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Sample records for related genera inferred

  1. Phylogenetic relationships between Bacillus species and related genera inferred from 16s rDNA sequences

    PubMed Central

    Wei Wang, Mi Sun

    2009-01-01

    Neighbor-joining, maximum-parsimony, minimum-evolution, maximum-likelihood and Bayesian trees constructed based on 16S rDNA sequences of 181 type strains of Bacillus species and related taxa manifested nine phylogenetic groups. The phylogenetic analysis showed that Bacillus was not a monophyletic group. B. subtilis was in Group 1. Group 4, 6 and 8 respectively consisted of thermophiles, halophilic or halotolerant bacilli and alkaliphilic bacilli. Group 2, 4 and 8 consisting of Bacillus species and related genera demonstrated that the current taxonomic system did not agree well with the 16S rDNA evolutionary trees. The position of Caryophanaceae and Planococcaceae in Group 2 suggested that they might be transferred into Bacillaceae, and the heterogeneity of Group 2 implied that some Bacillus species in it might belong to several new genera. Group 9 was mainly comprised of the genera (excluding Bacillus) of Bacillaceae, so some Bacillus species in Group 9: B. salarius, B. qingdaonensis and B. thermcloacae might not belong to Bacillus. Four Bacillus species, B. schlegelii, B. tusciae, B. edaphicus and B. mucilaginosus were clearly placed outside the nine groups. PMID:24031394

  2. 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...

  3. 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.

  4. 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

  5. The evolution of CMA bands in Citrus and related genera.

    PubMed

    e Silva, Ana Emília Barros; Marques, André; dos Santos, Karla G B; Guerra, Marcelo

    2010-06-01

    Most species of Citrus and related genera display a similar karyotype with 2n = 18 and a variable number of terminal heterochromatic blocks positively stained with chromomycin A(3) (CMA(+) bands). Some of these blocks are 45S rDNA sites, whereas others may correspond to the main GC-rich satellite DNA found in several Citrus species. In the present work, the distribution of the 45S rDNA and the main satellite DNA isolated from C. sinensis (CsSat) were investigated by in situ hybridization in seven species of Citrus, two species of closely related genera (Fortunella obovata and Poncirus trifoliata) and four species of the subfamily Aurantioideae, which were less related to Citrus (Atalantia monophylla, Murraya paniculata, Severinia buxifolia, and Triphasia trifolia). In Citrus, Fortunella, and Poncirus, most CMA(+) bands colocalized only with CsSat sites, whereas others colocalized only with rDNA sites. However, some of these species displayed a few CMA(+) bands that colocalized with sites of both probes and other CMA(+) bands that did not colocalized with any of the probes. On the other hand, in the four species less related to Citrus, no CsSat signal was found on chromosomes. On Southern blot, the CsSat probe hybridized with genomic DNA from Citrus, Fortunella, and Poncirus at high stringency only, while under the less stringent conditions, it also hybridized with distantly related species. Therefore, CsSat sequences are the principal component of the heterochromatic blocks of Citrus, Poncirus, and Fortunella, whereas CsSat-like sequences seem to be widespread in the subfamily Aurantioideae. These data further suggest that the variable number of terminal CMA(+) bands observed on chromosomes of Citrus and related genera are probably the consequence of amplification or reduction in the number of CsSat-like sequences distributed on chromosome termini, paralleled by mutation and homogenization events, as proposed by the library hypothesis.

  6. 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)...

  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. A molecular phylogeny and classification of Leptochloa (Poaceae: Chloridoideae: Chlorideae) sensu lato and related genera

    PubMed Central

    Peterson, Paul M.; Romaschenko, Konstantin; Snow, Neil; Johnson, Gabriel

    2012-01-01

    Background and Aims Leptochloa (including Diplachne) sensu lato (s.l.) comprises a diverse assemblage of C4 (NAD-ME and PCK) grasses with approx. 32 annual or perennial species. Evolutionary relationships and a modern classification of Leptochloa spp. based on the study of molecular characters have only been superficially investigated in four species. The goals of this study were to reconstruct the evolutionary history of Leptochloa s.l. with molecular data and broad taxon sampling. Methods A phylogenetic analysis was conducted of 130 species (mostly Chloridoideae), of which 22 are placed in Leptochloa, using five plastid (rpL32-trn-L, ndhA intron, rps16 intron, rps16-trnK and ccsA) and the nuclear ITS 1 and 2 (ribosomal internal transcribed spacer regions) to infer evolutionary relationships and revise the classification. Key results Leptochloa s.l. is polyphyletic and strong support was found for five lineages. Embedded within the Leptochloa sensu stricto (s.s.) clade are two Trichloris spp. and embedded in Dinebra are Drake-brockmania and 19 Leptochloa spp. Conclusions The molecular results support the dissolution of Leptochloa s.l. into the following five genera: Dinebra with 23 species, Diplachne with two species, Disakisperma with three species, Leptochloa s.s. with five species and a new genus, Trigonochloa, with two species. PMID:22628365

  9. 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.

  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. Redefining common endophytes and plant pathogens in Neofabraea, Pezicula, and related genera.

    PubMed

    Chen, Chen; Verkley, Gerard J M; Sun, Guangyu; Groenewald, Johannes Z; Crous, Pedro W

    2016-11-01

    Species in Neofabraea, Pezicula, and related genera have been reported as saprobes, plant pathogens or endophytes from a wide range of hosts. The asexual morphs of Neofabraea and Pezicula had been placed in Cryptosporiopsis, now a synonym of Pezicula, while Neofabraea was also linked to Phlyctema. Based on morphology and molecular data of the partial large subunit nrDNA (LSU), the internal transcribed spacer region with intervening 5.8S nrDNA (ITS), partial β-tubulin region (tub2), and the partial RNA polymerase II second largest subunit region (rpb2), the taxonomy and phylogenetic relationships of these fungi were investigated. Five new species were described in Pezicula based on morphology, while a further eight unnamed phylogenetic lineages revealed further diversity in the genus. Based on these results, the generic concept of Neofabraea was also emended. Phlyctema, which was previously associated with Neofabraea, formed a distinct clade, separate from Neofabraea s. str. Two new neofabraea-like genera, Parafabraea and Pseudofabraea were proposed, along with one new combination in Neofabraea s. str. To stabilise the application of these names, an epitype was designated for Pe. carpinea, the type species of Pezicula, and for N. malicorticis, the type species of Neofabraea.

  12. New insights into the phylogeny of Pleopeltis and related Neotropical genera (Polypodiaceae, Polypodiopsida).

    PubMed

    Otto, Elisabeth M; Janssen, Thomas; Kreier, Hans-Peter; Schneider, Harald

    2009-10-01

    The fern family Polypodiaceae plays an important role in Neotropical epiphyte diversity. Most of its American representatives are assembled in a monophyletic clade that, apart from the grammitids, nearly exclusively comprises species restricted to the New World. The phylogenetic relationships of these ferns are still insufficiently understood and many taxonomic problems, such as natural circumscriptions of the genera Polypodium and Pleopeltis, were unresolved. Here we address one of the two main lineages within New World Polypodiaceae including Pecluma, Phlebodium, Pleopeltis, and Polypodium. Our study is based on DNA sequence data from four plastid regions that were generated for 72 species representing all putative major taxonomic groups within this lineage. The analyses reveal three major clades: (1) Polypodium plus Pleurosoriopsis; (2) Pecluma plus Phlebodium, and some species of Polypodium; and (3) Pleopeltis and related genera. The last clade contains species of Pleopeltis and Polypodium as well as Microphlebodium, Neurodium, Dicranoglossum, and Pseudocolysis. All species included in the clade display conspicuous persistent peltate laminar scales that are not found in other species of this lineage. Our results suggest a reconsideration of the generic concept of Pleopeltis with peltate laminar scales being the genus' key character.

  13. Notes on the genus Libellulosoma Martin, 1906, and related genera (Odonata: Anisoptera: Corduliidae).

    PubMed

    Fleck, Günther; Legrand, Jean

    2013-12-09

    The holotype of Libellulosoma minuta, until now regarded as the unique specimen of this monotypic genus and considered lost for half a century, was found again in the dragonfly collection of the Muséum National d'Histoire Naturelle in Paris. A second specimen, also from Madagascar (probably East Madagascar) was found in the collection René Martin together with the holotype. A redescription, including the structure of the secondary copulatory apparatus, is provided. The genus Libellulosoma is closely related to the genera Pentathemis and Aeschnosoma, and its membership in the clade Aeschnosomata is well supported. Evidence from biogeography, the fossil record, and phylogeny indicates that this group, possible sister group of remaining Corduliidae s.s., was probably already present in the Early Cretaceous.

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

    PubMed Central

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

    2010-01-01

    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

  15. SOURCES OF THE ARCTIC FLORA: ORIGINS OF ARCTIC SPECIES IN RANUNCULUS AND RELATED GENERA.

    PubMed

    Hoffmann, Matthias H; von Hagen, K Bernhard; Hörandl, Elvira; Röser, Martin; Tkach, Natalia V

    2010-01-01

    The arctic biome is a relatively young ecosystem with ~2300 species of vascular plants. We studied the genus Ranunculus as an example of the origin and evolution of the arctic flora. For this purpose we used molecular phylogenetic and clock analyses based on evaluation of nuclear ITS and chloroplast matK-trnK DNA sequences in 194 taxa of Ranunculus and closely related genera. Taxa occurring in the Arctic arose form seven phylogenetic lineages of Ranunculus and also in the genera Coptidium and Halerpestes. Two clades of Ranunculus are species-rich in the Arctic, i.e., Ranunculus sect. Ranunculus and R. sect. Auricomus (both from R. subg. Ranunculus), but this is due to a number of arctic "microtaxa" morphologically barely separate from R. acris in the former clade and the widely agamospermic species complex of R. auricomus in the latter. Lineages with species adapted to wetlands or aquatic habitats are significant groups represented in the arctic flora (R. subg. Ranunculus sectt. Flammula and Hecatonia/Xanthobatrachium, R. subg. Batrachium, genus Coptidium) but show no clear signs of radiation in the Arctic or the northern boreal zone, except for sectt. Hecatonia/Xanthobatrachium, with R. hyperboreus and R. sceleratus subsp. reptabundus. Astonishingly few of the otherwise numerous lineages of Ranunculus with distributions in the higher mountain systems of Eurasia and North America have acted as "founding sources" for the arctic flora. The only clear example is that of the arctic-alpine R. glacialis and the Beringian R. chamissonis from the lineage of subg. R. sectt. Aconitifolii/Crymodes, although there might be others in sect. Auricomus not recovered in the current molecular data. Lineages that gave rise to arctic taxa diverged from each other from the early Miocene (R. glacialis/R. chamissonis, Coptidium, lineages in Halerpestes) and continued at an even rate throughout the Tertiary. There are no signs that the intense climate changes of the late Pliocene and the

  16. SOURCES OF THE ARCTIC FLORA: ORIGINS OF ARCTIC SPECIES IN RANUNCULUS AND RELATED GENERA

    PubMed Central

    Hoffmann, Matthias H.; von Hagen, K. Bernhard; Hörandl, Elvira; Röser, Martin; Tkach, Natalia V.

    2010-01-01

    The arctic biome is a relatively young ecosystem with ~2300 species of vascular plants. We studied the genus Ranunculus as an example of the origin and evolution of the arctic flora. For this purpose we used molecular phylogenetic and clock analyses based on evaluation of nuclear ITS and chloroplast matK-trnK DNA sequences in 194 taxa of Ranunculus and closely related genera. Taxa occurring in the Arctic arose form seven phylogenetic lineages of Ranunculus and also in the genera Coptidium and Halerpestes. Two clades of Ranunculus are species-rich in the Arctic, i.e., Ranunculus sect. Ranunculus and R. sect. Auricomus (both from R. subg. Ranunculus), but this is due to a number of arctic “microtaxa” morphologically barely separate from R. acris in the former clade and the widely agamospermic species complex of R. auricomus in the latter. Lineages with species adapted to wetlands or aquatic habitats are significant groups represented in the arctic flora (R. subg. Ranunculus sectt. Flammula and Hecatonia/Xanthobatrachium, R. subg. Batrachium, genus Coptidium) but show no clear signs of radiation in the Arctic or the northern boreal zone, except for sectt. Hecatonia/Xanthobatrachium, with R. hyperboreus and R. sceleratus subsp. reptabundus. Astonishingly few of the otherwise numerous lineages of Ranunculus with distributions in the higher mountain systems of Eurasia and North America have acted as “founding sources” for the arctic flora. The only clear example is that of the arctic-alpine R. glacialis and the Beringian R. chamissonis from the lineage of subg. R. sectt. Aconitifolii/Crymodes, although there might be others in sect. Auricomus not recovered in the current molecular data. Lineages that gave rise to arctic taxa diverged from each other from the early Miocene (R. glacialis/R. chamissonis, Coptidium, lineages in Halerpestes) and continued at an even rate throughout the Tertiary. There are no signs that the intense climate changes of the late Pliocene

  17. Toddlers infer higher-order relational principles in causal learning.

    PubMed

    Walker, Caren M; Gopnik, Alison

    2014-01-01

    Children make inductive inferences about the causal properties of individual objects from a very young age. When can they infer higher-order relational properties? In three experiments, we examined 18- to 30-month-olds' relational inferences in a causal task. Results suggest that at this age, children are able to infer a higher-order relational causal principle from just a few observations and use this inference to guide their own subsequent actions and bring about a novel causal outcome. Moreover, the children passed a revised version of the relational match-to-sample task that has proven very difficult for nonhuman primates. The findings are considered in light of their implications for understanding the nature of relational and causal reasoning, and their evolutionary origins.

  18. Development of novel chloroplast microsatellite markers to identify species in the Agrostis complex (Poaceae) and related genera.

    PubMed

    Zapiola, Maria L; Cronn, Richard C; Mallory-Smith, Carol A

    2010-07-01

    We needed a reliable way to identify species and confirm potential interspecific and intergeneric hybrids in a landscape level study of gene flow from transgenic glyphosate-resistant Agrostis stolonifera (Poaceae) to compatible relatives. We developed 12 new polymorphic chloroplast microsatellite markers to aid in identifying species recipient of transgenic pollen both within the Agrostis complex and the related genera Polypogon.

  19. 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

  20. Abietoid seed fatty acid compositions--a review of the genera Abies, Cedrus, Hesperopeuce, Keteleeria, Pseudolarix, and Tsuga and preliminary inferences on the taxonomy of Pinaceae.

    PubMed

    Wolff, Robert L; Lavialle, Olivier; Pédrono, Frédérique; Pasquier, Elodie; Destaillats, Frederic; Marpeau, Anne M; Angers, Paul; Aitzetmüller, Kurt

    2002-01-01

    The seed fatty acid (FA) compositions of Abietoids (Abies, Cedrus, Hesperopeuce, Keteleeria, Pseudolarix, and Tsuga) are reviewed in the present study in conclusion to our survey of Pinaceae seed FA compositions. Many unpublished data are given. Abietoids and Pinoids (Pinus, Larix, Picea, and Pseudotsuga)-constituting the family Pinaceae-are united by the presence of several delta5-olefinic acids, taxoleic (5,9-18:2), pinolenic (5,9,12-18:3), coniferonic (5,9,12,15-1 8:4), keteleeronic (5,11-20:2), and sciadonic (5,11,14-20:3) acids, and of 14-methyl hexadecanoic (anteiso-17:0) acid. These acids seldom occur in angiosperm seeds. The proportions of individual delta5-olefinic acids, however, differ between Pinoids and Abietoids. In the first group, pinolenic acid is much greater than taxoleic acid, whereas in the second group, pinolenic acid is greater than or equal to taxoleic acid. Moreover, taxoleic acid in Abietoids is much greater than taxoleic acid in Pinoids, an apparent limit between the two subfamilies being about 4.5% of that acid relative to total FA. Tsuga spp. appear to be a major exception, as their seed FA compositions are much like those of species from the Pinoid group. In this respect, Hesperopeuce mertensiana, also known as Tsuga mertensiana, has little in common with Abietoids and fits the general FA pattern of Pinoids well. Tsuga spp. and H. mertensiana, from their seed FA compositions, should perhaps be separated from the Abietoid group and their taxonomic position revised. It is suggested that a "Tsugoid" subfamily be created, with seed FA in compliance with the Pinoid pattern and other botanical and immunological criteria of the Abietoid type. All Pinaceae genera, with the exception of Pinus, are quite homogeneous when considering their overall seed FA compositions, including delta5-olefinic acids. In all cases but one (Pinus), variations from one species to another inside a given genus are of small amplitude. Pinus spp., on the other hand

  1. Delimitation of Neonectria and Cylindrocarpon (Nectriaceae, Hypocreales, Ascomycota) and related genera with Cylindrocarpon-like anamorphs

    PubMed Central

    Chaverri, P.; Salgado, C.; Hirooka, Y.; Rossman, A.Y.; Samuels, G.J.

    2011-01-01

    Neonectria is a cosmopolitan genus and it is, in part, defined by its link to the anamorph genus Cylindrocarpon. Neonectria has been divided into informal groups on the basis of combined morphology of anamorph and teleomorph. Previously, Cylindrocarpon was divided into four groups defined by presence or absence of microconidia and chlamydospores. Molecular phylogenetic analyses have indicated that Neonectria sensu stricto and Cylindrocarpon sensu stricto are phylogenetically congeneric. In addition, morphological and molecular data accumulated over several years have indicated that Neonectria sensu lato and Cylindrocarpon sensu lato do not form a monophyletic group and that the respective informal groups may represent distinct genera. In the present work, a multilocus analysis (act, ITS, LSU, rpb1, tef1, tub) was applied to representatives of the informal groups to determine their level of phylogenetic support as a first step towards taxonomic revision of Neonectria sensu lato. Results show five distinct highly supported clades that correspond to some extent with the informal Neonectria and Cylindrocarpon groups that are here recognised as genera: (1) N. coccinea-group and Cylindrocarpon groups 1 & 4 (Neonectria/Cylindrocarpon sensu stricto); (2) N. rugulosa-group (Rugonectria gen. nov.); (3) N. mammoidea/N. veuillotiana-groups and Cylindrocarpon group 2 (Thelonectria gen. nov.); (4) N. radicicola-group and Cylindrocarpon group 3 (Ilyonectria gen. nov.); and (5) anamorph genus Campylocarpon. Characteristics of the anamorphs and teleomorphs correlate with the five genera, three of which are newly described. New combinations are made for species where their classification is confirmed by phylogenetic data. PMID:21523189

  2. Intracranial EEG correlates of implicit relational inference within the hippocampus.

    PubMed

    Reber, T P; Do Lam, A T A; Axmacher, N; Elger, C E; Helmstaedter, C; Henke, K; Fell, J

    2016-01-01

    Drawing inferences from past experiences enables adaptive behavior in future situations. Inference has been shown to depend on hippocampal processes. Usually, inference is considered a deliberate and effortful mental act which happens during retrieval, and requires the focus of our awareness. Recent fMRI studies hint at the possibility that some forms of hippocampus-dependent inference can also occur during encoding and possibly also outside of awareness. Here, we sought to further explore the feasibility of hippocampal implicit inference, and specifically address the temporal evolution of implicit inference using intracranial EEG. Presurgical epilepsy patients with hippocampal depth electrodes viewed a sequence of word pairs, and judged the semantic fit between two words in each pair. Some of the word pairs entailed a common word (e.g., "winter-red," "red-cat") such that an indirect relation was established in following word pairs (e.g., "winter-cat"). The behavioral results suggested that drawing inference implicitly from past experience is feasible because indirect relations seemed to foster "fit" judgments while the absence of indirect relations fostered "do not fit" judgments, even though the participants were unaware of the indirect relations. A event-related potential (ERP) difference emerging 400 ms post-stimulus was evident in the hippocampus during encoding, suggesting that indirect relations were already established automatically during encoding of the overlapping word pairs. Further ERP differences emerged later post-stimulus (1,500 ms), were modulated by the participants' responses and were evident during encoding and test. Furthermore, response-locked ERP effects were evident at test. These ERP effects could hence be a correlate of the interaction of implicit memory with decision-making. Together, the data map out a time-course in which the hippocampus automatically integrates memories from discrete but related episodes to implicitly influence future

  3. Study of the bacterial load in a gelatine production process focussed on Bacillus and related endosporeforming genera.

    PubMed

    De Clerck, Elke; De Vos, Paul

    2002-12-01

    Gelatine is an animal protein with many industrial applications. Previous studies pointed out that endosporeforming bacteria, belonging to the genus Bacillus or related genera, might contaminate and survive the production process of gelatine, leading to products of low quality and safety. The aim of this study is to determine the bacterial diversity of contaminants isolated from a gelatine production chain with emphasis on aerobic endosporeforming bacteria. Contaminants were isolated from samples taken at five crucial points along two different production lines of a gelatine production process and from water supplies used for extraction and cooling. Gaschromatographic methyl ester analysis of fatty acids was performed to differentiate isolates at the genus level. Apart from members of the genus Bacillus or related endosporeforming genera, also members of Salmonella, Kluyvera, Staphylococcus, Burkholderia, Enterococcus, Pseudomonas, Yersinia, Streptococcus and Brevundimonas could be detected. Isolates identified as belonging to Bacillus and related endosporeforming genera were further characterised by gelatinase tests, rep-PCR and 16S rDNA sequencing. All these isolates showed the ability to liquefy gelatine. Endosporeforming isolates were assigned to Bacillus licheniformis, B. fumarioli, members of the B. cereus group, B. badius, B. coagulans, B. subtilis, Brevibacillus agri, Alicyclobacillus acidocaldarius and a yet undescribed Paenibacillus species.

  4. Phylogeny of the Southwest Asian Pimpinella and related genera based on nuclear and plastid sequences.

    PubMed

    Fereidounfar, S; Ghahremaninejad, F; Khajehpiri, M

    2016-10-24

    Pimpinella L. is a large genus and arguably one of the most complex genera in the family Apiaceae. In this study, the infra-generic relationship between Southwest Asian Pimpinella species and their generic allies in the tribe Pimpinelleae Spreng were investigated using sequence data from the cpDNA (chloroplast DNA) rps16 exon and rpL16 intron and nuclear ribosomal DNA internal transcribed spacer regions. In total, 185 accessions representing 52 species of Pimpinella, 8 species of Aegopodium, and the monotypic Opsicarpium Mozaff. were analyzed using maximum parsimony and Bayesian methods. In our phylogenetic study, Pimpinella and Opsicarpium were considered together as a monophyletic group within the tribe Pimpinelleae. As a result, Opsicarpium insignis Mozaff has been formally transferred to Pimpinella. Our results indicate that the genera Pimpinella and Reutera Boiss formed a monophyletic group and also supported merging the genus Reutera with Pimpinella. This study confirms the transfer of the Southwest Asian Pimpinella anthriscoides (Boiss.) F. Ghahrem., Khajepiri & Mozaff to the genus Aegopodium as Aegopodium tribracteolatum Schmalh.

  5. Person theories: their temporal stability and relation to intertrait inferences.

    PubMed

    Poon, Connie S K; Koehler, Derek J

    2008-07-01

    This article tests whether individual differences in inferring one trait from another (intertrait inferences) can be linked to lay beliefs about the malleability of personality (person theories). It finds that holding the belief that personality is malleable (incremental theory) rather than fixed (entity theory) at the time of inferences is associated with less extreme inferences involving semantically related (but not unrelated) traits. Although person theories have been assumed to be stable over time, existing short-term test-retest coefficients do not capture their instability over a longer period. These results can illuminate interrater discrepancies in assessments of personality pathology and job performance, enrich understanding of such phenomena as stereotyping and impression formation, refine the interpretation of past research involving person theories, and inform research planning.

  6. 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

  7. A molecular phylogenetic investigation of Opisthonecta and related genera (Ciliophora, Peritrichia, Sessilida).

    PubMed

    Williams, Daniel; Clamp, John C

    2007-01-01

    The gene encoding 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in the sessiline peritrichs Opisthonecta minima and Opisthonecta matiensis, whose free-swimming, paedomorphic trophonts resemble telotrochs. Using these new sequences, phylogenetic trees were constructed with four different methods to test a previously published association between Opisthonecta henneguyi and members of the families Vorticellidae and Astylozoidae. All trees had similar topologies, with O. minima, O. henneguyi, Vorticella microstoma, and Astylozoon enriquesi forming a well-supported, certainly monophyletic clade. On the basis of genetic evidence, genera of the families Opisthonectidae and Astylozoidae are assigned to the family Vorticellidae, which already includes some species with free-swimming morphotypes. The ssu rRNA sequence of O. matiensis places it in the family Epistylididae; its taxonomic revision will be left to another group of authors. A close association of Ophrydium versatile with members of the family Vorticellidae was confirmed, casting doubt on the validity of the family Ophrydiidae. Epistylis galea, Campanella umbellaria, and Opercularia microdiscum are confirmed as comprising an extremely distinct, monophyletic, but morphologically heterogeneous clade that is basal to other clades of sessiline peritrichs.

  8. Each flying fox on its own branch: a phylogenetic tree for Pteropus and related genera (Chiroptera: Pteropodidae).

    PubMed

    Almeida, Francisca C; Giannini, Norberto P; Simmons, Nancy B; Helgen, Kristofer M

    2014-08-01

    Pteropodidae is a diverse Old World family of non-echolocating, frugivorous and nectarivorous bats that includes the flying foxes (genus Pteropus) and allied genera. The subfamily Pteropodinae includes the largest living bats and is distributed across an immense geographic range from islands in East Africa to the Cook Islands of Polynesia. These bats are keystone species in their ecosystems and some carry zoonotic diseases that are increasingly a focus of interest in biomedical research. Here we present a comprehensive phylogeny for pteropodines focused on Pteropus. The analyses included 50 of the ∼63 species of Pteropus and 11 species from 7 related genera. We obtained sequences of the cytochrome b and the 12S rRNA mitochondrial genes for all species and sequences of the nuclear RAG1, vWF, and BRCA1 genes for a subsample of taxa. Some of the sequences of Pteropus were obtained from skin biopsies of museum specimens including that of an extinct species, P. tokudae. The resulting trees recovered Pteropus as monophyletic, although further work is needed to determine whether P. personatus belongs in the genus. Monophyly of the majority of traditionally-recognized Pteropus species groups was rejected, but statistical support was strong for several clades on which we based a new classification of the Pteropus species into 13 species groups. Other noteworthy results emerged regarding species status of several problematic taxa, including recognition of P. capistratus and P. ennisae as distinct species, paraphyly of the P. hypomelanus complex, and conspecific status of P. pelewensis pelewensis and P. p. yapensis. Relationships among the pteropodine genera were not completely resolved with the current dataset. Divergence time analysis suggests that Pteropus originated in the Miocene and that two independent bursts of diversification occurred in the Pleistocene in different regions of the Indo-Pacific realm.

  9. Closely related Wolbachia recovered from different genera of Mexican Thelytokous figitidae (Hymenoptera)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Closely related novel Wolbachia strains were recovered from the thelytokous figitids Odontosema anastrephae Borgmeier and Aganaspis alujai Ovruski et al. No Wolbachia were detected in a bi-sexual strain of O. anastrephae. While the presence or absence of Wolbachia does not demonstrate that Wolbachia...

  10. 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

  11. 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

  12. 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

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

    PubMed

    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.

  14. Causal Inference and Language Comprehension: Event-Related Potential Investigations

    ERIC Educational Resources Information Center

    Davenport, Tristan S.

    2014-01-01

    The most important information conveyed by language is often contained not in the utterance itself, but in the interaction between the utterance and the comprehender's knowledge of the world and the current situation. This dissertation uses psycholinguistic methods to explore the effects of a common type of inference--causal inference--on language…

  15. Diversity and functionality of Bacillus and related genera isolated from spontaneously fermented soybeans (Indian Kinema) and locust beans (African Soumbala).

    PubMed

    Sarkar, P K; Hasenack, B; Nout, M J R

    2002-08-25

    A total of 126 isolates of Bacillus and related genera from indigenous, spontaneously fermented soybeans (Kinema) and locust beans (Soumbala) were characterized with the purpose of defining interspecific, as well as intraspecific relationships among the components of their microflora. B. subtilis was the dominant species, and species diversity was more pronounced in Soumbala than in Kinema. While from Kinema, six species were isolated (B. subtilis, B. licheniformis, B. cereus, B. circulans, B. thuringiensis and B. sphaericus), in Soumbala, the species found were B. subtilis, B. thuringiensis, B. licheniformis, B. cereu, B. badius, Paenibacillus alvei, B. firmus, P. larvae, Brevibacillus laterosporus, B. megaterium, B. mycoides and B. sphaericus. Genomic diversity in the isolates of B. subtilis was investigated by random amplified polymorphic DNA (RAPD) analysis using the polymerase chain reaction (PCR). The RAPD-PCR fingerprint analysis showed a high level of diversity. With more than 90% similarity, all 52 RAPD subdivisions were source and continent-wise homogeneous. Profiles of carbon source fermentation also showed a wide but corresponding phenotypic diversity, largely corresponding with RAPD subdivisions. The various strains were tested for several criteria for functionality in soybean fermentation, viz. protein degradation, pH increase, and development of desirable stickiness caused by viscous exopolymers. Profiles of functionality, based upon estimations of pH, free amino nitrogen and stickiness were associated with genotypic and phenotypic profiles. Notwithstanding the heterogenous fermentation results for some genotypic profiles, a ranking of RAPD groups is possible and can be useful in the further selection and study of B. subtilis strains.

  16. Event-related potential correlates of emergent inference in human arbitrary relational learning.

    PubMed

    Wang, Ting; Dymond, Simon

    2013-01-01

    Two experiments investigated the functional-anatomical correlates of cognition supporting untrained, emergent relational inference in a stimulus equivalence task. In Experiment 1, after learning a series of conditional relations involving words and pseudowords, participants performed a relatedness task during which EEG was recorded. Behavioural performance was faster and more accurate on untrained, indirectly related symmetry (i.e., learn AB and infer BA) and equivalence trials (i.e., learn AB and AC and infer CB) than on unrelated trials, regardless of whether or not a formal test for stimulus equivalence relations had been conducted. Consistent with previous results, event related potentials (ERPs) evoked by trained and emergent trials at parietal and occipital sites differed only for those participants who had not received a prior equivalence test. Experiment 2 further replicated and extended these behavioural and ERP findings using arbitrary symbols as stimuli and demonstrated time and frequency differences for trained and untrained relatedness trials. Overall, the findings demonstrate convincingly the ERP correlates of intra-experimentally established stimulus equivalence relations consisting entirely of arbitrary symbols and offer support for a contemporary cognitive-behavioural model of symbolic categorisation and relational inference.

  17. 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

  18. 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

  19. Variational Bayesian Inference Algorithms for Infinite Relational Model of Network Data.

    PubMed

    Konishi, Takuya; Kubo, Takatomi; Watanabe, Kazuho; Ikeda, Kazushi

    2015-09-01

    Network data show the relationship among one kind of objects, such as social networks and hyperlinks on the Web. Many statistical models have been proposed for analyzing these data. For modeling cluster structures of networks, the infinite relational model (IRM) was proposed as a Bayesian nonparametric extension of the stochastic block model. In this brief, we derive the inference algorithms for the IRM of network data based on the variational Bayesian (VB) inference methods. After showing the standard VB inference, we derive the collapsed VB (CVB) inference and its variant called the zeroth-order CVB inference. We compared the performances of the inference algorithms using six real network datasets. The CVB inference outperformed the VB inference in most of the datasets, and the differences were especially larger in dense networks.

  20. Psychotic Experiences and Overhasty Inferences Are Related to Maladaptive Learning.

    PubMed

    Stuke, Heiner; Stuke, Hannes; Weilnhammer, Veith Andreas; Schmack, Katharina

    2017-01-01

    Theoretical accounts suggest that an alteration in the brain's learning mechanisms might lead to overhasty inferences, resulting in psychotic symptoms. Here, we sought to elucidate the suggested link between maladaptive learning and psychosis. Ninety-eight healthy individuals with varying degrees of delusional ideation and hallucinatory experiences performed a probabilistic reasoning task that allowed us to quantify overhasty inferences. Replicating previous results, we found a relationship between psychotic experiences and overhasty inferences during probabilistic reasoning. Computational modelling revealed that the behavioral data was best explained by a novel computational learning model that formalizes the adaptiveness of learning by a non-linear distortion of prediction error processing, where an increased non-linearity implies a growing resilience against learning from surprising and thus unreliable information (large prediction errors). Most importantly, a decreased adaptiveness of learning predicted delusional ideation and hallucinatory experiences. Our current findings provide a formal description of the computational mechanisms underlying overhasty inferences, thereby empirically substantiating theories that link psychosis to maladaptive learning.

  1. Psychotic Experiences and Overhasty Inferences Are Related to Maladaptive Learning

    PubMed Central

    Stuke, Heiner; Stuke, Hannes; Weilnhammer, Veith Andreas; Schmack, Katharina

    2017-01-01

    Theoretical accounts suggest that an alteration in the brain’s learning mechanisms might lead to overhasty inferences, resulting in psychotic symptoms. Here, we sought to elucidate the suggested link between maladaptive learning and psychosis. Ninety-eight healthy individuals with varying degrees of delusional ideation and hallucinatory experiences performed a probabilistic reasoning task that allowed us to quantify overhasty inferences. Replicating previous results, we found a relationship between psychotic experiences and overhasty inferences during probabilistic reasoning. Computational modelling revealed that the behavioral data was best explained by a novel computational learning model that formalizes the adaptiveness of learning by a non-linear distortion of prediction error processing, where an increased non-linearity implies a growing resilience against learning from surprising and thus unreliable information (large prediction errors). Most importantly, a decreased adaptiveness of learning predicted delusional ideation and hallucinatory experiences. Our current findings provide a formal description of the computational mechanisms underlying overhasty inferences, thereby empirically substantiating theories that link psychosis to maladaptive learning. PMID:28107344

  2. Fruit and seed anatomy of Chenopodium and related genera (Chenopodioideae, Chenopodiaceae/Amaranthaceae): implications for evolution and taxonomy.

    PubMed

    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.

  3. 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

  4. The absence of Arabidopsis-type telomeres in Cestrum and closely related genera Vestia and Sessea (Solanaceae): first evidence from eudicots.

    PubMed

    Sykorova, Eva; Lim, Kar Yoong; Chase, Mark W; Knapp, Sandra; Leitch, Ilia Judith; Leitch, Andrew Rowland; Fajkus, Jiri

    2003-05-01

    Using slot-blot and fluorescent in situ hybridization (FISH), we found no evidence for the presence of the Arabidopsis-type telomeric sequence (TTTAGGG)n at the chromosome termini in any of the Cestrum species we investigated. Probing for the human-type telomere (TTAGGG)n also revealed no signal. However, polymerase chain reaction experiments indicated that there are short lengths of the sequence TTTAGGG dispersed in the genome but that these sequences are almost certainly too short to act as functional telomeres even if they were at the chromosome termini. An analysis of related genera Vestia and Sessea indicates that they too lack the Arabidopsis-type telomere, and the sequences were lost in the common ancestor of these genera. We found that the Cestrum species investigated had particularly large mean chromosome sizes. We discuss whether this is a consequence of alternative telomere end maintenance systems.

  5. 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.

  6. 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

  7. 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

  8. Inferring facts from fiction: reading correct and incorrect information affects memory for related information.

    PubMed

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

    2012-07-01

    People can acquire both true and false knowledge about the world from fictional stories. 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. Participants 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 participants 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.

  9. The Madagascan endemic myrmicine ants related to Eutetramorium (Hymenoptera: Formicidae): taxonomy of the genera Eutetramorium Emery, Malagidris nom. n., Myrmisaraka gen. n., Royidris gen. n., and Vitsika gen. n.

    PubMed

    Bolton, Barry; Fisher, Brian L

    2014-04-24

    The monophyletic group of myrmicine ant genera related to Eutetramorium is described and its taxonomy is documented. The group is endemic in Madagascar and contains five genera: Eutetramorium Emery, 1899 (3 species, 1 of which is new); Malagidris nom. n., a replacement name for Brunella Forel, 1917, junior homonym of Brunella Smith, G.W. 1909 (Crustacea) (6 species, 5 of which are new); Myrmisaraka gen. n. (2 species, both new); Royidris gen. n. (15 species, 11 of which are new); Vitsika gen. n. (14 species, all of which are new). Keys to the worker caste are provided for all genera, and provisional keys to known males are given for Malagidris and Vitsika.

  10. 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.

  11. Development of a light microscopy stain for the sclerites of Gyrodactylus von Nordmann, 1832 (Monogenea) and related genera.

    PubMed

    García-Vásquez, A; Shinn, A P; Bron, J E

    2012-05-01

    Recent developments in semi-automated identification techniques and the increasing ability to rapidly access digital images and taxonomic descriptions offer to increase the range of individuals capable of performing taxonomic identifications. The present study details methodological approaches undertaken in developing a dedicated stain for the visualisation of monogenean haptoral skeletal elements and reproductive sclerites. The histochemical protocols centre around the use of fluorescent dyes and standard light and laser scanning confocal microscopy to support studies of the functional morphology of these hard structures in small, relatively uncompressed specimens, making these structures more amenable to semi-automated analysis and identification techniques. Staining of the sclerites was achieved using a tissue digestion step to remove the tegument and tissues enclosing the sclerites and then staining them in situ with 40 mM chromothrope 2R (C2R) containing 3 mM phosphotungstic acid (PTA) and 0.5% acetic acid (AA) at room temperature for up to 2 days. Visualisation of the armature of the male copulatory organ of warm water Gyrodactylus species was achieved using 40 mM C2R containing 3 mM PTA for 3 days, whilst cold water species were best stained in 6.4 mM C2R for 1 day without an NaOH pre-treatment. The developed techniques allow for good visualisation of the skeletal elements in a number of monogenean groups and promise to assist the preparation and identification/description of specimens. The 2D/3D digital images of specimens prepared in this manner should provide a useful resource for taxonomists and others needing material to assist specimen identification.

  12. Origin and diversification of the Milla Clade (Brodiaeoideae, Asparagaceae): a Neotropical group of six geophytic genera.

    PubMed

    Gándara, Etelvina; Specht, Chelsea D; Sosa, Victoria

    2014-06-01

    The Milla clade currently comprises six genera of geophytic plants distributed from Arizona to Guatemala. Three genera (Behria, Jaimehintonia and Petronymphe) are monotypic while the remaining genera (Bessera, Dandya and Milla) contain from two to ten (Milla) species. Parsimony, Maximum Likelihood and Bayesian Inference analyses were conducted with plastid and nuclear DNA sequences from a total of 181 plants belonging to 15 species in all six genera. Molecular dating was performed under a relaxed clock model. We examined the phylogenetic relationships of the genera and species, estimated origin-divergence times for the clade and genera and determined the ancestral distribution area of the clade by optimizing ancestral areas given current biogeographic distributions. The phylogenetic results suggest that final decisions on limits of the six genera in the Milla clade will have to be established until further taxonomic work is completed for Milla, in particular for the group of populations included under the name M. biflora. The later genus is rendered polyphyletic by other genera of the family. The origin of the Milla clade is estimated at 15.8Ma. Ancestral area of the clade most likely was located in the California Floristic Province and dispersal occurred most likely to the Chihuahuan-Coahuila Plateaus and the Trans-Mexican Volcanic Belt and from there to Baja California and the Sierra Madre del Sur. Two hypotheses that need further testing are proposed to explain complex relationships of genera and polyphyly of Milla, one in relation to fragmentation of populations and pollinator shifts and another suggesting that populations remained in refugia in the Trans-Mexican Volcanic Belt.

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

    PubMed

    Yin, Yu; Yao, Dezhong

    2016-07-08

    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.

  14. 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

  15. 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/.

  16. Structural mapping in statistical word problems: A relational reasoning approach to Bayesian inference.

    PubMed

    Johnson, Eric D; Tubau, Elisabet

    2016-09-27

    Presenting natural frequencies facilitates Bayesian inferences relative to using percentages. Nevertheless, many people, including highly educated and skilled reasoners, still fail to provide Bayesian responses to these computationally simple problems. We show that the complexity of relational reasoning (e.g., the structural mapping between the presented and requested relations) can help explain the remaining difficulties. With a non-Bayesian inference that required identical arithmetic but afforded a more direct structural mapping, performance was universally high. Furthermore, reducing the relational demands of the task through questions that directed reasoners to use the presented statistics, as compared with questions that prompted the representation of a second, similar sample, also significantly improved reasoning. Distinct error patterns were also observed between these presented- and similar-sample scenarios, which suggested differences in relational-reasoning strategies. On the other hand, while higher numeracy was associated with better Bayesian reasoning, higher-numerate reasoners were not immune to the relational complexity of the task. Together, these findings validate the relational-reasoning view of Bayesian problem solving and highlight the importance of considering not only the presented task structure, but also the complexity of the structural alignment between the presented and requested relations.

  17. 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.

  18. How to Infer Relative Fitness from a Sample of Genomic Sequences

    PubMed Central

    Dayarian, Adel; Shraiman, Boris I.

    2014-01-01

    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

  19. Phylogenetic relationships among phrynosomatid lizards as inferred from mitochondrial ribosomal DNA sequences: substitutional bias and information content of transitions relative to transversions.

    PubMed

    Reeder, T W

    1995-06-01

    The phylogenetic relationships among 40 species, representing all genera, within the North American lizard family Phrynosomatidae were inferred from mitochondrial ribosomal RNA gene sequences. Cladistic analysis of the DNA sequence data (779 bp; 162 informative characters) supported the monophyly of the sand lizards (Callisaurus, Cophosaurus, Holbrookia, and Uma), Petrosaurus, Phrynosoma, Urosaurus, and Uta. All the species of Sceloporus, except S. variabilis and S. chrysostictus, formed a clade. Except for a sand lizard + Phrynosoma clade, the intergeneric relationships inferred from the mtDNA were largely incongruent with recent cladistic analyses based on morphology. Sceloporus group monophyly was not supported, with Petrosaurus being a member of a clade containing Sator, Sceloporus, and Urosaurus, to the exclusion of Uta. The phylogenetic placement of Uta was ambiguous. The substitutional bias in the phrynosomatid mitochondrial rDNA sequences was examined, as well as the phylogenetic information content of transitions relative to transversions. There appeared to be a lower transition bias than observed in other vertebrate sequences, with some classes of transversions occurring as frequently as G <-> A transitions. Transitions were no less informative for phylogeny reconstruction than transversions. Therefore, transitions should not be down-weighted in phylogenetic analysis, as is often done.

  20. 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.

  1. 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

  2. The role of gender-related information and self-endorsement of traits in preadolescents' inferences and judgments.

    PubMed

    Lobel, T E; Bempechat, J; Gewirtz, J C; Shoken-Topaz, T; Bashe, E

    1993-08-01

    The major purpose of this study was to examine the effects of a target child's gender typicality on different aspects of preadolescents' inferences and judgments. The secondary purpose of the study was to investigate the relation between children's self-endorsement of traits and their inferences and judgments. Fifth and sixth graders were shown a video film, portraying a child playing either a gender-appropriate game with members of the same sex or a gender-inappropriate game with members of the other sex. In addition, subjects completed an adapted version of the BSRI and were categorized into sex-typed, androgynous, and undifferentiated subjects. Subjects made a number of different types of judgments and inferences about the target, including inferences about traits, popularity, choice of gift and name, and willingness to engage in activities with the target. All types of inferences and judgments were affected by the variations in the targets' gender-related behaviors, whereas self-endorsement of traits was not related to the inferences and judgments. The results suggest that the gender typicality of the target behavior is salient to preadolescents, regardless of their sex-role orientation.

  3. 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

  4. Fossil gaps inferred from phylogenies alter the apparent nature of diversification in dragonflies and their relatives

    PubMed Central

    2011-01-01

    Background The fossil record has suggested that clade growth may differ in marine and terrestrial taxa, supporting equilibrial models in the former and expansionist models in the latter. However, incomplete sampling may bias findings based on fossil data alone. To attempt to correct for such bias, we assemble phylogenetic supertrees on one of the oldest clades of insects, the Odonatoidea (dragonflies, damselflies and their extinct relatives), using MRP and MRC. We use the trees to determine when, and in what clades, changes in taxonomic richness have occurred. We then test whether equilibrial or expansionist models are supported by fossil data alone, and whether findings differ when phylogenetic information is used to infer gaps in the fossil record. Results There is broad agreement in family-level relationships between both supertrees, though with some uncertainty along the backbone of the tree regarding dragonflies (Anisoptera). "Anisozygoptera" are shown to be paraphyletic when fossil information is taken into account. In both trees, decreases in net diversification are associated with species-poor extant families (Neopetaliidae, Hemiphlebiidae), and an upshift is associated with Calopterygidae + Polythoridae. When ghost ranges are inferred from the fossil record, many families are shown to have much earlier origination dates. In a phylogenetic context, the number of family-level lineages is shown to be up to twice as high as the fossil record alone suggests through the Cretaceous and Cenozoic, and a logistic increase in richness is detected in contrast to an exponential increase indicated by fossils alone. Conclusions Our analysis supports the notion that taxa, which appear to have diversified exponentially using fossil data, may in fact have diversified more logistically. This in turn suggests that one of the major apparent differences between the marine and terrestrial fossil record may simply be an artifact of incomplete sampling. Our results also support

  5. 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.

  6. Free from mitochondrial DNA: Nuclear genes and the inference of species trees among closely related darter lineages (Teleostei: Percidae: Etheostomatinae).

    PubMed

    Near, Thomas J; Keck, Benjamin P

    2013-03-01

    Investigations into the phylogenetics of closely related animal species are dominated by the use of mitochondrial DNA (mtDNA) sequence data. However, the near-ubiquitous use of mtDNA to infer phylogeny among closely related animal lineages is tempered by an increasing number of studies that document high rates of transfer of mtDNA genomes among closely related species through hybridization, leading to substantial discordance between phylogenies inferred from mtDNA and nuclear gene sequences. In addition, the recent development of methods that simultaneously infer a species phylogeny and estimate divergence times, while accounting for incongruence among individual gene trees, has ushered in a new era in the investigation of phylogeny among closely related species. In this study we assess if DNA sequence data sampled from a modest number of nuclear genes can resolve relationships of a species-rich clade of North American freshwater teleost fishes, the darters. We articulate and expand on a recently introduced method to infer a time-calibrated multi-species coalescent phylogeny using the computer program (*)BEAST. Our analyses result in well-resolved and strongly supported time-calibrated darter species tree. Contrary to the expectation that mtDNA will provide greater phylogenetic resolution than nuclear gene data; the darter species tree inferred exclusively from nuclear genes exhibits a higher frequency of strongly supported nodes than the mtDNA time-calibrated gene tree.

  7. 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.

  8. 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.

  9. 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

  10. Spatial Frequencies Used in Landolt C Orientation Judgments: Relation to Inferred Magnocellular and Parvocellular Pathways

    PubMed Central

    McAnany, J. Jason; Alexander, Kenneth R.

    2008-01-01

    The purpose of this study was to define the spatial frequencies that underlie judgments of Landolt C orientation under test conditions designed to favor either the magnocellular (MC) or parvocellular (PC) pathway. Contrast thresholds of two observers were measured for briefly presented Landolt Cs of four sizes, using steady- and pulsed-pedestal paradigms to bias performance toward the MC and PC pathways, respectively. Contrast thresholds were derived from a two-alternative forced-choice orientation judgment task using the QUEST procedure. The Landolt Cs were either low-pass or high-pass Gaussian filtered with a range of cut-off object spatial frequencies (cycles per letter) to limit their frequency content. Center object frequencies were derived from plots of log contrast threshold for orientation judgments vs. log filter cutoff object frequency. The function relating center object frequency to Landolt C angular subtense was nonlinear on log-log coordinates for both the steady- and pulsed-pedestal paradigms, indicating that different object frequencies were used to judge Landolt C orientation at different optotype sizes. However, the function was substantially steeper under the pulsed-pedestal than under the steady-pedestal paradigm, such that a large change in optotype size produced a relatively small change in retinal spatial frequency (cycles per degree). The pattern of results is consistent with previously reported differences between the spatial contrast sensitivity functions of the inferred MC and PC pathways. PMID:18374385

  11. 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

  12. Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions

    PubMed Central

    Zhang, Yan-Cong; Lin, Kui

    2015-01-01

    Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms. PMID:26715828

  13. Bradykinin-related peptides (BRPs) from skin secretions of three genera of phyllomedusine leaf frogs and their comparative pharmacological effects on mammalian smooth muscles.

    PubMed

    Jiang, Yingchun; Xi, Xinping; Ge, Lilin; Yang, Nan; Hou, Xiaojuan; Ma, Jie; Ma, Chengbang; Wu, Yuxin; Guo, Xiaoxiao; Li, Renjie; Zhou, Mei; Wang, Lei; Chen, Tianbao; Shaw, Chris

    2014-02-01

    While bradykinin has been identified in the skin secretions from several species of amphibian, bradykinin-related peptides (BRPs) are more common constituents. These peptides display a plethora of primary structural variations from the type peptide which include single or multiple amino acid substitutions, N- and/or C-terminal extensions and post-translational modifications such as proline hydroxylation and tyrosine sulfation. Such modified peptides have been reported in species from many families, including Bombinatoridae, Hylidae and Ranidae. The spectrum of these peptides in a given species is thought to be reflective of its predator profile from different vertebrate taxa. Here we report the isolation of BRPs and parallel molecular cloning of their respective biosynthetic precursor-encoding cDNAs from the skin secretions of the Mexican leaf frog (Pachymedusa dacnicolor), the Central American red-eyed leaf frog (Agalychnis callidryas) and the South American orange-legged leaf frog (Phyllomedusa hypochondrialis). Additionally, the eight different BRPs identified were chemically synthesized and screened for bioactivity using four different mammalian smooth muscle preparations and their effects and rank potencies were found to be radically different in these with some acting preferentially through bradykinin B1-type receptors and others through B(2)-type receptors.

  14. 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

  15. Gene regulatory network inference and validation using relative change ratio analysis and time-delayed dynamic Bayesian network.

    PubMed

    Li, Peng; Gong, Ping; Li, Haoni; Perkins, Edward J; Wang, Nan; Zhang, Chaoyang

    2014-12-01

    The Dialogue for Reverse Engineering Assessments and Methods (DREAM) project was initiated in 2006 as a community-wide effort for the development of network inference challenges for rigorous assessment of reverse engineering methods for biological networks. We participated in the in silico network inference challenge of DREAM3 in 2008. Here we report the details of our approach and its performance on the synthetic challenge datasets. In our methodology, we first developed a model called relative change ratio (RCR), which took advantage of the heterozygous knockdown data and null-mutant knockout data provided by the challenge, in order to identify the potential regulators for the genes. With this information, a time-delayed dynamic Bayesian network (TDBN) approach was then used to infer gene regulatory networks from time series trajectory datasets. Our approach considerably reduced the searching space of TDBN; hence, it gained a much higher efficiency and accuracy. The networks predicted using our approach were evaluated comparatively along with 29 other submissions by two metrics (area under the ROC curve and area under the precision-recall curve). The overall performance of our approach ranked the second among all participating teams.

  16. 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.

  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. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Ecological Inference

    NASA Astrophysics Data System (ADS)

    King, Gary; Rosen, Ori; Tanner, Martin A.

    2004-09-01

    This collection of essays brings together a diverse group of scholars to survey the latest strategies for solving ecological inference problems in various fields. The last half-decade has witnessed an explosion of research in ecological inference--the process of trying to infer individual behavior from aggregate data. Although uncertainties and information lost in aggregation make ecological inference one of the most problematic types of research to rely on, these inferences are required in many academic fields, as well as by legislatures and the Courts in redistricting, by business in marketing research, and by governments in policy analysis.

  5. 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.

  6. 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

  7. 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.

  8. New genera of Australian stiletto flies (Diptera, Therevidae)

    PubMed Central

    Irwin, Michael E.; Winterton, Shaun L.

    2016-01-01

    Abstract Two new stiletto fly genera of Agapophytinae (Diptera: Therevidae) are described from Australia. Sidarena gen. n. comprises six new species (Sidarena aurantia sp. n., Sidarena flavipalpa sp. n., Sidarena geraldton sp. n., Sidarena hortorum sp. n., Sidarena macfarlandi sp. n., and Sidarena yallingup sp. n.) and is largely endemic to Western Australia. Zelothrix gen. n. is described based on two species; Zelothrix warrumbungles sp. n. is a locally abundant species in Eastern Australia, while Zelothrix yeatesi sp. n. is restricted to southwestern Western Australia. These sister genera are likely closely related to Taenogerella Winterton & Irwin and Actenomeros Winterton & Irwin. PMID:27853402

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

    PubMed

    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.

  11. 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

  12. 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.

  13. 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.

  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.

  15. Inference of Functional Relations in Predicted Protein Networks with a Machine Learning Approach

    PubMed Central

    Ezkurdia, Iakes; Andrés-León, Eduardo; Valencia, Alfonso

    2010-01-01

    Background Molecular biology is currently facing the challenging task of functionally characterizing the proteome. The large number of possible protein-protein interactions and complexes, the variety of environmental conditions and cellular states in which these interactions can be reorganized, and the multiple ways in which a protein can influence the function of others, requires the development of experimental and computational approaches to analyze and predict functional associations between proteins as part of their activity in the interactome. Methodology/Principal Findings We have studied the possibility of constructing a classifier in order to combine the output of the several protein interaction prediction methods. The AODE (Averaged One-Dependence Estimators) machine learning algorithm is a suitable choice in this case and it provides better results than the individual prediction methods, and it has better performances than other tested alternative methods in this experimental set up. To illustrate the potential use of this new AODE-based Predictor of Protein InterActions (APPIA), when analyzing high-throughput experimental data, we show how it helps to filter the results of published High-Throughput proteomic studies, ranking in a significant way functionally related pairs. Availability: All the predictions of the individual methods and of the combined APPIA predictor, together with the used datasets of functional associations are available at http://ecid.bioinfo.cnio.es/. Conclusions We propose a strategy that integrates the main current computational techniques used to predict functional associations into a unified classifier system, specifically focusing on the evaluation of poorly characterized protein pairs. We selected the AODE classifier as the appropriate tool to perform this task. AODE is particularly useful to extract valuable information from large unbalanced and heterogeneous data sets. The combination of the information provided by five

  16. 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

  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. Inferring relative tsunami magnitudes from inverse and forward sediment transport modeling of tsunami deposits in the Eastern Aleutian Islands.

    NASA Astrophysics Data System (ADS)

    Gelfenbaum, G. R.; La Selle, S.; Witter, R. C.; Jaffe, B. E.; Briggs, R. W.; Koehler, R. D., III; Engelhart, S. E.; Carver, G. A.

    2014-12-01

    Tsunami recurrence intervals can be determined by age dating paleotsunami deposits, but relative tsunami magnitude is more difficult to infer from deposit characteristics alone. Deposit thickness, grain size, and certain sedimentary structures are used to infer hydrodynamic conditions during deposition, which can be used as proxies for tsunami magnitude. Recent field studies in the eastern Alaska-Aleutian subduction zone have identified sequences of tsunami deposits from the 1957 Andreanof Islands earthquake (MW 8.6) and at least five other pre-historic tsunami events from the last 2,400 years. At Stardust Bay on the Pacific Coast of Sedanka Island, a sand-rich deposit attributed to the 1957 tsunami is 1-13 cm thick and is found at elevations up to 18.5 m. Older sand units are 6-50 cm thick and often have rounded gravel at the base of multiple, normally-graded sand beds. At Driftwood Bay on the south side of Umnak Island, about 200 km to the southeast of Stardust Bay, the 1957 deposit is 1 - 5.5 cm thick, underlain by a sequence of peat with up to 8 sandy deposits, some of which exhibit normally-graded beds up to 14 cm thick. Relatively thick deposits that exhibit suspension grading, a type of grading created by sediment falling out of suspension that is often observed in modern tsunami deposits, are typically formed under steady and uniform flow and are therefore good candidates for reconstructing flow conditions using inverse sediment transport models. By applying forward models of sediment transport, we will test how different tsunami waveforms, wave heights, sediment source distributions, roughness, and local slopes affect patterns of deposition. This will help us assess which deposits have characteristics that scale with tsunami wave heights used as initial conditions in the forward model, and are therefore more indicative of relative tsunami magnitude. Here, we attempt to determine if the tsunamis that created the pre-historic deposits found at Stardust and

  19. Relating the kick velocities of young pulsars with magnetic field growth time-scales inferred from braking indices

    NASA Astrophysics Data System (ADS)

    Güneydaş, A.; Ekşi, K. Y.

    2013-03-01

    A nascent neutron star may be exposed to fallback accretion soon after the proto-neutron star stage. This high-accretion episode can submerge the magnetic field deep in the crust. The diffusion of the magnetic field back to the surface will take hundreds to millions of years depending on the amount of mass accreted and the consequent depth the field is buried. Neutron stars with large kick velocities will accrete less amount of fallback material leading to shallower submergence of their fields and shorter time-scales for the growth of their fields. We obtain the relation τOhm ∝ v-1 between the space velocity of the neutron star and Ohmic time-scale for the growth of the magnetic field. We compare this with the relation between the measured transverse velocities, v⊥, and the field growth time-scales, μ /skew4dot{μ }, inferred from the measured braking indices. We find that the observational data are consistent with the theoretical prediction though the small number of data precludes a strong conclusion. Measurement of the transverse velocities of pulsars B1509-58, J1846-0258, J1119-6127 and J1734-3333 would increase the number of the data and strongly contribute to understanding whether pulsar fields grow following fallback accretion.

  20. 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

  1. 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

  2. Fault Geometry Inferred From High Precision Relative Locations of Microearthquake Clusters - An Example of Southeastern Sicily, Italy.

    NASA Astrophysics Data System (ADS)

    Scarfi, L.; Langer, H.; Gresta, S.

    clusters seem not affected seriously by random error. The hori- zontal extension of the first cluster in a NNW can be related major structures in the area such as, among others, the northern continuation of the Scicli line (Azzaro &Bar- bano, 2000). The direction of the P-axes of the focal mechanism of the first cluster is in agreement with compressional directions inferred from bore-hole breakouts found in the Gela Nappe (Ragg et. al, 1999).

  3. 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.

  4. 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

  5. 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…

  6. Elliptic genera from multi-centers

    NASA Astrophysics Data System (ADS)

    Gaddam, Nava

    2016-05-01

    I show how elliptic genera for various Calabi-Yau threefolds may be understood from supergravity localization using the quantization of the phase space of certain multi-center configurations. I present a simple procedure that allows for the enumeration of all multi-center configurations contributing to the polar sector of the elliptic genera — explicitly verifying this in the cases of the quintic in {P} 4, the sextic in {W}{P} (2,1,1,1,1), the octic in {W}{P} (4,1,1,1,1) and the dectic in {W}{P} (5,2,1,1,1). With an input of the corresponding `single-center' indices (Donaldson-Thomas invariants), the polar terms have been known to determine the elliptic genera completely. I argue that this multi-center approach to the low-lying spectrum of the elliptic genera is a stepping stone towards an understanding of the exact microscopic states that contribute to supersymmetric single center black hole entropy in {N} = 2 supergravity.

  7. Perceptual inference.

    PubMed

    Aggelopoulos, Nikolaos C

    2015-08-01

    Perceptual inference refers to the ability to infer sensory stimuli from predictions that result from internal neural representations built through prior experience. Methods of Bayesian statistical inference and decision theory model cognition adequately by using error sensing either in guiding action or in "generative" models that predict the sensory information. In this framework, perception can be seen as a process qualitatively distinct from sensation, a process of information evaluation using previously acquired and stored representations (memories) that is guided by sensory feedback. The stored representations can be utilised as internal models of sensory stimuli enabling long term associations, for example in operant conditioning. Evidence for perceptual inference is contributed by such phenomena as the cortical co-localisation of object perception with object memory, the response invariance in the responses of some neurons to variations in the stimulus, as well as from situations in which perception can be dissociated from sensation. In the context of perceptual inference, sensory areas of the cerebral cortex that have been facilitated by a priming signal may be regarded as comparators in a closed feedback loop, similar to the better known motor reflexes in the sensorimotor system. The adult cerebral cortex can be regarded as similar to a servomechanism, in using sensory feedback to correct internal models, producing predictions of the outside world on the basis of past experience.

  8. Evaluation of DNA barcodes in Codonopsis (Campanulaceae) and in some large angiosperm plant genera

    PubMed Central

    Xiang, Xiao-Guo; Huang, Lu-Qi; Jin, Xiao-Hua

    2017-01-01

    DNA barcoding is expected to be one of the most promising tools in biological taxonomy. However, there have been no agreements on which core barcode should be used in plants, especially in species-rich genera with wide geographical distributions. To evaluate their discriminatory power in large genera, four of the most widely used DNA barcodes, including three plastid regions (matK, rbcL, trnH-psbA) and nuclear internal transcribed spacer (nrITS), were tested in seven species-rich genera (Ficus, Pedicularis, Rhodiola, Rhododendron,Viburnum, Dendrobium and Lysimachia) and a moderate size genus, Codonopsis. All of the sequences from the aforementioned seven large genera were downloaded from NCBI. The related barcodes for Codonopsis were newly generated in this study. Genetics distances, DNA barcoding gaps and phylogenetic trees of the four single barcodes and their combinations were calculated and compared in the seven genera. As for single barcode, nrITS has the most variable sites, the clearest intra- and inter-specific divergences and the highest discrimination rates in the seven genera. Among the combinations of barcodes, ITS+matK performed better than all the single barcodes in most cases and even the three- and four-loci combinations in the seven genera. Therefore, we recommend ITS+matK as the core barcodes for large plant genera. PMID:28182623

  9. Statistical Inference

    NASA Astrophysics Data System (ADS)

    Khan, Shahjahan

    Often scientific information on various data generating processes are presented in the from of numerical and categorical data. Except for some very rare occasions, generally such data represent a small part of the population, or selected outcomes of any data generating process. Although, valuable and useful information is lurking in the array of scientific data, generally, they are unavailable to the users. Appropriate statistical methods are essential to reveal the hidden "jewels" in the mess of the row data. Exploratory data analysis methods are used to uncover such valuable characteristics of the observed data. Statistical inference provides techniques to make valid conclusions about the unknown characteristics or parameters of the population from which scientifically drawn sample data are selected. Usually, statistical inference includes estimation of population parameters as well as performing test of hypotheses on the parameters. However, prediction of future responses and determining the prediction distributions are also part of statistical inference. Both Classical or Frequentists and Bayesian approaches are used in statistical inference. The commonly used Classical approach is based on the sample data alone. In contrast, increasingly popular Beyesian approach uses prior distribution on the parameters along with the sample data to make inferences. The non-parametric and robust methods are also being used in situations where commonly used model assumptions are unsupported. In this chapter,we cover the philosophical andmethodological aspects of both the Classical and Bayesian approaches.Moreover, some aspects of predictive inference are also included. In the absence of any evidence to support assumptions regarding the distribution of the underlying population, or if the variable is measured only in ordinal scale, non-parametric methods are used. Robust methods are employed to avoid any significant changes in the results due to deviations from the model

  10. Statistical Inference

    NASA Astrophysics Data System (ADS)

    Khan, Shahjahan

    Often scientific information on various data generating processes are presented in the from of numerical and categorical data. Except for some very rare occasions, generally such data represent a small part of the population, or selected outcomes of any data generating process. Although, valuable and useful information is lurking in the array of scientific data, generally, they are unavailable to the users. Appropriate statistical methods are essential to reveal the hidden “jewels” in the mess of the row data. Exploratory data analysis methods are used to uncover such valuable characteristics of the observed data. Statistical inference provides techniques to make valid conclusions about the unknown characteristics or parameters of the population from which scientifically drawn sample data are selected. Usually, statistical inference includes estimation of population parameters as well as performing test of hypotheses on the parameters. However, prediction of future responses and determining the prediction distributions are also part of statistical inference. Both Classical or Frequentists and Bayesian approaches are used in statistical inference. The commonly used Classical approach is based on the sample data alone. In contrast, increasingly popular Beyesian approach uses prior distribution on the parameters along with the sample data to make inferences. The non-parametric and robust methods are also being used in situations where commonly used model assumptions are unsupported. In this chapter,we cover the philosophical andmethodological aspects of both the Classical and Bayesian approaches.Moreover, some aspects of predictive inference are also included. In the absence of any evidence to support assumptions regarding the distribution of the underlying population, or if the variable is measured only in ordinal scale, non-parametric methods are used. Robust methods are employed to avoid any significant changes in the results due to deviations from the model

  11. 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

  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.

  13. 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

  14. 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.

  15. Genera of Pentatomidae (Hemiptera: Pentatomoidea) from south India--an illustrated key to genera and checklist of species.

    PubMed

    Salini, S; Viraktamath, C A

    2015-02-25

    Family Pentatomidae is represented by four subfamilies (Asopinae, Pentatominae, Phyllocephalinae and Podopinae) and 86 genera in south India. Pentatominae are the dominant group represented by 29 tribes and 72 genera. An illustrated key including the habitus of majority of genera as well as illustrations of important diagnostic features are given for the subfamilies, tribes and genera occurring in south India. In addition, a key to families of Pentatomoidea and a checklist of species of Pentatomidae occurring in south India are also included.

  16. Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar.

    PubMed

    Bacon, Christine D; Simmons, Mark P; Archer, Robert H; Zhao, Liang-Cheng; Andriantiana, Jacky

    2016-01-01

    Of the 97 currently recognized genera of Celastraceae, 19 are native to Madagascar, including six endemics. In this study we conducted the most thorough phylogenetic analysis of Celastraceae yet completed with respect to both character and taxon sampling, and include representatives of five new endemic genera. Fifty-one new accessions, together with 328 previously used accessions of Celastrales, were sampled for morphological characters, two rDNA gene regions, and two plastid gene regions. The endemic Malagasy genera are resolved in two separate lineages-Xenodrys by itself and all other endemic genera in a clade that also includes four lineages inferred to have dispersed from Madagascar: Brexia madagascariensis (Mascarene Islands, coastal Africa), Elaeodendron (West Indies, Africa to New Caledonia), and Pleurostylia (Africa to New Caledonia). Of the 12 extant Malagasy Celastraceae lineages identified, eight are clearly of African origin. The origins of the remaining four lineages are less clear, but reasonable possibilities include America, Eurasia, Africa, southern India, Malesia, and Australia. Based on 95% credible age intervals from fossil-calibrated molecular dating, all 12 extant Malagasy Celastraceae lineages appear to have arisen following dispersal after the separation of Madagascar from other landmasses within the last 70 million years.

  17. Elliptic Genera and 3d Gravity

    SciTech Connect

    Benjamin, Nathan; Cheng, Miranda C. N.; Kachru, Shamit; Moore, Gregory W.; Paquette, Natalie M.

    2016-03-30

    We describe general constraints on the elliptic genus of a 2d supersymmetric conformal field theory which has a gravity dual with large radius in Planck units. We give examples of theories which do and do not satisfy the bounds we derive, by describing the elliptic genera of symmetric product orbifolds of K3, product manifolds, certain simple families of Calabi–Yau hypersurfaces, and symmetric products of the “Monster CFT”. We discuss the distinction between theories with supergravity duals and those whose duals have strings at the scale set by the AdS curvature. Under natural assumptions, we attempt to quantify the fraction of (2,2) supersymmetric conformal theories which admit a weakly curved gravity description, at large central charge.

  18. Elliptic genera and 3d gravity

    SciTech Connect

    Benjamin, Nathan; Cheng, Miranda C. N.; Kachru, Shamit; Moore, Gregory W.; Paquette, Natalie M.

    2016-03-30

    Here, we describe general constraints on the elliptic genus of a 2d supersymmetric conformal field theory which has a gravity dual with large radius in Planck units. We give examples of theories which do and do not satisfy the bounds we derive, by describing the elliptic genera of symmetric product orbifolds of K3, product manifolds, certain simple families of Calabi–Yau hypersurfaces, and symmetric products of the “Monster CFT”. We discuss the distinction between theories with supergravity duals and those whose duals have strings at the scale set by the AdS curvature. Under natural assumptions, we attempt to quantify the fraction of (2,2) supersymmetric conformal theories which admit a weakly curved gravity description, at large central charge.

  19. Elliptic genera and 3d gravity

    DOE PAGES

    Benjamin, Nathan; Cheng, Miranda C. N.; Kachru, Shamit; ...

    2016-03-30

    Here, we describe general constraints on the elliptic genus of a 2d supersymmetric conformal field theory which has a gravity dual with large radius in Planck units. We give examples of theories which do and do not satisfy the bounds we derive, by describing the elliptic genera of symmetric product orbifolds of K3, product manifolds, certain simple families of Calabi–Yau hypersurfaces, and symmetric products of the “Monster CFT”. We discuss the distinction between theories with supergravity duals and those whose duals have strings at the scale set by the AdS curvature. Under natural assumptions, we attempt to quantify the fractionmore » of (2,2) supersymmetric conformal theories which admit a weakly curved gravity description, at large central charge.« less

  20. Infering the Relation of Hydrometeorological Variability on the Durance Watershed (southeastern France) to Large Scale Circulation from Anatem Reconstructed Series

    NASA Astrophysics Data System (ADS)

    Fossa, M.; Mathevet, T.; Gailhard, J.; Massei, N.

    2015-12-01

    Understanding large spatio-temporal hydrometeorological variabilities is critical in the present context of climate change. Large scale information analyses require long and numerous times series as input data. It is often met with difficulty because good quality time series are scarce and often not available over a large area. Reconstructions offer an interesting alternative to alleviate this problem. An original reconstruction method for rainfall and temperature called ANATEM has been developed by Electricité de France in 2013 (Kuentz et al., 2015) combining both a nearby time series (TEM) and a climate field (i.e: geopotential height)(ANA) as predictors. By using large scale information, this method should allow improving on the TEM regression model both in spatial and temporal dimensions. ANATEM was used to reconstruct daily rainfall time series from 25 stations of the Durance watershed in South of France, spanning 1883-2010. This study focused on extracting the large scale information contained in the reconstructed series. Wavelet analyses were used to break down the signal and extract its long-term component (out of 4 different time scales) while composite map analyses enabled to show the links between mean rainfall over the durance and climate fields in the Euro-Atlantic sector. The study showed that ANATEM reconstruction can indeed improve on long term/large scale reconstructions and thus that reconstructions can be used to infer climate processes. Wavelet Multiresolution analysis over the Durance watershed showed a dip in long-term rainfall from 1950 to the end of the 20th century. Composite analysis revealed that rainfall variation (from low to high rainfall) over the Durance watershed is mainly associated with transition from positive NAO-like pattern to negative NAO-like one. The spatial large scale information shows a strong variability with season. In summer, large scale forcings seem less apparent. Long term oscillations showed distinct spatio

  1. Three Kanto Earthquakes Inferred from the Tsunami Deposits and the Relative Sea Level Change in the Miura Peninsula, Central Japan

    NASA Astrophysics Data System (ADS)

    Kim, H.; Shimazaki, K.; Chiba, T.; Ishibe, T.; Okamura, M.; Matsuoka, H.; Tsuji, Y.; Satake, K.

    2010-12-01

    The Kanto earthquake is a great interplate earthquake caused by subduction of the Philippine Sea Plate beneath the Japan Island along the Sagami Trough. The 1923 Kanto earthquake (M=7.9) and the 1703 Kanto earthquake (M~8.0) are two of the most devastating earthquake those struck Tokyo Metropolitan area, respectively. These earthquakes brought large (~5 m) tsunami to the coast area and uplifted the Miura peninsula by ~1.4 m. The tide gauge station, moreover, records the subsidence during the interseismic period before and after the 1923 earthquake. Present study clarifies the past Kanto earthquake prior to the 1703 earthquake based on the sedimentary analysis in the Koajiro bay of the southern Miura Peninsula. The continuous samples of inner bay fine sediments were taken by the boring survey using 3-m-long geoslicer. Three layers of coarse sediments, T1, T2, and T3 units from top toward bottom, are observed in the bay sediments at almost all the sites. These units are composed of mixture of materials such as shell fragments, rock clasts and gravel, and some of units have eroded the lower fine sediments, indicating the event deposits by the strong traction flow. The grain sizes of the bay sediments are grading upward and abruptly become larger after the deposition of the T1, T2 and T3 units. Very little diatom is observed in these units, but the total number of diatoms increase in the bay sediments. The ratio of the marine planktonic species against the benthic species gradually rises from the lower part to the upper part in the bay sediment. In the tidal flat sediment, the freshwater planktonic species appear in place of the marine planktonic diatom. The changes of grain size and diatom species make a presumption that the sea depth suddenly becomes shallow by the event and deeper during the interseismic period. The T1, T2 and T3 units, thus, are correlated with the tsunami deposits conveyed by the Kanto earthquake. The T1 and T2 units are inferred to be the tsunami

  2. Why Are Some Plant Genera More Invasive Than Others?

    PubMed Central

    Schmidt, John Paul; Drake, John M.

    2011-01-01

    Determining how biological traits are related to the ability of groups of organisms to become economically damaging when established outside of their native ranges is a major goal of population biology, and important in the management of invasive species. Little is known about why some taxonomic groups are more likely to become pests than others among plants. We investigated traits that discriminate vascular plant genera, a level of taxonomic generality at which risk assessment and screening could be more effectively performed, according to the proportion of naturalized species which are pests. We focused on the United States and Canada, and, because our purpose is ultimately regulatory, considered species classified as weeds or noxious. Using contingency tables, we identified 11 genera of vascular plants that are disproportionately represented by invasive species. Results from boosted regression tree analyses show that these categories reflect biological differences. In summary, approximately 25% of variation in genus proportions of weeds or noxious species was explained by biological covariates. Key explanatory traits included genus means for wetland habitat affinity, chromosome number, and seed mass. PMID:21494563

  3. 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

  4. 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...

  5. Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data

    PubMed Central

    2013-01-01

    Background Gibbons (Hylobatidae) are the most diverse group of living apes. They exist as geographically-contiguous species which diverged more rapidly than did their close relatives, the great apes (Hominidae). Of the four extant gibbon genera, the evolutionary histories of two polyspecific genera, Hylobates and Nomascus, have been the particular focus of research but the DNA sequence data used was largely derived from the maternally inherited mitochondrial DNA (mtDNA) locus. Results To investigate the evolutionary relationships and divergence processes of gibbon species, particularly those of the Hylobates genus, we produced and analyzed a total of 11.5 kb DNA of sequence at 14 biparentally inherited autosomal loci. We find that on average gibbon genera have a high average sequence diversity but a lower degree of genetic differentiation as compared to great ape genera. Our multilocus species tree features H. pileatus in a basal position and a grouping of the four Sundaic island species (H. agilis, H. klossii, H. moloch and H. muelleri). We conducted pairwise comparisons based on an isolation-with-migration (IM) model and detect signals of asymmetric gene flow between H. lar and H. moloch, between H. agilis and H. muelleri, and between N. leucogenys and N. siki. Conclusions Our multilocus analyses provide inferences of gibbon evolutionary histories complementary to those based on single gene data. The results of IM analyses suggest that the divergence processes of gibbons may be accompanied by gene flow. Future studies using analyses of multi-population model with samples of known provenance for Hylobates and Nomascus species would expand the understanding of histories of gene flow during divergences for these two gibbon genera. PMID:23586586

  6. 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

  7. 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.

  8. Compression fossil Mymaridae (Hymenoptera) from Kishenehn oil shales, with description of two new genera and review of Tertiary amber genera.

    PubMed

    Huber, John T; Greenwalt, Dale

    2011-01-01

    Compression fossils of three genera and six species of Mymaridae (Hymenoptera: Chalcidoidea) are described from 46 million year old Kishenehn oil shales in Montana, USA. Two new genera are described: Eoeustochus Huber, gen. n., with two included species, Eoeustochus kishenehn Huber (type species) and Eoeustochus borchersi Huber, sp. n., and Eoanaphes, gen. n., with Eoanaphes stethynioides Huber, sp. n. Three new species of Gonatocerus are also described, Gonatocerus greenwalti Huber, sp. n. , Gonatocerus kootenai Huber, sp. n., and Gonatocerus rasnitsyni Huber, sp. n. Previously described amber fossil genera are discussed and five genera in Baltic amber are tentatively recorded as fossils: Anagroidea, Camptoptera, Dorya, Eustochus, and Mimalaptus.

  9. 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.

  10. 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

  11. Ages and relative sizes of pre-2004 tsunamis in the Bay of Bengal inferred from geologic evidence in the Andaman and Nicobar Islands

    NASA Astrophysics Data System (ADS)

    Rajendran, C. P.; Rajendran, Kusala; Andrade, Vanessa; Srinivasalu, S.

    2013-04-01

    Geologic evidence along the northern part of the 2004 Aceh-Andaman rupture suggests that this region generated as many as five tsunamis in the prior 2000 years. We identify this evidence by drawing analogy with geologic records of land-level change and the tsunami in 2004 from the Andaman and Nicobar Islands (A&N). These analogs include subsided mangrove swamps, uplifted coral terraces, liquefaction, and organic soils coated by sand and coral rubble. The pre-2004 evidence varies in potency, and materials dated provide limiting ages on inferred tsunamis. The earliest tsunamis occurred between the second and sixth centuries A.D., evidenced by coral debris of the southern Car Nicobar Island. A subsequent tsunami, probably in the range A.D. 770-1040, is inferred from deposits both in A&N and on the Indian subcontinent. It is the strongest candidate for a 2004-caliber earthquake in the past 2000 years. A&N also contain tsunami deposits from A.D. 1250 to 1450 that probably match those previously reported from Sumatra and Thailand, and which likely date to the 1390s or 1450s if correlated with well-dated coral uplift offshore Sumatra. Thus, age data from A&N suggest that within the uncertainties in estimating relative sizes of paleo-earthquakes and tsunamis, the 1000 year interval can be divided in half by the earthquake or earthquakes of A.D. 1250-1450 of magnitude >8.0 and consequent tsunamis. Unlike the transoceanic tsunamis generated by full or partial rupture of the subduction interface, the A&N geology further provides evidence for the smaller-sized historical tsunamis of 1762 and 1881, which may have been damaging locally.

  12. Addressing reverse inference in psychiatric neuroimaging: Meta-analyses of task-related brain activation in common mental disorders.

    PubMed

    Sprooten, Emma; Rasgon, Alexander; Goodman, Morgan; Carlin, Ariella; Leibu, Evan; Lee, Won Hee; Frangou, Sophia

    2017-04-01

    Functional magnetic resonance imaging (fMRI) studies in psychiatry use various tasks to identify case-control differences in the patterns of task-related brain activation. Differently activated regions are often ascribed disorder-specific functions in an attempt to link disease expression and brain function. We undertook a systematic meta-analysis of data from task-fMRI studies to examine the effect of diagnosis and study design on the spatial distribution and direction of case-control differences on brain activation. We mapped to atlas regions coordinates of case-control differences derived from 537 task-fMRI studies in schizophrenia, bipolar disorder, major depressive disorder, anxiety disorders, and obsessive compulsive disorder comprising observations derived from 21,427 participants. The fMRI tasks were classified according to the Research Domain Criteria (RDoC). We investigated whether diagnosis, RDoC domain or construct and use of regions-of-interest or whole-brain analyses influenced the neuroanatomical pattern of results. When considering all primary studies, we found an effect of diagnosis for the amygdala and caudate nucleus and an effect of RDoC domains and constructs for the amygdala, hippocampus, putamen and nucleus accumbens. In contrast, whole-brain studies did not identify any significant effect of diagnosis or RDoC domain or construct. These results resonate with prior reports of common brain structural and genetic underpinnings across these disorders and caution against attributing undue specificity to brain functional changes when forming explanatory models of psychiatric disorders. Hum Brain Mapp 38:1846-1864, 2017. © 2017 Wiley Periodicals, Inc.

  13. Addressing reverse inference in psychiatric neuroimaging: Meta‐analyses of task‐related brain activation in common mental disorders

    PubMed Central

    Sprooten, Emma; Rasgon, Alexander; Goodman, Morgan; Carlin, Ariella; Leibu, Evan; Lee, Won Hee

    2017-01-01

    Abstract Functional magnetic resonance imaging (fMRI) studies in psychiatry use various tasks to identify case‐control differences in the patterns of task‐related brain activation. Differently activated regions are often ascribed disorder‐specific functions in an attempt to link disease expression and brain function. We undertook a systematic meta‐analysis of data from task‐fMRI studies to examine the effect of diagnosis and study design on the spatial distribution and direction of case‐control differences on brain activation. We mapped to atlas regions coordinates of case‐control differences derived from 537 task‐fMRI studies in schizophrenia, bipolar disorder, major depressive disorder, anxiety disorders, and obsessive compulsive disorder comprising observations derived from 21,427 participants. The fMRI tasks were classified according to the Research Domain Criteria (RDoC). We investigated whether diagnosis, RDoC domain or construct and use of regions‐of‐interest or whole‐brain analyses influenced the neuroanatomical pattern of results. When considering all primary studies, we found an effect of diagnosis for the amygdala and caudate nucleus and an effect of RDoC domains and constructs for the amygdala, hippocampus, putamen and nucleus accumbens. In contrast, whole‐brain studies did not identify any significant effect of diagnosis or RDoC domain or construct. These results resonate with prior reports of common brain structural and genetic underpinnings across these disorders and caution against attributing undue specificity to brain functional changes when forming explanatory models of psychiatric disorders. Hum Brain Mapp 38:1846–1864, 2017. © 2017 Wiley Periodicals, Inc. PMID:28067006

  14. Environmental niche conservatism explains the accumulation of species richness in Mediterranean-hotspot plant genera.

    PubMed

    Skeels, Alexander; Cardillo, Marcel

    2017-03-01

    The causes of exceptionally high plant diversity in Mediterranean-climate biodiversity hotspots are not fully understood. We asked whether a mechanism similar to the tropical niche conservatism hypothesis could explain the diversity of four large genera (Protea, Moraea, Banksia, and Hakea) with distributions within and adjacent to the Greater Cape Floristic Region (South Africa) or the Southwest Floristic Region (Australia). Using phylogenetic and spatial data we estimated the environmental niche of each species, and reconstructed the mode and dynamics of niche evolution, and the geographic history, of each genus. For three genera, there were strong positive relationships between the diversity of clades within a region and their inferred length of occupation of that region. Within genera, there was evidence for strong evolutionary constraint on niche axes associated with climatic seasonality and aridity, with different niche optima for hotspot and nonhotspot clades. Evolutionary transitions away from hotspots were associated with increases in niche breadth and elevated rates of niche evolution. Our results point to a process of "hotspot niche conservatism" whereby the accumulation of plant diversity in Mediterranean-type ecosystems results from longer time for speciation, with dispersal away from hotspots limited by narrow and phylogenetically conserved environmental niches.

  15. 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

  16. Relationships among genera of the Saccharomycotina (Ascomycota) from multigene phylogenetic analysis of type species.

    PubMed

    Kurtzman, Cletus P; Robnett, Christie J

    2013-02-01

    Relationships among ascomycetous yeast genera (subphylum Saccharomycotina, phylum Ascomycota) have been uncertain. In the present study, type species of 70 currently recognized genera are compared from divergence in the nearly entire nuclear gene sequences for large subunit rRNA, small subunit (SSU) rRNA, translation elongation factor-1α, and RNA polymerase II, subunits 1 (RPB1) and 2 (RPB2). The analysis substantiates earlier proposals that all known ascomycetous yeast genera now assigned to the Saccharomycotina represent a single clade. Maximum likelihood analysis resolved the taxa into eight large multigenus clades and four-one- and two-genus clades. Maximum parsimony and neighbor-joining analyses gave similar results. Genera of the family Saccharomycetaceae remain as one large clade as previously demonstrated, to which the genus Cyniclomyces is now assigned. Pichia, Saturnispora, Kregervanrija, Dekkera, Ogataea and Ambrosiozyma are members of a single large clade, which is separate from the clade that includes Barnettozyma, Cyberlindnera, Phaffomyces, Starmera and Wickerhamomyces. Other clades include Kodamaea, Metschnikowia, Debaryomyces, Cephaloascus and related genera, which are separate from the clade that includes Zygoascus, Trichomonascus, Yarrowia and others. This study once again demonstrates that there is limited congruence between a system of classification based on phenotype and a system determined from DNA sequences.

  17. The Psilostomidae Looss, 1900 (sensu stricto) (Digenea: Echinostomatoidea): description of three new genera and a key to the genera of the family.

    PubMed

    Kudlai, Olena; Kostadinova, Aneta; Pulis, Eric E; Tkach, Vasyl V

    2017-01-01

    Three new psilostomid genera, Byrdtrema n. g., Longisaccus n. g. and Macracetabulum n. g., each with a single species, are described from ducks, Aix sponsa (L.) and Bucephala albeola (L.) in North America. Byrdtrema n. g. and Macracetabulum n. g. possess a bipartite seminal vesicle and share this character with four psilostomid genera, Grysoma Byrd, Bogitsh & Maples, 1961, Neopsilotrema Kudlai, Pulis, Kostadinova & Tkach, 2016, Psilostomum Looss, 1899 and Psilotornus Byrd & Prestwood, 1969. Byrdtrema n. g. differs from Macracetabulum n. g. in the shape of the body (elongate vs elongate-oval); the position of the ventral sucker (in first third of body vs just pre-equatorial); the shorter forebody; as well as in the smaller size of the eggs in relation to body length. Both new genera differ from (i) Grysoma by the nature of the vitellarium (large, compact follicles with small vitelline cells vs weakly defined follicles with large vitelline cells, respectively) and the smaller size of the eggs in relation to body length; (ii) Psilostomum in the posterior extend of the cirrus-sac in relation to ventral sucker (slightly posterior vs more posterior), the location of the genital pore (at the level of oesophagus vs just postbifurcal), the shorter length of uterine and longer post-testicular fields in relation to body length, and the anterior limits of vitellarium (at the level of ventral sucker vs posterior to ventral sucker); (iii) Psilotornus by the presence of a muscular pharynx (vs absent or rudimentary) and the location of the cirrus-sac (antero-dorsal to ventral sucker or more posterior vs entirely anterior to ventral sucker) and ovary (in hindbody vs in forebody). Byrdtrema n. g. differs from Neopsilotrema in the shape of the body (elongate vs subspherical to elongate-oval) and ventral sucker (elongate-oval vs subspherical to transversely oval), the shorter forebody and smaller eggs in relation to body length. Macracetabulum n. g. differs from Neopsilotrema by the

  18. DNA barcoding and phylogenetic relationships of genera Picoides and Dendrocopos (Aves: Picidae).

    PubMed

    Huang, Z H; Tu, F Y; Liao, X J

    2015-12-28

    Picoides and Dendrocopos are two closely related genera of woodpeckers (family Picidae), and members of these genera have long been the subjects of phylogenetic debate. Mitochondrial cytochrome c oxidase subunit I (COI) is a powerful marker for the identification and phylogenetic study of animal species. In the present study, we analyzed the COI barcodes of 21 species from the two genera, and 222 variable sites were identified. Kimura two-parameter distances were calculated between barcodes. The average interspecific genetic distance was more than 20 times higher than the average intraspecific genetic distance. The neighbor-joining method was used to construct a phylogenetic tree, and all of the species could be discriminated by their distinct clades. Picoides arcticus was the first to split from the lineage, and the other species were grouped into two divergent clades. The results of this study indicated that the COI genetic data did not support the monophyly of Picoides and Dendrocopos.

  19. IRIS: Integrate, Relate. Infer. Share.

    DTIC Science & Technology

    2005-01-01

    share many of the goals and requirements for IRIS: Java-based, ontology-driven, user centric. We negotiated, and CEO Nova Spivack agreed to join the...Department of Interior-National Business Center (DOI-NBC). We would like to thank Nova Spivack and Jim Wissner at Radar Networks for their

  20. 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.

  1. Molecular phylogeny of microhylid frogs (Anura: Microhylidae) with emphasis on relationships among New World genera

    PubMed Central

    2012-01-01

    Background Over the last ten years we have seen great efforts focused on revising amphibian systematics. Phylogenetic reconstructions derived from DNA sequence data have played a central role in these revisionary studies but have typically under-sampled the diverse frog family Microhylidae. Here, we present a detailed phylogenetic study focused on expanding previous hypotheses of relationships within this cosmopolitan family. Specifically, we placed an emphasis on assessing relationships among New World genera and those taxa with uncertain phylogenetic affinities (i.e., incertae sedis). Results One mitochondrial and three nuclear genes (about 2.8 kb) were sequenced to assess phylogenetic relationships. We utilized an unprecedented sampling of 200 microhylid taxa representing 91% of currently recognized subfamilies and 95% of New World genera. Our analyses do not fully resolve relationships among subfamilies supporting previous studies that have suggested a rapid early diversification of this clade. We observed a close relationship between Synapturanus and Otophryne of the subfamily Otophryninae. Within the subfamily Gastrophryninae relationships between genera were well resolved. Conclusion Otophryninae is distantly related to all other New World microhylids that were recovered as a monophyletic group, Gastrophryninae. Within Gastrophryninae, five genera were recovered as non-monophyletic; we propose taxonomic re-arrangements to render all genera monophyletic. This hypothesis of relationships and updated classification for New World microhylids may serve as a guide to better understand the evolutionary history of this group that is apparently subject to convergent morphological evolution and chromosome reduction. Based on a divergence analysis calibrated with hypotheses from previous studies and fossil data, it appears that microhylid genera inhabiting the New World originated during a period of gradual cooling from the late Oligocene to mid Miocene. PMID:23228209

  2. The Pattern of Retinal Ganglion Cell Loss in OPA1-Related Autosomal Dominant Optic Atrophy Inferred From Temporal, Spatial, and Chromatic Sensitivity Losses

    PubMed Central

    Majander, Anna; João, Catarina; Rider, Andrew T.; Henning, G. Bruce; Votruba, Marcela; Moore, Anthony T.; Yu-Wai-Man, Patrick; Stockman, Andrew

    2017-01-01

    Purpose Progressive retinal ganglion cell (RGC) loss is the pathological hallmark of autosomal dominant optic atrophy (DOA) caused by pathogenic OPA1 mutations. The aim of this study was to conduct an in-depth psychophysical study of the visual losses in DOA and to infer any selective vulnerability of visual pathways subserved by different RGC subtypes. Methods We recruited 25 patients carrying pathogenic OPA1 mutations and age-matched healthy individuals. Spatial contrast sensitivity functions (SCSFs) and chromatic contrast sensitivity were quantified, the latter using the Cambridge Colour Test. In 11 patients, long (L) and short (S) wavelength–sensitive cone temporal acuities were measured as a function of target illuminance, and L-cone temporal contrast sensitivity (TCSF) as a function of temporal frequency. Results Spatial contrast sensitivity functions were abnormal, with the loss of sensitivity increasing with spatial frequency. Further, the highest L-cone temporal acuity fell on average by 10 Hz and the TCSFs by 0.66 log10 unit. Chromatic thresholds along the protan, deutan, and tritan axes were 8, 9, and 14 times higher than normal, respectively, with losses increasing with age and S-cone temporal acuity showing the most significant age-related decline. Conclusions Losses of midget parvocellular, parasol magnocellular, and bistratified koniocellular RGCs could account for the losses of high spatial frequency sensitivity and protan and deutan sensitivities, high temporal frequency sensitivity, and S-cone temporal and tritan sensitivities, respectively. The S-cone–related losses showed a significant deterioration with increasing patient age and could therefore prove useful biomarkers of disease progression in DOA. PMID:28125838

  3. A multilocus phylogeny of New World jay genera.

    PubMed

    Bonaccorso, Elisa; Peterson, A Townsend

    2007-02-01

    We studied phylogenetic relationships of the New World Jays (NWJs) based on DNA sequences from three mitochondrial and two nuclear loci. Sampling included at least two individuals from each of the seven NWJ genera and four outgroups of closely related corvids, as well as six of the 16 Cyanocorax species (including two representatives of the previously recognized "Cissilopha"). Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood, and Bayesian analyses for individual genes and a combined dataset. The combined phylogenetic analysis supports the basal position of Cyanolyca to all other NWJs, a (Cyanocorax (Calocitta, Psilorhinus)) clade, and a ((Cyanocitta, Aphelocoma) Gymnorhinus) clade that agrees with a novel morphological synapomorphy uniting Cyanocitta and Aphelocoma. Within Cyanocorax, C. yncas (former "Xanthoura") is basal to a split among former "Cyssilopha" species and the rest of the Cyanocorax species. To explore implications for the historical biogeography of the NJWs, we used Dispersal-Vicariance Analysis, which indicated that NWJs originated either in Mesoamerica or North America+Mesoamerica, with South American NWJs dispersing three times independently from Mesoamerica.

  4. 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.

  5. Dark septate endophytic pleosporalean genera from semiarid areas.

    PubMed

    Knapp, D G; Kovács, G M; Zajta, E; Groenewald, J Z; Crous, P W

    2015-12-01

    Dark septate endophytes (DSE) are distributed worldwide as root-colonising fungi, and frequent in environments with strong abiotic stress. DSE is not a taxon, but constitutes numerous fungal taxa belonging to several orders of Ascomycota. In this study we investigate three unidentified DSE lineages belonging to Pleosporales that were found previously in semiarid sandy grasslands. For molecular phylogenetic studies seven loci (ITS, partial 18S nrRNA, 28S nrRNA, actin, calmodulin, transcription-elongation factor 1- α and ß -tubulin genes) were amplified and sequenced. Based on morphology and the resulting molecular phylogeny these isolates were found to represent three novel genera within the Pleosporales, namely Aquilomyces, Flavomyces and Darksidea, with eight novel species. Molecular data revealed that monotypic Aquilomyces belongs to Morosphaeriaceae, monotypic Flavomyces represents an incertae sedis lineage related to Massarinaceae, and Darksidea, with six new species, is allied to the Lentitheciaceae. During this study we tested numerous conditions to induce sporulation, and managed for the first time to induce several DSE to form their sexual morphs.

  6. Palaearctic osmiine bees of the genera Hofferia and Stenoheriades (Megachilidae, Osmiini): biology, taxonomy and key to species.

    PubMed

    Müller, Andreas; Trunz, Vincent

    2014-02-17

    Hofferia and Stenoheriades are closely related, species-poor genera of the osmiine bees (Megachilidae). Analysis of female pollen loads and field observations indicate that species of both genera have a strong affinity to Asteraceae as pollen hosts. Both genera use insect burrows in dead wood as nesting site, and Hofferia schmiedeknechti was found to build cell walls and nest plug with resin partly mixed with small pebbles. The taxonomic revision of the Palaearctic Hofferia and Stenoheriades species revealed the existence of a still undescribed species in the Levant, Stenoheriades levantica spec. nov.. Stenoheriades hofferi (Tkalců, 1984) is synonymized with S. coelostoma (Benoist, 1935), which is distinct from S. asiatica (Friese, 1921), and Heriades integra Benoist, 1934, formerly considered a Stenoheriades species, is synonymized with Osmia (Hoplosmia) scutellaris Morawitz, 1868. Keys for the delimitation of Hofferia and Stenoheriades from the other Palaearctic osmiine bee genera and for the identification of the Palaearctic species are given. 

  7. Species concept and nomenclatural changes within the genera Elliptochloris and Pseudochlorella (Trebouxiophyceae) based on an integrative approach.

    PubMed

    Darienko, Tatyana; Gustavs, Lydia; Pröschold, Thomas

    2016-12-01

    The genera Elliptochloris and Pseudochlorella were erected for Chlorella-like green algae producing two types of autospores and cell packages, respectively. Both genera are widely distributed in different soil habitats, either as free living or as photobionts of lichens. The species of these genera are often difficult to identify because of the high phenotypic plasticity and occasional lack of characteristic features. The taxonomic and nomenclatural status of these species, therefore, remains unclear. In this study, 34 strains were investigated using an integrative approach. Phylogenetic analyses demonstrated that the isolates belong to two independent lineages of the Trebouxiophyceae (Elliptochloris and Prasiola clades) and confirmed that the genera are not closely related. The comparison of morphology, molecular phylogeny, and analyses of secondary structures of SSU and ITS rDNA sequences revealed that all of the strains belong to three genera: Elliptochloris, Pseudochlorella, and Edaphochlorella. As a consequence of the taxonomic revisions, we propose two new combinations (Elliptochloris antarctica and Pseudochlorella signiensis) and validate Elliptochloris reniformis, which is invalidly described according to the International Code for Nomenclature (ICN), by designating a holotype. To reflect the high phenotypic plasticity of P. signiensis, two new varieties were described: P. signiensis var. magna and P. signiensis var. communis. Chlorella mirabilis was not closely related to any of these genera and was, therefore, transferred to the new genus Edaphochlorella. All of the taxonomic changes were highly supported by all phylogenetic analyses and were confirmed by the ITS-2 Barcodes using the ITS-2/CBC approach.

  8. 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

  9. SU(2) WZW theory at higher genera

    NASA Astrophysics Data System (ADS)

    Gawędzki, Krzysztof

    1995-05-01

    We compute, by free field techniques, the scalar product of the SU(2) Chern-Simons states on genus >1 surfaces. The result is a finite-dimensional integral over positions of “screening charges” and one complex modular parameter. It uses an effective description of the CS states closely related to the one worked out by Bertram [1]. The scalar product formula allows to express the higher genus partition functions of the WZW conformal field theory by finite-dimensional integrals. It should provide the hermitian metric preserved by the Knizhnik-Zamolodchikov-Bernard connection describing the variations of the CS states under the change of the complex structure of the surface.

  10. 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.

  11. 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

  12. Causal Learning Mechanisms in Very Young Children: Two-, Three-, and Four-Year-Olds Infer Causal Relations from Patterns of Variation and Covariation.

    ERIC Educational Resources Information Center

    Gopnik, Alison; Sobel, David M.; Schulz, Laura E.; Glymour, Clark

    2001-01-01

    Investigated in 3 studies whether 2- to 4-year-olds make accurate causal inferences on the basis of patterns of variation and covariation. Found that all three age groups considered information from various patterns of variation and covariation in judgments regarding two objects and activation of a machine. Three- and 4-year-olds used the…

  13. Inference Generation during Discourse and Its Relation to Social Competence: An Online Investigation of Abilities of Children with and without Language Impairment

    ERIC Educational Resources Information Center

    Ford, Janet A.; Milosky, Linda A.

    2008-01-01

    Purpose: This study examined whether young children with typical language development (TL) and children with language impairment (LI) make emotion inferences online during the process of discourse comprehension, identified variables that predict emotion inferencing, and explored the relationship of these variables to social competence. Method:…

  14. 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

  15. 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

  16. Incomplete Lineage Sorting Is Common in Extant Gibbon Genera

    PubMed Central

    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. PMID:23341974

  17. 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.

  18. 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

  19. Phylogenetics and biogeography of the dung beetle genus Onthophagus inferred from mitochondrial genomes.

    PubMed

    Breeschoten, Thijmen; Doorenweerd, Camiel; Tarasov, Sergei; Vogler, Alfried P

    2016-12-01

    Phylogenetic relationships of dung beetles in the tribe Onthophagini, including the species-rich, cosmopolitan genus Onthophagus, were inferred using whole mitochondrial genomes. Data were generated by shotgun sequencing of mixed genomic DNA from >100 individuals on 50% of an Illumina MiSeq flow cell. Genome assembly of the mixed reads produced contigs of 74 (nearly) complete mitogenomes. The final dataset included representatives of Onthophagus from all biogeographic regions, closely related genera of Onthophagini, and the related tribes Onitini and Oniticellini. The analysis defined four major clades of Onthophagini, which was paraphyletic for Oniticellini, with Onitini as sister group to all others. Several (sub)genera considered as members of Onthophagus in the older literature formed separate deep lineages. All New World species of Onthophagus formed a monophyletic group, and the Australian taxa are confined to a single or two closely related clades, one of which forms the sister group of the New World species. Dating the tree by constraining the basal splits with existing calibrations of Scarabaeoidea suggests an origin of Onthophagini sensu lato in the Eocene and a rapid spread from an African ancestral stock into the Oriental region, and secondarily to Australia and the Americas at about 20-24 Mya. The successful assembly of mitogenomes and the well-supported tree obtained from these sequences demonstrates the power of shotgun sequencing from total genomic DNA of species pools as an efficient tool in genus-level phylogenetics.

  20. 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.).

  1. Inferring Learners' Knowledge from Their Actions

    ERIC Educational Resources Information Center

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

    2015-01-01

    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…

  2. Multiple Instance Fuzzy Inference

    DTIC Science & Technology

    2015-12-02

    INFERENCE A novel fuzzy learning framework that employs fuzzy inference to solve the problem of multiple instance learning (MIL) is presented. The...fuzzy learning framework that employs fuzzy inference to solve the problem of multiple instance learning (MIL) is presented. The framework introduces a...or learned from data. In multiple instance problems, the training data is ambiguously labeled. Instances are grouped into bags, labels of bags are

  3. 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

  4. 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...

  5. 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

  6. Total meltwater volume since the Last Glacial Maximum and viscosity structure of Earth's mantle inferred from relative sea level changes at Barbados and Bonaparte Gulf and GIA-induced J˙2

    NASA Astrophysics Data System (ADS)

    Nakada, Masao; Okuno, Jun'ichi; Yokoyama, Yusuke

    2016-02-01

    Inference of globally averaged eustatic sea level (ESL) rise since the Last Glacial Maximum (LGM) highly depends on the interpretation of relative sea level (RSL) observations at Barbados and Bonaparte Gulf, Australia, which are sensitive to the viscosity structure of Earth's mantle. Here we examine the RSL changes at the LGM for Barbados and Bonaparte Gulf ({{RSL}}_{{L}}^{{{Bar}}} and {{RSL}}_{{L}}^{{{Bon}}}), differential RSL for both sites (Δ {{RSL}}_{{L}}^{{{Bar}},{{Bon}}}) and rate of change of degree-two harmonics of Earth's geopotential due to glacial isostatic adjustment (GIA) process (GIA-induced J˙2) to infer the ESL component and viscosity structure of Earth's mantle. Differential RSL, Δ {{RSL}}_{{L}}^{{{Bar}},{{Bon}}} and GIA-induced J˙2 are dominantly sensitive to the lower-mantle viscosity, and nearly insensitive to the upper-mantle rheological structure and GIA ice models with an ESL component of about (120-130) m. The comparison between the predicted and observationally derived Δ {{RSL}}_{{L}}^{{{Bar}},{{Bon}}} indicates the lower-mantle viscosity higher than ˜2 × 1022 Pa s, and the observationally derived GIA-induced J˙2 of -(6.0-6.5) × 10-11 yr-1 indicates two permissible solutions for the lower mantle, ˜1022 and (5-10) × 1022 Pa s. That is, the effective lower-mantle viscosity inferred from these two observational constraints is (5-10) × 1022 Pa s. The LGM RSL changes at both sites, {{RSL}}_{{L}}^{{{Bar}}} and {{RSL}}_{{L}}^{{{Bon}}}, are also sensitive to the ESL component and upper-mantle viscosity as well as the lower-mantle viscosity. The permissible upper-mantle viscosity increases with decreasing ESL component due to the sensitivity of the LGM sea level at Bonaparte Gulf ({{RSL}}_{{L}}^{{{Bon}}}) to the upper-mantle viscosity, and inferred upper-mantle viscosity for adopted lithospheric thicknesses of 65 and 100 km is (1-3) × 1020 Pa s for ESL˜130 m and (4-10) × 1020 Pa s for ESL˜125 m. The former solution of (1-3) × 1020

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. Protein inference: A protein quantification perspective.

    PubMed

    He, Zengyou; Huang, Ting; Liu, Xiaoqing; Zhu, Peijun; Teng, Ben; Deng, Shengchun

    2016-08-01

    In mass spectrometry-based shotgun proteomics, protein quantification and protein identification are two major computational problems. To quantify the protein abundance, a list of proteins must be firstly inferred from the raw data. Then the relative or absolute protein abundance is estimated with quantification methods, such as spectral counting. Until now, most researchers have been dealing with these two processes separately. In fact, the protein inference problem can be regarded as a special protein quantification problem in the sense that truly present proteins are those proteins whose abundance values are not zero. Some recent published papers have conceptually discussed this possibility. However, there is still a lack of rigorous experimental studies to test this hypothesis. In this paper, we investigate the feasibility of using protein quantification methods to solve the protein inference problem. Protein inference methods aim to determine whether each candidate protein is present in the sample or not. Protein quantification methods estimate the abundance value of each inferred protein. Naturally, the abundance value of an absent protein should be zero. Thus, we argue that the protein inference problem can be viewed as a special protein quantification problem in which one protein is considered to be present if its abundance is not zero. Based on this idea, our paper tries to use three simple protein quantification methods to solve the protein inference problem effectively. The experimental results on six data sets show that these three methods are competitive with previous protein inference algorithms. This demonstrates that it is plausible to model the protein inference problem as a special protein quantification task, which opens the door of devising more effective protein inference algorithms from a quantification perspective. The source codes of our methods are available at: http://code.google.com/p/protein-inference/.

  12. 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.

  13. Comparative pharmacognostic evaluation of some species of the genera Suaeda and Salsola leaf (Chenopodiaceae).

    PubMed

    Munir, Uzma; Perveen, Anjum; Qamarunnisa, Syeda

    2014-09-01

    The genera Suaeda and Salsola are halophytic plants belong to the family Chenopodiaceae. Species of these genera have been extensively used in traditional medicines against many diseases due to their various bioactive compounds such as carotenoids, vitamins, sterol, phenolic compounds etc. The present research was carried out to establish detailed pharmacognosy of Suaeda fruticosa, Suaeda monoica, Salsola imbricata and Salsola tragus, which included macroscopy, microscopy, physico-chemical parameters and qualitative phytochemical screening of leaf samples extracted with methanol and chloroform. It was observed that macroscopic and microscopic characteristics were diagnostic features and can be used for distinction and identification of these closely related plant species. Phytochemically, these plant species are rich in constituents like anthraquinones, alkaloids, carbohydrates, cardiac glycosides, flavonoids, saponins, phenolic compounds and terpenoids. Physico-chemical parameters revealed that in all investigated plant species; methanol extractive values were higher than that of chloroform. Moreover, total ash values were found to be higher than other acid insoluble and water-soluble ash values, while a considerable amount of moisture was present in the species of both genera. On the basis of pharmacognosy, species of Suaeda were found to be more promising than Salsola. Present investigation will contribute towards establishment of pharmacognostic profile of these medicinally effective plants species.

  14. 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

  15. Reconsideration of the phylogenetic positions of five peritrich genera, Vorticella, Pseudovorticella, Zoothamnopsis, Zoothamnium, and Epicarchesium (Ciliophora, Peritrichia, Sessilida), based on small subunit rRNA gene sequences.

    PubMed

    Li, Lifang; Song, Weibo; Warren, Alan; Shin, Mann Kyoon; Chen, Zigui; Ji, Daode; Sun, Ping

    2008-01-01

    In order to re-evaluate the systematics of sessilid peritrich ciliates, small subunit (SSU) rRNA gene sequences were determined for 12 species belonging to five genera: Vorticella, Pseudovorticella, Epicarchesium, Zoothamnium, and Zoothamnopsis. Phylogenetic trees were deduced using Bayesian inference, maximum parsimony, and maximum likelihood methods. The phylogenetic analyses suggest that (1) sessilids which have stalks with continuous myonemes that contract in a zig-zag fashion form a separate clade from those which have stalks that contract independently and in a spiral fashion, supporting the separation of the family Zoothamniidae from the family Vorticellidae and (2) Epicarchesium and Pseudovorticella, both of which have reticulate silverline systems, are more closely related to each other than to other vorticellids, suggesting that differences in the silverline system (i.e. transverse vs. reticulate) may be the result of genuine evolutionary divergence among sessilid peritrichs. However, the newly sequenced Zoothamnopsis sinica, which has a reticulate silverline pattern, nests within the unresolved Zoothamnium species that have transverse silverline patterns. Thus, there were at least two evolutions of the reticulate silverline pattern character state from a plesiomorphic transverse state in the peritrichid ciliates. The molecular work demonstrates the genus Zoothamnium to be paraphyletic in relation to morphological studies, and suggests that Astylozoon, Opisthonecta, and Vorticella microstoma possibly share a SSU rRNA secondary structure in the helix E10-1 region.

  16. Inference of reversible tree languages.

    PubMed

    López, Damián; Sempere, José M; García, Pedro

    2004-08-01

    In this paper, we study the notion of k-reversibility and k-testability when regular tree languages are involved. We present an inference algorithm for learning a k-testable tree language that runs in polynomial time with respect to the size of the sample used. We also study the tree language classes in relation to other well known ones, and some properties of these languages are proven.

  17. Social Inference Through Technology

    NASA Astrophysics Data System (ADS)

    Oulasvirta, Antti

    Awareness cues are computer-mediated, real-time indicators of people’s undertakings, whereabouts, and intentions. Already in the mid-1970 s, UNIX users could use commands such as “finger” and “talk” to find out who was online and to chat. The small icons in instant messaging (IM) applications that indicate coconversants’ presence in the discussion space are the successors of “finger” output. Similar indicators can be found in online communities, media-sharing services, Internet relay chat (IRC), and location-based messaging applications. But presence and availability indicators are only the tip of the iceberg. Technological progress has enabled richer, more accurate, and more intimate indicators. For example, there are mobile services that allow friends to query and follow each other’s locations. Remote monitoring systems developed for health care allow relatives and doctors to assess the wellbeing of homebound patients (see, e.g., Tang and Venables 2000). But users also utilize cues that have not been deliberately designed for this purpose. For example, online gamers pay attention to other characters’ behavior to infer what the other players are like “in real life.” There is a common denominator underlying these examples: shared activities rely on the technology’s representation of the remote person. The other human being is not physically present but present only through a narrow technological channel.

  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. 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.

  20. 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.

  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. Two new species in the endemic Chinese leafhopper genera Flexocerus and Idioceroides (Hemiptera: Cicadellidae: Idiocerinae).

    PubMed

    Xue, Qingquan; Zhang, Yalin

    2015-02-24

    Two new species of endemic Chinese leafhopper genera (Flexocerus Kuoh & Fang and Idioceroides Matsumura), F. sinuatus sp. nov. and I. petaliformis sp. nov. are described and illustrated. Keys to species for both genera are provided.

  3. Capulavirus and Grablovirus: two new genera in the family Geminiviridae.

    PubMed

    Varsani, Arvind; Roumagnac, Philippe; Fuchs, Marc; Navas-Castillo, Jesús; Moriones, Enrique; Idris, Ali; Briddon, Rob W; Rivera-Bustamante, Rafael; Murilo Zerbini, F; Martin, Darren P

    2017-02-17

    Geminiviruses are plant-infecting single-stranded DNA viruses that occur in most parts of the world. Currently, there are seven genera within the family Geminiviridae (Becurtovirus, Begomovirus, Curtovirus, Eragrovirus, Mastrevirus, Topocuvirus and Turncurtovirus). The rate of discovery of new geminiviruses has increased significantly over the last decade as a result of new molecular tools and approaches (rolling-circle amplification and deep sequencing) that allow for high-throughput workflows. Here, we report the establishment of two new genera: Capulavirus, with four new species (Alfalfa leaf curl virus, Euphorbia caput-medusae latent virus, French bean severe leaf curl virus and Plantago lanceolata latent virus), and Grablovirus, with one new species (Grapevine red blotch virus). The aphid species Aphis craccivora has been shown to be a vector for Alfalfa leaf curl virus, and the treehopper species Spissistilus festinus is the likely vector of Grapevine red blotch virus. In addition, two highly divergent groups of viruses found infecting citrus and mulberry plants have been assigned to the new species Citrus chlorotic dwarf associated virus and Mulberry mosaic dwarf associated virus, respectively. These species have been left unassigned to a genus by the ICTV because their particle morphology and insect vectors are unknown.

  4. 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.

  5. 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.

  6. Phylogeny of the Baldratiina (Diptera: Cecidomyiidae) inferred from morphological, ecological and molecular data sources, and evolutionary patterns in plant-galler relationships.

    PubMed

    Dorchin, Netta; Freidberg, Amnon; Mokady, Ofer

    2004-03-01

    The phylogeny of the gall-midge subtribe Baldratiina (Diptera: Cecidomyiidae) was reconstructed from molecular (partial sequence of the mitochondrial 12S rDNA), morphological and ecological data sets, using 16 representative species of most of the genera. The morphological and ecological data were combined in a single character matrix and analyzed separately from the molecular data, resulting in an eco-morphological cladogram and a molecular cladogram. Attributes of galls and host associations were superimposed on the molecular cladogram in order to detect possible trends in the evolution of these traits. The cladograms resulting from the two independent analyses were statistically incongruent, although both provide evidence for the monophyly of the genera Baldratia and Careopalpis and the paraphyly of the genera Stefaniola and Izeniola. The results suggest a minor impact of the morphological characters traditionally used in the classification of the Baldratiina, whereas ecological data had a major impact on the phylogenetic inference. Mapping of gall and host attributes on the molecular cladogram suggests that multi-chambered stem galls constitute the ancestral state in the subtribe, with several subsequent shifts to leaf galls. It is concluded that in contrast to other studied groups of gall insects, related baldratiine species induce different types of galls, attesting to speciation driven by gall-type shifts at least as often as host shifts.

  7. Inference as Prediction

    ERIC Educational Resources Information Center

    Watson, Jane

    2007-01-01

    Inference, or decision making, is seen in curriculum documents as the final step in a statistical investigation. For a formal statistical enquiry this may be associated with sophisticated tests involving probability distributions. For young students without the mathematical background to perform such tests, it is still possible to draw informal…

  8. 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.

  9. 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.

  10. World reclassification of the Gonatocerus group of genera (Hymenoptera: Mymaridae).

    PubMed

    Huber, John T

    2015-06-08

    The 400+ nominal species of the worldwide genus Gonatocerus Nees are reclassified into 14 genera that are placed in Gonatocerini, which is defined by three putative autapomorphies. A key to the 13 extant genera of Gonatocerini is given, based on females. Five previously described genus-group taxa are recognized: Cosmocomoidea Howard stat. rev. (= ater group, of authors), Gahanopsis Ogloblin stat. rev. (= deficiens group, of authors), Gastrogonatocerus Ogloblin stat. n. (= membraciphagus group, of authors), Gonatocerus (= sulphuripes group, of authors), and Lymaenon Walker stat. rev. (= litoralis group, of authors). One new fossil genus, Archigonatocerus Huber gen. n., with two fossil species, A. balticus Huber sp. n., and A. longivena Huber sp. n. and one fossil species in Gonatocerus, G. janzeni Huber sp. n., are described, all from Baltic amber from the Eocene epoch. Eight new extant genera and 16 new extant species are described and their species keyed: Cosmocomopsis Huber gen. n., with C. flopsis Huber sp. n. and C. mopsis Huber sp. n.; Heptagonatocerus Huber gen. n., with H. madagascarensis Huber sp. n., H. magnificus Huber sp. n., H. parvus Huber sp. n., and H. pulchellus Huber sp. n.; Krateriske Huber gen. n., with K. ecuadorensis Huber sp. n., K. guianensis Huber sp. n., and K. peruensis Huber sp. n.; Octomicromeris Huber gen. n., with O. compacta Huber sp. n. and O. brevis Huber sp. n.; Pro-gonatocerus Huber gen. n., with P. albiclava Huber sp. n. and P. brunneiclava Huber sp. n; Tanyxiphium Huber gen. n., with T. breviovipositor Huber sp. n., T. longissimum Huber sp. n., and T. seychellense Huber sp. n. Yoshimotoana Huber gen. n. (= masneri group, of authors) with one included species and Zeyanus Huber, gen. n. (= asulcifrons group, of authors) with 9 included species. Keys to the species of seven genera: Archigonatocerus, Cosmocomopsis, Heptagonatocerus, Krateriske, Octomicromeris, Progonatocerus, and Tanyxiphium are provided. Information for each

  11. Identification and characterization of antimicrobial activity in two yeast genera.

    PubMed Central

    Bilinski, C A; Innamorato, G; Stewart, G G

    1985-01-01

    A general screening test for the expression of antibacterial activity was performed on over 400 cultures belonging to 31 yeast genera. Of these cultures, only two, Kluyveromyces thermotolerans and Kloeckera apiculata, were found to produce zones of inhibition of bacterial growth on Diagnostic Sensitivity Test Agar medium supplemented with 0.002% methylene blue. Of nine bacteria used as test organisms, only Lactobacillus plantarum and Bacillus megaterium were inhibited. No antibacterial activity was evident against four gram-negative bacteria used in this study. Optimal activities were found to be expressed after yeasts were grown at pH 6. A requirement for cultivation in the presence of methylene blue added to culture media for the expression of apparent antibacterial activity was demonstrated. Images PMID:3937494

  12. 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

    2016-08-10

    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.

  13. The boundaries of language and thought in deductive inference.

    PubMed

    Monti, Martin M; Parsons, Lawrence M; Osherson, Daniel N

    2009-07-28

    Is human thought fully embedded in language, or do some forms of thought operate independently? To directly address this issue, we focus on inference-making, a central feature of human cognition. In a 3T fMRI study we compare logical inferences relying on sentential connectives (e.g., not, or, if ... then) to linguistic inferences based on syntactic transformation of sentences involving ditransitive verbs (e.g., give, say, take). When contrasted with matched grammaticality judgments, logic inference alone recruited "core" regions of deduction [Brodmann area (BA) 10p and 8m], whereas linguistic inference alone recruited perisylvian regions of linguistic competence, among others (BA 21, 22, 37, 39, 44, and 45 and caudate). In addition, the two inferences commonly recruited a set of general "support" areas in frontoparietal cortex (BA 6, 7, 8, 40, and 47). The results indicate that logical inference is not embedded in natural language and confirm the relative modularity of linguistic processes.

  14. 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

  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. The role of causal models in analogical inference.

    PubMed

    Lee, Hee Seung; Holyoak, Keith J

    2008-09-01

    Computational models of analogy have assumed that the strength of an inductive inference about the target is based directly on similarity of the analogs and in particular on shared higher order relations. In contrast, work in philosophy of science suggests that analogical inference is also guided by causal models of the source and target. In 3 experiments, the authors explored the possibility that people may use causal models to assess the strength of analogical inferences. Experiments 1-2 showed that reducing analogical overlap by eliminating a shared causal relation (a preventive cause present in the source) from the target increased inductive strength even though it decreased similarity of the analogs. These findings were extended in Experiment 3 to cross-domain analogical inferences based on correspondences between higher order causal relations. Analogical inference appears to be mediated by building and then running a causal model. The implications of the present findings for theories of both analogy and causal inference are discussed.

  17. Optical Inference Machines

    DTIC Science & Technology

    1988-06-27

    de olf nessse end Id e ;-tl Sb ieeI smleo) ,Optical Artificial Intellegence ; Optical inference engines; Optical logic; Optical informationprocessing...common. They arise in areas such as expert systems and other artificial intelligence systems. In recent years, the computer science language PROLOG has...cal processors should in principle be well suited for : I artificial intelligence applications. In recent years, symbolic logic processing. , the

  18. Active inference and learning.

    PubMed

    Friston, Karl; FitzGerald, Thomas; Rigoli, Francesco; Schwartenbeck, Philipp; O'Doherty, John; Pezzulo, Giovanni

    2016-09-01

    This paper offers an active inference account of choice behaviour and learning. It focuses on the distinction between goal-directed and habitual behaviour and how they contextualise each other. We show that habits emerge naturally (and autodidactically) from sequential policy optimisation when agents are equipped with state-action policies. In active inference, behaviour has explorative (epistemic) and exploitative (pragmatic) aspects that are sensitive to ambiguity and risk respectively, where epistemic (ambiguity-resolving) behaviour enables pragmatic (reward-seeking) behaviour and the subsequent emergence of habits. Although goal-directed and habitual policies are usually associated with model-based and model-free schemes, we find the more important distinction is between belief-free and belief-based schemes. The underlying (variational) belief updating provides a comprehensive (if metaphorical) process theory for several phenomena, including the transfer of dopamine responses, reversal learning, habit formation and devaluation. Finally, we show that active inference reduces to a classical (Bellman) scheme, in the absence of ambiguity.

  19. 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).

  20. Seasonal and genera-specific variations in semen availability and semen characteristics in large parrots.

    PubMed

    Bublat, A; Fischer, D; Bruslund, S; Schneider, H; Meinecke-Tillmann, S; Wehrend, A; Lierz, M

    2017-03-15

    In large parrots electro-stimulation is suitable for collecting semen, and therefore, to facilitate semen examination and artificial insemination. Previous studies have detected differences in the semen collection success rate and semen parameters between psittacine genera. It remained unclear whether these differences were genera-related, seasonal variations or depend on the males' relationship status. To answer these questions, semen collection and spermatological analysis were performed for four psittacine groups (macaws, amazons, eclectus parrots and cockatoos) over 13 months. In one breeding facility, semen collection was attempted in 82 males using electro-stimulation twice monthly. A complete spermatological evaluation was performed on 435 semen samples. Volume, color, consistency, contamination and pH of semen, as well as motility, progressive motility, sperm concentration, total sperm count, viability, and morphology of spermatozoa were evaluated. Seasonality affected the collection success rate in macaws and amazons. Thereby, in amazons a distinct peak was observed several days before and around oviposition, whereas eclectus parrots and cockatoos produced semen all year round. The average sperm concentration was highest in eclectus parrots (2.7 × 10(6) sperm/μl) and lowest in macaws (35.6 × 10(3) sperm/μl). The differences in the semen collection success rate and semen parameters seem to coincide with the bird's breeding biology. The collected data allows a prognostic estimation when semen collection seems favorable, and may be taken as orientation values for semen analysis in these species.

  1. 18S rDNA phylogeny of lamproderma and allied genera (Stemonitales, Myxomycetes, Amoebozoa).

    PubMed

    Fiore-Donno, Anna Maria; Kamono, Akiko; Meyer, Marianne; Schnittler, Martin; Fukui, Manabu; Cavalier-Smith, Thomas

    2012-01-01

    The phylogenetic position of the slime-mould genus Lamproderma (Myxomycetes, Amoebozoa) challenges traditional taxonomy: although it displays the typical characters of the order Stemonitales, it appears to be sister to Physarales. This study provides a small subunit (18S or SSU) ribosomal RNA gene-based phylogeny of Lamproderma and its allies, with new sequences from 49 specimens in 12 genera. We found that the order Stemonitales and Lamproderma were both ancestral to Physarales and that Lamproderma constitutes several clades intermingled with species of Diacheopsis, Colloderma and Elaeomyxa. We suggest that these genera may have evolved from Lamproderma by multiple losses of fruiting body stalks and that many taxonomic revisions are needed. We found such high genetic diversity within three Lamproderma species that they probably consist of clusters of sibling species. We discuss the contrasts between genetic and morphological divergence and implications for the morphospecies concept, highlighting the phylogenetically most reliable morphological characters and pointing to others that have been overestimated. In addition, we showed that the first part (~600 bases) of the SSU rDNA gene is a valuable tool for phylogeny in Myxomycetes, since it displayed sufficient variability to distinguish closely related taxa and never failed to cluster together specimens considered of the same species.

  2. 18S rDNA Phylogeny of Lamproderma and Allied Genera (Stemonitales, Myxomycetes, Amoebozoa)

    PubMed Central

    Fiore-Donno, Anna Maria; Kamono, Akiko; Meyer, Marianne; Schnittler, Martin; Fukui, Manabu; Cavalier-Smith, Thomas

    2012-01-01

    The phylogenetic position of the slime-mould genus Lamproderma (Myxomycetes, Amoebozoa) challenges traditional taxonomy: although it displays the typical characters of the order Stemonitales, it appears to be sister to Physarales. This study provides a small subunit (18S or SSU) ribosomal RNA gene-based phylogeny of Lamproderma and its allies, with new sequences from 49 specimens in 12 genera. We found that the order Stemonitales and Lamproderma were both ancestral to Physarales and that Lamproderma constitutes several clades intermingled with species of Diacheopsis, Colloderma and Elaeomyxa. We suggest that these genera may have evolved from Lamproderma by multiple losses of fruiting body stalks and that many taxonomic revisions are needed. We found such high genetic diversity within three Lamproderma species that they probably consist of clusters of sibling species. We discuss the contrasts between genetic and morphological divergence and implications for the morphospecies concept, highlighting the phylogenetically most reliable morphological characters and pointing to others that have been overestimated. In addition, we showed that the first part (∼600 bases) of the SSU rDNA gene is a valuable tool for phylogeny in Myxomycetes, since it displayed sufficient variability to distinguish closely related taxa and never failed to cluster together specimens considered of the same species. PMID:22530009

  3. 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.

  4. Description of two genera and species of late Eocene Anthropoidea from Egypt.

    PubMed

    Simons, E L

    1989-12-01

    In 1987 and 1988 fossils of two previously unknown genera and species of Egyptian early Tertiary Anthropoidea were discovered in the Fayum Depression of Egypt. These are much older than all other Fayum, Oligocene primates and are believed to be Eocene in age. These genera, here named Catopithecus and Proteopithecus, come from a new Fayum site, L-41, and resemble Oligopithecus from the Jebel Qatrani Formation (lower sequence) at quarry E. They are here placed with the latter in a subfamily, Oligopithecinae, that is ranked in the Propliopithecidae. The level of L-41 is separated from quarry E by at least one major unconformity and 47 m of section. Only a maxilla of Proteopithecus is known. Its molars and premolars resemble those of later Fayum Propliopithecus and Aegyptopithecus and do not resemble those of Apidium and Parapithecus, all of which come from the Jebel Qatrani Formation, upper sequence. The type specimen of Catopithecus confirms a lower dental formula of 2-1-2-3, as in Catarrhini. These species appear to be the oldest primates undoubtedly related to humans. Their dental anatomy points to a derivation of Anthropoidea from Eocene adapids.

  5. Description of two genera and species of late Eocene Anthropoidea from Egypt.

    PubMed Central

    Simons, E L

    1989-01-01

    In 1987 and 1988 fossils of two previously unknown genera and species of Egyptian early Tertiary Anthropoidea were discovered in the Fayum Depression of Egypt. These are much older than all other Fayum, Oligocene primates and are believed to be Eocene in age. These genera, here named Catopithecus and Proteopithecus, come from a new Fayum site, L-41, and resemble Oligopithecus from the Jebel Qatrani Formation (lower sequence) at quarry E. They are here placed with the latter in a subfamily, Oligopithecinae, that is ranked in the Propliopithecidae. The level of L-41 is separated from quarry E by at least one major unconformity and 47 m of section. Only a maxilla of Proteopithecus is known. Its molars and premolars resemble those of later Fayum Propliopithecus and Aegyptopithecus and do not resemble those of Apidium and Parapithecus, all of which come from the Jebel Qatrani Formation, upper sequence. The type specimen of Catopithecus confirms a lower dental formula of 2-1-2-3, as in Catarrhini. These species appear to be the oldest primates undoubtedly related to humans. Their dental anatomy points to a derivation of Anthropoidea from Eocene adapids. Images PMID:2513576

  6. 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.

  7. 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 Central

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

    2011-01-01

    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 IC50s 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

  8. 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.

  9. 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.

  10. Inferring protein function from genomic sequence: Giardia lamblia expresses a phosphatidylinositol kinase-related kinase similar to yeast and mammalian TOR.

    PubMed

    Morrison, Hilary G; Zamora, Gus; Campbell, Robert K; Sogin, Mitchell L

    2002-12-01

    Functional assays of genes have historically led to insights about the activities of a protein or protein cascade. However, the rapid expansion of genomic and proteomic information for a variety of diverse taxa is an alternative and powerful means of predicting function by comparing the enzymes and metabolic pathways used by different organisms. As part of the Giardia lamblia genome sequencing project, we routinely survey the complement of predicted proteins and compare those found in this putatively early diverging eukaryote with those of prokaryotes and more recently evolved eukaryotic lineages. Such comparisons reveal the minimal composition of conserved metabolic pathways, suggest which proteins may have been acquired by lateral transfer, and, by their absence, hint at functions lost in the transition from a free-living to a parasitic lifestyle. Here, we describe the use of bioinformatic approaches to investigate the complement and conservation of proteins in Giardia involved in the regulation of translation. We compare an FK506 binding protein homologue and phosphatidylinositol kinase-related kinase present in Giardia to those found in other eukaryotes for which complete genomic sequence data are available. Our investigation of the Giardia genome suggests that PIK-related kinases are of ancient origin and are highly conserved.

  11. Relatively rapid emplacement of dome-forming magma inferred from strain analyses: The case of the acid Latian dome complexes (Central Italy)

    NASA Astrophysics Data System (ADS)

    Cimarelli, C.; de Rita, D.

    2006-11-01

    We have analysed the relationship between the volcanic substratum and magma body emplacement for the acid dome complexes of Latium, Central Italy. Our study shows that the volcanic edifices, which are mainly Pleistocene cryptodomes and related explosive products, were derived from mantle magmas contaminated by crustal materials. The Cimini, Tolfa and Cerite-Manziate dome complexes of Latium show the following characteristics: a shallow laccolith origin; emplacement in basins that have identical tectonic evolution and geological structure; the same magmatic composition and density contrast between magma and host rock; and geochronological data that are inconsistent with field evidence. In the Cimini and Tolfa dome complexes, the deformation induced by shallow intrusions was accompanied by ˜ 200 m uplift of the sedimentary cover. The estimated pluton infilling time for the Cimini and Tolfa domes is 10 2 years while the strain rate required to uplift their Pliocene overburden by 200 m is ɛm' ˜ 10 - 9 s - 1 . The rapid evolution of the dome complexes is consistent with field data that show no relevant interruptions in the volcanic activity and no significant compositional changes in the volcanic products related to the extrusion of the domes. For the Cerite-Manziate dome complex, the minimal input rate of magma favoured a monogenetic style of volcanism, independent of the regional stress conditions.

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

    PubMed

    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 mirabilisgen. nov., sp. nov. and Elasticomyces elasticusgen. 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.

  13. 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

  14. 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

  15. 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.

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

    PubMed

    Caterino, Michael S; Tishechkin, Alexey K

    2014-01-01

    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.

  17. 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

  18. New genera, species, and improved phylogeny of Glissomonadida (Cercozoa).

    PubMed

    Howe, Alexis T; Bass, David; Chao, Ema E; Cavalier-Smith, Thomas

    2011-11-01

    Glissomonadida is an important cercozoan order of predominantly biflagellate gliding bacterivores found largely in soil and freshwater. Their vast diversity is largely undescribed. We studied 23 mostly newly isolated strains by light microscopy and sequenced their 18S rDNA genes; nine represent new species. For two misidentified ATCC 'Heteromita triangularis' strains, we establish novel gliding genera and species: the sandonid Mollimonas lacrima, the only glissomonad forming anterior and posterior pseudopodia, and Dujardina stenomorpha, a strongly flattened member of the new family Dujardinidae. A new strain from Oxfordshire grassland soil is the first reliably identified isolate of the virtually uniflagellate, smooth-gliding glissomonad genus, AllantionSandon, 1924. Phylogenetic analysis and cytological features reveal Allantion to be a member of Allapsidae. Sandona limna and Bodomorpha prolixa from Lake Baikal and Sandona hexamutans from volcanic Costa Rican soil are described as new species. Fifteen glissomonad strains were from grassland beside Lake Baikal. We describe two as new species of Sandona (S. heptamutans and S. octamutans); the others included strains of Sandona and Allapsa species that have already been described; and three were new species of Sandona and Allapsa but these died before being described. We discuss the ecological and evolutionary significance of these new strains.

  19. Retropositional events consolidate the branching order among New World monkey genera.

    PubMed

    Osterholz, Martin; Walter, Lutz; Roos, Christian

    2009-03-01

    Due to contradicting relationships obtained from various morphological and genetic studies, phylogenetic relationships among New World monkey genera are highly disputed. In the present study, we analyzed the presence/absence pattern of 128 SINE integrations in all New World monkey genera. Among them, 70 were specific for only a single genus, whereas another 18 were present in all New World monkey genera. The 40 remaining insertions were informative to elucidate phylogenetic relationships among genera. Several of them confirmed the monophyly of the three families Cebidae, Atelidae and Pitheciidae as well as of the subfamily Callithrichinae. Further markers provided evidence for a sister grouping of Cebidae and Atelidae to the exclusion of Pitheciidae as well as for relationships among genera belonging to Callithrichinae and Atelidae. Although a close affiliation of Saimiri, Aotus and Cebus to Callithrichinae was shown, the relationships among the three genera remained unresolved due to three contradicting insertions.

  20. Comparison of Distribution- and Anchor-Based Approaches to Infer Changes in Health-Related Quality of Life of Prostate Cancer Survivors

    PubMed Central

    Jayadevappa, Ravishankar; Malkowicz, Stanley Bruce; Wittink, Marsha; Wein, Alan J; Chhatre, Sumedha

    2012-01-01

    Objective To determine the minimal important difference (MID) in generic and prostate-specific health-related quality of life (HRQoL) using distribution- and anchor-based methods. Study Design and Setting Prospective cohort study of 602 newly diagnosed prostate cancer patients recruited from an urban academic hospital and a Veterans Administration hospital. Participants completed generic (SF-36) and prostate-specific HRQoL surveys at baseline and at 3, 6, 12, and 24 months posttreatment. Anchor-based and distribution-based methods were used to develop MID estimates. We compared the proportion of participants returning to baseline based on MID estimates from the two methods. Results MID estimates derived from combining distribution- and anchor-based methods for the SF-36 subscales are physical function = 7, role physical = 14, role emotional = 12, vitality = 9, mental health = 6, social function = 9, bodily pain = 9, and general health = 8; and for the prostate-specific scales are urinary function = 8, bowel function = 7, sexual function = 8, urinary bother = 9, bowel bother = 8, and sexual bother = 11. Proportions of participants returning to baseline values corresponding to MID estimates from the two methods were comparable. Conclusions This is the first study to assess the MID for generic and prostate-specific HRQoL using anchor-based and distribution-based methods. Although variation exists in the MID estimates derived from these two methods, the recovery patterns corresponding to these estimates were comparable. PMID:22417225

  1. 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.

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

    PubMed

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

    2013-01-01

    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.

  3. Two new genera and two new species of eriophyoid mites (Acari: Eriophyoidea) from North Bengal, India.

    PubMed

    Chakrabarti, Samiran; Sur, Surajit; Roy, Sourav; Sarkar, Sanjay

    2017-02-21

    Two new genera and two new species of eriophyoid mites viz., Propeaciota genusetosis n. gen. and n. sp. infesting Acer sp. (Aceraceae) and Spinaephyes alnus n. gen. and n. sp. infesting Alnus nepalensis D. Don (Betulaceae) are described in the tribe Tegonotini (Eriophyidae: Phyllocoptinae) from North Bengal, India. Aciota secundum Flechtmann et al.1995 is re-assigned (n. comb.) to Propeaciota. Relationships of the new genera with other eriophyoid genera are discussed.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. New genera, species and records of Phaneropterinae (Orthoptera, Phaneropteridae) from sub-Saharan Africa

    PubMed Central

    Massa, Bruno

    2015-01-01

    Abstract The results of the study of many specimens preserved in different European museums are reported. The tribe Terpnistrini Brunner von Wattenwyl, 1878 is resurrected. The distribution of the following species is enhanced: Pardalota asymmetrica Karsch, 1896, Diogena denticulata Chopard, 1954, Diogena fausta (Burmeister, 1838), Plangiopsis adeps Karsch, 1896, Poreuomena sanghensis Massa, 2013 and Tylopsis continua (Walker, 1869). Further, for their peculiar characteristics, two African representatives of the American genus Symmetropleura Brunner von Wattenwyl, 1878 are included in two new genera: Symmetrokarschia africana (Brunner von Wattenwyl, 1878), comb. n. and Symmetroraggea dirempta (Karsch, 1889), comb. n. A new genus and species from the Democratic Republic of Congo, Angustithorax spiniger gen. n., sp. n., and a new genus and species from Tanzania, Arostratum oblitum gen. n., sp. n. are described. Finally Melidia claudiae sp. n. and Atlasacris brevipennis sp. n. are described and compared with related species. PMID:25632250

  15. Directions of strong winds on Mars inferred

    NASA Technical Reports Server (NTRS)

    Howard, A. D.

    1972-01-01

    Asymmetrical crater shadings and diffuse light and dark streaks visible on the photography returned by the 1969 Mars flyby of Mariners 6 and 7 are probably eolian in origin. Wind directions inferred from mapping of these features parallel motions of observed global dust storms or relate to expected patterns of topographic funneling of winds.

  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.

  17. 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.

  18. Cecembia lonarensis gen. nov., sp. nov., a haloalkalitolerant bacterium of the family Cyclobacteriaceae, isolated from a haloalkaline lake and emended descriptions of the genera Indibacter, Nitritalea and Belliella.

    PubMed

    Anil Kumar, P; Srinivas, T N R; Madhu, S; Sravan, R; Singh, Shashi; Naqvi, S W A; Mayilraj, S; Shivaji, S

    2012-09-01

    A novel Gram-staining-negative, rod-shaped, non-motile bacterium, designated strain LW9(T), was isolated from a water sample collected from Lonar Lake of Buldhana district, Maharashtra, India. Colonies and broth cultures were reddish orange due to the presence of carotenoid pigments. Strain LW9(T) was positive for catalase, ornithine decarboxylase and lysine decarboxylase activities and negative for gelatinase, oxidase, urease and lipase activities. The predominant fatty acids were iso-C(15 : 0) (31.3 %), iso-C(16 : 0) (9.3 %), anteiso-C(15 : 0) (7.3 %), iso-C(16 : 1) H (6.1 %), summed feature 3 (comprising C(16 : 1)ω7c/C(16 : 1)ω6c; 5.9 %), iso-C(17 : 1)ω9c (5.4 %) and iso-C(17 : 0) 3-OH (5.0 %). Strain LW9(T) contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids and seven unidentified lipids. The DNA G+C content of strain LW9(T) was 40.5 mol%. 16S rRNA gene sequence analysis indicated that the type strains of Indibacter alkaliphilus and Aquiflexum balticum, two members of the family Cyclobacteriaceae (phylum 'Bacteroidetes') were the most closely related strains with sequence similarities of 93.0 and 94.0 %, respectively. Other members of the family Cyclobacteriaceae showed sequence similarities <93.0 %. Based on these phenotypic characteristics and on phylogenetic inference, strain LW9(T) is proposed as the representative of novel species in a new genus, Cecembia lonarensis gen. nov., sp. nov. The type strain of the type species, Cecembia lonarensis, is LW9(T) (= CCUG 58316(T) = KCTC 22772(T)). Emended descriptions of the genera Indibacter, Nitritalea and Belliella are also proposed.

  19. Molecular characterization of the genera Proteus, Morganella, and Providencia by ribotyping.

    PubMed

    Pignato, S; Giammanco, G M; Grimont, F; Grimont, P A; Giammanco, G

    1999-09-01

    The so-called Proteus-Providencia group is constituted at present by three genera and 10 species. Several of the recognized species are common opportunistic pathogens for humans and animals. Different methods based on the study of phenotypic characters have been used in the past with variable levels of efficiency for typing some species for epidemiological purposes. We have determined the rRNA gene restriction patterns (ribotypes) for the type strains of the 10 different species of the genera Proteus, Morganella, and Providencia. Visual inspection of EcoRV- and HincII-digested DNA from the type strains showed remarkably different patterns for both enzymes, but EcoRV provided better differentiation. Both endonucleases were retained to study a large number of wild and collection strains belonging to the different species. Clinical isolates of Proteus mirabilis, Proteus penneri, Morganella morganii, and Providencia heimbachae showed patterns identical or very similar to those of the respective type strains, so that groups of related patterns (ribogroups) were found to correspond to the diverse species. On the contrary, distinct ribogroups were detected within Providencia alcalifaciens (two ribogroups with both enzymes), Providencia rettgeri (four ribogroups with EcoRV and five with HincII), Providencia stuartii (two ribogroups with EcoRV), Providencia rustigianii (two ribogroups with HincII), and Proteus vulgaris (two ribogroups with both enzymes). The pattern shown by the ancient P. vulgaris type strain NCTC 4175 differed considerably from both P. vulgaris ribogroups as well as from the newly proposed type strain ATCC 29905 and from any other strain in this study, thus confirming its atypical nature. Minor differences were frequently observed among patterns of strains belonging to the same ribogroup. These differences were assumed to define ribotypes within each ribogroup. No correlation was observed between ribogroups or ribotypes and biogroups of P. vulgaris, P

  20. Molecular Characterization of the Genera Proteus, Morganella, and Providencia by Ribotyping

    PubMed Central

    Pignato, S.; Giammanco, G. M.; Grimont, F.; Grimont, P. A. D.; Giammanco, G.

    1999-01-01

    The so-called Proteus-Providencia group is constituted at present by three genera and 10 species. Several of the recognized species are common opportunistic pathogens for humans and animals. Different methods based on the study of phenotypic characters have been used in the past with variable levels of efficiency for typing some species for epidemiological purposes. We have determined the rRNA gene restriction patterns (ribotypes) for the type strains of the 10 different species of the genera Proteus, Morganella, and Providencia. Visual inspection of EcoRV- and HincII-digested DNA from the type strains showed remarkably different patterns for both enzymes, but EcoRV provided better differentiation. Both endonucleases were retained to study a large number of wild and collection strains belonging to the different species. Clinical isolates of Proteus mirabilis, Proteus penneri, Morganella morganii, and Providencia heimbachae showed patterns identical or very similar to those of the respective type strains, so that groups of related patterns (ribogroups) were found to correspond to the diverse species. On the contrary, distinct ribogroups were detected within Providencia alcalifaciens (two ribogroups with both enzymes), Providencia rettgeri (four ribogroups with EcoRV and five with HincII), Providencia stuartii (two ribogroups with EcoRV), Providencia rustigianii (two ribogroups with HincII), and Proteus vulgaris (two ribogroups with both enzymes). The pattern shown by the ancient P. vulgaris type strain NCTC 4175 differed considerably from both P. vulgaris ribogroups as well as from the newly proposed type strain ATCC 29905 and from any other strain in this study, thus confirming its atypical nature. Minor differences were frequently observed among patterns of strains belonging to the same ribogroup. These differences were assumed to define ribotypes within each ribogroup. No correlation was observed between ribogroups or ribotypes and biogroups of P. vulgaris, P

  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. 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.

  3. The Role of Causal Models in Analogical Inference

    ERIC Educational Resources Information Center

    Lee, Hee Seung; Holyoak, Keith J.

    2008-01-01

    Computational models of analogy have assumed that the strength of an inductive inference about the target is based directly on similarity of the analogs and in particular on shared higher order relations. In contrast, work in philosophy of science suggests that analogical inference is also guided by causal models of the source and target. In 3…

  4. Hemispheric inference priming during comprehension of conversations and narratives.

    PubMed

    Powers, Chivon; Bencic, Rachel; Horton, William S; Beeman, Mark

    2012-09-01

    In this study we examined asymmetric semantic activation patterns as people listened to conversations and narratives that promoted causal inferences. Based on the hypothesis that understanding the unique features of conversational input may benefit from or require a modified pattern of conceptual activation during conversation, we compared semantic priming in both hemispheres for inferences embedded in conversations and in narratives. Participants named inference-related target words or unrelated words presented to the left visual field-right hemisphere (lvf-RH) or to the right visual field-left hemisphere (rvf-LH) at critical coherence points that required an inference in order to correctly understand an utterance in the context of the conversation or narrative. Fifty-seven undergraduates listened to 36 conversations or narratives and were tested at 100 target inference points. During narrative comprehension, inference-related priming was reliable and equally strong in both hemispheres. In contrast, during conversation comprehension, inference-related priming was only reliable for target words presented to lvf-RH. This work demonstrates that priming for inference-related concepts can be measured with input in conversational form and suggests the language processing style of the RH is advantageous for comprehending conversation.

  5. Debroyerella gen. nov. and Ulladulla gen. nov., two new lysianassoid genera (Crustacea, Amphipoda, Lysianassoidea).

    PubMed

    Lowry, J K; Kilgallen, N M

    2015-02-19

    Two new genera and a new species of lysianassoid amphipods are described. Debroyerella gen. nov. is described for three Antarctic species previously assigned to the genus Cheirimedon. Ulladulla gen. nov. is described to accommodate the new species U. selje, from Australian waters. Diagnostic descriptions are given for the genera and all species are described in full.

  6. Relationships among genera of the Saccharomycotina (Ascomycota) from multigene phylogenetic analysis of type species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phylogenetic relatedness among ascomycetous yeast genera (subphylum Saccharomycotina, phylum Ascomycota) has been uncertain. In the present study, type species of 70 currently recognized genera are compared from divergence in the nearly entire nuclear gene sequences for large subunit rRNA, small sub...

  7. 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…

  8. 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...

  9. 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…

  10. Eucoilinae of North America: A revised catalog of genera and described species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This is a catalog of North American taxa of Eucoilinae, with little resemblance to previous regional catalogs, which have been lagging behind in the recent systematic work in the group. The current catalog comprises 34 genera, arranged in six tribes. Of these genera, 9 have only unidentified or unde...

  11. 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

  12. 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

  13. 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.

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

    PubMed

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

    2016-01-01

    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.

  15. Definition and Revision of the Orthrius-group of genera (Coleoptera, Cleridae, Clerinae)

    PubMed Central

    Roland, Gerstmeier; Jonas, Eberle

    2011-01-01

    Abstract An “Orthrius-group” of genera is proposed, and defined to include Aphelochroa Quedenfeldt, 1885; Caridopus Schenkling, 1908; Dozocolletus Chevrolat, 1842; Gyponyx Gorham, 1883; Languropilus Pic, 1940; Orthrius Gorham, 1876; Pieleus Pic, 1940; Xenorthrius Gorham, 1892; plus three new genera Neorthrius gen. n., Nonalatus gen. n. and Pseudoastigmus gen. n. A phylogeny of the 11 constituent Orthrius-group genera (analysis of 22 morphological characters using Clerus Geoffroy as the out-group taxon was performed with TNT v1.1) is proposed. Four genera are synonymised: Burgeonus Pic, 1950, syn. n. (with Aphelochroa Quedenfeldt, 1885); Brinckodes Winkler, 1960, syn. n. and Quasibrinckodes Winkler, 1960, syn. n. (both with Dozocolletus Chevrolat, 1842); and Dedana Fairmaire, 1888, syn. n. (with Orthrius Gorham, 1876). The genera Falsoorthrius Pic, 1940 and Mimorthrius Pic, 1940 are transferred from Clerinae to the subfamily Tillinae. PMID:21594111

  16. 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

  17. 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.

  18. 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

  19. Mitogenomics phylogenetic relationships of the current sloth's genera and species (Bradypodidae and Megalonychidae).

    PubMed

    Ruiz-García, Manuel; Chacón, Diego; Plese, Tinka; Schuler, Ingrid; Shostell, Joseph Mark

    2017-01-27

    We sequenced the complete mitogenome of 39 sloths (19 Bradypus variegatus, 4 B. tridactylus, 1 B. pygmaeus, 1 B. torquatus, 4 Choloepus didactylus, and 10 C. hoffmanni). A Bayesian tree (BI) indicated a temporal split between Bradypus and Choloepus around 31 million years ago (MYA, Oligocene) and the other major splits within each genera during the Miocene and Pliocene. A haplotype network (MJN) estimated a lower temporal split between the sloth genera (around 23.5 MYA). Both methods detected the ancestor of B. torquatus as the first to diverge within Bradypus (21 for BI and 19 MJN), followed by that of the ancestor of B. tridactylus. The split of B. pygmaeus from the common ancestor with B. variegatus was around 12 MYA (BI) or 4.3 MYA (MJN). The splits among the previous populations of B. variegatus began around 8 MYA (BI) or 3.6 MYA (MJN). The trans-Andean population was the first to diverge from the remaining cis-Andean populations of B. variegatus. The genetic differentiation of the trans-Andean B. variegatus population relative to the cis-Andean B. variegatus is similar to that found for different species of sloths. The mitogenomic analysis resolved the differentiation of C. hoffmanni from the C. didactylus individuals of the Guiana Shield. However, one C. didactylus from the Colombian Amazon specimen was inside the C. hoffmanni clade. This could be the first example of possible natural hybridization in the Amazon of both Choloepus taxa or the existence of un-differentiable phenotypes of these two species in some Amazonian areas.

  20. 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

    2016-01-15

    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.

  1. 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.…

  2. 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…

  3. 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…

  4. 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

  5. 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

  6. 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.

  7. Right and Left Hemisphere Cooperation for Drawing Predictive and Coherence Inferences during Normal Story Comprehension

    PubMed Central

    Beeman, Mark Jung; Bowden, Edward M.; Gernsbacher, Morton Ann

    2015-01-01

    In three experiments, healthy young participants listened to stories promoting inferences and named inference-related test words presented to the right visual field-Left Hemisphere (rvf-LH) or to the left visual field-Right Hemisphere (lvf-RH). Participants showed priming for predictive inferences only for target words presented to the lvf-RH; in contrast, they showed priming for coherence inferences only for target words presented to the rvf-LH. These results, plus the fact that patients with RH brain damage have difficulty drawing coherence inferences and do not show inference-related priming, suggest that information capable of supporting predictive inferences is more likely to be initially activated in the RH than the LH, but following coherence breaks these concepts (now coherence inferences) are completed in the LH. These results are consistent with the theory that the RH engages in relatively coarse semantic coding, which aids full comprehension of discourse. PMID:10716864

  8. A morphology based key to the genera of the tribe Nemoriini (Lepidoptera: Geometridae, Geometrinae).

    PubMed

    Viidalepp, Jaan

    2017-02-23

    A diagrammatic key to the genera of the Nemoriini tribe (Lepidoptera, Geometridae) is presented and illustrated. The genera studied exhibit two main character sets, corresponding to the Nemoria lineage and the Phrudocentra lineage. The spatulate type of uncus is associated with multicolor wing markings on both hemispheres. A rod-shaped uncus, often slightly bulbed at its tip, is common in the Neotropics, the genera involved having their wing markings reduced to white lines or brown-grey vein marks on a plain green ground color.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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...

  14. Air-borne fungi in the air of Barcelona (Spain). IV. Various isolated genera.

    PubMed

    Calvo, M A; Guarro, J; Suarez, G; Ramírez, C

    1980-07-01

    During a two-year survey on the air-borne fungi in the atmosphere of Barcelona (Spain), the following genera were isolated in decreasing order: Aureobasidium, Rhizopus, Mucor, Arthrinium, Phoma, Fusarium, Trichoderma, and Botrytis.

  15. 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.

  16. Unified Theory of Inference for Text Understanding

    DTIC Science & Technology

    1986-11-25

    reataurant script is recognized, script application would lead to inferences such as identifying the waiter as ’ ’the waiter who is employed by the...relations between the objects. Objects have names as a convenience for the system modeler, but the names are not used for purposes other than...intent is that we can consider talking to be a frame with a talker slot which must be filled by a person. This is just a convenient notation; the

  17. A review of the families and genera of the superfamily PLATYSCELOIDEA Bowman & Gruner, 1973 (Crustacea: Amphipoda: Hyperiidea), together with keys to the families, genera and species.

    PubMed

    Zeidler, Wolfgang

    2016-11-13

    The systematics and phylogenetic relationships of the families and genera of the superfamily Platysceloidea are examined, following a thorough examination of the morphology of an example of the type species of each genus, or a substitute species if the true identity of the type species is in doubt. The mouthparts are described for each type species, often for the first time, providing additional characters for phylogenetic analysis. Genera are diagnosed using the taxonomic database program DELTA (Dalwitz et al. 1999). This database is also used for a phylogenetic analysis of the genera using PAUP (Swofford 2000). Proposed taxonomic changes resulting from this study are summarised as follows. The family Pronoidae is restricted to the monotypic genus Pronoe because it has some unique characters not found in any other platysceloidean. Paralycaea, previously in Pronoidae, has characters in common with Amphithyrus and Amphithyropsis gen. nov., a new genus proposed for Paralycaea platycephala Zeidler, 1998 (here re-determined a junior synonym of Tetrathyrus pulchellus Barnard, 1930), and together they form the proposed new family Amphithyridae fam. nov. Eupronoe and Parapronoe, also previously in Pronoidae, are similar in the morphology of the mouthparts, antennae and gnathopoda, and together form the proposed new family Eupronoidae fam. nov. The family Brachyscelidae is restricted to the genus Brachyscelus because Thamneus, previously included in Brachyscelidae, has a number of characters that differ considerably from any other genus of Hyperiidea and it is therefore placed in a family of its own, Thamneidae fam. nov. The status of the family Anapronoidae, for Anapronoe, is confirmed, as is the status of the family Tryphanidae for Tryphana. The family Lycaeidae is limited to Lycaea and Simorhynchotus. The family Oxycephalidae maybe polyphyletic but more work is required to resolve the systematic status of the eight genera currently recognised. Metalycaea globosa

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. Bayesian Inference of Galaxy Morphology

    NASA Astrophysics Data System (ADS)

    Yoon, Ilsang; Weinberg, M.; Katz, N.

    2011-01-01

    Reliable inference on galaxy morphology from quantitative analysis of ensemble galaxy images is challenging but essential ingredient in studying galaxy formation and evolution, utilizing current and forthcoming large scale surveys. To put galaxy image decomposition problem in broader context of statistical inference problem and derive a rigorous statistical confidence levels of the inference, I developed a novel galaxy image decomposition tool, GALPHAT (GALaxy PHotometric ATtributes) that exploits recent developments in Bayesian computation to provide full posterior probability distributions and reliable confidence intervals for all parameters. I will highlight the significant improvements in galaxy image decomposition using GALPHAT, over the conventional model fitting algorithms and introduce the GALPHAT potential to infer the statistical distribution of galaxy morphological structures, using ensemble posteriors of galaxy morphological parameters from the entire galaxy population that one studies.

  3. 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…

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

    PubMed

    Mtwana Nordlund, Lina; Koch, Evamaria W; 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.

  5. 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

  6. 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

  7. Statistical Inference in Graphical Models

    DTIC Science & Technology

    2008-06-17

    Probabilistic Network Library ( PNL ). While not fully mature, PNL does provide the most commonly-used algorithms for inference and learning with the efficiency...of C++, and also offers interfaces for calling the library from MATLAB and R 1361. Notably, both BNT and PNL provide learning and inference algorithms...mature and has been used for research purposes for several years, it is written in MATLAB and thus is not suitable to be used in real-time settings. PNL

  8. Statistical Inference: The Big Picture.

    PubMed

    Kass, Robert E

    2011-02-01

    Statistics has moved beyond the frequentist-Bayesian controversies of the past. Where does this leave our ability to interpret results? I suggest that a philosophy compatible with statistical practice, labelled here statistical pragmatism, serves as a foundation for inference. Statistical pragmatism is inclusive and emphasizes the assumptions that connect statistical models with observed data. I argue that introductory courses often mis-characterize the process of statistical inference and I propose an alternative "big picture" depiction.

  9. 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.

  10. Inferring the Why in Images

    DTIC Science & Technology

    2014-01-01

    images. To our knowledge, this challenging problem has not yet been extensively explored in computer vision. We present a novel learning based...automatically infers why people are performing actions in images by learning from visual data and written language. ∗denotes equal contribution 1 Report...explored in computer vision. We present a novel learning based framework that uses high-level visual recognition to infer why people are performing

  11. Spatial Patterns and Associations between Species Belonging to Four Genera of the Lauraceae Family

    PubMed Central

    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

  12. 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.

  13. 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

  14. 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.

  15. Causal inference and developmental psychology.

    PubMed

    Foster, E Michael

    2010-11-01

    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 the risk factor actually causes outcomes. Random assignment is not possible in many instances, and for that reason, psychologists must rely on observational studies. Such studies identify associations, and causal interpretation of such associations requires additional assumptions. Research in developmental psychology generally has relied on various forms of linear regression, but this methodology has limitations for causal inference. Fortunately, methodological developments in various fields are providing new tools for causal inference-tools that rely on more plausible assumptions. This article describes the limitations of regression for causal inference and describes how new tools might offer better causal inference. This discussion highlights the importance of properly identifying covariates to include (and exclude) from the analysis. This discussion considers the directed acyclic graph for use in accomplishing this task. With the proper covariates having been chosen, many of the available methods rely on the assumption of "ignorability." The article discusses the meaning of ignorability and considers alternatives to this assumption, such as instrumental variables estimation. Finally, the article considers the use of the tools discussed in the context of a specific research question, the effect of family structure on child development.

  16. Inferring Trust Based on Similarity with TILLIT

    NASA Astrophysics Data System (ADS)

    Tavakolifard, Mozhgan; Herrmann, Peter; Knapskog, Svein J.

    A network of people having established trust relations and a model for propagation of related trust scores are fundamental building blocks in many of today’s most successful e-commerce and recommendation systems. However, the web of trust is often too sparse to predict trust values between non-familiar people with high accuracy. Trust inferences are transitive associations among users in the context of an underlying social network and may provide additional information to alleviate the consequences of the sparsity and possible cold-start problems. Such approaches are helpful, provided that a complete trust path exists between the two users. An alternative approach to the problem is advocated in this paper. Based on collaborative filtering one can exploit the like-mindedness resp. similarity of individuals to infer trust to yet unknown parties which increases the trust relations in the web. For instance, if one knows that with respect to a specific property, two parties are trusted alike by a large number of different trusters, one can assume that they are similar. Thus, if one has a certain degree of trust to the one party, one can safely assume a very similar trustworthiness of the other one. In an attempt to provide high quality recommendations and proper initial trust values even when no complete trust propagation path or user profile exists, we propose TILLIT — a model based on combination of trust inferences and user similarity. The similarity is derived from the structure of the trust graph and users’ trust behavior as opposed to other collaborative-filtering based approaches which use ratings of items or user’s profile. We describe an algorithm realizing the approach based on a combination of trust inferences and user similarity, and validate the algorithm using a real large-scale data-set.

  17. Scope Ambiguity and Inference

    DTIC Science & Technology

    1991-07-01

    sentence (1) is followed by sentence (4), and that the system is able to conclude that her is anaphoric to an undergrad in (1). It could immediately conclude...the system is able to conclude that her in the second sentence is anaphoric to an undergrad in the first sentence, it will also be able to conclude... anaphoric relations [Schubert and Pelletier, 1988; Groenendijk and Stokhof, 1990]. 4.2 A Relational Semantics for DRT The Syntax of DRT0 The set of

  18. Evolution of bidirectional sex change and gonochorism in fishes of the gobiid genera Trimma, Priolepis, and Trimmatom.

    PubMed

    Sunobe, Tomoki; Sado, Tetsuya; Hagiwara, Kiyoshi; Manabe, Hisaya; Suzuki, Toshiyuki; Kobayashi, Yasuhisa; Sakurai, Makoto; Dewa, Shin-Ichi; Matsuoka, Midori; Shinomiya, Akihiko; Fukuda, Kazuya; Miya, Masaki

    2017-04-01

    Size-advantage and low-density models have been used to explain how mating systems favor hermaphroditism or gonochorism. However, these models do not indicate historical transitions in sexuality. Here, we investigate the evolution of bidirectional sex change and gonochorism by phylogenetic analysis using the mitochondrial gene of the gobiids Trimma (31 species), Priolepis (eight species), and Trimmatom (two species). Trimma and Priolepis formed a clade within the sister group Trimmatom. Gonadal histology and rearing experiments revealed that Trimma marinae, Trimma nasa, and Trimmatom spp. were gonochoric, whereas all other Trimma and Priolepis spp. were bidirectional sex changers or inferred ones. A maximum-likelihood reconstruction analysis demonstrated that the common ancestor of the three genera was gonochoristic. Bidirectional sex change probably evolved from gonochorism in a common ancestor of Trimma and Priolepis. As the gonads of bidirectional sex changers simultaneously contain mature ovarian and immature testicular components or vice versa, individuals are always potentially capable of functioning as females or males, respectively. Monogamy under low-density conditions may have been the ecological condition for the evolution of bidirectional sex change in a common ancestor. As T. marinae and T. nasa are a monophyletic group, gonochorism should have evolved from bidirectional sex change in a common ancestor.

  19. Evolution of bidirectional sex change and gonochorism in fishes of the gobiid genera Trimma, Priolepis, and Trimmatom

    NASA Astrophysics Data System (ADS)

    Sunobe, Tomoki; Sado, Tetsuya; Hagiwara, Kiyoshi; Manabe, Hisaya; Suzuki, Toshiyuki; Kobayashi, Yasuhisa; Sakurai, Makoto; Dewa, Shin-ichi; Matsuoka, Midori; Shinomiya, Akihiko; Fukuda, Kazuya; Miya, Masaki

    2017-04-01

    Size-advantage and low-density models have been used to explain how mating systems favor hermaphroditism or gonochorism. However, these models do not indicate historical transitions in sexuality. Here, we investigate the evolution of bidirectional sex change and gonochorism by phylogenetic analysis using the mitochondrial gene of the gobiids Trimma (31 species), Priolepis (eight species), and Trimmatom (two species). Trimma and Priolepis formed a clade within the sister group Trimmatom. Gonadal histology and rearing experiments revealed that Trimma marinae, Trimma nasa, and Trimmatom spp. were gonochoric, whereas all other Trimma and Priolepis spp. were bidirectional sex changers or inferred ones. A maximum-likelihood reconstruction analysis demonstrated that the common ancestor of the three genera was gonochoristic. Bidirectional sex change probably evolved from gonochorism in a common ancestor of Trimma and Priolepis. As the gonads of bidirectional sex changers simultaneously contain mature ovarian and immature testicular components or vice versa, individuals are always potentially capable of functioning as females or males, respectively. Monogamy under low-density conditions may have been the ecological condition for the evolution of bidirectional sex change in a common ancestor. As T. marinae and T. nasa are a monophyletic group, gonochorism should have evolved from bidirectional sex change in a common ancestor.

  20. Phylogenetic relationships of Cranichidinae and Prescottiinae (Orchidaceae, Cranichideae) inferred from plastid and nuclear DNA sequences

    PubMed Central

    Salazar, Gerardo A.; Cabrera, Lidia I.; Madriñán, Santiago; Chase, Mark W.

    2009-01-01

    Background and Aims Phylogenetic relationships of subtribes Cranichidinae and Prescottiinae, two diverse groups of neotropical terrestrial orchids, are not satisfactorily understood. A previous molecular phylogenetic study supported monophyly for Cranichidinae, but Prescottiinae consisted of two clades not sister to one another. However, that analysis included only 11 species and eight genera of these subtribes. Here, plastid and nuclear DNA sequences are analysed for an enlarged sample of genera and species of Cranichidinae and Prescottiinae with the aim of clarifying their relationships, evaluating the phylogenetic position of the monospecific genera Exalaria, Ocampoa and Pseudocranichis and examining the value of various structural traits as taxonomic markers. Methods Approx. 6000 bp of nucleotide sequences from nuclear ribosomal (ITS) and plastid DNA (rbcL, matK-trnK and trnL-trnF) were analysed with cladistic parsimony and Bayesian inference for 45 species/14 genera of Cranichidinae and Prescottiinae (plus suitable outgroups). The utility of flower orientation, thickenings of velamen cell walls, hamular viscidium and pseudolabellum to mark clades recovered by the molecular analysis was assessed by tracing these characters on the molecular trees. Key Results Spiranthinae, Cranichidinae, paraphyletic Prescottia (with Pseudocranichis embedded), and a group of mainly Andean ‘prescottioid’ genera (the ‘Stenoptera clade’) were strongly supported. Relationships among these clades were unresolved by parsimony but the Bayesian tree provided moderately strong support for the resolution (Spiranthinae–(Stenoptera clade-(Prescottia/Pseudocranichis–Cranichidinae))). Three of the four structural characters mark clades on the molecular trees, but the possession of a pseudolabellum is variable in the polyphyletic Ponthieva. Conclusions No evidence was found for monophyly of Prescottiinae and the reinstatement of Cranichidinae s.l. (including the genera of

  1. 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

  2. Isolation and characterization of microsatellite loci in Sisyrinchium (Iridaceae) and cross amplification in other genera.

    PubMed

    Miz, R B; Tacuatiá, L O; Cidade, F W; de Souza, A P; Bered, F; Eggers, L; de Souza-Chies, T T

    2016-09-16

    Recent phylogenetic studies on Sisyrinchium strongly suggest that species classified in section Hydastylus and section Viperella belong to a single group of plants in recent adaptive radiation (Clade IV). These species neither present clear morphological differentiation among them nor show clear identification using DNA barcode markers. Thus, the main goal of this study was to develop a set of polymorphic microsatellite markers compatible for representative species of both sections to ensure variability that could be revealed by SSR markers. Therefore, microsatellite primers were isolated and characterized for Sisyrinchium palmifolium and S. marchioides. In addition, transferability of the developed primers was tested in Iridoideae, primarily in closely related species of Sisyrinchium. Sixteen microsatellite loci were developed from enriched genomic libraries, of which ten were polymorphic. GST values indicated higher differentiation among subpopulations of S. palmifolium than those from S. marchioides. Major transferability was obtained using primers isolated from S. marchioides. All primers exhibited higher rates of cross-amplification for species belonging to Clade IV of Sisyrinchium, as well as to the genera Calydorea and Herbertia. These developed microsatellite markers can be used as an efficient tool for characterization of genetic variability in species belonging to Iridoideae, as well as for studies on population dynamics, genetic structure, and mating system in other Sisyrinchium species.

  3. The comparative biology of diving in two genera of European Dytiscidae (Coleoptera).

    PubMed

    Calosi, P; Bilton, D T; Spicer, J I; Verberk, W C E P; Atfield, A; Garland, T

    2012-02-01

    Surfacing behaviour is fundamental in the ecology of aquatic air-breathing organisms; however, it is only in vertebrates that the evolutionary ecology of diving has been well characterized. Here, we explore the diving behaviour of dytiscid beetles, a key group of surface-exchanging freshwater invertebrates, by comparing the dive responses of 25 taxa (Deronectes and Ilybius spp.) acclimated at two temperatures. The allometric slopes of dive responses in these dytiscids appear similar to those of vertebrate ectotherms, supporting the notion that metabolic mode shapes the evolution of diving performance. In both genera, beetles spend more time submerged than on the surface, and surface time does not vary with the temperature of acclimation. However, presumably in order to meet increased oxygen demand at higher temperatures, Deronectes species increase surfacing frequency, whereas Ilybius species decrease dive time, an example of 'multiple solutions.' Finally, widespread northern species appear to possess higher diving performances than their geographically restricted southern relatives, something which may have contributed to their range expansion ability.

  4. 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

  5. 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

  6. Diatoms from the Colombian and Peruvian Amazon: the Genera Encyonema, Encyonopsis and Gomphonema (Cymbellales: Bacillariophyceae).

    PubMed

    Vouilloud, Amelia A; Sala, Silvia E; Avellaneda, Marcela Núñez; Duque, Santiago R

    2010-03-01

    The diatom flora of the Colombian and Peruvian Amazon is far less studied than the flora of the Brazilian sector of the basin. Here we present results related to the genera Encyonema, Encyonopsis and Gomphonema. Plankton and periphyton samples were collected in lotic and lentic waterbodies from the Amazonian-Andean region, the Amazon River, Japurá River and Porvenir River basins during 1993, 1994, 2001 and 2003. At each sampling station pH, temperature, water transparency and conductivity were registered. Samples were analyzed with phase contrast microscope (LM) and scanning electron microscope (SEM). Ten taxa are new records for the area; Encyonema for the Peruvian and Colombian Amazon and Encyonopsis for the Colombian Sector. Encyonema neogracile var. tenuipunctatum, E. vulgare, Encyonopsis frequentis, Gomphonema augur var. sphaerophorum and G. contraturris are recorded for the first time in Colombia; Encyonema venezolanum and G. neoapiculatum in Colombia and Peru and the latter also for Amazonia. E. angustecapitatum was mentioned in Colombia before at a pond located at 3000 m asl. We describe a new species from Porvenir River, Amazonas, Colombia: Encyonema amazonianum.

  7. 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

  8. Phylogenetic relationships of the genera of the Pronocephalidae Looss, 1902 (Digenea: Paramphistomiformes).

    PubMed

    Pérez Ponce de León, G; Brooks, D R

    1995-04-01

    Quantitative phylogenetic analysis of 20 nominal genera of the Pronocephalidae based on 47 morphological transformation series produced 6 equally parsimonious trees, each with a consistency index of 77.8%. All trees agree that Adenogaster is the sister group to the rest of the pronocephalids, and a new subfamily is proposed for it. The Pronocephalinae comprises Pronocephalus, Ruicephalus, Neopronocephalus, Macravestibulum, Choanophorus, Cetiosaccus, and Metacetabulum. The Charaxicephalinae comprises Charaxicephalus, Desmogonius, Diaschistorchis, Pleurogonius, Iguanacola, Renigonius, Parapleurogonius, Himasomum, Pyelosomum, Cricocephalus, Barisomum, and Pseudobarisomum. An amended diagnosis for Himasomum is presented. The trees differ only in the placements of Pleurogonius, Renigonius + Parapleurogonius, Iguanacola, and Himasomum relative to each other. Parapronocephalum and Notocotyloides are members of the clade containing the Notocotylidae. The phylogenetic tree supports interpretations of 3-4 transitions from marine to freshwater turtles, 3 host switches from marine turtles to the Galapagos marine iguana and 3 from marine turtles to the French angelfish, and widespread host switching among marine chelonians. No switches to non-chelonian hosts coincide with transitions from marine to freshwater.

  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. 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.

  11. Spectral likelihood expansions for Bayesian inference

    NASA Astrophysics Data System (ADS)

    Nagel, Joseph B.; Sudret, Bruno

    2016-03-01

    A spectral approach to Bayesian inference is presented. It pursues the emulation of the posterior probability density. The starting point is a series expansion of the likelihood function in terms of orthogonal polynomials. From this spectral likelihood expansion all statistical quantities of interest can be calculated semi-analytically. The posterior is formally represented as the product of a reference density and a linear combination of polynomial basis functions. Both the model evidence and the posterior moments are related to the expansion coefficients. This formulation avoids Markov chain Monte Carlo simulation and allows one to make use of linear least squares instead. The pros and cons of spectral Bayesian inference are discussed and demonstrated on the basis of simple applications from classical statistics and inverse modeling.

  12. Brain imaging, forward inference, and theories of reasoning.

    PubMed

    Heit, Evan

    2014-01-01

    This review focuses on the issue of how neuroimaging studies address theoretical accounts of reasoning, through the lens of the method of forward inference (Henson, 2005, 2006). After theories of deductive and inductive reasoning are briefly presented, the method of forward inference for distinguishing between psychological theories based on brain imaging evidence is critically reviewed. Brain imaging studies of reasoning, comparing deductive and inductive arguments, comparing meaningful versus non-meaningful material, investigating hemispheric localization, and comparing conditional and relational arguments, are assessed in light of the method of forward inference. Finally, conclusions are drawn with regard to future research opportunities.

  13. On the elliptic genera of manifolds of Spin(7) holonomy

    SciTech Connect

    Benjamin, Nathan; Harrison, Sarah M.; Kachru, Shamit; Paquette, Natalie M.; Whalen, Daniel

    2015-12-16

    Superstring compactification on a manifold of Spin(7) holonomy gives rise to a 2d worldsheet conformal field theory with an extended supersymmetry algebra. The N=1 superconformal algebra is extended by additional generators of spins 2 and 5/2, and instead of just superconformal symmetry one has a c = 12 realization of the symmetry group SW(3/2,2). In this paper, we compute the characters of this supergroup and decompose the elliptic genus of a general Spin(7) compactification in terms of these characters. Here, we find suggestive relations to various sporadic groups, which are made more precise in a companion paper.

  14. On the Elliptic Genera of Manifolds of Spin(7) Holonomy

    SciTech Connect

    Benjamin, Nathan; Harrison, Sarah M.; Kachru, Shamit; Paquette, Natalie M.; Whalen, Daniel

    2015-12-16

    Superstring compactification on a manifold of Spin(7) holonomy gives rise to a 2d worldsheet conformal field theory with an extended supersymmetry algebra. The N=1N=1 superconformal algebra is extended by additional generators of spins 2 and 5/2, and instead of just superconformal symmetry one has a c = 12 realization of the symmetry group SW(3/2,2)SW(3/2,2) . In this paper, we compute the characters of this supergroup and decompose the elliptic genus of a general Spin(7) compactification in terms of these characters. We find suggestive relations to various sporadic groups, which are made more precise in a companion paper.

  15. Three new genera of rhinebothriidean cestodes from stingrays in Southeast Asia.

    PubMed

    Caira, Janine N; Healy, Claire J; Marques, Fernando P L; Jensen, Kirsten

    2017-04-04

    Three genera of rhinebothriideans, previously referred to as New genus 1, New genus 2 and New genus 4, are erected in the the Anthocephaliidae. New genus 1 is established as Divaricobothrium gen. n., with Divaricobothrium tribelum sp. n. as its type species; Echeneibothrium trifidum Shipley et Hornell, 1906 is transferred to the genus as Divaricobothrium trifidum (Shipley et Hornell, 1906) comb. n. This genus is unique among rhinebothriidean genera in bearing bothridia that are posteriorly deeply divided into two lobes with facial loculi but no apical sucker, and a vagina that extends to near the anterior margin of the proglottid. Its species parasitise Indo-Pacific members of the genera Brevitrygon Last, Naylor et Manjaji-Matsumoto, Maculabatis Last, Naylor et Manjaji-Matsumoto and Pateobatis Last, Naylor et Manjaji-Matsumoto. New genus 2 is established as Barbeaucestus gen. n., with Barbeaucestus jockuschae sp. n. as its type species; Barbeaucestus ralickiae sp. n. is also described. Anthobothrium sexorchidum Williams, 1964 and Rhinebothrium shipleyi Southwell, 1912 are transferred to the genus as Barbeaucestus sexorchidus (Williams, 1964) comb. n. and Barbeaucestus shipleyi (Southwell, 1912) comb. n., respectively. This genus is unique among rhinebothriidean genera in that its bothridia are substantially wider than long, bear an apical sucker and at least one row of two or more facial loculi in their anterior half. Its species parasitise the genera Neotrygon Castelnau and Taeniura Müller et Henle. New genus 4 is established as Sungaicestus gen. n. with transfer of Rhinebothrium kinabatanganensis Healy, 2006, as Sungaicestus kinabatanganensis (Healy, 2006) comb. n., as its type species. Among the genera of its order, this genus most closely resembles Rhinebothrium Linton, 1890, however, despite the original description, the bothridia were found to bear, rather than lack, apical suckers. This monotypic genus is known only from the freshwater stingray Urogymnus

  16. Rapid detection of human fecal Eubacterium species and related genera by nested PCR method.

    PubMed

    Kageyama, A; Benno, Y

    2001-01-01

    PCR procedures based on 16S rDNA gene sequence specific for seven Eubacterium spp. and Eggerthella lenta that predominate in the human intestinal tract were developed, and used for direct detection of these species in seven human feces samples. Three species of Eggerthella lenta, Eubacterium rectale, and Eubacterium eligens were detected from seven fecal samples. Eubacterium biforme was detected from six samples. It was reported that E. rectale, E. eligens, and E. biforme were difficult to detect by traditional culture method, but the nested PCR method is available for the detection of these species. This result shows that the nested PCR method utilizing a universal primer pair, followed by amplification with species-specific primers, would allow rapid detection of Eubacterium species in human feces.

  17. 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...

  18. 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'.

  19. Statistical inference and string theory

    NASA Astrophysics Data System (ADS)

    Heckman, Jonathan J.

    2015-09-01

    In this paper, we expose some surprising connections between string theory and statistical inference. We consider a large collective of agents sweeping out a family of nearby statistical models for an M-dimensional manifold of statistical fitting parameters. When the agents making nearby inferences align along a d-dimensional grid, we find that the pooled probability that the collective reaches a correct inference is the partition function of a nonlinear sigma model in d dimensions. Stability under perturbations to the original inference scheme requires the agents of the collective to distribute along two dimensions. Conformal invariance of the sigma model corresponds to the condition of a stable inference scheme, directly leading to the Einstein field equations for classical gravity. By summing over all possible arrangements of the agents in the collective, we reach a string theory. We also use this perspective to quantify how much an observer can hope to learn about the internal geometry of a superstring compactification. Finally, we present some brief speculative remarks on applications to the AdS/CFT correspondence and Lorentzian signature space-times.

  20. Genera of euophryine jumping spiders (Araneae: Salticidae), with a combined molecular-morphological phylogeny.

    PubMed

    Zhang, Junxia; Maddison, Wayne P

    2015-03-27

    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.

  1. Active inference and robot control: a case study.

    PubMed

    Pio-Lopez, Léo; Nizard, Ange; Friston, Karl; Pezzulo, Giovanni

    2016-09-01

    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.

  2. 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

  3. Locative inferences in medical texts.

    PubMed

    Mayer, P S; Bailey, G H; Mayer, R J; Hillis, A; Dvoracek, J E

    1987-06-01

    Medical research relies on epidemiological studies conducted on a large set of clinical records that have been collected from physicians recording individual patient observations. These clinical records are recorded for the purpose of individual care of the patient with little consideration for their use by a biostatistician interested in studying a disease over a large population. Natural language processing of clinical records for epidemiological studies must deal with temporal, locative, and conceptual issues. This makes text understanding and data extraction of clinical records an excellent area for applied research. While much has been done in making temporal or conceptual inferences in medical texts, parallel work in locative inferences has not been done. This paper examines the locative inferences as well as the integration of temporal, locative, and conceptual issues in the clinical record understanding domain by presenting an application that utilizes two key concepts in its parsing strategy--a knowledge-based parsing strategy and a minimal lexicon.

  4. 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.

  5. Functional neuroanatomy of intuitive physical inference

    PubMed Central

    Mikhael, John G.; Tenenbaum, Joshua B.; Kanwisher, Nancy

    2016-01-01

    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

  6. A phylogeny of the schoenoid sedges (Cyperaceae: Schoeneae) based on plastid DNA sequences, with special reference to the genera found in Africa.

    PubMed

    Verboom, G Anthony

    2006-01-01

    Despite its large size (about 700 species), the australy-centred sedge tribe Schoeneae has received little explicit phylogenetic study, especially using molecular data. As a result, generic relationships are poorly understood, and even the monophyly of the tribe is open to question. In this study, plastid DNA sequences (rbcL, trnL-trnF, and rps16) drawn from a broad array of Schoeneae are analysed using Bayesian and parsimony-based approaches to infer a framework phylogeny for the tribe. Both analytical methods broadly support the monophyly of Schoeneae, Bayesian methods doing so with good support. Within the schoenoid clade, there is strong support for a series of monophyletic generic groupings whose interrelationships are unclear. These lineages form a large polytomy at the base of Schoeneae that may be indicative of past radiation, probably following the fragmentation of Gondwana. Most of these lineages contain both African and non-African members, suggesting a history of intercontinental dispersal. The results of this study clearly identify the relationships of the African-endemic schoenoid genera and demonstrate that the African-Australasian genus Tetraria, like Costularia, is polyphyletic. This pattern is morphologically consistent and suggests that these genera require realignment.

  7. 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

  8. 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

  9. 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

  10. Polyphyly of the hawk genera Leucopternis and Buteogallus (Aves, Accipitridae): multiple habitat shifts during the Neotropical buteonine diversification

    PubMed Central

    do Amaral, Fabio S Raposo; Miller, Matthew J; Silveira, Luís Fábio; Bermingham, Eldredge; Wajntal, Anita

    2006-01-01

    Background The family Accipitridae (hawks, eagles and Old World vultures) represents a large radiation of predatory birds with an almost global distribution, although most species of this family occur in the Neotropics. Despite great morphological and ecological diversity, the evolutionary relationships in the family have been poorly explored at all taxonomic levels. Using sequences from four mitochondrial genes (12S, ATP8, ATP6, and ND6), we reconstructed the phylogeny of the Neotropical forest hawk genus Leucopternis and most of the allied genera of Neotropical buteonines. Our goals were to infer the evolutionary relationships among species of Leucopternis, estimate their relationships to other buteonine genera, evaluate the phylogenetic significance of the white and black plumage patterns common to most Leucopternis species, and assess general patterns of diversification of the group with respect to species' affiliations with Neotropical regions and habitats. Results Our molecular phylogeny for the genus Leucopternis and its allies disagrees sharply with traditional taxonomic arrangements for the group, and we present new hypotheses of relationships for a number of species. The mtDNA phylogenetic trees derived from analysis of the combined data posit a polyphyletic relationship among species of Leucopternis, Buteogallus and Buteo. Three highly supported clades containing Leucopternis species were recovered in our phylogenetic reconstructions. The first clade consisted of the sister pairs L. lacernulatus and Buteogallus meridionalis, and Buteogallus urubitinga and Harpyhaliaetus coronatus, in addition to L. schistaceus and L. plumbeus. The second clade included the sister pair Leucopternis albicollis and L. occidentalis as well as L. polionotus. The third lineage comprised the sister pair L. melanops and L. kuhli, in addition to L. semiplumbeus and Buteo buteo. According to our results, the white and black plumage patterns have evolved at least twice in the group

  11. Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)

    PubMed Central

    Mishra, Priyanka; Kumar, Amit; Rodrigues, Vereena; Shukla, Ashutosh K.

    2016-01-01

    Premise of the Study The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae. Methodology A combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA. Principal Findings Based on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed

  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.

  13. One, four or 100 genera? A new classification of the cone snails.

    PubMed

    Puillandre, N; Duda, T F; Meyer, C; Olivera, B M; Bouchet, P

    2015-02-01

    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.

  14. 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.

  15. 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

  16. Inference and validation of predictive gene networks from biomedical literature and gene expression data.

    PubMed

    Olsen, Catharina; Fleming, Kathleen; Prendergast, Niall; Rubio, Renee; Emmert-Streib, Frank; Bontempi, Gianluca; Haibe-Kains, Benjamin; Quackenbush, John

    2014-01-01

    Although many methods have been developed for inference of biological networks, the validation of the resulting models has largely remained an unsolved problem. Here we present a framework for quantitative assessment of inferred gene interaction networks using knock-down data from cell line experiments. Using this framework we are able to show that network inference based on integration of prior knowledge derived from the biomedical literature with genomic data significantly improves the quality of inferred networks relative to other approaches. Our results also suggest that cell line experiments can be used to quantitatively assess the quality of networks inferred from tumor samples.

  17. Verbal framing of statistical evidence drives children's preference inferences.

    PubMed

    Garvin, Laura E; Woodward, Amanda L

    2015-05-01

    Although research has shown that statistical information can support children's inferences about specific psychological causes of others' behavior, previous work leaves open the question of how children interpret statistical information in more ambiguous situations. The current studies investigated the effect of specific verbal framing information on children's ability to infer mental states from statistical regularities in behavior. We found that preschool children inferred others' preferences from their statistically non-random choices only when they were provided with verbal information placing the person's behavior in a specifically preference-related context, not when the behavior was presented in a non-mentalistic action context or an intentional choice context. Furthermore, verbal framing information showed some evidence of supporting children's mental state inferences even from more ambiguous statistical data. These results highlight the role that specific, relevant framing information can play in supporting children's ability to derive novel insights from statistical information.

  18. Inference of seasonal and pandemic influenza transmission dynamics

    PubMed Central

    Yang, Wan; Lipsitch, Marc; Shaman, Jeffrey

    2015-01-01

    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

  19. 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.

  20. How Forgetting Aids Heuristic Inference

    ERIC Educational Resources Information Center

    Schooler, Lael J.; Hertwig, Ralph

    2005-01-01

    Some theorists, ranging from W. James (1890) to contemporary psychologists, have argued that forgetting is the key to proper functioning of memory. The authors elaborate on the notion of beneficial forgetting by proposing that loss of information aids inference heuristics that exploit mnemonic information. To this end, the authors bring together 2…

  1. 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…

  2. The mechanisms of temporal inference

    NASA Technical Reports Server (NTRS)

    Fox, B. R.; Green, S. R.

    1987-01-01

    The properties of a temporal language are determined by its constituent elements: the temporal objects which it can represent, the attributes of those objects, the relationships between them, the axioms which define the default relationships, and the rules which define the statements that can be formulated. The methods of inference which can be applied to a temporal language are derived in part from a small number of axioms which define the meaning of equality and order and how those relationships can be propagated. More complex inferences involve detailed analysis of the stated relationships. Perhaps the most challenging area of temporal inference is reasoning over disjunctive temporal constraints. Simple forms of disjunction do not sufficiently increase the expressive power of a language while unrestricted use of disjunction makes the analysis NP-hard. In many cases a set of disjunctive constraints can be converted to disjunctive normal form and familiar methods of inference can be applied to the conjunctive sub-expressions. This process itself is NP-hard but it is made more tractable by careful expansion of a tree-structured search space.

  3. Statistical inference and Aristotle's Rhetoric.

    PubMed

    Macdonald, Ranald R

    2004-11-01

    Formal logic operates in a closed system where all the information relevant to any conclusion is present, whereas this is not the case when one reasons about events and states of the world. Pollard and Richardson drew attention to the fact that the reasoning behind statistical tests does not lead to logically justifiable conclusions. In this paper statistical inferences are defended not by logic but by the standards of everyday reasoning. Aristotle invented formal logic, but argued that people mostly get at the truth with the aid of enthymemes--incomplete syllogisms which include arguing from examples, analogies and signs. It is proposed that statistical tests work in the same way--in that they are based on examples, invoke the analogy of a model and use the size of the effect under test as a sign that the chance hypothesis is unlikely. Of existing theories of statistical inference only a weak version of Fisher's takes this into account. Aristotle anticipated Fisher by producing an argument of the form that there were too many cases in which an outcome went in a particular direction for that direction to be plausibly attributed to chance. We can therefore conclude that Aristotle would have approved of statistical inference and there is a good reason for calling this form of statistical inference classical.

  4. Word Learning as Bayesian Inference

    ERIC Educational Resources Information Center

    Xu, Fei; Tenenbaum, Joshua B.

    2007-01-01

    The authors present a Bayesian framework for understanding how adults and children learn the meanings of words. The theory explains how learners can generalize meaningfully from just one or a few positive examples of a novel word's referents, by making rational inductive inferences that integrate prior knowledge about plausible word meanings with…

  5. Starfish: Robust spectroscopic inference tools

    NASA Astrophysics Data System (ADS)

    Czekala, Ian; Andrews, Sean M.; Mandel, Kaisey S.; Hogg, David W.; Green, Gregory M.

    2015-05-01

    Starfish is a set of tools used for spectroscopic inference. It robustly determines stellar parameters using high resolution spectral models and uses Markov Chain Monte Carlo (MCMC) to explore the full posterior probability distribution of the stellar parameters. Additional potential applications include other types of spectra, such as unresolved stellar clusters or supernovae spectra.

  6. 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)…

  7. 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…

  8. 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.

  9. Flexible retrieval: When true inferences produce false memories.

    PubMed

    Carpenter, Alexis C; Schacter, Daniel L

    2017-03-01

    Episodic memory involves flexible retrieval processes that allow us to link together distinct episodes, make novel inferences across overlapping events, and recombine elements of past experiences when imagining future events. However, the same flexible retrieval and recombination processes that underpin these adaptive functions may also leave memory prone to error or distortion, such as source misattributions in which details of one event are mistakenly attributed to another related event. To determine whether the same recombination-related retrieval mechanism supports both successful inference and source memory errors, we developed a modified version of an associative inference paradigm in which participants encoded everyday scenes comprised of people, objects, and other contextual details. These scenes contained overlapping elements (AB, BC) that could later be linked to support novel inferential retrieval regarding elements that had not appeared together previously (AC). Our critical experimental manipulation concerned whether contextual details were probed before or after the associative inference test, thereby allowing us to assess whether (a) false memories increased for successful versus unsuccessful inferences, and (b) any such effects were specific to after compared with before participants received the inference test. In each of 4 experiments that used variants of this paradigm, participants were more susceptible to false memories for contextual details after successful than unsuccessful inferential retrieval, but only when contextual details were probed after the associative inference test. These results suggest that the retrieval-mediated recombination mechanism that underlies associative inference also contributes to source misattributions that result from combining elements of distinct episodes. (PsycINFO Database Record

  10. Molecular characterisation of potexviruses isolated from three different genera in the family Cactaceae.

    PubMed

    Koenig, R; Pleij, C W A; Loss, S; Burgermeister, W; Aust, H; Schiemann, J

    2004-05-01

    The genome properties of three potexviruses which previously had been isolated from different genera in the family Cactaceae and had been found to be only distantly related serologically have been studied. The sequence of the 3040 3' terminal nucleotides of the genomic RNA of isolate K11 from Schlumbergera bridgesii and the complete RNA sequences of isolates B1 and CC10 from Zygocactus sp. and Opuntia sp., respectively, were determined. Starting sequences were obtained by means of immunocapture reverse transcription PCR using primers derived from highly conserved sequences in other potexviral RNAs. The known parts of the sequences were extended by means of random-primed cDNAs and specific primers derived from the known parts of the sequences. The genome structure of the three viruses resembles that of other potexviruses. The conserved motifs typical for replication-associated proteins, triple gene block (TGB) proteins and coat proteins of potexviruses were readily identified in the translation products of the five open reading frames. The 3' untranslated regions of the three RNAs are folded into secondary structures containing three characteristic hairpins. Rather low percentages of amino acid sequence identities ranging from 62% to 76% for the coat proteins and 41% to 49% for TGB proteins 3 suggest that these viruses should be regarded as distinct virus species for which the names Zygocactus virus X, Schlumbergera virus X and Opuntia virus X are proposed. It is also suggested that the name Cactus virus X which originally was coined for all three virus isolates should no longer be used.

  11. 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.

  12. Towards General Algorithms for Grammatical Inference

    NASA Astrophysics Data System (ADS)

    Clark, Alexander

    Many algorithms for grammatical inference can be viewed as instances of a more general algorithm which maintains a set of primitive elements, which distributionally define sets of strings, and a set of features or tests that constrain various inference rules. Using this general framework, which we cast as a process of logical inference, we re-analyse Angluin's famous lstar algorithm and several recent algorithms for the inference of context-free grammars and multiple context-free grammars. Finally, to illustrate the advantages of this approach, we extend it to the inference of functional transductions from positive data only, and we present a new algorithm for the inference of finite state transducers.

  13. 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

  14. 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 ...

  15. 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...

  16. 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.

  17. 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...

  18. 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...

  19. 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...

  20. Type species of genera in Aphididae (Hemiptera Sternorrhyncha) with two new generic synonymies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The type species of genus-group taxa in the insect family Aphididae are summarized. Type species designations of 16 available genera are amended to adhere to international nomenclatural standards and two synonymies incorrectly recorded in the literature are corrected: Neorhizobius Del Guercio is a s...

  1. DNA extraction protocols from dormant buds of twelve woody plant genera

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Standard plant DNA extraction protocols call for samples of newly expanding leaves and shoots yet analysis is sometimes needed when plants are dormant. We evaluated three DNA extraction protocols using dormant buds from 40 species and four hybrids of 12 genera. Two protocols were from ready-to-use ...

  2. Evolution and Biogeography of the Slipper Orchids: Eocene Vicariance of the Conduplicate Genera in the Old and New World Tropics

    PubMed Central

    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. PMID:22685605

  3. 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.

  4. Proposed update to the taxonomy of the genera Hepacivirus and Pegivirus within the Flaviviridae family.

    PubMed

    Smith, Donald B; Becher, Paul; Bukh, Jens; Gould, Ernest A; Meyers, Gregor; Monath, Thomas; Muerhoff, A Scott; Pletnev, Alexander; Rico-Hesse, Rebecca; Stapleton, Jack T; Simmonds, Peter

    2016-11-01

    Proposals are described for the assignment of recently reported viruses, infecting rodents, bats and other mammalian species, to new species within the Hepacivirus and Pegivirus genera (family Flaviviridae). Assignments into 14 Hepacivirus species (Hepacivirus A-N) and 11 Pegivirus species (Pegivirus A-K) are based on phylogenetic relationships and sequence distances between conserved regions extracted from complete coding sequences for members of each proposed taxon. We propose that the species Hepatitis C virus is renamed Hepacivirus C in order to acknowledge its unique historical position and so as to minimize confusion. Despite the newly documented genetic diversity of hepaciviruses and pegiviruses, members of these genera remain phylogenetically distinct, and differ in hepatotropism and the possession of a basic core protein; pegiviruses in general lack these features. However, other characteristics that were originally used to support their division into separate genera are no longer definitive; there is overlap between the two genera in the type of internal ribosomal entry site and the presence of miR-122 sites in the 5' UTR, the predicted number of N-linked glycosylation sites in the envelope E1 and E2 proteins, the presence of poly U tracts in the 3' UTR and the propensity of viruses to establish a persistent infection. While all classified hepaciviruses and pegiviruses have mammalian hosts, the recent description of a hepaci-/pegi-like virus from a shark and the likely existence of further homologues in other non-mammalian species indicate that further species or genera remain to be defined in the future.

  5. 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

  6. 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

  7. Fused Regression for Multi-source Gene Regulatory Network Inference

    PubMed Central

    Lam, Kari Y.; Westrick, Zachary M.; Müller, Christian L.; Christiaen, Lionel; Bonneau, Richard

    2016-01-01

    Understanding gene regulatory networks is critical to understanding cellular differentiation and response to external stimuli. Methods for global network inference have been developed and applied to a variety of species. Most approaches consider the problem of network inference independently in each species, despite evidence that gene regulation can be conserved even in distantly related species. Further, network inference is often confined to single data-types (single platforms) and single cell types. We introduce a method for multi-source network inference that allows simultaneous estimation of gene regulatory networks in multiple species or biological processes through the introduction of priors based on known gene relationships such as orthology incorporated using fused regression. This approach improves network inference performance even when orthology mapping and conservation are incomplete. We refine this method by presenting an algorithm that extracts the true conserved subnetwork from a larger set of potentially conserved interactions and demonstrate the utility of our method in cross species network inference. Last, we demonstrate our method’s utility in learning from data collected on different experimental platforms. PMID:27923054

  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. 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...

  10. 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

  11. Statistical learning and selective inference.

    PubMed

    Taylor, Jonathan; Tibshirani, Robert J

    2015-06-23

    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.

  12. Inferring Centrality from Network Snapshots

    NASA Astrophysics Data System (ADS)

    Shao, Haibin; Mesbahi, Mehran; Li, Dewei; Xi, Yugeng

    2017-01-01

    The topology and dynamics of a complex network shape its functionality. However, the topologies of many large-scale networks are either unavailable or incomplete. Without the explicit knowledge of network topology, we show how the data generated from the network dynamics can be utilised to infer the tempo centrality, which is proposed to quantify the influence of nodes in a consensus network. We show that the tempo centrality can be used to construct an accurate estimate of both the propagation rate of influence exerted on consensus networks and the Kirchhoff index of the underlying graph. Moreover, the tempo centrality also encodes the disturbance rejection of nodes in a consensus network. Our findings provide an approach to infer the performance of a consensus network from its temporal data.

  13. 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

  14. 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

  15. System Support for Forensic Inference

    NASA Astrophysics Data System (ADS)

    Gehani, Ashish; Kirchner, Florent; Shankar, Natarajan

    Digital evidence is playing an increasingly important role in prosecuting crimes. The reasons are manifold: financially lucrative targets are now connected online, systems are so complex that vulnerabilities abound and strong digital identities are being adopted, making audit trails more useful. If the discoveries of forensic analysts are to hold up to scrutiny in court, they must meet the standard for scientific evidence. Software systems are currently developed without consideration of this fact. This paper argues for the development of a formal framework for constructing “digital artifacts” that can serve as proxies for physical evidence; a system so imbued would facilitate sound digital forensic inference. A case study involving a filesystem augmentation that provides transparent support for forensic inference is described.

  16. Inferring Centrality from Network Snapshots

    PubMed Central

    Shao, Haibin; Mesbahi, Mehran; Li, Dewei; Xi, Yugeng

    2017-01-01

    The topology and dynamics of a complex network shape its functionality. However, the topologies of many large-scale networks are either unavailable or incomplete. Without the explicit knowledge of network topology, we show how the data generated from the network dynamics can be utilised to infer the tempo centrality, which is proposed to quantify the influence of nodes in a consensus network. We show that the tempo centrality can be used to construct an accurate estimate of both the propagation rate of influence exerted on consensus networks and the Kirchhoff index of the underlying graph. Moreover, the tempo centrality also encodes the disturbance rejection of nodes in a consensus network. Our findings provide an approach to infer the performance of a consensus network from its temporal data. PMID:28098166

  17. Bayesian inference for agreement measures.

    PubMed

    Vidal, Ignacio; de Castro, Mário

    2016-08-25

    The agreement of different measurement methods is an important issue in several disciplines like, for example, Medicine, Metrology, and Engineering. In this article, some agreement measures, common in the literature, were analyzed from a Bayesian point of view. Posterior inferences for such agreement measures were obtained based on well-known Bayesian inference procedures for the bivariate normal distribution. As a consequence, a general, simple, and effective method is presented, which does not require Markov Chain Monte Carlo methods and can be applied considering a great variety of prior distributions. Illustratively, the method was exemplified using five objective priors for the bivariate normal distribution. A tool for assessing the adequacy of the model is discussed. Results from a simulation study and an application to a real dataset are also reported.

  18. The relationships within the Chaitophorinae and Drepanosiphinae (Hemiptera, Aphididae) inferred from molecular-based phylogeny and comprehensive morphological data

    PubMed Central

    Wieczorek, Karina; Lachowska-Cierlik, Dorota; Kajtoch, Łukasz; Kanturski, Mariusz

    2017-01-01

    The Chaitophorinae is a bionomically diverse Holarctic subfamily of Aphididae. The current classification includes two tribes: the Chaitophorini associated with deciduous trees and shrubs, and Siphini that feed on monocotyledonous plants. We present the first phylogenetic hypothesis for the subfamily, based on molecular and morphological datasets. Molecular analyses were based on the mitochondrial gene cytochrome oxidase subunit I (COI) and the nuclear gene elongation factor-1α (EF-1α). Phylogenetic inferences were obtained individually on each of genes and joined alignments using Bayesian inference (BI) and Maximum likelihood (ML). In phylogenetic trees reconstructed on the basis of nuclear and mitochondrial genes as well as a morphological dataset, the monophyly of Siphini and the genus Chaitophorus was supported. Periphyllus forms independent lineages from Chaitophorus and Siphini. Within this genus two clades comprising European and Asiatic species, respectively, were indicated. Concerning relationships within the subfamily, EF-1α and joined COI and EF-1α genes analysis strongly supports the hypothesis that Chaitophorini do not form a monophyletic clade. Periphyllus is a sister group to a clade containing Chaitophorus and Siphini. The Asiatic unit of Periphyllus also includes Trichaitophorus koyaensis. The analysis of morphological dataset under equally weighted parsimony also supports the view that Chaitophorini is an artificial taxon, as Lambersaphis pruinosae and Pseudopterocomma hughi, both traditionally included in the Chaitophorini, formed independent lineages. COI analyses support consistent groups within the subfamily, but relationships between groups are poorly resolved. These analyses were extended to include the species of closely related and phylogenetically unstudied subfamily Drepanosiphinae, which produced congruent results. Genera Drepanosiphum and Depanaphis are monophyletic and sister. The position of Yamatocallis tokyoensis differs in the

  19. Fast, Flexible, Rational Inductive Inference

    DTIC Science & Technology

    2013-08-23

    learning phonetic categories – the sounds that make up speech – learning the words that those sounds appear in provides sufficiently strong constraints...first to be able to infer realistic phonetic categories directly from simulated speech data. Objective 2.2: Forming feature-based representations...lexicon in phonetic category acquisition. Psychological Review. Griffiths, T. L., Austerweil, J. L., & Berthiaume, V. G. (2012). Comparing the

  20. A revision of the haploporinae nicoll, 1914 (digenea: haploporidae) from mullets (mugilidae): two new haploporine genera and a key to the genera of the subfamily.

    PubMed

    Blasco-Costa, Isabel; Montero, Francisco E; Gibson, David I; Balbuena, Juan Antonio; Kostadinova, Aneta

    2009-03-01

    Two new haploporine genera are established for parasites of mullets. Ragaia n. g. is erected for R. lizae n. sp. from Liza ramado in the Ebro Delta on the Mediterranean Coast of Spain. This new genus is distinguished by the unique combination of the following characters: a strongly muscular ventral sucker which is twice as large as the oral sucker; a large, muscular hermaphroditic sac similar in length to the ventral sucker; a saccular, thick-walled internal seminal vesicle which is larger than the external seminal vesicle; and the ovary and vitellarium located rather close to the posterior extremity. Pseudodicrogaster n. g. is erected to accommodate Dicrogaster japonica Machida, 1996, as P. japonica (Machida, 1996) n. comb., a parasite of Mugil cephalus L. off Fukaura, Japan. This genus is recognised on the basis of: the tubular condition of both the internal and external seminal vesicles, the latter being much shorter than the former; the sucker ratio; the massive pyriform hermaphroditic sac; the location of the testis; and the presence of two eye-spots in developed miracidia. A key to the nine recognised genera of the Haploporinae is presented.

  1. 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.

  2. An introduction to causal inference.

    PubMed

    Pearl, Judea

    2010-02-26

    This paper summarizes recent advances in causal inference and underscores the paradigmatic shifts that must be undertaken in moving from traditional statistical analysis to causal analysis of multivariate data. Special emphasis is placed on the assumptions that underlie all causal inferences, the languages used in formulating those assumptions, the conditional nature of all causal and counterfactual claims, and the methods that have been developed for the assessment of such claims. These advances are illustrated using a general theory of causation based on the Structural Causal Model (SCM) described in Pearl (2000a), which subsumes and unifies other approaches to causation, and provides a coherent mathematical foundation for the analysis of causes and counterfactuals. In particular, the paper surveys the development of mathematical tools for inferring (from a combination of data and assumptions) answers to three types of causal queries: those about (1) the effects of potential interventions, (2) probabilities of counterfactuals, and (3) direct and indirect effects (also known as "mediation"). Finally, the paper defines the formal and conceptual relationships between the structural and potential-outcome frameworks and presents tools for a symbiotic analysis that uses the strong features of both. The tools are demonstrated in the analyses of mediation, causes of effects, and probabilities of causation.

  3. 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

  4. Phylogeny of minute carabid beetles and their relatives based upon DNA sequence data (Coleoptera, Carabidae, Trechitae).

    PubMed

    Maddison, David R; Ober, Karen A

    2011-01-01

    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.

  5. 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

  6. Inferring causal structure: a quantum advantage

    NASA Astrophysics Data System (ADS)

    Ried, Katja; Spekkens, Robert

    2014-03-01

    The problem of inferring causal relations from observed correlations is central to science, and extensive study has yielded both important conceptual insights and widely used practical applications. Yet some of the simplest questions are impossible to answer classically: for instance, if one observes correlations between two variables (such as taking a new medical treatment and the subject's recovery), does this show a direct causal influence, or is it due to some hidden common cause? We develop a framework for quantum causal inference, and show how quantum theory provides a unique advantage in this decision problem. The key insight is that certain quantum correlations can only arise from specific causal structures, whereas pairs of classical variables can exhibit any pattern of correlation regardless of whether they have a common cause or a direct-cause relation. For example, suppose one measures the same Pauli observable on two qubits. If they share a common cause, such as being prepared in an entangled state, then one never finds perfect (positive) correlations in every basis, whereas perfect anticorrelations are possible (if one prepares the singlet state). Conversely, if a channel connects the qubits, hence a direct causal influence, perfect anticorrelations are impossible.

  7. Inferring epigenetic dynamics from kin correlations

    PubMed Central

    Hormoz, Sahand; Desprat, Nicolas; Shraiman, Boris I.

    2015-01-01

    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

  8. Representing Documents via Latent Keyphrase Inference

    PubMed Central

    Liu, Jialu; Ren, Xiang; Shang, Jingbo; Cassidy, Taylor; Voss, Clare R.; Han, Jiawei

    2017-01-01

    Many text mining approaches adopt bag-of-words or n-grams models to represent documents. Looking beyond just the words, i.e., the explicit surface forms, in a document can improve a computer’s understanding of text. Being aware of this, researchers have proposed concept-based models that rely on a human-curated knowledge base to incorporate other related concepts in the document representation. But these methods are not desirable when applied to vertical domains (e.g., literature, enterprise, etc.) due to low coverage of in-domain concepts in the general knowledge base and interference from out-of-domain concepts. In this paper, we propose a data-driven model named Latent Keyphrase Inference (LAKI) that represents documents with a vector of closely related domain keyphrases instead of single words or existing concepts in the knowledge base. We show that given a corpus of in-domain documents, topical content units can be learned for each domain keyphrase, which enables a computer to do smart inference to discover latent document keyphrases, going beyond just explicit mentions. Compared with the state-of-art document representation approaches, LAKI fills the gap between bag-of-words and concept-based models by using domain keyphrases as the basic representation unit. It removes dependency on a knowledge base while providing, with keyphrases, readily interpretable representations. When evaluated against 8 other methods on two text mining tasks over two corpora, LAKI outperformed all. PMID:28229132

  9. Children's and adults' evaluation of the certainty of deductive inferences, inductive inferences, and guesses.

    PubMed

    Pillow, Bradford H

    2002-01-01

    Two experiments investigated kindergarten through fourth-grade children's and adults' (N = 128) ability to (1) evaluate the certainty of deductive inferences, inductive inferences, and guesses; and (2) explain the origins of inferential knowledge. When judging their own cognitive state, children in first grade and older rated deductive inferences as more certain than guesses; but when judging another person's knowledge, children did not distinguish valid inferences from invalid inferences and guesses until fourth grade. By third grade, children differentiated their own deductive inferences from inductive inferences and guesses, but only adults both differentiated deductive inferences from inductive inferences and differentiated inductive inferences from guesses. Children's recognition of their own inferences may contribute to the development of knowledge about cognitive processes, scientific reasoning, and a constructivist epistemology.

  10. 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.

  11. 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.

  12. [Comparative Analysis of DNA Homology in Pericentric Regions of Chromosomes of Wood Mice from Genera Apodemus and Sylvaemus].

    PubMed

    Rubtsov, N B; Karamysheva, T V; Bogdanov, A S; Kartavtseva, I V; Bochkarev, M N; Iwasa, M A

    2015-12-01

    In the present study, an analysis of the DNA homology of the pericentric chromosomal regions and pericentric heterochromatin in distantly related species of wood mice (species from the Apodemus genus, as well as from the Apodemus and Sylvaemus genera) was conducted by fluorescent in situ hybridization (FISH) with microdissected DNA probes obtained from the corresponding chromosomal regions of these species. Cross-hybridization of microdissected DNA probes obtained from pericentric C-positive blocks of chromosomes of Sylvaemus species with chromosomes of Apodemus species, as well as DNA probes from pericentric C-positive blocks of chromosomes of Apodemus species with chromosomes of Apodemus and Sylvaemus species, showed that DNA repeats homologous to the pericentric regions in other species represented. dispersed repeats in C-negative chromosomal regions, as well as in several regions bordering pericentric C-positive and C-negative regions in heterochromosomes and autosomes and in distal regions in the long arms of several autosomes. The results indicate that the level of DNA homology in pericentric chromosomal regions decreases with an increase in the differentiation level and a decrease in the kinship between the compared forms and species of wood mice. Most likely, degeneration of the DNA repeats is accompanied by a gradual destruction of repeat clusters and their replacement by new, nonhomologous repeats in almost all pericentric regions (some old repetitive sequences might be "extruded" into interstitial or telomeric regions of chromosomes). These processes, which are observed in some species from Sylvaemus genus in distantly related species of Sylvaemus and Apodemus genera, have almost achieved the final stages.

  13. A Full Bayesian Approach for Boolean Genetic Network Inference

    PubMed Central

    Han, Shengtong; Wong, Raymond K. W.; Lee, Thomas C. M.; Shen, Linghao; Li, Shuo-Yen R.; Fan, Xiaodan

    2014-01-01

    Boolean networks are a simple but efficient model for describing gene regulatory systems. A number of algorithms have been proposed to infer Boolean networks. However, these methods do not take full consideration of the effects of noise and model uncertainty. In this paper, we propose a full Bayesian approach to infer Boolean genetic networks. Markov chain Monte Carlo algorithms are used to obtain the posterior samples of both the network structure and the related parameters. In addition to regular link addition and removal moves, which can guarantee the irreducibility of the Markov chain for traversing the whole network space, carefully constructed mixture proposals are used to improve the Markov chain Monte Carlo convergence. Both simulations and a real application on cell-cycle data show that our method is more powerful than existing methods for the inference of both the topology and logic relations of the Boolean network from observed data. PMID:25551820

  14. Phylogenomic and molecular demarcation of the core members of the polyphyletic pasteurellaceae genera actinobacillus, haemophilus, and pasteurella.

    PubMed

    Naushad, Sohail; Adeolu, Mobolaji; Goel, Nisha; Khadka, Bijendra; Al-Dahwi, Aqeel; Gupta, Radhey S

    2015-01-01

    The genera Actinobacillus, Haemophilus, and Pasteurella exhibit extensive polyphyletic branching in phylogenetic trees and do not represent coherent clusters of species. In this study, we have utilized molecular signatures identified through comparative genomic analyses in conjunction with genome based and multilocus sequence based phylogenetic analyses to clarify the phylogenetic and taxonomic boundary of these genera. We have identified large clusters of Actinobacillus, Haemophilus, and Pasteurella species which represent the "sensu stricto" members of these genera. We have identified 3, 7, and 6 conserved signature indels (CSIs), which are specifically shared by sensu stricto members of Actinobacillus, Haemophilus, and Pasteurella, respectively. We have also identified two different sets of CSIs that are unique characteristics of the pathogen containing genera Aggregatibacter and Mannheimia, respectively. It is now possible to demarcate the genera Actinobacillus sensu stricto, Haemophilus sensu stricto, and Pasteurella sensu stricto on the basis of discrete molecular signatures. The other members of the genera Actinobacillus, Haemophilus, and Pasteurella that do not fall within the "sensu stricto" clades and do not contain these molecular signatures should be reclassified as other genera. The CSIs identified here also provide useful diagnostic targets for the identification of current and novel members of the indicated genera.

  15. Review of the grass-feeding leafhopper genera Miradeltaphus Dash & Viraktamath and Yuanamia Zhang & Duan (Hemiptera: Cicadellidae: Deltocephalinae: Deltocephalini).

    PubMed

    Duan, Yani; Dietrich, Christopher H; Zhang, Yalin

    2016-04-05

    Miradeltaphus Dash & Viraktamath and Yuanamia Zhang & Duan are revised, one new species M. sanogae sp. n. is described and Parayuanamia Xing & Li is considered a junior synonym of Yuanamia Zhang & Duan syn. n. Both genera are newly recorded from Thailand. A revised key to the Palearctic and Oriental genera of Deltocephalini is provided.

  16. Phylogenomic and Molecular Demarcation of the Core Members of the Polyphyletic Pasteurellaceae Genera Actinobacillus, Haemophilus, and Pasteurella

    PubMed Central

    Naushad, Sohail; Adeolu, Mobolaji; Goel, Nisha; Khadka, Bijendra; Al-Dahwi, Aqeel; Gupta, Radhey S.

    2015-01-01

    The genera Actinobacillus, Haemophilus, and Pasteurella exhibit extensive polyphyletic branching in phylogenetic trees and do not represent coherent clusters of species. In this study, we have utilized molecular signatures identified through comparative genomic analyses in conjunction with genome based and multilocus sequence based phylogenetic analyses to clarify the phylogenetic and taxonomic boundary of these genera. We have identified large clusters of Actinobacillus, Haemophilus, and Pasteurella species which represent the “sensu stricto” members of these genera. We have identified 3, 7, and 6 conserved signature indels (CSIs), which are specifically shared by sensu stricto members of Actinobacillus, Haemophilus, and Pasteurella, respectively. We have also identified two different sets of CSIs that are unique characteristics of the pathogen containing genera Aggregatibacter and Mannheimia, respectively. It is now possible to demarcate the genera Actinobacillus sensu stricto, Haemophilus sensu stricto, and Pasteurella sensu stricto on the basis of discrete molecular signatures. The other members of the genera Actinobacillus, Haemophilus, and Pasteurella that do not fall within the “sensu stricto” clades and do not contain these molecular signatures should be reclassified as other genera. The CSIs identified here also provide useful diagnostic targets for the identification of current and novel members of the indicated genera. PMID:25821780

  17. Characteristics of Immunochemical Interrelations between Cellular Components Included into the Composition of Allergenoactive Fractions of Enterobacteria of Various Genera,

    DTIC Science & Technology

    Cellular components which form allergenoactive fractions include antigens common to enterobacteria of different genera. In Escherichia, Shigella...The degree of immunochemical community is expressed identically for individual examples of enterobacteria . According to the number of common antigens...in the allergenic fractions, enterobacteria can be divided into four immunochemical types: Escherichia (combines the genera Escherichia, Salmonella

  18. 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.

  19. Seasonal constraints on inferred planetary heat content

    NASA Astrophysics Data System (ADS)

    McKinnon, Karen A.; Huybers, Peter

    2016-10-01

    Planetary heating can be quantified using top of the atmosphere energy fluxes or through monitoring the heat content of the Earth system. It has been difficult, however, to compare the two methods with each other because of biases in satellite measurements and incomplete spatial coverage of ocean observations. Here we focus on the the seasonal cycle whose amplitude is large relative to satellite biases and observational errors. The seasonal budget can be closed through inferring contributions from high-latitude oceans and marginal seas using the covariance structure of National Center for Atmospheric Research (NCAR) Community Earth System Model (CESM1). In contrast, if these regions are approximated as the average across well-observed regions, the amplitude of the seasonal cycle is overestimated relative to satellite constraints. Analysis of the same CESM1 simulation indicates that complete measurement of the upper ocean would increase the magnitude and precision of interannual trend estimates in ocean heating more than fully measuring the deep ocean.

  20. Making inference from wildlife collision data: inferring predator absence from prey strikes.

    PubMed

    Caley, Peter; Hosack, Geoffrey R; Barry, Simon C

    2017-01-01

    Wildlife collision data are ubiquitous, though challenging for making ecological inference due to typically irreducible uncertainty relating to the sampling process. We illustrate a new approach that is useful for generating inference from predator data arising from wildlife collisions. By simply conditioning on a second prey species sampled via the same collision process, and by using a biologically realistic numerical response functions, we can produce a coherent numerical response relationship between predator and prey. This relationship can then be used to make inference on the population size of the predator species, including the probability of extinction. The statistical conditioning enables us to account for unmeasured variation in factors influencing the runway strike incidence for individual airports and to enable valid comparisons. A practical application of the approach for testing hypotheses about the distribution and abundance of a predator species is illustrated using the hypothesized red fox incursion into Tasmania, Australia. We estimate that conditional on the numerical response between fox and lagomorph runway strikes on mainland Australia, the predictive probability of observing no runway strikes of foxes in Tasmania after observing 15 lagomorph strikes is 0.001. We conclude there is enough evidence to safely reject the null hypothesis that there is a widespread red fox population in Tasmania at a population density consistent with prey availability. The method is novel and has potential wider application.

  1. Making inference from wildlife collision data: inferring predator absence from prey strikes

    PubMed Central

    Hosack, Geoffrey R.; Barry, Simon C.

    2017-01-01

    Wildlife collision data are ubiquitous, though challenging for making ecological inference due to typically irreducible uncertainty relating to the sampling process. We illustrate a new approach that is useful for generating inference from predator data arising from wildlife collisions. By simply conditioning on a second prey species sampled via the same collision process, and by using a biologically realistic numerical response functions, we can produce a coherent numerical response relationship between predator and prey. This relationship can then be used to make inference on the population size of the predator species, including the probability of extinction. The statistical conditioning enables us to account for unmeasured variation in factors influencing the runway strike incidence for individual airports and to enable valid comparisons. A practical application of the approach for testing hypotheses about the distribution and abundance of a predator species is illustrated using the hypothesized red fox incursion into Tasmania, Australia. We estimate that conditional on the numerical response between fox and lagomorph runway strikes on mainland Australia, the predictive probability of observing no runway strikes of foxes in Tasmania after observing 15 lagomorph strikes is 0.001. We conclude there is enough evidence to safely reject the null hypothesis that there is a widespread red fox population in Tasmania at a population density consistent with prey availability. The method is novel and has potential wider application. PMID:28243534

  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. 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

  4. The freshwater snails (Gastropoda) of Iran, with descriptions of two new genera and eight new species.

    PubMed

    Glöer, Peter; Pešić, Vladimir

    2012-01-01

    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.

  5. 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

  6. 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.

  7. 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.

  8. Composition and distribution of selected munnopsid genera (Crustacea, Isopoda, Asellota) in Icelandic waters

    NASA Astrophysics Data System (ADS)

    Schnurr, Sarah; Brandt, Angelika; Brix, Saskia; Fiorentino, Dario; Malyutina, Marina; Svavarsson, Jörundur

    2014-02-01

    The Greenland-Scotland Ridge (GSR) is a major topographic feature, extending from Greenland to Scotland. It constrains the water exchange between the northernmost North Atlantic Ocean and the Greenland, Iceland and Norwegian Seas (GIN Seas) and thus forms a potential barrier for faunal exchange from the Arctic to the North Atlantic (and vice versa). Recently an increase in Atlantic water inflow has been observed, leading to changes in physical parameters (i.e. temperature and salinity), which may have an impact on the resident fauna. In this study, we analyzed the composition and distribution of six selected genera of the isopod family Munnopsidae (Crustacea) occurring north and south of the GSR. We examined 82 epibenthic sledge samples and 26 additional sub-samples taken in the course of the Benthic Invertebrates of Icelandic Waters (BIOICE) and Icelandic Marine Animals: Genetics and Ecology (IceAGE) projects, respectively, covering a total depth range from 103 to 2752 m depth. Overall, 58 of the evaluated stations originated in the area north of the GSR, while the remaining 50 samples were collected south of the ridge. In total, 10517 individuals could be assigned to 15 species, most belonging to the genus EurycopeSars, 1864. Due to the presence of the GSR as well as differences in the environment, we expected significant dissimilarities in faunal composition between the two study areas. However, most species (8) occurred on both sides of the ridge, while four species were restricted to the region north of Iceland, and three to the region south of the ridge. Depth (or factors related to depth) appeared to be the most important factor in driving distributional patterns of the studied species. Temperature was also an important driver, but not to the same extent as depth. On the contrary, salinity and sediment type did not have much influence on munnopsid distribution patterns. Hence, the presence of the ridge does not restrict faunal exchange between the northern

  9. Monilochaetes and allied genera of the Glomerellales, and a reconsideration of families in the Microascales

    PubMed Central

    Réblová, M.; Gams, W.; Seifert, K.A.

    2011-01-01

    We examined the phylogenetic relationships of two species that mimic Chaetosphaeria in teleomorph and anamorph morphologies, Chaetosphaeria tulasneorum with a Cylindrotrichum anamorph and Australiasca queenslandica with a Dischloridium anamorph. Four data sets were analysed: a) the internal transcribed spacer region including ITS1, 5.8S rDNA and ITS2 (ITS), b) nc28S (ncLSU) rDNA, c) nc18S (ncSSU) rDNA, and d) a combined data set of ncLSU-ncSSU-RPB2 (ribosomal polymerase B2). The traditional placement of Ch. tulasneorum in the Microascales based on ncLSU sequences is unsupported and Australiasca does not belong to the Chaetosphaeriaceae. Both holomorph species are nested within the Glomerellales. A new genus, Reticulascus, is introduced for Ch. tulasneorum with associated Cylindrotrichum anamorph; another species of Reticulascus and its anamorph in Cylindrotrichum are described as new. The taxonomic structure of the Glomerellales is clarified and the name is validly published. As delimited here, it includes three families, the Glomerellaceae and the newly described Australiascaceae and Reticulascaceae. Based on ITS and ncLSU rDNA sequence analyses, we confirm the synonymy of the anamorph genera Dischloridium with Monilochaetes. Consequently Dischloridium laeënse, type species of the genus, and three related species are transferred to the older genus Monilochaetes. The teleomorph of D. laeënse is described in Australiasca as a new species. The Plectosphaerellaceae, to which the anamorph genus Stachylidium is added, is basal to the Glomerellales in the three-gene phylogeny. Stilbella annulata also belongs to this family and is newly combined in Acrostalagmus. Phylogenetic analyses based on ncLSU, ncSSU, and combined ncLSU-ncSSU-RPB2 sequences clarify family relationships within the Microascales. The family Ceratocystidaceae is validated as a strongly supported monophyletic group consisting of Ceratocystis, Cornuvesica, Thielaviopsis, and the type species of

  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. 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.

  12. 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.

  13. 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

  14. Evolution of Lecythidaceae with an emphasis on the circumscription of neotropical genera: information from combined ndhF and trnL-F sequence data.

    PubMed

    Mori, Scott A; Tsou, Chi-Hua; Wu, Chi-Chih; Cronholm, Bodil; Anderberg, Arne A

    2007-03-01

    The Lecythidaceae comprise a pantropical family best known for the edible seeds of the Brazil nut (Bertholletia excelsa) and the cannon-ball tree (Couroupita guianensis), which is planted as a botanical curiosity in subtropical and tropical gardens. In addition, species of the family are often among the most common in neotropical forests, especially in the Amazon Basin. The Brazil nut family is diverse and abundant in the Amazon and is considered to be an indicator of undisturbed or scarcely disturbed lowland forests; thus, what is learned about its evolution, ecology, and biogeography may suggest similar patterns for other Amazonian tree families. We used combined data sets derived from the ndhF and trnL-F genes to elucidate relationships of genera in both the Old and New Worlds that have been associated with Lecythidaceae. Our molecular tree agrees with the recognition of Napoleonaeaceae and Scytopetalaceae. Within the Lecythidaceae, there is molecular support for recognizing three subfamilies: Foetidioideae, Planchonioideae, and Lecythidoideae. We then focused on genera of the Lecythidoideae and found support for recognizing Allantoma (when the actinomorphic-flowered species of Cariniana are included in it), Grias, Gustavia, Corythophora, Couratari, and Couroupita, but conclude that Cariniana, Lecythis, and Eschweilera are not monoyphyletic. Because the position of the monotypic Bertholletia excelsa in relation to the other zygomorphic-flowered genera is not resolved, we are not able to comment on its generic relationships.

  15. Two new genera, Hoffmannanthus and Jeffreycia, mostly from East Africa (Erlangeinae, Vernonieae, Asteraceae)

    PubMed Central

    Robinson, Harold; Keeley, Sterling C.; Skvarla, John J.; Chan, Raymund

    2014-01-01

    Abstract Two genera of Vernonieae subtribe Erlangeinae with Type A pollen, 5-ribbed achenes, and blunt-tipped sweeping hairs on the styles are described as new, Hoffmannanthus with one species and with Vernonia brachycalyx O. Hoffm. as type, and Jeffreycia with five known species, with Vernonia zanzibarensis Less. as type. Vernonia abbotiana O. Hoffm. is neotypified and is an older name for V. brachycalyx. PMID:25197225

  16. 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.

  17. 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.

  18. At Least 23 Genera Instead of One: The Case of Iris L. s.l. (Iridaceae)

    PubMed Central

    Mavrodiev, Evgeny V.; Martínez-Azorín, Mario; Dranishnikov, Peter; Crespo, Manuel B.

    2014-01-01

    Background Iris L. s.l. is one of the most diverse and well-known genera in the Asparagales, with approximately 250–300 circumscribed species and significant economic impact. The taxonomy of the genus has suffered dramatic changes in the last century, particularly in the last decades after the application of molecular techniques. As a result several contrasting systematic arrangements are currently available to taxonomists. Many genera that were split from Iris s.str. in the past, on the basis of morphology (e.g., Hermodactylus, Iridodictyum, Juno, Pardanthopsis, and Xiphion, among others), are now a priori re-included in a very widely circumscribed Iris s.l. (incl. Belamcanda). This resulted in a more heterogeneous genus that is more difficult to define on morphological grounds. Testing congruence between taxonomic treatments and the results of recent molecular studies of Iris has never been performed, mostly due to the lack of proper taxonomic context. Results We generated several conventional phylogenies for Iris & outgroups using extensive sampling of taxa (187) and characters (10 plastid loci). We demonstrate that the natural history of Iris, written either as conventional molecular phylogenies or, if viewing in the context of the comparative approach, as a nested most parsimonious hierarchy of patterns, appear to be fully congruent with the narrow taxonomical treatment of the genus, restricted to the rhizomatous “bearded” taxa. The resulting topologies place Belamcanda, Pardanthopsis, and Gattenhofia as sisters to Iris s.str. and genus Siphonostylis as sister to Iris s.l. Conclusion The present study clearly justifies the splitting of Iris s.l. into at least 23 genera, 18 of which have already been accepted in the past by numerous authorities. These genera are characterized by unique combinations of partly overlapping morphological characters and biogeography. Moreover, nearly the same entities, which we here recognize at a generic rank, were for

  19. Statistical inference for inverse problems

    NASA Astrophysics Data System (ADS)

    Bissantz, Nicolai; Holzmann, Hajo

    2008-06-01

    In this paper we study statistical inference for certain inverse problems. We go beyond mere estimation purposes and review and develop the construction of confidence intervals and confidence bands in some inverse problems, including deconvolution and the backward heat equation. Further, we discuss the construction of certain hypothesis tests, in particular concerning the number of local maxima of the unknown function. The methods are illustrated in a case study, where we analyze the distribution of heliocentric escape velocities of galaxies in the Centaurus galaxy cluster, and provide statistical evidence for its bimodality.

  20. 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

  1. 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.

  2. Molecular approach for the rapid detection of Bacillus and Pseudomonas genera--dominant antagonistic groups--from diverse ecological niches using colony multiplex PCR.

    PubMed

    Nair, Anusree V; Pradeep, M A; Vijayan, K K

    2014-07-01

    Bacillus and Pseudomonas are the dominant groups of bacteria known for their antagonistic potential against many plant and animal pathogens. Presently, exploration of these genera with antagonistic property for disease management of aquaculture system is gaining more importance to overcome the use of antibiotics and related resistance issues. Rapid screening and identification of these genera from diverse bacterial populations by conventional methods is laborious, cost-intensive, and time-consuming. To overcome these limiting factors, in the present study, a colony multiplex PCR (cmPCR) method was developed and evaluated for the rapid detection of Bacillus and Pseudomonas. The technique amplifies the partial 16S rRNA gene of Bacillus and Pseudomonas with a product size of ~1,100 and ~375 bp, respectively, using single forward (BSF2) and two reverse primers (PAGSR and BK1R). Reliability of the cmPCR method was confirmed by screening 472 isolates obtained from ten different eco-stations, of which 133 isolates belonged to Bacillus and 32 to Pseudomonas. The cmPCR method also helped to identify six different Pseudomonas spp. and 14 different Bacillus spp. from environmental samples. Of the total 472 isolates studied, 46 showed antagonistic activity, among which 63 % were Bacillus and 17.4 % were Pseudomonas. Thus, the newly developed molecular approach provides a quick, sensitive, and potential screening tool to detect novel, antagonistically important Bacillus and Pseudomonas genera for their use in aquaculture. Further, it can also act as a taxonomic tool to understand the distribution of these genera from wide ecological niches and their exploitation for diverse biotechnological applications.

  3. Revision of the stiletto fly genera Acupalpa Kröber and Pipinnipons Winterton (Diptera, Therevidae, Agapophytinae) using cybertaxonomic methods, with a key to Australasian genera

    PubMed Central

    Winterton, Shaun L.

    2011-01-01

    Abstract Australian stiletto flies of the sister-genera Acupalpa Kröber, 1912 and Pipinnipons Winterton, 2001 (Diptera: Therevidae: Agapophytinae) are revised. Twelve new species of Acupalpa are described, while Acupalpa imitans (White, 1915), comb. n. is transferred from Pipinnipons and Acupalpa albimanis (Kröber, 1914), comb. n. is transferred from Ectinorhynchus Macquart as a senior synonym of Acupalpa pollinosa Mann. The total number of species of Acupalpa is therefore increased to 19: Acupalpa albimanis (Kröber), comb. n., Acupalpa albitarsa Mann, Acupalpa boharti sp. n., Acupalpa divisa (Walker), Acupalpa dolichorhyncha sp. n., Acupalpa glossa sp. n., Acupalpa imitans (White), comb. n., Acupalpa irwini Winterton, Acupalpa melanophaeos sp. n., Acupalpa miaboolya sp. n., Acupalpa minuta sp. n., Acupalpa minutoides sp. n., Acupalpa notomelas sp. n., Acupalpa novayamarna sp. n., Acupalpa rostrata Kröber, Acupalpa semirufa Mann, Acupalpa westralica sp. n., Acupalpa yalgoo sp. n. and Acupalpa yanchep sp. n. Three new species of Pipinnipons are described, increasing the total number of species to five: Pipinnipons chauncyvallis sp. n., Pipinnipons fascipennis (Kröber), Pipinnipons kampmeierae sp. n., Pipinnipons kroeberi Winterton, and P. sphecoda sp. n. Pipinnipons and Acupalpa are rediagnosed in light of the new species presented herein and revised keys to species are included. A dichotomous key to genera of Australasian Therevidae is included. As an empirical example of cybertaxonomy, taxonomic descriptions were composed using a character matrix developed in Lucid Builder (in Structured Descriptive Data (SDD) format) to generate natural language descriptions supplemented by online specimen and image databases. Web resources are provided throughout the document including: a) links to high resolution colour images of all species on Morphbank, b) registration of authors, publications, taxon names and other nomenclatural acts in Zoobank, with assignment of Life

  4. Revision of the stiletto fly genera Acupalpa Kröber and Pipinnipons Winterton (Diptera, Therevidae, Agapophytinae) using cybertaxonomic methods, with a key to Australasian genera.

    PubMed

    Winterton, Shaun L

    2011-05-04

    Australian stiletto flies of the sister-genera Acupalpa Kröber, 1912 and Pipinnipons Winterton, 2001 (Diptera: Therevidae: Agapophytinae) are revised. Twelve new species of Acupalpa are described, while Acupalpa imitans (White, 1915), comb. n. is transferred from Pipinnipons and Acupalpa albimanis (Kröber, 1914), comb. n. is transferred from Ectinorhynchus Macquart as a senior synonym of Acupalpa pollinosa Mann. The total number of species of Acupalpa is therefore increased to 19: Acupalpa albimanis (Kröber), comb. n., Acupalpa albitarsa Mann, Acupalpa bohartisp. n., Acupalpa divisa (Walker), Acupalpa dolichorhynchasp. n., Acupalpa glossasp. n., Acupalpa imitans (White), comb. n., Acupalpa irwini Winterton, Acupalpa melanophaeossp. n.,Acupalpa miaboolyasp. n., Acupalpa minutasp. n., Acupalpa minutoidessp. n., Acupalpa notomelassp. n., Acupalpa novayamarnasp. n., Acupalpa rostrata Kröber, Acupalpa semirufa Mann, Acupalpa westralicasp. n., Acupalpa yalgoosp. n. and Acupalpa yanchepsp. n. Three new species of Pipinnipons are described, increasing the total number of species to five: Pipinnipons chauncyvallissp. n., Pipinnipons fascipennis (Kröber), Pipinnipons kampmeieraesp. n., Pipinnipons kroeberi Winterton, and P. sphecodasp. n.Pipinnipons and Acupalpa are rediagnosed in light of the new species presented herein and revised keys to species are included. A dichotomous key to genera of Australasian Therevidae is included. As an empirical example of cybertaxonomy, taxonomic descriptions were composed using a character matrix developed in Lucid Builder (in Structured Descriptive Data (SDD) format) to generate natural language descriptions supplemented by online specimen and image databases. Web resources are provided throughout the document including: a) links to high resolution colour images of all species on Morphbank, b) registration of authors, publications, taxon names and other nomenclatural acts in Zoobank, with assignment of Life Science Identifiers (LSIDs

  5. Broadly reactive aptamers targeting bacteria belonging to different genera using a sequential toggle cell-SELEX

    PubMed Central

    Song, Min Young; Nguyen, Dung; Hong, Seok Won; Kim, Byoung Chan

    2017-01-01

    Conventional cell-SELEX aims to isolate aptamers to a single unique target bacteria species. We propose a method to isolate single-stranded DNA aptamers that have broad reactivity to multiple bacterial targets belonging to different genera. The key of the proposed method is that targets of interest are changed sequentially at each SELEX round. The general scheme was examined using six bacteria from different genera, Escherichia coli, Enterobacter aerogenes, Klebsiella pneumoniae, Citrobacter freundii, Bacillus subtilis, and Staphylococcus epidermidis (four gram-negative and two gram-positive bacteria). In the first round of SELEX, the DNA library was incubated with E. coli and amplicons bound to E. coli were separated. The amplicons were sequentially separated by incubation with E. aerogenes, K. pneumoniae, C. freundii, B. subtilis, and S. epidermidis at each SELEX. The amplicons obtained using the last bacterial species were incubated again with the first bacterial species and this loop was repeated two more times. We refer to this method as sequential toggle cell-SELEX (STC-SELEX). The isolated aptamers had dissociation constants of 9.22–38.5 nM and had no affinity to other bacteria that were not included in STC-SELEX. These results demonstrate the potential to isolate aptamers with broad affinity to bacterial taxa in different genera. PMID:28272554

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Kalapuya brunnea gen. & sp. nov. and its relationship to the other sequestrate genera in Morchellaceae.

    PubMed

    Trappe, Matthew J; Trappe, James M; Bonito, Gregory M

    2010-01-01

    Kalapuya is described as a new, monotypic truffle genus in the Morchellaceae known only from the Pacific northwestern United States. Its relationship to other hypogeous genera within Morchellaceae is explored by phylogenetic analysis of the ribosomal LSU and EF1alpha protein coding region. The type species, K. brunnea, occurs in Douglas-fir forests up to about 50 y old on the west slope of the Cascade Range in Oregon and in the Coastal Ranges of Oregon and northern California. It has a roughened, warty, reddish brown to brown peridium, a solid whitish gleba that develops grayish brown mottling as the spores mature, and produces a cheesy-garlicky odor at maturity. Its smooth, ellipsoid spores resemble those of Morchella spp. but are much larger. The four hypogeous genera known in the Morchellaceae, Kalapuya, Fischerula, Imaia and Leucangium, are distinct from the epigeous genera Morchella and Verpa, but it is uncertain whether they resulted from a single transition to a hypogeous fruiting habit or from multiple independent transitions. Kalapuya, locally known as the Oregon brown truffle, has been commercially harvested for culinary use.

  11. Sympatry inference and network analysis in biogeography.

    PubMed

    Dos Santos, Daniel A; Fernández, Hugo R; Cuezzo, María Gabriela; Domínguez, Eduardo

    2008-06-01

    A new approach for biogeography to find patterns of sympatry, based on network analysis, is proposed. Biogeographic analysis focuses basically on sympatry patterns of species. Sympatry is a network (= relational) datum, but it has never been analyzed before using relational tools such as Network Analysis. Our approach to biogeographic analysis consists of two parts: first the sympatry inference and second the network analysis method (NAM). The sympatry inference method was designed to propose sympatry hypothesis, constructing a basal sympatry network based on punctual data, independent of a priori distributional area determination. In this way, two or more species are considered sympatric when there is interpenetration and relative proximity among their records of occurrence. In nature, groups of species presenting within-group sympatry and between-group allopatry constitute natural units (units of co-occurrence). These allopatric units are usually connected by intermediary species. The network analysis method (NAM) that we propose here is based on the identification and removal of intermediary species to segregate units of co-occurrence, using the betweenness measure and the clustering coefficient. The species ranges of the units of co-occurrence obtained are transferred to a map, being considered as candidates to areas of endemism. The new approach was implemented on three different real complex data sets (one of them a classic example previously used in biogeography) resulting in (1) independence of predefined spatial units; (2) definition of co-occurrence patterns from the sympatry network structure, not from species range similarities; (3) higher stability in results despite scale changes; (4) identification of candidates to areas of endemism supported by strictly endemic species; (5) identification of intermediary species with particular biological attributes.

  12. 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.

  13. Bayesian inference for radio observations

    NASA Astrophysics Data System (ADS)

    Lochner, Michelle; Natarajan, Iniyan; Zwart, Jonathan T. L.; Smirnov, Oleg; Bassett, Bruce A.; Oozeer, Nadeem; Kunz, Martin

    2015-06-01

    New telescopes like the Square Kilometre Array (SKA) will push into a new sensitivity regime and expose systematics, such as direction-dependent effects, that could previously be ignored. Current methods for handling such systematics rely on alternating best estimates of instrumental calibration and models of the underlying sky, which can lead to inadequate uncertainty estimates and biased results because any correlations between parameters are ignored. These deconvolution algorithms produce a single image that is assumed to be a true representation of the sky, when in fact it is just one realization of an infinite ensemble of images compatible with the noise in the data. In contrast, here we report a Bayesian formalism that simultaneously infers both systematics and science. Our technique, Bayesian Inference for Radio Observations (BIRO), determines all parameters directly from the raw data, bypassing image-making entirely, by sampling from the joint posterior probability distribution. This enables it to derive both correlations and accurate uncertainties, making use of the flexible software MEQTREES to model the sky and telescope simultaneously. We demonstrate BIRO with two simulated sets of Westerbork Synthesis Radio Telescope data sets. In the first, we perform joint estimates of 103 scientific (flux densities of sources) and instrumental (pointing errors, beamwidth and noise) parameters. In the second example, we perform source separation with BIRO. Using the Bayesian evidence, we can accurately select between a single point source, two point sources and an extended Gaussian source, allowing for `super-resolution' on scales much smaller than the synthesized beam.

  14. 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.

  15. Dopamine, Affordance and Active Inference

    PubMed Central

    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. PMID:22241972

  16. Phylogeny of Barnadesioideae (Asteraceae) inferred from DNA sequence data and morphology.

    PubMed

    Gruenstaeudl, Michael; Urtubey, Estrella; Jansen, Robert K; Samuel, Rosabelle; Barfuss, Michael H J; Stuessy, Tod F

    2009-06-01

    Subfamily Barnadesioideae (Asteraceae) consists of nine genera and 91 species endemic to South America. They include annual and perennial herbs, arching shrubs and trees up to 30m tall. Presumed sister to all other Asteraceae, its intergeneric relationships are key to understanding the early evolution of the family. Results of the only molecular study on the subfamily conflict with relationships inferred from morphology. We investigate inter- and intrageneric relationships in Barnadesioideae with novel DNA sequence data and morphological characters using parsimony, likelihood and Bayesian inference. All results verify Barnadesioideae as monophyletic and sister to the rest of the family. A basal split within the subfamily is recognized, with Chuquiraga, Doniophyton and Duseniella in one clade, and Arnaldoa, Barnadesia, Dasyphyllum, Fulcaldea, Huarpea and possibly Schlechtendalia in another. The largest genus, Dasyphyllum, is revealed as biphyletic with the two clades separating along subgeneric and geographic lines. Schlechtendalia, suggested as the earliest diverging lineage of the subfamily by morphological studies and parsimony analyses, is found in a more derived position under model-based inference methods. Competing phylogenetic hypotheses, both previous and present, are evaluated using likelihood-based tests. Evolutionary trends within Barnadesioideae are inferred: hummingbird pollination has developed convergently at least three times. An early vicariance in the subfamily's distribution is revealed. X=9 is supported as the ancestral base chromosome number for both Barnadesioideae and the family as a whole.

  17. 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

  18. Feature Inference and the Causal Structure of Categories

    ERIC Educational Resources Information Center

    Rehder, B.; Burnett, R.C.

    2005-01-01

    The purpose of this article was to establish how theoretical category knowledge-specifically, knowledge of the causal relations that link the features of categories-supports the ability to infer the presence of unobserved features. Our experiments were designed to test proposals that causal knowledge is represented psychologically as Bayesian…

  19. A Review of Children's Use of Causal Inference Principles.

    ERIC Educational Resources Information Center

    Sedlak, Andrea J.; Kurtz, Susan T.

    1981-01-01

    Examines cues which guide the discovery of simple cause-effect relations, beginning with the properties (suggested by Hume) of temporal precedence, covariation and contiguity; explores variables which can influence simple causal judgments; and discusses developmental evidence regarding inference principles associated with causal schemata.…

  20. Social Inference Skills in Learning Disabled and Nondisabled Children.

    ERIC Educational Resources Information Center

    Saloner, Michele R.; Gettinger, Maribeth

    1985-01-01

    Examined the performance of 30 learning disabled and 30 nondisabled children in grades one through seven on the Test of Social Inference (TSI). Results indicated that disabled students obtained lower TSI total scores than did nondisabled students; they also performed relatively lower on TSI items requiring more verbal expression. (NRB)

  1. Quantum inferring acausal structures and the Monty Hall problem

    NASA Astrophysics Data System (ADS)

    Kurzyk, Dariusz; Glos, Adam

    2016-12-01

    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.

  2. A Study of Inference Problems in Distributed Databases

    DTIC Science & Technology

    2002-01-01

    524. [6] Denning, D. (1980) \\Secure Statistical Database with Random Sample Queries," ACM Transaction on Database Systems, 5(3), pp. 291-315. [7] Dobra ...1996) "Analyzing FD Inference in Relational Databases", Data and Knowledge Engineering Journal, vol. 18, pp. 167-183. [10] Heckerman, D. (1996) \\Bayesian...No. 3-4, pp. 225-241. [16] Marks, D. (1996) \\Inference in MLS Database Systems," IEEE Trans. Knowledge and Data Engineering , Vol 8, No. 1, pp. 46-55

  3. Quantitative evaluation of statistical inference in resting state functional MRI.

    PubMed

    Yang, Xue; Kang, Hakmook; Newton, Allen; Landman, Bennett A

    2012-01-01

    Modern statistical inference techniques may be able to improve the sensitivity and specificity of resting state functional MRI (rs-fMRI) connectivity analysis through more realistic characterization of distributional assumptions. In simulation, the advantages of such modern methods are readily demonstrable. However quantitative empirical validation remains elusive in vivo as the true connectivity patterns are unknown and noise/artifact distributions are challenging to characterize with high fidelity. Recent innovations in capturing finite sample behavior of asymptotically consistent estimators (i.e., SIMulation and EXtrapolation - SIMEX) have enabled direct estimation of bias given single datasets. Herein, we leverage the theoretical core of SIMEX to study the properties of inference methods in the face of diminishing data (in contrast to increasing noise). The stability of inference methods with respect to synthetic loss of empirical data (defined as resilience) is used to quantify the empirical performance of one inference method relative to another. We illustrate this new approach in a comparison of ordinary and robust inference methods with rs-fMRI.

  4. Generalizing memories over time: sleep and reinforcement facilitate transitive inference.

    PubMed

    Werchan, Denise M; Gómez, Rebecca L

    2013-02-01

    The use of reinforcement and rewards is known to enhance memory retention. However, the impact of reinforcement on higher-order forms of memory processing, such as integration and generalization, has not been directly manipulated in previous studies. Furthermore, there is evidence that sleep enhances the integration and generalization of memory, but these studies have only used reinforcement learning paradigms and have not examined whether reinforcement impacts or is critical for memory integration and generalization during sleep. Thus, the aims of the current study were to examine: (1) whether reinforcement during learning impacts the integration and generalization of memory; and (2) whether sleep and reinforcement interact to enhance memory integration and generalization. We investigated these questions using a transitive inference (TI) task, which is thought to require the integration and generalization of disparate relational memories in order to make novel inferences. To examine whether reinforcement influences or is required for the formation of inferences, we compared performance using a reinforcement or an observation based TI task. We examined the impact of sleep by comparing performance after a 12-h delay containing either wake or sleep. Our results showed that: (1) explicit reinforcement during learning is required to make transitive inferences and that sleep further enhances this effect; (2) sleep does not make up for the inability to make inferences when reinforcement does not occur during learning. These data expand upon previous findings and suggest intriguing possibilities for the mechanisms involved in sleep-dependent memory transformation.

  5. 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.

  6. 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.

  7. Acquiring a naive theory of kinship through inference.

    PubMed

    Springer, K

    1995-04-01

    The present study focused on how children acquire a naive theory of kinship. Young children appear to have theoretical beliefs about the biological meaning of kinship relations. It was argued here that these beliefs reflect inductive inferences from simple facts about prenatal growth (e.g, where babies grow). An informal model of the inferences linking facts to theory was proposed and tested. In Experiment 1, 4-7-year-olds who knew the basic facts of prenatal growth were most likely to also express the naive theory of kinship. Virtually none of the children who expressed the theory were unaware of the basic facts. In Experiment 2, teaching the facts to a sample of preschoolers led to some increase in their acceptance of the kinship theory. Overall, the results implicate a type of theory building that involves inferences from preexisting knowledge rather than structural change, use of analogy, or acquisition of new knowledge.

  8. 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.

  9. 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.

  10. Automated adaptive inference of phenomenological dynamical models

    NASA Astrophysics Data System (ADS)

    Daniels, Bryan C.; Nemenman, Ilya

    2015-08-01

    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.

  11. 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

  12. 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

  13. Inferring orthologous gene regulatory networks using interspecies data fusion

    PubMed Central

    Penfold, Christopher A.; Millar, Jonathan B. A.; Wild, David L.

    2015-01-01

    Motivation: The ability to jointly learn gene regulatory networks (GRNs) in, or leverage GRNs between related species would allow the vast amount of legacy data obtained in model organisms to inform the GRNs of more complex, or economically or medically relevant counterparts. Examples include transferring information from Arabidopsis thaliana into related crop species for food security purposes, or from mice into humans for medical applications. Here we develop two related Bayesian approaches to network inference that allow GRNs to be jointly inferred in, or leveraged between, several related species: in one framework, network information is directly propagated between species; in the second hierarchical approach, network information is propagated via an unobserved ‘hypernetwork’. In both frameworks, information about network similarity is captured via graph kernels, with the networks additionally informed by species-specific time series gene expression data, when available, using Gaussian processes to model the dynamics of gene expression. Results: Results on in silico benchmarks demonstrate that joint inference, and leveraging of known networks between species, offers better accuracy than standalone inference. The direct propagation of network information via the non-hierarchical framework is more appropriate when there are relatively few species, while the hierarchical approach is better suited when there are many species. Both methods are robust to small amounts of mislabelling of orthologues. Finally, the use of Saccharomyces cerevisiae data and networks to inform inference of networks in the budding yeast Schizosaccharomyces pombe predicts a novel role in cell cycle regulation for Gas1 (SPAC19B12.02c), a 1,3-beta-glucanosyltransferase. Availability and implementation: MATLAB code is available from http://go.warwick.ac.uk/systemsbiology/software/. Contact: d.l.wild@warwick.ac.uk Supplementary information: Supplementary data are available at Bioinformatics

  14. 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.

  15. Spontaneous Trait Inferences on Social Media

    PubMed Central

    Utz, Sonja

    2016-01-01

    The present research investigates whether spontaneous trait inferences occur under conditions characteristic of social media and networking sites: nonextreme, ostensibly self-generated content, simultaneous presentation of multiple cues, and self-paced browsing. We used an established measure of trait inferences (false recognition paradigm) and a direct assessment of impressions. Without being asked to do so, participants spontaneously formed impressions of people whose status updates they saw. Our results suggest that trait inferences occurred from nonextreme self-generated content, which is commonly found in social media updates (Experiment 1) and when nine status updates from different people were presented in parallel (Experiment 2). Although inferences did occur during free browsing, the results suggest that participants did not necessarily associate the traits with the corresponding status update authors (Experiment 3). Overall, the findings suggest that spontaneous trait inferences occur on social media. We discuss implications for online communication and research on spontaneous trait inferences. PMID:28123646

  16. Inferring echolocation in ancient bats.

    PubMed

    Simmons, Nancy B; Seymour, Kevin L; Habersetzer, Jörg; Gunnell, Gregg F

    2010-08-19

    Laryngeal echolocation, used by most living bats to form images of their surroundings and to detect and capture flying prey, is considered to be a key innovation for the evolutionary success of bats, and palaeontologists have long sought osteological correlates of echolocation that can be used to infer the behaviour of fossil bats. Veselka et al. argued that the most reliable trait indicating echolocation capabilities in bats is an articulation between the stylohyal bone (part of the hyoid apparatus that supports the throat and larynx) and the tympanic bone, which forms the floor of the middle ear. They examined the oldest and most primitive known bat, Onychonycteris finneyi (early Eocene, USA), and argued that it showed evidence of this stylohyal-tympanic articulation, from which they concluded that O. finneyi may have been capable of echolocation. We disagree with their interpretation of key fossil data and instead argue that O. finneyi was probably not an echolocating bat.

  17. Motion Inference During +Gz Acceleration

    DTIC Science & Technology

    2006-09-01

    AFRL-HW-WP-TP-2006-0091 Motion Inference During +Gz Acceleration Lloyd D . Tripp Jr. Richard A. McKinley Robert L. Esken Air Force Research Laboratory...5c. PROGRAM ELEMENT NUMBER 62202F 6. AUTHOR(S) 5d. PROJECT NUMBER Lloyd D . Tripp Jr 7184 Richard A. McKinley 5e. TASK NUMBER Robert L. Esken 03 5f...CD A Cj CL.C2 C 0~ 0. D 0 0~G)C00.E)’ca)4-100 ( 0 Eo12 E a 0 0L0mm 0a0 " C0 U) U) LUr o CLI.,a @ .- . : ) 0 " 0 C CL.. 70 E- 0 M 0.0 toE-C .- 0)c .2 0UL

  18. Inferred properties of stellar granulation

    SciTech Connect

    Gray, D.F.; Toner, C.G.

    1985-06-01

    Apparent characteristics of stellar granulation in F and G main-sequence stars are inferred directly from observed spectral-line asymmetries and from comparisons of numerical simulations with the observations: (1) the apparent granulation velocity increases with effective temperature, (2) the dispersion of granule velocities about their mean velocity of rise increases with the apparent granulation velocity, (3) the mean velocity of rise of granules must be less than the total line broadening, (4) the apparent velocity difference between granules and dark lanes corresponds to the granulation velocity deduced from stellar line bisectors, (5) the dark lanes show velocities of fall approximately twice as large as the granule rise velocities, (6) the light contributed to the stellar flux by the granules is four to ten times more than the light from the dark lanes. Stellar rotation is predicted to produce distortions in the line bisectors which may give information on the absolute velocity displacements of the line bisectors. 37 references.

  19. Synaptic Computation Underlying Probabilistic Inference

    PubMed Central

    Soltani, Alireza; Wang, Xiao-Jing

    2010-01-01

    In this paper we propose that synapses may be the workhorse of neuronal computations that underlie probabilistic reasoning. We built a neural circuit model for probabilistic inference when information provided by different sensory cues needs to be integrated, and the predictive powers of individual cues about an outcome are deduced through experience. We found that bounded synapses naturally compute, through reward-dependent plasticity, the posterior probability that a choice alternative is correct given that a cue is presented. Furthermore, a decision circuit endowed with such synapses makes choices based on the summated log posterior odds and performs near-optimal cue combination. The model is validated by reproducing salient observations of, and provide insights into, a monkey experiment using a categorization task. Our model thus suggests a biophysical instantiation of the Bayesian decision rule, while predicting important deviations from it similar to ‘base-rate neglect’ observed in human studies when alternatives have unequal priors. PMID:20010823

  20. 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.…

  1. Children's Causal Inferences from Indirect Evidence: Backwards Blocking and Bayesian Reasoning in Preschoolers

    ERIC Educational Resources Information Center

    Sobel, David M.; Tenenbaum, Joshua B.; Gopnik, Alison

    2004-01-01

    Previous research suggests that children can infer causal relations from patterns of events. However, what appear to be cases of causal inference may simply reduce to children recognizing relevant associations among events, and responding based on those associations. To examine this claim, in Experiments 1 and 2, children were introduced to a…

  2. Generic comparison of protein inference engines.

    PubMed

    Claassen, Manfred; Reiter, Lukas; Hengartner, Michael O; Buhmann, Joachim M; Aebersold, Ruedi

    2012-04-01

    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.

  3. 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.

  4. 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

  5. New taxa, including three new genera show uniqueness of Neotropical Nepticulidae (Lepidoptera).

    PubMed

    van Nieukerken, Erik J; Doorenweerd, Camiel; Nishida, Kenji; Snyers, Chris

    2016-01-01

    After finding distinct clades in a molecular phylogeny for Nepticulidae that could not be placed in any known genera and discovering clear apomorphic characters that define these clades, as well as a number of Neotropical species that could be placed in known genera but were undescribed, three new genera and nine new species are here described from the Neotropics: Stigmella gallicola van Nieukerken & Nishida, sp. n. reared from galls on Hampea appendiculata (Malvaceae) in Costa Rica, representing the first example of a gall making Stigmella; Stigmella schinivora van Nieukerken, sp. n. reared from leafmines on Schinus terebinthifolia (Anacardiaceae) in Argentina, Misiones; Stigmella costaricensis van Nieukerken & Nishida, sp. n. and Stigmella intronia van Nieukerken & Nishida, sp. n. each from a single specimen collected the same night in Costa Rica, Parque Nacional Chirripó; Stigmella molinensis van Nieukerken & Snyers, sp. n. reared from leafmines on Salix humboldtiana, Peru, Lima, the first Neotropical species of the Stigmella salicis group sensu stricto; Ozadelpha van Nieukerken, gen. n. with type species Ozadelpha conostegiae van Nieukerken & Nishida, sp. n., reared from leafmines on Conostegia oerstediana (Melastomataceae) from Costa Rica; Neotrifurcula van Nieukerken, gen. n. with type species Neotrifurcula gielisorum van Nieukerken, sp. n. from Chile; Hesperolyra van Nieukerken, gen. n.. with type species Fomoria diskusi Puplesis & Robinson, 2000; Hesperolyra saopaulensis van Nieukerken, sp. n., reared from an unidentified Myrtaceae, Sao Paulo, Brasil; and Acalyptris janzeni van Nieukerken & Nishida, sp. n. from Costa Rica, Guanacaste. Five new combinations are made: Ozadelpha ovata (Puplesis & Robinson, 2000), comb. n. and Ozadelpha guajavae (Puplesis & Diškus, 2002), comb. n., Hesperolyra diskusi (Puplesis & Robinson, 2000), comb. n., Hesperolyra molybditis (Zeller, 1877), comb. n. and Hesperolyra repanda (Puplesis & Diškus, 2002), comb. n. Three

  6. New taxa, including three new genera show uniqueness of Neotropical Nepticulidae (Lepidoptera)

    PubMed Central

    van Nieukerken, Erik J.; Doorenweerd, Camiel; Nishida, Kenji; Snyers, Chris

    2016-01-01

    Abstract After finding distinct clades in a molecular phylogeny for Nepticulidae that could not be placed in any known genera and discovering clear apomorphic characters that define these clades, as well as a number of Neotropical species that could be placed in known genera but were undescribed, three new genera and nine new species are here described from the Neotropics: Stigmella gallicola van Nieukerken & Nishida, sp. n. reared from galls on Hampea appendiculata (Malvaceae) in Costa Rica, representing the first example of a gall making Stigmella; Stigmella schinivora van Nieukerken, sp. n. reared from leafmines on Schinus terebinthifolia (Anacardiaceae) in Argentina, Misiones; Stigmella costaricensis van Nieukerken & Nishida, sp. n. and Stigmella intronia van Nieukerken & Nishida, sp. n. each from a single specimen collected the same night in Costa Rica, Parque Nacional Chirripó; Stigmella molinensis van Nieukerken & Snyers, sp. n. reared from leafmines on Salix humboldtiana, Peru, Lima, the first Neotropical species of the Stigmella salicis group sensu stricto; Ozadelpha van Nieukerken, gen. n. with type species Ozadelpha conostegiae van Nieukerken & Nishida, sp. n., reared from leafmines on Conostegia oerstediana (Melastomataceae) from Costa Rica; Neotrifurcula van Nieukerken, gen. n. with type species Neotrifurcula gielisorum van Nieukerken, sp. n. from Chile; Hesperolyra van Nieukerken, gen. n.. with type species Fomoria diskusi Puplesis & Robinson, 2000; Hesperolyra saopaulensis van Nieukerken, sp. n., reared from an unidentified Myrtaceae, Sao Paulo, Brasil; and Acalyptris janzeni van Nieukerken & Nishida, sp. n. from Costa Rica, Guanacaste. Five new combinations are made: Ozadelpha ovata (Puplesis & Robinson, 2000), comb. n. and Ozadelpha guajavae (Puplesis & Diškus, 2002), comb. n., Hesperolyra diskusi (Puplesis & Robinson, 2000), comb. n., Hesperolyra molybditis (Zeller, 1877), comb. n. and Hesperolyra repanda (Puplesis & Diškus, 2002), comb. n

  7. 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.

  8. Aoteasalda and Kiwisaldula, two new genera of Saldidae (Hemiptera: Heteroptera), with a key to New Zealand genera and a new synonymy in Zemacrosaldula.

    PubMed

    Larivière, Marie-Claude; Larochelle, André

    2016-03-04

    Aoteasalda new genus, is described with Saldula maculipennis Cobben, 1961, as type species, resulting in the following new combination Aoteasalda maculipennis (Cobben, 1961). Kiwisaldula new genus, is described with Saldula parvula Cobben, 1961, as type species. The following new combinations are made: Kiwisaldula parvula (Cobben, 1961); Kiwisaldula butleri (White, 1878); Kiwisaldula laelaps (White, 1878); Kiwisaldula stoneri (Drake & Hoberlandt, 1950). Two species are described as new: Kiwisaldula manawatawhi new species, Kiwisaldula porangahau new species. A lectotype is designated for Salda laelaps White, 1878. The holotype of Salda butleri White, 1878, and the type series of Saldula trivialis Cobben, 1961, and Saldula maculipennis Cobben, 1961, are documented. A new synonymy is established in the genus Zemacrosaldula (valid name listed after equal sign): Saldula trivialis Cobben, 1961 = Zemacrosaldula australis (White, 1876). A revision of the taxonomy of Aoteasalda and Kiwisaldula species occurring on New Zealand's North Island and nearby offshore islands, is presented. Morphological descriptions are provided, with illustrations emphasising the most significant diagnostic features of the external morphology and male genitalia. Information is given on synonymy, type data, material examined, geographic distribution, and biology. Species of Kiwisaldula and genera of Saldidae recognised for New Zealand, are keyed.

  9. Taxonomic study on Korean Aphyllophorales (5) - on some unrecorded genera and species -

    PubMed Central

    Lee, Jin Sung

    2006-01-01

    A total of 149 species and 209 strains of Korean Aphyllophorales in Seoul National University Fungus Collection (SFC) were analyzed by taxonomic and phylogenetic methods. Among those examined fungal specimens, 9 genera Abundisporus, Antrodiella, Cyphellopsis, Dendrothele, Dichomitus, Laxitextum, Piloderma, Skeletocutis and Tubulicrinis, and 23 species, Abundisporus fuscopurpureus, Antrodiella semisupina, Auriporia pileata, Cantharellus subalbidus, Clavulina cinerea, Cyphellopsis confusa, Dendrothele acerina, Dichomitus campestris, Haplotrichum aureum, Heterobasidion annosum, Hyphoderma argillaceum, Hyphodontia tropica, Inonotus dryophilus, Ischnoderma benzoinum, Laxitextum bicolor, Phanerochaete radicata, Phellinus lonicericola, Piloderma byssinum, Skeletocutis nivea, Tomentella terrestris, Trametes elegans, Trametes tenuis, and Tubulicrinis accedens were confirmed as new to Korea and registered here with descriptions. PMID:24039493

  10. Terfezia disappears from the American truffle mycota as two new genera and Mattirolomyces species emerge.

    PubMed

    Kovács, Gábor M; Trappe, James M; Alsheikh, Abdulmagid M; Hansen, Karen; Healy, Rosanne A; Vági, Pál

    2011-01-01

    Reexamination and molecular phylogenetic analyses of American Terfezia species and Mattirolomyces tiffanyae revealed that their generic assignments were wrong. Therefore we here propose these combinations: Mattirolomyces spinosus comb. nov. (≡ Terfezia spinosa), Stouffera longii gen. & comb. nov. (≡ Terfezia longii) and Temperantia tiffanyae gen. & comb. nov. (≡ Mattirolomyces tiffanyae). In addition we describe a new species, Mattirolomyces mexicanus spec. nov. All species belong to the Pezizaceae. Based on these results Terfezia is not known from North America, Mattirolomyces is represented by two species and two new monotypic genera are present.

  11. Spatial partitioning of host habitat by chewing lice of the genera Geomydoecus and Thomomydoecus (Phthiraptera: Trichodectidae).

    PubMed

    Reed, D L; Hafner, M S; Allen, S K; Smith, M B

    2000-10-01

    Chewing lice, Geomydoecus and Thomomydoecus, coexist on pocket gophers, Thomomys spp. We investigated the spatial distribution of the 2 genera on their hosts and explored possible mechanisms of resource partitioning by chewing lice. Chewing lice appear to partition available host resources spatially, with Geomydoecus occurring primarily on the lateral and dorsal regions of the host, and Thomomydoecus occurring primarily on the lateral and ventral regions. Although spatial partitioning of the host habitat is evident, it does not appear to be explained by hair diameter. Spatial partitioning of the host's body could be the result of some other factor, possibly temperature or humidity gradients of the host's body.

  12. 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.

  13. 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

  14. Synaptic and nonsynaptic plasticity approximating probabilistic inference

    PubMed Central

    Tully, Philip J.; Hennig, Matthias H.; Lansner, Anders

    2014-01-01

    Learning and memory operations in neural circuits are believed to involve molecular cascades of synaptic and nonsynaptic changes that lead to a diverse repertoire of dynamical phenomena at higher levels of processing. Hebbian and homeostatic plasticity, neuromodulation, and intrinsic excitability all conspire to form and maintain memories. But it is still unclear how these seemingly redundant mechanisms could jointly orchestrate learning in a more unified system. To this end, a Hebbian learning rule for spiking neurons inspired by Bayesian statistics is proposed. In this model, synaptic weights and intrinsic currents are adapted on-line upon arrival of single spikes, which initiate a cascade of temporally interacting memory traces that locally estimate probabilities associated with relative neuronal activation levels. Trace dynamics enable synaptic learning to readily demonstrate a spike-timing dependence, stably return to a set-point over long time scales, and remain competitive despite this stability. Beyond unsupervised learning, linking the traces with an external plasticity-modulating signal enables spike-based reinforcement learning. At the postsynaptic neuron, the traces are represented by an activity-dependent ion channel that is shown to regulate the input received by a postsynaptic cell and generate intrinsic graded persistent firing levels. We show how spike-based Hebbian-Bayesian learning can be performed in a simulated inference task using integrate-and-fire (IAF) neurons that are Poisson-firing and background-driven, similar to the preferred regime of cortical neurons. Our results support the view that neurons can represent information in the form of probability distributions, and that probabilistic inference could be a functional by-product of coupled synaptic and nonsynaptic mechanisms operating over several timescales. The model provides a biophysical realization of Bayesian computation by reconciling several observed neural phenomena whose

  15. Spurious correlations and inference in landscape genetics.

    PubMed

    Cushman, Samuel A; Landguth, Erin L

    2010-09-01

    Reliable interpretation of landscape genetic analyses depends on statistical methods that have high power to identify the correct process driving gene flow while rejecting incorrect alternative hypotheses. Little is known about statistical power and inference in individual-based landscape genetics. Our objective was to evaluate the power of causal-modelling with partial Mantel tests in individual-based landscape genetic analysis. We used a spatially explicit simulation model to generate genetic data across a spatially distributed population as functions of several alternative gene flow processes. This allowed us to stipulate the actual process that is in action, enabling formal evaluation of the strength of spurious correlations with incorrect models. We evaluated the degree to which naïve correlational approaches can lead to incorrect attribution of the driver of observed genetic structure. Second, we evaluated the power of causal modelling with partial Mantel tests on resistance gradients to correctly identify the explanatory model and reject incorrect alternative models. Third, we evaluated how rapidly after the landscape genetic process is initiated that we are able to reliably detect the effect of the correct model and reject the incorrect models. Our analyses suggest that simple correlational analyses between genetic data and proposed explanatory models produce strong spurious correlations, which lead to incorrect inferences. We found that causal modelling was extremely effective at rejecting incorrect explanations and correctly identifying the true causal process. We propose a generalized framework for landscape genetics based on analysis of the spatial genetic relationships among individual organisms relative to alternative hypotheses that define functional relationships between landscape features and spatial population processes.

  16. Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands.

    PubMed

    Vinuesa, Pablo; Silva, Claudia; Lorite, María José; Izaguirre-Mayoral, María Luisa; Bedmar, Eulogio J; Martínez-Romero, Esperanza

    2005-10-01

    A well-resolved rhizobial species phylogeny with 51 haplotypes was inferred from a combined atpD + recA data set using Bayesian inference with best-fit, gene-specific substitution models. Relatively dense taxon sampling for the genera Rhizobium and Mesorhizobium was achieved by generating atpD and recA sequences for six type and 24 reference strains not previously available in GenBank. This phylogeny was used to classify nine nodule isolates from Sesbania exasperata, S. punicea and S. sericea plants native to seasonally flooded areas of Venezuela, and compared with a PCR-RFLP analysis of rrs plus rrl genes and large maximum likelihood rrs and nifH phylogenies. We show that rrs phylogenies are particularly sensitive to strain choice due to the high levels of sequence mosaicism found at this locus. All analyses consistently identified the Sesbania isolates as Mesorhizobium plurifarium or Rhizobium huautlense. Host range experiments on ten legume species coupled with plasmid profiling uncovered potential novel biovarieties of both species. This study demonstrates the wide geographic and environmental distribution of M. plurifarium, that R. galegae and R. huautlense are sister lineages, and the synonymy of R. gallicum, R. mongolense and R. yanglingense. Complex and diverse phylogeographic, inheritance and host-association patterns were found for the symbiotic nifH locus. The results and the analytical approaches used herein are discussed in the context of rhizobial taxonomy and molecular systematics.

  17. 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.

  18. 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

  19. Persanura hyrcanica, a new genus and species of Neanurinae (Collembola: Neanuridae) from Iran, with a key to genera of the tribe Neanurini.

    PubMed

    Mayvan, Mahmood Mehrafroz; Shayanmehr, Masoumeh; Smolis, Adrian; Skarżyński, Dariusz

    2015-02-13

    Persanura hyrcanica, a new genus and species of Neanurini from Iran is described and illustrated. It has a unique suite of morphological characters: labrum with only 4 chaetae, fusion of tubercles So and L on head, tubercle Di on th. II-III with 2 chaetae and separation of tubercles Di on abd. V. The erected genus is closely related to Neanura MacGillivray, 1893, Kalanura Smolis, 2007 and Xylanura Smolis, 2011. An updated key to genera of the tribe Neanurini is given.

  20. MonotomidGen – A matrix-based interactive key to the New World genera of Monotomidae (Coleoptera, Cucujoidea)

    PubMed Central

    McElrath, Thomas C.; Boyd, Olivia F.; McHugh, Joseph V.

    2016-01-01

    Abstract A matrix-based LucidTM key is presented for the twelve genera of Monotomidae (Coleoptera: Cucujoidea) represented in the New World. A general overview is given for the features and technical specifications of an original interactive key for the identification of these genera. The list of terminal taxa included with the key provides a current summary of monotomid generic diversity for the Nearctic and Neotropical regions. PMID:27917049

  1. A Comparison of Two Student Instructional Rating Forms Utilizing High-Inference Versus Moderate Inference Items.

    ERIC Educational Resources Information Center

    Wilson, Pamela W.

    Two types of items used in student evaluations of college teaching were compared: high-inference items, which require considerable inferring from what is seen or heard in the classroom to labelling of teacher behavior; and moderate-inference items, such as "teacher listens carefully." Two instruments were administered to random halves of…

  2. 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.

  3. Discovering the Unknown: Improving Detection of Novel Species and Genera from Short Reads

    DOE PAGES

    Rosen, Gail L.; Polikar, Robi; Caseiro, Diamantino 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

  4. Description of new genera and species of marine cyanobacteria from the Portuguese Atlantic coast.

    PubMed

    Brito, Ângela; Ramos, Vitor; Mota, Rita; Lima, Steeve; Santos, Arlete; Vieira, Jorge; Vieira, Cristina P; Kaštovský, Jan; Vasconcelos, Vitor M; Tamagnini, Paula

    2017-03-06

    Aiming at increasing the knowledge on marine cyanobacteria from temperate regions, we previously isolated and characterized 60 strains from the Portuguese foreshore and evaluate their potential to produce secondary metabolites. About 15% of the obtained 16S rRNA gene sequences showed less than 97% similarity to sequences in the databases revealing novel biodiversity. Herein, seven of these strains were extensively characterized and their classification was re-evaluated. The present study led to the proposal of five new taxa, three genera (Geminobacterium, Lusitaniella, and Calenema) and two species (Hyella patelloides and Jaaginema litorale). Geminobacterium atlanticum LEGE 07459 is a chroococcalean that shares morphological characteristics with other unicellular cyanobacterial genera but has a distinct phylogenetic position and particular ultrastructural features. The description of the Pleurocapsales Hyella patelloides LEGE 07179 includes novel molecular data for members of this genus. The filamentous isolates of Lusitaniella coriacea - LEGE 07167, 07157 and 06111 - constitute a very distinct lineage, and seem to be ubiquitous on the Portuguese coast. Jaaginema litorale LEGE 07176 has distinct characteristics compared to their marine counterparts, and our analysis indicates that this genus is polyphyletic. The Synechococcales Calenema singularis possess wider trichomes than Leptolyngbya, and its phylogenetic position reinforces the establishment of this new genus.

  5. Invalidation of Hyperamoeba by transferring its species to other genera of Myxogastria.

    PubMed

    Fiore-Donno, Anna Maria; Kamono, Akiko; Chao, Ema E; Fukui, Manabu; Cavalier-Smith, Thomas

    2010-01-01

    The genus Hyperamoeba Alexeieff, 1923 was established to accommodate an aerobic amoeba exhibiting three life stages-amoeba, flagellate, and cyst. As more species/strains were isolated, it became increasingly evident from small subunit (SSU) gene phylogenies and ultrastructure that Hyperamoeba is polyphyletic and its species occupy different positions within the class Myxogastria. To pinpoint Hyperamoeba strains within other myxogastrid genera we aligned numerous myxogastrid sequences: whole small subunit ribosomal (SSU or 18S rRNA) gene for 50 dark-spored (i.e. Stemonitida and Physarida) Myxogastria (including a new "Hyperamoeba"/Didymium sequence) and a approximately 400-bp SSU fragment for 147 isolates assigned to 10 genera of the order Physarida. Phylogenetic analyses show unambiguously that the type species Hyperamoeba flagellata is a Physarum (Physarum flagellatum comb. nov.) as it nests among other Physarum species as robust sister to Physarum didermoides. Our trees also allow the following allocations: five Hyperamoeba strains to the genus Stemonitis; Hyperamoeba dachnaya, Pseudodidymium cryptomastigophorum, and three other Hyperamoeba strains to the genus Didymium; and two further Hyperamoeba strains to the family Physaridae. We therefore abandon the polyphyletic and redundant genus Hyperamoeba. We discuss the implications for the ecology and evolution of Myxogastria, whose amoeboflagellates are more widespread than previous inventories supposed, being now found in freshwater and even marine environments.

  6. Dominant genera of cyanobacteria in Lake Taihu and their relationships with environmental factors.

    PubMed

    Feng, Lijun; Liu, Shiyou; Wu, Wenxian; Ma, Jiawen; Li, Pei; Xu, Hailing; Li, Na; Feng, Yaoyu

    2016-07-01

    Cyanobacterial blooms in freshwaters have become one of the most widespread of environmental problems and threaten water resources worldwide. Previous studies on cyanobacteria in Lake Taihu often collected samples from one site (like Meiliang Bay or Zhushan Bay) and focused on the variation in patterns or abundance of Microcystis during the blooming season. However, the distribution of cyanobacteria in Lake Taihu shows differing pattern in various seasons. In this study, water samples were collected monthly for one year at five sites in Lake Taihu with different trophic status and a physicochemical analysis and denaturing gradient gel electrophoresis (DGGE) were conducted. DGGE fingerprint analysis showed that Microcystis (7/35 bands) and Synechococcus (12/35 bands) were the two most dominant genera present during the study period at all five sites. Cyanobium (3/35 bands) was the third most common genus which has seldom been previously reported in Lake Taihu. Redundancy analysis (RDA) indicated that the cyanobacterial community structure was significantly correlated with NO3 (-)-N, CODMn, and NH4 (+)-N in the winter and spring, whereas it was correlated with water temperature in the summer and autumn. Limiting the nutrient input (especially of N and C loading) in Lake Taihu would be a key factor in controlling the growth of different genera of cyanobacteria.

  7. Discovering the unknown: improving detection of novel species and genera from short reads.

    PubMed

    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 their 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 the performance of several algorithms on a real acid mine drainage dataset.

  8. Discovering the Unknown: Improving Detection of Novel Species and Genera from Short Reads

    PubMed Central

    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 their 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 the performance of several algorithms on a real acid mine drainage dataset. PMID:21541181

  9. Phylogenetic relationships and divergence dates of the whole mitochondrial genome sequences among three gibbon genera.

    PubMed

    Matsudaira, Kazunari; Ishida, Takafumi

    2010-05-01

    Phylogenetic relationships of gibbons (4 genera, 12 species) deduced from short/partial mitochondrial DNA sequences were with low resolution and inconsistent. Their divergence over the short period of time may require longer sequences for the higher resolution. To solve the problems, we newly sequenced the whole mitochondrial genome of Hylobates agilis, Hylobates pileatus, Nomascus sp. and Symphalangus syndactylus. A highly resolved phylogenetic tree was obtained for the mitochondrial genome in the neighbor-joining, maximum-parsimony and maximum-likelihood analyses. The divergence dates of mitochondrial genome were estimated by Bayesian method; Nomascus and the other two genera to 8.0 million years ago (MYA), Symphalangus and Hylobates to 7.0 MYA, Hylobates pileatus and the other two Hylobates species to 3.9 MYA and Hylobates lar and Hylobates agilis to 3.3 MYA. Our results support the generic rank of Nomascus, Symphalangus and Hylobates, and proposed a new scenario that the Hylobates gibbons diverged in the Pliocene. This study shows the potential of the whole mitochondrial genome analyses to reveal detailed divergence history of gibbons.

  10. 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.

  11. Forward and Backward Inference in Spatial Cognition

    PubMed Central

    Penny, Will D.; Zeidman, Peter; Burgess, Neil

    2013-01-01

    This paper shows that the various computations underlying spatial cognition can be implemented using statistical inference in a single probabilistic model. Inference is implemented using a common set of ‘lower-level’ computations involving forward and backward inference over time. For example, to estimate where you are in a known environment, forward inference is used to optimally combine location estimates from path integration with those from sensory input. To decide which way to turn to reach a goal, forward inference is used to compute the likelihood of reaching that goal under each option. To work out which environment you are in, forward inference is used to compute the likelihood of sensory observations under the different hypotheses. For reaching sensory goals that require a chaining together of decisions, forward inference can be used to compute a state trajectory that will lead to that goal, and backward inference to refine the route and estimate control signals that produce the required trajectory. We propose that these computations are reflected in recent findings of pattern replay in the mammalian brain. Specifically, that theta sequences reflect decision making, theta flickering reflects model selection, and remote replay reflects route and motor planning. We also propose a mapping of the above computational processes onto lateral and medial entorhinal cortex and hippocampus. PMID:24348230

  12. Application of Transformations in Parametric Inference

    ERIC Educational Resources Information Center

    Brownstein, Naomi; Pensky, Marianna

    2008-01-01

    The objective of the present paper is to provide a simple approach to statistical inference using the method of transformations of variables. We demonstrate performance of this powerful tool on examples of constructions of various estimation procedures, hypothesis testing, Bayes analysis and statistical inference for the stress-strength systems.…