rps16-matK plus matK, and trnL-F). Maximum parsimony, maximum likelihood, and Bayesian inference are used to analyze 115 individuals, representing ca. 56 species of Tectaria s.l. and 36 species of ten related genera. The results strongly support the monophyly of Tectaria in a broad sense, in which Ctenitopsis, Hemigramma, Heterogonium, Psomiocarpa, Quercifilix, Stenosemia, and Tectaridium should be submerged. Such broadly circumscribed Tectaria is supported by the arising pattern of veinlets and the base chromosome number (x=40). Four primary clades are well resolved within Tectaria, one from the Neotropic (T. trifoliata clade) and three from the Old World (T. subtriphylla clade, Ctenitopsis clade, and T. crenata clade). Tectaria crenata clade is the largest one including six subclades. Of the genera previously recognized as tectarioid ferns, Ctenitis, Lastreopsis, and Pleocnemia, are confirmed to be members in Dryopteridaceae; while Pteridrys and Triplophyllum are supported in Tectariaceae. To infer morphological evolution, 13 commonly used characters are optimized on the resulting phylogenetic trees and in result, are all homoplastic in Tectaria.

  20. Leaf-inhabiting genera of the Gnomoniaceae, Diaporthales

    PubMed Central

    Sogonov, M.V.; Castlebury, L.A.; Rossman, A.Y.; Mejía, L.C.; White, J.F.

    2008-01-01

    The Gnomoniaceae are characterised by ascomata that are generally immersed, solitary, without a stroma, or aggregated with a rudimentary stroma, in herbaceous plant material especially in leaves, twigs or stems, but also in bark or wood. The ascomata are black, soft-textured, thin-walled, and pseudoparenchymatous with one or more central or eccentric necks. The asci usually have a distinct apical ring. The Gnomoniaceae includes species having ascospores that are small, mostly less than 25 μm long, although some are longer, and range in septation from non-septate to one-septate, rarely multi-septate. Molecular studies of the Gnomoniaceae suggest that the traditional classification of genera based on characteristics of the ascomata such as position of the neck and ascospores such as septation have resulted in genera that are not monophyletic. In this paper the concepts of the leaf-inhabiting genera in the Gnomoniaceae are reevaluated using multiple genes, specifically nrLSU, translation elongation factor 1-alpha (tef1-α), and RNA polymerase II second largest subunit (rpb2) for 64 isolates. ITS sequences were generated for 322 isolates. Six genera of leaf-inhabiting Gnomoniaceae are defined based on placement of their type species within the multigene phylogeny. The new monotypic genus Ambarignomonia is established for an unusual species, A. petiolorum. A key to 59 species of leaf-inhabiting Gnomoniaceae is presented and 22 species of Gnomoniaceae are described and illustrated. PMID:19287541

  1. Catalog of the Aphid Genera Described from the New World

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This manuscript presents a synthesis and catalogue of the genera of New World aphids (sensu stricto) from 1758 to 2004. It includes information on 215 generic and subgeneric names, type localities, bibliographic information, etymology, as well as synonymic and other nomenclatural data. Two nomencl...

  2. The Botryosphaeriaceae: genera and species known from culture

    PubMed Central

    Phillips, A.J.L.; Alves, A.; Abdollahzadeh, J.; Slippers, B.; Wingfield, M.J.; Groenewald, J.Z.; Crous, P.W.

    2013-01-01

    In this paper we give an account of the genera and species in the Botryosphaeriaceae. We consider morphological characters alone as inadequate to define genera or identify species, given the confusion it has repeatedly introduced in the past, their variation during development, and inevitable overlap as representation grows. Thus it seems likely that all of the older taxa linked to the Botryosphaeriaceae, and for which cultures or DNA sequence data are not available, cannot be linked to the species in this family that are known from culture. Such older taxa will have to be disregarded for future use unless they are epitypified. We therefore focus this paper on the 17 genera that can now be recognised phylogenetically, which concentrates on the species that are presently known from culture. Included is a historical overview of the family, the morphological features that define the genera and species and detailed descriptions of the 17 genera and 110 species. Keys to the genera and species are also provided. Phylogenetic relationships of the genera are given in a multi-locus tree based on combined SSU, ITS, LSU, EF1-α and β-tubulin sequences. The morphological descriptions are supplemented by phylogenetic trees (ITS alone or ITS + EF1-α) for the species in each genus. Taxonomic novelties: New species - Neofusicoccum batangarum Begoude, Jol. Roux & Slippers. New combinations - Botryosphaeria fabicerciana (S.F. Chen, D. Pavlic, M.J. Wingf. & X.D. Zhou) A.J.L. Phillips & A. Alves, Botryosphaeria ramosa (Pavlic, T.I. Burgess, M.J. Wingf.) A.J.L. Phillips & A. Alves, Cophinforma atrovirens (Mehl & Slippers) A. Alves & A.J.L. Phillips, Cophinforma mamane (D.E. Gardner) A.J.L. Phillips & A. Alves, Dothiorella pretoriensis (Jami, Gryzenh., Slippers & M.J. Wingf.) Abdollahz. & A.J.L. Phillips, Dothiorella thailandica (D.Q. Dai., J.K. Liu & K.D. Hyde) Abdollahz., A.J.L. Phillips & A. Alves, Dothiorella uruguayensis (C.A. Pérez, Blanchette, Slippers & M.J. Wingf.) Abdollahz

  3. Phylogenetics and systematics of Angiostrongylus lungworms and related taxa (Nematoda: Metastrongyloidea) inferred from the nuclear small subunit (SSU) ribosomal DNA sequences.

    PubMed

    Eamsobhana, P; Lim, P E; Yong, H S

    2015-05-01

    The Angiostrongylus lungworms are of public health and veterinary concern in many countries. At the family level, the Angiostrongylus lungworms have been included in the family Angiostrongylidae or the family Metastrongylidae. The present study was undertaken to determine the usefulness and suitability of the nuclear 18S (small subunit, SSU) rDNA sequences for differentiating various taxa of the genus Angiostrongylus, as well as to determine the systematics and phylogenetic relationship of Angiostrongylus species and other metastrongyloid taxa. This study revealed six 18S (SSU) haplotypes in A. cantonensis, indicating considerable genetic diversity. The uncorrected pairwise 'p' distances among A. cantonensis ranged from 0 to 0.86%. The 18S (SSU) rDNA sequences unequivocally distinguished the five Angiostrongylus species, confirmed the close relationship of A. cantonensis and A. malaysiensis and that of A. costaricensis and A. dujardini, and were consistent with the family status of Angiostrongylidae and Metastrongylidae. In all cases, the congeneric metastrongyloid species clustered together. There was no supporting evidence to include the genus Skrjabingylus as a member of Metastrongylidae. The genera Aelurostrongylus and Didelphostrongylus were not recovered with Angiostrongylus, indicating polyphyly of the Angiostrongylidae. Of the currently recognized families of Metastrongyloidea, only Crenosomatidae appeared to be monophyletic. In view of the unsettled questions regarding the phylogenetic relationships of various taxa of the metastrongyloid worms, further analyses using more markers and more taxa are warranted.

  4. Preliminary cladistic analysis of genera of the cestode order Trypanorhyncha Diesing, 1863.

    PubMed

    Beveridge, I; Campbell, R A; Palm, H W

    1999-01-01

    A preliminary cladistic analysis was carried out on the 49 currently recognised genera of the order Trypanorhyncha. Forty-four characters were analysed; a functional outgroup was used for scolex and strobilar characters, while Nybelinia was utilised to polarise characters related to the rhyncheal system. Eight well-resolved clades were evident in the resultant cladogram, which is compared with existing phenetic classifications. An analysis of families resulted in a similar clustering of taxa to that observed in the case of the genera. The results suggest that two key characters used in existing classifications, namely the presence of sensory fossettes on the bothridia and the development of atypical heteroacanth and poeciloacanth armatures from typical heteroacanth armatures, have occurred on several occasions. Some clades provide support for the arrangements used in current classifications. Suggestions are made for future avenues of research which might provide more robust phylogenetic data for the Trypanorhyncha.

  5. On Pulchritia new genus, with a reappraisal of the genera of Trichotriidae (Rotifera, Monogononta)

    PubMed Central

    Luo, Yongting; Segers, Hendrik

    2013-01-01

    Abstract During the study of rotifers collected in Eastern DR Congo, we rediscovered specimens that correspond to Monostyla dorsicornuta Van Oye, 1926. This species, which we redescribe, had not been seen since it’s summary description, and lacked type material. Our analysis reveals that the animal belongs to Trichotriidae rather than to Lecane (presently considered to include Monostyla) or Lecanidae, but is nevertheless characterised by a foot structure that is remarkably convergent to that of Lecanidae, and different from all other genera of Trichotriidae. We conclude that the species and the closely related South American Macrochaetus kostei (José de Paggi, Branco & Kozlowsky-Suzuki, 2000) belong to a new genus of Trichotriidae; the two offer a rare example of African-South American vicariance in rotifers.We further provide emended diagnoses of the remaining genera of Trichotriidae, to conform these to the new information and to address some inconsistencies in these. PMID:24194651

  6. Hepatozoon infection prevalence in four snake genera: influence of diet, prey parasitemia levels, or parasite type?

    PubMed

    Tomé, Beatriz; Maia, João P M C; Harris, D James

    2012-10-01

    Hepatozoon spp. (Apicomplexa: Haemogregarinidae) are the most commonly reported hemoparasites from snakes. Of over 300 Hepatozoon species identified, more than 120 were described from snakes. However, recent genetic assessments have found Hepatozoon lineages recovered from both prey and predators, indicating that diet may play an important role in the infection of final vertebrate hosts. Here 4 different snake genera with different diets were assessed. Hepatozoon spp. prevalence varied greatly between the genera, but only lineages already identified from potential prey, i.e., gecko and lacertid lizards, were recovered from the snakes. Interestingly, the Hepatozoon spp. lineage known from geckos was the most common in the snakes, but this does not reflect their diet. Higher parasitemia levels, reported for some geckos relative to lacertid lizards, may play a role. Alternatively, this lineage may be more effective at parasitizing snakes or may occur, despite being unrecorded, in other vertebrate groups consumed by snakes. PMID:22551400

  7. Three proposed new bacteriophage genera of staphylococcal phages: "3alikevirus", "77likevirus" and "Phietalikevirus".

    PubMed

    Gutiérrez, Diana; Adriaenssens, Evelien M; Martínez, Beatriz; Rodríguez, Ana; Lavigne, Rob; Kropinski, Andrew M; García, Pilar

    2014-02-01

    To date, most members of the Siphoviridae family of bacteriophages remain unclassified, including the 46 staphylococcal phages for which the complete genome sequences have been deposited in public databases. Comparative nucleotide and protein sequence analysis, in addition to available data on phage morphology, allowed us to propose three new phage genera within the family Siphoviridae: "3alikevirus", "77likevirus" and "Phietalikevirus", which include related phages infecting Staphylococcus aureus and Staphylococcus epidermidis. However, six phages infecting S. aureus, Staphylococcus pasteuri, Staphylococcus hominis and Staphylococcus capitis strains remain to be classified (orphan phages). Overall, the former phages share morphological features and genome organization. The three groups have conserved domains containing peptidoglycan hydrolytic activities clearly identified as part of tape measure proteins ("3alikevirus" and "77likevirus") or as individual virionassociated proteins ("Phietalikevirus"). In addition, bacteriophages belonging to the genus "3alikevirus" share closely related DNA-processing and packaging proteins, while bacteriophages included in the genus "Phietalikevirus" encode specific tail proteins for host interaction. These properties are considered distinctive for these genera. Orphan phages seem to have a more divergent organization, but they share some properties with members of these proposed genera.

  8. Review of the genera Anelaphinis Kolbe, 1892 and Atrichelaphinis Kraatz, 1898 (Coleoptera, Scarabaeidae, Cetoniinae)

    PubMed Central

    Rojkoff, Sébastien; Perissinotto, Renzo

    2015-01-01

    Abstract New material collected recently throughout the Afrotropical region has led to a major reassessment of taxa within the genera Anelaphinis Kolbe, 1892, Atrichelaphinis Kraatz, 1898 and other closely related genera. As a result, the name Megalleucosma Antoine, 1989 is here synonymised with Anelaphinis and a lectotype is designated for the type species, Cetonia dominula Harold, 1879. The genus Atrichelaphinis is redefined and a new subgenus, Atrichelaphinis (Eugeaphinis), is proposed for Elaphinis simillima Ancey, 1883, Elaphinis vermiculata Fairmaire, 1894, Niphetophora rhodesiana Péringuey, 1907, Atrichelaphinis deplanata Moser, 1907 (with Anelaphinis kwangensis Burgeon, 1931 as junior synonym) and Anelaphinis sternalis Moser, 1914. Additionally, three new species and one new subspecies are recognised and described in this new subgenus: Atrichelaphinis (Eugeaphinis) bomboesbergica sp. n. from South Africa; Atrichelaphinis (Eugeaphinis) bjornstadi sp. n. from Tanzania; Atrichelaphinis (Eugeaphinis) garnieri sp. n. from south–east Africa (Tanzania, Zimbabwe); and Atrichelaphinis (Eugeaphinis) deplanata minettii ssp. n. from central Africa (Malawi, Mozambique, Congo-Kinshasa, Congo-Brazzaville, South Africa, Rwanda, Zambia, Zimbabwe). The genus Atrichelaphinis is compared to its closest relatives and two separate keys are proposed, one for Atrichelaphinis and one for the sub-Saharan genera exhibiting completely or partially fused parameres. PMID:25709532

  9. Causal inference based on counterfactuals

    PubMed Central

    Höfler, M

    2005-01-01

    Background The counterfactual or potential outcome model has become increasingly standard for causal inference in epidemiological and medical studies. Discussion This paper provides an overview on the counterfactual and related approaches. A variety of conceptual as well as practical issues when estimating causal effects are reviewed. These include causal interactions, imperfect experiments, adjustment for confounding, time-varying exposures, competing risks and the probability of causation. It is argued that the counterfactual model of causal effects captures the main aspects of causality in health sciences and relates to many statistical procedures. Summary Counterfactuals are the basis of causal inference in medicine and epidemiology. Nevertheless, the estimation of counterfactual differences pose several difficulties, primarily in observational studies. These problems, however, reflect fundamental barriers only when learning from observations, and this does not invalidate the counterfactual concept. PMID:16159397

  10. Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms.

    PubMed

    Sabath, Niv; Goldberg, Emma E; Glick, Lior; Einhorn, Moshe; Ashman, Tia-Lynn; Ming, Ray; Otto, Sarah P; Vamosi, Jana C; Mayrose, Itay

    2016-02-01

    Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious and nondioecious species. We then applied a probabilistic approach that accounts for differential speciation, extinction, and transition rates between states to examine whether there is an association between dioecy and lineage diversification. We found a bimodal distribution, whereby dioecious lineages exhibited higher diversification in certain genera but lower diversification in others. Additional analyses did not uncover an ecological or life history trait that could explain a context-dependent effect of dioecy on diversification. Furthermore, in-depth simulations of neutral characters demonstrated that such bimodality is also found when simulating neutral characters across the observed trees. Our analyses suggest that - at least for these genera with the currently available data - dioecy neither consistently places a strong brake on diversification nor is a strong driver.

  11. Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms.

    PubMed

    Sabath, Niv; Goldberg, Emma E; Glick, Lior; Einhorn, Moshe; Ashman, Tia-Lynn; Ming, Ray; Otto, Sarah P; Vamosi, Jana C; Mayrose, Itay

    2016-02-01

    Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious and nondioecious species. We then applied a probabilistic approach that accounts for differential speciation, extinction, and transition rates between states to examine whether there is an association between dioecy and lineage diversification. We found a bimodal distribution, whereby dioecious lineages exhibited higher diversification in certain genera but lower diversification in others. Additional analyses did not uncover an ecological or life history trait that could explain a context-dependent effect of dioecy on diversification. Furthermore, in-depth simulations of neutral characters demonstrated that such bimodality is also found when simulating neutral characters across the observed trees. Our analyses suggest that - at least for these genera with the currently available data - dioecy neither consistently places a strong brake on diversification nor is a strong driver. PMID:26467174

  12. Somatic Embryogenesis in Two Orchid Genera (Cymbidium, Dendrobium).

    PubMed

    da Silva, Jaime A Teixeira; Winarto, Budi

    2016-01-01

    The protocorm-like body (PLB) is the de facto somatic embryo in orchids. Here we describe detailed protocols for two orchid genera (hybrid Cymbidium Twilight Moon 'Day Light' and Dendrobium 'Jayakarta', D. 'Gradita 31', and D. 'Zahra FR 62') for generating PLBs. These protocols will most likely have to be tweaked for different cultivars as the response of orchids in vitro tends to be dependent on genotype. In addition to primary somatic embryogenesis, secondary (or repetitive) somatic embryogenesis is also described for both genera. The use of thin cell layers as a sensitive tissue assay is outlined for hybrid Cymbidium while the protocol outlined is suitable for bioreactor culture of D. 'Zahra FR 62'.

  13. Unusual larval habitats and life history of chironomid (Diptera) genera

    USGS Publications Warehouse

    Hudson, Patrick L.

    1987-01-01

    Ninety-three genera, representing all subfamilies of Chironomidae, are organized into 9 categories of unusual habitats or life history including hygropetric, riparian (bank, floodplain, upland), hyporheic, symbiotic, and intertidal; others live in water held in plants or mine into unusual substrates. In riparian zones precise location of optimum habitat is difficult to determine as is definition of habitat within the continuum from shoreline to upland areas. The ecological importance of the riparian group appears to lie in its processing of coarse particulate matter along the floodplain of streams and rivers. All riparian genera are zoogeographically useful and can be used in reconstructing evolutionary dispersal pathways because they are adapted to unique habits that have remained largely undisturbed by human activities.

  14. Somatic Embryogenesis in Two Orchid Genera (Cymbidium, Dendrobium).

    PubMed

    da Silva, Jaime A Teixeira; Winarto, Budi

    2016-01-01

    The protocorm-like body (PLB) is the de facto somatic embryo in orchids. Here we describe detailed protocols for two orchid genera (hybrid Cymbidium Twilight Moon 'Day Light' and Dendrobium 'Jayakarta', D. 'Gradita 31', and D. 'Zahra FR 62') for generating PLBs. These protocols will most likely have to be tweaked for different cultivars as the response of orchids in vitro tends to be dependent on genotype. In addition to primary somatic embryogenesis, secondary (or repetitive) somatic embryogenesis is also described for both genera. The use of thin cell layers as a sensitive tissue assay is outlined for hybrid Cymbidium while the protocol outlined is suitable for bioreactor culture of D. 'Zahra FR 62'. PMID:26619873

  15. Temperate Pollen Genera in the Eocene (Claiborne) Flora, Alabama.

    PubMed

    Gray, J

    1960-09-23

    Pollen, spores, hystrichospherids, dinoflagellates, and the fresh-water alga Pediastrum occur in marine clays at the classic Claiborne Bluffs locality, Alabama. The presence of Ephedra pollen provides the first documented Tertiary record of this genus from the southeastern states. The occurrence of several characteristically temperate genera lends support to the idea that a deciduous hardwood forest was present in the Appalachian uplands during the Eocene.

  16. New species of the spider genera Aysenia and Aysenoides from Chile and Argentina: description and phylogenetic relationships (Araneae: Anyphaenidae, Amaurobioidinae).

    PubMed

    Laborda, Alvaro; Ramírez, Martín J; Pizarro-Araya, Jaime

    2013-01-01

    New spider species of the genera Aysenia Tullgren and Aysenoides Ramírez are described and their phylogenetic relationships discussed. The new species Aysenia paposo, from the coastal desert in northern Chile is sister to Aysenia araucana Ramírez. The diagnosis of Aysenia araucana is updated and new somatic variability is reported for the species. We present new records for other species of Aysenia and Aysenoides. The new species Aysenoides simoi, from temperate forests in Chile and adjacent Argentina is sister to Aysenoides nahuel. The phylogenetic analysis confirmed the monophyly of both genera. The support values of the genera are relatively high, but some internal branches show low support values. The genus Aysenia is supported by three synapomorphies, two of these from leg spination and one from the male genitalia. Aysenoides is supported by three synapomorphies from male and female genitalia. PMID:25277558

  17. Phylogenetic relationships in the coral family acroporidae, reassessed by inference from mitochondrial genes.

    PubMed

    Fukami, H; Omori, M; Hatta, M

    2000-07-01

    Phylogenetic relationships within the dominant reef coral family Acroporidae were inferred from the mitochondrial genes cytochrome b and ATPase 6. The rate of nucleotide substitution in the genes gave proper resolution to deduce genetic relationships between the genera in this family. The molecular phylogeny divided this family into three major lineages: the genera Astreopora, Montipora and Acropora. The genus Anacropora was included in the same clade as the genus Montipora, suggesting its recent speciation from Montipora. The subgenus Isopora was significantly distant from the subgenus Acropora. Taken together with morphological and reproductive differences, we propose that these two subgenera be classified as independent genera. The divergence times deduced from the genetic distances were consistent with the fossil record for the major genera. The results also suggest that the extant reef corals speciated and expanded very recently, probably after the Miocene, from single lineage which survived repeated extinction by climate changes during the Cenozoic era. PMID:18517306

  18. Magnetospheric convection strength inferred from inner edge of the electron plasma sheet and its relation to the polar cap potential drop

    NASA Astrophysics Data System (ADS)

    Jiang, F.; Kivelson, M. G.; Walker, R. J.; Khurana, K. K.; Angelopoulos, V.

    2010-12-01

    The sharp inner edge of the nightside electron plasma sheet observed by the THEMIS spacecraft is shown to provide a measure of the effective convection strength that transports plasma sheet plasma into the inner magnetosphere. The effective convection strength is characterized by the difference of potential between the magnetopause terminators at dawn and at dusk. We have surveyed inner boundary crossings of the electron plasma sheet measured by three THEMIS probes on orbits from Nov. 2007 to Apr. 2009. The values of the convection electric potential are inferred from the locations of the inner edge for different energy channels using a steady-state drift boundary model with a dipole magnetic field and a Volland-Stern electric field. When plotted against the solar wind electric field ( ), the convection electric potential is found to have a quasi-linear relationship with the driving solar wind electric field for the range of values tested (meaningful statistics only for Esw < 1.5 mV/m). Reasonably good agreement is found between the convection electric potential and the polar-cap potential drop calculated from model of Boyle et al. [1997] when the degree of shielding in the Volland-Stern potential is selected as gamma=1.5.

  19. Revision of the genus Ficiana Ghauri and its relationship to other genera in Empoascini (Hemiptera, Cicadellidae, Typhlocybinae)

    PubMed Central

    Xu, Ye; Suo, Hui-feng; Qin, Dao-zheng

    2015-01-01

    Abstract The empoascine genus Ficiana Ghauri is reviewed based on specimens from China. One new Ficiana species, Ficiana aurantia sp. n. is described from Guangxi in south China. An identification key to all species in this genus is provided. The morphological characters of Ficiana and related genera in this tribe are discussed. PMID:26798281

  20. Molecular phylogeny of porcelain crabs (Porcellanidae: Petrolisthes and allies) from the south eastern Pacific: the genera Allopetrolisthes and Liopetrolisthes are not natural entities.

    PubMed

    Baeza, J Antonio

    2016-01-01

    Porcelain crabs from the closely related genera Petrolisthes, Liopetrolisthes, and Allopetrolisthes are known for their diversity of lifestyles, habitats, and coloration. The evolutionary relationships among the species belonging to these three genera is not fully resolved. A molecular phylogeny of the group may help to resolve the long-standing taxonomic question about the validity of the genera Allopetrolisthes and Liopetrolisthes. Using both 'total evidence' and single-marker analyses based on a 362-bp alignment of the 16S rRNA mitochondrial DNA and a 328-bp alignment of the Histone 3 nuclear DNA, the phylogenetic relationships among 11 species from Petrolisthes (6 species), Liopetrolisthes (2 species), and Allopetrolisthes (3 species), all native to the south eastern Pacific, were examined. The analyses supported three pairs of sister species: L. mitra + L. patagonicus, P. tuberculatus + P. tuberculosus, and A. angulosus + A. punctatus. No complete segregation of species, according to genera, was evident from tree topologies. Bayesian-factor analyses revealed strong support for the unconstrained tree instead of an alternative tree in which monophyly of the three genera was forced. Thus, the present molecular phylogeny does not support the separation of the species within this complex into the genera Petrolisthes, Liopetrolisthes, and Allopetrolisthes. Taking into account the above and other recent molecular phylogenetic analyses focused on other representatives from the family Porcellanidae, it is tentatively proposed to eliminate the genera Liopetrolisthes and Allopetrolisthes, and to transfer their members to the genus Petrolisthes. PMID:26989636

  1. Molecular phylogeny of porcelain crabs (Porcellanidae: Petrolisthes and allies) from the south eastern Pacific: the genera Allopetrolisthes and Liopetrolisthes are not natural entities

    PubMed Central

    2016-01-01

    Porcelain crabs from the closely related genera Petrolisthes, Liopetrolisthes, and Allopetrolisthes are known for their diversity of lifestyles, habitats, and coloration. The evolutionary relationships among the species belonging to these three genera is not fully resolved. A molecular phylogeny of the group may help to resolve the long-standing taxonomic question about the validity of the genera Allopetrolisthes and Liopetrolisthes. Using both ‘total evidence’ and single-marker analyses based on a 362-bp alignment of the 16S rRNA mitochondrial DNA and a 328-bp alignment of the Histone 3 nuclear DNA, the phylogenetic relationships among 11 species from Petrolisthes (6 species), Liopetrolisthes (2 species), and Allopetrolisthes (3 species), all native to the south eastern Pacific, were examined. The analyses supported three pairs of sister species: L. mitra + L. patagonicus, P. tuberculatus + P. tuberculosus, and A. angulosus + A. punctatus. No complete segregation of species, according to genera, was evident from tree topologies. Bayesian-factor analyses revealed strong support for the unconstrained tree instead of an alternative tree in which monophyly of the three genera was forced. Thus, the present molecular phylogeny does not support the separation of the species within this complex into the genera Petrolisthes, Liopetrolisthes, and Allopetrolisthes. Taking into account the above and other recent molecular phylogenetic analyses focused on other representatives from the family Porcellanidae, it is tentatively proposed to eliminate the genera Liopetrolisthes and Allopetrolisthes, and to transfer their members to the genus Petrolisthes. PMID:26989636

  2. The Bayes Inference Engine

    SciTech Connect

    Hanson, K.M.; Cunningham, G.S.

    1996-04-01

    The authors are developing a computer application, called the Bayes Inference Engine, to provide the means to make inferences about models of physical reality within a Bayesian framework. The construction of complex nonlinear models is achieved by a fully object-oriented design. The models are represented by a data-flow diagram that may be manipulated by the analyst through a graphical programming environment. Maximum a posteriori solutions are achieved using a general, gradient-based optimization algorithm. The application incorporates a new technique of estimating and visualizing the uncertainties in specific aspects of the model.

  3. Twelve previously unknown phage genera are ubiquitous in global oceans

    SciTech Connect

    Holmfeldt, Karin; Solonenko, Natalie; Shah, Manesh B; Corrier, Kristen L; Riemann, Lasse; Verberkmoes, Nathan C; Sullivan, Matthew B

    2013-01-01

    Viruses are fundamental to ecosystems ranging from oceans to humans, yet our ability to study them is bottlenecked by the lack of ecologically relevant isolates, resulting in unknowns dominating culture-independent surveys. Here we present genomes from 31 phages infecting multiple strains of the aquatic bacterium Cellulophaga baltica (Bacteroidetes) to provide data for an underrepresented and environmentally abundant bacterial lineage. Comparative genomics delineated 12 phage groups that (i) each represent a new genus, and (ii) represent one novel and four wellknown viral families. This diversity contrasts the few well-studied marine phage systems, but parallels the diversity of phages infecting human-associated bacteria. Although all 12 Cellulophaga phages represent new genera, the podoviruses and icosahedral, nontailed ssDNA phages were exceptional, with genomes up to twice as large as those previously observed for each phage type. Structural novelty was also substantial, requiring experimental phage proteomics to identify 83% of the structural proteins. The presence of uncommon nucleotide metabolism genes in four genera likely underscores the importance of scavenging nutrient-rich molecules as previously seen for phages in marine environments. Metagenomic recruitment analyses suggest that these particular Cellulophaga phages are rare and may represent a first glimpse into the phage side of the rare biosphere. However, these analyses also revealed that these phage genera are widespread, occurring in 94% of 137 investigated metagenomes. Together, this diverse and novel collection of phages identifies a small but ubiquitous fraction of unknown marine viral diversity and provides numerous environmentally relevant phage host systems for experimental hypothesis testing.

  4. Twelve previously unknown phage genera are ubiquitous in global oceans

    PubMed Central

    Holmfeldt, Karin; Solonenko, Natalie; Shah, Manesh; Corrier, Kristen; Riemann, Lasse; VerBerkmoes, Nathan C.; Sullivan, Matthew B.

    2013-01-01

    Viruses are fundamental to ecosystems ranging from oceans to humans, yet our ability to study them is bottlenecked by the lack of ecologically relevant isolates, resulting in “unknowns” dominating culture-independent surveys. Here we present genomes from 31 phages infecting multiple strains of the aquatic bacterium Cellulophaga baltica (Bacteroidetes) to provide data for an underrepresented and environmentally abundant bacterial lineage. Comparative genomics delineated 12 phage groups that (i) each represent a new genus, and (ii) represent one novel and four well-known viral families. This diversity contrasts the few well-studied marine phage systems, but parallels the diversity of phages infecting human-associated bacteria. Although all 12 Cellulophaga phages represent new genera, the podoviruses and icosahedral, nontailed ssDNA phages were exceptional, with genomes up to twice as large as those previously observed for each phage type. Structural novelty was also substantial, requiring experimental phage proteomics to identify 83% of the structural proteins. The presence of uncommon nucleotide metabolism genes in four genera likely underscores the importance of scavenging nutrient-rich molecules as previously seen for phages in marine environments. Metagenomic recruitment analyses suggest that these particular Cellulophaga phages are rare and may represent a first glimpse into the phage side of the rare biosphere. However, these analyses also revealed that these phage genera are widespread, occurring in 94% of 137 investigated metagenomes. Together, this diverse and novel collection of phages identifies a small but ubiquitous fraction of unknown marine viral diversity and provides numerous environmentally relevant phage–host systems for experimental hypothesis testing. PMID:23858439

  5. Twelve previously unknown phage genera are ubiquitous in global oceans.

    PubMed

    Holmfeldt, Karin; Solonenko, Natalie; Shah, Manesh; Corrier, Kristen; Riemann, Lasse; Verberkmoes, Nathan C; Sullivan, Matthew B

    2013-07-30

    Viruses are fundamental to ecosystems ranging from oceans to humans, yet our ability to study them is bottlenecked by the lack of ecologically relevant isolates, resulting in "unknowns" dominating culture-independent surveys. Here we present genomes from 31 phages infecting multiple strains of the aquatic bacterium Cellulophaga baltica (Bacteroidetes) to provide data for an underrepresented and environmentally abundant bacterial lineage. Comparative genomics delineated 12 phage groups that (i) each represent a new genus, and (ii) represent one novel and four well-known viral families. This diversity contrasts the few well-studied marine phage systems, but parallels the diversity of phages infecting human-associated bacteria. Although all 12 Cellulophaga phages represent new genera, the podoviruses and icosahedral, nontailed ssDNA phages were exceptional, with genomes up to twice as large as those previously observed for each phage type. Structural novelty was also substantial, requiring experimental phage proteomics to identify 83% of the structural proteins. The presence of uncommon nucleotide metabolism genes in four genera likely underscores the importance of scavenging nutrient-rich molecules as previously seen for phages in marine environments. Metagenomic recruitment analyses suggest that these particular Cellulophaga phages are rare and may represent a first glimpse into the phage side of the rare biosphere. However, these analyses also revealed that these phage genera are widespread, occurring in 94% of 137 investigated metagenomes. Together, this diverse and novel collection of phages identifies a small but ubiquitous fraction of unknown marine viral diversity and provides numerous environmentally relevant phage-host systems for experimental hypothesis testing. PMID:23858439

  6. Dynamical Logic Driven by Classified Inferences Including Abduction

    NASA Astrophysics Data System (ADS)

    Sawa, Koji; Gunji, Yukio-Pegio

    2010-11-01

    We propose a dynamical model of formal logic which realizes a representation of logical inferences, deduction and induction. In addition, it also represents abduction which is classified by Peirce as the third inference following deduction and induction. The three types of inference are represented as transformations of a directed graph. The state of a relation between objects of the model fluctuates between the collective and the distinctive. In addition, the location of the relation in the sequence of the relation influences its state.

  7. Phylogenetic relationships of yellowjackets inferred from nine loci (Hymenoptera: Vespidae, Vespinae, Vespula and Dolichovespula).

    PubMed

    Lopez-Osorio, Federico; Pickett, Kurt M; Carpenter, James M; Ballif, Bryan A; Agnarsson, Ingi

    2014-04-01

    Eusociality has arisen repeatedly and independently in the history of insects, often leading to evolutionary success and ecological dominance. Eusocial wasps of the genera Vespula and Dolichovespula, or yellowjackets, have developed advanced social traits in a relatively small number of species. The origin of traits such as effective paternity and colony size has been interpreted with reference to an established phylogenetic hypothesis that is based on phenotypic data, while the application of molecular evidence to phylogenetic analysis within yellowjackets has been limited. Here, we investigate the evolutionary history of yellowjackets on the basis of mitochondrial and nuclear markers (nuclear: 28S, EF1α, Pol II, and wg; mitochondrial: 12S, 16S, COI, COII, and Cytb). We use these data to test the monophyly of yellowjackets and species groups, and resolve species-level relationships within each genus using parsimony and Bayesian inference. Our results indicate that a yellowjacket clade is either weakly supported (parsimony) or rejected (Bayesian inference). However, the monophyly of each yellowjacket genus as well as species groups are strongly supported and concordant between methods. Our results agree with previous studies regarding the monophyly of the Vespula vulgaris group and the sister relationship between the V. rufa and V. squamosa groups. This suggests convergence of large colony size and high effective paternity in the vulgaris group and V. squamosa, or a single origin of both traits in the most recent common ancestor of all Vespula species and their evolutionary reversal in the rufa group. PMID:24462637

  8. Population analysis of the genera buildup on some commercially important vegetable crops grown in Kashmir Valley.

    PubMed

    Sheikh, Javaid Hassan; Chishti, M Z; Rasheed, Majidah; Tak, Irfan-Ur-Rauf; Dar, Shoaib Ali; Lal, Eugenia P; Mohiuddin, Dawood

    2016-09-01

    In order to list the genera buildup on Brassica oleracea (Cauliflower), Capsicum frustscens (Chillies), Spinacia oleracea (Spinach) and Phaseolus vulgaris (Farash bean) a general survey was carried in the summer season of 2013. On examining the soil samples as well as root samples of Cauliflower Boleodorus, Psilenchus, Helicotylenchus, Merlinius, Aglenchus and Filenchus were encountered with their absolute density of 18, 31, 34.5, 35, 35 and 31.5 %. On Chillies, Tylenchus, Helicotylenchus, Psilenchus, Pratylenchus and Hirschmaniella with their absolute frequency of 86, 96.6, 100, 100 and 96.6 % respectively were collected. Among these five genera recorded on Chillies the Relative prominence value of 16 % is lowest for Psilenchus and 26.7 % for Helicotylenchus. Merlinius, Psilenchus, Aglenchus, and Boleodorus were encountered on examining the soil and root samples of Spinach during the period of study. Boleodorus was met with the highest percentage of frequency of 90 % as well as highest proportion of absolute density of 37 % and lowest value of 24 % in case of Merlinius and Psilenchus. Soil samples as well as root samples of Farash bean, Aglenchus, Tylenchus, Hirschmaniella, Helicotylenchus and Psilenchus were encountered with their absolute density of 27, 19.5, 33, 33 and 35.4 %. The absolute frequency of 100 % was found in Tylenchus with the lowest frequency of 70 % in Helicotylenchus. Among the genera recorded on Farash bean relative prominence value happened to be highest in Hirschmaniella with the value as 23.6 % and lowest on Tylenchus with the value of 14.2 %.

  9. Population analysis of the genera buildup on some commercially important vegetable crops grown in Kashmir Valley.

    PubMed

    Sheikh, Javaid Hassan; Chishti, M Z; Rasheed, Majidah; Tak, Irfan-Ur-Rauf; Dar, Shoaib Ali; Lal, Eugenia P; Mohiuddin, Dawood

    2016-09-01

    In order to list the genera buildup on Brassica oleracea (Cauliflower), Capsicum frustscens (Chillies), Spinacia oleracea (Spinach) and Phaseolus vulgaris (Farash bean) a general survey was carried in the summer season of 2013. On examining the soil samples as well as root samples of Cauliflower Boleodorus, Psilenchus, Helicotylenchus, Merlinius, Aglenchus and Filenchus were encountered with their absolute density of 18, 31, 34.5, 35, 35 and 31.5 %. On Chillies, Tylenchus, Helicotylenchus, Psilenchus, Pratylenchus and Hirschmaniella with their absolute frequency of 86, 96.6, 100, 100 and 96.6 % respectively were collected. Among these five genera recorded on Chillies the Relative prominence value of 16 % is lowest for Psilenchus and 26.7 % for Helicotylenchus. Merlinius, Psilenchus, Aglenchus, and Boleodorus were encountered on examining the soil and root samples of Spinach during the period of study. Boleodorus was met with the highest percentage of frequency of 90 % as well as highest proportion of absolute density of 37 % and lowest value of 24 % in case of Merlinius and Psilenchus. Soil samples as well as root samples of Farash bean, Aglenchus, Tylenchus, Hirschmaniella, Helicotylenchus and Psilenchus were encountered with their absolute density of 27, 19.5, 33, 33 and 35.4 %. The absolute frequency of 100 % was found in Tylenchus with the lowest frequency of 70 % in Helicotylenchus. Among the genera recorded on Farash bean relative prominence value happened to be highest in Hirschmaniella with the value as 23.6 % and lowest on Tylenchus with the value of 14.2 %. PMID:27605801

  10. Two new Nirvanini genera from China (Hemiptera: Cicadellidae).

    PubMed

    Gao, Min; Dai, Wu; Zhang, Yalin

    2014-01-01

    Two new Nirvanini genera, Decursusnirvana gen. nov. (type species: Decursusnirvana fasciiformis sp. nov.) and Sinonirvana gen. nov. (type species: Sinonirvana hirsuta sp. nov.), including two new species, D. fasciiformis sp. nov. and S. hirsuta, sp. nov. from China are described. One new combination, Decursusnirvana excelsa (Melichar) n. comb., is also proposed. Decursusnirvana most closely resembles Oniella Matsumura, but it may be distinguished from the latter by the aedeagus lacking an atrium and with the shaft with its basal half straight and apical half strongly curved ventrally, with a pair of processes. Sinonirvana gen. nov is similar to Decursusnirvana gen. nov., differs from the latter as follows: head more elongate with anteclypeus much broader and not extended beyond margin of gena. Also, the pygofer lobe is solid (not divided in two places like the latter) and the subgenital plate has numerous long, fine setae. Detailed morphological descriptions and illustrations of all three species are given and a key to all male species in two genera is also provided. 

  11. Inference is bliss: using evolutionary relationship to guide categorical inferences.

    PubMed

    Novick, Laura R; Catley, Kefyn M; Funk, Daniel J

    2011-01-01

    Three experiments, adopting an evolutionary biology perspective, investigated subjects' inferences about living things. Subjects were told that different enzymes help regulate cell function in two taxa and asked which enzyme a third taxon most likely uses. Experiment 1 and its follow-up, with college students, used triads involving amphibians, reptiles, and mammals (reptiles and mammals are most closely related evolutionarily) and plants, fungi, and animals (fungi are more closely related to animals than to plants). Experiment 2, with 10th graders, also included triads involving mammals, birds, and snakes/crocodilians (birds and snakes/crocodilians are most closely related). Some subjects received cladograms (hierarchical diagrams) depicting the evolutionary relationships among the taxa. The effect of providing cladograms depended on students' background in biology. The results illuminate students' misconceptions concerning common taxa and constraints on their willingness to override faulty knowledge when given appropriate evolutionary evidence. Implications for introducing tree thinking into biology curricula are discussed. PMID:21463358

  12. Inferred Propositions and the Expression of the Evidence Relation in Natural Language Evidentiality in Central Alaskan Yup'ik Eskimo and English

    ERIC Educational Resources Information Center

    Krawczyk, Elizabeth A.

    2012-01-01

    Evidentiality has usually been defined as the grammaticalized expression of a speaker's evidence source for a proposition, where "evidence" is conceptualized as a speaker's source-type for a particular proposition (Aikhenvald 2004). How this evidence source-type and the evidential are related has yet to be formally modeled in…

  13. Five vicarious genera from Gondwana: the Velloziaceae as shown by molecules and morphology

    PubMed Central

    Mello-Silva, Renato; Santos, Déborah Yara A. C.; Salatino, Maria Luiza F.; Motta, Lucimar B.; Cattai, Marina B.; Sasaki, Denise; Lovo, Juliana; Pita, Patrícia B.; Rocini, Cintia; Rodrigues, Cristiane D. N.; Zarrei, Mehdi; Chase, Mark W.

    2011-01-01

    Background and Aims The amount of data collected previously for Velloziaceae neither clarified relationships within the family nor helped determine an appropriate classification, which has led to huge discordance among treatment by different authors. To achieve an acceptable phylogenetic result and understand the evolution and roles of characters in supporting groups, a total evidence analysis was developed which included approx. 20 % of the species and all recognized genera and sections of Velloziaceae, plus outgroups representatives of related families within Pandanales. Methods Analyses were undertaken with 48 species of Velloziaceae, representing all ten genera, with DNA sequences from the atpB-rbcL spacer, trnL-trnF spacer, trnL intron, trnH-psbA spacer, ITS ribosomal DNA spacers and morphology. Key Results Four groups consistently emerge from the analyses. Persistent leaves, two phloem strands, stem cortex divided in three regions and violet tepals support Acanthochlamys as sister to Velloziaceae s.s., which are supported mainly by leaves with marginal bundles, transfusion tracheids and inflorescence without axis. Within Velloziaceae s.s., an African Xerophyta + Talbotia clade is uniquely supported by basal loculicidal capsules; an American clade, Barbacenia s.l. + Barbaceniopsis + Nanuza + Vellozia, is supported by only homoplastic characters. Barbacenia s.l. (= Aylthonia + Barbacenia + Burlemarxia + Pleurostima) is supported by a double sheath in leaf vascular bundles and a corona; Barbaceniopsis + Nanuza + Vellozia is not supported by an unambiguous character, but Barbaceniopsis is supported by five characters, including diclinous flowers, Nanuza + Vellozia is supported mainly by horizontal stigma lobes and stem inner cortex cells with secondary walls, and Vellozia alone is supported mainly by pollen in tetrads. Conclusions The results imply recognition of five genera (Acanthochlamys (Xerophyta (Barbacenia (Barbaceniopsis, Vellozia)))), solving the long

  14. Molecular systematics of two enigmatic genera Psittacella and Pezoporus illuminate the ecological radiation of Australo-Papuan parrots (Aves: Psittaciformes).

    PubMed

    Joseph, Leo; Toon, Alicia; Schirtzinger, Erin E; Wright, Timothy F

    2011-06-01

    The platycercine parrots of Australia, usually recognized as the Platycercinae or Platycercini, are the broad-tailed parrots and their allies typified by the rosellas Platycercus spp. Debate concerning their circumscription has most recently centerd on the position of four genera, Neophema, Neopsephotus, Pezoporus and Psittacella, the last two having never been adequately included in sequence-based analyses. We use broad taxon sampling, mitochondrial and nuclear DNA sequence data from seven independent loci (two linked mitochondrial loci and six nuclear loci), and both gene tree and species tree approaches to reconstruct phylogenies and so determine the systematic placement all four genera. Analyses of two data sets, one of 48 taxa and five loci and one of 27 taxa and the same five plus three additional loci produced broadly congruent and consistently well-resolved phylogenies. We reject placement of any of these four genera within core platycercines. Pezoporus is closely allied to Neophema and Neopsephotus. These three genera are the likely sister group to core platycercines and we advocate their recognition as a subfamily. Psittacella is the sole extant representative of a lineage that branched very early in the history of Australo-Papuan parrot fauna and is not closely related to any of the mostly south-east Asian and Indonesian psittaculine taxa with which it is more often linked. We present a revised view of the extraordinary phylogenetic, phenotypic and ecological diversity that is the adaptive radiation of Australo-Papuan parrots. Finally, our analyses highlight the likely paraphyly of Mayr's (2008) Loricoloriinae.

  15. Decision generation tools and Bayesian inference

    NASA Astrophysics Data System (ADS)

    Jannson, Tomasz; Wang, Wenjian; Forrester, Thomas; Kostrzewski, Andrew; Veeris, Christian; Nielsen, Thomas

    2014-05-01

    Digital Decision Generation (DDG) tools are important software sub-systems of Command and Control (C2) systems and technologies. In this paper, we present a special type of DDGs based on Bayesian Inference, related to adverse (hostile) networks, including such important applications as terrorism-related networks and organized crime ones.

  16. On the criticality of inferred models

    NASA Astrophysics Data System (ADS)

    Mastromatteo, Iacopo; Marsili, Matteo

    2011-10-01

    Advanced inference techniques allow one to reconstruct a pattern of interaction from high dimensional data sets, from probing simultaneously thousands of units of extended systems—such as cells, neural tissues and financial markets. We focus here on the statistical properties of inferred models and argue that inference procedures are likely to yield models which are close to singular values of parameters, akin to critical points in physics where phase transitions occur. These are points where the response of physical systems to external perturbations, as measured by the susceptibility, is very large and diverges in the limit of infinite size. We show that the reparameterization invariant metrics in the space of probability distributions of these models (the Fisher information) are directly related to the susceptibility of the inferred model. As a result, distinguishable models tend to accumulate close to critical points, where the susceptibility diverges in infinite systems. This region is the one where the estimate of inferred parameters is most stable. In order to illustrate these points, we discuss inference of interacting point processes with application to financial data and show that sensible choices of observation time scales naturally yield models which are close to criticality.

  17. Recent Speciation in Three Closely Related Sympatric Specialists: Inferences Using Multi-Locus Sequence, Post-Mating Isolation and Endosymbiont Data

    PubMed Central

    Xue, Huai-Jun; Li, Wen-Zhu; Nie, Rui-E; Yang, Xing-Ke

    2011-01-01

    Shifting between unrelated host plants is relatively rare for phytophagous insects, and distinct host specificity may play crucial roles in reproductive isolation. However, the isolation status and the relationship between parental divergence and post-mating isolation among closely related sympatric specialists are still poorly understood. Here, multi-locus sequence were used to estimate the relationship among three host plant–specific closely related flea beetles, Altica cirsicola, A. fragariae and A. viridicyanea (abbreviated as AC, AF and AV respectively). The tree topologies were inconsistent using different gene or different combinations of gene fragments. The relationship of AF+(AC+AV) was supported, however, by both gene tree and species tree based on concatenated data. Post-mating reproductive data on the results of crossing these three species are best interpreted in the light of a well established phylogeny. Nuclear-induced but not Wolbachia-induced unidirectional cytoplasmic incompatibility, which was detected in AC-AF and AF-AV but not in AC-AV, may also suggest more close genetic affinity between AC and AV. Prevalence of Wolbachia in these three beetles, and the endosymbiont in most individuals of AV and AC sharing a same wsp haplotype may give another evidence of AF+(AC+AV). Our study also suggested that these three flea beetles diverged in a relative short time (0.94 My), which may be the result of shifting between unrelated host plants and distinct host specificity. Incomplete post-mating isolation while almost complete lineage sorting indicated that effective pre-mating isolation among these three species should have evolved. PMID:22110767

  18. OH(v=1 to 9) Relative Population Levels Inferred from VIRTIS/Rosetta Airglow Observations in the Earth's Atmosphere (Invited)

    NASA Astrophysics Data System (ADS)

    Migliorini, A.; Gerard, J. C.; Soret, L.; Piccioni, G.; Capaccioni, F.; Filacchione, G.; Snels, M.

    2015-08-01

    On its way to the comet 67P/Churyumov-Gerasimenko, the Rosetta spacecraft performed three flybys with the Earth, in March 2005, November 2007 and November 2009. The last one was quite suitable to observe the nightside of our planet. The Visible and Infrared Thermal Imaging Spectrometer (VIRTIS) on board Rosetta was especially adapted to study the hydroxyl nightglow emissions in the infrared spectral range. The OH v=1,2 sequences were measured simultaneously. We thus investigate the relative population levels of the v=1 to 9 vibrational levels at the same time. Results, obtained using our simple 1-dimension model, are presented for the relative population levels; in particular, the value of level v=1 is derived for the first time, relative to levels up to 9. The vibrational population decreases with increasing vibrational quantum number. Our results are in satisfactorily agreement with previous observations and models developed for mid-latitudes conditions. They favor the models where sudden death deactivation by atomic oxygen is the major process controlling the vibrational population. The observed behavior results to be distinctly different than the OH airglow observations made in the Venus atmosphere with the VIRTIS instrument on board Venus Express, where quenching by CO2 seems to occur with collisional cascades. The authors thank ESA, ASI and all the national space agencies, which support the Rosetta mission (Grants: ASI-INAF I/062/08/0 and ASI-INAF I/050/10/0).

  19. New angiosperm genera from cretaceous sections of northern Asia

    NASA Astrophysics Data System (ADS)

    Alekseev, P. I.; Herman, A. B.; Shchepetov, S. V.

    2014-11-01

    The Cretaceous floras of northern Asia represented by the Antibes flora of the Chulym-Yenisei area of West Siberia, Kaivayam flora of northwestern Kamchatka, and Grebenka flora of the Anadyr River basin in Chukotka are reviewed. These floras characterize the Late Cretaceous Siberian-Canadian Paleofloristic Region, where they developed in humid warm temperate climatic environments. Two new angiosperm genera are described: genus Chachlovia P. Alekseev et Herman with species C. kiyensis P. Alekseev, sp. nov. and C. dombeyopsoida (Herman) Herman, comb. nov. and genus Soninia Herman et Shczepetov with species S. asiatica P. Alekseev, sp. nov. and S. integerrima Herman et Shczepetov, sp. nov. The species Chachlovia kiyensis and Soninia asiatica were characteristic components of the Antibes flora. Chachlovia dombeyopsoida and Soninia integerrima were constituents of the Kaivayam and Grebenka floras, respectively.

  20. [Two new genera of land snails (Stylommatophora: Arionacea) from Chile].

    PubMed

    Vargas-Almonacid, Patricio; Stuardo, José R

    2007-06-01

    We describe two new genera of land molluscs found under wet leaf litter in isolated fragments of a secondary native forest at the Hualpén Botanical Park (36 degrees 45'-36 degrees 49' S, 73 degrees 9'-73 degrees 13' W), University of Concepción, Chile. The new taxa are Pichikadi gen.n., of Punctidae, and Chellius gen.n., of Charopidae, with the following new species: Pichikadi hualpensis sp.n., and Chellius piramidalis sp.n. English diagnosis are presented for all taxa, together with an English identification key and English versions of figure captions and table headings. To facilitate subsequent studies and interpretations, we follow recent authors in using mainly shell characters, an approach that has favored the present taxonomic stability of the world's land micromollusca. The diagnosis and observations are complemented with a key for the species of these families inhabiting continental Chile.

  1. New unidentate jumping spider genera (Araneae: Salticidae) from Australia.

    PubMed

    Richardson, Barry J

    2013-01-01

    The Australian fauna includes large numbers of undescribed, tiny, litter-living, jumping spiders. In this paper four monotypic new genera (Ananeon howardensis n. g. n. sp., Barraina anfracta n. g. n.sp., Frewena maculata n.g. n.s., and Pungalina weiri n.g, n.sp.) are described. Two species (Neon taylori n.sp. and Neon australis n. sp.) representing the two distinctive morphological patterns found in Australian species of this genus are also described. The former, similar in the morphology of the palp and genitalia to that found in many species from eastern Australia, is most similar in morphology to N. sumatranus Logunov 1998 from Indonesia and N. kovblyuki Logunov 2004 from the Crimea. The latter, and other similar species from South Australia and Western Australia, has palp morphology and fringing on L1 very similar to that seen in N. nojimai Ikeda 1995 from Japan. PMID:26106785

  2. Phylogenetic relationships of the genera of Ptiloneuridae (Psocodea, 'Psocoptera', Epipsocetae) and a test on the monophyly of Brasineura Silva-Neto & García Aldrete and Loneuroides García Aldrete.

    PubMed

    Silva-Neto, Alberto Moreira Da; Aldrete, Alfonso N García; Rafael, José Albertino

    2016-01-01

    The phylogenetic relationships of the genera of Ptiloneuridae were inferred on the basis of morphological characters of adult specimens. Two distinct clades are recognized: one, including Belicania, Euplocania, Omilneura, Perucania, Timnewia and Triplocania, and the other, including Brasineura, Loneura, Loneuroides, Ptiloneura, Ptiloneuropsis and Willreevesia. Brasineura and Loneuroides are recognized as monophyletic. A correction of nomenclature for the parts of the phallosome in Brasineura was made; we also modified the identification key to the genera of Ptiloneuridae, in the couplets that separate Loneura from Brasineura. PMID:27515646

  3. Possible migration front of gas-related fluid inferred from interpretation on 3D-seismic data in the eastern Nankai Trough

    NASA Astrophysics Data System (ADS)

    Otsuka, H.; Morita, S.; Tanahashi, M.; Ashi, J.; Nagakubo, S.; Fujii, T.

    2008-12-01

    High resolution 3D seismic survey, "Tokai-oki to Kumano-nada", was conducted for methane hydrate exploration in the eastern Nankai Trough by METI in 2002. Our study focuses on zigzag-shaped specific reflectors on BSR margins, which have been recognized by JOGMEC on the 3D data. We call the reflectors "gFoldback Reflectors (FBRs)"h in this study. From the edge of BSR, the 1st FBR generally extends down to lower formation below the BSR crossing sedimentary horizons. The following FBRs (often the 2nd, sometimes 3rd and above) extend down from the edge of the last FBR forming bellows-like shape. The 1st FBR indicates normal polarity (antiphase of BSR), and the following FBRs change their polarities alternately. FBRs are mostly developed in the well-stratified formation but not in the area of frequent fractures and the area of major lateral lithological change. FBR generally corresponds to lateral seismic facies boundary between BSR distribution area and outside the BSR area. The formation beneath the BSR shows dimmed facies characterized by relatively low amplitude and lack of high frequency components in contrast to outside the BSR area of normal facies. Seismic velocity analysis (JOGMEC, personal communication) suggests that FBRs correspond to velocity boundaries, where the dimmed faceis below the BSR coinsides with relatively low velocity. The polarities of FBRs are also consistent with such velocity changes. Such dimmed facies with low velocity and low amplitude anomaly suggests relation to gas components in the formation water. The lowest FBR does not cross major unconformities, which often exhibit negative polarity suggesting fluid migration from the lower unit. In this case, the lowest FBR which shows negative polarity and reaches the unconformity is to be merged to the negative reflection of the unconformity. In addition, high amplitude layers are sometimes recognized at foldbacks convex to the outside the BSR area. These high amplitude layers probably having

  4. Developing tools for risk assessment in protected species: Relative potencies inferred from competitive binding of halogenated aromatic hydrocarbons to aryl hydrocarbon receptors from beluga (Delphinapterus leucas) and mouse.

    PubMed

    Jensen, Brenda A; Reddy, Christopher M; Nelson, Robert K; Hahn, Mark E

    2010-11-01

    Persistent organic pollutants such as halogenated aromatic hydrocarbons (HAHs) biomagnify in food webs and accumulate to high concentrations in top predators like odontocete cetaceans (toothed whales). The most toxic HAHs are the 2,3,7,8-substituted halogenated dibenzo-p-dioxins and furans, and non-ortho-substituted polychlorinated biphenyls (PCBs), which exert their effects via the aryl hydrocarbon receptor (AHR). Understanding the impact of HAHs in wildlife is limited by the lack of taxon-specific information about the relative potencies of toxicologically important congeners. To assess whether Toxic Equivalency Factors (TEFs) determined in rodents are predictive of HAH relative potencies in a cetacean, we used beluga and mouse AHRs expressed in vitro from cloned cDNAs to measure the relative AHR-binding affinities of ten HAHs from five different structural classes. The rank order of mean IC(50)s for competitive binding to beluga AHR was: TCDDrelative to those of an AHR from a dioxin-responsive mouse suggests that beluga, and perhaps cetaceans in general, may be particularly sensitive to the toxic effects of AHR agonists. Further study is warranted in order to more fully address this important question affecting protected and endangered species.

  5. Developing tools for risk assessment in protected species: Relative potencies inferred from competitive binding of halogenated aromatic hydrocarbons to aryl hydrocarbon receptors from beluga (Delphinapterus leucas) and mouse.

    PubMed

    Jensen, Brenda A; Reddy, Christopher M; Nelson, Robert K; Hahn, Mark E

    2010-11-01

    Persistent organic pollutants such as halogenated aromatic hydrocarbons (HAHs) biomagnify in food webs and accumulate to high concentrations in top predators like odontocete cetaceans (toothed whales). The most toxic HAHs are the 2,3,7,8-substituted halogenated dibenzo-p-dioxins and furans, and non-ortho-substituted polychlorinated biphenyls (PCBs), which exert their effects via the aryl hydrocarbon receptor (AHR). Understanding the impact of HAHs in wildlife is limited by the lack of taxon-specific information about the relative potencies of toxicologically important congeners. To assess whether Toxic Equivalency Factors (TEFs) determined in rodents are predictive of HAH relative potencies in a cetacean, we used beluga and mouse AHRs expressed in vitro from cloned cDNAs to measure the relative AHR-binding affinities of ten HAHs from five different structural classes. The rank order of mean IC(50)s for competitive binding to beluga AHR was: TCDDrelative to those of an AHR from a dioxin-responsive mouse suggests that beluga, and perhaps cetaceans in general, may be particularly sensitive to the toxic effects of AHR agonists. Further study is warranted in order to more fully address this important question affecting protected and endangered species. PMID:20728228

  6. Towards Context Sensitive Information Inference.

    ERIC Educational Resources Information Center

    Song, D.; Bruza, P. D.

    2003-01-01

    Discusses information inference from a psychologistic stance and proposes an information inference mechanism that makes inferences via computations of information flow through an approximation of a conceptual space. Highlights include cognitive economics of information processing; context sensitivity; and query models for information retrieval.…

  7. Multimodel inference and adaptive management

    USGS Publications Warehouse

    Rehme, S.E.; Powell, L.A.; Allen, C.R.

    2011-01-01

    Ecology is an inherently complex science coping with correlated variables, nonlinear interactions and multiple scales of pattern and process, making it difficult for experiments to result in clear, strong inference. Natural resource managers, policy makers, and stakeholders rely on science to provide timely and accurate management recommendations. However, the time necessary to untangle the complexities of interactions within ecosystems is often far greater than the time available to make management decisions. One method of coping with this problem is multimodel inference. Multimodel inference assesses uncertainty by calculating likelihoods among multiple competing hypotheses, but multimodel inference results are often equivocal. Despite this, there may be pressure for ecologists to provide management recommendations regardless of the strength of their study’s inference. We reviewed papers in the Journal of Wildlife Management (JWM) and the journal Conservation Biology (CB) to quantify the prevalence of multimodel inference approaches, the resulting inference (weak versus strong), and how authors dealt with the uncertainty. Thirty-eight percent and 14%, respectively, of articles in the JWM and CB used multimodel inference approaches. Strong inference was rarely observed, with only 7% of JWM and 20% of CB articles resulting in strong inference. We found the majority of weak inference papers in both journals (59%) gave specific management recommendations. Model selection uncertainty was ignored in most recommendations for management. We suggest that adaptive management is an ideal method to resolve uncertainty when research results in weak inference.

  8. Phylogenies from genetic and morphological characters do not support a revision of Gigasporaceae (Glomeromycota) into four families and five genera.

    PubMed

    Morton, Joseph B; Msiska, Zola

    2010-10-01

    The family Gigasporaceae consisted of the two genera Gigaspora and Scutellospora when first erected. In a recent revision of this classification, Scutellospora was divided into three families and four genera based on two main lines of evidence: (1) phylogenetic patterns of coevolving small and large rRNA genes and (2) morphology of spore germination shields. The rRNA trees were assumed to accurately reflect species evolution, and shield characters were selected because they correlated with gene trees. These characters then were used selectively to support gene trees and validate the classification. To test this new classification, a phylogenetic tree was reconstructed from concatenated 25S rRNA and β-tubulin gene sequences using 35% of known species in Gigasporaceae. A tree also was reconstructed from 23 morphological characters represented in 71% of known species. Results from both datasets showed that the revised classification was untenable. The classification also failed to accurately represent sister group relationships amongst higher taxa. Only two clades were fully resolved and congruent among datasets: Gigaspora and Racocetra (a clade consisting of species with spores having one inner germinal wall). Other clades were unresolved, which was attributed in part to undersampling of species. Topology of the morphology-based phylogeny was incongruent with gene evolution. Five shield characters were reduced to three, of which two were phylogenetically uninformative because they were homoplastic. Therefore, most taxa erected in the new classification are rejected. The classification is revised to restore the family Gigasporaceae, within which are the three genera Gigaspora, Racocetra, and Scutellospora. This classification does not reflect strict topology of either gene or morphological evolution. Further revisions must await sampling of additional characters and taxa to better ascertain congruence between datasets and infer a more accurate phylogeny of this

  9. Weak-lensing-inferred scaling relations of galaxy clusters in the RCS2: mass-richness, mass-concentration, mass-bias, and more

    NASA Astrophysics Data System (ADS)

    van Uitert, Edo; Gilbank, David G.; Hoekstra, Henk; Semboloni, Elisabetta; Gladders, Michael D.; Yee, Howard K. C.

    2016-02-01

    We study a sample of ~104 galaxy clusters in the redshift range 0.2 5×1013 h70-1 M⊙, discovered in the second Red-sequence Cluster Survey (RCS2). The depth and excellent image quality of the RCS2 enabled us to detect the cluster-mass cross-correlation up to z ~ 0.7. To obtain cluster masses, concentrations, and halo biases, we fit a cluster halo model simultaneously to the lensing signal and to the projected density profile of red-sequence cluster members, because the latter provides tight constraints on the cluster miscentring distribution. We parametrised the mass-richness relation as M200 = A × (N200/ 20)α and find A =(15.0±0.8)×1013 h70-1 M⊙ and α = 0.73 ± 0.07 at low redshift (0.2 < z < 0.35). At intermediate redshift (0.35 < z < 0.55), we find a higher normalisation, which points towards a fractional increase in the richness towards lower redshift caused by the build-up of the red sequence. The miscentring distribution is well constrained. Only ~30% of our BCGs coincide with the peak of the dark matter distribution. The distribution of the remaining BCGs are modelled with a 2D-Gaussian, whose width increases from 0.2 to 0.4 h70-1 Mpc towards higher masses. The ratio of width and r200 is constant with mass and has an average value of 0.44 ± 0.01. The mass-concentration and mass-bias relations agree fairly well with literature results at low redshift, but have a higher normalisation at higher redshifts, possibly because of selection and projection effects. The concentration of the satellite distribution decreases with mass and is correlated to the concentration of the halo.

  10. A three-parameter model for classifying anurans into four genera based on advertisement calls.

    PubMed

    Gingras, Bruno; Fitch, William Tecumseh

    2013-01-01

    The vocalizations of anurans are innate in structure and may therefore contain indicators of phylogenetic history. Thus, advertisement calls of species which are more closely related phylogenetically are predicted to be more similar than those of distant species. This hypothesis was evaluated by comparing several widely used machine-learning algorithms. Recordings of advertisement calls from 142 species belonging to four genera were analyzed. A logistic regression model, using mean values for dominant frequency, coefficient of variation of root-mean square energy, and spectral flux, correctly classified advertisement calls with regard to genus with an accuracy above 70%. Similar accuracy rates were obtained using these parameters with a support vector machine model, a K-nearest neighbor algorithm, and a multivariate Gaussian distribution classifier, whereas a Gaussian mixture model performed slightly worse. In contrast, models based on mel-frequency cepstral coefficients did not fare as well. Comparable accuracy levels were obtained on out-of-sample recordings from 52 of the 142 original species. The results suggest that a combination of low-level acoustic attributes is sufficient to discriminate efficiently between the vocalizations of these four genera, thus supporting the initial premise and validating the use of high-throughput algorithms on animal vocalizations to evaluate phylogenetic hypotheses. PMID:23297926

  11. Patterns of diversification in islands: A comparative study across three gecko genera in the Socotra Archipelago.

    PubMed

    Garcia-Porta, Joan; Morales, Hernán E; Gómez-Díaz, Elena; Sindaco, Roberto; Carranza, Salvador

    2016-05-01

    In this study we used the complete fauna of geckos of the Socotra Archipelago to test whether the three gecko genera co-occurring in the islands (Pristurus, Hemidactylus and Haemodracon) produced similar outcomes of morphological and climatic diversification. To test this, we produced a time-calibrated tree of 346 geckos including all 16 endemic species of the archipelago and 26 potential close-relatives in the continent. Our dating estimates revealed that most of the diversity of geckos in the archipelago was the consequence of in situ diversification. However not all genera shared similar patterns of diversification. While in Hemidactylus and Haemodracon this involved great differences in body size and low levels of climatic diversification (mostly involving sympatric distributions), an opposite pattern appeared in Pristurus in which most of the diversification involved shifts in climatic envelopes (mostly involving allopatric and parapatric distributions) but almost no size differentiation. Consistently with this, Pristurus was the only genus in which rates of size diversification in islands were substantially lower than in the continent. This illustrates how different groups can greatly differ in their patterns of intra-island diversification and highlights the importance of taxon-dependent factors at determining different patterns of diversification in the same insular context. PMID:26911521

  12. A cladistic analysis of the genera in the subfamily Pudicinae (Nematoda, Trichostrongyloidea, Heligmonellidae).

    PubMed

    Durette-Desset, M C; Justine, J L

    1991-09-01

    A parsimony analysis was performed on 37 specific taxa belonging to the subfamily Pudicinae (family Heligmonellidae), which contains parasites mainly from South American caviomorph rodents. Thirteen characters were used from the synlophe (rotation of axis, presence of carene, carene asymmetry, presence of comaretes, single ventral comarete length, ridge discontinuity, ventral ridge numbers, presence of a peculiar posterior synlophe, presence of supernumerary spines) and the male caudal bursa (relative length of rays 9 and 10, caudal bursa type, division of the dorsal ray, divergence of the 10th rays). The cladogram shows a consistency index of 1.0. The subfamily Pudicinae has two synapomorphies. Two suprageneric groups are recognized. Suprageneric group 1 shows one synapomorphy and contains Heligmostrongylus, Fuellebornema, Sciurodendrium and Pseudoheligmosomum; suprageneric group 2 shows two synapomorphies and contains Pudica, Acanthostrongylus, Justinema and Durettestrongylus. Five genera are defined on the basis of synapomorphies. The genera Heligmostrongylus, Sciurodendrium and Pudica which are considered paraphyletic, however, are retained due to lack of knowledge as to their relationships.

  13. Patterns of diversification in islands: A comparative study across three gecko genera in the Socotra Archipelago.

    PubMed

    Garcia-Porta, Joan; Morales, Hernán E; Gómez-Díaz, Elena; Sindaco, Roberto; Carranza, Salvador

    2016-05-01

    In this study we used the complete fauna of geckos of the Socotra Archipelago to test whether the three gecko genera co-occurring in the islands (Pristurus, Hemidactylus and Haemodracon) produced similar outcomes of morphological and climatic diversification. To test this, we produced a time-calibrated tree of 346 geckos including all 16 endemic species of the archipelago and 26 potential close-relatives in the continent. Our dating estimates revealed that most of the diversity of geckos in the archipelago was the consequence of in situ diversification. However not all genera shared similar patterns of diversification. While in Hemidactylus and Haemodracon this involved great differences in body size and low levels of climatic diversification (mostly involving sympatric distributions), an opposite pattern appeared in Pristurus in which most of the diversification involved shifts in climatic envelopes (mostly involving allopatric and parapatric distributions) but almost no size differentiation. Consistently with this, Pristurus was the only genus in which rates of size diversification in islands were substantially lower than in the continent. This illustrates how different groups can greatly differ in their patterns of intra-island diversification and highlights the importance of taxon-dependent factors at determining different patterns of diversification in the same insular context.

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

    PubMed

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

    2008-12-01

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

  15. Distribution of the genus Cyclotella in relation to pH in Precambrian Shield lakes: implications for diatom-inferred pH

    SciTech Connect

    Taylor, M.C.; Duthie, H.C.; Smith, S.M.

    1987-12-01

    Recent research on relationships between diatoms and pH suggest that the genus Cyclotella exhibits a strong relationship with lake acidity, being almost totally absent below pH 5.5. This decline has been used as an indicator of lake acidification in paleolimnological studies. In this study C. stelligera V.H. and C. kuetzingiana Thwaites were abundant in Precambrian Sheild lakes with pH as low as 4.5. Cyclotella comta (Ehr.) Kuetz. was found in lakes of pH <5.5, but maximum abundance was observed in lakes of pH >5.5. Cyclotella michiganiana Skv. was found in lakes of pH >6.0. These results indicate that the use of C. stelligera, C. kuetzingiana, and possibly C. comta, in paleolimnological investigations of lake acidification, should be approached with caution. These taxa may exhibit a decline in abundance with decreasing lake water pH, but this is partially a morphometric effect not necessarily related to anthropogenic acidification.

  16. Geographical and ecological distribution of marine halacarid genera and species (Acari: Halacaridae).

    PubMed

    Bartsch, Ilse

    2004-01-01

    At the end of 2002, the number of marine halacarid species was 1018, that of genera 51. A single genus, Copidognathus contains 33% of all species (336). Eleven genera are monotypic. Geographical provinces with a large number of species are the tropical western Pacific, temperate northeastern Atlantic, temperate southeastern Pacific, and Mediterranean-Black Sea. Most records of halacarid species are from temperate and tropical areas; 10% of species are known from polar zones. On a generic level, 29 genera are recorded from tropical and temperate but not from polar provinces, five genera are restricted to the tropics, and none to polar regions. The majority (920 species or 90%) of all species live in the upper 200 m. Records of genera with exclusively algivorous or brackish/fresh water species are bound to littoral habitats; all the other genera occur in more than one depth zone. Arenicolous genera, though most abundant in the littoral zone, have representatives in the bathyal. Four marine genera (Copidognathus, Halacarellus, Isobactrus, Lohmannella) have representatives in coastal fresh water, and three genera, Acarothrix, Caspihalacarus and Peregrinacarus, are predominantly inhabitants of diluted brackish and fresh water. None of the free-living halacarid genera of the world's oceans appears to be endemic to one geographical province.

  17. Visual Inference Programming

    NASA Technical Reports Server (NTRS)

    Wheeler, Kevin; Timucin, Dogan; Rabbette, Maura; Curry, Charles; Allan, Mark; Lvov, Nikolay; Clanton, Sam; Pilewskie, Peter

    2002-01-01

    The goal of visual inference programming is to develop a software framework data analysis and to provide machine learning algorithms for inter-active data exploration and visualization. The topics include: 1) Intelligent Data Understanding (IDU) framework; 2) Challenge problems; 3) What's new here; 4) Framework features; 5) Wiring diagram; 6) Generated script; 7) Results of script; 8) Initial algorithms; 9) Independent Component Analysis for instrument diagnosis; 10) Output sensory mapping virtual joystick; 11) Output sensory mapping typing; 12) Closed-loop feedback mu-rhythm control; 13) Closed-loop training; 14) Data sources; and 15) Algorithms. This paper is in viewgraph form.

  18. Graphical inference for Infovis.

    PubMed

    Wickham, Hadley; Cook, Dianne; Hofmann, Heike; Buja, Andreas

    2010-01-01

    How do we know if what we see is really there? When visualizing data, how do we avoid falling into the trap of apophenia where we see patterns in random noise? Traditionally, infovis has been concerned with discovering new relationships, and statistics with preventing spurious relationships from being reported. We pull these opposing poles closer with two new techniques for rigorous statistical inference of visual discoveries. The "Rorschach" helps the analyst calibrate their understanding of uncertainty and "line-up" provides a protocol for assessing the significance of visual discoveries, protecting against the discovery of spurious structure.

  19. Inferring the degree of incipient speciation in secondary contact zones of closely related lineages of Palearctic green toads (Bufo viridis subgroup)

    PubMed Central

    Dufresnes, C; Bonato, L; Novarini, N; Betto-Colliard, C; Perrin, N; Stöck, M

    2014-01-01

    Reproductive isolation between lineages is expected to accumulate with divergence time, but the time taken to speciate may strongly vary between different groups of organisms. In anuran amphibians, laboratory crosses can still produce viable hybrid offspring >20 My after separation, but the speed of speciation in closely related anuran lineages under natural conditions is poorly studied. Palearctic green toads (Bufo viridis subgroup) offer an excellent system to address this question, comprising several lineages that arose at different times and form secondary contact zones. Using mitochondrial and nuclear markers, we previously demonstrated that in Sicily, B. siculus and B. balearicus developed advanced reproductive isolation after Plio-Pleistocene divergence (2.6 My, 3.3–1.9), with limited historic mtDNA introgression, scarce nuclear admixture, but low, if any, current gene flow. Here, we study genetic interactions between younger lineages of early Pleistocene divergence (1.9 My, 2.5–1.3) in northeastern Italy (B. balearicus, B. viridis). We find significantly more, asymmetric nuclear and wider, differential mtDNA introgression. The population structure seems to be molded by geographic distance and barriers (rivers), much more than by intrinsic genomic incompatibilities. These differences of hybridization between zones may be partly explained by differences in the duration of previous isolation. Scattered research on other anurans suggests that wide hybrid zones with strong introgression may develop when secondary contacts occur <2 My after divergence, whereas narrower zones with restricted gene flow form when divergence exceeds 3 My. Our study strengthens support for this rule of thumb by comparing lineages with different divergence times within the same radiation. PMID:24713825

  20. Late Quaternary environmental change inferred from phytoliths and other soil-related proxies: Case studies from the central and southern Great Plains, USA

    USGS Publications Warehouse

    Cordova, C.E.; Johnson, W.C.; Mandel, R.D.; Palmer, M.W.

    2011-01-01

    This study investigates stable carbon isotopes (??13C), opal phytolith assemblages, burnt phytoliths, microscopic charcoal and Sporormiella spores from modern soils and paleosols in Kansas and Oklahoma. Grass and dicot phytoliths in combination with ??13C are used as proxies for reconstructing the structure of grasslands and woodlands. Burnt grass phytoliths and microscopic charcoal are evaluated as proxies for reconstructing paleofire incidence. Concentrations of the fungal spore Sporormiella are used as a proxy for assessing large herbivore activity. These proxies were tested on various modern grassland communities of the central and southern Great Plains, including areas with bison, cattle, and small herbivores, and areas under different fire frequencies.Opal phytolith assemblages and ??13C values show that before cal 11ka, C3 grasses and woody plants predominated in areas that today are dominated by C4 grasses. The origin of the shortgrass prairie dates back to about cal 10ka. The origin of the tallgrass prairie, however, is not clear as phytolith data show variable assemblages throughout the Holocene (mixed-grass, tallgrass, and tallgrass-woodland mosaic). Different proxies (burnt phytoliths vs. charcoal) reveal different fire frequencies, but it is apparent that microfossil evidence for fire incidence is closely related to the abundance of woody plants in the landscape.Before cal 12. ka, soils show somewhat elevated concentration of Sporormiella, but lower concentrations than the modern high-density bison and cattle grazing areas. Throughout the Holocene, Sporormiella frequencies are low, which suggests lower large ungulate densities and perhaps high mobility. ?? 2010 Elsevier B.V.

  1. Age- and position-related changes in hydraulic versus mechanical dysfunction of xylem: inferring the design criteria for Douglas-fir wood structure.

    PubMed

    Domec, J C; Gartner, B L

    2002-02-01

    We do not know why trees exhibit changes in wood characteristics as a function of cambial age. In part, the answer may lie in the existence of a tradeoff between hydraulic properties and mechanical support. In conifers, longitudinal tracheids represent 92% of the cells comprising the wood and are involved in both water transport and mechanical support. We used three hydraulic parameters to estimate hydraulic safety factors at several vertical and radial locations in the trunk and branches: vulnerability to cavitation; variation in xylem water potential (psi); and xylem relative water content. The hydraulic safety factors for 12 and 88 percent loss of conductivity (S(H12) and S(H88), representing the hydraulic safety factors for the air entry point and full embolism point, respectively) were determined. We also estimated the mechanical safety factor for maximum tree height and for buckling. We estimated the dimensionless hydraulic and mechanical safety factors for six seedlings (4 years old), six saplings (10 years old) and six mature trees (> 110 years old) of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco). Over the natural range of psi, S(H12) decreased linearly from treetop to a minimum of 0.95 at the tree base. Young and mature trees had S(H12) values 1.4 and 1.3 times higher, respectively, at their tips (juvenile wood) than at their bases (mature wood). Modeling analyses indicated that if trees were made entirely of mature wood, S(H12) at the stem base would be only 0.7. The mechanical safety factor was 1.2 times higher for the base of the tree than for the rest of the tree. The minimum mechanical safety factor-1.6 for the critical buckling height and 2.2 for the critical buckling load-occurred at the base of the live crown. Modeling analysis indicated that if trees were made only of mature wood, these values would increase to 1.7 and 2.3, respectively. Hydraulic safety factors had values that were less than half those for mechanical safety factors

  2. Drought meets acid: three new genera in a dothidealean clade of extremotolerant fungi

    PubMed Central

    Selbmann, L.; de Hoog, G.S.; Zucconi, L.; Isola, D.; Ruisi, S.; van den Ende, A.H.G. Gerrits; Ruibal, C.; De Leo, F.; Urzì, C.; Onofri, S.

    2008-01-01

    Fungal strains isolated from rocks and lichens collected in the Antarctic ice-free area of the Victoria Land, one of the coldest and driest habitats on earth, were found in two phylogenetically isolated positions within the subclass Dothideomycetidae. They are here reported as new genera and species, Recurvomyces mirabilis gen. nov., sp. nov. and Elasticomyces elasticus gen. nov., sp. nov. The nearest neighbours within the clades were other rock-inhabiting fungi from dry environments, either cold or hot. Plant-associated Mycosphaerella-like species, known as invaders of leathery leaves in semi-arid climates, are also phylogenetically related with the new taxa. The clusters are also related to the halophilic species Hortaea werneckii, as well as to acidophilic fungi. One of the latter, able to grow at pH 0, is Scytalidium acidophilum, which is ascribed here to the newly validated genus Acidomyces. The ecological implications of this finding are discussed. PMID:19287523

  3. Comprehensive phylogeny, biogeography and new classification of the diverse bee tribe Megachilini: Can we use DNA barcodes in phylogenies of large genera?

    PubMed

    Trunz, V; Packer, L; Vieu, J; Arrigo, N; Praz, C J

    2016-10-01

    Classification and evolutionary studies of particularly speciose clades pose important challenges, as phylogenetic analyses typically sample a small proportion of the existing diversity. We examine here one of the largest bee genera, the genus Megachile - the dauber and leafcutting bees. Besides presenting a phylogeny based on five nuclear genes (5480 aligned nucleotide positions), we attempt to use the phylogenetic signal of mitochondrial DNA barcodes, which are rapidly accumulating and already include a substantial proportion of the known species diversity in the genus. We used barcodes in two ways: first, to identify particularly divergent lineages and thus to guide taxon sampling in our nuclear phylogeny; second, to augment taxon sampling by combining nuclear markers (as backbone for ancient divergences) with DNA barcodes. Our results indicate that DNA barcodes bear phylogenetic signal limited to very recent divergences (3-4 my before present). Sampling within clades of very closely related species may be augmented using this technique, but our results also suggest statistically supported, but incongruent placements of some taxa. However, the addition of one single nuclear gene (LW-rhodopsin) to the DNA barcode data was enough to recover meaningful placement with high clade support values for nodes up to 15 million years old. We discuss different proposals for the generic classification of the tribe Megachilini. Finding a classification that is both in agreement with our phylogenetic hypotheses and practical in terms of diagnosability is particularly challenging as our analyses recover several well-supported clades that include morphologically heterogeneous lineages. We favour a classification that recognizes seven morphologically well-delimited genera in Megachilini: Coelioxys, Gronoceras, Heriadopsis, Matangapis, Megachile, Noteriades and Radoszkowskiana. Our results also lead to the following classification changes: the groups known as Dinavis, Neglectella

  4. Comprehensive phylogeny, biogeography and new classification of the diverse bee tribe Megachilini: Can we use DNA barcodes in phylogenies of large genera?

    PubMed

    Trunz, V; Packer, L; Vieu, J; Arrigo, N; Praz, C J

    2016-10-01

    Classification and evolutionary studies of particularly speciose clades pose important challenges, as phylogenetic analyses typically sample a small proportion of the existing diversity. We examine here one of the largest bee genera, the genus Megachile - the dauber and leafcutting bees. Besides presenting a phylogeny based on five nuclear genes (5480 aligned nucleotide positions), we attempt to use the phylogenetic signal of mitochondrial DNA barcodes, which are rapidly accumulating and already include a substantial proportion of the known species diversity in the genus. We used barcodes in two ways: first, to identify particularly divergent lineages and thus to guide taxon sampling in our nuclear phylogeny; second, to augment taxon sampling by combining nuclear markers (as backbone for ancient divergences) with DNA barcodes. Our results indicate that DNA barcodes bear phylogenetic signal limited to very recent divergences (3-4 my before present). Sampling within clades of very closely related species may be augmented using this technique, but our results also suggest statistically supported, but incongruent placements of some taxa. However, the addition of one single nuclear gene (LW-rhodopsin) to the DNA barcode data was enough to recover meaningful placement with high clade support values for nodes up to 15 million years old. We discuss different proposals for the generic classification of the tribe Megachilini. Finding a classification that is both in agreement with our phylogenetic hypotheses and practical in terms of diagnosability is particularly challenging as our analyses recover several well-supported clades that include morphologically heterogeneous lineages. We favour a classification that recognizes seven morphologically well-delimited genera in Megachilini: Coelioxys, Gronoceras, Heriadopsis, Matangapis, Megachile, Noteriades and Radoszkowskiana. Our results also lead to the following classification changes: the groups known as Dinavis, Neglectella

  5. Inferring horizontal gene transfer.

    PubMed

    Ravenhall, Matt; Škunca, Nives; Lassalle, Florent; Dessimoz, Christophe

    2015-05-01

    Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages. Computational identification of HGT events relies upon the investigation of sequence composition or evolutionary history of genes. Sequence composition-based ("parametric") methods search for deviations from the genomic average, whereas evolutionary history-based ("phylogenetic") approaches identify genes whose evolutionary history significantly differs from that of the host species. The evaluation and benchmarking of HGT inference methods typically rely upon simulated genomes, for which the true history is known. On real data, different methods tend to infer different HGT events, and as a result it can be difficult to ascertain all but simple and clear-cut HGT events. PMID:26020646

  6. Moment inference from tomograms

    USGS Publications Warehouse

    Day-Lewis, F. D.; Chen, Y.; Singha, K.

    2007-01-01

    Time-lapse geophysical tomography can provide valuable qualitative insights into hydrologic transport phenomena associated with aquifer dynamics, tracer experiments, and engineered remediation. Increasingly, tomograms are used to infer the spatial and/or temporal moments of solute plumes; these moments provide quantitative information about transport processes (e.g., advection, dispersion, and rate-limited mass transfer) and controlling parameters (e.g., permeability, dispersivity, and rate coefficients). The reliability of moments calculated from tomograms is, however, poorly understood because classic approaches to image appraisal (e.g., the model resolution matrix) are not directly applicable to moment inference. Here, we present a semi-analytical approach to construct a moment resolution matrix based on (1) the classic model resolution matrix and (2) image reconstruction from orthogonal moments. Numerical results for radar and electrical-resistivity imaging of solute plumes demonstrate that moment values calculated from tomograms depend strongly on plume location within the tomogram, survey geometry, regularization criteria, and measurement error. Copyright 2007 by the American Geophysical Union.

  7. Inferring Horizontal Gene Transfer

    PubMed Central

    Lassalle, Florent; Dessimoz, Christophe

    2015-01-01

    Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages [1]. Computational identification of HGT events relies upon the investigation of sequence composition or evolutionary history of genes. Sequence composition-based ("parametric") methods search for deviations from the genomic average, whereas evolutionary history-based ("phylogenetic") approaches identify genes whose evolutionary history significantly differs from that of the host species. The evaluation and benchmarking of HGT inference methods typically rely upon simulated genomes, for which the true history is known. On real data, different methods tend to infer different HGT events, and as a result it can be difficult to ascertain all but simple and clear-cut HGT events. PMID:26020646

  8. Phylogenetic relationships and ancestral areas of the bustards (Gruiformes: Otididae), inferred from mitochondrial DNA and nuclear intron sequences.

    PubMed

    Pitra, Christian; Lieckfeldt, Dietmar; Frahnert, Sylke; Fickel, Joerns

    2002-04-01

    The taxonomy of the bustards is poorly understood phylogenetically and has not been extensively evaluated using molecular methods. We sequenced part of the mitochondrial cytochrome b gene, the control region (central domain II), and an intron-exon crossing fragment of the nuclear chromo-helicase-DNA binding gene (CHD1) in 27 bustard taxa (including multiple subspecies) representing 11 genera and four gruiform outgroup species. Molecular datings suggest a Miocene origin for the family. Inferred phylogenetic relationships include the following: (i) the basal polytomy consists of 10 branches (mostly consistent with traditional genera), suggesting a rapid early radiation; (ii) sister relationships between several couplets of genera include Ardeotis with Neotis, Afrotis with Eupodotis (excluding E. rueppellii), Otis with Chlamydotis, and Houbaropsis with Sypheotides; (iii) the genus Eupodotis may be polyphyletic; and (iv) the currently delimited genera Ardeotis and Neotis do not form independent monophyletic lineages. Molecular evidence for the Afro-tropical origin of the Otididae is provided. PMID:12182403

  9. Phylogenetic and molecular clock inferences of cyanobacterial strains within Rivulariaceae from distant environments.

    PubMed

    Domínguez-Escobar, Julia; Beltrán, Yislem; Bergman, Birgitta; Díez, Beatriz; Ininbergs, Karolina; Souza, Valeria; Falcón, Luisa I

    2011-03-01

    Heterocyst-forming cyanobacteria are important players at both evolutionary and ecological scales, but to date it has been difficult to establish their phylogenetic affiliations. We present data from a phylogenetic and molecular clock analysis of heterocystous cyanobacteria within the family Rivulariaceae, including the genera Calothrix, Rivularia, Gloeotrichia and Tolypothrix. The strains were isolated from distant geographic regions including fresh and brackish water bodies, microbial mats from beach rock, microbialites, pebble beaches, plus PCC strains 7103 and 7504. Phylogenetic inferences (distance, likelihood and Bayesian) suggested the monophyly of genera Calothrix and Rivularia. Molecular clock estimates indicate that Calothrix and Rivularia originated ∼1500 million years ago (MYA) ago and species date back to 400-300 MYA while Tolypothrix and Gloeotrichia are younger genera (600-400 MYA).

  10. A new family and four new genera in Rhizophydiales (Chytridiomycota).

    PubMed

    Letcher, Peter M; Powell, Martha J; Davis, William J

    2015-01-01

    Many chytrid phylogenies contain lineages representing a lone taxon or a few organisms. One such lineage in recent molecular phylogenies of Rhizophydiales contained two marine chytrids, Rhizophydium littoreum and Rhizophydium aestuarii. To better understand the relationship between these organisms, we increased sampling such that the R. littoreum/R. aestuarii lineage included 10 strains of interest. To place this lineage in Rhizophydiales, we constructed a molecular phylogeny from partial nuc 28S rDNA D1-D3 domains (28S) of these and 80 additional strains in Rhizophydiales and examined thallus morphology and zoospore ultrastructure of our strains of interest. We also analyzed sequences of the nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS) of our 10 strains of interest to assess sequence similarity and phylogenetic placement of strains within the lineage. The 10 strains grouped together in three well supported clades: (i) Rhizophydium littoreum+Phlyctochytrium mangrovei, (ii) three strains of Rhizophydium aestuarii and (iii) five previously unidentified strains. Light microscopic observations revealed four distinct thallus morphologies, and zoospore ultrastructural analyses revealed four distinct constellations of ultrastructural features. On the bases of morphological, ultrastructural and molecular evidence we place these strains in the new family Halomycetaceae and four new genera (Halomyces, Paludomyces, Ulkenomyces, Paranamyces) in Rhizophydiales. PMID:25911694

  11. New genera and species of Neotropical Exosternini (Coleoptera, Histeridae)

    PubMed Central

    Caterino, Michael S.; Tishechkin, Alexey K.

    2014-01-01

    Abstract We describe the following 8 new genera and 23 new species of Neotropical Exosternini. Conocassis gen. n. (Conocassis minor sp. n. [type species], Conocassis dromedaria sp. n., Conocassis trisulcata sp. n., and Conocassis invaginata sp. n.), Enkyosoma gen. n. (Enkyosoma rockwelli sp. n.), Pluricosta gen. n. (Pluricosta onthophiloides sp. n.), Pyxister gen. n. (Pyxister devorator sp. n. [type species] and Pyxister labralis sp. n.), Chapischema gen. n. (Chapischema doppelganger sp. n.), Scaptorus gen. n. (Scaptorus pyramus sp. n.), Lacrimorpha gen. n. (Lacrimorpha glabra sp. n. [type species], Lacrimorpha balbina sp. n., Lacrimorpha subdepressa sp. n., and Lacrimorpha acuminata sp. n.), Crenulister gen. n. (Crenulister grossus sp. n. [type species], Crenulister explanatus sp. n., Crenulister dentatus sp. n., Crenulister impar sp. n., Crenulister umbrosus sp. n., Crenulister simplex sp. n., Crenulister paucitans sp. n., Crenulister spinipes sp. n., and Crenulister seriatus sp. n.) These all represent highly distinctive and phylogenetically isolated forms, almost invariably known from very few specimens. All but one species have been collected only by passive flight intercept traps, and nothing significant is known about the biology of any of them. PMID:24624014

  12. 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

  13. 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

  14. A key to the Mexican and Central America Genera of Anthonomini (Curculionidae, Curculioninae)

    PubMed Central

    Hernández, Macotulio Soto; Jones, Robert W.; Castillo, Pedro Reyes

    2013-01-01

    Abstract Presently the only keys available for identification of genera of Anthonomini are limited to those of the United States of America and Canada. A dichotomous key is presented to identify all genera of Mexican and Central American Anthonomini. Previous keys do not include the genera Achia, Botanebius, Loncophorus, Loncophorellus and Melexerus. A brief synopsis is given for each genus and photographs of representative species are included. PMID:23717181

  15. Inferring learners' knowledge from their actions.

    PubMed

    Rafferty, Anna N; LaMar, Michelle M; Griffiths, Thomas L

    2015-04-01

    Watching another person take actions to complete a goal and making inferences about that person's knowledge is a relatively natural task for people. This ability can be especially important in educational settings, where the inferences can be used for assessment, diagnosing misconceptions, and providing informative feedback. In this paper, we develop a general framework for automatically making such inferences based on observed actions; this framework is particularly relevant for inferring student knowledge in educational games and other interactive virtual environments. Our approach relies on modeling action planning: We formalize the problem as a Markov decision process in which one must choose what actions to take to complete a goal, where choices will be dependent on one's beliefs about how actions affect the environment. We use a variation of inverse reinforcement learning to infer these beliefs. Through two lab experiments, we show that this model can recover people's beliefs in a simple environment, with accuracy comparable to that of human observers. We then demonstrate that the model can be used to provide real-time feedback and to model data from an existing educational game.

  16. Inferring learners' knowledge from their actions.

    PubMed

    Rafferty, Anna N; LaMar, Michelle M; Griffiths, Thomas L

    2015-04-01

    Watching another person take actions to complete a goal and making inferences about that person's knowledge is a relatively natural task for people. This ability can be especially important in educational settings, where the inferences can be used for assessment, diagnosing misconceptions, and providing informative feedback. In this paper, we develop a general framework for automatically making such inferences based on observed actions; this framework is particularly relevant for inferring student knowledge in educational games and other interactive virtual environments. Our approach relies on modeling action planning: We formalize the problem as a Markov decision process in which one must choose what actions to take to complete a goal, where choices will be dependent on one's beliefs about how actions affect the environment. We use a variation of inverse reinforcement learning to infer these beliefs. Through two lab experiments, we show that this model can recover people's beliefs in a simple environment, with accuracy comparable to that of human observers. We then demonstrate that the model can be used to provide real-time feedback and to model data from an existing educational game. PMID:25155381

  17. A synoptic review of the ant genera (Hymenoptera, Formicidae) of the Philippines

    PubMed Central

    General, David M.; Alpert, Gary D.

    2012-01-01

    Abstract An overview of the history of myrmecology in the Philippine archipelago is presented. Keys are provided to the 11 ant subfamilies and the 92 ant genera known from the Philippines. Eleven ant genera (12%), including 3 undescribed genera, are recorded for the first time from the Philippines. The biology and ecology of the 92 genera, illustrated by full-face and profile photo-images, of Philippine ants are summarized in the form of brief generic accounts. A bibliography of significant taxonomic and behavioral papers on Philippine ants and a checklist of valid species and subspecies and their island distributions are provided. PMID:22767999

  18. Three new monotypic genera of Trichopolydesmidae from Croatia, Balkan Peninsula (Diplopoda, Polydesmida).

    PubMed

    Antić, Dragan Ž; Reip, Hans S; Dražina, Tvrtko; Rađa, Tonći; Makarov, Slobodan E

    2014-11-13

    Three new monotypic genera are described from underground habitats in Croatia: Balkanodesmus biokovensis gen. n., sp. n., Solentanodesmus insularis gen. n., sp. n. and Velebitodesmus cavernicolus gen. n., sp. n. In all three new genera the prefemoral part of the gonopods is orientated transversely to the main body axis, and all three new genera possess numerous metatergal setae arranged in a few transverse irregular rows, a condition observed in several European trichopolydesmids. These three new genera are very close to the genus Verhoeffodesmus. A distribution map and a brief discussion about the relationship with congeners are provided.

  19. Nonintentional analogical inference in text comprehension.

    PubMed

    Day, Samuel B; Gentner, Dedre

    2007-01-01

    We present findings suggesting that analogical inference processes can play a role in fluent comprehension and interpretation. Participants were found to use information from a prior relationally similar example in understanding the content of a later example, but they reported that they were not aware of having done so. These inference processes were sensitive to structural mappings between the two instances, ruling out explanations based solely on more general kinds of activation, such as priming. Reading speed measures were consistent with the possibility that these inferences had taken place during encoding of the target rather than during the later recognition test. These findings suggest that analogical mapping, though often viewed as an explicit deliberative process, can sometimes operate without intent or even awareness.

  20. Bayesian inference in geomagnetism

    NASA Technical Reports Server (NTRS)

    Backus, George E.

    1988-01-01

    The inverse problem in empirical geomagnetic modeling is investigated, with critical examination of recently published studies. Particular attention is given to the use of Bayesian inference (BI) to select the damping parameter lambda in the uniqueness portion of the inverse problem. The mathematical bases of BI and stochastic inversion are explored, with consideration of bound-softening problems and resolution in linear Gaussian BI. The problem of estimating the radial magnetic field B(r) at the earth core-mantle boundary from surface and satellite measurements is then analyzed in detail, with specific attention to the selection of lambda in the studies of Gubbins (1983) and Gubbins and Bloxham (1985). It is argued that the selection method is inappropriate and leads to lambda values much larger than those that would result if a reasonable bound on the heat flow at the CMB were assumed.

  1. BIE: Bayesian Inference Engine

    NASA Astrophysics Data System (ADS)

    Weinberg, Martin D.

    2013-12-01

    The Bayesian Inference Engine (BIE) is an object-oriented library of tools written in C++ designed explicitly to enable Bayesian update and model comparison for astronomical problems. To facilitate "what if" exploration, BIE provides a command line interface (written with Bison and Flex) to run input scripts. The output of the code is a simulation of the Bayesian posterior distribution from which summary statistics e.g. by taking moments, or determine confidence intervals and so forth, can be determined. All of these quantities are fundamentally integrals and the Markov Chain approach produces variates heta distributed according to P( heta|D) so moments are trivially obtained by summing of the ensemble of variates.

  2. Molecular phylogeny of oligotrich genera Omegastrombidium and Novistrombidium (Protozoa, Ciliophora) for the systematical relationships within Family Strombidiidae

    NASA Astrophysics Data System (ADS)

    Zhang, Qianqian; Yi, Zhenzhen; Xu, Dapeng; Al-Rasheid, Khaled A. S.; Gong, Jun; Song, Weibo

    2010-07-01

    The phylogeny of the oligotrich ciliates is currently a hot debate despite the availability of both morphological and molecular data. In the present paper, further small subunit rRNA (SS rRNA) genes were analyzed from the Genera Omegastrombidium and Novistrombidium, as well as from Strombidium, and combined with three new SS rRNA sequences from Strombidium basimorphum, S. sulcatum population QD-1, and Novistrombidium testaceum population GD. The phylogenetic positions of these organisms were inferred using Bayesian inference, Maximum Likelihood, and Maximum Parsimony methods. The main results are: (1) the SS rRNA gene sequence analyses match the recent findings about the molecular evolution of oligotrichs, indicating that the family Strombidiidae is paraphyletic; (2) the Genus Omegastrombidium is separated from the Genus Strombidium, as shown in recent cladistic analyses; (3) morphospecies in Genus Novistrombidium, based on similarity of somatic ciliature, are separated from each other in all topological trees, indicating that this genus could be a paraphyletic group; (4) the molecular data indicate a possibility of paraphyly for the genus Strombidium; and (5) the similarities of the SS rRNA gene of specimens identified as S. sulcatum and S. inclinatum are 99.8%-100%. However, present knowledge on the oligotrichs sensu stricto is still insufficient and further studies based on both molecular and other technologies are required.

  3. New and already known acanthocephalans mostly from mammals in Vietnam, with descriptions of two new genera and species in Archiacanthocephala.

    PubMed

    Amin, Omar M; Ha, Ngyuen Van; Heckmann, Richard A

    2008-02-01

    Adults of 2 new species and 2 new genera of acanthocephalans in class Archiacanthocephala, collected between 1998 and 2004 in Vietnam from the intestines of mammals, are described, i.e., Cucullanorhynchus constrictruncatus n. gen., n. sp. (Oligacanthorhynchidae) from a leopard Panthera pardus (Linnaeus) (Mammalia: Felidae) and Paraprosthenorchis ornatus n. gen. n. sp. (Oligacanthorhynchidae) from the Chinese pangolin Manis pentadactyla (Linnaeus) (Mammalia: Manidae). Adult Sphaerechinorhynchus macropisthospinus Amin, Wongsawad, Marayong, Saehoong, Suwattanacoupt, and Sey, 1998 (Plagiorhynchidae) are described for the first time from 2 females collected from a tiger Panthera tigris (Linnaeus) (Mammalia: Felidae) and from 1 male from a water monitor Varanus salvator Laurenti (Reptilia: Varanidae). Characteristic features distinguishing the new species or genera from related taxa are as follows. The trunk of C. constrictruncatus has an anterior hood in both sexes and a posterior constriction in females. The anterior trunk of P. ornatus has many small festoons and proboscis hooks are inserted in elevated papillae separated by beady, near hexagonal, ornate grids.

  4. Bayes factors and multimodel inference

    USGS Publications Warehouse

    Link, W.A.; Barker, R.J.; Thomson, David L.; Cooch, Evan G.; Conroy, Michael J.

    2009-01-01

    Multimodel inference has two main themes: model selection, and model averaging. Model averaging is a means of making inference conditional on a model set, rather than on a selected model, allowing formal recognition of the uncertainty associated with model choice. The Bayesian paradigm provides a natural framework for model averaging, and provides a context for evaluation of the commonly used AIC weights. We review Bayesian multimodel inference, noting the importance of Bayes factors. Noting the sensitivity of Bayes factors to the choice of priors on parameters, we define and propose nonpreferential priors as offering a reasonable standard for objective multimodel inference.

  5. Mahseers genera Tor and Neolissochilus (Teleostei: Cyprinidae) from southern Vietnam.

    PubMed

    Hoàng, Huy Đức; Phạm, Hùng Mạnh; Durand, Jean-Dominique; Trần, Ngân Trọng; Phan, Phúc Đình

    2015-08-25

    Two new species and two new basin records of mahseers in the genera Tor and Neolissochilus are described from the upper Krong No and middle Đồng Nai drainages of the Langbiang Plateau in southern Vietnam. These new species and new records are known from streams and rivers in montane mixed pine and evergreen forests between 140 and 1112 m. Their populations are isolated in the Sre Pok River of the Mekong basin, the middle of the Đồng Nai basin, and the An Lão River. Both new species are differentiated from their congeners by a combination of the following characters: 23-24 lateral scales, 9-10 predorsal scales, 2/7 or 1/8 pelvic-fin rays, mouth position, median lobe of lower lip, rostral hood, colour in life and by divergent mitochondrial DNA. Tor mekongensis sp. nov. is differentiated from Tor dongnaiensis sp. nov. by the number of transverse scale rows (3/1/2 vs. 4/1/2), number of pelvic-fin rays (2/7 vs. 1/8), a blunt rostral hood vs. pointed, caudal-fin lobes that are equal vs. unequal, and by mitochondrial DNA (0.7% sequence divergence). Molecular evidence identifies both species as members of the genus Tor and distinct from all congeners sampled (uncorrected sequence divergences >1.9% for all Tor species for which homologous COI sequences are available). Tor sinensis is recorded in the Krong No and the Sre Pok rivers, further south of its known distribution. Polymorphism is described in Neolissochilus stracheyi with a Tor-like morph and a Neolissochilus-like morph.

  6. Phylogenetic and morphotaxonomic revision of Ramichloridium and allied genera

    PubMed Central

    Arzanlou, M.; Groenewald, J.Z.; Gams, W.; Braun, U.; Shin, H.-D; Crous, P.W.

    2007-01-01

    The phylogeny of the genera Periconiella, Ramichloridium, Rhinocladiella and Veronaea was explored by means of partial sequences of the 28S (LSU) rRNA gene and the ITS region (ITS1, 5.8S rDNA and ITS2). Based on the LSU sequence data, ramichloridium-like species segregate into eight distinct clusters. These include the Capnodiales (Mycosphaerellaceae and Teratosphaeriaceae), the Chaetothyriales (Herpotrichiellaceae), the Pleosporales, and five ascomycete clades with uncertain affinities. The type species of Ramichloridium, R. apiculatum, together with R. musae, R. biverticillatum, R. cerophilum, R. verrucosum, R. pini, and three new species isolated from Strelitzia, Musa and forest soil, respectively, reside in the Capnodiales clade. The human-pathogenic species R. mackenziei and R. basitonum, together with R. fasciculatum and R. anceps, cluster with Rhinocladiella (type species: Rh. atrovirens, Herpotrichiellaceae, Chaetothyriales), and are allocated to this genus. Veronaea botryosa, the type species of the genus Veronaea, also resides in the Chaetothyriales clade, whereas Veronaea simplex clusters as a sister taxon to the Venturiaceae (Pleosporales), and is placed in a new genus, Veronaeopsis. Ramichloridium obovoideum clusters with Carpoligna pleurothecii (anamorph: Pleurothecium sp., Chaetosphaeriales), and a new combination is proposed in Pleurothecium. Other ramichloridium-like clades include R. subulatum and R. epichloës (incertae sedis, Sordariomycetes), for which a new genus, Radulidium is erected. Ramichloridium schulzeri and its varieties are placed in a new genus, Myrmecridium (incertae sedis, Sordariomycetes). The genus Pseudovirgaria (incertae sedis) is introduced to accommodate ramichloridium-like isolates occurring on various species of rust fungi. A veronaea-like isolate from Bertia moriformis with phylogenetic affinity to the Annulatascaceae (Sordariomycetidae) is placed in a new genus, Rhodoveronaea. Besides Ramichloridium, Periconiella is also

  7. Phylogenetic and morphotaxonomic revision of Ramichloridium and allied genera.

    PubMed

    Arzanlou, M; Groenewald, J Z; Gams, W; Braun, U; Shin, H-D; Crous, P W

    2007-01-01

    The phylogeny of the genera Periconiella, Ramichloridium, Rhinocladiella and Veronaea was explored by means of partial sequences of the 28S (LSU) rRNA gene and the ITS region (ITS1, 5.8S rDNA and ITS2). Based on the LSU sequence data, ramichloridium-like species segregate into eight distinct clusters. These include the Capnodiales (Mycosphaerellaceae and Teratosphaeriaceae), the Chaetothyriales (Herpotrichiellaceae), the Pleosporales, and five ascomycete clades with uncertain affinities. The type species of Ramichloridium, R. apiculatum, together with R. musae, R. biverticillatum, R. cerophilum, R. verrucosum, R. pini, and three new species isolated from Strelitzia, Musa and forest soil, respectively, reside in the Capnodiales clade. The human-pathogenic species R. mackenziei and R. basitonum, together with R. fasciculatum and R. anceps, cluster with Rhinocladiella (type species: Rh. atrovirens, Herpotrichiellaceae, Chaetothyriales), and are allocated to this genus. Veronaea botryosa, the type species of the genus Veronaea, also resides in the Chaetothyriales clade, whereas Veronaea simplex clusters as a sister taxon to the Venturiaceae (Pleosporales), and is placed in a new genus, Veronaeopsis. Ramichloridium obovoideum clusters with Carpoligna pleurothecii (anamorph: Pleurothecium sp., Chaetosphaeriales), and a new combination is proposed in Pleurothecium. Other ramichloridium-like clades include R. subulatum and R. epichloës (incertae sedis, Sordariomycetes), for which a new genus, Radulidium is erected. Ramichloridium schulzeri and its varieties are placed in a new genus, Myrmecridium (incertae sedis, Sordariomycetes). The genus Pseudovirgaria (incertae sedis) is introduced to accommodate ramichloridium-like isolates occurring on various species of rust fungi. A veronaea-like isolate from Bertia moriformis with phylogenetic affinity to the Annulatascaceae (Sordariomycetidae) is placed in a new genus, Rhodoveronaea. Besides Ramichloridium, Periconiella is also

  8. A phylogenetic and biogeographic analysis of the genera of Spirorchinae (Digenea: Spirorchidae) parasitic in freshwater turtles.

    PubMed

    Platt, T R

    1992-08-01

    Cladistic analysis of the freshwater genera of Spirorchinae (Schistosomatoidea: Spirorchidae sensu Yamaguti, 1971) plus Haematotrema Stunkard, 1923, and Aphanospirorchis Platt, 1990, was completed. The Spirorchinae were considered monophyletic based on synapomorphies of the esophagus. Three lineages, Spirhapalum (Europe/Asia), Plasmiorchis+Hemiorchis (India), and Spirorchis + Henotosoma + Haematotrema + Aphanospirorchis (North America), were identified. Nelsen consensus analysis was used as the basis for recognizing 3 valid monophyletic genera: Spirhapalum, Plasmiorchis, and Spirorchis. Hapalotrematinae sensu Smith, 1972 (e.g., Hapalorhynchus/Coeuritrema), is considered the most plesiomorphic group of spirorchids. Freshwater representatives of the hapalotrematines have been reported from 7 of 12 extant turtle families, including the relatively primitive Pelomedusidae (Pleurodira) and exhibit a worldwide distribution. It is hypothesized that this group arose in the early Triassic period, prior to the breakup of Pangea. Thus, it represents a primitive lineage that was present during the diversification of turtle lineages in the mid-Mesozoic era. Spirorchinae arose later (late Cretaceous period) as a Laurasian component parasitic in the more recent pond turtles (Emydidae + Bataguridae). Species of Spirhapalum retained a relatively plesiomorphic distribution, and they are found in emydids (Europe) and batagurids (Asia). Species of Spirorchis arose and diversified with North America emydids following the separation of North America and Europe in the late Cretaceous or early Tertiary periods. Species of Plasmiorchis are hypothesized to be derived from Asian ancestors that accompanied the colonization of India by Asian batagurids during the early Tertiary period. The presence of Spirorchis species in snapping turtles (Chelydridae/North America) and of Plasmiorchis species in Indian soft-shelled turtle (Trionychidae) are considered independent colonization events. PMID

  9. A phylogenetic and biogeographic analysis of the genera of Spirorchinae (Digenea: Spirorchidae) parasitic in freshwater turtles.

    PubMed

    Platt, T R

    1992-08-01

    Cladistic analysis of the freshwater genera of Spirorchinae (Schistosomatoidea: Spirorchidae sensu Yamaguti, 1971) plus Haematotrema Stunkard, 1923, and Aphanospirorchis Platt, 1990, was completed. The Spirorchinae were considered monophyletic based on synapomorphies of the esophagus. Three lineages, Spirhapalum (Europe/Asia), Plasmiorchis+Hemiorchis (India), and Spirorchis + Henotosoma + Haematotrema + Aphanospirorchis (North America), were identified. Nelsen consensus analysis was used as the basis for recognizing 3 valid monophyletic genera: Spirhapalum, Plasmiorchis, and Spirorchis. Hapalotrematinae sensu Smith, 1972 (e.g., Hapalorhynchus/Coeuritrema), is considered the most plesiomorphic group of spirorchids. Freshwater representatives of the hapalotrematines have been reported from 7 of 12 extant turtle families, including the relatively primitive Pelomedusidae (Pleurodira) and exhibit a worldwide distribution. It is hypothesized that this group arose in the early Triassic period, prior to the breakup of Pangea. Thus, it represents a primitive lineage that was present during the diversification of turtle lineages in the mid-Mesozoic era. Spirorchinae arose later (late Cretaceous period) as a Laurasian component parasitic in the more recent pond turtles (Emydidae + Bataguridae). Species of Spirhapalum retained a relatively plesiomorphic distribution, and they are found in emydids (Europe) and batagurids (Asia). Species of Spirorchis arose and diversified with North America emydids following the separation of North America and Europe in the late Cretaceous or early Tertiary periods. Species of Plasmiorchis are hypothesized to be derived from Asian ancestors that accompanied the colonization of India by Asian batagurids during the early Tertiary period. The presence of Spirorchis species in snapping turtles (Chelydridae/North America) and of Plasmiorchis species in Indian soft-shelled turtle (Trionychidae) are considered independent colonization events.

  10. Transdimensional inference in the geosciences.

    PubMed

    Sambridge, M; Bodin, T; Gallagher, K; Tkalcic, H

    2013-02-13

    Seismologists construct images of the Earth's interior structure using observations, derived from seismograms, collected at the surface. A common approach to such inverse problems is to build a single 'best' Earth model, in some sense. This is despite the fact that the observations by themselves often do not require, or even allow, a single best-fit Earth model to exist. Interpretation of optimal models can be fraught with difficulties, particularly when formal uncertainty estimates become heavily dependent on the regularization imposed. Similar issues occur across the physical sciences with model construction in ill-posed problems. An alternative approach is to embrace the non-uniqueness directly and employ an inference process based on parameter space sampling. Instead of seeking a best model within an optimization framework, one seeks an ensemble of solutions and derives properties of that ensemble for inspection. While this idea has itself been employed for more than 30 years, it is now receiving increasing attention in the geosciences. Recently, it has been shown that transdimensional and hierarchical sampling methods have some considerable benefits for problems involving multiple parameter types, uncertain data errors and/or uncertain model parametrizations, as are common in seismology. Rather than being forced to make decisions on parametrization, the level of data noise and the weights between data types in advance, as is often the case in an optimization framework, the choice can be informed by the data themselves. Despite the relatively high computational burden involved, the number of areas where sampling methods are now feasible is growing rapidly. The intention of this article is to introduce concepts of transdimensional inference to a general readership and illustrate with particular seismological examples. A growing body of references provide necessary detail. PMID:23277604

  11. Declarative memory, awareness, and transitive inference.

    PubMed

    Smith, Christine; Squire, Larry R

    2005-11-01

    A characteristic usually attributed to declarative memory is that what is learned is accessible to awareness. Recently, the relationship between awareness and declarative (hippocampus-dependent) memory has been questioned on the basis of findings from transitive inference tasks. In transitive inference, participants are first trained on overlapping pairs of items (e.g., A+B-, B+C-, C+D-, and D+E-, where + and - indicate correct and incorrect choices). Later, participants who choose B over D when presented with the novel pair BD are said to demonstrate transitive inference. The ability to exhibit transitive inference is thought to depend on the fact that participants have represented the stimulus elements hierarchically (i.e., A>B>C>D>E). We found that performance on five-item and six-item transitive inference tasks was closely related to awareness of the hierarchical relationship among the elements of the training pairs. Participants who were aware of the hierarchy performed near 100% correct on all tests of transitivity, but participants who were unaware of the hierarchy performed poorly (e.g., on transitive pair BD in the five-item problem; on transitive pairs BD, BE, and CE in the six-item problem). When the five-item task was administered to memory-impaired patients with damage thought to be limited to the hippocampal region, the patients were impaired at learning the training pairs. All patients were unaware of the hierarchy and, like unaware controls, performed poorly on the BD pair. The findings indicate that awareness is critical for robust performance on tests of transitive inference and support the view that awareness of what is learned is a fundamental characteristic of declarative memory.

  12. NEW RECORDS AND RANGE EXTENSIONS FOR SEVERAL CHIRONOMID GENERA IN LAKE SUPERIOR

    EPA Science Inventory

    Recent USEPA investigations of Lake Superior benthos in Minnesota, Wisconsin, and Michigan waters have resulted in the discovery of six uncommon genera of Chironomidae. Five new records of genera for Lake Superior and five significant Nearctic range extensions are reported. New r...

  13. Evidence of Possible Evolutionary Divergence in Plant Genera Based on Antioxidant Properties

    ERIC Educational Resources Information Center

    Asai, Elizabeth; Cao, Sharon

    2009-01-01

    The purpose of this investigation was to determine if three Western species of the Panax, Lycium, and Astragalus genera had antibacterial and/or antioxidant properties, and how their properties compared to Eastern herbs in the same genera. The group hypothesized that when compared, the corresponding herbs would have identical antibacterial and…

  14. New genera, species and host plant records of Nearctic and Neotropical Tephritidae (Diptera)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three new genera and 5 new species of Tephritidae (Diptera) are described from the Nearctic and Neotropical Regions. The new genera are: Agallamyia Norrbom (type species: A. pendula Norrbom, n. sp.), Neosphaeniscus Norrbom (type species: Euribia m-nigrum Hendel), and Phacelochaeta Norrbom (type spec...

  15. Keys to the Common Genera of Marine Plants Taken Aboard the Orange County Floating Marine Laboratory.

    ERIC Educational Resources Information Center

    Williams, H. R.

    Provided is a dichotomous key to the common genera of marine algae and angiosperms which are taken aboard the Orange County Floating Marine Laboratory. It is designed primarily for use by junior and senior high school students. Drawings of representative members of the various genera are included. This work was prepared under an ESEA Title III…

  16. Learning to Observe "and" Infer

    ERIC Educational Resources Information Center

    Hanuscin, Deborah L.; Park Rogers, Meredith A.

    2008-01-01

    Researchers describe the need for students to have multiple opportunities and social interaction to learn about the differences between observation and inference and their role in developing scientific explanations (Harlen 2001; Simpson 2000). Helping children develop their skills of observation and inference in science while emphasizing the…

  17. Feature Inference Learning and Eyetracking

    ERIC Educational Resources Information Center

    Rehder, Bob; Colner, Robert M.; Hoffman, Aaron B.

    2009-01-01

    Besides traditional supervised classification learning, people can learn categories by inferring the missing features of category members. It has been proposed that feature inference learning promotes learning a category's internal structure (e.g., its typical features and interfeature correlations) whereas classification promotes the learning of…

  18. Improving Inferences from Multiple Methods.

    ERIC Educational Resources Information Center

    Shotland, R. Lance; Mark, Melvin M.

    1987-01-01

    Multiple evaluation methods (MEMs) can cause an inferential challenge, although there are strategies to strengthen inferences. Practical and theoretical issues involved in the use by social scientists of MEMs, three potential problems in drawing inferences from MEMs, and short- and long-term strategies for alleviating these problems are outlined.…

  19. Causal Inference in Retrospective Studies.

    ERIC Educational Resources Information Center

    Holland, Paul W.; Rubin, Donald B.

    1988-01-01

    The problem of drawing causal inferences from retrospective case-controlled studies is considered. A model for causal inference in prospective studies is applied to retrospective studies. Limitations of case-controlled studies are formulated concerning relevant parameters that can be estimated in such studies. A coffee-drinking/myocardial…

  20. Causal Inference and Developmental Psychology

    ERIC Educational Resources Information Center

    Foster, E. Michael

    2010-01-01

    Causal inference is of central importance to developmental psychology. Many key questions in the field revolve around improving the lives of children and their families. These include identifying risk factors that if manipulated in some way would foster child development. Such a task inherently involves causal inference: One wants to know whether…

  1. Home at last: the enigmatic genera Eriachaenium and Adenocaulon (Compositae, Mutisioideae, Mutisieae, Adenocaulinae)

    PubMed Central

    Funk, Vicki A.; Pasini, Eduardo; Bonifacino, J. Mauricio; Katinas, Liliana

    2016-01-01

    Abstract The genera Eriachaenium and Adenocaulon (Compositae) have distinct but complex histories and both have been placed in a number of tribes across the family. For the first time the two genera are included in a molecular study and the results show that they are best placed in the tribe Mutisieae s.s. and are the only genera in the re-instated subtribe Adenocaulinae. When described, this subtribe contained only Adenocaulon and was found in the Inuleae. The study also confirms one of the conclusions of a recent morphological study that Eriachaenium and Adenocaulon are sister taxa. Past difficulties in tribal assignment are attributed to the distinct and unusual morphology of each genus. Both genera and the subtribe are described and a key to separate the genera is provided. PMID:27081341

  2. Discrimination of lichen genera and species using element concentrations

    USGS Publications Warehouse

    Bennett, J.P.

    2008-01-01

    The importance of organic chemistry in the classification of lichens is well established, but inorganic chemistry has been largely overlooked. Six lichen species were studied over a period of 23 years that were growing in 11 protected areas of the northern Great Lakes ecoregion, which were not greatly influenced by anthropogenic particulates or gaseous air pollutants. The elemental data from these studies were aggregated in order to test the hypothesis that differences among species in tissue element concentrations were large enough to discriminate between taxa faithfully. Concentrations of 16 chemical elements that were found in tissue samples from Cladonia rangiferina, Evernia mesomorpha, Flavopunctelia flaventior, Hypogymnia physodes, Parmelia sulcata, and Punctelia rudecta were analyzed statistically using multivariate discriminant functions and CART analyses, as well as t-tests. Genera and species were clearly separated in element space, and elemental discriminant functions were able to classify 91-100 of the samples correctly into species. At the broadest level, a Zn concentration of 51 ppm in tissues of four of the lichen species effectively discriminated foliose from fruticose species. Similarly, a S concentration of 680 ppm discriminated C. rangiferina and E. mesomorpha, and a Ca concentration of 10 436 ppm discriminated H. physodes from P. sulcata. For the three parmelioid species, a Ca concentration >32 837 ppm discriminated Punctelia rudecta from the other two species, while a Zn concentration of 56 ppm discriminated Parmelia sulcata from F. flaventior. Foliose species also had higher concentrations than did fruticose species of all elements except Na. Elemental signatures for each of the six species were developed using standardized means. Twenty-four mechanisms explaining the differences among species are summarized. Finally, the relationships of four species based on element concentrations, using additive-trees clustering of a Euclidean

  3. Discrimination of lichen genera and species using element concentrations

    USGS Publications Warehouse

    Bennett, James P.

    2008-01-01

    The importance of organic chemistry in the classification of lichens is well established, but inorganic chemistry has been largely overlooked. Six lichen species were studied over a period of 23 years that were growing in 11 protected areas of the northern Great Lakes ecoregion, which were not greatly influenced by anthropogenic particulates or gaseous air pollutants. The elemental data from these studies were aggregated in order to test the hypothesis that differences among species in tissue element concentrations were large enough to discriminate between taxa faithfully. Concentrations of 16 chemical elements that were found in tissue samples from Cladonia rangiferina, Evernia mesomorpha, Flavopunctelia flaventior, Hypogymnia physodes, Parmelia sulcata, and Punctelia rudecta were analyzed statistically using multivariate discriminant functions and CART analyses, as well as t-tests. Genera and species were clearly separated in element space, and elemental discriminant functions were able to classify 91-100 of the samples correctly into species. At the broadest level, a Zn concentration of 51 ppm in tissues of four of the lichen species effectively discriminated foliose from fruticose species. Similarly, a S concentration of 680 ppm discriminated C. rangiferina and E. mesomorpha, and a Ca concentration of 10 436 ppm discriminated H. physodes from P. sulcata. For the three parmelioid species, a Ca concentration >32 837 ppm discriminated Punctelia rudecta from the other two species, while a Zn concentration of 56 ppm discriminated Parmelia sulcata from F. flaventior. Foliose species also had higher concentrations than did fruticose species of all elements except Na. Elemental signatures for each of the six species were developed using standardized means. Twenty-four mechanisms explaining the differences among species are summarized. Finally, the relationships of four species based on element concentrations, using additive-trees clustering of a Euclidean

  4. Genetic Diversity and Host Specificity Varies across Three Genera of Blood Parasites in Ducks of the Pacific Americas Flyway

    PubMed Central

    Reeves, Andrew B.; Smith, Mathew M.; Meixell, Brandt W.; Fleskes, Joseph P; Ramey, Andrew M.

    2015-01-01

    Birds of the order Anseriformes, commonly referred to as waterfowl, are frequently infected by Haemosporidia of the genera Haemoproteus, Plasmodium, and Leucocytozoon via dipteran vectors. We analyzed nucleotide sequences of the Cytochrome b (Cytb) gene from parasites of these genera detected in six species of ducks from Alaska and California, USA to characterize the genetic diversity of Haemosporidia infecting waterfowl at two ends of the Pacific Americas Flyway. In addition, parasite Cytb sequences were compared to those available on a public database to investigate specificity of genetic lineages to hosts of the order Anseriformes. Haplotype and nucleotide diversity of Haemoproteus Cytb sequences was lower than was detected for Plasmodium and Leucocytozoon parasites. Although waterfowl are presumed to be infected by only a single species of Leucocytozoon, L. simondi, diversity indices were highest for haplotypes from this genus and sequences formed five distinct clades separated by genetic distances of 4.9%–7.6%, suggesting potential cryptic speciation. All Haemoproteus and Leucocytozoon haplotypes derived from waterfowl samples formed monophyletic clades in phylogenetic analyses and were unique to the order Anseriformes with few exceptions. In contrast, waterfowl-origin Plasmodium haplotypes were identical or closely related to lineages found in other avian orders. Our results suggest a more generalist strategy for Plasmodium parasites infecting North American waterfowl as compared to those of the genera Haemoproteus and Leucocytozoon. PMID:25710468

  5. Genetic diversity and host specificity varies across three genera of blood parasites in ducks of the Pacific Americas Flyway

    USGS Publications Warehouse

    Reeves, Andrew B.; Smith, Matthew M.; Meixell, Brandt W.; Fleskes, Joseph P.; Ramey, Andrew M.

    2015-01-01

    Birds of the order Anseriformes, commonly referred to as waterfowl, are frequently infected by Haemosporidia of the genera Haemoproteus, Plasmodium, and Leucocytozoon via dipteran vectors. We analyzed nucleotide sequences of the Cytochrome b (Cytb) gene from parasites of these genera detected in six species of ducks from Alaska and California, USA to characterize the genetic diversity of Haemosporidia infecting waterfowl at two ends of the Pacific Americas Flyway. In addition, parasite Cytb sequences were compared to those available on a public database to investigate specificity of genetic lineages to hosts of the order Anseriformes. Haplotype and nucleotide diversity of Haemoproteus Cytb sequences was lower than was detected for Plasmodium and Leucocytozoon parasites. Although waterfowl are presumed to be infected by only a single species of Leucocytozoon, L. simondi, diversity indices were highest for haplotypes from this genus and sequences formed five distinct clades separated by genetic distances of 4.9%–7.6%, suggesting potential cryptic speciation. All Haemoproteus andLeucocytozoon haplotypes derived from waterfowl samples formed monophyletic clades in phylogenetic analyses and were unique to the order Anseriformes with few exceptions. In contrast, waterfowl-origin Plasmodium haplotypes were identical or closely related to lineages found in other avian orders. Our results suggest a more generalist strategy for Plasmodiumparasites infecting North American waterfowl as compared to those of the generaHaemoproteus and Leucocytozoon.

  6. Observations on the biology of Afrotropical Hesperiidae (Lepidoptera). Part 9. Hesperiinae incertae sedis: Zingiberales feeders, genera of unknown biology and an overview of the Hesperiinae incertae sedis.

    PubMed

    Cock, Matthew J W; Congdon, T Colin E; Collins, Steve C

    2016-01-01

    The Afrotropical genera that have been recorded to feed on Zingiberales are documented. Partial life histories are presented for Erionota torus Evans (a South-East Asian species established in Mauritius), Semalea arela (Mabille), S. pulvina (Plötz), Xanthodisca vibius (Hewitson), X. rega (Mabille), Hypoleucis ophiusa (Hewitson), Caenides dacena (Hewitson), Osmodes adon (Mabille), Gretna cylinda (Hewitson) and Moltena fiara (Butler). Additional notes from the literature are provided on the genera Leona and Rhabdomantis. Notes on natural enemies of E. torus and M. fiara are included. We find that the Zingiberaceae and Costaceae feeding genera, Semalea, Xanthodiscus, Hypoleucis and Caenides (part) are united by a C-shaped raised rim to the prothoracic spiracle of the pupa. The pupa of Osmodes adon indicates this genus may have no close affinities to other Afrotropical genera for which the life history is known. The pupa of G. cylinda is unlike any other that we have documented and may reflect that this is the only species which we have found to be formed on the open leaf under surface rather than in a shelter. The early stages of M. fiara indicate affinities with Zophopetes and related genera. The paper concludes with a brief comparative discussion of the early stages of the Afrotropical Hesperiinae incertae sedis as a whole. There appear to be useful characters to group species by the ova and pupae but less so by the caterpillars. Based on pupae alone, the Hesperiinae incertae sedis might be divided into nine groups. PMID:27395548

  7. Multigene Molecular Phylogeny and Biogeographic Diversification of the Earth Tongue Fungi in the Genera Cudonia and Spathularia (Rhytismatales, Ascomycota)

    PubMed Central

    Ge, Zai-Wei; Yang, Zhu L.; Pfister, Donald H.; Carbone, Matteo; Bau, Tolgor; Smith, Matthew E.

    2014-01-01

    The family Cudoniaceae (Rhytismatales, Ascomycota) was erected to accommodate the “earth tongue fungi” in the genera Cudonia and Spathularia. There have been no recent taxonomic studies of these genera, and the evolutionary relationships within and among these fungi are largely unknown. Here we explore the molecular phylogenetic relationships within Cudonia and Spathularia using maximum likelihood and Bayesian inference analyses based on 111 collections from across the Northern Hemisphere. Phylogenies based on the combined data from ITS, nrLSU, rpb2 and tef-1α sequences support the monophyly of three main clades, the /flavida, /velutipes, and /cudonia clades. The genus Cudonia and the family Cudoniaceae are supported as monophyletic groups, while the genus Spathularia is not monophyletic. Although Cudoniaceae is monophyletic, our analyses agree with previous studies that this family is nested within the Rhytismataceae. Our phylogenetic analyses circumscribes 32 species-level clades, including the putative recognition of 23 undescribed phylogenetic species. Our molecular phylogeny also revealed an unexpectedly high species diversity of Cudonia and Spathularia in eastern Asia, with 16 (out of 21) species-level clades of Cudonia and 8 (out of 11) species-level clades of Spathularia. We estimate that the divergence time of the Cudoniaceae was in the Paleogene approximately 28 Million years ago (Mya) and that the ancestral area for this group of fungi was in Eastern Asia based on the current data. We hypothesize that the large-scale geological and climatic events in Oligocene (e.g. the global cooling and the uplift of the Tibetan plateau) may have triggered evolutionary radiations in this group of fungi in East Asia. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of Cudonia and Spathularia and highlights the need for more molecular studies on collections from Europe and North America. PMID:25084276

  8. Phylogenomics and Divergence Dating of Fungus-Farming Ants (Hymenoptera: Formicidae) of the Genera Sericomyrmex and Apterostigma

    PubMed Central

    Ješovnik, Ana; González, Vanessa L.; Schultz, Ted R.

    2016-01-01

    Fungus-farming ("attine") ants are model systems for studies of symbiosis, coevolution, and advanced eusociality. A New World clade of nearly 300 species in 15 genera, all attine ants cultivate fungal symbionts for food. In order to better understand the evolution of ant agriculture, we sequenced, assembled, and analyzed transcriptomes of four different attine ant species in two genera: three species in the higher-attine genus Sericomyrmex and a single lower-attine ant species, Apterostigma megacephala, representing the first genomic data for either genus. These data were combined with published genomes of nine other ant species and the honey bee Apis mellifera for phylogenomic and divergence-dating analyses. The resulting phylogeny confirms relationships inferred in previous studies of fungus-farming ants. Divergence-dating analyses recovered slightly older dates than most prior analyses, estimating that attine ants originated 53.6–66.7 million of years ago, and recovered a very long branch subtending a very recent, rapid radiation of the genus Sericomyrmex. This result is further confirmed by a separate analysis of the three Sericomyrmex species, which reveals that 92.71% of orthologs have 99% - 100% pairwise-identical nucleotide sequences. We searched the transcriptomes for genes of interest, most importantly argininosuccinate synthase and argininosuccinate lyase, which are functional in other ants but which are known to have been lost in seven previously studied attine ant species. Loss of the ability to produce the amino acid arginine has been hypothesized to contribute to the obligate dependence of attine ants upon their cultivated fungi, but the point in fungus-farming ant evolution at which these losses occurred has remained unknown. We did not find these genes in any of the sequenced transcriptomes. Although expected for Sericomyrmex species, the absence of arginine anabolic genes in the lower-attine ant Apterostigma megacephala strongly suggests that

  9. Phylogenomics and Divergence Dating of Fungus-Farming Ants (Hymenoptera: Formicidae) of the Genera Sericomyrmex and Apterostigma.

    PubMed

    Ješovnik, Ana; González, Vanessa L; Schultz, Ted R

    2016-01-01

    Fungus-farming ("attine") ants are model systems for studies of symbiosis, coevolution, and advanced eusociality. A New World clade of nearly 300 species in 15 genera, all attine ants cultivate fungal symbionts for food. In order to better understand the evolution of ant agriculture, we sequenced, assembled, and analyzed transcriptomes of four different attine ant species in two genera: three species in the higher-attine genus Sericomyrmex and a single lower-attine ant species, Apterostigma megacephala, representing the first genomic data for either genus. These data were combined with published genomes of nine other ant species and the honey bee Apis mellifera for phylogenomic and divergence-dating analyses. The resulting phylogeny confirms relationships inferred in previous studies of fungus-farming ants. Divergence-dating analyses recovered slightly older dates than most prior analyses, estimating that attine ants originated 53.6-66.7 million of years ago, and recovered a very long branch subtending a very recent, rapid radiation of the genus Sericomyrmex. This result is further confirmed by a separate analysis of the three Sericomyrmex species, which reveals that 92.71% of orthologs have 99% - 100% pairwise-identical nucleotide sequences. We searched the transcriptomes for genes of interest, most importantly argininosuccinate synthase and argininosuccinate lyase, which are functional in other ants but which are known to have been lost in seven previously studied attine ant species. Loss of the ability to produce the amino acid arginine has been hypothesized to contribute to the obligate dependence of attine ants upon their cultivated fungi, but the point in fungus-farming ant evolution at which these losses occurred has remained unknown. We did not find these genes in any of the sequenced transcriptomes. Although expected for Sericomyrmex species, the absence of arginine anabolic genes in the lower-attine ant Apterostigma megacephala strongly suggests that the

  10. Evolutionary inference via the Poisson Indel Process.

    PubMed

    Bouchard-Côté, Alexandre; Jordan, Michael I

    2013-01-22

    We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114-124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments.

  11. Model averaging, optimal inference, and habit formation

    PubMed Central

    FitzGerald, Thomas H. B.; Dolan, Raymond J.; Friston, Karl J.

    2014-01-01

    Postulating that the brain performs approximate Bayesian inference generates principled and empirically testable models of neuronal function—the subject of much current interest in neuroscience and related disciplines. Current formulations address inference and learning under some assumed and particular model. In reality, organisms are often faced with an additional challenge—that of determining which model or models of their environment are the best for guiding behavior. Bayesian model averaging—which says that an agent should weight the predictions of different models according to their evidence—provides a principled way to solve this problem. Importantly, because model evidence is determined by both the accuracy and complexity of the model, optimal inference requires that these be traded off against one another. This means an agent's behavior should show an equivalent balance. We hypothesize that Bayesian model averaging plays an important role in cognition, given that it is both optimal and realizable within a plausible neuronal architecture. We outline model averaging and how it might be implemented, and then explore a number of implications for brain and behavior. In particular, we propose that model averaging can explain a number of apparently suboptimal phenomena within the framework of approximate (bounded) Bayesian inference, focusing particularly upon the relationship between goal-directed and habitual behavior. PMID:25018724

  12. The Nearctic genera of Agathidinae (Hymenoptera: Braconidae) with a phylogenetic analysis, illustrated generic key, and the description of three new genera.

    PubMed

    Sharkey, Michael J; Chapman, Eric G

    2015-08-13

    The genera of Nearctic Agathidinae are revised based on a phylogenetic analysis of COI and 28S sequence data; 151 ingroup taxa are included. Three new genera are proposed, i.e., Aphelagathis Sharkey n. gen., Pneumagathis Sharkey n. gen. and Gelastagathis Sharkey n. gen.. The enigmatic species Agathis verticalis Cresson is identified and placed in Aphelagathis, Aphelagathis verticalis (Cresson) n. comb., and a neotype for the species is designated. Two species are described, i.e., Gelastagathis grisselli Sharkey n. sp. and G. frosti Sharkey n. sp. Two new combinations are proposed, Bassus spiracularis Muesebeck and Bassus brooksi Sharkey are transferred to Pneumagathis, Pneumagathis spiracularis (Muesebeck) n. comb., Pneumagathis brooksi (Sharkey) n. comb. An illustrated key to the Nearctic genera of Agathidinae is provided.

  13. Dinoflagellate Phylogeny as Inferred from Heat Shock Protein 90 and Ribosomal Gene Sequences

    PubMed Central

    Hoppenrath, Mona; Leander, Brian S.

    2010-01-01

    Background Interrelationships among dinoflagellates in molecular phylogenies are largely unresolved, especially in the deepest branches. Ribosomal DNA (rDNA) sequences provide phylogenetic signals only at the tips of the dinoflagellate tree. Two reasons for the poor resolution of deep dinoflagellate relationships using rDNA sequences are (1) most sites are relatively conserved and (2) there are different evolutionary rates among sites in different lineages. Therefore, alternative molecular markers are required to address the deeper phylogenetic relationships among dinoflagellates. Preliminary evidence indicates that the heat shock protein 90 gene (Hsp90) will provide an informative marker, mainly because this gene is relatively long and appears to have relatively uniform rates of evolution in different lineages. Methodology/Principal Findings We more than doubled the previous dataset of Hsp90 sequences from dinoflagellates by generating additional sequences from 17 different species, representing seven different orders. In order to concatenate the Hsp90 data with rDNA sequences, we supplemented the Hsp90 sequences with three new SSU rDNA sequences and five new LSU rDNA sequences. The new Hsp90 sequences were generated, in part, from four additional heterotrophic dinoflagellates and the type species for six different genera. Molecular phylogenetic analyses resulted in a paraphyletic assemblage near the base of the dinoflagellate tree consisting of only athecate species. However, Noctiluca was never part of this assemblage and branched in a position that was nested within other lineages of dinokaryotes. The phylogenetic trees inferred from Hsp90 sequences were consistent with trees inferred from rDNA sequences in that the backbone of the dinoflagellate clade was largely unresolved. Conclusions/Significance The sequence conservation in both Hsp90 and rDNA sequences and the poor resolution of the deepest nodes suggests that dinoflagellates reflect an explosive

  14. An emergent approach to analogical inference

    NASA Astrophysics Data System (ADS)

    Thibodeau, Paul H.; Flusberg, Stephen J.; Glick, Jeremy J.; Sternberg, Daniel A.

    2013-03-01

    In recent years, a growing number of researchers have proposed that analogy is a core component of human cognition. According to the dominant theoretical viewpoint, analogical reasoning requires a specific suite of cognitive machinery, including explicitly coded symbolic representations and a mapping or binding mechanism that operates over these representations. Here we offer an alternative approach: we find that analogical inference can emerge naturally and spontaneously from a relatively simple, error-driven learning mechanism without the need to posit any additional analogy-specific machinery. The results also parallel findings from the developmental literature on analogy, demonstrating a shift from an initial reliance on surface feature similarity to the use of relational similarity later in training. Variants of the model allow us to consider and rule out alternative accounts of its performance. We conclude by discussing how these findings can potentially refine our understanding of the processes that are required to perform analogical inference.

  15. Quantum-Like Representation of Non-Bayesian Inference

    NASA Astrophysics Data System (ADS)

    Asano, M.; Basieva, I.; Khrennikov, A.; Ohya, M.; Tanaka, Y.

    2013-01-01

    This research is related to the problem of "irrational decision making or inference" that have been discussed in cognitive psychology. There are some experimental studies, and these statistical data cannot be described by classical probability theory. The process of decision making generating these data cannot be reduced to the classical Bayesian inference. For this problem, a number of quantum-like coginitive models of decision making was proposed. Our previous work represented in a natural way the classical Bayesian inference in the frame work of quantum mechanics. By using this representation, in this paper, we try to discuss the non-Bayesian (irrational) inference that is biased by effects like the quantum interference. Further, we describe "psychological factor" disturbing "rationality" as an "environment" correlating with the "main system" of usual Bayesian inference.

  16. Melanelixia and Melanohalea, two new genera segregated from Melanelia (Parmeliaceae) based on molecular and morphological data.

    PubMed

    Blanco, Oscar; Crespo, Ana; Divakar, Pradeep K; Esslinger, Theodore L; Hawksworth, David L; Lumbsch, H Thorsten

    2004-08-01

    This paper continues a revision of generic concepts in the parmelioid lichens using molecular data in order to reach a consensus among lichenologists over which segregates proposed over the last two decades should be accepted. Here we employ data from three gene portions to provide a basis for a revised generic concept of the brown parmelioid lichens hitherto classified in Melanelia. The phylogeny was studied using a Bayesian analysis of a combined data set of nuclear ITS, LSU rDNA and mitochondrial SSU rDNA sequences. 173 new sequences were obtained from 38 specimens of 15 Melanelia species, 37 related parmelioid species, and eight non-parmelioid species. The results indicate that Melanelia is not monophyletic but falls into four different clades. The genus Melanelia is restricted here to a small group of saxicolous lichens related to the type species M. stygia, and with bifusiform conidia, while the remaining species, most of which are primarily corticolous and have mainly cylindrical to filiform conidia, belong to two other clades recognised as two new genera: Melanelixia and Melanohalea, to accommodate the M. exasperata and M. glabra groups, respectively. 27 new combinations are made. The epicortex of Melanelixia species have pores or special structures termed here 'fenestrations', while most Melanohalea species are pseudocyphellate. Pleurosticta links to the Melanohalea clade but without strong support, and the phylogenetic position of M. disjuncta and its related species remains uncertain, linking with the Xanthoparmelia (syn. Neofuscelia) clade but also without strong support.

  17. Ancestral state reconstruction infers phytopathogenic origins of sooty blotch and flyspeck fungi on apple.

    PubMed

    Ismail, Siti Izera; Batzer, Jean Carlson; Harrington, Thomas C; Crous, Pedro W; Lavrov, Dennis V; Li, Huanyu; Gleason, Mark L

    2016-01-01

    Members of the sooty blotch and flyspeck (SBFS) complex are epiphytic fungi in the Ascomycota that cause economically damaging blemishes of apples worldwide. SBFS fungi are polyphyletic, but approx. 96% of SBFS species are in the Capnodiales. Evolutionary origins of SBFS fungi remain unclear, so we attempted to infer their origins by means of ancestral state reconstruction on a phylogenetic tree built utilizing genes for the nuc 28S rDNA (approx. 830 bp from near the 59 end) and the second largest subunit of RNA polymerase II (RPB2). The analyzed taxa included the well-known genera of SBFS as well as non-SBFS fungi from seven families within the Capnodiales. The non-SBFS taxa were selected based on their distinct ecological niches, including plant-parasitic and saprophytic species. The phylogenetic analyses revealed that most SBFS species in the Capnodiales are closely related to plant-parasitic fungi. Ancestral state reconstruction provided strong evidence that plant-parasitic fungi were the ancestors of the major SBFS lineages. Knowledge gained from this study may help to better understand the ecology and evolution of epiphytic fungi.

  18. Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity.

    PubMed

    Alström, Per; Barnes, Keith N; Olsson, Urban; Barker, F Keith; Bloomer, Paulette; Khan, Aleem Ahmed; Qureshi, Masood Ahmed; Guillaumet, Alban; Crochet, Pierre-André; Ryan, Peter G

    2013-12-01

    The Alaudidae (larks) is a large family of songbirds in the superfamily Sylvioidea. Larks are cosmopolitan, although species-level diversity is by far largest in Africa, followed by Eurasia, whereas Australasia and the New World have only one species each. The present study is the first comprehensive phylogeny of the Alaudidae. It includes 83.5% of all species and representatives from all recognised genera, and was based on two mitochondrial and three nuclear loci (in total 6.4 kbp, although not all loci were available for all species). In addition, a larger sample, comprising several subspecies of some polytypic species was analysed for one of the mitochondrial loci. There was generally good agreement in trees inferred from different loci, although some strongly supported incongruences were noted. The tree based on the concatenated multilocus data was overall well resolved and well supported by the data. We stress the importance of performing single gene as well as combined data analyses, as the latter may obscure significant incongruence behind strong nodal support values. The multilocus tree revealed many unpredicted relationships, including some non-monophyletic genera (Calandrella, Mirafra, Melanocorypha, Spizocorys). The tree based on the extended mitochondrial data set revealed several unexpected deep divergences between taxa presently treated as conspecific (e.g. within Ammomanes cinctura, Ammomanes deserti, Calandrella brachydactyla, Eremophila alpestris), as well as some shallow splits between currently recognised species (e.g. Certhilauda brevirostris-C. semitorquata-C. curvirostris; Calendulauda barlowi-C. erythrochlamys; Mirafra cantillans-M. javanica). Based on our results, we propose a revised generic classification, and comment on some species limits. We also comment on the extraordinary morphological adaptability in larks, which has resulted in numerous examples of parallel evolution (e.g. in Melanocorypha mongolica and Alauda leucoptera [both

  19. Another Look At The Canon of Plausible Inference

    NASA Astrophysics Data System (ADS)

    Solana-Ortega, Alberto; Solana, Vicente

    2005-11-01

    Systematic study of plausible inference is very recent. Axiomatics have been traditionally limited to the development of uninterpreted pure calculi for comparing individual inferences, ignoring the need of formalisms to solve each of these inferences and leaving the interpretation and application of such calculi to ad hoc statistical criteria which are open to inconsistencies. Here we defend a different viewpoint, regarding plausible inference in a holistic manner. Specifically we consider that all tasks involved in it, including the formalization of languages in which to pose problems, the definitions and axiomatics leading to calculation rules and those for deriving inference procedures or assignment rules, ought to be based on common grounds. For this purpose a set of elementary requirements establishing desirable properties so fundamental any theory of scientific inference should satisfy is proposed under the name of plausible inference canon. Its logical status as an extramathematical foundation is investigated, together with the different roles it plays as constructive guideline, standard for contrasting frameworks or normative stipulation. We also highlight the novelties it introduces with respect to similar proposals by other authors. In particular we concentrate on those aspects of the canon related to the critical issue of adequately incorporating basic evidential knowledge to inference.

  20. Causal Inference in Public Health

    PubMed Central

    Glass, Thomas A.; Goodman, Steven N.; Hernán, Miguel A.; Samet, Jonathan M.

    2014-01-01

    Causal inference has a central role in public health; the determination that an association is causal indicates the possibility for intervention. We review and comment on the long-used guidelines for interpreting evidence as supporting a causal association and contrast them with the potential outcomes framework that encourages thinking in terms of causes that are interventions. We argue that in public health this framework is more suitable, providing an estimate of an action’s consequences rather than the less precise notion of a risk factor’s causal effect. A variety of modern statistical methods adopt this approach. When an intervention cannot be specified, causal relations can still exist, but how to intervene to change the outcome will be unclear. In application, the often-complex structure of causal processes needs to be acknowledged and appropriate data collected to study them. These newer approaches need to be brought to bear on the increasingly complex public health challenges of our globalized world. PMID:23297653

  1. Bayesian Inference: with ecological applications

    USGS Publications Warehouse

    Link, William A.; Barker, Richard J.

    2010-01-01

    This text provides a mathematically rigorous yet accessible and engaging introduction to Bayesian inference with relevant examples that will be of interest to biologists working in the fields of ecology, wildlife management and environmental studies as well as students in advanced undergraduate statistics.. This text opens the door to Bayesian inference, taking advantage of modern computational efficiencies and easily accessible software to evaluate complex hierarchical models.

  2. Epilachnini (Coleoptera: Coccinellidae)-A Revision of the World Genera.

    PubMed

    Tomaszewska, Wioletta; Szawaryn, Karol

    2016-01-01

    Based on the recent revised generic classification of the tribe Epilachnini (Szawaryn et al. 2015), all 27 genera are re-described, diagnosed, illustrated, and included in an identification key. The following nomenclatural changes are made: Epilachna (Hypsa) Mulsant 1850, Epilachna (Cleta) Mulsant 1850, Solanophila Weise 1898, Epilachna (Aparodentata) Wang and Cao 1993, and Epilachna (Uniparodentata) Wang and Cao 1993 are removed from synonymy of Epilachna Chervolat 1837. The subgenus Cleta of Epilachna is raised to the genus level, as Cleta Mulsant 1850 stat. nov.; the subgenus Uniparodentata of Epilachna is raised to the genus level, as Uniparodentata Wang and Cao 1993 stat. nov. Chazeauiana Tomaszewska and Szawaryn 2015 (type species, Epilachna sahlbergi Mulsant 1850), and Epilachna (Hypsa) Mulsant 1850 (type species, Epilachna nigrolimbata Thomson 1875) are synonymized here under the name Cleta Mulsant 1850 (type species, Epilachna eckloni Mulsant 1850)-new synonyms; Fuerschia Tomaszewska and Szawaryn 2015 (type species, Coccinella canina Fabricius 1781) is synonymized with Solanophila Weise 1898 (type species, Epilachna gibbosa Crotch 1874)-new synonym; Ryszardia Tomaszewska and Szawaryn 2015 (type species, Epilachna decipiens Crotch 1874) and Epilachna (Aparodentata) Wang and Cao, 1993 (type species, Epilachna yongshanensis Cao and Xiao 1984) are synonymized under the name Uniparodentata Wang and Cao 1993 (type species, Epilachna paramagna Pang and Mao 1979)-new synonyms. Henosepilachna (Elateria) Fürsch 1964 (type species: Coccinella elaterii Rossi 1794) is removed from synomyms of Henosepilachna Li 1961 [type species, Coccinella sparsa Herbst 1786 (=Coccinella vigintioctopunctata Fabricius 1775)] and is synonymized here with Chnootriba Chevrolat 1837 (type species: Coccinella similis Thunberg 1781)-new synonym. Coccinella flavofasciata Laporte 1840, Epilachna aequatorialis Gordon 1975, E. bizonata Crotch 1874, E. convergens Crotch 1874, E. cruciata Mulsant

  3. Epilachnini (Coleoptera: Coccinellidae)-A Revision of the World Genera.

    PubMed

    Tomaszewska, Wioletta; Szawaryn, Karol

    2016-01-01

    Based on the recent revised generic classification of the tribe Epilachnini (Szawaryn et al. 2015), all 27 genera are re-described, diagnosed, illustrated, and included in an identification key. The following nomenclatural changes are made: Epilachna (Hypsa) Mulsant 1850, Epilachna (Cleta) Mulsant 1850, Solanophila Weise 1898, Epilachna (Aparodentata) Wang and Cao 1993, and Epilachna (Uniparodentata) Wang and Cao 1993 are removed from synonymy of Epilachna Chervolat 1837. The subgenus Cleta of Epilachna is raised to the genus level, as Cleta Mulsant 1850 stat. nov.; the subgenus Uniparodentata of Epilachna is raised to the genus level, as Uniparodentata Wang and Cao 1993 stat. nov. Chazeauiana Tomaszewska and Szawaryn 2015 (type species, Epilachna sahlbergi Mulsant 1850), and Epilachna (Hypsa) Mulsant 1850 (type species, Epilachna nigrolimbata Thomson 1875) are synonymized here under the name Cleta Mulsant 1850 (type species, Epilachna eckloni Mulsant 1850)-new synonyms; Fuerschia Tomaszewska and Szawaryn 2015 (type species, Coccinella canina Fabricius 1781) is synonymized with Solanophila Weise 1898 (type species, Epilachna gibbosa Crotch 1874)-new synonym; Ryszardia Tomaszewska and Szawaryn 2015 (type species, Epilachna decipiens Crotch 1874) and Epilachna (Aparodentata) Wang and Cao, 1993 (type species, Epilachna yongshanensis Cao and Xiao 1984) are synonymized under the name Uniparodentata Wang and Cao 1993 (type species, Epilachna paramagna Pang and Mao 1979)-new synonyms. Henosepilachna (Elateria) Fürsch 1964 (type species: Coccinella elaterii Rossi 1794) is removed from synomyms of Henosepilachna Li 1961 [type species, Coccinella sparsa Herbst 1786 (=Coccinella vigintioctopunctata Fabricius 1775)] and is synonymized here with Chnootriba Chevrolat 1837 (type species: Coccinella similis Thunberg 1781)-new synonym. Coccinella flavofasciata Laporte 1840, Epilachna aequatorialis Gordon 1975, E. bizonata Crotch 1874, E. convergens Crotch 1874, E. cruciata Mulsant

  4. Active inference, communication and hermeneutics.

    PubMed

    Friston, Karl J; Frith, Christopher D

    2015-07-01

    Hermeneutics refers to interpretation and translation of text (typically ancient scriptures) but also applies to verbal and non-verbal communication. In a psychological setting it nicely frames the problem of inferring the intended content of a communication. In this paper, we offer a solution to the problem of neural hermeneutics based upon active inference. In active inference, action fulfils predictions about how we will behave (e.g., predicting we will speak). Crucially, these predictions can be used to predict both self and others--during speaking and listening respectively. Active inference mandates the suppression of prediction errors by updating an internal model that generates predictions--both at fast timescales (through perceptual inference) and slower timescales (through perceptual learning). If two agents adopt the same model, then--in principle--they can predict each other and minimise their mutual prediction errors. Heuristically, this ensures they are singing from the same hymn sheet. This paper builds upon recent work on active inference and communication to illustrate perceptual learning using simulated birdsongs. Our focus here is the neural hermeneutics implicit in learning, where communication facilitates long-term changes in generative models that are trying to predict each other. In other words, communication induces perceptual learning and enables others to (literally) change our minds and vice versa.

  5. Active inference, communication and hermeneutics☆

    PubMed Central

    Friston, Karl J.; Frith, Christopher D.

    2015-01-01

    Hermeneutics refers to interpretation and translation of text (typically ancient scriptures) but also applies to verbal and non-verbal communication. In a psychological setting it nicely frames the problem of inferring the intended content of a communication. In this paper, we offer a solution to the problem of neural hermeneutics based upon active inference. In active inference, action fulfils predictions about how we will behave (e.g., predicting we will speak). Crucially, these predictions can be used to predict both self and others – during speaking and listening respectively. Active inference mandates the suppression of prediction errors by updating an internal model that generates predictions – both at fast timescales (through perceptual inference) and slower timescales (through perceptual learning). If two agents adopt the same model, then – in principle – they can predict each other and minimise their mutual prediction errors. Heuristically, this ensures they are singing from the same hymn sheet. This paper builds upon recent work on active inference and communication to illustrate perceptual learning using simulated birdsongs. Our focus here is the neural hermeneutics implicit in learning, where communication facilitates long-term changes in generative models that are trying to predict each other. In other words, communication induces perceptual learning and enables others to (literally) change our minds and vice versa. PMID:25957007

  6. Active inference, communication and hermeneutics.

    PubMed

    Friston, Karl J; Frith, Christopher D

    2015-07-01

    Hermeneutics refers to interpretation and translation of text (typically ancient scriptures) but also applies to verbal and non-verbal communication. In a psychological setting it nicely frames the problem of inferring the intended content of a communication. In this paper, we offer a solution to the problem of neural hermeneutics based upon active inference. In active inference, action fulfils predictions about how we will behave (e.g., predicting we will speak). Crucially, these predictions can be used to predict both self and others--during speaking and listening respectively. Active inference mandates the suppression of prediction errors by updating an internal model that generates predictions--both at fast timescales (through perceptual inference) and slower timescales (through perceptual learning). If two agents adopt the same model, then--in principle--they can predict each other and minimise their mutual prediction errors. Heuristically, this ensures they are singing from the same hymn sheet. This paper builds upon recent work on active inference and communication to illustrate perceptual learning using simulated birdsongs. Our focus here is the neural hermeneutics implicit in learning, where communication facilitates long-term changes in generative models that are trying to predict each other. In other words, communication induces perceptual learning and enables others to (literally) change our minds and vice versa. PMID:25957007

  7. Analogical and Category-Based Inference: A Theoretical Integration with Bayesian Causal Models

    ERIC Educational Resources Information Center

    Holyoak, Keith J.; Lee, Hee Seung; Lu, Hongjing

    2010-01-01

    A fundamental issue for theories of human induction is to specify constraints on potential inferences. For inferences based on shared category membership, an analogy, and/or a relational schema, it appears that the basic goal of induction is to make accurate and goal-relevant inferences that are sensitive to uncertainty. People can use source…

  8. Key to the recognition of normapolles and some morphologically similar pollen genera

    USGS Publications Warehouse

    Batten, D.J.; Christopher, R.A.

    1981-01-01

    A dichotomous key to the recognition of 86 Normapolles and morphologically similar pollen genera is presented. The key is accompanied by line drawings of each genus and an illustrated glossary of descriptive terms. ?? 1981.

  9. New genera and species of leaf beetles (Coleoptera: Chrysomelidae) from China and South Korea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two new genera from China (Taumaceroides Lopatin and Yunnaniata Lopatin) and 11 new species (Smaragdina quadrimaculata Lopatin, Smaragdina oblongum Lopatin, Hyphaenia volkovitshi Lopatin, Arthrotus daliensis Lopatin, Taumaceroides sinicus Lopatin, Yunnaniata konstantinovi Lopatin, Calomicrus yunnanu...

  10. A taxonomic review of the genera of the aphelenchoidea (fuchs, 1937) thorne, 1949 (nematoda: tylenchida).

    PubMed

    Nickle, W R

    1970-10-01

    This generic level taxonomic review of the nematode superfamily Aphelenchoidea is based upon a study of specimens from 24 of the 28 described genera. The diagnoses of these genera are presented, and some are emended with new information. One new genus, Huntaphelenchoides, and five new combinations are proposed. The families Paraphelenchidae and Anomyctidae are placed in synonymy with Aphelenchidae and Aphelenchoididae, respectively. The genera Asteroaphelenchoides and Pseudaphelencboides are placed in synonymy under the genus Aphelenchoides. Rare male and/or female specimens of Peraphelenchus, Anomyctus, Laimaphelenchus, Aphelenchus, Cryptaphelenchoides, Megadorus, Tylaphelenchus, and Entaphelenchus, are redescribed and illustrated. Four plates, containing 106 original drawings of the males, females, stylets, and spicules of representatives of 22 aphelenchoid genera, are presented.

  11. A Taxonomic Review of the Genera of the Aphelenchoidea (Fuchs, 1937) Thorne, 1949 (Nematoda: Tylenchida)

    PubMed Central

    Nickle, W. R.

    1970-01-01

    This generic level taxonomic review of the nematode superfamily Aphelenchoidea is based upon a study of specimens from 24 of the 28 described genera. The diagnoses of these genera are presented, and some are emended with new information. One new genus, Huntaphelenchoides, and five new combinations are proposed. The families Paraphelenchidae and Anomyctidae are placed in synonymy with Aphelenchidae and Aphelenchoididae, respectively. The genera Asteroaphelenchoides and Pseudaphelencboides are placed in synonymy under the genus Aphelenchoides. Rare male and/or female specimens of Peraphelenchus, Anomyctus, Laimaphelenchus, Aphelenchus, Cryptaphelenchoides, Megadorus, Tylaphelenchus, and Entaphelenchus, are redescribed and illustrated. Four plates, containing 106 original drawings of the males, females, stylets, and spicules of representatives of 22 aphelenchoid genera, are presented. PMID:19322328

  12. Two new high altitude genera of Camiarini (Coleoptera: Leiodidae: Camiarinae) from Australia and New Zealand.

    PubMed

    Seago, Ainsley E; Leschen, Richard A B; Newton, Alfred F

    2015-01-01

    Two new leiodid genera and species, Camisolus ptinoides gen. nov., sp. nov. and Camiarodes nunni gen. nov., sp. nov. are described from southeastern Australia and New Zealand, respectively. Each new species is placed within its own genus on the basis of morphological uniqueness within Camiarini (Camiarinae) based on the presence of an enlarged maxillary palpomere 4 and metanepisternum with a lateral, tongue-like process that overlaps the elytron in repose. A key to the described genera is provided for world Camiarini. The tribe, new to Australia, is otherwise known only from New Zealand (six genera including one new) and southern South America (one genus). Both new genera are found exclusively in high altitude areas. PMID:26249077

  13. Two new species of Dryophthorinae in the genera Metamasius and Melchus from the Lesser Antilles (Coleoptera: urculionidae).

    PubMed

    Anderson, Robert S

    2013-12-20

    Metamasius planatus and Melchus jessae, are described and illustrated from the Lesser Antilles islands of Dominica and St. Lucia.  Metamasius planatus (Dominica) is distinguished by a relatively flat profile and presence of dense, very fine, golden micropilosity covering most of the dorsal surface.  Melchus jessae (Dominica and St. Lucia) is the sixth species known in the genus and is distinguished by the cylindrical rostrum (not laterally compressed apically).  Information on natural history for both species is limited: some Metamasius planatus and one Melchus jessae were collected in bases of Euterpe globosa fronds. A revised key to genera of Neotropical Litosomini is presented.

  14. A new genus of fossil Mymaridae (Hymenoptera) from Cretaceous amber and key to Cretaceous mymarid genera.

    PubMed

    Poinar, George; Huber, John T

    2011-01-01

    Myanmymar aresconoidesgen n., sp. n. is described from one female in Burmese amber, dated as about 100 my. It is similar to Arescon on wing features but is unique among Mymaridae in having distinctly segmented palpi. It is the fifth mymarid genus definitely referable to the Cretaceous period. A key to Cretaceous mymarid genera is presented and the features of Myanmymar are compared with the other Cretaceous and extant mymarid genera.

  15. MOSCHweb - a matrix-based interactive key to the genera of the Palaearctic Tachinidae (Insecta, Diptera).

    PubMed

    Cerretti, Pierfilippo; Tschorsnig, Hans-Peter; Lopresti, Massimo; Giovanni, Filippo Di

    2012-01-01

    We provide a general overview of features and technical specifications of an original interactive key web application for the identification of Palaearctic Tachinidae genera. The full list of terminal taxa included in the key, which is the most updated list of genera currently recorded for the Palaearctic Region, is given. We also briefly discuss the need for dealing with detailed and standardized taxa descriptions as a base to keep matrix-based interactive tools easily updated, by proposing a standardized protocol.

  16. A new genus of fossil Mymaridae (Hymenoptera) from Cretaceous amber and key to Cretaceous mymarid genera.

    PubMed

    Poinar, George; Huber, John T

    2011-01-01

    Myanmymar aresconoidesgen n., sp. n. is described from one female in Burmese amber, dated as about 100 my. It is similar to Arescon on wing features but is unique among Mymaridae in having distinctly segmented palpi. It is the fifth mymarid genus definitely referable to the Cretaceous period. A key to Cretaceous mymarid genera is presented and the features of Myanmymar are compared with the other Cretaceous and extant mymarid genera. PMID:22259293

  17. A comparative morphological study of the kinorhynch genera Antygomonas and Semnoderes (Kinorhyncha: Cyclorhagida)

    NASA Astrophysics Data System (ADS)

    Sørensen, Martin V.; Heiner, Iben; Hansen, Jesper G.

    2009-06-01

    Detailed information revealed through combined use of light- and scanning electron microscopy, is given for two species of kinorhynchs, representing the cyclorhagid genera Semnoderes and Antygomonas. The two species have not previously been examined using SEM, and the new observations point out several similarities between species of the two genera, which could indicate a potential close relationship. The generated data is meant to be incorporated in a future phylogenetic analysis in order to clarify the phylogenetic relationships among kinorhynchs.

  18. Biogeography and evolutionary diversification in one of the most widely distributed and species rich genera of the Pacific.

    PubMed

    Cantley, Jason T; Markey, Adrienne S; Swenson, Nathan G; Keeley, Sterling C

    2016-01-01

    The historical biogeography of many lineages-of both terrestrial and marine ocean habitats-remains poorly investigated even though remote ocean habitat covers approximately 66% of the Earth's surface. One such lineage with poorly understood biogeographic affinities across vast ocean habitat is the genus Coprosma (Rubiaceae) with numerous species, and a widespread and disjunct distribution among the far-flung insular localities of multiple Pacific Islands. Here, the first taxonomically robust phylogeny for Coprosma s.s. was dated using molecular clock techniques and indicated Coprosma s.s. diverged from its sister genus Nertera likely during or shortly after the Oligocene Marine Transgression of New Zealand. Diversification of the five major clades identified occurred in New Zealand during the Miocene, which was then followed by multiple independent dispersals from New Zealand to various localities in many directions. The pattern of Coprosma's distribution in the Pacific appears stochastic both temporally and spatially, but evolution of an orange to red fruit colour prior to nearly all inferred dispersals hints at endozoochory by birds. The number of inferred long-distance dispersals of Coprosma s.s. (>30), and number of repeated dispersals to the same insular locality from unrelated Coprosma s.s. sublineages (>8) is perhaps the most currently known for a remote Pacific-centred genus investigated to date. A New Zealand origin for a Pacific-wide dispersal of taxa is not novel, but the manner in which the temporal and spatial distribution for Coprosma s.s. was achieved contributes to a novel understanding of the historical biogeography of widespread Pacific genera that have origins in the Southern Hemisphere.

  19. Biogeography and evolutionary diversification in one of the most widely distributed and species rich genera of the Pacific

    PubMed Central

    Cantley, Jason T.; Markey, Adrienne S.; Swenson, Nathan G.; Keeley, Sterling C.

    2016-01-01

    The historical biogeography of many lineages—of both terrestrial and marine ocean habitats—remains poorly investigated even though remote ocean habitat covers approximately 66% of the Earth’s surface. One such lineage with poorly understood biogeographic affinities across vast ocean habitat is the genus Coprosma (Rubiaceae) with numerous species, and a widespread and disjunct distribution among the far-flung insular localities of multiple Pacific Islands. Here, the first taxonomically robust phylogeny for Coprosma s.s. was dated using molecular clock techniques and indicated Coprosma s.s. diverged from its sister genus Nertera likely during or shortly after the Oligocene Marine Transgression of New Zealand. Diversification of the five major clades identified occurred in New Zealand during the Miocene, which was then followed by multiple independent dispersals from New Zealand to various localities in many directions. The pattern of Coprosma’s distribution in the Pacific appears stochastic both temporally and spatially, but evolution of an orange to red fruit colour prior to nearly all inferred dispersals hints at endozoochory by birds. The number of inferred long-distance dispersals of Coprosma s.s. (>30), and number of repeated dispersals to the same insular locality from unrelated Coprosma s.s. sublineages (>8) is perhaps the most currently known for a remote Pacific-centred genus investigated to date. A New Zealand origin for a Pacific-wide dispersal of taxa is not novel, but the manner in which the temporal and spatial distribution for Coprosma s.s. was achieved contributes to a novel understanding of the historical biogeography of widespread Pacific genera that have origins in the Southern Hemisphere. PMID:27339053

  20. Biogeography and evolutionary diversification in one of the most widely distributed and species rich genera of the Pacific.

    PubMed

    Cantley, Jason T; Markey, Adrienne S; Swenson, Nathan G; Keeley, Sterling C

    2016-01-01

    The historical biogeography of many lineages-of both terrestrial and marine ocean habitats-remains poorly investigated even though remote ocean habitat covers approximately 66% of the Earth's surface. One such lineage with poorly understood biogeographic affinities across vast ocean habitat is the genus Coprosma (Rubiaceae) with numerous species, and a widespread and disjunct distribution among the far-flung insular localities of multiple Pacific Islands. Here, the first taxonomically robust phylogeny for Coprosma s.s. was dated using molecular clock techniques and indicated Coprosma s.s. diverged from its sister genus Nertera likely during or shortly after the Oligocene Marine Transgression of New Zealand. Diversification of the five major clades identified occurred in New Zealand during the Miocene, which was then followed by multiple independent dispersals from New Zealand to various localities in many directions. The pattern of Coprosma's distribution in the Pacific appears stochastic both temporally and spatially, but evolution of an orange to red fruit colour prior to nearly all inferred dispersals hints at endozoochory by birds. The number of inferred long-distance dispersals of Coprosma s.s. (>30), and number of repeated dispersals to the same insular locality from unrelated Coprosma s.s. sublineages (>8) is perhaps the most currently known for a remote Pacific-centred genus investigated to date. A New Zealand origin for a Pacific-wide dispersal of taxa is not novel, but the manner in which the temporal and spatial distribution for Coprosma s.s. was achieved contributes to a novel understanding of the historical biogeography of widespread Pacific genera that have origins in the Southern Hemisphere. PMID:27339053

  1. Seagrass Ecosystem Services and Their Variability across Genera and Geographical Regions

    PubMed Central

    Mtwana Nordlund, Lina; Barbier, Edward B.; Creed, Joel C.

    2016-01-01

    Threats to and loss of seagrass ecosystems globally, impact not only natural resources but also the lives of people who directly or indirectly depend on these systems. Seagrass ecosystems play a multi-functional role in human well-being, e.g. food through fisheries, control of erosion and protection against floods. Quantifying these services reveals their contributions to human well-being and helps justify seagrass conservation. There has been no comprehensive assessment as to whether seagrass ecosystem services are perceived to vary over the globe or amongst genera. Our study compiles the most complete list of ecosystem services provided by seagrasses so far, including bioregional- and genus-specific information from expert opinion and published studies. Several seagrass ecosystem services vary considerably in their (known) provision across genera and over the globe. Seagrasses genera are clearly not all equal with regard to the ecosystem services they provide. As seagrass genera are not evenly distributed over all bioregions, the presence of an ecosystem service sometimes depends on the genera present. Larger sized seagrass genera (e.g. Posidonia, Enhalus) are perceived to provide more substantial and a wider variety of ecosystem services than smaller species (e.g. Halophila, Lepilaena). Nevertheless, smaller species provide important services. Our findings point out data gaps, provide new insight for more efficient management and recommend caution in economic valuation of seagrass services worldwide. PMID:27732600

  2. Molecular phylogenetic studies of Brassica, rorippa, arabidopsis and allied genera based on the internal transcribed spacer region of 18S-25S rDNA.

    PubMed

    Yang, Y W; Lai, K N; Tai, P Y; Ma, D P; Li, W H

    1999-12-01

    The phylogenetic relationships of nine genera in four tribes of the family Brassicaceae were estimated from the sequences of the internal transcribed spacer region (ITS) of the 18S-25S nuclear ribosomal DNA. The entire ITS region of 16 accessions belonging to 10 species of seven genera was sequenced. Eight published sequences of Brassicaceae were also used. A total of 27 sequences were included in this study; four of them were found to be pseudogenes. Both the neighbor-joining and the parsimony trees suggest that the nine genera can be divided into three groups: (1) Arabidopsis, Cardaminopsis, Capsella, and Lepidium; (2) Rorippa and Cardamine; and (3) Brassica, Sinapis, and Raphanus. In contradiction to the proposal that Cardaminopsis and Arabidopsis be put into an expanded tribe Arabideae, our data show that these two genera are more closely related to Capsella and Lepidium (tribe Lepidieae) than to Rorippa and Cardamine (tribe Arabideae). Further, our data show that within the tribe Brassiceae, Raphanus is more closely related to B. nigra than to the B. oleracea/B. rapa clade. This result is in agreement with the nuclear data obtained in several studies, but is in conflict with the RFLP data of mitochondrial and chloroplast DNA. As pointed out by previous authors, it is possible that Raphanus is a hybrid between the B. nigra and B. oleracea/B. rapa lineages with the latter as the maternal parent.

  3. Pantanalinema gen. nov. and Alkalinema gen. nov.: novel pseudanabaenacean genera (Cyanobacteria) isolated from saline-alkaline lakes.

    PubMed

    Vieira Vaz, Marcelo Gomes Marçal; Genuário, Diego Bonaldo; Andreote, Ana Paula Dini; Malone, Camila Francieli Silva; Sant'Anna, Célia Leite; Barbiero, Laurent; Fiore, Marli Fátima

    2015-01-01

    The genus Leptolyngbya Anagnostidis & Komárek (1988) was described from a set of strains identified as 'LPP-group B'. The morphology within this group is not particularly informative and underestimates the group's genetic diversity. In the present study, two new pseudanabaenacean genera related to Leptolyngbya morphotypes, Pantanalinema gen. nov. and Alkalinema gen. nov., are described under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants, based on a polyphasic approach. Pantanalinema gen. nov. (type species Pantanalinema rosaneae sp. nov.) has sheaths and trichomes with slight gliding motility, which distinguish this genus from Alkalinema gen. nov. (type species Alkalinema pantanalense sp. nov.), which possesses trichomes arranged in an ornate (interwoven) pattern. 16S rRNA gene sequences of strains of Pantanalinema and Alkalinema exhibited low identity to each other (≤91.6 %) and to other sequences from known pseudanabaenacean genera (≤94.3 and 93.7 %, respectively). In a phylogenetic reconstruction, six sequences from strains of Pantanalinema and four from strains of Alkalinema formed two separate and robust clades (99 % bootstrap value), with the genera Oculatella and Phormidesmis, respectively, as the closest related groups. 16S-23S rRNA intergenic spacer sequences and secondary structures of strains of Pantanalinema and Alkalinema did not correspond to any previous descriptions. The strains of Pantanalinema and Alkalinema were able to survive and produce biomass at a range of pH (pH 4-11) and were also able to alter the culture medium to pH values ranging from pH 8.4 to 9.9. These data indicate that cyanobacterial communities in underexplored environments, such as the Pantanal wetlands, are promising sources of novel taxa.

  4. Spatial patterns and associations between species belonging to four genera of the Lauraceae family.

    PubMed

    Li, Lin; Ye, Wan Hui; Wei, Shi Guang; Lian, Ju Yu; Huang, Zhong Liang

    2014-01-01

    Spatial distribution pattern of biological related species present unique opportunities and challenges to explain species coexistence. In this study, we explored the spatial distributions and associations among congeneric species at both the species and genus levels to explain their coexistence through examining the similarities and differences at these two levels. We first used DNA and cluster analysis to confirmed the relative relationship of eight species within a 20 ha subtropical forest in southern China. We compared Diameter at breast height (DBH) classes, aggregation intensities and spatial patterns, associations, and distributions of four closely related species pairs to reveal similarities and differences at the species and genus levels. These comparisons provided insight into the mechanisms of coexistence of these congeners. O-ring statistics were used to measure spatial patterns of species. Ω0-10, the mean conspecific density within 10 m of a tree, was used as a measure of the intensity of aggregation of a species, and g-function was used to analyze spatial associations. Our results suggested that spatial aggregations were common, but the differences between spatial patterns were reduced at the genus level. Aggregation intensity clearly reduced at the genus level. Negative association frequencies decreased at the genus level, such that independent association was commonplace among all four genera. Relationships between more closely related species appeared to be more competitive at both the species and genus levels. The importance of competition on interactions is most likely influenced by similarity in lifestyle, and the habitat diversity within the species' distribution areas. Relatives with different lifestyles likely produce different distribution patterns through different interaction process. In order to fully understand the mechanisms generating spatial distributions of coexisting siblings, further research is required to determine the spatial

  5. Inferences of competence from faces predict election outcomes.

    PubMed

    Todorov, Alexander; Mandisodza, Anesu N; Goren, Amir; Hall, Crystal C

    2005-06-10

    We show that inferences of competence based solely on facial appearance predicted the outcomes of U.S. congressional elections better than chance (e.g., 68.8% of the Senate races in 2004) and also were linearly related to the margin of victory. These inferences were specific to competence and occurred within a 1-second exposure to the faces of the candidates. The findings suggest that rapid, unreflective trait inferences can contribute to voting choices, which are widely assumed to be based primarily on rational and deliberative considerations.

  6. Active Inference for Binary Symmetric Hidden Markov Models

    NASA Astrophysics Data System (ADS)

    Allahverdyan, Armen E.; Galstyan, Aram

    2015-10-01

    We consider active maximum a posteriori (MAP) inference problem for hidden Markov models (HMM), where, given an initial MAP estimate of the hidden sequence, we select to label certain states in the sequence to improve the estimation accuracy of the remaining states. We focus on the binary symmetric HMM, and employ its known mapping to 1d Ising model in random fields. From the statistical physics viewpoint, the active MAP inference problem reduces to analyzing the ground state of the 1d Ising model under modified external fields. We develop an analytical approach and obtain a closed form solution that relates the expected error reduction to model parameters under the specified active inference scheme. We then use this solution to determine most optimal active inference scheme in terms of error reduction, and examine the relation of those schemes to heuristic principles of uncertainty reduction and solution unicity.

  7. Semiparametric Bayesian Inference for Multilevel Repeated Measurement Data

    PubMed Central

    Müller, Peter; Quintana, Fernando A.; Rosner, Gary L.

    2011-01-01

    Summary We discuss inference for data with repeated measurements at multiple levels. The motivating example is data with blood counts from cancer patients undergoing multiple cycles of chemotherapy, with days nested within cycles. Some inference questions relate to repeated measurements over days within cycle, while other questions are concerned with the dependence across cycles. When the desired inference relates to both levels of repetition, it becomes important to reflect the data structure in the model. We develop a semiparametric Bayesian modeling approach, restricting attention to two levels of repeated measurements. For the top-level longitudinal sampling model we use random effects to introduce the desired dependence across repeated measurements. We use a nonparametric prior for the random effects distribution. Inference about dependence across second-level repetition is implemented by the clustering implied in the nonparametric random effects model. Practical use of the model requires that the posterior distribution on the latent random effects be reasonably precise. PMID:17447954

  8. Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria (the strawberry)

    PubMed Central

    Vilanova, Santiago; Sargent, Daniel J; Arús, Pere; Monfort, Amparo

    2008-01-01

    Background The Rosaceae encompass a large number of economically-important diploid and polyploid fruit and ornamental species in many different genera. The basic chromosome numbers of these genera are x = 7, 8 and 9 and all have compact and relatively similar genome sizes. Comparative mapping between distantly-related genera has been performed to a limited extent in the Rosaceae including a comparison between Malus (subfamily Maloideae) and Prunus (subfamily Prunoideae); however no data has been published to date comparing Malus or Prunus to a member of the subfamily Rosoideae. In this paper we compare the genome of Fragaria, a member of the Rosoideae, to Prunus, a member of the Prunoideae. Results The diploid genomes of Prunus (2n = 2x = 16) and Fragaria (2n = 2x = 14) were compared through the mapping of 71 anchor markers – 40 restriction fragment length polymorphisms (RFLPs), 29 indels or single nucleotide polymorphisms (SNPs) derived from expressed sequence tags (ESTs) and two simple-sequence repeats (SSRs) – on the reference maps of both genera. These markers provided good coverage of the Prunus (78%) and Fragaria (78%) genomes, with maximum gaps and average densities of 22 cM and 7.3 cM/marker in Prunus and 32 cM and 8.0 cM/marker in Fragaria. Conclusion Our results indicate a clear pattern of synteny, with most markers of each chromosome of one of these species mapping to one or two chromosomes of the other. A large number of rearrangements (36), most of which produced by inversions (27) and the rest (9) by translocations or fission/fusion events could also be inferred. We have provided the first framework for the comparison of the position of genes or DNA sequences of these two economically valuable and yet distantly-related genera of the Rosaceae. PMID:18564412

  9. Australian Marsh Beetles (Coleoptera: Scirtidae) 4. Two new genera, Austrocyphon and Tasmanocyphon.

    PubMed

    Zwick, Peter

    2013-01-01

    The related new genera Austrocyphon and Tasmanocyphon are erected for 42 small Australian marsh beetles resembling members of the genus Cyphon Paykull in habitus. They are distinguished from Cyphon. Only males are known of most species but for two of them larvae and pupae are also available. Austrocyphon species occur in all Australian Federal States, and one species is Australasian and shared with Papua New Guinea. The following species are included: Austrocyphon acaciae sp. n., A. aculeatus sp. n., A. acustropicus sp. n., A. adelaidae (Blackburn), A. asper sp. n., A. bidens sp. n., A. bifidus sp. n., A. charon sp. n., A. crinitus (Klausnitzer), A. curvispina, sp. n., A. deserticola sp. n., A. doctus (Lea), A. enigmaticus sp. n., A. excisus sp. n., A. fenestratus (Blackburn), A. flagellifer sp. n., A. furcatus sp. n., A. hamatus sp. n., A. harpago sp. n., A. leptophallus sp. n., A. linguatus sp. n., A. lobatus sp. n., A. neptunus sp. n., A. noctua sp. n., A. ovensensis (Blackburn), A. papilio sp. n., A. perdoctus sp. n., A. pictus (Blackburn), A. quadridens sp. n., A. quinquespinosus sp. n., A. robustus sp. n., A. setifer sp. n., A. spiculifer sp. n., A. stylatus sp. n., A. stylifer sp. n., A. submersus sp. n., A. tinea sp. n., A. tomweiri sp. n., A. tribulator sp. n., A. tropicus sp. n., A. unguiculatus sp. n., A. wattsi sp. n.Tasmanocyphon is endemic to Tasmania, and only the adult male is known. The genus is monotypic, including only T. heideae, sp. n.

  10. Parallel molecular routes to cold adaptation in eight genera of New Zealand stick insects

    PubMed Central

    Dennis, Alice B.; Dunning, Luke T.; Sinclair, Brent J.; Buckley, Thomas R.

    2015-01-01

    The acquisition of physiological strategies to tolerate novel thermal conditions allows organisms to exploit new environments. As a result, thermal tolerance is a key determinant of the global distribution of biodiversity, yet the constraints on its evolution are not well understood. Here we investigate parallel evolution of cold tolerance in New Zealand stick insects, an endemic radiation containing three montane-occurring species. Using a phylogeny constructed from 274 orthologous genes, we show that stick insects have independently colonized montane environments at least twice. We compare supercooling point and survival of internal ice formation among ten species from eight genera, and identify both freeze tolerance and freeze avoidance in separate montane lineages. Freeze tolerance is also verified in both lowland and montane populations of a single, geographically widespread, species. Transcriptome sequencing following cold shock identifies a set of structural cuticular genes that are both differentially regulated and under positive sequence selection in each species. However, while cuticular proteins in general are associated with cold shock across the phylogeny, the specific genes at play differ among species. Thus, while processes related to cuticular structure are consistently associated with adaptation for cold, this may not be the consequence of shared ancestral genetic constraints. PMID:26355841

  11. Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle.

    PubMed

    Yue, Jia-Xing; Kozmikova, Iryna; Ono, Hiroki; Nossa, Carlos W; Kozmik, Zbynek; Putnam, Nicholas H; Yu, Jr-Kai; Holland, Linda Z

    2016-01-01

    Cephalochordates, the sister group of vertebrates + tunicates, are evolving particularly slowly. Therefore, genome comparisons between two congeners of Branchiostoma revealed so many conserved noncoding elements (CNEs), that it was not clear how many are functional regulatory elements. To more effectively identify CNEs with potential regulatory functions, we compared noncoding sequences of genomes of the most phylogenetically distant cephalochordate genera, Asymmetron and Branchiostoma, which diverged approximately 120-160 million years ago. We found 113,070 noncoding elements conserved between the two species, amounting to 3.3% of the genome. The genomic distribution, target gene ontology, and enriched motifs of these CNEs all suggest that many of them are probably cis-regulatory elements. More than 90% of previously verified amphioxus regulatory elements were re-captured in this study. A search of the cephalochordate CNEs around 50 developmental genes in several vertebrate genomes revealed eight CNEs conserved between cephalochordates and vertebrates, indicating sequence conservation over >500 million years of divergence. The function of five CNEs was tested in reporter assays in zebrafish, and one was also tested in amphioxus. All five CNEs proved to be tissue-specific enhancers. Taken together, these findings indicate that even though Branchiostoma and Asymmetron are distantly related, as they are evolving slowly, comparisons between them are likely optimal for identifying most of their tissue-specific cis-regulatory elements laying the foundation for functional characterizations and a better understanding of the evolution of developmental regulation in cephalochordates. PMID:27412606

  12. Natural Products from Antarctic Colonial Ascidians of the Genera Aplidium and Synoicum: Variability and Defensive Role

    PubMed Central

    Núñez-Pons, Laura; Carbone, Marianna; Vázquez, Jennifer; Rodríguez, Jaime; Nieto, Rosa María; Varela, María Mercedes; Gavagnin, Margherita; Avila, Conxita

    2012-01-01

    Ascidians have developed multiple defensive strategies mostly related to physical, nutritional or chemical properties of the tunic. One of such is chemical defense based on secondary metabolites. We analyzed a series of colonial Antarctic ascidians from deep-water collections belonging to the genera Aplidium and Synoicum to evaluate the incidence of organic deterrents and their variability. The ether fractions from 15 samples including specimens of the species A. falklandicum, A. fuegiense, A. meridianum, A. millari and S. adareanum were subjected to feeding assays towards two relevant sympatric predators: the starfish Odontaster validus, and the amphipod Cheirimedon femoratus. All samples revealed repellency. Nonetheless, some colonies concentrated defensive chemicals in internal body-regions rather than in the tunic. Four ascidian-derived meroterpenoids, rossinones B and the three derivatives 2,3-epoxy-rossinone B, 3-epi-rossinone B, 5,6-epoxy-rossinone B, and the indole alkaloids meridianins A–G, along with other minoritary meridianin compounds were isolated from several samples. Some purified metabolites were tested in feeding assays exhibiting potent unpalatabilities, thus revealing their role in predation avoidance. Ascidian extracts and purified compound-fractions were further assessed in antibacterial tests against a marine Antarctic bacterium. Only the meridianins showed inhibition activity, demonstrating a multifunctional defensive role. According to their occurrence in nature and within our colonial specimens, the possible origin of both types of metabolites is discussed. PMID:23015772

  13. Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle

    PubMed Central

    Yue, Jia-Xing; Kozmikova, Iryna; Ono, Hiroki; Nossa, Carlos W.; Kozmik, Zbynek; Putnam, Nicholas H.; Yu, Jr-Kai; Holland, Linda Z.

    2016-01-01

    Cephalochordates, the sister group of vertebrates + tunicates, are evolving particularly slowly. Therefore, genome comparisons between two congeners of Branchiostoma revealed so many conserved noncoding elements (CNEs), that it was not clear how many are functional regulatory elements. To more effectively identify CNEs with potential regulatory functions, we compared noncoding sequences of genomes of the most phylogenetically distant cephalochordate genera, Asymmetron and Branchiostoma, which diverged approximately 120–160 million years ago. We found 113,070 noncoding elements conserved between the two species, amounting to 3.3% of the genome. The genomic distribution, target gene ontology, and enriched motifs of these CNEs all suggest that many of them are probably cis-regulatory elements. More than 90% of previously verified amphioxus regulatory elements were re-captured in this study. A search of the cephalochordate CNEs around 50 developmental genes in several vertebrate genomes revealed eight CNEs conserved between cephalochordates and vertebrates, indicating sequence conservation over >500 million years of divergence. The function of five CNEs was tested in reporter assays in zebrafish, and one was also tested in amphioxus. All five CNEs proved to be tissue-specific enhancers. Taken together, these findings indicate that even though Branchiostoma and Asymmetron are distantly related, as they are evolving slowly, comparisons between them are likely optimal for identifying most of their tissue-specific cis-regulatory elements laying the foundation for functional characterizations and a better understanding of the evolution of developmental regulation in cephalochordates. PMID:27412606

  14. The maxillary sinus in three genera of new world monkeys: factors that constrain secondary pneumatization.

    PubMed

    Smith, Timothy D; Rossie, James B; Cooper, Gregory M; Carmody, Kelly A; Schmieg, Robin M; Bonar, Christopher J; Mooney, Mark P; Siegel, Michael I

    2010-01-01

    The air filled cavities of paranasal sinuses are thought by some to appear opportunistically in spatial "gaps" within the craniofacial complex. Anthropoid primates provide excellent natural experiments for testing this model, since not all species possess a full complement of paranasal sinuses. In this study, two genera of monkeys (Saguinus and Cebuella) which form maxillary sinuses (MS) as adults were compared to squirrel monkeys (Saimiri spp.), in which a MS does not form. Using microCT and histomorphometric methods, the spatial position of paranasal spaces was assessed and size of the adjacent dental sacs was measured. In Saguinus, secondary pneumatization is underway perinatally, and the sinus extends alongside deciduous premolars (dp). The MS overlaps all permanent molars in the adult. In Saimiri, the homologous space (maxillary recess) extends no farther posterior than the first deciduous premolar at birth and extends no farther than the last premolar in the adult. Differences in dental size and position may account for this finding. For example, Saimiri has significantly larger relative dp volumes, and enlarged orbits, which encroach on the internasal space to a greater degree when compared to Saguinus. These factors limit space for posterior expansion of the maxillary recess. These findings support the hypothesis that secondary pneumatization is a novel, opportunistic growth mechanism that removes "unneeded" bone. Moreover, paranasal spaces occur in association with semiautonomous skeletal elements that border more than one functional matrix, and the spatial dynamics of these units can act as a constraint on pneumatic expansion of paranasal spaces.

  15. Genetic diversity of rhizobial symbionts isolated from legume species within the genera Astragalus, Oxytropis, and Onobrychis.

    PubMed

    Laguerre, G; van Berkum, P; Amarger, N; Prévost, D

    1997-12-01

    The genetic diversity of 44 rhizobial isolates from Astragalus, Oxytropis, and Onobrychis spp. originating from different geographic locations was evaluated by mapped restriction site polymorphism (MRSP) analysis of 16S rRNA genes and by PCR DNA fingerprinting with repetitive sequences (REP-PCR). A comparison of tree topologies of reference strains constructed with data obtained by MRSP and by 16S rRNA gene sequence analyses showed that the topologies were in good agreement, indicating that the MSRP approach results in reasonable estimates of rhizobial phylogeny. The isolates were distributed into 14 distinct 16S rRNA gene types clustering into three major groups which corresponded with three of the genera within the legume symbionts. Most of the isolates were within the genus Mesorhizobium. Five were identified with different genomic species nodulating Lotus spp. and Cicer arietinum. Three Astragalus isolates were classified as Bradyrhizobium, one being similar to Bradyrhizobium elkanii and another being similar to Bradyrhizobium japonicum. Six of the isolates were related to species within the genus Rhizobium. Two were similar to Rhizobium leguminosarum, and the remainder were identified as Rhizobium gallicum. DNA fingerprinting by REP-PCR revealed a high level of diversity within single 16S ribosomal DNA types. The 44 isolates were distributed into 34 REP groups. Rhizobial classification at the genus and probably also the species levels was independent of geographic origin and host plant affinity.

  16. Association of Growth Substrates and Bacterial Genera with Benzo[a]pyrene Mineralization in Contaminated Soil

    PubMed Central

    Jones, Maiysha D.; Rodgers-Vieira, Elyse A.; Hu, Jing; Aitken, Michael D.

    2014-01-01

    Abstract Benzo[a]pyrene (BaP) is a carcinogenic polycyclic aromatic hydrocarbon (PAH) that is not known to be a bacterial growth substrate. Organisms capable of cometabolizing BaP in complex field-contaminated systems have not previously been identified. We evaluated BaP mineralization by a bacterial community from a bioreactor treating PAH-contaminated soil during coincubation with or after pre-enrichment on various PAHs as growth substrates. Pyrosequence libraries of 16S rRNA genes were used to identify bacteria that were enriched on the added growth substrate as a means of associating specific organisms with BaP mineralization. Coincubating the bioreactor-treated soil with naphthalene, phenanthrene, or pyrene inhibited BaP mineralization, whereas pre-enriching the soil on the same three PAHs enhanced BaP mineralization. Combined, these results suggest that bacteria in the bioreactor community that are capable of growing on naphthalene, phenanthrene, and/or pyrene can metabolize BaP, with coincubation competitively inhibiting BaP metabolism. Anthracene, fluoranthene, and benz[a]anthracene had little effect on BaP mineralization compared to incubations without an added growth substrate under either coincubation or pre-enrichment conditions. Substantial increases in relative abundance after pre-enrichment with phenanthrene, naphthalene, or pyrene, but not the other PAHs, suggest that members of the genera Cupriavidus and Luteimonas may have been associated with BaP mineralization. PMID:25469077

  17. Parallel molecular routes to cold adaptation in eight genera of New Zealand stick insects.

    PubMed

    Dennis, Alice B; Dunning, Luke T; Sinclair, Brent J; Buckley, Thomas R

    2015-09-10

    The acquisition of physiological strategies to tolerate novel thermal conditions allows organisms to exploit new environments. As a result, thermal tolerance is a key determinant of the global distribution of biodiversity, yet the constraints on its evolution are not well understood. Here we investigate parallel evolution of cold tolerance in New Zealand stick insects, an endemic radiation containing three montane-occurring species. Using a phylogeny constructed from 274 orthologous genes, we show that stick insects have independently colonized montane environments at least twice. We compare supercooling point and survival of internal ice formation among ten species from eight genera, and identify both freeze tolerance and freeze avoidance in separate montane lineages. Freeze tolerance is also verified in both lowland and montane populations of a single, geographically widespread, species. Transcriptome sequencing following cold shock identifies a set of structural cuticular genes that are both differentially regulated and under positive sequence selection in each species. However, while cuticular proteins in general are associated with cold shock across the phylogeny, the specific genes at play differ among species. Thus, while processes related to cuticular structure are consistently associated with adaptation for cold, this may not be the consequence of shared ancestral genetic constraints.

  18. Genetic diversity of rhizobial symbionts isolated from legume species within the genera Astragalus, Oxytropis, and Onobrychis.

    PubMed Central

    Laguerre, G; van Berkum, P; Amarger, N; Prévost, D

    1997-01-01

    The genetic diversity of 44 rhizobial isolates from Astragalus, Oxytropis, and Onobrychis spp. originating from different geographic locations was evaluated by mapped restriction site polymorphism (MRSP) analysis of 16S rRNA genes and by PCR DNA fingerprinting with repetitive sequences (REP-PCR). A comparison of tree topologies of reference strains constructed with data obtained by MRSP and by 16S rRNA gene sequence analyses showed that the topologies were in good agreement, indicating that the MSRP approach results in reasonable estimates of rhizobial phylogeny. The isolates were distributed into 14 distinct 16S rRNA gene types clustering into three major groups which corresponded with three of the genera within the legume symbionts. Most of the isolates were within the genus Mesorhizobium. Five were identified with different genomic species nodulating Lotus spp. and Cicer arietinum. Three Astragalus isolates were classified as Bradyrhizobium, one being similar to Bradyrhizobium elkanii and another being similar to Bradyrhizobium japonicum. Six of the isolates were related to species within the genus Rhizobium. Two were similar to Rhizobium leguminosarum, and the remainder were identified as Rhizobium gallicum. DNA fingerprinting by REP-PCR revealed a high level of diversity within single 16S ribosomal DNA types. The 44 isolates were distributed into 34 REP groups. Rhizobial classification at the genus and probably also the species levels was independent of geographic origin and host plant affinity. PMID:9406393

  19. Children's Category-Based Inferences Affect Classification

    ERIC Educational Resources Information Center

    Ross, Brian H.; Gelman, Susan A.; Rosengren, Karl S.

    2005-01-01

    Children learn many new categories and make inferences about these categories. Much work has examined how children make inferences on the basis of category knowledge. However, inferences may also affect what is learned about a category. Four experiments examine whether category-based inferences during category learning influence category knowledge…

  20. Causal inference from observational data.

    PubMed

    Listl, Stefan; Jürges, Hendrik; Watt, Richard G

    2016-10-01

    Randomized controlled trials have long been considered the 'gold standard' for causal inference in clinical research. In the absence of randomized experiments, identification of reliable intervention points to improve oral health is often perceived as a challenge. But other fields of science, such as social science, have always been challenged by ethical constraints to conducting randomized controlled trials. Methods have been established to make causal inference using observational data, and these methods are becoming increasingly relevant in clinical medicine, health policy and public health research. This study provides an overview of state-of-the-art methods specifically designed for causal inference in observational data, including difference-in-differences (DiD) analyses, instrumental variables (IV), regression discontinuity designs (RDD) and fixed-effects panel data analysis. The described methods may be particularly useful in dental research, not least because of the increasing availability of routinely collected administrative data and electronic health records ('big data'). PMID:27111146

  1. We infer light in space.

    PubMed

    Schirillo, James A

    2013-10-01

    In studies of lightness and color constancy, the terms lightness and brightness refer to the qualia corresponding to perceived surface reflectance and perceived luminance, respectively. However, what has rarely been considered is the fact that the volume of space containing surfaces appears neither empty, void, nor black, but filled with light. Helmholtz (1866/1962) came closest to describing this phenomenon when discussing inferred illumination, but previous theoretical treatments have fallen short by restricting their considerations to the surfaces of objects. The present work is among the first to explore how we infer the light present in empty space. It concludes with several research examples supporting the theory that humans can infer the differential levels and chromaticities of illumination in three-dimensional space. PMID:23435628

  2. Analysis of the ICE-6G (VM5a) global GIA model performance with respect to geological inferences of relative sea-level history: from Barbados to the US East Coast

    NASA Astrophysics Data System (ADS)

    Roy, K.; Peltier, W. R.

    2013-12-01

    Models of the glacial isostatic adjustment process require two fundamental inputs: a history of ice-sheet loading and a model of the radial variation of mantle viscosity. These models, which are dominated by the influence of the Late Pleistocene cycle of glaciation and deglaciation, may be tested and refined by comparing relative sea-level history predictions to geological inferences based upon appropriate sea level indicators. Datasets of high-quality relative sea-level history reconstructions are available for many globally distributed regions and were crucial in the development of the existing spherically symmetric visco-elastic models of the internal structure of Earth's mantle. These reconstructions have also proven to be essential in the development of ice sheet histories for the Late Quaternary, such as the most recent ICE-6G(VM5a) model. This latest model is a refinement of the ICE-5G(VM2) structure, which has been made possible by the increased availability of accurate space geodetic constraints from previously ice-covered regions and from peripheral regions dominated by the process of forebulge collapse, in particular in the continental United States. A geologically derived sea level record of particular importance in the development of these models has been the coral based record from the island of Barbados in the Caribbean Sea, which has provided, once corrected for tectonics, a very accurate estimate of the globally averaged ice equivalent (eustatic) history of sea level change from the Last Glacial Maximum (LGM) onwards. However, a recent analysis by Austermann et al. (2013, Nature Geoscience) has led these authors to suggest an alternative interpretation that centers on the notion that a large amount of North American ice might be missing from the ICE-5G (VM2) model at LGM. In this paper, we demonstrate this alternative interpretation to be incorrect and thereby reinforce the original interpretation of the tectonics corrected record from Barbados as

  3. Closely related Wolbachia (Rickettsiales:Rickettsiaceae) recovered from different genera of Mexican Thelytokous figitidae (Hymenoptera)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thelytokous parasitoid strains are theoretically advantageous when utilized for biological control, as the absence of males should reduce production costs and potentially increase field efficacy. The maternally inherited intracellular bacterium, Wolbachia pipientis, is capable of inducing thelytokou...

  4. A new species of Furculanurida (Collembola: Neanuridae) from Ivory Coast, with comments on related genera.

    PubMed

    Zon, Serge Demeango; Tano, Yao; Deharveng, Louis

    2014-10-29

    A new species of Pseudachorutinae, Furculanurida emucronata sp. nov., is described from Lamto in the Ivory Coast. It differs from all known Pseudachorutinae species by the presence of a strong lateral tooth on the claw of leg I, and from other species of the genus Furculanurida by the absence of a mucro. It is provisionally assigned to the genus Furculanurida which is redefined accordingly. The heterogeneity of the genus is stressed, and its relationships with Arlesiella, Kenyura, Pseudachorutes and Stachorutes are discussed.

  5. Eyespot evolution: phylogenetic insights from Junonia and related butterfly genera (Nymphalidae: Junoniini).

    PubMed

    Kodandaramaiah, Ullasa

    2009-01-01

    Butterfly eyespots have been the focus of a number of developmental and evolutionary studies. However, a phylogenetic component has rarely been explicitly incorporated in these studies. In this study, I utilize a phylogeny to trace the evolution of eyespot number and position on the wing in a group of nymphalid butterflies, the subtribe Junoniini. These butterflies have two kinds of eyespot arrangements which I refer to as Serial and Individual. In the Serial arrangement, eyespots are placed in a series on compartments 1-6 (counting from the anterior wing margin). In the Individual arrangement, eyespots are isolated on specific compartments, ranging from 1 to 4 in number. This can be divided into four subtypes based on the number and positions of eyespots. I map the evolution of these five arrangements over a phylogeny of Junoniini reconstructed with ca. 3000 base pairs of sequence data from three genes. The results show that almost all arrangements have evolved at least twice, with multiple shifts between them by addition and deletion of eyespots. I propose a model involving genetic or developmental coupling between eyespots in specific compartments to explain these shifts. I discuss their evolution in light of existing knowledge about their development. I also discuss potential explanations for functional significance of the eyespot patterns found in the group. Differential selection for and against eyespots, both at different times over the phylogeny and in different regions, have driven the evolution of eyespot arrangements. The study throws open many questions about the adaptive significance of eyespots and the developmental underpinnings of the various arrangements. PMID:19754706

  6. Transduction of plasmid DNA in Streptomyces spp. and related genera by bacteriophage FP43.

    PubMed

    McHenney, M A; Baltz, R H

    1988-05-01

    A segment (hft) of bacteriophage FP43 DNA cloned into plasmid pIJ702 mediated high-frequency transduction of the resulting plasmid (pRHB101) by FP43 in Streptomyces griseofuscus. The transducing particles contained linear concatemers of plasmid DNA. Lysates of FP43 prepared on S. griseofuscus containing pRHB101 also transduced many other Streptomyces species, including several that restrict plaque formation by FP43 and at least two that produce restriction endonucleases that cut pRHB101 DNA. Transduction efficiencies in different species were influenced by the addition of anti-FP43 antiserum to the transduction plates, the temperature for cell growth before transduction, the multiplicity of infection, and the host on which the transducing lysate was prepared. FP43 lysates prepared on S. griseofuscus(pRHB101) also transduced species of Streptoverticillium, Chainia, and Saccharopolyspora.

  7. Eyespot evolution: phylogenetic insights from Junonia and related butterfly genera (Nymphalidae: Junoniini).

    PubMed

    Kodandaramaiah, Ullasa

    2009-01-01

    Butterfly eyespots have been the focus of a number of developmental and evolutionary studies. However, a phylogenetic component has rarely been explicitly incorporated in these studies. In this study, I utilize a phylogeny to trace the evolution of eyespot number and position on the wing in a group of nymphalid butterflies, the subtribe Junoniini. These butterflies have two kinds of eyespot arrangements which I refer to as Serial and Individual. In the Serial arrangement, eyespots are placed in a series on compartments 1-6 (counting from the anterior wing margin). In the Individual arrangement, eyespots are isolated on specific compartments, ranging from 1 to 4 in number. This can be divided into four subtypes based on the number and positions of eyespots. I map the evolution of these five arrangements over a phylogeny of Junoniini reconstructed with ca. 3000 base pairs of sequence data from three genes. The results show that almost all arrangements have evolved at least twice, with multiple shifts between them by addition and deletion of eyespots. I propose a model involving genetic or developmental coupling between eyespots in specific compartments to explain these shifts. I discuss their evolution in light of existing knowledge about their development. I also discuss potential explanations for functional significance of the eyespot patterns found in the group. Differential selection for and against eyespots, both at different times over the phylogeny and in different regions, have driven the evolution of eyespot arrangements. The study throws open many questions about the adaptive significance of eyespots and the developmental underpinnings of the various arrangements.

  8. Evolutionary inferences from the analysis of exchangeability

    PubMed Central

    Hendry, Andrew P.; Kaeuffer, Renaud; Crispo, Erika; Peichel, Catherine L.; Bolnick, Daniel I.

    2013-01-01

    Evolutionary inferences are usually based on statistical models that compare mean genotypes and phenotypes (or their frequencies) among populations. An alternative is to use the actual distribution of genotypes and phenotypes to infer the “exchangeability” of individuals among populations. We illustrate this approach by using discriminant functions on principal components to classify individuals among paired lake and stream populations of threespine stickleback in each of six independent watersheds. Classification based on neutral and non-neutral microsatellite markers was highest to the population of origin and next-highest to populations in the same watershed. These patterns are consistent with the influence of historical contingency (separate colonization of each watershed) and subsequent gene flow (within but not between watersheds). In comparison to this low genetic exchangeability, ecological (diet) and morphological (trophic and armor traits) exchangeability was relatively high – particularly among populations from similar habitats. These patterns reflect the role of natural selection in driving parallel changes adaptive changes when independent populations colonize similar habitats. Importantly, however, substantial non-parallelism was also evident. Our results show that analyses based on exchangeability can confirm inferences based on statistical analyses of means or frequencies, while also refining insights into the drivers of – and constraints on – evolutionary diversification. PMID:24299398

  9. Functional neuroanatomy of intuitive physical inference.

    PubMed

    Fischer, Jason; Mikhael, John G; Tenenbaum, Joshua B; Kanwisher, Nancy

    2016-08-23

    To engage with the world-to understand the scene in front of us, plan actions, and predict what will happen next-we must have an intuitive grasp of the world's physical structure and dynamics. How do the objects in front of us rest on and support each other, how much force would be required to move them, and how will they behave when they fall, roll, or collide? Despite the centrality of physical inferences in daily life, little is known about the brain mechanisms recruited to interpret the physical structure of a scene and predict how physical events will unfold. Here, in a series of fMRI experiments, we identified a set of cortical regions that are selectively engaged when people watch and predict the unfolding of physical events-a "physics engine" in the brain. These brain regions are selective to physical inferences relative to nonphysical but otherwise highly similar scenes and tasks. However, these regions are not exclusively engaged in physical inferences per se or, indeed, even in scene understanding; they overlap with the domain-general "multiple demand" system, especially the parts of that system involved in action planning and tool use, pointing to a close relationship between the cognitive and neural mechanisms involved in parsing the physical content of a scene and preparing an appropriate action. PMID:27503892

  10. Active inference and robot control: a case study

    PubMed Central

    Nizard, Ange; Friston, Karl; Pezzulo, Giovanni

    2016-01-01

    Active inference is a general framework for perception and action that is gaining prominence in computational and systems neuroscience but is less known outside these fields. Here, we discuss a proof-of-principle implementation of the active inference scheme for the control or the 7-DoF arm of a (simulated) PR2 robot. By manipulating visual and proprioceptive noise levels, we show under which conditions robot control under the active inference scheme is accurate. Besides accurate control, our analysis of the internal system dynamics (e.g. the dynamics of the hidden states that are inferred during the inference) sheds light on key aspects of the framework such as the quintessentially multimodal nature of control and the differential roles of proprioception and vision. In the discussion, we consider the potential importance of being able to implement active inference in robots. In particular, we briefly review the opportunities for modelling psychophysiological phenomena such as sensory attenuation and related failures of gain control, of the sort seen in Parkinson's disease. We also consider the fundamental difference between active inference and optimal control formulations, showing that in the former the heavy lifting shifts from solving a dynamical inverse problem to creating deep forward or generative models with dynamics, whose attracting sets prescribe desired behaviours. PMID:27683002

  11. Perception, illusions and Bayesian inference.

    PubMed

    Nour, Matthew M; Nour, Joseph M

    2015-01-01

    Descriptive psychopathology makes a distinction between veridical perception and illusory perception. In both cases a perception is tied to a sensory stimulus, but in illusions the perception is of a false object. This article re-examines this distinction in light of new work in theoretical and computational neurobiology, which views all perception as a form of Bayesian statistical inference that combines sensory signals with prior expectations. Bayesian perceptual inference can solve the 'inverse optics' problem of veridical perception and provides a biologically plausible account of a number of illusory phenomena, suggesting that veridical and illusory perceptions are generated by precisely the same inferential mechanisms.

  12. Inferring biotic interactions from proxies.

    PubMed

    Morales-Castilla, Ignacio; Matias, Miguel G; Gravel, Dominique; Araújo, Miguel B

    2015-06-01

    Inferring biotic interactions from functional, phylogenetic and geographical proxies remains one great challenge in ecology. We propose a conceptual framework to infer the backbone of biotic interaction networks within regional species pools. First, interacting groups are identified to order links and remove forbidden interactions between species. Second, additional links are removed by examination of the geographical context in which species co-occur. Third, hypotheses are proposed to establish interaction probabilities between species. We illustrate the framework using published food-webs in terrestrial and marine systems. We conclude that preliminary descriptions of the web of life can be made by careful integration of data with theory.

  13. Novel cultured protists identify deep-branching environmental DNA clades of cercozoa: New Genera Tremula, Micrometopion, Minimassisteria, Nudifila, Peregrinia.

    PubMed

    Howe, Alexis T; Bass, David; Scoble, Josephine M; Lewis, Rhodri; Vickerman, Keith; Arndt, Hartmut; Cavalier-Smith, Thomas

    2011-04-01

    We describe three new orders of filosan Cercozoa, five new deep-branching genera, eight new species of Thaumatomonas, Reckertia, Spongomonas, Rhogostoma, Agitata, Neoheteromita and Paracercomonas, sequence their 18S rDNA, and construct 18S rDNA trees for 148 Cercozoa. Our phylogeny indicates that Filosa were ancestrally gliding flagellates; non-flagellate filose amoebae evolved from them five times independently. The new genera are more closely related to environmental DNA sequences than cultured organisms. Tremula longifila, a zooflagellate glider on both flagella (unlike other Cercozoa), is the most divergent filosan (Tremulida ord. n.). Micrometopion nutans is a eukaryote-eating gliding zooflagellate like Metopion and Metromonas. Minimassisteria diva is a widespread trimorphic marine amoeboflagellate granofilosan. Peregrinia clavideferens, a non-testate, scale-bearing, filose amoeba, branches deeply in Thaumatomonadida, which are probably sisters to Spongomonadida. Nudifila producta is a filose amoeboflagellate related to Clautriavia and Marimonadida (ord. n., e.g. Pseudopirsonia, Auranticordis). We substantially revise Imbricatea, now including Spongomonadida, and Thecofilosea to include Phaeodaria. Thecofilosea and Imbricatea and Thecofilosea are sisters, both arguably ancestrally rigid gliding flagellates with ventral pseudopod-emitting grooves. Scale-free Ovulinata parva is sister to Paulinella, so imbricate silica scales can be lost. Internal hollow silica skeletons evolved twice in Thecofilosea (Ebriida, Phaeodaria) or were multiply lost. Protaspa replaces preoccupied 'Protaspis'.

  14. Impacts of Terraces on Phylogenetic Inference.

    PubMed

    Sanderson, Michael J; McMahon, Michelle M; Stamatakis, Alexandros; Zwickl, Derrick J; Steel, Mike

    2015-09-01

    Terraces are sets of trees with precisely the same likelihood or parsimony score, which can be induced by missing sequences in partitioned multi-locus phylogenetic data matrices. The potentially large set of trees on a terrace can be characterized by enumeration algorithms or consensus methods that exploit the pattern of partial taxon coverage in the data, independent of the sequence data themselves. Terraces can add ambiguity and complexity to phylogenetic inference, particularly in settings where inference is already challenging: data sets with many taxa and relatively few loci. In this article we present five new findings about terraces and their impacts on phylogenetic inference. First, we clarify assumptions about partitioning scheme model parameters that are necessary for the existence of terraces. Second, we explore the dependence of terrace size on partitioning scheme and indicate how to find the partitioning scheme associated with the largest terrace containing a given tree. Third, we highlight the impact of terrace size on bootstrap estimates of confidence limits in clades, and characterize the surprising result that the bootstrap proportion for a clade, as it is usually calculated, can be entirely determined by the frequency of bipartitions on a terrace, with some bipartitions receiving high support even when incorrect. Fourth, we dissect some effects of prior distributions of edge lengths on the computed posterior probabilities of clades on terraces, to understand an example in which long edges "attract" each other in Bayesian inference. Fifth, we describe how assuming relationships between edge-lengths of different loci, as an attempt to avoid terraces, can also be problematic when taxon coverage is partial, specifically when heterotachy is present. Finally, we discuss strategies for remediation of some of these problems. One promising approach finds a minimal set of taxa which, when deleted from the data matrix, reduces the size of a terrace to a

  15. Inferring the temperature dependence of population parameters: the effects of experimental design and inference algorithm

    PubMed Central

    Palamara, Gian Marco; Childs, Dylan Z; Clements, Christopher F; Petchey, Owen L; Plebani, Marco; Smith, Matthew J

    2014-01-01

    Understanding and quantifying the temperature dependence of population parameters, such as intrinsic growth rate and carrying capacity, is critical for predicting the ecological responses to environmental change. Many studies provide empirical estimates of such temperature dependencies, but a thorough investigation of the methods used to infer them has not been performed yet. We created artificial population time series using a stochastic logistic model parameterized with the Arrhenius equation, so that activation energy drives the temperature dependence of population parameters. We simulated different experimental designs and used different inference methods, varying the likelihood functions and other aspects of the parameter estimation methods. Finally, we applied the best performing inference methods to real data for the species Paramecium caudatum. The relative error of the estimates of activation energy varied between 5% and 30%. The fraction of habitat sampled played the most important role in determining the relative error; sampling at least 1% of the habitat kept it below 50%. We found that methods that simultaneously use all time series data (direct methods) and methods that estimate population parameters separately for each temperature (indirect methods) are complementary. Indirect methods provide a clearer insight into the shape of the functional form describing the temperature dependence of population parameters; direct methods enable a more accurate estimation of the parameters of such functional forms. Using both methods, we found that growth rate and carrying capacity of Paramecium caudatum scale with temperature according to different activation energies. Our study shows how careful choice of experimental design and inference methods can increase the accuracy of the inferred relationships between temperature and population parameters. The comparison of estimation methods provided here can increase the accuracy of model predictions, with important

  16. Inferring the temperature dependence of population parameters: the effects of experimental design and inference algorithm.

    PubMed

    Palamara, Gian Marco; Childs, Dylan Z; Clements, Christopher F; Petchey, Owen L; Plebani, Marco; Smith, Matthew J

    2014-12-01

    Understanding and quantifying the temperature dependence of population parameters, such as intrinsic growth rate and carrying capacity, is critical for predicting the ecological responses to environmental change. Many studies provide empirical estimates of such temperature dependencies, but a thorough investigation of the methods used to infer them has not been performed yet. We created artificial population time series using a stochastic logistic model parameterized with the Arrhenius equation, so that activation energy drives the temperature dependence of population parameters. We simulated different experimental designs and used different inference methods, varying the likelihood functions and other aspects of the parameter estimation methods. Finally, we applied the best performing inference methods to real data for the species Paramecium caudatum. The relative error of the estimates of activation energy varied between 5% and 30%. The fraction of habitat sampled played the most important role in determining the relative error; sampling at least 1% of the habitat kept it below 50%. We found that methods that simultaneously use all time series data (direct methods) and methods that estimate population parameters separately for each temperature (indirect methods) are complementary. Indirect methods provide a clearer insight into the shape of the functional form describing the temperature dependence of population parameters; direct methods enable a more accurate estimation of the parameters of such functional forms. Using both methods, we found that growth rate and carrying capacity of Paramecium caudatum scale with temperature according to different activation energies. Our study shows how careful choice of experimental design and inference methods can increase the accuracy of the inferred relationships between temperature and population parameters. The comparison of estimation methods provided here can increase the accuracy of model predictions, with important

  17. Genera of euophryine jumping spiders (Araneae: Salticidae), with a combined molecular-morphological phylogeny.

    PubMed

    Zhang, Junxia; Maddison, Wayne P

    2015-01-01

    Morphological traits of euophryine jumping spiders were studied to clarify generic limits in the Euophryinae and to permit phylogenetic classification of genera lacking molecular data. One hundred and eight genera are recognized within the subfamily. Euophryine generic groups and the delimitation of some genera are reviewed in detail. In order to explore the effect of adding formal morphological data to previous molecular phylogenetic studies, and to find morphological synapomorphies, eighty-two morphological characters were scored for 203 euophryine species and seven outgroup species. The morphological dataset does not perform as well as the molecular dataset (genes 28S, Actin 5C; 16S-ND1, COI) in resolving the phylogeny of Euophryinae, probably because of frequent convergence and reversal. The formal morphological data were mapped on the phylogeny in order to seek synapomorphies, in hopes of extending the phylogeny to include taxa for which molecular data are not available. Because of homoplasy, few globally-applicable morphological synapomorphies for euophryine clades were found. However, synapomorphies that are unique locally in subclades still help to delimit euophryine generic groups and genera. The following synonyms of euophryine genera are proposed: Maeotella with Anasaitis; Dinattus with Corythalia; Paradecta with Compsodecta; Cobanus, Chloridusa and Wallaba with Sidusa; Tariona with Mopiopia; Nebridia with Amphidraus; Asaphobelis and Siloca with Coryphasia; Ocnotelus with Semnolius; Palpelius with Pristobaeus; Junxattus with Laufeia; Donoessus with Colyttus; Nicylla, Pselcis and Thianitara with Thiania. The new genus Saphrys is erected for misplaced species from southern South America. PMID:25947489

  18. Carbon Monitoring Satellite (CarbonSat): assessment of scattering related atmospheric CO2 and CH4 retrieval errors and first results on implications for inferring city CO2 emissions

    NASA Astrophysics Data System (ADS)

    Buchwitz, M.; Reuter, M.; Bovensmann, H.; Pillai, D.; Heymann, J.; Schneising, O.; Rozanov, V.; Krings, T.; Burrows, J. P.; Boesch, H.; Gerbig, C.; Meijer, Y.; Löscher, A.

    2013-05-01

    Carbon Monitoring Satellite (CarbonSat) is one of two candidate missions for ESA's Earth Explorer 8 (EE8) satellite - the selected one to be launched around the end of this decade. The objective of the CarbonSat mission is to improve our understanding of natural and anthropogenic sources and sinks of the two most important anthropogenic greenhouse gases (GHG) carbon dioxide (CO2) and methane (CH4). The unique feature of CarbonSat is its "GHG imaging capability", which is achieved via a combination of high spatial resolution (2 km × 2 km) and good spatial coverage (wide swath and gap-free across- and along-track ground sampling). This capability enables global imaging of localized strong emission source such as cities, power plants, methane seeps, landfills and volcanos and better disentangling of natural and anthropogenic GHG sources and sinks. Source/sink information can be derived from the retrieved atmospheric column-averaged mole fractions of CO2 and CH4, i.e. XCO2 and XCH4, via inverse modeling. Using the most recent instrument and mission specification, an error analysis has been performed using the BESD/C retrieval algorithm. We focus on systematic errors due to aerosols and thin cirrus clouds, as this is the dominating error source especially with respect to XCO2 systematic errors. To compute the errors for each single CarbonSat observation in a one year time period, we have developed an error parameterization scheme based on six relevant input parameters: we consider solar zenith angle, surface albedo in two bands, aerosol and cirrus optical depth, and cirrus altitude variations but neglect, for example, aerosol type variations. Using this method we have generated and analyzed one year of simulated CarbonSat observations. Using this data set we estimate that scattering related systematic errors are mostly (approx. 85%) below 0.3 ppm for XCO2 (<0.5 ppm: 99.5%) and below 2 ppb for XCH4 (<4 ppb: 99.3%). We also show that the single measurement precision is

  19. Perceptual Inference and Autistic Traits

    ERIC Educational Resources Information Center

    Skewes, Joshua C; Jegindø, Else-Marie; Gebauer, Line

    2015-01-01

    Autistic people are better at perceiving details. Major theories explain this in terms of bottom-up sensory mechanisms or in terms of top-down cognitive biases. Recently, it has become possible to link these theories within a common framework. This framework assumes that perception is implicit neural inference, combining sensory evidence with…

  20. Science Shorts: Observation versus Inference

    ERIC Educational Resources Information Center

    Leager, Craig R.

    2008-01-01

    When you observe something, how do you know for sure what you are seeing, feeling, smelling, or hearing? Asking students to think critically about their encounters with the natural world will help to strengthen their understanding and application of the science-process skills of observation and inference. In the following lesson, students make…

  1. Sample Size and Correlational Inference

    ERIC Educational Resources Information Center

    Anderson, Richard B.; Doherty, Michael E.; Friedrich, Jeff C.

    2008-01-01

    In 4 studies, the authors examined the hypothesis that the structure of the informational environment makes small samples more informative than large ones for drawing inferences about population correlations. The specific purpose of the studies was to test predictions arising from the signal detection simulations of R. B. Anderson, M. E. Doherty,…

  2. Improving Explanatory Inferences from Assessments

    ERIC Educational Resources Information Center

    Diakow, Ronli Phyllis

    2013-01-01

    This dissertation comprises three papers that propose, discuss, and illustrate models to make improved inferences about research questions regarding student achievement in education. Addressing the types of questions common in educational research today requires three different "extensions" to traditional educational assessment: (1)…

  3. A phylogenetic and evolutionary justification for three genera of Geminiviridae.

    PubMed

    Rybicki, E P

    1994-01-01

    Gene-by-gene phylogenetic analyses of all of the viruses for which sequences are known, as well as analysis of the coding capacities, clearly demonstrated that there are two major groups of viruses in the taxonomic family Geminiviridae. These are of the Subgroup I type, with one genomic component, which mainly infect monocots and are leafhopper-transmitted; and of the Subgroup III type, with one or two genomic components, which infect dicots and are whitefly-transmitted. The existence of "New World" and "Old World" clusters of Subgroup III viruses was confirmed, as well as the possession by the latter of an AV1 ORF not present in New World viruses. A third minor generic group is defined by viruses of the Subgroup II type, which have a single genomic component, infect dicots, and are leafhopper-transmitted. The latter group appear to be the result of an ancient recombination event between a Subgroup III-like and a Subgroup I-like virus. The question of whether one- and two-component Subgroup III viruses should be in the same taxon appears hard to resolve: the only distinguishing feature of the one-component Subgroup III viruses is that they apparently have no second component, as gene-for-gene comparisons of the "A" components of the viruses with other Subgroup III viruses place them within a larger Old World group of viruses, most of which are two component. The possibility exists that these viruses may either have independently lost their B components, or possess a B component that has simply not yet been found. Possible nomenclatural changes to accommodate viruses with the same name which are not closely related to one another, and possible evolutionary scenarios to account for the observed familial, generic and specific diversity of geminiviruses, are discussed.

  4. Inference of seasonal and pandemic influenza transmission dynamics.

    PubMed

    Yang, Wan; Lipsitch, Marc; Shaman, Jeffrey

    2015-03-01

    The inference of key infectious disease epidemiological parameters is critical for characterizing disease spread and devising prevention and containment measures. The recent emergence of surveillance records mined from big data such as health-related online queries and social media, as well as model inference methods, permits the development of new methodologies for more comprehensive estimation of these parameters. We use such data in conjunction with Bayesian inference methods to study the transmission dynamics of influenza. We simultaneously estimate key epidemiological parameters, including population susceptibility, the basic reproductive number, attack rate, and infectious period, for 115 cities during the 2003-2004 through 2012-2013 seasons, including the 2009 pandemic. These estimates discriminate key differences in the epidemiological characteristics of these outbreaks across 10 y, as well as spatial variations of influenza transmission dynamics among subpopulations in the United States. In addition, the inference methods appear to compensate for observational biases and underreporting inherent in the surveillance data. PMID:25730851

  5. Global history of the ancient monocot family Araceae inferred with models accounting for past continental positions and previous ranges based on fossils.

    PubMed

    Nauheimer, Lars; Metzler, Dirk; Renner, Susanne S

    2012-09-01

    The family Araceae (3790 species, 117 genera) has one of the oldest fossil records among angiosperms. Ecologically, members of this family range from free-floating aquatics (Pistia and Lemna) to tropical epiphytes. Here, we infer some of the macroevolutionary processes that have led to the worldwide range of this family and test how the inclusion of fossil (formerly occupied) geographical ranges affects biogeographical reconstructions. Using a complete genus-level phylogeny from plastid sequences and outgroups representing the 13 other Alismatales families, we estimate divergence times by applying different clock models and reconstruct range shifts under different models of past continental connectivity, with or without the incorporation of fossil locations. Araceae began to diversify in the Early Cretaceous (when the breakup of Pangea was in its final stages), and all eight subfamilies existed before the K/T boundary. Early lineages persist in Laurasia, with several relatively recent entries into Africa, South America, South-East Asia and Australia. Water-associated habitats appear to be ancestral in the family, and DNA substitution rates are especially high in free-floating Araceae. Past distributions inferred when fossils are included differ in nontrivial ways from those without fossils. Our complete genus-level time-scale for the Araceae may prove to be useful for ecological and physiological studies.

  6. Immatures of the New World treehopper tribe Amastrini (Hemiptera, Membracidae, Smiliinae) with a key to genera.

    PubMed

    McKamey, Stuart H; Wallner, Adam M; Porter, Mitchell J

    2015-01-01

    The immatures stages of 8 of the 11 genera (Amastris Stål, Bajulata Ball, Erosne Stål, Harmonides Kirkaldy, Idioderma Van Duzee, Neotynelia Creão-Duarte & Sakakibara, Tynelia Stål, and Vanduzea Goding) of the tribe Amastrini are described for the first time along with brief diagnoses of Membracidae and the subfamily Smiliinae. A key to genera and notes on biology are provided. Multiple species of most genera are illustrated. Based on its distinct nymphal morphology, Vanduzea laeta nolina Ball is elevated to specific rank as Vanduzea nolina stat. n., and Bajulata, despite the superficial similarity of its adults to those of Vanduzea, is confirmed as warranting generic rank based on its unique nymphal morphology. Colombia is a new country record for Tynelia.

  7. Provisional keys to the genera of seaweeds of Micronesia, with new records for Guam and Yap

    PubMed Central

    LOBBAN, CHRISTOPHER S.; N'YEURT, ANTOINE D.R.

    2008-01-01

    Artificial keys to the genera of blue-green, red, brown, and green marine benthic algae of Micronesia are given, including virtually all the genera reported from Palau, Guam, Commonwealth of the Northern Marianas, Federated States of Micronesia and the Marshall Islands. Twenty-two new species or genera are reported here for Guam and 7 for Yap; 11 of these are also new for Micronesia. Note is made of several recent published records for Guam and 2 species recently raised from varietal status. Finally, a list is given of nomenclatural changes that affect the 2003 revised checklist. An interactive version of the keys is included in the algal biodiversity website at http://university.uog.edu/botany/474. PMID:18958300

  8. Immatures of the New World treehopper tribe Amastrini (Hemiptera, Membracidae, Smiliinae) with a key to genera

    PubMed Central

    McKamey, Stuart H.; Wallner, Adam M.; Porter, Mitchell J.

    2015-01-01

    Abstract The immatures stages of 8 of the 11 genera (Amastris Stål, Bajulata Ball, Erosne Stål, Harmonides Kirkaldy, Idioderma Van Duzee, Neotynelia Creão-Duarte & Sakakibara, Tynelia Stål, and Vanduzea Goding) of the tribe Amastrini are described for the first time along with brief diagnoses of Membracidae and the subfamily Smiliinae. A key to genera and notes on biology are provided. Multiple species of most genera are illustrated. Based on its distinct nymphal morphology, Vanduzea laeta nolina Ball is elevated to specific rank as Vanduzea nolina stat. n., and Bajulata, despite the superficial similarity of its adults to those of Vanduzea, is confirmed as warranting generic rank based on its unique nymphal morphology. Colombia is a new country record for Tynelia. PMID:26478706

  9. Genera of conjoined bases of linear Hamiltonian systems and limit characterization of principal solutions at infinity

    NASA Astrophysics Data System (ADS)

    Šepitka, Peter; Šimon Hilscher, Roman

    2016-04-01

    In this paper we derive a general limit characterization of principal solutions at infinity of linear Hamiltonian systems under no controllability assumption. The main result is formulated in terms of a limit involving antiprincipal solutions at infinity of the system. The novelty lies in the fact that the principal and antiprincipal solutions at infinity may belong to two different genera of conjoined bases, i.e., the eventual image of their first components is not required to be the same as in the known literature. For this purpose we extend the theory of genera of conjoined bases, which was recently initiated by the authors. We show that the orthogonal projector representing each genus of conjoined bases satisfies a symmetric Riccati matrix differential equation. This result then leads to an exact description of the structure of the set of all genera, in particular it forms a complete lattice. We also provide several examples, which illustrate our new theory.

  10. Provisional keys to the genera of seaweeds of Micronesia, with new records for Guam and Yap.

    PubMed

    Lobban, Christopher S; N'yeurt, Antoine D R

    2006-01-01

    Artificial keys to the genera of blue-green, red, brown, and green marine benthic algae of Micronesia are given, including virtually all the genera reported from Palau, Guam, Commonwealth of the Northern Marianas, Federated States of Micronesia and the Marshall Islands. Twenty-two new species or genera are reported here for Guam and 7 for Yap; 11 of these are also new for Micronesia. Note is made of several recent published records for Guam and 2 species recently raised from varietal status. Finally, a list is given of nomenclatural changes that affect the 2003 revised checklist. An interactive version of the keys is included in the algal biodiversity website at http://university.uog.edu/botany/474. PMID:18958300

  11. New spider flies from the Neotropical Region (Diptera, Acroceridae) with a key to New World genera

    PubMed Central

    Schlinger, Evert I.; Gillung, Jessica P.; Borkent, Christopher J.

    2013-01-01

    Abstract Two new genera and five new species of spider flies (Diptera: Acroceridae) are described from the Neotropical Region. A new genus of Philopotinae (Neophilopota brevirostris Schlinger gen. et sp. n.) is described from Mexico, while an unusual new species of Sphaerops Philippi, 1865 (Acrocerinae: Sphaerops micella Schlinger sp. n.) is described from Chile. A new Panopinae genus near Lasia Wiedemann, 1824 (Coquena stangei Schlinger gen. et sp. n.), is described from Argentina and two new species of Pialea Erichson, 1840 (Pialea brunea Schlinger sp. n. and Pialea corbiculata Schlinger sp. n.)are described from Venezuela. Each genus is diagnosed and figured, and a key to species provided. The Neotropical fauna presently includes 19 genera, containing approximately 100 species. A key to New World genera is also included. PMID:23730188

  12. Molecular phylogenetics and diversification of trap-jaw ants in the genera Anochetus and Odontomachus (Hymenoptera: Formicidae).

    PubMed

    Larabee, Fredrick J; Fisher, Brian K; Schmidt, Chris A; Matos-Maraví, Pável; Janda, Milan; Suarez, Andrew V

    2016-10-01

    Ants in the genera Anochetus and Odontomachus belong to one of the largest clades in the subfamily Ponerinae, and are one of four lineages of ants possessing spring-loaded "trap-jaws." Here we present results from the first global species-level molecular phylogenetic analysis of these trap-jaw ants, reconstructed from one mitochondrial, one ribosomal RNA, and three nuclear protein-coding genes. Bayesian and likelihood analyses strongly support reciprocal monophyly for the genera Anochetus and Odontomachus. Additionally, we found strong support for seven trap-jaw ant clades (four in Anochetus and three in Odontomachus) mostly concordant with geographic distribution. Ambiguity remains concerning the closest living non-trap-jaw ant relative of the Anochetus+Odontomachus clade, but Bayes factor hypothesis testing strongly suggests that trap-jaw ants evolved from a short mandible ancestor. Ponerine trap-jaw ants originated in the early Eocene (52.5Mya) in either South America or Southeast Asia, where they have radiated rapidly in the last 30million years, and subsequently dispersed multiple times to Africa and Australia. These results will guide future taxonomic work on the group and act as a phylogenetic framework to study the macroevolution of extreme ant mouthpart specialization. PMID:27450781

  13. Molecular phylogenetics and diversification of trap-jaw ants in the genera Anochetus and Odontomachus (Hymenoptera: Formicidae).

    PubMed

    Larabee, Fredrick J; Fisher, Brian K; Schmidt, Chris A; Matos-Maraví, Pável; Janda, Milan; Suarez, Andrew V

    2016-10-01

    Ants in the genera Anochetus and Odontomachus belong to one of the largest clades in the subfamily Ponerinae, and are one of four lineages of ants possessing spring-loaded "trap-jaws." Here we present results from the first global species-level molecular phylogenetic analysis of these trap-jaw ants, reconstructed from one mitochondrial, one ribosomal RNA, and three nuclear protein-coding genes. Bayesian and likelihood analyses strongly support reciprocal monophyly for the genera Anochetus and Odontomachus. Additionally, we found strong support for seven trap-jaw ant clades (four in Anochetus and three in Odontomachus) mostly concordant with geographic distribution. Ambiguity remains concerning the closest living non-trap-jaw ant relative of the Anochetus+Odontomachus clade, but Bayes factor hypothesis testing strongly suggests that trap-jaw ants evolved from a short mandible ancestor. Ponerine trap-jaw ants originated in the early Eocene (52.5Mya) in either South America or Southeast Asia, where they have radiated rapidly in the last 30million years, and subsequently dispersed multiple times to Africa and Australia. These results will guide future taxonomic work on the group and act as a phylogenetic framework to study the macroevolution of extreme ant mouthpart specialization.

  14. Phylogenetic and morphological diversity of novel soil cercomonad species with a description of two new genera (Nucleocercomonas and Metabolomonas).

    PubMed

    Brabender, Marian; Kiss, Aron Keve; Domonell, Anne; Nitsche, Frank; Arndt, Hartmut

    2012-07-01

    Cercomonads are important components of microbial food webs in soils and aquatic sediments. Here, we investigated the general morphology, behaviour, life cycle and 18S rDNA phylogeny of cercomonad cultures from a German grassland soil habitat. We describe ten new species including two new genera from 23 strains. Three Cercomonas, two Eocercomonas and three Paracercomonas species are described. Based on large phylogenetic distance and distinct morphology, we erect two novel clade B genera near the root of the cercomonad tree. Nucleocercomonas nov. gen. bears a number of characters unusual for cercomonads: Its anterior flagellum is extremely long, it mostly does not glide, and in its most frequent life stage the cell body does not attach to the substratum, but produces unattached pseudopodia. Furthermore, it has a unique nucleus with a peripheral nucleolus that attaches to the nuclear envelope opposite the basal body connection. Metabolomonas nov. gen. is extremely metabolic. It is characterized by a very high beating frequency of the anterior flagellum, fast gliding, rapid changes in shape and strong cytoplasmic streams. A new genus Brevimastigomonas is erected for the previously described species Paracercomonas anaerobica. The general morphology of cercomonad species often does not correspond with their phylogenetic position: closely related species may have a very different morphology.

  15. New and already known acanthocephalans mostly from mammals in Vietnam, with descriptions of two new genera and species in Archiacanthocephala.

    PubMed

    Amin, Omar M; Ha, Ngyuen Van; Heckmann, Richard A

    2008-02-01

    Adults of 2 new species and 2 new genera of acanthocephalans in class Archiacanthocephala, collected between 1998 and 2004 in Vietnam from the intestines of mammals, are described, i.e., Cucullanorhynchus constrictruncatus n. gen., n. sp. (Oligacanthorhynchidae) from a leopard Panthera pardus (Linnaeus) (Mammalia: Felidae) and Paraprosthenorchis ornatus n. gen. n. sp. (Oligacanthorhynchidae) from the Chinese pangolin Manis pentadactyla (Linnaeus) (Mammalia: Manidae). Adult Sphaerechinorhynchus macropisthospinus Amin, Wongsawad, Marayong, Saehoong, Suwattanacoupt, and Sey, 1998 (Plagiorhynchidae) are described for the first time from 2 females collected from a tiger Panthera tigris (Linnaeus) (Mammalia: Felidae) and from 1 male from a water monitor Varanus salvator Laurenti (Reptilia: Varanidae). Characteristic features distinguishing the new species or genera from related taxa are as follows. The trunk of C. constrictruncatus has an anterior hood in both sexes and a posterior constriction in females. The anterior trunk of P. ornatus has many small festoons and proboscis hooks are inserted in elevated papillae separated by beady, near hexagonal, ornate grids. PMID:18372641

  16. Phylogenetic relationships between some members of the genera Deleya, Halomonas, and Halovibrio.

    PubMed

    Dobson, S J; McMeekin, T A; Franzmann, P D

    1993-10-01

    The genera Halomonas and Deleya, which constitute the family Halomonadaceae, are difficult to differentiate on the basis of phenotypic and chemotaxonomic attributes. DNA-rRNA hybridization studies have indicated that some Halomonas spp. have the same level of relationship to the type species of the genus Deleya as some Deleya spp. A phylogenetic analysis of the 16S rRNA sequences of seven members of the Halomonadaceae indicated that the members of the genera Halomonas and Deleya do not form separate monophyletic subgroups, confirming the lack of any phylogenetic support for retention of these taxa as separate genera. A phylogenetic analysis of the 16S rRNA sequence of Halovibrio variabilis confirmed that this species belongs in the Halomonadaceae. All of the members of the Halomonadaceae examined and Halovibrio variabilis possess a cytosine residue at position 486 (Escherichia coli numbering), which is an extremely rare attribute among the prokaryotes and has been reported in only one other species, Listonella anguillarum. Several other signature characteristics which define this group in the gamma subclass of the Proteobacteria are identified. The Jukes-Cantor distances between members of the family Halomonadaceae, including Halovibrio variabilis, range from 0.086 to 0.000 (the levels of similarity between the 16S rRNA sequences range from 92.6 to 100%). The members of the genera Halomonas, Deleya, and Halovibrio form a monophyletic group and share common chemotaxonomic and phenotypic characteristics. Subgroups containing members of the genera Halomonas, Deleya, and Halovibrio cannot be resolved on the basis of phylogenetic, chemotaxonomic, or phenotypic data. Our data indicate that the members of the genera Halomonas, Deleya, and Halovibrio should be united in a single genus.

  17. Three New Monotypic Genera of the Caloplacoid Lichens (Teloschistaceae, Lichen-Forming Ascomycetes).

    PubMed

    Kondratyuk, Sergii Y; Lőkös, Lászlo; Kim, Jung A; Kondratiuk, Anna S; Jeong, Min Hye; Jang, Seol Hwa; Oh, Soon-Ok; Hur, Jae-Seoun

    2015-09-01

    Three monophyletic branches are strongly supported in a phylogenetic analysis of the Teloschistaceae based on combined data sets of internal transcribed spacer and large subunit nrDNA and 12S small subunit mtDNA sequences. These are described as new monotypic genera: Jasonhuria S. Y. Kondr., L. Lőkös et S. -O. Oh, Loekoesia S. Y. Kondr., S. -O. Oh et J. -S. Hur and Olegblumia S. Y. Kondr., L. Lőkös et J. -S. Hur. Three new combinations for the type species of these genera are proposed.

  18. Tanaidaceans (Crustacea) from the Central Pacific Manganese Nodule Province. I. The genera Collettea, Robustochelia and Tumidochelia

    PubMed Central

    Larsen, Kim

    2011-01-01

    Abstract Three new species of are described from the manganese nodule province between the Clarion and the Clipperton Fracture Zone of the equatorial North Pacific Ocean, and collected during the Nodinaut expedition on board the r/v l´Atalante in the summer of 2004. The new species belongs to three genera as: Collettea (Collettea longisetosa), Robustochelia (Robustochelia pacifica), and Tumidochelia (Tumidochelia tuberculata). A key to the genus Tumidochelia is presented and the validity of the genera Robustochelia and Collettea is discussed. PMID:21594100

  19. Three New Monotypic Genera of the Caloplacoid Lichens (Teloschistaceae, Lichen-Forming Ascomycetes)

    PubMed Central

    Lőkös, Lászlo; Kim, Jung A.; Kondratiuk, Anna S.; Jeong, Min Hye; Jang, Seol Hwa; Oh, Soon-Ok; Hur, Jae-Seoun

    2015-01-01

    Three monophyletic branches are strongly supported in a phylogenetic analysis of the Teloschistaceae based on combined data sets of internal transcribed spacer and large subunit nrDNA and 12S small subunit mtDNA sequences. These are described as new monotypic genera: Jasonhuria S. Y. Kondr., L. Lőkös et S. -O. Oh, Loekoesia S. Y. Kondr., S. -O. Oh et J. -S. Hur and Olegblumia S. Y. Kondr., L. Lőkös et J. -S. Hur. Three new combinations for the type species of these genera are proposed. PMID:26539034

  20. Atractosporocybe, Leucocybe and Rhizocybe: three new clitocyboid genera in the Tricholomatoid clade (Agaricales) with notes on Clitocybe and Lepista.

    PubMed

    Alvarado, Pablo; Moreno, Gabriel; Vizzini, Alfredo; Consiglio, Giovanni; Manjón, José Luis; Setti, Ledo

    2015-01-01

    A molecular multigene analysis (ITS, 18S and 28S nrLSU ribosomal DNA, tef1, rpb2) was used to support the proposition of three new genera of clitocyboid fungi. Leucocybe is proposed to accommodate the clade formed by Clitocybe connata and C. candicans. Clitocybe inornata is invested as type species of Atractosporocybe, while the new genus, Rhizocybe, is proposed for the former species of section Vernae of Clitocybe, C. vermicularis, C. pruinosa and C. rhizoides. The three lineages are related to the families Lyophyllaceae and Entolomataceae and independent from the Clitocybeae clade. Morphologically Rhizocybe is characterized by the presence of conspicuous rhizomorphs, while Atractosporocybe presents long fusiform spores. Leucocybe includes two whitish species in the former section Candicantes of Clitocybe, but no relevant shared characteristic feature was detected. Other whitish clitocyboid species, such as C. phyllophila (= C. cerussata), C. dealbata, C. rivulosa, and Singerocybe hydrogramma, are shown to be genetically related to the core lineage of the Clitocybeae.

  1. On the scientific inference from clinical trials.

    PubMed

    Holmberg, L; Baum, M; Adami, H O

    1999-05-01

    We have not been able to describe clearly how we generalize findings from a study to our own 'everyday patients'. This difficulty is not surprising, since generalization deals with how empirical observations are related to the growth of scientific knowledge, which is a major philosophical problem. An argument, sometimes used to discard evidence from a trial, is that the patient sample was too selected and therefore not 'representative' enough for the results to be meaningful for generalization. In this paper, we discuss issues of representativeness and generalizability. Other authors have shown that generalization cannot only depend on statistical inference. Then, how do randomized clinical trials contribute to the growth of knowledge? We discuss three aspects of the randomized clinical trial (Mant 1999), First, the trial is an empirical experiment set up to study the intervention on the question as specifically and as much in isolation from other -- biasing and confounding -- factors as possible (Rothman & Greenland 1998). Second, the trial is set up to challenge our prevailing hypotheses (or prejudices) and the trial is above all a help in error elimination (Popper 1992). Third, we need to learn to see new, unexpected and thought-provoking patterns in the data from a trial. Point one -- and partly point two -- refers to the paradigm of the controlled experiment in scientific method. How much a study contributes to our knowledge, with respect to points two and three, relates to its originality. In none of these respects is the representativeness of the patients, or the clinical situations, crucial for judging the study and its possible inferences. However, we also discuss that the biological domain of disease that was studied in a particular trial has to be taken into account. Thus, the inference drawn from a clinical study is not only a question of statistical generalization, but must include a jump from the world of experiences into the world of reason

  2. Network Plasticity as Bayesian Inference

    PubMed Central

    Legenstein, Robert; Maass, Wolfgang

    2015-01-01

    General results from statistical learning theory suggest to understand not only brain computations, but also brain plasticity as probabilistic inference. But a model for that has been missing. We propose that inherently stochastic features of synaptic plasticity and spine motility enable cortical networks of neurons to carry out probabilistic inference by sampling from a posterior distribution of network configurations. This model provides a viable alternative to existing models that propose convergence of parameters to maximum likelihood values. It explains how priors on weight distributions and connection probabilities can be merged optimally with learned experience, how cortical networks can generalize learned information so well to novel experiences, and how they can compensate continuously for unforeseen disturbances of the network. The resulting new theory of network plasticity explains from a functional perspective a number of experimental data on stochastic aspects of synaptic plasticity that previously appeared to be quite puzzling. PMID:26545099

  3. Bayesian inference on proportional elections.

    PubMed

    Brunello, Gabriel Hideki Vatanabe; Nakano, Eduardo Yoshio

    2015-01-01

    Polls for majoritarian voting systems usually show estimates of the percentage of votes for each candidate. However, proportional vote systems do not necessarily guarantee the candidate with the most percentage of votes will be elected. Thus, traditional methods used in majoritarian elections cannot be applied on proportional elections. In this context, the purpose of this paper was to perform a Bayesian inference on proportional elections considering the Brazilian system of seats distribution. More specifically, a methodology to answer the probability that a given party will have representation on the chamber of deputies was developed. Inferences were made on a Bayesian scenario using the Monte Carlo simulation technique, and the developed methodology was applied on data from the Brazilian elections for Members of the Legislative Assembly and Federal Chamber of Deputies in 2010. A performance rate was also presented to evaluate the efficiency of the methodology. Calculations and simulations were carried out using the free R statistical software.

  4. Bayesian Inference on Proportional Elections

    PubMed Central

    Brunello, Gabriel Hideki Vatanabe; Nakano, Eduardo Yoshio

    2015-01-01

    Polls for majoritarian voting systems usually show estimates of the percentage of votes for each candidate. However, proportional vote systems do not necessarily guarantee the candidate with the most percentage of votes will be elected. Thus, traditional methods used in majoritarian elections cannot be applied on proportional elections. In this context, the purpose of this paper was to perform a Bayesian inference on proportional elections considering the Brazilian system of seats distribution. More specifically, a methodology to answer the probability that a given party will have representation on the chamber of deputies was developed. Inferences were made on a Bayesian scenario using the Monte Carlo simulation technique, and the developed methodology was applied on data from the Brazilian elections for Members of the Legislative Assembly and Federal Chamber of Deputies in 2010. A performance rate was also presented to evaluate the efficiency of the methodology. Calculations and simulations were carried out using the free R statistical software. PMID:25786259

  5. Statistical learning and selective inference

    PubMed Central

    Taylor, Jonathan; Tibshirani, Robert J.

    2015-01-01

    We describe the problem of “selective inference.” This addresses the following challenge: Having mined a set of data to find potential associations, how do we properly assess the strength of these associations? The fact that we have “cherry-picked”—searched for the strongest associations—means that we must set a higher bar for declaring significant the associations that we see. This challenge becomes more important in the era of big data and complex statistical modeling. The cherry tree (dataset) can be very large and the tools for cherry picking (statistical learning methods) are now very sophisticated. We describe some recent new developments in selective inference and illustrate their use in forward stepwise regression, the lasso, and principal components analysis. PMID:26100887

  6. Development, characterization, and cross-species/genera transferability of SSR markers for rubber tree (Hevea brasiliensis).

    PubMed

    Yu, Fei; Wang, Bao-Hua; Feng, Su-Ping; Wang, Jing-Yi; Li, Wei-Guo; Wu, Yao-Ting

    2011-03-01

    Genomic simple sequence repeat (SSR) markers are particularly valuable in studies of genetic diversity, evolution, genetic linkage map construction, quantitative trait loci tagging, and marker-assisted selection because of their multi-allelic nature, reproducibility, co-dominant inheritance, high abundance, and extensive genome coverage. The traditional methods of SSR marker development, such as genomic-SSR hybrid screening and microsatellite enrichment, have the disadvantages of high cost and complex operation. The selectively amplified microsatellite method is less costly and highly efficient as well as being simple and convenient. In this study, 252 sequences with SSRs were cloned from the rubber tree (Hevea brasiliensis) genome from which 258 SSR loci were obtained. The average repeat number was six. There were only 10 (3.9%) mononucleotide, trinucleotide, and pentanucleotide repeats, whereas the remaining 248 (96.1%) were dinucleotide repeats, including 128 (49.6%) GT/CA repeats, 118 (45.7%) GA/CT repeats, and 2 (0.8%) AT/TA repeats. A total of 126 primer pairs (see ESM) were successfully designed of which 36 primer pairs generated polymorphic products from 12 accessions of the cultivated species, 4 related species, and 3 species of the family Euphorbiaceae. In addition, investigations based on four genomic SSRs (GAR4, ACR22, CTR25, and GTR28) by cloning and sequencing provided evidence for cross-species/genera applicability, and homologous sequences were obtained from the rubber tree and Euphorbiaceae. Further analysis about the variation of the flanking regions of the four markers was carried out. PMID:20960206

  7. Phialide arrangement and character evolution in the helotialean anamorph genera Cadophora and Phialocephala.

    PubMed

    Day, Melissa J; Hall, Jocelyn C; Currah, Randolph S

    2012-01-01

    The dematiaceous hyphomycete genera Cadophora and Phialocephala are anamorphs associated with mollisioid inoperculate discomycetes (Helotiales) and are delineated based on the complexity of the phialide arrangement with members of Cadophora producing solitary phialides and species of Phialocephala producing complex heads of multiple phialides. A third phylogenetically related taxon, Leptodontidium orchidicola, produces mostly indehiscent conidia that may represent non-functional phialides. Morphological characteristics of both sexual and asexual states of these and other fungi in a focal group of helotialean taxa were re-examined, in light of relationships shown by molecular phylogenetic analyses of rDNA ITS sequences, to determine the evolutionary significance of phialide arrangement. The focal species of Phialocephala formed a monophyletic clade, while five of six species of Cadophora including the type were in a separate clade along with L. orchidicola. C. finlandica was placed in a third clade with species of Meliniomyces and Rhizoscyphus. We hypothesized that the ancestral state for species in Cadophora and Phialocephala is the production of sclerotium-like heads of multiple phialides, which has been retained in most species assignable to Phialocephala. A reduction to solitary phialides occurred in the lineage leading to the clade containing most of the Cadophora species. Two possible reductions to non-functional phialides were identified: one in the Meliniomyces-C. finlandica-Chloridium paucisporum clade and another in the L. orchidicola and Mollisia "rhizophila": clade. A reversion to increased phialide complexity might have occurred in the clade containing C. finlandica and Ch. paucisporum. Our data and analyses also show a previously unrecognized relationship between teleomorph and anamorph morphology in that Mollisia species with smaller asci would be expected to have Phialocephala states while those with larger asci would be expected to have Cadophora

  8. LOWER LEVEL INFERENCE CONTROL IN STATISTICAL DATABASE SYSTEMS

    SciTech Connect

    Lipton, D.L.; Wong, H.K.T.

    1984-02-01

    An inference is the process of transforming unclassified data values into confidential data values. Most previous research in inference control has studied the use of statistical aggregates to deduce individual records. However, several other types of inference are also possible. Unknown functional dependencies may be apparent to users who have 'expert' knowledge about the characteristics of a population. Some correlations between attributes may be concluded from 'commonly-known' facts about the world. To counter these threats, security managers should use random sampling of databases of similar populations, as well as expert systems. 'Expert' users of the DATABASE SYSTEM may form inferences from the variable performance of the user interface. Users may observe on-line turn-around time, accounting statistics. the error message received, and the point at which an interactive protocol sequence fails. One may obtain information about the frequency distributions of attribute values, and the validity of data object names from this information. At the back-end of a database system, improved software engineering practices will reduce opportunities to bypass functional units of the database system. The term 'DATA OBJECT' should be expanded to incorporate these data object types which generate new classes of threats. The security of DATABASES and DATABASE SySTEMS must be recognized as separate but related problems. Thus, by increased awareness of lower level inferences, system security managers may effectively nullify the threat posed by lower level inferences.

  9. Cortical circuits for perceptual inference.

    PubMed

    Friston, Karl; Kiebel, Stefan

    2009-10-01

    This paper assumes that cortical circuits have evolved to enable inference about the causes of sensory input received by the brain. This provides a principled specification of what neural circuits have to achieve. Here, we attempt to address how the brain makes inferences by casting inference as an optimisation problem. We look at how the ensuing recognition dynamics could be supported by directed connections and message-passing among neuronal populations, given our knowledge of intrinsic and extrinsic neuronal connections. We assume that the brain models the world as a dynamic system, which imposes causal structure on the sensorium. Perception is equated with the optimisation or inversion of this internal model, to explain sensory input. Given a model of how sensory data are generated, we use a generic variational approach to model inversion to furnish equations that prescribe recognition; i.e., the dynamics of neuronal activity that represents the causes of sensory input. Here, we focus on a model whose hierarchical and dynamical structure enables simulated brains to recognise and predict sequences of sensory states. We first review these models and their inversion under a variational free-energy formulation. We then show that the brain has the necessary infrastructure to implement this inversion and present stimulations using synthetic birds that generate and recognise birdsongs.

  10. Cortical circuits for perceptual inference.

    PubMed

    Friston, Karl; Kiebel, Stefan

    2009-10-01

    This paper assumes that cortical circuits have evolved to enable inference about the causes of sensory input received by the brain. This provides a principled specification of what neural circuits have to achieve. Here, we attempt to address how the brain makes inferences by casting inference as an optimisation problem. We look at how the ensuing recognition dynamics could be supported by directed connections and message-passing among neuronal populations, given our knowledge of intrinsic and extrinsic neuronal connections. We assume that the brain models the world as a dynamic system, which imposes causal structure on the sensorium. Perception is equated with the optimisation or inversion of this internal model, to explain sensory input. Given a model of how sensory data are generated, we use a generic variational approach to model inversion to furnish equations that prescribe recognition; i.e., the dynamics of neuronal activity that represents the causes of sensory input. Here, we focus on a model whose hierarchical and dynamical structure enables simulated brains to recognise and predict sequences of sensory states. We first review these models and their inversion under a variational free-energy formulation. We then show that the brain has the necessary infrastructure to implement this inversion and present stimulations using synthetic birds that generate and recognise birdsongs. PMID:19635656

  11. [Microflora of the atmosphere in the city of Trujillo (Peru). III. Genera isolated during the year 1971].

    PubMed

    Requejo, H

    1975-07-30

    There were 1762 fungi isolated from the atmosphere of Trujillo city (Peru) during the year 1971. These isolants belonged to 23 genera of fungi. The most frequently isolated were: Cladosporium, Penicillium, Fusarium, Stemphylium, Alternaria, Helminthosporium, Aspergillus and Tilachlidium. Nine genera are reported for first time from the air of the city (Tilachlidium, Cephalosporium, Mucor, Aureobasidium, Hormiscium, Trichoderma, Stachybotrys, Paecilomyces and Fisidium). Six genera may be alergenic for asthmatic patients of Trujillo city.

  12. Systematic revision and phylogeny of the genera Blakeius Ashmead, 1903 and Liomutilla André, 1907, with description of two new genera (Hymenoptera: Mutillidae, Myrmillinae).

    PubMed

    Turrisi, Giuseppe Fabrizio; Palmerini, Maurizio Matteini; Brothers, Denis J

    2015-09-01

    Nine species of Palaearctic Myrmillinae with females bearing two round spots on the second metasomal tergite, currently assigned to two genera, Blakeius Ashmead, 1903 and Liomutilla André, 1907, are revised and their phylogenetic relationships are investigated. The cladistic analyses demonstrate that Blakeius is not strictly monophyletic but includes three distinct lineages: Blakeius s. str., containing three species, an additional two genera proposed as new (Bidecoloratilla Turrisi & Matteini Palmerini, gen. nov., with four species, type species Mutilla chiesi Spinola, 1839, and Bimaculatilla Turrisi & Matteini Palmerini, gen. nov., including only type species Myrmilla invreai Suárez, 1958), and the monotypic genus Liomutilla is nested within the former Blakeius. A new status is proposed for Bla. cobosi (Suárez, 1958), stat. nov., and the specific status of Bid. iberica (Suárez, 1958), is confirmed. New combinations are proposed for Bim. invreai (Suárez, 1958), comb. nov. (from Myrmilla), Bid. chiesi (Spinola, 1839), comb. nov., Bid. iberica (Suárez, 1958), comb. nov., Bid. leopoldina (Invrea, 1955), comb. nov. Bid. negrei (Suárez, 1958), comb. nov. (all from Blakeius). Lectotypes are designated for Myr. otini Giner Marí, 1959 (♀) and Myr. leopoldina Invrea, 1955 (♂). Redescriptions of all treated taxa, based also on material belonging to the type series, are provided, along with illustrations of both sexes. Based on extensive material of relevant museum collections and personal collections, the distributions of all treated taxa are revised and illustrated through distributional maps. A revised key to genera of the subfamily Myrmillinae of the Palaearctic Region is given.

  13. Inferring epigenetic dynamics from kin correlations.

    PubMed

    Hormoz, Sahand; Desprat, Nicolas; Shraiman, Boris I

    2015-05-01

    Populations of isogenic embryonic stem cells or clonal bacteria often exhibit extensive phenotypic heterogeneity that arises from intrinsic stochastic dynamics of cells. The phenotypic state of a cell can be transmitted epigenetically in cell division, leading to correlations in the states of cells related by descent. The extent of these correlations is determined by the rates of transitions between the phenotypic states. Therefore, a snapshot of the phenotypes of a collection of cells with known genealogical structure contains information on phenotypic dynamics. Here, we use a model of phenotypic dynamics on a genealogical tree to define an inference method that allows extraction of an approximate probabilistic description of the dynamics from observed phenotype correlations as a function of the degree of kinship. The approach is tested and validated on the example of Pyoverdine dynamics in Pseudomonas aeruginosa colonies. Interestingly, we find that correlations among pairs and triples of distant relatives have a simple but nontrivial structure indicating that observed phenotypic dynamics on the genealogical tree is approximately conformal--a symmetry characteristic of critical behavior in physical systems. The proposed inference method is sufficiently general to be applied in any system where lineage information is available. PMID:25902540

  14. Immatures of the New World Treehopper Tribe Amastrini (Hemiptera: Membracidae: Smiliinae) with a key to genera

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The immatures stages of 9 of the 11 genera (Amastris Stål, Bajulata Ball, Erosne Stål, Harmonides Kirkaldy, Idioderma Van Duzee, Lallemandia Funkhouser, Neotynelia Creão-Duarte & Sakakibara, Tynelia Stål, and Vanduzea Goding) of the tribe Amastrini are described for the first time long with brief di...

  15. Protoptiline Caddisfly Genera Endemic to the Southern Cone Region of South America (Trichoptera: Glossosomatidae)

    NASA Astrophysics Data System (ADS)

    Robertson, D. R.; Holzenthal, R. W.

    2005-05-01

    The Trichoptera fauna of the Southern Cone region of South America (Argentina, Chile, Uruguay, Paraguay, and SE Brazil) is well known for its high degree of endemism, at both the species and genus level. This is also true for the saddle or tortoise case-making family Glossosomatidae, represented entirely in the region by members of the subfamily Protoptilinae. The Southern Cone includes six endemic protoptiline genera: Canoptila, Itauara, Mastigoptila, Merionoptila, Scotiotrichia, and Tolhuaca, containing 19 described species. Although not particularly species diverse when compared to the rest of the Neotropical Trichoptera fauna, these endemics are note-worthy: some genera display morphological characteristics that may be considered very primitive and others are very evolutionarily derived. Additionally, there are at least 11 new species whose placement is uncertain. This points out the need to reexamine the taxonomy and evaluate the evolutionary relationships among these genera. Recently several new species of Mastigoptila and Tolhuaca were described, including some females. Taxonomic revisions of the remaining genera based on careful examination of the male and female genitalia, wing venation, and other adult morphological characters, are currently underway. Included in the revisions are descriptions of new species, new illustrations of previously described species, and a phylogenetic assessment.

  16. MEMBRANE FILTER PROCEDURE FOR ENUMERATING THE COMPONENT GENERA OF THE COLIFORM GROUP IN SEAWATER

    EPA Science Inventory

    A facile, quantitative, membrane filter procedure (mC) for defining the distribution of coliform populations in seawater according to the component genera was developed. The procedure, which utilizes a series of in situ substrate tests to obviate the picking of colonies for ident...

  17. New flat mite genera (Acari: Trombidiformes: Tenuipalpidae) associated with Australian sedges (Cyperaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two new genera, Gahniacarus and Cyperacarus, and four new species, G. gersonus, G. tuberculatus, C. naomae and C. foliatus, are described from native Australian sedge species in the genus Gahnia (Cyperaceae). Leg chaetotaxy is provided for all stages of each species. The importance of taxonomic ch...

  18. New species of the Eastern Hemisphere genera Afroheriades and Noteriades (Hymenoptera: Megachilidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New species of the rarely encountered megachilid genera Afroheriades Peters from South Africa, A. hyalinus sp. n., and Noteriades Cockerell from Myanmar and Thailand, N. jenniferae sp. n. and N. spinosus sp. n., are described and illustrated. The species are described to make their names available i...

  19. An illustrated key to the genera of Thripinae (Thysanoptera, Thripidae) from Iran

    PubMed Central

    Mirab-balou, Majid; Minaei, Kambiz; Chen, Xue-Xin

    2013-01-01

    Abstract An illustrated key is provided for the identification of 35 genera of Thripinae (Thysanoptera: Thripidae) from Iran with comments for each genus. Chirothrips maximi Ananthakrishnan and Limothrips cerealium Haliday are recorded from Iran for the first time. A checklist is provided of Thripinae recorded from this country. PMID:23950669

  20. Two new genera and two new species of Mantophasmatodea (Insecta, Polyneoptera) from Namibia

    PubMed Central

    Wipfler, Benjamin; Pohl, Hans; Predel, Reinhard

    2012-01-01

    Abstract Two new species and two new genera (Pachyphasma, Striatophasma) of Mantophasmatodea are described from Namibia. Pachyphasma brandbergense is endemic to the Brandberg massif; Striatophasma occupies an extensive area south of the region inhabited by Mantophasma. Phylogenetic analyses (see Predel et al. in press) suggest a sistergroup relationship of Striatophasma and the South African Austrophasmatidae. PMID:22328860

  1. Synopsis of warty leaf beetles genera of the world (Coleoptera: Chrysomelidae: Cryptocephalinae: Chlamisini)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    World genera of Chlamisini are reviewed, diagnosed, and illustrated. A key for their dentification is provided. A replacement name, Kakita Chamorro-Lacayo and Konstantinov is presented for Ceratochlamys Bokermann which is a junior homonym of Ceratochlamys Habe, 1946 (Mollusca). Chlamisus rousei M...

  2. New Records and Range Extensions for Several Chironomid Genera from Lake Superior

    EPA Science Inventory

    Five genera of chironomids have been reported for the first time in Lake Superior. Chironomids are small flying insects with a sediment-dwelling aquatic larval stage. The chironomids were collected by scientists at the Mid-Continent Ecology Division as part of a research program ...

  3. The assassin bug genera Nagustoides and Stenolemus (Hemiptera: Heteroptera: Reduviidae) newly recorded from Japan.

    PubMed

    Ishikawa, Tadashi; Naka, Takeru

    2016-01-01

    Two assassin bug genera, Nagustoides Miller, 1954 of Harpactorinae and Stenolemus Signoret, 1858 of Emesinae (Hemiptera: Heteroptera: Reduviidae), are recorded from Japan for the first time, with the presence of the representative species N. lii Zhao, Cai & Ren, 2006 and S. alikakay Rédei & Tsai, 2010. Distribution ranges of the two species are revised by the present finding. PMID:27615956

  4. Entropic Biological Score: a cell cycle investigation for GRNs inference.

    PubMed

    Lopes, Fabrício M; Ray, Shubhra Sankar; Hashimoto, Ronaldo F; Cesar, Roberto M

    2014-05-15

    Inference of gene regulatory networks (GRNs) is one of the most challenging research problems of Systems Biology. In this investigation, a new GRNs inference methodology, called Entropic Biological Score (EBS), which linearly combines the mean conditional entropy (MCE) from expression levels and a Biological Score (BS), obtained by integrating different biological data sources, is proposed. The EBS is validated with the Cell Cycle related functional annotation information, available from Munich Information Center for Protein Sequences (MIPS), and compared with some existing methods like MRNET, ARACNE, CLR and MCE for GRNs inference. For real networks, the performance of EBS, which uses the concept of integrating different data sources, is found to be superior to the aforementioned inference methods. The best results for EBS are obtained by considering the weights w1=0.2 and w2=0.8 for MCE and BS values, respectively, where approximately 40% of the inferred connections are found to be correct and significantly better than related methods. The results also indicate that expression profile is able to recover some true connections, that are not present in biological annotations, thus leading to the possibility of discovering new relations between its genes. PMID:24631265

  5. Evolution and biogeography of the slipper orchids: Eocene vicariance of the conduplicate genera in the Old and New World Tropics.

    PubMed

    Guo, Yan-Yan; Luo, Yi-Bo; Liu, Zhong-Jian; Wang, Xiao-Quan

    2012-01-01

    Intercontinental disjunctions between tropical regions, which harbor two-thirds of the flowering plants, have drawn great interest from biologists and biogeographers. Most previous studies on these distribution patterns focused on woody plants, and paid little attention to herbs. The Orchidaceae is one of the largest families of angiosperms, with a herbaceous habit and a high species diversity in the Tropics. Here we investigate the evolutionary and biogeographical history of the slipper orchids, which represents a monophyletic subfamily (Cypripedioideae) of the orchid family and comprises five genera that are disjunctly distributed in tropical to temperate regions. A relatively well-resolved and highly supported phylogeny of slipper orchids was reconstructed based on sequence analyses of six maternally inherited chloroplast and two low-copy nuclear genes (LFY and ACO). We found that the genus Cypripedium with a wide distribution in the northern temperate and subtropical zones diverged first, followed by Selenipedium endemic to South America, and finally conduplicate-leaved genera in the Tropics. Mexipedium and Phragmipedium from the neotropics are most closely related, and form a clade sister to Paphiopedilum from tropical Asia. According to molecular clock estimates, the genus Selenipedium originated in Palaeocene, while the most recent common ancestor of conduplicate-leaved slipper orchids could be dated back to the Eocene. Ancestral area reconstruction indicates that vicariance is responsible for the disjunct distribution of conduplicate slipper orchids in palaeotropical and neotropical regions. Our study sheds some light on mechanisms underlying generic and species diversification in the orchid family and tropical disjunctions of herbaceous plant groups. In addition, we suggest that the biogeographical study should sample both regional endemics and their widespread relatives.

  6. Category Representation for Classification and Feature Inference

    ERIC Educational Resources Information Center

    Johansen, Mark K.; Kruschke, John K.

    2005-01-01

    This research's purpose was to contrast the representations resulting from learning of the same categories by either classifying instances or inferring instance features. Prior inference learning research, particularly T. Yamauchi and A. B. Markman (1998), has suggested that feature inference learning fosters prototype representation, whereas…

  7. On the identity of Mastacanthus Suffrian, 1852 and Sternoglosus Suffrian, 1866 and key to world genera of Pachybrachina (Chrysomelidae: Cryptocephalinae: Cryptocephalini)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pachybrachina includes 8 genera worldwide. The identity of the two Neotropical genera Mastacanthus Suffrian and Sternoglosus Suffrian is established. Redescription of the type species of both genera and an illustrated key to world genera are provided. Type species of Sternoglosus and the lectotype f...

  8. Revision of the paraphyletic genus Koerneria Meyl, 1960 and resurrection of two other genera of Diplogastridae (Nematoda)

    PubMed Central

    Kanzaki, Natsumi; Ragsdale, Erik J.; Giblin-Davis, Robin M.

    2014-01-01

    Abstract Recent inferences of phylogeny from molecular characters, as well as a reexamination of morphological and biological characters, reject the monophyly of the nematode genus Koerneria Meyl, 1960 (Diplogastridae). Here, Koerneria sensu lato is revised. The genus, which previously consisted of 40 species, is separated into three genera. Almost all of the transferred species are moved to the resurrected genus Allodiplogaster Paramonov & Sobolev in Skrjabin et al. (1954). Koerneria and Allodiplogaster are distinguished from each other by a weakly vs. clearly striated body surface, an undivided vs. divided stomatal cheilostom, and arrangement of the terminal ventral triplet of male genital papillae, namely in that v5 and v6 are paired and separated from v7 vs. v5–v7 being close to each other. Allodiplogaster is further divided into two groups of species, herein called the henrichae and striata groups, based on both morphological and life-history traits. The henrichae group is characterized by papilliform labial sensilla and male genital papillae, a conical tail in both males and females, and an association with terrestrial habitats and insects, whereas the striata group is characterized by setiform labial sensilla and male genital papillae, an elongated conical tail in both sexes, and an association with aquatic habitats. A second genus, Anchidiplogaster Paramonov, 1952, is resurrected to include a single species that is characterized by its miniscule stoma and teeth, unreflexed testis, and a distinct lack of male genital papillae or stomatal apodemes. Lastly, one further species that was previously included in Koerneria sensu lato is transferred to the genus Pristionchus Kreis, 1932. The revision of Koerneria sensu lato is necessitated by the great variability in its subordinate taxa, which occupy a variety of habitats, in addition to the increased attention to Diplogastridae as a model system for comparative mechanistic biology. PMID:25349487

  9. One, four or 100 genera? A new classification of the cone snails

    PubMed Central

    Puillandre, N.; Duda, T. F.; Meyer, C.; Olivera, B. M.; Bouchet, P.

    2015-01-01

    We present a new classification for the genus Conus sensu lato (family Conidae), based on molecular phylogenetic analyses of 329 species. This classification departs from both the traditional classification in only one genus and from a recently proposed shell- and radula-based classification scheme that separates members of this group into five families and 115 genera. Roughly 140 genus-group names are available for Recent cone snails. We propose to place all cone snails within a single family (Conidae) containing four genera—Conus, Conasprella, Profundiconus and Californiconus (with Conus alone encompassing about 85% of known species)—based on the clear separation of cone snails into four distinct and well-supported groups/lineages in molecular phylogenetic analyses. Within Conus and Conasprella, we recognize 57 and 11 subgenera, respectively, that represent well-supported subgroupings within these genera, which we interpret as evidence of intrageneric distinctiveness. We allocate the 803 Recent species of Conidae listed as valid in the World Register of Marine Species into these four genera and 71 subgenera, with an estimate of the confidence for placement of species in these taxonomic categories based on whether molecular or radula and/or shell data were used in these determinations. Our proposed classification effectively departs from previous schemes by (1) limiting the number of accepted genera, (2) retaining the majority of species within the genus Conus and (3) assigning members of these genera to species groups/subgenera to enable the effective communication of these groups, all of which we hope will encourage acceptance of this scheme. PMID:26300576

  10. Comparative descriptions of non-adult stages of four genera of Gordiids (Phylum: Nematomorpha).

    PubMed

    Szmygiel, Cleo; Schmidt-Rhaesa, Andreas; Hanelt, Ben; Bolek, Matthew G

    2014-02-25

    Freshwater hairworms infect terrestrial arthropods as larvae but are free-living in aquatic habitats as adults. Estimates suggest that only 18% of hairworm species have been described globally and biodiversity studies on this group have been hindered by unreliable ways of collecting adult free living worms over large geographical areas. However, recent work indicates that non-adult cyst stages of hairworms may be the most commonly encountered stages of gordiids in the environment, and can be used for discovering the hidden diversity of this group. Unfortunately, little information is available on the morphological characteristics of non-adult stages of hairworms. To address this problem, we describe and compare morphological characteristics of non-adult stages for nine species of African and North American gordiids from four genera (Chordodes, Gordius, Paragordius, and Neochordodes). Observations were made on the oviposition behavior of adult worms and morphological characteristics were recorded for egg strings, larvae and cysts using light and differential interference contrast microscopy and/or scanning electron microscopy. Our study indicates that three distinct types of oviposition behaviors and three distinct morphological types of egg string, larva, and cysts were present among the four genera of gordiids. Although species identification based on cyst characteristics was not always possible among different species of gordiids, cyst morphology was conserved among some genera and all clades of gordiids. More importantly, our work indicates that gordiid larval morphology can be used for predicting cyst morphology among other gordiid genera. The capability to identify and predict gordiid genera and/or clades based on cyst morphology will be useful for culturing gordiids in the laboratory from field collected cysts and these new techniques will undoubtedly allow others to discover new species of gordiids from around the world.

  11. Phylogeny of minute carabid beetles and their relatives based upon DNA sequence data (Coleoptera, Carabidae, Trechitae)

    PubMed Central

    Maddison, David R.; Ober, Karen A.

    2011-01-01

    Abstract The phylogeny of ground beetles of supertribe Trechitae is inferred using DNA sequences of genes that code for 28S ribosomal RNA, 18S ribosomal RNA, and wingless. Within the outgroups, austral psydrines are inferred to be monophyletic, and separate from the three genera of true Psydrina (Psydrus, Nomius, Laccocenus); the austral psydrines are formally removed from Psydrini and are treated herein as their own tribe, Moriomorphini Sloane. All three genes place Gehringia with Psydrina. Trechitae is inferred to be monophyletic, and sister to Patrobini. Within trechites, evidence is presented that Tasmanitachoides is not a tachyine, but is instead a member of Trechini. Perileptus is a member of subtribe Trechodina. Against Erwin’s hypothesis of anillines as a polyphyletic lineage derived from the tachyine genus Paratachys, the anillines sampled are monophyletic, and not related to Paratachys. Zolini, Pogonini, Tachyina, and Xystosomina are all monophyletic, with the latter two being sister groups. The relationships of the subtribe Bembidiina were studied in greater detail. Phrypeus is only distantly related to Bembidion, and there is no evidence from sequence data that it belongs within Bembidiina. Three groups that have been recently considered to be outside of the large genus Bembidion are shown to be derived members of Bembidion, related to subgroups: Cillenus is related to the Ocydromus complex of Bembidion, Zecillenus is related to the New Zealand subgenus Zeplataphus, and Hydrium is close to subgenus Metallina. The relationships among major lineages of Trechitae are not, however, resolved with these data. PMID:22379388

  12. Revisions of the genera Lurama Schaus, 1928 and Ulmara Schaus, 1928 (Lepidoptera, Mimallonoidea, Mimallonidae) with the descriptions of three new Ulmara species and a new genus

    PubMed Central

    St. Laurent, Ryan A.

    2016-01-01

    Abstract The Andean genera Lurama Schaus, 1928 and Ulmara Schaus, 1928 are revised. Lurama poses difficulty for revision due to lost male genitalia of the types of both described species. Ulmara conjuncta sp. n., Ulmara azurula sp. n., and Ulmara dombroskiei sp. n. are described as new in the genus Ulmara. A lectotype is designated for Lurama quindiuna Schaus, 1928 and Ulmara rotunda (Dognin, 1916). A new monotypic genus, Cunicumara gen. n., which is externally similar to Ulmara, is described to include the new species Cunicumara anae sp. n. from low elevations of Bolivia and Paraguay. Male genital morphology does not support a close association of Cunicumara with Lurama or Ulmara. The latter two genera, however, are closely related based on similarities of male genitalia and biogeography. PMID:27594799

  13. Revisions of the genera Lurama Schaus, 1928 and Ulmara Schaus, 1928 (Lepidoptera, Mimallonoidea, Mimallonidae) with the descriptions of three new Ulmara species and a new genus

    PubMed Central

    St. Laurent, Ryan A.

    2016-01-01

    Abstract The Andean genera Lurama Schaus, 1928 and Ulmara Schaus, 1928 are revised. Lurama poses difficulty for revision due to lost male genitalia of the types of both described species. Ulmara conjuncta sp. n., Ulmara azurula sp. n., and Ulmara dombroskiei sp. n. are described as new in the genus Ulmara. A lectotype is designated for Lurama quindiuna Schaus, 1928 and Ulmara rotunda (Dognin, 1916). A new monotypic genus, Cunicumara gen. n., which is externally similar to Ulmara, is described to include the new species Cunicumara anae sp. n. from low elevations of Bolivia and Paraguay. Male genital morphology does not support a close association of Cunicumara with Lurama or Ulmara. The latter two genera, however, are closely related based on similarities of male genitalia and biogeography.

  14. Revisions of the genera Lurama Schaus, 1928 and Ulmara Schaus, 1928 (Lepidoptera, Mimallonoidea, Mimallonidae) with the descriptions of three new Ulmara species and a new genus.

    PubMed

    St Laurent, Ryan A

    2016-01-01

    The Andean genera Lurama Schaus, 1928 and Ulmara Schaus, 1928 are revised. Lurama poses difficulty for revision due to lost male genitalia of the types of both described species. Ulmara conjuncta sp. n., Ulmara azurula sp. n., and Ulmara dombroskiei sp. n. are described as new in the genus Ulmara. A lectotype is designated for Lurama quindiuna Schaus, 1928 and Ulmara rotunda (Dognin, 1916). A new monotypic genus, Cunicumara gen. n., which is externally similar to Ulmara, is described to include the new species Cunicumara anae sp. n. from low elevations of Bolivia and Paraguay. Male genital morphology does not support a close association of Cunicumara with Lurama or Ulmara. The latter two genera, however, are closely related based on similarities of male genitalia and biogeography.

  15. Revisions of the genera Lurama Schaus, 1928 and Ulmara Schaus, 1928 (Lepidoptera, Mimallonoidea, Mimallonidae) with the descriptions of three new Ulmara species and a new genus.

    PubMed

    St Laurent, Ryan A

    2016-01-01

    The Andean genera Lurama Schaus, 1928 and Ulmara Schaus, 1928 are revised. Lurama poses difficulty for revision due to lost male genitalia of the types of both described species. Ulmara conjuncta sp. n., Ulmara azurula sp. n., and Ulmara dombroskiei sp. n. are described as new in the genus Ulmara. A lectotype is designated for Lurama quindiuna Schaus, 1928 and Ulmara rotunda (Dognin, 1916). A new monotypic genus, Cunicumara gen. n., which is externally similar to Ulmara, is described to include the new species Cunicumara anae sp. n. from low elevations of Bolivia and Paraguay. Male genital morphology does not support a close association of Cunicumara with Lurama or Ulmara. The latter two genera, however, are closely related based on similarities of male genitalia and biogeography. PMID:27594799

  16. In situ hybridization analysis of gibbon chromosomes suggests that amplification of alpha satellite DNA in the telomere region is confined to two of the four genera.

    PubMed

    Baicharoen, Sudarath; Arsaithamkul, Visit; Hirai, Yuriko; Hara, Toru; Koga, Akihiko; Hirai, Hirohisa

    2012-11-01

    The siamang (Symphalangus syndactylus), a species of the family Hylobatidae (gibbons), carries large blocks of constitutive heterochromatin in the telomere region of chromosomes. We recently found that alpha satellite DNA constitutes these heterochromatin blocks as a main component. Alpha satellite DNA, tandem repeat sequences of 171-bp repeat units, is a major component of centromeres in primates. In addition to the siamang, the white-cheeked gibbon (Nomascus leucogenys) was previously found to carry the alpha satellite DNA in the telomere region, although not as large a scale as the siamang. Gibbons comprise four genera: Hoolock, Hylobates, Nomascus, and Symphalangus. Here, we report that the amplification of alpha satellite DNA in the telomere region is probably confined to two genera: Nomascus and Symphalangus. We examined one species of Hoolock and four species of Hylobates and obtained evidence against such an amplification event in these species. The phylogenetic relationship of the four gibbon genera remains unclear. One simple explanation for the current distribution of the telomere region alpha satellite DNA would be that Nomascus and Symphalangus are relatively closely related and the amplification occurred in their common ancestor.

  17. Prefrontal Cortex: Role in Acquisition of Overlapping Associations and Transitive Inference

    ERIC Educational Resources Information Center

    DeVito, Loren M.; Lykken, Christine; Kanter, Benjamin R.; Eichenbaum, Howard

    2010-01-01

    "Transitive inference" refers to the ability to judge from memory the relationships between indirectly related items that compose a hierarchically organized series, and this capacity is considered a fundamental feature of relational memory. Here we explored the role of the prefrontal cortex in transitive inference by examining the performance of…

  18. Molecular phylogeny and systematics of Polyblastia (Verrucariaceae, Eurotiomycetes) and allied genera.

    PubMed

    Savić, Sanja; Tibell, Leif; Gueidan, Cécile; Lutzoni, François

    2008-11-01

    Phylogenetic relationships of the lichen genus Polyblastia and closely related taxa in the family Verrucariaceae (Verrucariales, Chaetothyriomycetidae) were studied. A total of 130 sets of sequences (nuLSU rDNA, nuITS rDNA and RPB1 region A-D), including 129 newly generated sequences, were analysed. Phylogenetic relationships were inferred using a Bayesian approach based on two datasets. A first analysis of a larger, two-locus dataset (nuLSU and RPB1) for 128 members of the Verrucariaceae, confirmed the polyphyly of Polyblastia, Thelidium, Staurothele, and Verrucaria, as currently construed. The second analysis focused on 56 Polyblastia and allied taxa, but using an additional locus (nuITS rDNA) and two closely related outgroup taxa. The latter analysis revealed strongly supported groups, such as Polyblastia s. str., the Thelidium group (a mixture of Polyblastia, Thelidium, Staurothele and Verrucaria species). The genus Sporodictyon, which is here accepted, also accommodates Sporodictyon terrestre comb. nov. Morphological features traditionally used for characterizing Polyblastia, Thelidium, Staurothele and Verrucaria, such as spore septation and colour, occurrence of hymenial photobiont, involucrellum structure, and substrate preference, were found to be only partially consistent within the strongly supported clades, and thus are not always reliable features for characterizing natural groups. PMID:18945603

  19. Differences between forest type and vertical strata in the diversity and composition of hymenopteran families and mymarid genera in northeastern temperate forests.

    PubMed

    Vance, C C; Smith, S M; Malcolm, J R; Huber, J; Bellocq, M I

    2007-10-01

    Most insects' assemblages differ with forest type and show vertical stratification. We tested for differences in richness, abundance and composition of hymenopteran families and mymarid genera between sugar maple (Acer saccharum) and white pine (Pinus strobus) stands and between canopy and understory in northeastern temperate forests in Canada. We used flight interception traps (modified malaise traps) suspended in the canopy and the understory in a split-split block design, with forest type as the main factor, forest stratum as the first split factor, and collection bottle location as the second split factor. Hymenopteran families and mymarid genera differed in their diversity depending on forest type and stratum. Both family and genera richness were higher in maple than in pine forests, whereas family richness was higher in the canopy and top bottles and generic richness was higher in the understory and bottom bottles. Multivariate analysis separated samples by forest type, vegetation stratum, and bottle location. Family composition showed 77% similarity between forest types and 73% between the canopy and understory. At the lower taxa level, mymarid genera showed only 47% similarity between forest types and 40% between forest strata, indicating vertical stratification and relatively high beta-diversity. Our study suggests that hymenopteran diversity and composition is strongly dependent on forest type and structure, making flying members of this order particularly vulnerable to forest management practices. It also shows that insect assemblage composition (especially at low-taxon levels), rather than relative abundance and richness, is the community attribute most sensitive to forest type and vertical stratification.

  20. Multi-locus phylogenetic inference among New World Vultures (Aves: Cathartidae).

    PubMed

    Johnson, Jeff A; Brown, Joseph W; Fuchs, Jérôme; Mindell, David P

    2016-12-01

    New World Vultures are large-bodied carrion feeding birds in the family Cathartidae, currently consisting of seven species from five genera with geographic distributions in North and South America. No study to date has included all cathartid species in a single phylogenetic analysis. In this study, we investigated the phylogenetic relationships among all cathartid species using five nuclear (nuc; 4060bp) and two mitochondrial (mt; 2165bp) DNA loci with fossil calibrated gene tree (27 outgroup taxa) and coalescent-based species tree (2 outgroup taxa) analyses. We also included an additional four nuclear loci (2578bp) for the species tree analysis to explore changes in nodal support values. Although the stem lineage is inferred to have originated ∼69 million years ago (Ma; 74.5-64.9 credible interval), a more recent basal split within Cathartidae was recovered at ∼14Ma (17.1-11.1 credible interval). Two primary clades were identified: (1) Black Vulture (Coragyps atratus) together with the three Cathartes species (Lesser C. burrovianus and Greater C. melambrotus Yellow-headed Vultures, and Turkey Vulture C. aura), and (2) King Vulture (Sarcoramphus papa), California (Gymnogyps californianus) and Andean (Vultur gryphus) Condors. Support for taxon relationships within the two basal clades were inconsistent between analyses with the exception of Black Vulture sister to a monophyletic Cathartes clade. Increased support for a yellow-headed vulture clade was recovered in the species tree analysis using the four additional nuclear loci. Overall, these results are in agreement with cathartid life history (e.g. olfaction ability and behavior) and contrasting habitat affinities among sister taxa with overlapping geographic distributions. More research is needed using additional molecular loci to further resolve the phylogenetic relationships within the two basal cathartid clades, as speciation appeared to have occurred in a relatively short period of time.

  1. Multi-locus phylogenetic inference among New World Vultures (Aves: Cathartidae).

    PubMed

    Johnson, Jeff A; Brown, Joseph W; Fuchs, Jérôme; Mindell, David P

    2016-12-01

    New World Vultures are large-bodied carrion feeding birds in the family Cathartidae, currently consisting of seven species from five genera with geographic distributions in North and South America. No study to date has included all cathartid species in a single phylogenetic analysis. In this study, we investigated the phylogenetic relationships among all cathartid species using five nuclear (nuc; 4060bp) and two mitochondrial (mt; 2165bp) DNA loci with fossil calibrated gene tree (27 outgroup taxa) and coalescent-based species tree (2 outgroup taxa) analyses. We also included an additional four nuclear loci (2578bp) for the species tree analysis to explore changes in nodal support values. Although the stem lineage is inferred to have originated ∼69 million years ago (Ma; 74.5-64.9 credible interval), a more recent basal split within Cathartidae was recovered at ∼14Ma (17.1-11.1 credible interval). Two primary clades were identified: (1) Black Vulture (Coragyps atratus) together with the three Cathartes species (Lesser C. burrovianus and Greater C. melambrotus Yellow-headed Vultures, and Turkey Vulture C. aura), and (2) King Vulture (Sarcoramphus papa), California (Gymnogyps californianus) and Andean (Vultur gryphus) Condors. Support for taxon relationships within the two basal clades were inconsistent between analyses with the exception of Black Vulture sister to a monophyletic Cathartes clade. Increased support for a yellow-headed vulture clade was recovered in the species tree analysis using the four additional nuclear loci. Overall, these results are in agreement with cathartid life history (e.g. olfaction ability and behavior) and contrasting habitat affinities among sister taxa with overlapping geographic distributions. More research is needed using additional molecular loci to further resolve the phylogenetic relationships within the two basal cathartid clades, as speciation appeared to have occurred in a relatively short period of time. PMID:27601346

  2. Predicting Inference Processes during Reading: A Multilevel Analysis of Text-Based and Reader-Based Factors

    ERIC Educational Resources Information Center

    Todaro, Stacey Ann

    2010-01-01

    Inferences are important because not everything in the text is explicit. Therefore, the reader must generate inferences that fill in "missing" information. Various factors can influence inference processes, including those that are related to the text and reader. Moreover, these two factors are likely to interact in highly complex ways, although…

  3. sick: The Spectroscopic Inference Crank

    NASA Astrophysics Data System (ADS)

    Casey, Andrew R.

    2016-03-01

    There exists an inordinate amount of spectral data in both public and private astronomical archives that remain severely under-utilized. The lack of reliable open-source tools for analyzing large volumes of spectra contributes to this situation, which is poised to worsen as large surveys successively release orders of magnitude more spectra. In this article I introduce sick, the spectroscopic inference crank, a flexible and fast Bayesian tool for inferring astrophysical parameters from spectra. sick is agnostic to the wavelength coverage, resolving power, or general data format, allowing any user to easily construct a generative model for their data, regardless of its source. sick can be used to provide a nearest-neighbor estimate of model parameters, a numerically optimized point estimate, or full Markov Chain Monte Carlo sampling of the posterior probability distributions. This generality empowers any astronomer to capitalize on the plethora of published synthetic and observed spectra, and make precise inferences for a host of astrophysical (and nuisance) quantities. Model intensities can be reliably approximated from existing grids of synthetic or observed spectra using linear multi-dimensional interpolation, or a Cannon-based model. Additional phenomena that transform the data (e.g., redshift, rotational broadening, continuum, spectral resolution) are incorporated as free parameters and can be marginalized away. Outlier pixels (e.g., cosmic rays or poorly modeled regimes) can be treated with a Gaussian mixture model, and a noise model is included to account for systematically underestimated variance. Combining these phenomena into a scalar-justified, quantitative model permits precise inferences with credible uncertainties on noisy data. I describe the common model features, the implementation details, and the default behavior, which is balanced to be suitable for most astronomical applications. Using a forward model on low-resolution, high signal

  4. Universum Inference and Corpus Homogeneity

    NASA Astrophysics Data System (ADS)

    Vogel, Carl; Lynch, Gerard; Janssen, Jerom

    Universum Inference is re-interpreted for assessment of corpus homogeneity in computational stylometry. Recent stylometric research quantifies strength of characterization within dramatic works by assessing the homogeneity of corpora associated with dramatic personas. A methodological advance is suggested to mitigate the potential for the assessment of homogeneity to be achieved by chance. Baseline comparison analysis is constructed for contributions to debates by nonfictional participants: the corpus analyzed consists of transcripts of US Presidential and Vice-Presidential debates from the 2000 election cycle. The corpus is also analyzed in translation to Italian, Spanish and Portuguese. Adding randomized categories makes assessments of homogeneity more conservative.

  5. Cooperative inference: Features, objects, and collections.

    PubMed

    Searcy, Sophia Ray; Shafto, Patrick

    2016-10-01

    Cooperation plays a central role in theories of development, learning, cultural evolution, and education. We argue that existing models of learning from cooperative informants have fundamental limitations that prevent them from explaining how cooperation benefits learning. First, existing models are shown to be computationally intractable, suggesting that they cannot apply to realistic learning problems. Second, existing models assume a priori agreement about which concepts are favored in learning, which leads to a conundrum: Learning fails without precise agreement on bias yet there is no single rational choice. We introduce cooperative inference, a novel framework for cooperation in concept learning, which resolves these limitations. Cooperative inference generalizes the notion of cooperation used in previous models from omission of labeled objects to the omission values of features, labels for objects, and labels for collections of objects. The result is an approach that is computationally tractable, does not require a priori agreement about biases, applies to both Boolean and first-order concepts, and begins to approximate the richness of real-world concept learning problems. We conclude by discussing relations to and implications for existing theories of cognition, cognitive development, and cultural evolution. (PsycINFO Database Record PMID:27379575

  6. An Ada inference engine for expert systems

    NASA Technical Reports Server (NTRS)

    Lavallee, David B.

    1986-01-01

    The purpose is to investigate the feasibility of using Ada for rule-based expert systems with real-time performance requirements. This includes exploring the Ada features which give improved performance to expert systems as well as optimizing the tradeoffs or workarounds that the use of Ada may require. A prototype inference engine was built using Ada, and rule firing rates in excess of 500 per second were demonstrated on a single MC68000 processor. The knowledge base uses a directed acyclic graph to represent production lines. The graph allows the use of AND, OR, and NOT logical operators. The inference engine uses a combination of both forward and backward chaining in order to reach goals as quickly as possible. Future efforts will include additional investigation of multiprocessing to improve performance and creating a user interface allowing rule input in an Ada-like syntax. Investigation of multitasking and alternate knowledge base representations will help to analyze some of the performance issues as they relate to larger problems.

  7. Toddlers infer unobserved causes for spontaneous events

    PubMed Central

    Muentener, Paul; Schulz, Laura

    2014-01-01

    Previous research suggests that children infer the presence of unobserved causes when objects appear to move spontaneously. Are such inferences limited to motion events or do children assume that unexplained physical events have causes more generally? Here we introduce an apparently spontaneous event and ask whether, even in the absence of spatiotemporal and co-variation cues linking the events, toddlers treat a plausible variable as a cause of the event. Toddlers (24 months) saw a toy that appeared to light up either spontaneously or after an experimenter’s action. Toddlers were also introduced to a button but were not shown any predictive relation between the button and the light. Across three different dependent measures of exploration, predictive looking (Study 1), prompted intervention (Study 2), and spontaneous exploration (Study 3), toddlers were more likely to represent the button as a cause of the light when the event appeared to occur spontaneously. In Study 4, we found that even in the absence of a plausible candidate cause, toddlers engaged in selective exploration when the light appeared to activate spontaneously. These results suggest that toddlers’ exploration is guided by the causal explanatory power of events. PMID:25566161

  8. Inferring differentiation pathways from gene expression

    PubMed Central

    Costa, Ivan G.; Roepcke, Stefan; Hafemeister, Christoph; Schliep, Alexander

    2008-01-01

    Motivation: The regulation of proliferation and differentiation of embryonic and adult stem cells into mature cells is central to developmental biology. Gene expression measured in distinguishable developmental stages helps to elucidate underlying molecular processes. In previous work we showed that functional gene modules, which act distinctly in the course of development, can be represented by a mixture of trees. In general, the similarities in the gene expression programs of cell populations reflect the similarities in the differentiation path. Results: We propose a novel model for gene expression profiles and an unsupervised learning method to estimate developmental similarity and infer differentiation pathways. We assess the performance of our model on simulated data and compare it with favorable results to related methods. We also infer differentiation pathways and predict functional modules in gene expression data of lymphoid development. Conclusions: We demonstrate for the first time how, in principal, the incorporation of structural knowledge about the dependence structure helps to reveal differentiation pathways and potentially relevant functional gene modules from microarray datasets. Our method applies in any area of developmental biology where it is possible to obtain cells of distinguishable differentiation stages. Availability: The implementation of our method (GPL license), data and additional results are available at http://algorithmics.molgen.mpg.de/Supplements/InfDif/ Contact: filho@molgen.mpg.de, schliep@molgen.mpg.de Supplementary information: Supplementary data is available at Bioinformatics online. PMID:18586709

  9. Models for inference in dynamic metacommunity systems

    USGS Publications Warehouse

    Dorazio, Robert M.; Kery, Marc; Royle, J. Andrew; Plattner, Matthias

    2010-01-01

    A variety of processes are thought to be involved in the formation and dynamics of species assemblages. For example, various metacommunity theories are based on differences in the relative contributions of dispersal of species among local communities and interactions of species within local communities. Interestingly, metacommunity theories continue to be advanced without much empirical validation. Part of the problem is that statistical models used to analyze typical survey data either fail to specify ecological processes with sufficient complexity or they fail to account for errors in detection of species during sampling. In this paper, we describe a statistical modeling framework for the analysis of metacommunity dynamics that is based on the idea of adopting a unified approach, multispecies occupancy modeling, for computing inferences about individual species, local communities of species, or the entire metacommunity of species. This approach accounts for errors in detection of species during sampling and also allows different metacommunity paradigms to be specified in terms of species- and location-specific probabilities of occurrence, extinction, and colonization: all of which are estimable. In addition, this approach can be used to address inference problems that arise in conservation ecology, such as predicting temporal and spatial changes in biodiversity for use in making conservation decisions. To illustrate, we estimate changes in species composition associated with the species-specific phenologies of flight patterns of butterflies in Switzerland for the purpose of estimating regional differences in biodiversity.

  10. Models for inference in dynamic metacommunity systems

    USGS Publications Warehouse

    Dorazio, R.M.; Kery, M.; Royle, J. Andrew; Plattner, M.

    2010-01-01

    A variety of processes are thought to be involved in the formation and dynamics of species assemblages. For example, various metacommunity theories are based on differences in the relative contributions of dispersal of species among local communities and interactions of species within local communities. Interestingly, metacommunity theories continue to be advanced without much empirical validation. Part of the problem is that statistical models used to analyze typical survey data either fail to specify ecological processes with sufficient complexity or they fail to account for errors in detection of species during sampling. In this paper, we describe a statistical modeling framework for the analysis of metacommunity dynamics that is based on the idea of adopting a unified approach, multispecies occupancy modeling, for computing inferences about individual species, local communities of species, or the entire metacommunity of species. This approach accounts for errors in detection of species during sampling and also allows different metacommunity paradigms to be specified in terms of species-and location-specific probabilities of occurrence, extinction, and colonization: all of which are estimable. In addition, this approach can be used to address inference problems that arise in conservation ecology, such as predicting temporal and spatial changes in biodiversity for use in making conservation decisions. To illustrate, we estimate changes in species composition associated with the species-specific phenologies of flight patterns of butterflies in Switzerland for the purpose of estimating regional differences in biodiversity. ?? 2010 by the Ecological Society of America.

  11. Seed plant genera endemic to the Caribbean Island biodiversity hotspot: A review and a molecular phylogentic perspective

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Caribbean Island Biodiversity Hotspot is composed primarily by the Bahamas and Greater and Lesser Antilles. A total of 178 genera (722 spp., ca. 9% of the species endemic to the Antilles) are restricted to this hotspot. Most of these genera are unispecific (53%), a pattern that is also found o...

  12. Phylogenetic position of Indian termites (Isoptera: Termitidae) with their respective genera inferred from DNA sequence analysis of the mitochondrial cytochrome oxidase gene subunit I compared to subunit II.

    PubMed

    Sharma, Vijay Lakshmi; Singla, Mandakini; Sobti, Ranbir Chander

    2013-08-20

    The present work was aimed to investigate the phylogenetic analysis of different species of Indian termites belonging to the family termitidae based on mitochondrial genes COI and COII. The sequences so obtained from public database revealed grouping of termites according to their ecological distribution. The sequences of the species under investigation were characterized on the basis of frequencies of nucleotide bases and in most of the species, a significantly high percentage of A+T base composition was observed. Phylogenetic tree revealed positioning of species according to the analysis of their cytochrome oxidase subunits.

  13. SYMBOLIC INFERENCE OF XENOBIOTIC METABOLISM

    PubMed Central

    MCSHAN, D.C.; UPDADHAYAYA, M.; SHAH, I.

    2009-01-01

    We present a new symbolic computational approach to elucidate the biochemical networks of living systems de novo and we apply it to an important biomedical problem: xenobiotic metabolism. A crucial issue in analyzing and modeling a living organism is understanding its biochemical network beyond what is already known. Our objective is to use the available metabolic information in a representational framework that enables the inference of novel biochemical knowledge and whose results can be validated experimentally. We describe a symbolic computational approach consisting of two parts. First, biotransformation rules are inferred from the molecular graphs of compounds in enzyme-catalyzed reactions. Second, these rules are recursively applied to different compounds to generate novel metabolic networks, containing new biotransformations and new metabolites. Using data for 456 generic reactions and 825 generic compounds from KEGG we were able to extract 110 biotransformation rules, which generalize a subset of known biocatalytic functions. We tested our approach by applying these rules to ethanol, a common substance of abuse and to furfuryl alcohol, a xenobiotic organic solvent, which is absent in metabolic databases. In both cases our predictions on the fate of ethanol and furfuryl alcohol are consistent with the literature on the metabolism of these compounds. PMID:14992532

  14. Bayesian inference for OPC modeling

    NASA Astrophysics Data System (ADS)

    Burbine, Andrew; Sturtevant, John; Fryer, David; Smith, Bruce W.

    2016-03-01

    The use of optical proximity correction (OPC) demands increasingly accurate models of the photolithographic process. Model building and inference techniques in the data science community have seen great strides in the past two decades which make better use of available information. This paper aims to demonstrate the predictive power of Bayesian inference as a method for parameter selection in lithographic models by quantifying the uncertainty associated with model inputs and wafer data. Specifically, the method combines the model builder's prior information about each modelling assumption with the maximization of each observation's likelihood as a Student's t-distributed random variable. Through the use of a Markov chain Monte Carlo (MCMC) algorithm, a model's parameter space is explored to find the most credible parameter values. During parameter exploration, the parameters' posterior distributions are generated by applying Bayes' rule, using a likelihood function and the a priori knowledge supplied. The MCMC algorithm used, an affine invariant ensemble sampler (AIES), is implemented by initializing many walkers which semiindependently explore the space. The convergence of these walkers to global maxima of the likelihood volume determine the parameter values' highest density intervals (HDI) to reveal champion models. We show that this method of parameter selection provides insights into the data that traditional methods do not and outline continued experiments to vet the method.

  15. Dopamine, affordance and active inference.

    PubMed

    Friston, Karl J; Shiner, Tamara; FitzGerald, Thomas; Galea, Joseph M; Adams, Rick; Brown, Harriet; Dolan, Raymond J; Moran, Rosalyn; Stephan, Klaas Enno; Bestmann, Sven

    2012-01-01

    The role of dopamine in behaviour and decision-making is often cast in terms of reinforcement learning and optimal decision theory. Here, we present an alternative view that frames the physiology of dopamine in terms of Bayes-optimal behaviour. In this account, dopamine controls the precision or salience of (external or internal) cues that engender action. In other words, dopamine balances bottom-up sensory information and top-down prior beliefs when making hierarchical inferences (predictions) about cues that have affordance. In this paper, we focus on the consequences of changing tonic levels of dopamine firing using simulations of cued sequential movements. Crucially, the predictions driving movements are based upon a hierarchical generative model that infers the context in which movements are made. This means that we can confuse agents by changing the context (order) in which cues are presented. These simulations provide a (Bayes-optimal) model of contextual uncertainty and set switching that can be quantified in terms of behavioural and electrophysiological responses. Furthermore, one can simulate dopaminergic lesions (by changing the precision of prediction errors) to produce pathological behaviours that are reminiscent of those seen in neurological disorders such as Parkinson's disease. We use these simulations to demonstrate how a single functional role for dopamine at the synaptic level can manifest in different ways at the behavioural level.

  16. Trandimensional Inference in the Geosciences

    NASA Astrophysics Data System (ADS)

    Bodin, Thomas

    2016-04-01

    An inverse problem is the task often occurring in many branches of Earth sciences, where the values of some model parameters describing the Earth must be obtained given noisy observations made at the surface. In all applications of inversion, assumptions are made about the nature of the model parametrisation and data noise characteristics, and results can significantly depend on those assumptions. These quantities are often manually `tuned' by means of subjective trial-and-error procedures, and this prevents to accurately quantify uncertainties in the solution. A Bayesian approach allows these assumptions to be relaxed by incorporating relevant parameters as unknowns in the inference problem. Rather than being forced to make decisions on parametrisation, the level of data noise and the weights between data types in advance, as is often the case in an optimization framework, the choice can be informed by the data themselves. Probabilistic sampling techniques such as transdimensional Markov chain Monte Carlo, allow sampling over complex posterior probability density functions, thus providing information on constraint, trade-offs and uncertainty in the unknowns. This presentation will present a review of transdimensional inference, and its application to different problems, ranging from Geochemistry to Solid Earth Geophysics.

  17. Quantum Inference on Bayesian Networks

    NASA Astrophysics Data System (ADS)

    Yoder, Theodore; Low, Guang Hao; Chuang, Isaac

    2014-03-01

    Because quantum physics is naturally probabilistic, it seems reasonable to expect physical systems to describe probabilities and their evolution in a natural fashion. Here, we use quantum computation to speedup sampling from a graphical probability model, the Bayesian network. A specialization of this sampling problem is approximate Bayesian inference, where the distribution on query variables is sampled given the values e of evidence variables. Inference is a key part of modern machine learning and artificial intelligence tasks, but is known to be NP-hard. Classically, a single unbiased sample is obtained from a Bayesian network on n variables with at most m parents per node in time (nmP(e) - 1 / 2) , depending critically on P(e) , the probability the evidence might occur in the first place. However, by implementing a quantum version of rejection sampling, we obtain a square-root speedup, taking (n2m P(e) -1/2) time per sample. The speedup is the result of amplitude amplification, which is proving to be broadly applicable in sampling and machine learning tasks. In particular, we provide an explicit and efficient circuit construction that implements the algorithm without the need for oracle access.

  18. Effect of Conway Medium and f/2 Medium on the growth of six genera of South China Sea marine microalgae.

    PubMed

    Lananan, Fathurrahman; Jusoh, Ahmad; Ali, Nora'aini; Lam, Su Shiung; Endut, Azizah

    2013-08-01

    A study was performed to determine the effect of Conway and f/2 media on the growth of microalgae genera. Genera of Chlorella sp., Dunaliella sp., Isochrysis sp., Chaetoceros sp., Pavlova sp. and Tetraselmis sp. were isolated from the South China Sea. During the cultivation period, the density of cells were determined using Syringe Liquid Sampler Particle Measuring System (SLS-PMS) that also generated the population distribution curve based on the size of the cells. The population of the microalgae genera is thought to consist of mother and daughter generations since these microalgae genera reproduce by releasing small non-motile reproductive cells (autospores). It was found that the reproduction of Tetraselmis sp., Dunaliella sp. and Pavlova sp. could be sustained longer in f/2 Medium. Higher cell density was achieved by genus Dunaliella, Chlorella and Isochrysis in Conway Medium. Different genera of microalgae had a preference for different types of cultivation media.

  19. Endiandric Acid Derivatives and Other Constituents of Plants from the Genera Beilschmiedia and Endiandra (Lauraceae)

    PubMed Central

    Ndjakou Lenta, Bruno; Chouna, Jean Rodolphe; Nkeng-Efouet, Pepin Alango; Sewald, Norbert

    2015-01-01

    Plants of the Lauraceae family are widely used in traditional medicine and are sources of various classes of secondary metabolites. Two genera of this family, Beilschmiedia and Endiandra, have been the subject of numerous investigations over the past decades because of their application in traditional medicine. They are the only source of bioactive endiandric acid derivatives. Noteworthy is that their biosynthesis contains two consecutive non-enzymatic electrocyclic reactions. Several interesting biological activities for this specific class of secondary metabolites and other constituents of the two genera have been reported, including antimicrobial, enzymes inhibitory and cytotoxic properties. This review compiles information on the structures of the compounds described between January 1960 and March 2015, their biological activities and information on endiandric acid biosynthesis, with 104 references being cited. PMID:26117852

  20. Seven New Recorded Species in Five Genera of the Strophariaceae in Korea

    PubMed Central

    Cho, Hae Jin; Lee, Hyun; Park, Jae Young; Park, Myung Soo; Kim, Nam Kyu; Eimes, John A.; Kim, Changmu; Han, Sang-Kuk

    2016-01-01

    Most known species in the Strophariaceae are decomposers and grow on various kind of organic matter. Approximately 18 genera and 1,316 species in the Strophariaceae have been reported worldwide. Through an ongoing survey of indigenous fungi in Korea, 29 specimens belonging to the Strophariaceae were collected from 2012 to 2016. These specimens were identified based on morphological characteristics and molecular analysis of internal transcribed spacer sequences. Fifteen taxa were confirmed, with eight species matching those previously recorded. Seven species in five genera were shown to be new records in Korea: Galerina marginata, Gymnopilus crociphyllus, Gymnopilus picreus, Hebeloma birrus, Hebeloma cavipes, Pholiota multicingulata, and Psilocybe thaizapoteca. In this study, we provide detailed morphological descriptions of these species and investigate their evolutionary relationships by constructing phylogenetic trees. PMID:27790064

  1. Systematic review of genera and subgenera of Rhopalopsyllinae (Siphonaptera: Rhopalopsyllidae) by phenetic and cladistic methods.

    PubMed

    Linardi, P M; Guimarães, L R

    1993-01-01

    A systematic review of genera and subgenera of Siphonaptera Rhopalopsyllinae comprising nine operating taxonomic units is presented based on phenetic and cladistic analysis. Twenty-seven characters of adults were analyzed and the character states were determined for each character by the out-group method. Phenogram and cladograms indicated two tribes, each with two subtribes. Systematic changes proposed as a result of this study include the raising of the subgeneric status of Gephyropsylla, Hechteilla, and Ayeshaepsylla to independent genera; the recognition of a new genus, Neotropsylla, to include Polygenis guimaraesi Linardi; the division of the genus Polygenis Jordan into two subgenera: Neopolygenis subgen. n., to include species of the atopus group, and Polygenis s. str., for remaining species.

  2. The freshwater snails (Gastropoda) of Iran, with descriptions of two new genera and eight new species

    PubMed Central

    Glöer, Peter; Pešić, Vladimir

    2012-01-01

    Abstract Using published records and original data from recent field work and revision of Iranian material of certain species deposited in the collections of the Natural History Museum Basel, the Zoological Museum Berlin, and Natural History Museum Vienna, a checklist of the freshwater gastropod fauna of Iran was compiled. This checklist contains 73 species from 34 genera and 14 families of freshwater snails; 27 of these species (37%) are endemic to Iran. Two new genera, Kaskakia and Sarkhia, and eight species, i.e., Bithynia forcarti, Bithynia starmuehlneri, Bithynia mazandaranensis, Pseudamnicola georgievi, Kaskakia khorrasanensis, Sarkhia sarabensis, Valvata nowsharensis and Acroloxus pseudolacustris are described as new to science; Ecrobia grimmi (Clessin & Dybowski, 1888), Heleobia dalmatica (Radoman, 1974) and Hippeutis complanatus (Linnaeus, 1758) are reported for the first time from Iran. Additional field work is highly desirable for a more appropriate evaluation of the extant freshwater snail biodiversity in Iran. PMID:22977349

  3. Sex Pheromone Evolution Is Associated with Differential Regulation of the Same Desaturase Gene in Two Genera of Leafroller Moths

    PubMed Central

    Albre, Jérôme; Liénard, Marjorie A.; Sirey, Tamara M.; Schmidt, Silvia; Tooman, Leah K.; Carraher, Colm; Greenwood, David R.; Löfstedt, Christer; Newcomb, Richard D.

    2012-01-01

    Chemical signals are prevalent in sexual communication systems. Mate recognition has been extensively studied within the Lepidoptera, where the production and recognition of species-specific sex pheromone signals are typically the defining character. While the specific blend of compounds that makes up the sex pheromones of many species has been characterized, the molecular mechanisms underpinning the evolution of pheromone-based mate recognition systems remain largely unknown. We have focused on two sets of sibling species within the leafroller moth genera Ctenopseustis and Planotortrix that have rapidly evolved the use of distinct sex pheromone blends. The compounds within these blends differ almost exclusively in the relative position of double bonds that are introduced by desaturase enzymes. Of the six desaturase orthologs isolated from all four species, functional analyses in yeast and gene expression in pheromone glands implicate three in pheromone biosynthesis, two Δ9-desaturases, and a Δ10-desaturase, while the remaining three desaturases include a Δ6-desaturase, a terminal desaturase, and a non-functional desaturase. Comparative quantitative real-time PCR reveals that the Δ10-desaturase is differentially expressed in the pheromone glands of the two sets of sibling species, consistent with differences in the pheromone blend in both species pairs. In the pheromone glands of species that utilize (Z)-8-tetradecenyl acetate as sex pheromone component (Ctenopseustis obliquana and Planotortrix octo), the expression levels of the Δ10-desaturase are significantly higher than in the pheromone glands of their respective sibling species (C. herana and P. excessana). Our results demonstrate that interspecific sex pheromone differences are associated with differential regulation of the same desaturase gene in two genera of moths. We suggest that differential gene regulation among members of a multigene family may be an important mechanism of molecular innovation in

  4. Palynological study of the genera Ruellia, Ecbolium, Asystasia, Blepharis and Dicliptera (Acanthaceae) of Yemen

    SciTech Connect

    Al-Hakimi, S. Anisa; Maideen, Haja; Latiff, A.

    2013-11-27

    Pollen morphology of five genera of the family Acanthaceae, namely Ruellia, Blepharis, Asystasia, Ecbolium and Dicliptera (Acanthaceae) of Yemen has been examined using light and scanning electron microscope. Pollen descriptions were provided with two shapes distinguished, spheroidal and prolate. Most of the pollen grains were tricolporate amd psuedocolpi except those of Blepharis which are colpate. The surface is coarsely reticulate, in addition to the lumina that varies in size.

  5. Genetic relatedness between intracisternal A particles and other major oncovirus genera.

    PubMed

    Chiu, I M; Huang, R C; Aaronson, S A

    1985-07-01

    Intracisternal A particles represent a major oncovirus genus. By reciprocal hybridization between molecularly cloned A particles and representatives of other oncovirus genera, we established pol gene homology with type B, type D and avian type C viruses. The most extensive homology was with mammalian type D viruses. The transcriptional orientation of the IAP genome was determined, as well as evidence indicating that its pol gene, which is apparently defective, contains coding regions for both reverse transcriptase and endonuclease proteins.

  6. Palynological study of the genera Ruellia, Ecbolium, Asystasia, Blepharis and Dicliptera (Acanthaceae) of Yemen

    NASA Astrophysics Data System (ADS)

    Al-Hakimi, S. Anisa; Maideen, Haja; Latiff, A.

    2013-11-01

    Pollen morphology of five genera of the family Acanthaceae, namely Ruellia, Blepharis, Asystasia, Ecbolium and Dicliptera (Acanthaceae) of Yemen has been examined using light and scanning electron microscope. Pollen descriptions were provided with two shapes distinguished, spheroidal and prolate. Most of the pollen grains were tricolporate amd psuedocolpi except those of Blepharis which are colpate. The surface is coarsely reticulate, in addition to the lumina that varies in size.

  7. Male sleeping aggregation of multiple Eucerini bee genera (Hymenoptera: Apidae) in Chapada Diamantina, Bahia, Brazil

    PubMed Central

    Hipólito, Juliana; de Oliveira, Favízia F.

    2014-01-01

    Abstract Males of some groups of bees have to find a place outside the nests to sleep, sometimes forming “male sleeping aggregations”. Here we report the first record of “dense” male sleeping aggregation of two different genera of Eucerini bees observed in Bahia, Brazil. We discuss the possible aim of this kind of aggregation as well the plant utilized on aggregate. PMID:25349523

  8. New genera, species and records of Doryctinae (Hymenoptera: Braconidae) from Brazil.

    PubMed

    Gadelha, Sian De Souza; Nunes, Juliano Fiorelini; Oliveira, Marcio Luiz De

    2016-01-01

    Two new genera of Doryctinae (Hymenoptera: Braconidae) are described, Parsteres n. gen., Tuberatra n. gen., and are added to the identification key of Marsh (1997). Three new species are also described: P. pilosus n. sp., T. curvicauda n. sp., and Barbalhoa longicaudus n. sp. An identification key to the species of Barbalhoa Marsh, 2002 is presented, and nine species of the subfamily have their first record for Brazil. PMID:27394235

  9. Molecular data and phylogeny of Nosema infecting lepidopteran forest defoliators in the genera Choristoneura and Malacosoma.

    PubMed

    Kyei-Poku, George; Gauthier, Debbie; van Frankenhuyzen, Kees

    2008-01-01

    Nosema isolates from five lepidopteran forest defoliators, Nosema fumiferanae from spruce budworm, Choristoneura fumiferana; a Nosema sp. from jack pine budworm, Choristoneura pinus pinus and western spruce budworm, Choristoneura occidentalis (Nosema sp. CPP and Nosema sp. CO, respectively); Nosema thomsoni from large aspen tortrix, Choristoneura conflictana; and Nosema disstriae, from the forest tent caterpillar, Malacosoma disstria were compared based on their small subunit (SSU) ribosomal RNA (rRNA) gene sequences. Four of the species sequenced, N. fumiferanae, Nosema sp. CPP, Nosema sp. CO, and N. disstriae have a high SSU rDNA sequence identity (0.6%-1.5%) and are members of the "true Nosema" clade. They all showed the reverse arrangement of the (large subunit [LSU]-internal transcribed spacer [ITS]-SSU) of the rRNA gene. The fifth species, N. thomsoni has the usual (SSU-ITS-LSU) arrangement and is not a member of this clade showing only an 82% sequence similarity. We speculate, therefore, that a genetic reversal may have occurred in the common ancestor to the "true Nosema" clade. Although, the mechanism for rearrangement of the rRNA gene subunits is not known we provide a possible explanation for the localization. N. fumiferanae, Nosema sp. CPP, and Nosema sp. CO clustered together on the inferred phylogenetic tree. The high sequence similarities, the reverse arrangement in the rRNA gene subunits, and the phylogenetic clustering suggest that these three species are closely related but separate species.

  10. The Blicket Within: Preschoolers' Inferences about Insides and Causes

    ERIC Educational Resources Information Center

    Sobel, David M.; Yoachim, Caroline M.; Gopnik, Alison; Meltzoff, Andrew N.; Blumenthal, Emily J.

    2007-01-01

    Four experiments examined children's inferences about the relation between objects' internal parts and their causal properties. In Experiment 1, 4-year-olds recognized that objects with different internal parts had different causal properties, and those causal properties transferred if the internal part moved to another object. In Experiment 2,…

  11. How Far Is "Near"? Inferring Distance from Spatial Descriptions

    ERIC Educational Resources Information Center

    Carlson, Laura A.; Covey, Eric S.

    2005-01-01

    A word may mean different things in different contexts. The current study explored the changing denotations of spatial terms, focusing on how the distance inferred from a spatial description varied as a function of the size of the objects being spatially related. We examined both terms that explicitly convey distance (i.e., topological terms such…

  12. How Generalization Inferences Are Constructed in Expository Text Comprehension

    ERIC Educational Resources Information Center

    Ritchey, Kristin A.

    2011-01-01

    Three questions regarding adult readers' processing of generalization inferences (conceptually broad statements that subsume several specific statements) are investigated. College students (N=193) read expository texts containing target statements that were consistent, inconsistent, or off-topic in relation to a generalization implied by one…

  13. Do Readers with Autism Make Bridging Inferences from World Knowledge?

    ERIC Educational Resources Information Center

    Saldana, David; Frith, Uta

    2007-01-01

    Individuals with autism frequently show impairments in text reading comprehension. This often is attributed to poor ability to draw inferences during reading and to inadequate access to relevant knowledge. The current study tested this hypothesis by measuring the time taken to read the same question, relating to either physical or social world…

  14. Temporal Integration and Inferences About Televised Social Behavior.

    ERIC Educational Resources Information Center

    Collins, W. Andrew

    This paper discusses research on age related aspects of children's processing and comprehension of the narrative content of family oriented television programs. In one study, the temporal integration necessary to make inferences about audiovisually presented information was examined in 254 second, fifth and eighth grade children. Subjects were…

  15. Quantum inferring acausal structures and the Monty Hall problem

    NASA Astrophysics Data System (ADS)

    Kurzyk, Dariusz; Glos, Adam

    2016-09-01

    This paper presents a quantum version of the Monty Hall problem based upon the quantum inferring acausal structures, which can be identified with generalization of Bayesian networks. Considered structures are expressed in formalism of quantum information theory, where density operators are identified with quantum generalization of probability distributions. Conditional relations between quantum counterpart of random variables are described by quantum conditional operators. Presented quantum inferring structures are used to construct a model inspired by scenario of well-known Monty Hall game, where we show the differences between classical and quantum Bayesian reasoning.

  16. Apocynaceae species with antiproliferative and/or antiplasmodial properties: a review of ten genera.

    PubMed

    Chan, Eric Wei Chiang; Wong, Siu Kuin; Chan, Hung Tuck

    2016-07-01

    Apocynaceae is a large family of tropical trees, shrubs and vines with most species producing white latex. Major metabolites of species are triterpenoids, iridoids, alkaloids and cardenolides, which are known for a wide range of biological and pharmacological activities such as cardioprotective, hepatoprotective, neuroprotective, anti-inflammatory, anticancer and antimalarial properties. Prompted by their anticancer and antimalarial properties, the current knowledge on ten genera (Allamanda, Alstonia, Calotropis, Catharanthus, Cerbera, Dyera, Kopsia, Nerium, Plumeria and Vallaris) is updated. Major classes of metabolites are described using some species as examples. Species with antiproliferative (APF) and/or antiplasmodial (APM) properties have been identified. With the exception of the genus Dyera, nine genera of 22 species possess APF activity. Seven genera (Alstonia, Calotropis, Catharanthus, Dyera, Kopsia, Plumeria and Vallaris) of 13 species have APM properties. Among these species, Alstonia angustiloba, Alstonia macrophylla, Calotropis gigantea, Calotropis procera, Catharanthus roseus, Plumeria alba and Vallaris glabra displayed both APF and APM properties. The chemical constituents of these seven species are compiled for assessment and further research.

  17. Apocynaceae species with antiproliferative and/or antiplasmodial properties: a review of ten genera.

    PubMed

    Chan, Eric Wei Chiang; Wong, Siu Kuin; Chan, Hung Tuck

    2016-07-01

    Apocynaceae is a large family of tropical trees, shrubs and vines with most species producing white latex. Major metabolites of species are triterpenoids, iridoids, alkaloids and cardenolides, which are known for a wide range of biological and pharmacological activities such as cardioprotective, hepatoprotective, neuroprotective, anti-inflammatory, anticancer and antimalarial properties. Prompted by their anticancer and antimalarial properties, the current knowledge on ten genera (Allamanda, Alstonia, Calotropis, Catharanthus, Cerbera, Dyera, Kopsia, Nerium, Plumeria and Vallaris) is updated. Major classes of metabolites are described using some species as examples. Species with antiproliferative (APF) and/or antiplasmodial (APM) properties have been identified. With the exception of the genus Dyera, nine genera of 22 species possess APF activity. Seven genera (Alstonia, Calotropis, Catharanthus, Dyera, Kopsia, Plumeria and Vallaris) of 13 species have APM properties. Among these species, Alstonia angustiloba, Alstonia macrophylla, Calotropis gigantea, Calotropis procera, Catharanthus roseus, Plumeria alba and Vallaris glabra displayed both APF and APM properties. The chemical constituents of these seven species are compiled for assessment and further research. PMID:27417173

  18. Two new genera and three new species of freshwater crabs (Crustacea: Pseudothelphusidae: Potamocarcinini) from Chiapas, Mexico.

    PubMed

    Villalobos, José Luis; Álvarez, Fernando

    2013-01-01

    Two new genera, Sylvathelphusa n. gen. and Tzotzilthelphusa n. gen., and three new species, Sylvathelphusa kalebi n. sp., S. cavernicola n. sp. and Tzotzilthelphusa villarosalensis n. sp., of the tribe Potamocarcinini, family Pseudothelphusidae, are described from Chiapas, Mexico. Sylvathelphusa n. gen. is characterized by a male gonopod with the marginal plate between the caudal and mesial surfaces abruptly widening distally and forming a triangular apical projection; and a mesial process as a strong, acute spine forming a 90º angle with respect to the principal axis of the gonopod. Tzotzilthelphusa n. gen. exhibits a male gonopod strongly bent laterally in the distal third, and a mesial surface rounded distally with acute spinules. Sylvathelphusa n. gen. is similar to Potamocarcinus in gonopod morphology, in both straight and with a mesial process developed as strong tooth in a similar shape and position. Tzotzilthelphusa n. gen. is similar to Phrygiopilus in that the gonopods of both genera develop a supra-apical process that is a continuation of the mesial surface. The new taxa come from the Los Altos de Chiapas region and bring the total number of pseudothelphusid genera in Chiapas to 11. PMID:24613999

  19. Myxozoan genera: definition and notes on taxonomy, life-cycle terminology and pathogenic species.

    PubMed

    Lom, Jirí; Dyková, Iva

    2006-03-01

    A list of myxozoan genera is presented in the current taxonomical scheme. These genera are defined; their type species and most important pathogens along with their hosts are listed. Simultaneously, definitions of actinospore stages representing sexual stages of the myxosporean life cycle are given; altogether, 17 actinospore collective groups with 180 types have been described. Life cycles of the two classes of the phylum Myxozoa, Malacosporea and Myxosporea, are briefly outlined with specification of the appropriate terms. Up to now, 4 malacosporean and 2,180 myxosporean species assigned to a total of 62 genera, have been established. The surviving classification of myxosporeans, based on spore morphology, is discussed in the context of the still fragmentary data resulting from SSU rDNA sequence analyses. The main task for the future is a rigorous, detailed morphological description combined with molecular techniques in establishment of new species and in revision of the existing ones. Establishment of a classification acceptable from morphological, biological and phylogenetical viewpoints is necessary.

  20. Phylogenetic relationships of Echinolaena and Ichnanthus within Panicoideae (Poaceae) reveal two new genera of tropical grasses.

    PubMed

    Silva, Christian; Snak, Cristiane; Schnadelbach, Alessandra Selbach; van den Berg, Cássio; Oliveira, Reyjane Patrícia

    2015-12-01

    Echinolaena and Ichnanthus are two tropical grass genera distributed mostly in the Americas, characterized by the presence of rachilla appendages in the shape of convex swellings, scars or wings at the base of the upper anthecium. However, recent studies have shown that rachilla appendages arose several times independently in several groups within Paniceae and Paspaleae (Panicoideae). Thus, this study aimed to assess the monophyly of Echinolaena and Ichnanthus and their relationship to other genera of Paniceae and Paspaleae, especially those including species with rachilla appendages. Parsimony and Bayesian analyses of the cpDNA regions ndhF, rpl16, trnH-(rps19)-psbA, trnL-trnF, trnS-(psbZ)-trnG, and the rDNA ITS region included 29 of the 39 known species of Echinolaena and Ichnanthus, 23 of which were sampled for the first time. The multiple loci analyses indicated that Echinolaena and Ichnanthus are polyphyletic in their current circumscriptions, with species in four distinct lineages within subtribe Paspalinae, each one characterized by a single type of rachilla appendage. Thus, Echinolaena and Ichnanthus are each circumscribed in a narrow sense, and the other two lineages excluded from them are proposed as the new genera Hildaea and Oedochloa, resulting in 15 new combinations and the restablishment of I. oplismenoides Munro ex Döll.

  1. Jurassic-Early Cretaceous Gondwanan homoxylous woods: a nomenclatural revision of the genera with taxonomic notes.

    PubMed

    Bamford, M K.; Philippe, M

    2001-04-01

    The homoxylous fossil woods occurring in the Gondwanan continents of South America, Australia, Africa, India and Antarctica during the Jurassic and Early Cretaceous period are considered here. Original descriptions of the genera and wherever possible, the type material, have been consulted. Applying the rules of the International Code of Botanical Nomenclature, the generic names of the homoxylous woods have been revised from a nomenclatural point of view. According to this review, out of 31 generic names used for woods from the given time interval and area, 6 are illegitimate later nomenclatural synonyms, 1 is a later homonym, and 5 can be considered as taxonomical synonyms. Moreover, 9 genera have been used erroneously. We propose one new generic name (Protaxodioxylon n. gen.) and elsewhere we will propose for conservation, with a conserved type one of the illegitimate names and one of the taxonomic synonyms. As a result, we consider that there are only eighteen generic names correctly quoted for the Jurassic-Early Cretaceous of Gondwana, and we provide a taxonomic key for the corresponding genera. This revision is the first step in systematically comparing northern and southern hemisphere woods. PMID:11179718

  2. Jurassic-Early Cretaceous Gondwanan homoxylous woods: a nomenclatural revision of the genera with taxonomic notes.

    PubMed

    Bamford, M K.; Philippe, M

    2001-04-01

    The homoxylous fossil woods occurring in the Gondwanan continents of South America, Australia, Africa, India and Antarctica during the Jurassic and Early Cretaceous period are considered here. Original descriptions of the genera and wherever possible, the type material, have been consulted. Applying the rules of the International Code of Botanical Nomenclature, the generic names of the homoxylous woods have been revised from a nomenclatural point of view. According to this review, out of 31 generic names used for woods from the given time interval and area, 6 are illegitimate later nomenclatural synonyms, 1 is a later homonym, and 5 can be considered as taxonomical synonyms. Moreover, 9 genera have been used erroneously. We propose one new generic name (Protaxodioxylon n. gen.) and elsewhere we will propose for conservation, with a conserved type one of the illegitimate names and one of the taxonomic synonyms. As a result, we consider that there are only eighteen generic names correctly quoted for the Jurassic-Early Cretaceous of Gondwana, and we provide a taxonomic key for the corresponding genera. This revision is the first step in systematically comparing northern and southern hemisphere woods.

  3. Two new genera and three new species of freshwater crabs (Crustacea: Pseudothelphusidae: Potamocarcinini) from Chiapas, Mexico.

    PubMed

    Villalobos, José Luis; Álvarez, Fernando

    2013-01-09

    Two new genera, Sylvathelphusa n. gen. and Tzotzilthelphusa n. gen., and three new species, Sylvathelphusa kalebi n. sp., S. cavernicola n. sp. and Tzotzilthelphusa villarosalensis n. sp., of the tribe Potamocarcinini, family Pseudothelphusidae, are described from Chiapas, Mexico. Sylvathelphusa n. gen. is characterized by a male gonopod with the marginal plate between the caudal and mesial surfaces abruptly widening distally and forming a triangular apical projection; and a mesial process as a strong, acute spine forming a 90º angle with respect to the principal axis of the gonopod. Tzotzilthelphusa n. gen. exhibits a male gonopod strongly bent laterally in the distal third, and a mesial surface rounded distally with acute spinules. Sylvathelphusa n. gen. is similar to Potamocarcinus in gonopod morphology, in both straight and with a mesial process developed as strong tooth in a similar shape and position. Tzotzilthelphusa n. gen. is similar to Phrygiopilus in that the gonopods of both genera develop a supra-apical process that is a continuation of the mesial surface. The new taxa come from the Los Altos de Chiapas region and bring the total number of pseudothelphusid genera in Chiapas to 11.

  4. On the Inference of Functional Circadian Networks Using Granger Causality

    PubMed Central

    Pourzanjani, Arya; Herzog, Erik D.; Petzold, Linda R.

    2015-01-01

    Being able to infer one way direct connections in an oscillatory network such as the suprachiastmatic nucleus (SCN) of the mammalian brain using time series data is difficult but crucial to understanding network dynamics. Although techniques have been developed for inferring networks from time series data, there have been no attempts to adapt these techniques to infer directional connections in oscillatory time series, while accurately distinguishing between direct and indirect connections. In this paper an adaptation of Granger Causality is proposed that allows for inference of circadian networks and oscillatory networks in general called Adaptive Frequency Granger Causality (AFGC). Additionally, an extension of this method is proposed to infer networks with large numbers of cells called LASSO AFGC. The method was validated using simulated data from several different networks. For the smaller networks the method was able to identify all one way direct connections without identifying connections that were not present. For larger networks of up to twenty cells the method shows excellent performance in identifying true and false connections; this is quantified by an area-under-the-curve (AUC) 96.88%. We note that this method like other Granger Causality-based methods, is based on the detection of high frequency signals propagating between cell traces. Thus it requires a relatively high sampling rate and a network that can propagate high frequency signals. PMID:26413748

  5. Learning and retention through predictive inference and classification.

    PubMed

    Sakamoto, Yasuaki; Love, Bradley C

    2010-12-01

    Work in category learning addresses how humans acquire knowledge and, thus, should inform classroom practices. In two experiments, we apply and evaluate intuitions garnered from laboratory-based research in category learning to learning tasks situated in an educational context. In Experiment 1, learning through predictive inference and classification were compared for fifth-grade students using class-related materials. Making inferences about properties of category members and receiving feedback led to the acquisition of both queried (i.e., tested) properties and nonqueried properties that were correlated with a queried property (e.g., even if not queried, students learned about a species' habitat because it correlated with a queried property, like the species' size). In contrast, classifying items according to their species and receiving feedback led to knowledge of only the property most diagnostic of category membership. After multiple-day delay, the fifth-graders who learned through inference selectively retained information about the queried properties, and the fifth-graders who learned through classification retained information about the diagnostic property, indicating a role for explicit evaluation in establishing memories. Overall, inference learning resulted in fewer errors, better retention, and more liking of the categories than did classification learning. Experiment 2 revealed that querying a property only a few times was enough to manifest the full benefits of inference learning in undergraduate students. These results suggest that classroom teaching should emphasize reasoning from the category to multiple properties rather than from a set of properties to the category. PMID:21198253

  6. Phylogeographic ancestral inference using the coalescent model on haplotype trees.

    PubMed

    Manolopoulou, Ioanna; Emerson, Brent C

    2012-06-01

    Phylogeographic ancestral inference is issue frequently arising in population ecology that aims to understand the geographical roots and structure of species. Here, we specifically address relatively small scale mtDNA datasets (typically less than 500 sequences with fewer than 1000 nucleotides), focusing on ancestral location inference. Our approach uses a coalescent modelling framework projected onto haplotype trees in order to reduce computational complexity, at the same time adhering to complex evolutionary processes. Statistical innovations of the last few years have allowed for computationally feasible yet accurate inferences in phylogenetic frameworks. We implement our methods on a set of synthetic datasets and show how, despite high uncertainty in terms of identifying the root haplotype, estimation of the ancestral location naturally encompasses lower uncertainty, allowing us to pinpoint the Maximum A Posteriori estimates for ancestral locations. We exemplify our methods on a set of synthetic datasets and then combine our inference methods with the phylogeographic clustering approach presented in Manolopoulou et al. (2011) on a real dataset from weevils in the Iberian peninsula in order to infer ancestral locations as well as population substructure.

  7. Learning and retention through predictive inference and classification.

    PubMed

    Sakamoto, Yasuaki; Love, Bradley C

    2010-12-01

    Work in category learning addresses how humans acquire knowledge and, thus, should inform classroom practices. In two experiments, we apply and evaluate intuitions garnered from laboratory-based research in category learning to learning tasks situated in an educational context. In Experiment 1, learning through predictive inference and classification were compared for fifth-grade students using class-related materials. Making inferences about properties of category members and receiving feedback led to the acquisition of both queried (i.e., tested) properties and nonqueried properties that were correlated with a queried property (e.g., even if not queried, students learned about a species' habitat because it correlated with a queried property, like the species' size). In contrast, classifying items according to their species and receiving feedback led to knowledge of only the property most diagnostic of category membership. After multiple-day delay, the fifth-graders who learned through inference selectively retained information about the queried properties, and the fifth-graders who learned through classification retained information about the diagnostic property, indicating a role for explicit evaluation in establishing memories. Overall, inference learning resulted in fewer errors, better retention, and more liking of the categories than did classification learning. Experiment 2 revealed that querying a property only a few times was enough to manifest the full benefits of inference learning in undergraduate students. These results suggest that classroom teaching should emphasize reasoning from the category to multiple properties rather than from a set of properties to the category.

  8. On the Inference of Functional Circadian Networks Using Granger Causality.

    PubMed

    Pourzanjani, Arya; Herzog, Erik D; Petzold, Linda R

    2015-01-01

    Being able to infer one way direct connections in an oscillatory network such as the suprachiastmatic nucleus (SCN) of the mammalian brain using time series data is difficult but crucial to understanding network dynamics. Although techniques have been developed for inferring networks from time series data, there have been no attempts to adapt these techniques to infer directional connections in oscillatory time series, while accurately distinguishing between direct and indirect connections. In this paper an adaptation of Granger Causality is proposed that allows for inference of circadian networks and oscillatory networks in general called Adaptive Frequency Granger Causality (AFGC). Additionally, an extension of this method is proposed to infer networks with large numbers of cells called LASSO AFGC. The method was validated using simulated data from several different networks. For the smaller networks the method was able to identify all one way direct connections without identifying connections that were not present. For larger networks of up to twenty cells the method shows excellent performance in identifying true and false connections; this is quantified by an area-under-the-curve (AUC) 96.88%. We note that this method like other Granger Causality-based methods, is based on the detection of high frequency signals propagating between cell traces. Thus it requires a relatively high sampling rate and a network that can propagate high frequency signals.

  9. Molecular phylogeny of the nettle family (Urticaceae) inferred from multiple loci of three genomes and extensive generic sampling.

    PubMed

    Wu, Zeng-Yuan; Monro, Alex K; Milne, Richard I; Wang, Hong; Yi, Ting-Shuang; Liu, Jie; Li, De-Zhu

    2013-12-01

    Urticaceae is one of the larger Angiosperm families, but relationships within it remain poorly known. This study presents the first densely sampled molecular phylogeny of Urticaceae, using maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) to analyze the DNA sequence data from two nuclear (ITS and 18S), four chloroplast (matK, rbcL, rpll4-rps8-infA-rpl36, trnL-trnF) and one mitochondrial (matR) loci. We sampled 169 accessions representing 122 species, representing 47 of the 54 recognized genera within Urticaceae, including four of the six sometimes separated as Cecropiaceae. Major results included: (1) Urticaceae including Cecropiaceae was monophyletic; (2) Cecropiaceae was biphyletic, with both lineages nested within Urticaceae; (3) Urticaceae can be divided into four well-supported clades; (4) previously erected tribes or subfamilies were broadly supported, with some additions and alterations; (5) the monophyly of many genera was supported, whereas Boehmeria, Pellionia, Pouzolzia and Urera were clearly polyphyletic, while Urtica and Pilea each had a small genus nested within them; (6) relationships between genera were clarified, mostly with substantial support. These results clarify that some morphological characters have been overstated and others understated in previous classifications of the family, and provide a strong foundation for future studies on biogeography, character evolution, and circumscription of difficult genera.

  10. Methods for causal inference from gene perturbation experiments and validation

    PubMed Central

    Meinshausen, Nicolai; Hauser, Alain; Mooij, Joris M.; Peters, Jonas; Versteeg, Philip; Bühlmann, Peter

    2016-01-01

    Inferring causal effects from observational and interventional data is a highly desirable but ambitious goal. Many of the computational and statistical methods are plagued by fundamental identifiability issues, instability, and unreliable performance, especially for large-scale systems with many measured variables. We present software and provide some validation of a recently developed methodology based on an invariance principle, called invariant causal prediction (ICP). The ICP method quantifies confidence probabilities for inferring causal structures and thus leads to more reliable and confirmatory statements for causal relations and predictions of external intervention effects. We validate the ICP method and some other procedures using large-scale genome-wide gene perturbation experiments in Saccharomyces cerevisiae. The results suggest that prediction and prioritization of future experimental interventions, such as gene deletions, can be improved by using our statistical inference techniques. PMID:27382150

  11. Bayesian multimodel inference for dose-response studies

    USGS Publications Warehouse

    Link, W.A.; Albers, P.H.

    2007-01-01

    Statistical inference in dose?response studies is model-based: The analyst posits a mathematical model of the relation between exposure and response, estimates parameters of the model, and reports conclusions conditional on the model. Such analyses rarely include any accounting for the uncertainties associated with model selection. The Bayesian inferential system provides a convenient framework for model selection and multimodel inference. In this paper we briefly describe the Bayesian paradigm and Bayesian multimodel inference. We then present a family of models for multinomial dose?response data and apply Bayesian multimodel inferential methods to the analysis of data on the reproductive success of American kestrels (Falco sparveriuss) exposed to various sublethal dietary concentrations of methylmercury.

  12. Methods for causal inference from gene perturbation experiments and validation.

    PubMed

    Meinshausen, Nicolai; Hauser, Alain; Mooij, Joris M; Peters, Jonas; Versteeg, Philip; Bühlmann, Peter

    2016-07-01

    Inferring causal effects from observational and interventional data is a highly desirable but ambitious goal. Many of the computational and statistical methods are plagued by fundamental identifiability issues, instability, and unreliable performance, especially for large-scale systems with many measured variables. We present software and provide some validation of a recently developed methodology based on an invariance principle, called invariant causal prediction (ICP). The ICP method quantifies confidence probabilities for inferring causal structures and thus leads to more reliable and confirmatory statements for causal relations and predictions of external intervention effects. We validate the ICP method and some other procedures using large-scale genome-wide gene perturbation experiments in Saccharomyces cerevisiae The results suggest that prediction and prioritization of future experimental interventions, such as gene deletions, can be improved by using our statistical inference techniques. PMID:27382150

  13. SERIES - Satellite Emission Range Inferred Earth Surveying

    NASA Technical Reports Server (NTRS)

    Macdoran, P. F.; Spitzmesser, D. J.; Buennagel, L. A.

    1983-01-01

    The Satellite Emission Range Inferred Earth Surveying (SERIES) concept is based on the utilization of NAVSTAR Global Positioning System (GPS) radio transmissions without any satellite modifications and in a totally passive mode. The SERIES stations are equipped with lightweight 1.5 m diameter dish antennas mounted on trailers. A series baseline measurement accuracy demonstration is considered, taking into account a 100 meter baseline estimation from approximately one hour of differential Doppler data. It is planned to conduct the next phase of experiments on a 150 m baseline. Attention is given to details regarding future baseline measurement accuracy demonstrations, aspects of ionospheric calibration in connection with subdecimeter baseline accuracy requirements of geodesy, and advantages related to the use of the differential Doppler or pseudoranging mode.

  14. Automated adaptive inference of phenomenological dynamical models

    PubMed Central

    Daniels, Bryan C.; Nemenman, Ilya

    2015-01-01

    Dynamics of complex systems is often driven by large and intricate networks of microscopic interactions, whose sheer size obfuscates understanding. With limited experimental data, many parameters of such dynamics are unknown, and thus detailed, mechanistic models risk overfitting and making faulty predictions. At the other extreme, simple ad hoc models often miss defining features of the underlying systems. Here we develop an approach that instead constructs phenomenological, coarse-grained models of network dynamics that automatically adapt their complexity to the available data. Such adaptive models produce accurate predictions even when microscopic details are unknown. The approach is computationally tractable, even for a relatively large number of dynamical variables. Using simulated data, it correctly infers the phase space structure for planetary motion, avoids overfitting in a biological signalling system and produces accurate predictions for yeast glycolysis with tens of data points and over half of the interacting species unobserved. PMID:26293508

  15. Structural inference for uncertain networks

    NASA Astrophysics Data System (ADS)

    Martin, Travis; Ball, Brian; Newman, M. E. J.

    2016-01-01

    In the study of networked systems such as biological, technological, and social networks the available data are often uncertain. Rather than knowing the structure of a network exactly, we know the connections between nodes only with a certain probability. In this paper we develop methods for the analysis of such uncertain data, focusing particularly on the problem of community detection. We give a principled maximum-likelihood method for inferring community structure and demonstrate how the results can be used to make improved estimates of the true structure of the network. Using computer-generated benchmark networks we demonstrate that our methods are able to reconstruct known communities more accurately than previous approaches based on data thresholding. We also give an example application to the detection of communities in a protein-protein interaction network.

  16. Systematics and phylogenetics of Indo-Pacific Luciolinae fireflies (Coleoptera: Lampyridae) and the description of new genera.

    PubMed

    Ballantyne, Lesly A; Lambkin, Christine L

    2013-01-01

    This revision completes a taxonomic survey of fireflies (Coleoptera: Lampyridae) in the area encompassed by Australia, the Republic of Palau, Federated States of Micronesia, Papua New Guinea, Indonesia (West Irian/Papua), Solomon Islands, New Caledonia, Vanuatu and Fiji. It finalises the taxonomic issues arising from the 1969–70 voyage of the scientific vessel Alpha Helix to New Guinea. The firefly fauna of this area is exclusively Luciolinae. The scope of the revision was extended to include all known Luciolinae genera and certain species from SE Asia, and a phylogenetic analysis of 436 morphological characters of males, females, and associated larvae includes 142 Luciolinae species (Ballantyne & Lambkin 2009, and Fu et al. 2012a). The phylogenetic analyses infer four major groups within the Luciolinae. The monotypic Missimia Ballantyne is sister to all remaining Luciolinae and forms a grade to Aquatica Fu etBallantyne. The large clade of Curtos Motschulsky, Photuroluciola Pic, Colophotia Motschulsky, Poluninius gen. nov., Pyrophanes Olivier, Pteroptyx s. str. Olivier, Medeopteryx gen. nov., Trisinuata gen. nov., and Australoluciola gen. nov.forms a grade to the clade of Luciola s. str. Laporte (including Bourgeoisia Olivier). The monotypic Emeia Fu et al.forms a grade with a clade of Luciola and Pygoluciola Wittmer, sister to a large clade of Convexa Ballantyne, Pacifica gen. nov., Magnalata Ballantyne, Lloydiella Ballantyne, Asymmetricata Ballantyne, Pygatyphella s. str. Ballantyne, Atyphella Olliff, Aquilonia Ballantyne, and Gilvainsula Ballantyne. Luciola is paraphyletic, found in up to six clades across the tree. Together with Luciola, Magnalata, Aquilonia, and Gilvainsula render Atyphella paraphyletic. The new genera described here are all monophyletic and supported in the phylogenetic analyses that also provide evidence for the inclusion of taxa within them. Twenty-three genera including five new ones, and ten new species, are recognised and keys are

  17. Statistical Mechanics of Optimal Convex Inference in High Dimensions

    NASA Astrophysics Data System (ADS)

    Advani, Madhu; Ganguli, Surya

    2016-07-01

    ML and MAP while still outperforming them. For example, such optimal M-estimation algorithms can lead to as much as a 20% reduction in the amount of data to achieve the same performance relative to MAP. Moreover, we demonstrate a prediction of replica theory that no inference procedure whatsoever can outperform our optimal M-estimation procedure when signal and noise distributions are log-concave, by uncovering an equivalence between optimal M-estimation and optimal Bayesian inference in this setting. Our analysis also reveals insights into the nature of generalization and predictive power in high dimensions, information theoretic limits on compressed sensing, phase transitions in quadratic inference, and connections to central mathematical objects in convex optimization theory and random matrix theory.

  18. Occurrence and evolutionary inferences about Kranz anatomy in Cyperaceae (Poales).

    PubMed

    Martins, Shirley; Alves, Marccus; Scatena, Vera L

    2015-01-01

    Cyperaceae is an angiosperm family with the greatest diversity of species with Kranz anatomy. Four different types of Kranz anatomy (chlorocyperoid, eleocharoid, fimbristyloid and rhynchosporoid) have been described for this angiosperm family, and the occurrence and structural characteristics of these types are important to trace evolutionary hypotheses. The purpose of this study was to examine the available data on Cyperaceae Kranz anatomy, emphasizing taxonomy, geographic distribution, habitat and anatomy, to infer the potential origin of the Kranz anatomy in this family. The results showed that the four types of Kranz anatomy (associated with C4 photosynthesis) in Cyperaceae emerged numerous times in unrelated phylogenetic groups. However, the convergence of these anatomical types, except rhynchosporoid, was observed in certain groups. Thus, the diverse origin of these species might result from different environmental pressures that promote photorespiration. Greater variation in occurrence of Kranz anatomy and anatomical types was observed in Eleocharis, whose emergence of the C4 pathway was recent compared with other genera in the family, and the species of this genus are located in aquatic environments. PMID:26628020

  19. Bayesian Nonparametric Inference – Why and How

    PubMed Central

    Müller, Peter; Mitra, Riten

    2013-01-01

    We review inference under models with nonparametric Bayesian (BNP) priors. The discussion follows a set of examples for some common inference problems. The examples are chosen to highlight problems that are challenging for standard parametric inference. We discuss inference for density estimation, clustering, regression and for mixed effects models with random effects distributions. While we focus on arguing for the need for the flexibility of BNP models, we also review some of the more commonly used BNP models, thus hopefully answering a bit of both questions, why and how to use BNP. PMID:24368932

  20. Generic Comparison of Protein Inference Engines*

    PubMed Central

    Claassen, Manfred; Reiter, Lukas; Hengartner, Michael O.; Buhmann, Joachim M.; Aebersold, Ruedi

    2012-01-01

    Protein identifications, instead of peptide-spectrum matches, constitute the biologically relevant result of shotgun proteomics studies. How to appropriately infer and report protein identifications has triggered a still ongoing debate. This debate has so far suffered from the lack of appropriate performance measures that allow us to objectively assess protein inference approaches. This study describes an intuitive, generic and yet formal performance measure and demonstrates how it enables experimentalists to select an optimal protein inference strategy for a given collection of fragment ion spectra. We applied the performance measure to systematically explore the benefit of excluding possibly unreliable protein identifications, such as single-hit wonders. Therefore, we defined a family of protein inference engines by extending a simple inference engine by thousands of pruning variants, each excluding a different specified set of possibly unreliable identifications. We benchmarked these protein inference engines on several data sets representing different proteomes and mass spectrometry platforms. Optimally performing inference engines retained all high confidence spectral evidence, without posterior exclusion of any type of protein identifications. Despite the diversity of studied data sets consistently supporting this rule, other data sets might behave differently. In order to ensure maximal reliable proteome coverage for data sets arising in other studies we advocate abstaining from rigid protein inference rules, such as exclusion of single-hit wonders, and instead consider several protein inference approaches and assess these with respect to the presented performance measure in the specific application context. PMID:22057310

  1. Image-Data Compression Using Edge-Optimizing Algorithm for WFA Inference.

    ERIC Educational Resources Information Center

    Culik, Karel II; Kari, Jarkko

    1994-01-01

    Presents an inference algorithm that produces a weighted finite automata (WFA), in particular, the grayness functions of graytone images. Image-data compression results based on the new inference algorithm produces a WFA with a relatively small number of edges. Image-data compression results alone and in combination with wavelets are discussed.…

  2. Occurrence of Physical Dormancy in Seeds of Australian Sapindaceae: A Survey of 14 Species in Nine Genera

    PubMed Central

    Cook, A.; Turner, S. R.; Baskin, J. M.; Baskin, C. C.; Steadman, K. J.; Dixon, K. W.

    2008-01-01

    Background and Aims Sapindaceae is one of 16 angiosperm families whose seeds have physical dormancy (PY). However, the extent and nature of PY within this family is poorly known. The primary aims of this study were: (1) to evaluate seed characteristics and determine presence (or not) of PY within nine genera of Australian Sapindaceae; and (2) to compare the frequency of PY across the phylogenetic tree within Australian Sapindaceae. Methods Viability, imbibition and seed characteristics were assessed for 14 taxa from nine genera of Sapindaceae. For five species of Dodonaea, optimal conditions for germination and dormancy break were evaluated. An in situ burial experiment was performed on D. hackettiana seeds to identify the factor(s) responsible for overcoming PY. Classes of dormancy and of non-dormancy for 26 genera of Sapindaceae were mapped onto a phylogenetic tree for the family. Key Results Mean seed viability across all taxa was 69·7 %. Embryos were fully developed and folded (seven genera) or bent (two genera); no endosperm was present. Seeds of all five Dodonaea spp. and of Distichostemon hispidulus had PY. Hot-water treatment released PY in these six species. Optimal germination temperature for seeds of the four Dodonaea spp. that germinated was 15–20 °C. Following 5 months burial in soil, 36·4 % of D. hackettiana seeds had lost PY and germinated by the beginning of the winter wet season (May). Laboratory and field data indicate that dormancy was broken by warm, moist temperatures (≥50 °C) during summer. Conclusions PY occurs infrequently in genera of Sapindaceae native to Australia. Seeds of Dodonaea and Distichostemon had PY, whereas those of the other seven genera did not. Seeds of these two genera and of Diplopeltis (a previous study) are the only three of the 20 native Australian genera of Sapindaceae for which germination has been studied that have PY; all three belong to subfamily Dodonaeoideae. PMID:18369237

  3. The ventral pallidum and orbitofrontal cortex support food pleasantness inferences

    PubMed Central

    Simmons, W. Kyle; Rapuano, Kristina M.; Ingeholm, John E.; Avery, Jason; Kallman, Seth; Hall, Kevin D.; Martin, Alex

    2013-01-01

    Food advertisements often promote choices that are driven by inferences about the hedonic pleasures of eating a particular food. Given the individual and public health consequences of obesity, it is critical to address unanswered questions about the specific neural systems underlying these hedonic inferences. For example, although regions such as the orbitofrontal cortex (OFC) are frequently observed to respond more to pleasant food images than less hedonically pleasing stimuli, one important hedonic brain region in particular has largely remained conspicuously absent among human studies of hedonic response to food images. Based on rodent research demonstrating that activity in the ventral pallidum underlies the hedonic pleasures experienced upon eating food rewards, one might expect that activity in this important ‘hedonic hotspot’ might also track inferred food pleasantness. To date, however, no human studies have assessed this question. We thus asked human subjects to undergo fMRI and make item-by-item ratings of how pleasant it would be to eat particular visually perceived foods. Activity in the ventral pallidum was strongly modulated with pleasantness inferences. Additionally, activity within a region of the orbitofrontal cortex that tracks the pleasantness of tastes was also modulated with inferred pleasantness. Importantly, the reliability of these findings is demonstrated by their replication when we repeated the experiment at a new site with new subjects. These two experiments demonstrate that the ventral pallidum, in addition to the OFC, plays a central role in the moment-to-moment hedonic inferences that influence food-related decision-making. PMID:23397317

  4. Working memory and inferences: Evidence from eye fixations during reading.

    PubMed

    Calvo, Manuel G.

    2001-07-01

    Eye fixations during reading were monitored to examine the relationship between individual differences in working memory capacity-as assessed by the reading span task-and inferences about predictable events. Context sentences predicting likely events, or non-predicting control sentences, were presented. They were followed by continuation sentences in which a target word represented an event to be inferred (inferential word) or an unlikely event (non-predictable word). A main effect of reading span showed that high working memory capacity was related to shorter gaze durations across sentence regions. More specific findings involved an interaction between context, target, and reading span on late processing measures and regions. Thus, for high- but not for low-span readers, the predicting condition, relative to the control condition, facilitated reanalysis of the continuation sentence that represented the inference concept. This effect was revealed by a reduction in regression-path reading time in the last region of the sentence, involving less time reading that region and fewer regressions from it. These results indicate that working memory facilitates elaborative inferences during reading, but that this occurs at late text-integration processes, rather than at early lexical-access processes.

  5. Working memory and inferences: evidence from eye fixations during reading.

    PubMed

    Calvo, M G

    2001-01-01

    Eye fixations during reading were monitored to examine the relationship between individual differences in working memory capacity-as assessed by the reading span task-and inferences about predictable events. Context sentences predicting likely events, or non-predicting control sentences, were presented. They were followed by continuation sentences in which a target word represented an event to be inferred (inferential word) or an unlikely event (non-predictable word). A main effect of reading span showed that high working memory capacity was related to shorter gaze durations across sentence regions. More specific findings involved an interaction between context, target, and reading span on late processing measures and regions. Thus, for high- but not for low-span readers, the predicting condition, relative to the control condition, facilitated reanalysis of the continuation sentence that represented the inference concept. This effect was revealed by a reduction in regression-path reading time in the last region of the sentence, involving less time reading that region and fewer regressions from it. These results indicate that working memory facilitates elaborative inferences during reading, but that this occurs at late text-integration processes, rather than at early lexical-access processes.

  6. Phylogeny of Bembidion and related ground beetles (Coleoptera: Carabidae: Trechinae: Bembidiini: Bembidiina).

    PubMed

    Maddison, David R

    2012-06-01

    The phylogeny of the large genus Bembidion and related genera is inferred from four nuclear protein-coding genes (CAD, wingless, arginine kinase, and topoisomerase I), ribosomal DNA (28S and 18S), and the mitochondrial gene cytochrome oxidase I (COI). 230 of the more than 1200 species of Bembidion are sampled, as well as 26 species of five related genera, and 14 outgroups. Nuclear copies (numts) of COI were found sparsely scattered through sampled species. The resulting phylogeny, based upon individual gene analyses and combined analyses using maximum likelihood and parsimony, is very well supported at most nodes. Additional analyses explored the evidence, and corroborate the phylogeny. Seven analyses, each with one of the seven genes removed from the combined matrix, were also conducted, and yielded maximum likelihood bootstrap trees sharing over 92% of their nodes with the original, well-resolved bootstrap trees based on the complete set of seven genes. All key nodes were present in all seven analyses missing a single gene, indicating that support for these nodes comes from at least two genes. In addition, the inferred maximum likelihood tree based on the combined matrix is well-behaved and self-predicting, in that simulated evolution of sequences on the inferred tree under the inferred model of evolution yields a matrix from which all but one of the model tree's clades are recovered with bootstrap value >50, suggesting that internal branches in the tree may be of a length to yield sequences sufficient to allow their inference. All likelihood analyses were conducted under both a proportion-invariable plus gamma site-to-site rate variation model, as well as a simpler gamma model. The choice of model did not have a major effect on inferred phylogenies or their bootstrap values. The inferred phylogeny shows that Bembidarenas is not closely related to Bembidiina, and Phrypeus is likely distant as well; the remaining genera of Bembidiina form a monophyletic group

  7. A QUICK KEY TO THE SUBFAMILIES AND GENERA OF ANTS OF THE SAVANNAH RIVER SITE

    SciTech Connect

    Martin, D

    2007-09-04

    This taxonomic key was devised to support development of a Rapid Bioassessment Protocol using ants at the Savannah River Site. The emphasis is on 'rapid' and, because the available keys contained a very large number of genera not known to occur at the Savannah River Site, we found that the available keys were unwieldy. Because these keys contained many more genera than we would ever encounter and because this larger number of genera required more couplets in the key and often required examination of characters that are difficult to assess without higher magnifications (60X or higher), more time was required to process samples. In developing this set of keys I emphasized character states that are easier for nonspecialists to recognize. I recognize that the character sets used may lead to some errors but I believe that the error rate will be small and, for the purpose of rapid bioassessment, this error rate will be acceptable provided that overall sample sizes are adequate. Oliver and Beattie (1996a, 1996b) found that for rapid assessment of biodiversity the same results were found when identifications were done to morphospecies by people with minimal expertise as when the same data sets were identified by subject matter experts. Basset et al. (2004) concluded that it was not as important to correctly identify all species as it was to be sure that the study included as many functional groups as possible. If your study requires high levels of accuracy, it is highly recommended that, when you key out a specimen and have any doubts concerning the identification, you should refer to keys in Bolton (1994) or to the other keys used to develop this area specific taxonomic key.

  8. Endemicity and evolutionary value: a study of Chilean endemic vascular plant genera.

    PubMed

    Scherson, Rosa A; Albornoz, Abraham A; Moreira-Muñoz, Andrés S; Urbina-Casanova, Rafael

    2014-03-01

    This study uses phylogeny-based measures of evolutionary potential (phylogenetic diversity and community structure) to evaluate the evolutionary value of vascular plant genera endemic to Chile. Endemicity is regarded as a very important consideration for conservation purposes. Taxa that are endemic to a single country are valuable conservation targets, as their protection depends upon a single government policy. This is especially relevant in developing countries in which conservation is not always a high resource allocation priority. Phylogeny-based measures of evolutionary potential such as phylogenetic diversity (PD) have been regarded as meaningful measures of the "value" of taxa and ecosystems, as they are able to account for the attributes that could allow taxa to recover from environmental changes. Chile is an area of remarkable endemism, harboring a flora that shows the highest number of endemic genera in South America. We studied PD and community structure of this flora using a previously available supertree at the genus level, to which we added DNA sequences of 53 genera endemic to Chile. Using discrepancy values and a null model approach, we decoupled PD from taxon richness, in order to compare their geographic distribution over a one-degree grid. An interesting pattern was observed in which areas to the southwest appear to harbor more PD than expected by their generic richness than those areas to the north of the country. In addition, some southern areas showed more PD than expected by chance, as calculated with the null model approach. Geological history as documented by the study of ancient floras as well as glacial refuges in the coastal range of southern Chile during the quaternary seem to be consistent with the observed pattern, highlighting the importance of this area for conservation purposes. PMID:24683462

  9. Endemicity and evolutionary value: a study of Chilean endemic vascular plant genera

    PubMed Central

    Scherson, Rosa A; Albornoz, Abraham A; Moreira-Muñoz, Andrés S; Urbina-Casanova, Rafael

    2014-01-01

    This study uses phylogeny-based measures of evolutionary potential (phylogenetic diversity and community structure) to evaluate the evolutionary value of vascular plant genera endemic to Chile. Endemicity is regarded as a very important consideration for conservation purposes. Taxa that are endemic to a single country are valuable conservation targets, as their protection depends upon a single government policy. This is especially relevant in developing countries in which conservation is not always a high resource allocation priority. Phylogeny-based measures of evolutionary potential such as phylogenetic diversity (PD) have been regarded as meaningful measures of the “value” of taxa and ecosystems, as they are able to account for the attributes that could allow taxa to recover from environmental changes. Chile is an area of remarkable endemism, harboring a flora that shows the highest number of endemic genera in South America. We studied PD and community structure of this flora using a previously available supertree at the genus level, to which we added DNA sequences of 53 genera endemic to Chile. Using discrepancy values and a null model approach, we decoupled PD from taxon richness, in order to compare their geographic distribution over a one-degree grid. An interesting pattern was observed in which areas to the southwest appear to harbor more PD than expected by their generic richness than those areas to the north of the country. In addition, some southern areas showed more PD than expected by chance, as calculated with the null model approach. Geological history as documented by the study of ancient floras as well as glacial refuges in the coastal range of southern Chile during the quaternary seem to be consistent with the observed pattern, highlighting the importance of this area for conservation purposes. PMID:24683462

  10. Stable isotope data of selected gastropod genera as proxies for seawater chemistry of the Central Paratethys

    NASA Astrophysics Data System (ADS)

    Latal, C.; Piller, W. E.; Harzhauser, M.

    2003-04-01

    Geodynamic processes influenced the complex evolution of the Paratethys, an extended marginal sea, which is characterised by intermittently open and closed marine seaways with its surrounding oceans. Especially in the Miocene, this led to substantial changes in marine environments and ecosystems by changing basin geometries, water circulation, water depth, water chemistry, climate etc. Investigations of stable isotopes of fossil carbonate shells provide information about paleoenvironmental parameters of the ancient seawater. Oxygen and carbon isotope data of selected gastropod genera, mainly Turritellidae, are used to reconstruct paleoenvironmental parameters of different time slices of the Miocene of Austrian Neogene basins. Recent Turritellidae live in a wide range of environments, mainly shallow infaunal or epifaunal, but prefer fully marine conditions. Stable isotope investigations of recent specimens support their usefulness as isotopic indicators for environmental parameters. For detecting diagenetic alterations of the aragonitic gastropod shells, samples were analysed for their shell mineralogy and microstructures with X-ray diffraction analyses and scanning electron microscopy prior to stable isotope analyses. Several microsamples for isotope analyses of each shell were taken to test the intrashell variability. Oxygen and carbon isotopes for Karpatian and Badenian turritellids from the Vienna Basin and the Korneuburg Basin show slightly lighter oxygen and carbon isotope values for the Karpatian. In addition to turritellids, two other gastropod genera (Ocenebra and Granulolabium), both preferring an intertidal habitat and tolerating some salinity fluctuations, were investigated, yielding information about mixing of seawater with freshwater. So parameters for different environments can be obtained, and also comparisons of different gastropod genera are possible. The study was supported by the Austrian Science Foundation (FWF), project "Stable isotopes and

  11. The Impact of Disablers on Predictive Inference

    ERIC Educational Resources Information Center

    Cummins, Denise Dellarosa

    2014-01-01

    People consider alternative causes when deciding whether a cause is responsible for an effect (diagnostic inference) but appear to neglect them when deciding whether an effect will occur (predictive inference). Five experiments were conducted to test a 2-part explanation of this phenomenon: namely, (a) that people interpret standard predictive…

  12. Local and Global Thinking in Statistical Inference

    ERIC Educational Resources Information Center

    Pratt, Dave; Johnston-Wilder, Peter; Ainley, Janet; Mason, John

    2008-01-01

    In this reflective paper, we explore students' local and global thinking about informal statistical inference through our observations of 10- to 11-year-olds, challenged to infer the unknown configuration of a virtual die, but able to use the die to generate as much data as they felt necessary. We report how they tended to focus on local changes…

  13. Causal inference in economics and marketing.

    PubMed

    Varian, Hal R

    2016-07-01

    This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual-a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference.

  14. Genetic Network Inference Using Hierarchical Structure

    PubMed Central

    Kimura, Shuhei; Tokuhisa, Masato; Okada-Hatakeyama, Mariko

    2016-01-01

    Many methods for inferring genetic networks have been proposed, but the regulations they infer often include false-positives. Several researchers have attempted to reduce these erroneous regulations by proposing the use of a priori knowledge about the properties of genetic networks such as their sparseness, scale-free structure, and so on. This study focuses on another piece of a priori knowledge, namely, that biochemical networks exhibit hierarchical structures. Based on this idea, we propose an inference approach that uses the hierarchical structure in a target genetic network. To obtain a reasonable hierarchical structure, the first step of the proposed approach is to infer multiple genetic networks from the observed gene expression data. We take this step using an existing method that combines a genetic network inference method with a bootstrap method. The next step is to extract a hierarchical structure from the inferred networks that is consistent with most of the networks. Third, we use the hierarchical structure obtained to assign confidence values to all candidate regulations. Numerical experiments are also performed to demonstrate the effectiveness of using the hierarchical structure in the genetic network inference. The improvement accomplished by the use of the hierarchical structure is small. However, the hierarchical structure could be used to improve the performances of many existing inference methods. PMID:26941653

  15. The Reasoning behind Informal Statistical Inference

    ERIC Educational Resources Information Center

    Makar, Katie; Bakker, Arthur; Ben-Zvi, Dani

    2011-01-01

    Informal statistical inference (ISI) has been a frequent focus of recent research in statistics education. Considering the role that context plays in developing ISI calls into question the need to be more explicit about the reasoning that underpins ISI. This paper uses educational literature on informal statistical inference and philosophical…

  16. Reinforcement learning or active inference?

    PubMed

    Friston, Karl J; Daunizeau, Jean; Kiebel, Stefan J

    2009-01-01

    This paper questions the need for reinforcement learning or control theory when optimising behaviour. We show that it is fairly simple to teach an agent complicated and adaptive behaviours using a free-energy formulation of perception. In this formulation, agents adjust their internal states and sampling of the environment to minimize their free-energy. Such agents learn causal structure in the environment and sample it in an adaptive and self-supervised fashion. This results in behavioural policies that reproduce those optimised by reinforcement learning and dynamic programming. Critically, we do not need to invoke the notion of reward, value or utility. We illustrate these points by solving a benchmark problem in dynamic programming; namely the mountain-car problem, using active perception or inference under the free-energy principle. The ensuing proof-of-concept may be important because the free-energy formulation furnishes a unified account of both action and perception and may speak to a reappraisal of the role of dopamine in the brain.

  17. Active inference and epistemic value.

    PubMed

    Friston, Karl; Rigoli, Francesco; Ognibene, Dimitri; Mathys, Christoph; Fitzgerald, Thomas; Pezzulo, Giovanni

    2015-01-01

    We offer a formal treatment of choice behavior based on the premise that agents minimize the expected free energy of future outcomes. Crucially, the negative free energy or quality of a policy can be decomposed into extrinsic and epistemic (or intrinsic) value. Minimizing expected free energy is therefore equivalent to maximizing extrinsic value or expected utility (defined in terms of prior preferences or goals), while maximizing information gain or intrinsic value (or reducing uncertainty about the causes of valuable outcomes). The resulting scheme resolves the exploration-exploitation dilemma: Epistemic value is maximized until there is no further information gain, after which exploitation is assured through maximization of extrinsic value. This is formally consistent with the Infomax principle, generalizing formulations of active vision based upon salience (Bayesian surprise) and optimal decisions based on expected utility and risk-sensitive (Kullback-Leibler) control. Furthermore, as with previous active inference formulations of discrete (Markovian) problems, ad hoc softmax parameters become the expected (Bayes-optimal) precision of beliefs about, or confidence in, policies. This article focuses on the basic theory, illustrating the ideas with simulations. A key aspect of these simulations is the similarity between precision updates and dopaminergic discharges observed in conditioning paradigms. PMID:25689102

  18. Brazilian Histerini (Coleoptera, Histeridae, Histerinae): a new species, key to the genera, and checklist of species.

    PubMed

    Leivas, Fernando W T; Moura, Daniel P; Caterino, Michael S

    2015-01-01

    A new species of the Hister coenosus group from southern Brazil is described. Hister lucia sp. nov. is the largest Hister sp. in the New World, and is also distinguished by its dorsally and laterally concave mandibles. The three genera of Histerini recorded from Brazil are keyed, and a checklist of species of the tribe recorded from Brazil is presented. In total, seventeen described species of Histerini are recorded from Brazil, including fifteen of Hister Linnaeus, one of Atholus C. Thomson, and one of Margarinotus Marseul.

  19. Representatives of genera Malbosiceras and Pomeliceras (Neocomitidae, Ammonoidea) from the Berriasian of the Crimean Mountains

    NASA Astrophysics Data System (ADS)

    Arkad'Ev, V. V.; Bogdanova, T. N.; Lysenko, N. I.

    2007-06-01

    The revised representatives of ammonite genera Malbosiceras and Pomeliceras from the Berriasian of the Crimean Mountains are classed with seven species, four of the first genus [ M. malbosi (Pictet), M. chaperi (Pictet), M. broussei (Mazenot), M. pictetiforme Tavera] and three of the second one [ P. aff. boisseti Nikolov, P. breveti (Pomel), P. (?) funduklense Lysenko et Arkadiev sp. nov.]. The identified species are described. The genus Mazenoticeras is considered as synonym of Malbosiceras. The above species prove that all the Berriasian zones ( jacobi, occitanica and boissieri) are characteristic of corresponding deposits in the Crimean Mountains.

  20. Elliptic Genera of Two-Dimensional Gauge Theories with Rank-One Gauge Groups

    NASA Astrophysics Data System (ADS)

    Benini, Francesco; Eager, Richard; Hori, Kentaro; Tachikawa, Yuji

    2014-04-01

    We compute the elliptic genera of two-dimensional and -gauged linear sigma models via supersymmetric localization, for rank-one gauge groups. The elliptic genus is expressed as a sum over residues of a meromorphic function whose argument is the holonomy of the gauge field along both the spatial and the temporal directions of the torus. We illustrate our formulas by a few examples including the quintic Calabi-Yau, SU(2) and O(2) gauge theories coupled to N fundamental chiral multiplets, and a geometric model.

  1. [Metabolites of Toxigenic Fungi in Lichens of Genera Alectoria, Bryoria, Evernia, Pseudevernia, and Usnea].

    PubMed

    Burkin, A A; Kononenko, G P

    2015-01-01

    Complexes of mycotoxins in fruticose lichens of 14 species belonging to five genera of the family Parmeliaceae were characterized by size, composition, and content of individual components. It was shown that species of the genus Bryoria always contain five mycotoxins (sterigmatocystin, mycophenolic acid, citrinin, emodin, and alternariol). In Evernia and Pseudevernia, this list is supplemented with zearalenone, diacetoxyscirpenol, and cyclopiazonic acid or fumonisins. It was noted that Alectoria and Usnea are distinguished by a peculiar set of toxic metabolites and occupy an intermediate position according to their number. The similarities and distinctions of the mycotoxin profile in species belonging to the same genus and in specimens from different habitats are discussed.

  2. Inference-based constraint satisfaction supports explanation

    SciTech Connect

    Sqalli, M.H.; Freuder, E.C.

    1996-12-31

    Constraint satisfaction problems are typically solved using search, augmented by general purpose consistency inference methods. This paper proposes a paradigm shift in which inference is used as the primary problem solving method, and attention is focused on special purpose, domain specific inference methods. While we expect this approach to have computational advantages, we emphasize here the advantages of a solution method that is more congenial to human thought processes. Specifically we use inference-based constraint satisfaction to support explanations of the problem solving behavior that are considerably more meaningful than a trace of a search process would be. Logic puzzles are used as a case study. Inference-based constraint satisfaction proves surprisingly powerful and easily extensible in this domain. Problems drawn from commercial logic puzzle booklets are used for evaluation. Explanations are produced that compare well with the explanations provided by these booklets.

  3. Spionidae (Annelida) from Lizard Island, Great Barrier Reef, Australia: the genera Aonides, Dipolydora, Polydorella, Prionospio, Pseudopolydora, Rhynchospio, and Tripolydora.

    PubMed

    Radashevsky, Vasily I

    2015-01-01

    Nineteen species in seven genera of spionid polychaetes are described and illustrated based on new material collected from the intertidal and shallow waters around the Lizard Island Group, northern Great Barrier Reef. Only one of these species had been previously reported from the Reef. Six species are described as new to science, and the taxonomy of seven species should be clarified in the future. Prionospio sensu lato is the most diverse group with 11 species identified in the present study. One species is identified in each of the genera Dipolydora, Polydorella, Rhynchospio and Tripolydora, and two species are identified in each of the genera Aonides and Pseudopolydora. The fauna of spionid polychaetes of the Great Barrier Reef seems to be more diverse than previously described and more species are expected to be found in the future. An identification key is provided to 16 genera of Spionidae reported from or likely to be found on the Great Barrier Reef. PMID:26624082

  4. Spionidae (Annelida) from Lizard Island, Great Barrier Reef, Australia: the genera Aonides, Dipolydora, Polydorella, Prionospio, Pseudopolydora, Rhynchospio, and Tripolydora.

    PubMed

    Radashevsky, Vasily I

    2015-09-18

    Nineteen species in seven genera of spionid polychaetes are described and illustrated based on new material collected from the intertidal and shallow waters around the Lizard Island Group, northern Great Barrier Reef. Only one of these species had been previously reported from the Reef. Six species are described as new to science, and the taxonomy of seven species should be clarified in the future. Prionospio sensu lato is the most diverse group with 11 species identified in the present study. One species is identified in each of the genera Dipolydora, Polydorella, Rhynchospio and Tripolydora, and two species are identified in each of the genera Aonides and Pseudopolydora. The fauna of spionid polychaetes of the Great Barrier Reef seems to be more diverse than previously described and more species are expected to be found in the future. An identification key is provided to 16 genera of Spionidae reported from or likely to be found on the Great Barrier Reef.

  5. A revision and key to the genera of Afrotropical Mantispidae (Neuropterida, Neuroptera), with the description of a new genus.

    PubMed

    Snyman, Louwtjie P; Ohl, Michael; Mansell, Mervyn W; Scholtz, Clarke H

    2012-01-01

    The Afrotropical Mantispidae genera have previously been neglected and are poorly known. The genera are revised and redescribed. A new genus Afromantispa Snyman and Ohl is described with Afromantispa tenellacomb. n.as type species. Perlamantispa (Handschin, 1960) is synonymised with Sagittalata Handschin, 1959. The new combinations within the genus include Sagittalata austroafricacomb. n., Sagittalata bequaerticomb. n., Sagittalata dorsaliscomb. n., Sagittalata girardicomb. n., Sagittalata nubilacomb. n.,Sagittalata perlacomb. n.,Sagittalata pusillacomb. n., Sagittalata similatacomb. n., Sagittalata royicomb. n., Sagittalata tinctacomb. n. andSagittalata vasseicomb. n. An illustrated key to the genera Afromantispagen. n., Sagittalata Handschin, 1959, Mantispa Illiger, 1798, Cercomantispa Handschin, 1959, Rectinerva Handschin, 1959, Nampista Navás, 1914, and Pseudoclimaciella Handschin, 1960 is provided. The wing venation of Mantispidae is redescribed. Similarities between the genera are discussed. Subsequent studies will focus on revising the taxonomic status of species, which are not dealt with in this study. PMID:22573953

  6. Prevalence and differential host-specificity of two avian blood parasite genera in the Australo-Papuan region

    USGS Publications Warehouse

    Beadell, J.S.; Gering, E.; Austin, J.; Dumbacher, J.P.; Peirce, M.A.; Pratt, T.K.; Atkinson, C.T.; Fleischer, R.C.

    2004-01-01

    The degree to which widespread avian blood parasites in the genera Plasmodium and Haemoproteus pose a threat to novel hosts depends in part on the degree to which they are constrained to a particular host or host family. We examined the host distribution and host-specificity of these parasites in birds from two relatively understudied and isolated locations: Australia and Papua New Guinea. Using polymerase chain reaction (PCR), we detected infection in 69 of 105 species, representing 44% of individuals surveyed (n = 428). Across host families, prevalence of Haemoproteus ranged from 13% (Acanthizidae) to 56% (Petroicidae) while prevalence of Plasmodium ranged from 3% (Petroicidae) to 47% (Ptilonorhynchidae). We recovered 78 unique mitochondrial lineages from 155 sequences. Related lineages of Haemoproteus were more likely to derive from the same host family than predicted by chance at shallow (average LogDet genetic distance = 0, n = 12, P = 0.001) and greater depths (average distance = 0.014, n = 11, P < 0.001) within the parasite phylogeny. Within two major Haemoproteus subclades identified in a maximum likelihood phylogeny, host-specificity was evident up to parasite genetic distances of 0.029 and 0.007 based on logistic regression. We found no significant host relationship among lineages of Plasmodium by any method of analysis. These results support previous evidence of strong host-family specificity in Haemoproteus and suggest that lineages of Plasmodium are more likely to form evolutionarily-stable associations with novel hosts.

  7. Phylogenetic affinities of Phobetinus to other pirate spider genera (Araneae: Mimetidae) as indicated by spinning field morphology.

    PubMed

    Townley, Mark A; Harms, Danilo; Benjamin, Suresh P

    2013-09-01

    Spinnerets from Phobetinus sagittifer and an undescribed Phobetinus species were examined by scanning electron microscopy to gain a better understanding of this genus' relationships to other genera in the family Mimetidae. Consistent with placement of Phobetinus in Mimetinae, females possessed two synapomorphies of this subfamily; enlarged cylindrical silk gland spigots with domed shafts and a single cylindrical spigot per posterior lateral spinneret (PLS). Spinning field features overall suggest Phobetinus is most closely related to Mimetus, followed by Australomimetus, then Ero. A possible synapomorphy of a clade including Mimetus and Phobetinus is a pair of modified piriform silk gland spigots on each anterior lateral spinneret of adult males located adjacent to the secondary major ampullate silk gland tartipore. These spigots were present in P. sagittifer; however, similarly positioned spigots in the undescribed species were not obviously modified (i.e., wider or with larger openings relative to the other piriform spigots). Close affinity to Mimetus was also indicated by tartipore-accommodated PLS aciniform silk glands in both Phobetinus species. These have been consistently observed in Mimetus, but not in Australomimetus or Ero. Somatic and genitalic drawings of P. sagittifer are provided to aid identification and similarities are noted between male pedipalps of Mimetus and Phobetinus.

  8. SSU rRNA-based phylogenetic position of the genera Amoeba and Chaos (Lobosea, Gymnamoebia): the origin of gymnamoebae revisited.

    PubMed

    Bolivar, I; Fahrni, J F; Smirnov, A; Pawlowski, J

    2001-12-01

    Naked lobose amoebae (gymnamoebae) are among the most abundant group of protists present in all aquatic and terrestrial biotopes. Yet, because of lack of informative morphological characters, the origin and evolutionary history of gymnamoebae are poorly known. The first molecular studies revealed multiple origins for the amoeboid lineages and an extraordinary diversity of amoebae species. Molecular data, however, exist only for a few species of the numerous taxa belonging to this group. Here, we present the small-subunit (SSU) rDNA sequences of four species of typical large gymnamoebae: Amoeba proteus, Amoeba leningradensis, Chaos nobile, and Chaos carolinense. Sequence analysis suggests that the four species are closely related to the species of genera Saccamoeba, Leptomyxa, Rhizamoeba, Paraflabellula, Hartmannella, and Echinamoeba. All of them form a relatively well-supported clade, which corresponds to the subclass Gymnamoebia, in agreement with morphology-based taxonomy. The other gymnamoebae cluster in small groups or branch separately. Their relationships change depending on the type of analysis and the model of nucleotide substitution. All gymnamoebae branch together in Neighbor-Joining analysis with corrections for among-site rate heterogeneity and proportion of invariable sites. This clade, however, is not statistically supported by SSU rRNA gene sequences and further analysis of protein sequence data will be necessary to test the monophyly of gymnamoebae.

  9. Oil-producing flowers within the Iridoideae (Iridaceae): evolutionary trends in the flowers of the New World genera

    PubMed Central

    Chauveau, Olivier; Eggers, Lilian; Souza-Chies, Tatiana T.; Nadot, Sophie

    2012-01-01

    Background and Aims Oil-producing flowers related to oil-bee pollination are a major innovation in Neotropical and Mexican Iridaceae. In this study, phylogenetic relationships were investigated among a wide array of New World genera of the tribes Sisyrinchieae, Trimezieae and Tigridieae (Iridaceae: Iridoideae) and the evolution of floral glandular structures, which are predominantly trichomal elaiophores, was examined in relation to the diversification of New World Iridaceae. Methods Phylogenetic analyses based on seven molecular markers obtained from 97 species were conducted to produce the first extensive phylogeny of the New World tribes of subfamily Iridoideae. The resulting phylogenetic hypothesis was used to trace the evolutionary history of glandular structures present in the flowers of numerous species in each tribe. Hypotheses of differential diversification rates among lineages were also investigated using both topological and Binary-State Speciation and Extinction methods. Key Results and Conclusions Floral glandular structures and especially trichomal elaiophores evolved multiple times independently in the American tribes of Iridoideae. The distribution pattern of species displaying glandular trichomes across the phylogeny reveals lability in the pollination system and suggests that these structures may have played a significant role in the diversification of the Iridoideae on the American continent. PMID:22782239

  10. An illustrated key to the genera and subgenera of the Recent azooxanthellate Scleractinia (Cnidaria, Anthozoa), with an attached glossary

    PubMed Central

    Cairns, Stephen D.; Kitahara, Marcelo V.

    2012-01-01

    Abstract The 120 presently recognized genera and seven subgenera of the azooxanthellate Scleractinia are keyed using gross morphological characters of the corallum. All genera are illustrated with calicular and side views of coralla. All termes used in the key are defined in an illustrated glossary. A table of all species-level keys, both comprehensive and faunistic, is provided covering the last 40 years. PMID:23166463

  11. Number of genera as a potential screening tool for assessing quality of bryophyte communities in Ohio wetlands

    USGS Publications Warehouse

    Schumacher, William; Stapanian, Martin A.; Andreas, Barbara; Gara, Brian

    2016-01-01

    Bryophytes (mosses, liverworts, and hornworts) have numerous advantages as indicators of environmental quality. A quality assessment index for bryophyte species assemblages (BQAI) was developed for the State of Ohio, USA. Reliable identification of bryophytes to species often requires considerable training, practice, and time. In contrast, reliable identification to genera for most bryophytes in Ohio requires much less training. We identified 110 bryophyte species (14 liverworts and 96 mosses) belonging to 69 genera (13 liverwort and 56 moss) in 45 wetlands (27 emergent, 13 forested, and 5 shrub) in Ohio. As expected, there were more genera and higher BQAI scores in forested than in emergent wetlands. Number of genera was highly correlated (r ≥ 0.9) with BQAI in emergent and forested wetlands and for the combined set of wetlands. Number of genera and BQAI responded almost identically to an index of wetland disturbance. The results suggest that number of genera has potential as a screening tool for assessing bryophyte community quality in wetlands in some regions.

  12. If he can do it, so can they: exposure to counterstereotypically successful exemplars prompts automatic inferences.

    PubMed

    Critcher, Clayton R; Risen, Jane L

    2014-03-01

    After incidental exposure to Blacks who succeeded in counterstereotypical domains (e.g., Brown University President Ruth Simmons, Nobel Laureate Toni Morrison), participants drew an automatic inference that race was not a success-inhibiting factor in modern society. Of note, participants' automatic inferences were not simply guided by their explicit reasoning (i.e., their beliefs about what these exemplars signify about the state of race relations). Studies 1-3 demonstrated the basic automatic inference effect and provided evidence that such effects unfolded automatically, without intention or awareness. Study 4 replicated the effect in non-race-related domains. Subsequent studies examined what features of exemplars (Studies 5 and 6) and inference makers (Studies 7 and 8) prompt automatic inferences. Study 5 suggested that counterstereotypically successful exemplars prompt racism-denying inferences because they signal what is possible, even if not typical. Study 6 demonstrated that when these exemplars succeed in a stereotypical domain (e.g., Blacks in athletics), similar automatic inferences are not drawn. Those most likely to draw automatic inferences are people predisposed to approach the world with inferential thinking: participants dispositionally high in need for cognition (Study 7) or experimentally primed to think inferentially (Study 8).

  13. Electrophysiological time course and brain areas of spontaneous and intentional trait inferences

    PubMed Central

    Van Duynslaeger, Marijke; Verstraeten, Edwin

    2007-01-01

    This study measured event-related potentials during spontaneous and intentional trait inferences. Participants read sentences describing the behavior of a target person from which a strong moral trait could be inferred. The last word of each sentence determined the consistency with the trait induced during an introductory paragraph. In comparison with behaviors that were consistent with the implied trait, a P300 waveform was obtained when the behaviors were evaluative inconsistent with that trait. This dependency on behavioral consistency indicates that trait inferences were made previously while reading the preceding behaviors, irrespective of the participants’ spontaneous or intentional goals. Overall, the P300 shows considerable parallels between spontaneous and intentional inferences, indicating that the type and timing of the inconsistency process is very similar. In contrast, source localization (LORETA) of the event-related potentials suggest that spontaneous inferences show greater activation in the temporo-parietal junction compared to intentional inferences following an inconsistency. Memory measures taken after the presentation of the stimulus material involved sentence completion and trait-cued recall, and supported the occurrence of trait inferences associated with the actor. They also showed significant correlations with the neural components (i.e. P300 and its current density at the temporo-parietal junction) predominantly following spontaneous instructions, indicating that these components are valid neural indices of spontaneous inferences. PMID:18985139

  14. Probabilistic phylogenetic inference with insertions and deletions.

    PubMed

    Rivas, Elena; Eddy, Sean R

    2008-01-01

    A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non-reversible generative (birth-death) evolutionary model for insertions and deletions. The model assumes that insertion and deletion events occur one residue at a time. We apply this model to phylogenetic tree inference by extending the program dnaml in phylip. Using standard benchmarking methods on simulated data and a new "concordance test" benchmark on real ribosomal RNA alignments, we show that the extended program dnamlepsilon improves accuracy relative to the usual approach of ignoring gaps, while retaining the computational efficiency of the Felsenstein peeling algorithm. PMID:18787703

  15. Fine structure of body wall cuticle of females of eight genera of heteroderidae.

    PubMed

    Cliff, G M; Baldwin, J G

    1985-07-01

    Body wall cuticle of adult females of eight genera within the Heteroderidae was examined by transmission electron microscopy for comparison with previously studied species within the family. Cuticle structure was used to test some current hypotheses of phylogeny of Heteroderidae and to evaluate intrageneric variability in cuticle layering. Verutus, Rhizonema, and Meloidodera possess striated cuticle surfaces and have the simplest layering, suggesting that striations have not necessarily arisen repeatedly in Heteroderidae through convergent or parallel evolution. Atalodera and Thecavermiculatus possess similar cuticles with derived characteristics, strengthening the hypothesis that the two genera are sister groups. Similarly, the cuticle of Cactodera resembles the specialized cuticle of Globodera and Punctodera in having a basal layer (D) and a surface layer infused with electron-dense substance. Heterodera betulae has a unique cuticle in which the thickest layer (C) is infiltrated with an electron-dense matrix. Little intrageneric difference was found between cuticles of two species of Meloidodera or between two species of Atalodera. However, Atalodera ucri has a basal layer (E) not found in other Heteroderidae. The most striking intrageneric variation in cuticle structure was observed between the thin three-layered cuticle of Sarisodera africana and the much thicker four-layered cuticle of Sarisodera hydrophila; results do not support monophyly of Sarisodera.

  16. Nematode Genera in Forest Soil Respond Differentially to Elevated CO2

    PubMed Central

    Neher, Deborah A.; Weicht, Thomas R.

    2013-01-01

    Previous reports suggest that fungivorous nematodes are the only trophic group in forest soils affected by elevated CO2. However, there can be ambiguity within trophic groups, and we examined data at a genus level to determine whether the conclusion remains similar. Nematodes were extracted from roots and soil of loblolly pine (Pinus taeda) and sweet gum (Liquidambar styraciflua) forests fumigated with either ambient air or CO2-enriched air. Root length and nematode biomass were estimated using video image analysis. Most common genera included Acrobeloides, Aphelenchoides, Cephalobus, Ditylenchus, Ecphyadorphora, Filenchus, Plectus, Prismatolaimus, and Tylencholaimus. Maturity Index values and diversity increased with elevated CO2 in loblolly pine but decreased with elevated CO2 in sweet gum forests. Elevated CO2 treatment affected the occurrence of more nematode genera in sweet gum than loblolly pine forests. Numbers were similar but size of Xiphinema decreased in elevated CO2. Abundance, but not biomass, of Aphelenchoides was reduced by elevated CO2. Treatment effects were apparent at the genus levels that were masked at the trophic level. For example, bacterivores were unaffected by elevated CO2, but abundance of Cephalobus was affected by CO2 treatment in both forests. PMID:24115786

  17. Discovering the Unknown: Improving Detection of Novel Species and Genera from Short Reads

    DOE PAGESBeta

    Rosen, Gail L.; Polikar, Robi; Caseiro, Diamantino A.; Essinger, Steven D.; Sokhansanj, Bahrad A.

    2011-01-01

    High-throughput sequencing technologies enable metagenome profiling, simultaneous sequencing of multiple microbial species present within an environmental sample. Since metagenomic data includes sequence fragments (“reads”) from organisms that are absent from any database, new algorithms must be developed for the identification and annotation of novel sequence fragments. Homology-based techniques have been modified to detect novel species and genera, but, composition-based methods, have not been adapted. We develop a detection technique that can discriminate between “known” and “unknown” taxa, which can be used with composition-based methods, as well as a hybrid method. Unlike previous studies, we rigorously evaluate all algorithms for theirmore » ability to detect novel taxa. First, we show that the integration of a detector with a composition-based method performs significantly better than homology-based methods for the detection of novel species and genera, with best performance at finer taxonomic resolutions. Most importantly, we evaluate all the algorithms by introducing an “unknown” class and show that the modified version of PhymmBL has similar or better overall classification performance than the other modified algorithms, especially for the species-level and ultrashort reads. Finally, we evaluate theperformance of several algorithms on a real acid mine drainage dataset.« less

  18. Fine Structure of Body Wall Cuticle of Females of Eight Genera of Heteroderidae

    PubMed Central

    Cliff, G. M.; Baldwin, J. G.

    1985-01-01

    Body wall cuticle of adult females of eight genera within the Heteroderidae was examined by transmission electron microscopy for comparison with previously studied species within the family. Cuticle structure was used to test some current hypotheses of phylogeny of Heteroderidae and to evaluate intrageneric variability in cuticle layering. Verutus, Rhizonema, and Meloidodera possess striated cuticle surfaces and have the simplest layering, suggesting that striations have not necessarily arisen repeatedly in Heteroderidae through convergent or parallel evolution. Atalodera and Thecavermiculatus possess similar cuticles with derived characteristics, strengthening the hypothesis that the two genera are sister groups. Similarly, the cuticle of Cactodera resembles the specialized cuticle of Globodera and Punctodera in having a basal layer (D) and a surface layer infused with electron-dense substance. Heterodera betulae has a unique cuticle in which the thickest layer (C) is infiltrated with an electron-dense matrix. Little intrageneric difference was found between cuticles of two species of Meloidodera or between two species of Atalodera. However, Atalodera ucri has a basal layer (E) not found in other Heteroderidae. The most striking intrageneric variation in cuticle structure was observed between the thin three-layered cuticle of Sarisodera africana and the much thicker four-layered cuticle of Sarisodera hydrophila; results do not support monophyly of Sarisodera. PMID:19294096

  19. Two new genera of Lumbriculidae (Annelida, Clitellata) from North Carolina, USA

    USGS Publications Warehouse

    Fend, S.V.; Lenat, D.R.

    2007-01-01

    Recent benthic macroinvertebrate collections from North Carolina contained many undescribed oligochaete taxa, mostly belonging to the family Lumbriculidae. Three of the new species had arrangements of spermathecae and atria previously unreported for the family, and were assigned to new two genera. Pilaridrilus is distinguished by the location of spermathecal pores five segments behind the male pores. The single species, Pilaridrilus uliginosus, also has unusually complex penes and spermathecae. Martinidrilus is distinguished by spermathecae beginning more than two segments anterior to the atrial segment, and also by the the vasa deferentia, which join a common duct before joining the atria. The two Martinidrilus species also have unusual digitiform blood vessels in posterior segments. Martinidrilus carolinensis has lateral spermathecae in VI, and Martinidrilus arenosus has dorsolateral spermathecae in VII and VIII. Because arrangement and morphology of reproductive organs do not resemble those of described lumbriculids, the phylogenetic affinities of the new species are not clear. These new genera and species were generally collected from areas of high water quality, suggesting that lumbriculids can be useful in water quality monitoring and conservation evaluation. Copyright ?? 2007 Magnolia Press.

  20. Two New Genera of Fish Blood Flukes (Digenea: Aporocotylidae) from Catfishes in the Peruvian Amazon.

    PubMed

    Orélis-Ribeiro, Raphael; Bullard, Stephen A

    2016-06-01

    Cladocaecum tomasscholzi n. gen., n. sp. infects the heart (lumen of ventricle) of driftwood catfish, Ageneiosus inermis Linnaeus, 1766 (Siluriformes: Auchenipteridae) from the Nanay River (Amazon River Basin, near Iquitos, Peru). It differs from all other aporocotylid genera by having a highly branched intestine comprising a central cecum that terminates immediately anterior to the ovary and that has numerous laterally directed diverticula. Kritsky platyrhynchi ( Guidelli, Isaac, and Pavanelli, 2002 ) n. gen., n. comb. (= Plehniella p.) is redescribed based on paratypes plus new specimens collected from the body cavity of the type host (porthole shovelnose catfish, Hemisorubim platyrhynchos Valenciennes, 1840) (Pimelodidae) from the nearby Itaya River. Kritsky differs from Sanguinicola Plehn, 1905 , Plehniella Szidat, 1951 , Nomasanguinicola Truong and Bullard, 2013 , and Cladocaecum by the combination of having a spinous anterior sucker, an intestine comprising 6 asymmetrical ceca, a lanceolate body, a straight vas deferens, an ovary with finger-like lateral projections, a small and spheroid oötype, numerous, minute, spheroid uterine eggs, and separate genital pores. An updated list of hosts, tissues infected, and geographic localities for the catfish blood flukes (9 spp.; 5 genera) is provided. This is the first report of a fish blood fluke infecting a member of Auchenipteridae and first proposal of a new genus of blood fluke (Schistosomatoidea) from South America in 64 yr. It brings the total number of Amazonian fish blood flukes to a mere 4 species.