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Sample records for cylindrocladium anamorphs species

  1. Calonectria species and their Cylindrocladium anamorphs: species with clavate vesicles

    PubMed Central

    Crous, Pedro W.; Groenewald, Johannes Z.; Risède, Jean-Michel; Simoneau, Philippe; Hyde, Kevin D.

    2006-01-01

    The present study compares all known species of Cylindrocladium that have clavate vesicles. Several isolates were obtained from baited soils collected in various parts of the world, while others were associated with leaf litter or symptomatic plant hosts. Isolates were compared based on morphology, as well as DNA sequence data from their β-tubulin and histone gene H3 regions. Cylindrocladium australiense and Cy. ecuadoriae, are described as new species, a decision based on morphology and molecular data. A group of isolates associated with toppling disease of banana in the West Indies is identified as Cy. flexuosum. An epitype is designated for Cy. ilicicola, and a new name, Curvicladiella, proposed to replace the anamorphic genus Curvicladium, which is a homonym. PMID:18490981

  2. Taxonomy and phylogenetic relationships of nine species of Hypocrea with anamorphs assignable to Trichoderma section Hypocreanum

    PubMed Central

    Overton, Barrie E.; Stewart, Elwin L.; Geiser, David M.

    2006-01-01

    Morphological studies and phylogenetic analyses of DNA sequences from the internal transcribed spacer (ITS) regions of the nuclear ribosomal gene repeat, a partial sequence of RNA polymerase II subunit (rpb2), and a partial sequence of the large exon of tef1 (LEtef1) were used to investigate the taxonomy and systematics of nine Hypocrea species with anamorphs assignable to Trichoderma sect. Hypocreanum. Hypocrea corticioides and H. sulphurea are reevaluated. Their Trichoderma anamorphs are described and the phylogenetic positions of these species are determined. Hypocrea sulphurea and H. subcitrina are distinct species based on studies of the type specimens. Hypocrea egmontensis is a facultative synonym of the older name H. subcitrina. Hypocrea with anamorphs assignable to Trichoderma sect. Hypocreanum formed a well-supported clade. Five species with anamorphs morphologically similar to sect. Hypocreanum, H. avellanea, H. parmastoi, H. megalocitrina, H. alcalifuscescens, and H. pezizoides, are not located in this clade. Protocrea farinosa belongs to Hypocrea s.s. PMID:18490989

  3. Two new Ophiostoma species with Sporothrix anamorphs from Austria and Azerbaijan.

    PubMed

    Aghayeva, Dilzara N; Wingfield, Michael J; de Beer, Z Wilhelm; Kirisits, Thomas

    2004-01-01

    The genus Ophiostoma includes numerous species of primarily insect-vectored, wood-staining fungi. Several anamorph genera that differ in their micronematous or macronematous conidiogenous cells have been associated with Ophiostoma species. Among the former group, Sporothrix is associated with many species and is characterized by conidiogenous cells that arise laterally or terminally from any place on the hyphae and produce nonseptate conidia on sympodially developing denticles. The purpose of this study was to characterize ophiostomatoid isolates with Sporothrix anamorphs recently collected in Austria and Azerbaijan. The isolates were characterized based on comparisons of rDNA and β-tubulin sequence data. Morphology, growth in culture, and sexual reproductive mode were also considered. Phylogenetic analyses of the combined sequence data showed that the isolates formed two distinct groups, one including isolates from Austria and the other isolates from Austria and Azerbaijan. Growth at 25 C and morphology revealed some differences between the two groups, and supported the view that they represent two new species, which we describe here as Ophiostoma fusiforme sp. nov. and Ophiostoma lunatum sp. nov. Both these groups phylogenetically were related to, but distinct from, Ophiostoma stenoceras.

  4. Polyphasic taxonomy of the basidiomycetous yeast genus Rhodosporidium: Rhodosporidium kratochvilovae and related anamorphic species.

    PubMed

    Sampaio, J P; Gadanho, M; Santos, S; Duarte, F L; Pais, C; Fonseca, A; Fell, J W

    2001-03-01

    The phenotypic and genetic heterogeneity of the basidiomycetous yeast species Rhodosporidium kratochvilovae was investigated in a group of recent isolates and collection strains. A polyphasic taxonomic approach was followed which included micromorphological studies, nuclear staining, determination of sexual compatibility, physiological characterization, comparison of electrophoretic isoenzyme patterns, PCR fingerprinting, determination of mol% G+C, DNA-DNA reassociation experiments and 26S and ITS rDNA sequence analysis. The results allowed a more natural circumscription of the species, both from the genetic and phenotypic perspectives. The relationships with anamorphic species of the genus Rhodotorula were studied and isolates previously identified as Rhodotorula glutinis were found to belong to Rhodosporidium kratochvilovae. Other isolates included in the study were found to represent members of Rhodotorula glutinis var. dairenensis. Rhodosporidium kratochvilovae was found to include heterothallic strains, besides those already known to be self-sporulating. A total of 17 isolates, which were found to belong to this species, were heterothallic, self-sporulating and anamorphic strains. It is anticipated that integrated polyphasic studies of basidiomycetous yeasts will provide a more coherent classification system and the basis for accurate identification schemes, which in turn are essential for detailed ecological studies.

  5. Anamorphic Art

    ERIC Educational Resources Information Center

    Foster, Colin

    2006-01-01

    During the 17th century, Baroque decoration used anamorphism to combine actual architectural elements with illusionistic painting. When viewed from a particular point in space, the architecture blends with painting to form a combined image. In this article, Julian Beever, a leading anamorphic pavement artist, explains to the author the principles…

  6. Cryptococcus rajasthanensis sp. nov., an anamorphic yeast species related to Cryptococcus laurentii, isolated from Rajasthan, India.

    PubMed

    Saluja, Puja; Prasad, G S

    2007-02-01

    Two novel anamorphic yeast strains (S-15LT and 3-C1) were isolated from the inflorescences of plants collected in two different towns in Rajasthan State, India. Sequencing of the D1/D2 domains of the large-subunit (LSU) rDNA and the internal transcribed spacer (ITS) regions suggested they are strains of the same species. Phenotypic characteristics such as the absence of fermentation, the absence of sexual structures and ballistoconidia, the assimilation of myo-inositol and d-glucuronate, and positive Diazonium blue B and urease reactions indicated that these strains belong to the genus Cryptococcus. The novel strains differed from Cryptococcus laurentii in six physiological tests and differed from other related species in more than six tests. A phylogenetic analysis of the sequences of the D1/D2 domains of the LSU rDNA and the ITS regions placed these strains in the Bulleromyces clade within the order Tremellales, with C. laurentii as their closest described relative. The novel strains showed 1.6 and 7.5 % divergence in the D1/D2 domain of the LSU rDNA and ITS regions, respectively, with respect to C. laurentii. The divergence from other species was more than 3 % for the D1/D2 domain and more than 9 % for the ITS region. On the basis of the phenotypic and molecular data, strains S-15LT and 3-C1 represent a novel species within the genus Cryptococcus, for which the name Cryptococcus rajasthanensis sp. nov. is proposed. The type strain is S-15LT (=MTCC 7075T=CBS 10406T).

  7. A revision of Cyanonectria and Geejayessia gen. nov., and related species with Fusarium-like anamorphs

    PubMed Central

    Schroers, H.-J.; Gräfenhan, T.; Nirenberg, H.I.; Seifert, K.A.

    2011-01-01

    A revision of Fusarium-like species associated with the plant genus Buxus led to a reconsideration of generic concepts in the Fusarium clade of the Nectriaceae. Phylogenetic analyses of the partial second largest subunit of the RNA polymerase II (rpb2) and the larger subunit of the ATP citrate lyase (acl1) gene exons confirm the existence of a clade, here called the terminal Fusarium clade, that includes genera such as Fusarium sensu stricto (including its Gibberella teleomorphs), Albonectria, Cyanonectria, “Haematonectria”, the newly described genus Geejayessia, and “Nectria” albida. Geejayessia accommodates five species. Four were previously classified in Nectria sensu lato, namely the black perithecial, KOH–species G. atrofusca and the orange or reddish, KOH+ G. cicatricum, G. desmazieri and G. zealandica. Geejayessia celtidicola is newly described. Following our phylogenetic analyses showing its close relationship with Cyanonectria cyanostoma, the former Gibbera buxi is recombined as the second species of Cyanonectria. A three gene phylogenetic analysis of multiple strains of each morphological species using translation elongation factor 1 α (tef-1), rpb2 and acl1 gene exons and introns confirms their status as distinct phylogenetic species. Internal transcribed spacer of the ribosomal RNA gene cluster and nuclear large ribosomal subunit sequences were generated as additional DNA barcodes for selected strains. The connection of Fusarium buxicola, often erroneously reported as the anamorph of G. desmazieri, with the bluish black and KOH+ perithecial species C. buxi is reinstated. Most Cyanonectria and Geejayessia species exhibit restricted host ranges on branches or twigs of Buxus species, Celtis occidentalis, or Staphylea trifolia. Their perithecia form caespitose clusters on well-developed, mostly erumpent stromata on the bark or outer cortex of the host and are relatively thin-walled, mostly smooth, and therefore reminiscent of the more or less

  8. Botryosphaeria corticola, sp. nov. on Quercus species, with notes and description of Botryosphaeria stevensii and its anamorph, Diplodia mutila.

    PubMed

    Alves, Artur; Correia, António; Luque, Jordi; Phillips, Alan

    2004-01-01

    Botr yosphaeria stevensii frequently has been associated with dieback and canker diseases of oak, mainly in the western Mediterranean area but more rarely in other regions. The species concept of B. stevensii has been unclear, and it is possible that some collections were identified incorrectly. A collection of fungal strains isolated from diseased oak trees and initially identified as B. stevensii was characterized on the basis of morphology and ITS nucleotide sequences. Morphology was compared with the type specimens of Physalospora mutila (= B. stevensii) and its anamorph, Diplodia mutila. It was concluded that the isolates from oak differed from B. stevensii in having larger ascospores and conidia as well as different spore shapes and represented an as yet undescribed species, which is described here as B. corticola. Moreover, ITS sequence data separated B. corticola from all other known species of Botryosphaeria. Amended descriptions of B. stevensii and its anamorph are provided to differentiate B. stevensii from B. corticola and to clarify some of the earlier taxonomic uncertainties.

  9. Ovularia puerariae Sawada is the hyphomycetous anamorph of a new Marasmius species on living leaves of kudzu (Pueraria montana, Fabaceae).

    PubMed

    Kirschner, Roland; Lee, I-Shu; Chen, Chee-Jen

    2013-01-01

    An arthroconidial hyphomycete on living leaves of kudzu (Pueraria montana, Fabaceae), originally described by Sawada in 1959 as Ovularia puerariae, was rediscovered. This anamorph is connected to an unknown Marasmius teleomorph belonging to section Globulares, which develops on the same living leaves. Ultrastructure and LSU rDNA sequence analysis of the anamorph confirm this connection. The fungus does not have only a unique biology among agarics, comparable only to Mycena citricolor, but also has the potential for application as a control agent of kudzu. During comparison with similar anamorph genera, Illosporium graminicola was found to be a synonym for Beniowskia sphaeroidea.

  10. Hannaella siamensis sp. nov. and Hannaella phetchabunensis sp. nov., two new anamorphic basidiomycetous yeast species isolated from plants.

    PubMed

    Kaewwichian, Rungluk; Jindamorakot, Sasitorn; Am-In, Somjit; Sipiczki, Matthias; Limtong, Savitree

    2015-04-01

    Eight strains, representing two novel anamorphic yeast species, consisted of five strains isolated from the external surfaces of rice leaves (DMKU-RP72(T), DMKU-RP109, DMKU-RP119, YE-124 and YE-156) and one from a corn leaf (DMKU-CP430(T))4 collected in Thailand, and one strain isolated from each of a composite flower (11-1114) and a fallen dead leaf (12-301); the latter two were collected in Belize. On the basis of sequence analysis of the D1/D2 region of the large subunit rRNA gene and the internal transcribed spacer (ITS) region, they were suggested to be two novel species of the genus Hannaella. Seven strains (DMKU-RP72(T), DMKU-RP109, DMKU-RP119, YE-124, YE-156, 11-1114 and 12-301) differed from each other by 0-3 nt substitutions in the D1/D2 region and by 0-1 nt substitutions in the ITS region. In terms of pairwise sequence similarities of the D1/D2 region these seven strains were closest to Hannaella zeae, but with 1.2-1.7% (7-9) nucleotide substitutions. The sequences of the ITS region of these seven strains differed from H. zeae by 3.7-3.9% (16-17) nucleotide substitutions. Therefore, they were assigned to a single novel species and the name Hannaella siamensis sp. nov. has been proposed. The type strain is DMKU-RP72(T) ( = BCC 69493(T) = NBRC 110425(T) = CBS 13533(T)). Strain DMKU-CP430(T) represents the second novel species and was also most closely related to H. zeae, but with 1.0% (6) nucleotide substitutions in the D1/D2 region and 3.2% (14) nucleotide substitutions in the ITS region. It was assigned to the proposed novel species, Hannaella phetchabunensis sp. nov. (type strain DMKU-CP430(T) = BCC 69492(T) = NBRC 110424(T) = CBS 13386(T)).

  11. Candida kuoi sp. nov., a new anamorphic species of the Starmerella yeast clade that synthesizes sophorolipids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Candida kuoii sp. nov. (NRRL Y-27208T, CBS 7267T, type strain) is described from a strain isolated from concentrated grape juice in Cape Province, South Africa. Analysis of sequences from the D1/D2 domains of the nuclear large subunit rRNA gene separated the proposed new species from Starmerella bom...

  12. Candida xinjiangensis sp. nov., a new anamorphic yeast species isolated from Scolytus scheryrewi Semenov in China.

    PubMed

    Zhu, Xiao-Feng; Zhang, Dian-Peng; Yang, Sen; Zhang, Qing-Wen

    2017-03-01

    Three yeast strains designated as S44, XF1 and XF2, respectively, were isolated from Scolytus scheryrewi Semenov of apricot tree in Shule County, Xinjiang, China, and were demonstrated to be a new member of the genus Candida by sequence comparisons of 26S rRNA gene D1/D2 domain and internal transcribed spacer (ITS) region. BLASTn alignments on NCBI showed that the similarity of 26S rRNA gene sequences of S44 (type strain) to all sequences of other Candida yeasts was very low (≦93 %). The phylogenetic tree based on the 26S rRNA gene D1/D2 domain and ITS region sequences revealed that the strain S44 is closely related to C. blattae, C. dosseyi, C. pruni, C. asparagi, C. fructus and C. musae. However, the strain S44 is distinguished from these Candida species by the physiological characteristics. Moreover, the strain S44 formed typical pseudohyphae when grown on cornmeal agar at 25 °C for 7 days, but did not form ascospores in sporulation medium for 3-4 weeks. Therefore, the name Candida xinjiangensis is proposed for the novel species, with S44 (=KCTC(T)27747) as the type strain.

  13. Two new ascomycetous anamorphic yeast species related to Candida friedrichii--Candida jaroonii sp. nov., and Candida songkhlaensis sp. nov.--isolated in Thailand.

    PubMed

    Imanishi, Yumi; Jindamorakot, Sasitorn; Mikata, Kozaburo; Nakagiri, Akira; Limtong, Savitree; Potacharoen, Wanchern; Tanticharoen, Morakot; Nakase, Takashi

    2008-08-01

    In a study of yeast diversity in Thailand, eight strains of hitherto undescribed anamorphic yeasts were isolated: four from insect frass, two from Marasmius sp. fruiting bodies, one from a flower, and one from jackfruit exudates. Phylogenetic analysis of the D1/D2 domain of 26S ribosomal DNA nucleotide sequences indicated that the eight strains represented two new species related to Candida friedrichii. Genetic separation of the two new species was further supported by DNA-DNA hybridization analysis, which resulted in between-species similarity values of less than 48%, and by electrophoretic karyotyping. The two new species are C. jaroonii sp. nov. (type strain, ST-300(T) = NBRC 103209(T) = BCC 11783(T) = CBS 10790(T)) and C. songkhlaensis sp. nov. (type strain, ST-328(T) = NBRC 103214(T) = BCC 11804(T) = CBS 10791(T)).

  14. The anamorphic universe

    NASA Astrophysics Data System (ADS)

    Ijjas, Anna; Steinhardt, Paul J.

    2015-10-01

    We introduce ``anamorphic'' cosmology, an approach for explaining the smoothness and flatness of the universe on large scales and the generation of a nearly scale-invariant spectrum of adiabatic density perturbations. The defining feature is a smoothing phase that acts like a contracting universe based on some Weyl frame-invariant criteria and an expanding universe based on other frame-invariant criteria. An advantage of the contracting aspects is that it is possible to avoid the multiverse and measure problems that arise in inflationary models. Unlike ekpyrotic models, anamorphic models can be constructed using only a single field and can generate a nearly scale-invariant spectrum of tensor perturbations. Anamorphic models also differ from pre-big bang and matter bounce models that do not explain the smoothness. We present some examples of cosmological models that incorporate an anamorphic smoothing phase.

  15. The anamorphic universe

    SciTech Connect

    Ijjas, Anna; Steinhardt, Paul J. E-mail: steinh@princeton.edu

    2015-10-01

    We introduce ''anamorphic'' cosmology, an approach for explaining the smoothness and flatness of the universe on large scales and the generation of a nearly scale-invariant spectrum of adiabatic density perturbations. The defining feature is a smoothing phase that acts like a contracting universe based on some Weyl frame-invariant criteria and an expanding universe based on other frame-invariant criteria. An advantage of the contracting aspects is that it is possible to avoid the multiverse and measure problems that arise in inflationary models. Unlike ekpyrotic models, anamorphic models can be constructed using only a single field and can generate a nearly scale-invariant spectrum of tensor perturbations. Anamorphic models also differ from pre-big bang and matter bounce models that do not explain the smoothness. We present some examples of cosmological models that incorporate an anamorphic smoothing phase.

  16. Comparison of use of phenotypic and genotypic characteristics for identification of species of the anamorph genus Candida and related teleomorph yeast species.

    PubMed

    Latouche, G N; Daniel, H M; Lee, O C; Mitchell, T G; Sorrell, T C; Meyer, W

    1997-12-01

    A total of 49 type and neotype isolates and 32 clinical isolates of the anamorph genus Candida and related teleomorph genera were obtained from different culture collections and clinical laboratories. Isolates were subjected to two phenotypic methods of identification, Vitek yeast biochemical card (YBC) and API ID 32C, both based on carbohydrate assimilation, and one genotypic method, PCR fingerprinting, based on the detection of DNA polymorphisms between minisatellite-specific sequences with the primer M13 (5' GAGGGTGGCGGTTCT 3'). The correct identification of a strain at the Centraalbureau voor Schimmelcultures was used as the gold standard for the identification of an isolate. When the study was restricted to species included in the respective biochemical databases, the Vitek YBC and API ID 32C systems performed adequately with positive identification rates of 87.3 and 76.8%, respectively. When uncommon species were added to the study, several of which are not included in the databases, the identification efficiencies were 76.5 and 77.5%, respectively. By comparison, all isolates were correctly identified by PCR fingerprinting, with 63 reference species profiles in the databank. Sufficient polymorphisms among the total set of banding patterns were observed, with adequate similarity in the major patterns obtained from a given species, to allow each isolate to be assigned unambiguously to a particular species. In addition, variations in minor bands allowed for differentiation to the strain level. PCR fingerprinting was found to be rapid, reproducible, and more cost-effective than either biochemical approach. Our results provide reference laboratories with an improved identification method for yeasts based on genotypic rather than phenotypic markers.

  17. Comparison of use of phenotypic and genotypic characteristics for identification of species of the anamorph genus Candida and related teleomorph yeast species.

    PubMed Central

    Latouche, G N; Daniel, H M; Lee, O C; Mitchell, T G; Sorrell, T C; Meyer, W

    1997-01-01

    A total of 49 type and neotype isolates and 32 clinical isolates of the anamorph genus Candida and related teleomorph genera were obtained from different culture collections and clinical laboratories. Isolates were subjected to two phenotypic methods of identification, Vitek yeast biochemical card (YBC) and API ID 32C, both based on carbohydrate assimilation, and one genotypic method, PCR fingerprinting, based on the detection of DNA polymorphisms between minisatellite-specific sequences with the primer M13 (5' GAGGGTGGCGGTTCT 3'). The correct identification of a strain at the Centraalbureau voor Schimmelcultures was used as the gold standard for the identification of an isolate. When the study was restricted to species included in the respective biochemical databases, the Vitek YBC and API ID 32C systems performed adequately with positive identification rates of 87.3 and 76.8%, respectively. When uncommon species were added to the study, several of which are not included in the databases, the identification efficiencies were 76.5 and 77.5%, respectively. By comparison, all isolates were correctly identified by PCR fingerprinting, with 63 reference species profiles in the databank. Sufficient polymorphisms among the total set of banding patterns were observed, with adequate similarity in the major patterns obtained from a given species, to allow each isolate to be assigned unambiguously to a particular species. In addition, variations in minor bands allowed for differentiation to the strain level. PCR fingerprinting was found to be rapid, reproducible, and more cost-effective than either biochemical approach. Our results provide reference laboratories with an improved identification method for yeasts based on genotypic rather than phenotypic markers. PMID:9399515

  18. Cordyceps bassiana and production of stromata in vitro showing Beauveria anamorph in Korea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A Cordyceps species was found with Beauveria anamorph state on larval insect cadavers on Obong Mountsin in Gangwon Pronvince, Republic of Korea. Cultures from discharged ascospores formed an anamorph identifiable as Beauveria bassiana. This teleomorph-anamorph connection was also confirmed by the in...

  19. Description of Taphrina antarctica f.a. sp. nov., a new anamorphic ascomycetous yeast species associated with Antarctic endolithic microbial communities and transfer of four Lalaria species in the genus Taphrina.

    PubMed

    Selbmann, Laura; Turchetti, Benedetta; Yurkov, Andrey; Cecchini, Clarissa; Zucconi, Laura; Isola, Daniela; Buzzini, Pietro; Onofri, Silvano

    2014-07-01

    In the framework of a large-scale rock sampling in Continental Antarctica, a number of yeasts have been isolated. Two strains that are unable to grow above 20 °C and that have low ITS sequence similarities with available data in the public domain were found. The D1/D2 LSU molecular phylogeny placed them in an isolated position in the genus Taphrina, supporting their affiliation to a not yet described species. Because the new species is able to grow in its anamorphic state only, the species Taphrina antarctica f.a. (forma asexualis) sp. nov. has been proposed to accommodate both strains (type strain DBVPG 5268(T), DSM 27485(T) and CBS 13532(T)). Lalaria and Taphrina species are dimorphic ascomycetes, where the anamorphic yeast represents the saprotrophic state and the teleomorph is the parasitic counterpart on plants. This is the first record for this genus in Antarctica; since plants are absent on the continent, we hypothesize that the fungus may have focused on the saprotrophic part of its life cycle to overcome the absence of its natural host and adapt environmental constrains. Following the new International Code of Nomenclature for Algae, Fungi and Plants (Melbourne Code 2011) the reorganization of Taphrina-Lalaria species in the teleomorphic genus Taphrina is proposed. We emend the diagnosis of the genus Taphrina to accommodate asexual saprobic states of these fungi. Taphrina antarctica was registered in MycoBank under MB 808028.

  20. Candida alocasiicola sp. nov., Candida hainanensis sp. nov., Candida heveicola sp. nov. and Candida musiphila sp. nov., novel anamorphic, ascomycetous yeast species isolated from plants.

    PubMed

    Wang, Shi-An; Jia, Jian-Hua; Bai, Feng-Yan

    2008-08-01

    In a taxonomic study on the ascomycetous yeasts isolated from plant materials collected in tropical forests in Yunnan and Hainan Provinces, southern China, four strains isolated from tree sap (YJ2E(T)) and flowers (YF9E(T), YWZH3C(T) and YYF2A(T)) were revealed to represent four undescribed yeast species. Molecular phylogenetic analysis based on the large subunit (26S) rRNA gene D1/D2 domain sequences showed that strain YJ2E(T) was located in a clade together with Candida haemulonii and C. pseudohaemulonii. Strain YF9E(T) was most closely related to C. azyma and strain YWZH3C(T) to C. sorbophila and C. spandovensis. Strain YYF2A(T) was clustered in a clade containing small-spored Metschnikowia species and related anamorphic Candida species. The new strains differed from their closely related described species by more than 10% mismatches in the D1/D2 domain. No sexual states were observed for the four strains on various sporulation media. The new species are therefore assigned to the genus Candida and described as Candida alocasiicola sp. nov. (type strain, YF9E(T) = AS 2.3484(T) = CBS 10702(T)), Candida hainanensis sp. nov. (type strain, YYF2A(T) = AS 2.3478(T) = CBS 10696(T)), Candida heveicola sp. nov. (type strain, YJ2E(T) = AS 2.3483(T) = CBS 10701(T)) and Candida musiphila sp. nov. (type strain, YWZH3C(T) = AS 2.3479(T) = CBS 10697(T)).

  1. Rhodotorula subericola sp. nov., an anamorphic basidiomycetous yeast species isolated from bark of Quercus suber (cork oak).

    PubMed

    Belloch, C; Villa-Carvajal, M; Alvarez-Rodríguez, M L; Coque, J J R

    2007-07-01

    Two yeasts strains, Y-31(T) and Y-20B, pertaining to a previously unknown yeast species were isolated from bark of cork oak in Spain. Physiological characterization revealed a pattern of assimilation of carbon and nitrogen compounds compatible with members of the genus Rhodotorula. From sequence analysis of the D1/D2 region of the 26S rRNA gene, Rhodotorula cycloclastica and Rhodotorula philyla were related to the unknown species. Phylogenetic reconstruction based on the D1/D2 region of the 26S rRNA gene showed that the novel species clustered in a branch together with R. cycloclastica. The name Rhodotorula subericola sp. nov. is proposed, with isolate Y-31(T) (=CECT 11976(T)=CBS 10442(T)) the type strain of this novel taxon in the Microbotryum lineage, subclass Microbotryomycetidae, class Urediniomycetes of basidiomycetous yeasts.

  2. Anamorphs of the Bolbitiaceae (Basidiomycota, Agaricales).

    PubMed

    Walther, Grit; Weiss, Michael

    2006-01-01

    We describe and illustrate thallic conidiogenesis in 14 species of the Bolbitiaceae sensu Singer studied in culture. Conidiogenesis of 12 species is shown for the first time. Bolbitius vitellinus and the investigated species of Conocybe (C. albipes, C. appendiculata, C. magnicapitata, C. semiglobata, C. subovalis, C. subpubescens, C. sulcatipes and C. teneroides) possessed a similar mode of conidiogenesis. Species of both genera formed mostly coiled conidiogenous hyphae arising sympodially from differentiated conidiophores. The anamorphs of the Agrocybe species were not uniform and predominantly differed from those of Conocybe and Bolbitius. The conidia of Agrocybe dura, A. firma and A. praecox developed by the simple fragmentation of normally branched hyphae. Sympodially proliferating conidiophores occurred in Agrocybe arvalis and A. aegerita. Secretory cells of different size and shape were found in Agrocybe and in Conocybe. Our results corroborate a close phylogenetic relationship between Bolbitius and Conocybe as well as the polyphyly of the Bolbitiaceae as currently treated, which is consistent with recent molecular phylogenetic studies. Consequently we emend the family concept based on anamorphic characters.

  3. Mycocrystallization of gold ions by the fungus Cylindrocladium floridanum.

    PubMed

    Narayanan, Kannan Badri; Sakthivel, Natarajan

    2013-11-01

    The size and morphology determines the thermodynamic, physical and electronic properties of metal nanoparticles. The extracellular synthesis of gold nanoparticles by fungus, Cylindrocladium floridanum, which acts as a source of reducing and stabilizing agent has been described. The synthesized nanoparticles were characterized using techniques such as UV-Vis spectroscopy, X-ray diffraction (XRD), scanning electron microscopy, energy dispersive X-ray analysis (EDAX), and high-resolution transmission electron microscopy (HR-TEM). Based on the evidence of HR-TEM, the synthesized particles were found to be spherical with an average size of 19.05 nm. Powder XRD pattern proved the formation of (111)-oriented face-centered cubic crystals of metallic gold. This microbial approach by fungus for the green synthesis of spherical gold nanoparticles has many advantages such as economic viability, scaling up and environment friendliness.

  4. Cryptococcus allantoinivorans sp.nov., an anamorphic basidiomycetous yeast (Tremellales) physiologically resembling other species of the Cryptococcus laurentii complex that degrade polysaccharides and C2 compounds.

    PubMed

    Middelhoven, Wouter J

    2005-02-01

    A novel Cryptococcus species is proposed to accommodate a yeast strain (CBS 9604) able to assimilate allantoin as sole carbon source, a characteristic very uncommon among yeasts. By traditional methods, the strain could not be distinguished from Cryptococcus laurentii, but nucleotide sequences of the D1D2 region of the large subunit (26S) and of the ITS region of ribosomal DNA showed relationship to the Bulleromyces clade of the genus Cryptococcus (order Tremellales) with some Tremella spp. as the closest relatives. A traditional morphological and physiological description of the strain is given. Data on the assimilation of some C2 compounds and polysaccharides are provided and compared with those of other type strains of novel species of the C. laurentii complex.

  5. Compact Reflective Imaging Spectrometer Design Utilizing An Immersed Grating And Anamorphic Mirror

    DOEpatents

    Lerner, Scott A.

    2006-01-10

    A compact imaging spectrometer comprising an entrance slit, an anamorphic mirror, a grating, and a detector array. The entrance slit directs light to the anamorphic mirror. The anamorphic mirror receives the light and directs the light to the grating. The grating receives the light from the anamorphic mirror and defracts the light back onto the anamorphic mirror. The anamorphic mirror focuses the light onto a detector array.

  6. A monograph of the entomopathogenic genera Hypocrella, Moelleriella, and Samuelsia gen. nov. (Ascomycota, Hypocreales, Clavicipitaceae), and their aschersonia-like anamorphs in the Neotropics

    PubMed Central

    Chaverri, P.; Liu, M.; Hodge, K.T.

    2008-01-01

    The present taxonomic revision deals with Neotropical species of three entomopathogenic genera that were once included in Hypocrella s. l.: Hypocrella s. str. (anamorph Aschersonia), Moelleriella (anamorph aschersonia-like), and Samuelsia gen. nov (anamorph aschersonia-like). Species of Hypocrella, Moelleriella, and Samuelsia are pathogens of scale insects (Coccidae and Lecaniidae, Homoptera) and whiteflies (Aleyrodidae, Homoptera) and are common in tropical regions. Phylogenetic analyses of DNA sequences from nuclear ribosomal large subunit (28S), translation elongation factor 1-α (TEF 1-α), and RNA polymerase II subunit 1 (RPB1) and analyses of multiple morphological characters demonstrate that the three segregated genera can be distinguished by the disarticulation of the ascospores and shape and size of conidia. Moelleriella has filiform multi-septate ascospores that disarticulate at the septa within the ascus and aschersonia-like anamorphs with fusoid conidia. Hypocrella s. str. has filiform to long-fusiform ascospores that do not disarticulate and Aschersonia s. str. anamorphs with fusoid conidia. The new genus proposed here, Samuelsia, has filiform to long-fusiform ascospores that do not disarticulate and aschersonia-like anamorphs with small allantoid conidia. In addition, the present study presents and discusses the evolution of species, morphology, and ecology in Hypocrella, Moelleriella, and Samuelsia based on multigene phylogenetic analyses. PMID:18490956

  7. Phylogeny and taxonomic revision of the Planistromellaceae including its coelomycetous anamorphs: contributions towards a monograph of the genus Kellermania

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The core species of the family Planistromellaceae are included in the teleomorphic genera Planistroma and Planistromella and their anamorphic, coelomycetous genera Alpakesa, Kellermania, and Piptarthron. These genera have been defined primarily on the basis of ascospore septation or number of conidi...

  8. High-Resolution Anamorphic SPECT Imaging

    PubMed Central

    Durko, Heather L.; Barrett, Harrison H.; Furenlid, Lars R.

    2015-01-01

    We have developed a gamma-ray imaging system that combines a high-resolution silicon detector with two sets of movable, half-keel-edged copper-tungsten blades configured as crossed slits. These apertures can be positioned independently between the object and detector, producing an anamorphic image in which the axial and transaxial magnifications are not constrained to be equal. The detector is a 60 mm × 60 mm, one-millimeter-thick, one-megapixel silicon double-sided strip detector with a strip pitch of 59 μm. The flexible nature of this system allows the application of adaptive imaging techniques. We present system details; calibration, acquisition, and reconstruction methods; and imaging results. PMID:26160983

  9. 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

  10. A monograph of Allantonectria, Nectria, and Pleonectria (Nectriaceae, Hypocreales, Ascomycota) and their pycnidial, sporodochial, and synnematous anamorphs

    PubMed Central

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

    2012-01-01

    Although Nectria is the type genus of Nectriaceae (Hypocreales, Sordariomycetes, Pezizomycotina, Ascomycota), the systematics of the teleomorphic and anamorphic state of Nectria sensu Rossman has not been studied in detail. The objectives of this study are to 1) provide a phylogenetic overview to determine if species of Nectria with Gyrostroma, Tubercularia, and Zythiostroma anamorphs form a monophyletic group; 2) define Nectria, segregate genera, and their species using morphologically informative characters of teleomorphic and anamorphic states; and 3) provide descriptions and illustrations of these genera and species. To accomplish these objectives, results of phylogenetic analyses of DNA sequence data from six loci (act, ITS, LSU, rpb1, tef1 and tub), were integrated with morphological characterisations of anamorphs and teleomorphs. Results from the phylogenetic analyses demonstrate that species previously regarded as the genus Nectria having Gyrostroma, Tubercularia, and Zythiostroma anamorphs belong in two major paraphyletic clades. The first major clade regarded as the genus Pleonectria contains 26 species with ascoconidia produced by ascospores in asci, perithecial walls having bright yellow scurf, and immersed or superficial pycnidial anamorphs (Zythiostroma = Gyrostroma). A lineage basal to the Pleonectria clade includes Nectria miltina having very small, aseptate ascospores, and trichoderma-like conidiophores and occurring on monocotyledonous plants. These characteristics are unusual in Pleonectria, thus we recognise the monotypic genus Allantonectria with Allantonectria miltina. The second major clade comprises the genus Nectria sensu stricto including the type species, N. cinnabarina, and 28 additional species. Within the genus Nectria, four subclades exist. One subclade includes species with sporodochial anamorphs and another with synnematous anamorphs. The other two paraphyletic subclades include species that produce abundant stromata in which the

  11. Dynamics of cosmological perturbations and reheating in the anamorphic universe

    NASA Astrophysics Data System (ADS)

    Graef, L. L.; Hipólito-Ricaldi, W. S.; Ferreira, Elisa G. M.; Brandenberger, Robert

    2017-04-01

    We discuss scalar-tensor realizations of the Anamorphic cosmological scenario recently proposed by Ijjas and Steinhardt [1]. Through an analysis of the dynamics of cosmological perturbations we obtain constraints on the parameters of the model. We also study gravitational Parker particle production in the contracting Anamorphic phase and we compute the fraction between the energy density of created particles at the end of the phase and the background energy density. We find that, as in the case of inflation, a new mechanism is required to reheat the universe.

  12. Seed-borne Botryosphaeria spp. from native Prunus and Podocarpus trees in Ethiopia, with a description of the anamorph Diplodia rosulata sp. nov.

    PubMed

    Gure, Abdella; Slippers, Bernard; Stenlid, Jan

    2005-09-01

    Botryosphaeria spp. from seeds of the native afromontane forest tree species, Podocarpus falcatus and Prunus africana, in Ethiopia have been identified. This is achieved by combining anamorph morphological characters and ITS sequence data. From a relatively small sample, four Botryosphaeria spp. were encountered. Two of the species from P. falcatus and the one from P. africana have not been previously described. The two species from P. falcatus were represented by only one isolate each and are not named here. The morphology of their Diplodia and Dothiorella anamorphs is, however, characterised. The anamorph of the other Botryosphaeria sp. from P. africana is described here as Diplodia rosulata sp. nov. Furthermore, B. parva is identified from P. falcatus based on ITS phylogeny. This species is also an important pathogen of various commercially important tree species in Ethiopia and elsewhere. This study highlights the ability of Botryosphaeria spp. to infect seeds and the possibility that they might be distributed in this way. The study also contributes to recent attempts to stabilize the taxonomy of Botryosphaeria anamorphs, especially regarding Diplodia, which is currently in taxonomic disarray.

  13. Draft Genome Sequence of the Formaldehyde-Resistant Fungus Byssochlamys spectabilis No. 5 (Anamorph Paecilomyces variotii No. 5) (NBRC109023)

    PubMed Central

    Ekino, Keisuke; Fukuda, Kohsai; Nomura, Yoshiyuki

    2014-01-01

    Byssochlamys spectabilis no. 5 (anamorph Paecilomyces variotii no. 5) (NBRC109023) was isolated from a soil sample in 2001 in Kumamoto Prefecture, Japan. This fungus is highly resistant to formaldehyde. Here, we report a draft genome sequence of P. variotii no. 5; this draft was produced with the intent of investigating the mechanism of formaldehyde resistance. This is the first report of the genome sequence of any Paecilomyces species. PMID:24407650

  14. Phylogenetic reassessment of Mycosphaerella spp. and their anamorphs occurring on Eucalyptus. II.

    PubMed Central

    Crous, Pedro W.; Wingfield, Michael J.; Mansilla, J. Pedro; Alfenas, Acelino C.; Groenewald, Johannes Z.

    2006-01-01

    Species of Eucalyptus are widely planted as exotics in the tropics and Southern Hemisphere and to some extent in southern Europe, for timber and fibre production. Species of Mycosphaerella are commonly associated with leaves and twigs of Eucalyptus and can result in defoliation, dieback, and even tree death. In the present study, numerous isolates of Mycosphaerella species were collected from leaf litter, living leaves exhibiting leaf spot symptoms or severe Mycosphaerella leaf blotch symptoms. Isolates were compared based on DNA sequence data for the internal transcribed spacer region (ITS1 & ITS2) and the 5.8S gene. These data, together with characteristics of the fungal growth on three different media, morphology of the anamorph and teleomorph structures as well as ascospore germination patterns were used to describe 21 new species. PMID:18490974

  15. Cryptococcus ibericus sp. nov., Cryptococcus aciditolerans sp. nov. and Cryptococcus metallitolerans sp. nov., a new ecoclade of anamorphic basidiomycetous yeast species from an extreme environment associated with acid rock drainage in São Domingos pyrite mine, Portugal.

    PubMed

    Gadanho, Mário; Sampaio, José Paulo

    2009-09-01

    In this report, we describe three novel asexual basidiomycetous yeast species, Cryptococcus aciditolerans sp. nov. (type strain CBS 10872T=SDY 081T), Cryptococcus ibericus sp. nov. (type strain CBS 10871T=SDY 022T) and Cryptococcus metallitolerans sp. nov. (type strain CBS 10873T=SDY 190T), which were isolated from acid rock drainage collected at the São Domingos mine in southern Portugal. Phylogenetic analysis of molecular sequence data indicated that the novel species belong to the order Filobasidiales of the class Tremellomycetes and form a well-separated clade, next to Cryptococcus gastricus and Cryptococcus gilvescens. Since the novel species also share a peculiar ecology, being able to thrive under extreme environmental conditions characterized by very low pH and high concentrations of heavy metals, we designate this combination of phylogenetic and ecological characteristics as an ecoclade.

  16. Redisposition of phoma-like anamorphs in Pleosporales

    PubMed Central

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

    2013-01-01

    The anamorphic genus Phoma was subdivided into nine sections based on morphological characters, and included teleomorphs in Didymella, Leptosphaeria, Pleospora and Mycosphaerella, suggesting the polyphyly of the genus. Recent molecular, phylogenetic studies led to the conclusion that Phoma should be restricted to Didymellaceae. The present study focuses on the taxonomy of excluded Phoma species, currently classified in Phoma sections Plenodomus, Heterospora and Pilosa. Species of Leptosphaeria and Phoma section Plenodomus are reclassified in Plenodomus, Subplenodomus gen. nov., Leptosphaeria and Paraleptosphaeria gen. nov., based on the phylogeny determined by analysis of sequence data of the large subunit 28S nrDNA (LSU) and Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS). Phoma heteromorphospora, type species of Phoma section Heterospora, and its allied species Phoma dimorphospora, are transferred to the genus Heterospora stat. nov. The Phoma acuta complex (teleomorph Leptosphaeria doliolum), is revised based on a multilocus sequence analysis of the LSU, ITS, small subunit 18S nrDNA (SSU), β-tubulin (TUB), and chitin synthase 1 (CHS-1) regions. Species of Phoma section Pilosa and allied Ascochyta species were determined to belong to Pleosporaceae based on analysis of actin (ACT) sequence data. Anamorphs that are similar morphologically to Phoma and described in Ascochyta, Asteromella, Coniothyrium, Plectophomella, Pleurophoma and Pyrenochaeta are included in this study. Phoma-like species, which grouped outside the Pleosporineae based on a LSU sequence analysis, are transferred to the genera Aposphaeria, Paraconiothyrium and Westerdykella. The genera Medicopsis gen. nov. and Nigrograna gen. nov. are introduced to accommodate the medically important species formerly known as Pyrenochaeta romeroi and Pyrenochaeta mackinnonii, respectively. Taxonomic novelties: New genera: Medicopsis Gruyter, Verkley & Crous, Nigrograna Gruyter, Verkley & Crous

  17. Anamorphic integral field spectrometer for diffuse ultraviolet astronomy.

    PubMed

    Cook, Timothy

    2013-12-20

    We present the design of a novel anamorphic integral field spectrometer for diffuse ultraviolet astronomy. The system is designed to be able to measure emissions from faint diffuse astrophysical sources across a large field with good spectral resolving power. The design uses a standard focal plane image slicer and an anamorphic relay mirror and spectrometer to achieve an exceptional area, field of view, resolving power (AΩR) product, the key figure of merit for a spectroscopic system intended to study line emission from extended or diffuse sources. We present a typical design with R∼1000 and an effective etendue (AΩ) of 1.5×10(-4)cm2 sr.

  18. Imaging performance of the EUV high NA anamorphic system

    NASA Astrophysics Data System (ADS)

    van Ingen Schenau, Koen; Bottiglieri, Gerardo; van Schoot, Jan; Neumann, Jens-Timo; Roesch, Matthias

    2015-09-01

    This paper presents the predicted imaging performance for an anamorphic EUV high NA (>0.5) exposure system with a 4x magnification in X orientation and a 8x magnification in Y orientation. It has a half field size with which the productivity requirements can be maintained. The main findings of the study are that horizontal and vertical features have very similar process window sizes despite magnification difference. A new definition of the Mask Error Factor (MEF) is introduced that is more relevant for anamorphic imaging; it shows that reticle CD errors have 2x larger impact for vertical compared to horizontal features. For dark field horizontal two-bar trenches relatively small mask induced focus shift was observed compared to the 0.33NA case, probably due to the relatively small Mask Angle of Incidence in the Y orientation with the 8x magnification. Finally a Ni type absorber has potential to further improve imaging performance.

  19. Three common bryophilous fungi with meristematic anamorphs and phylogenetic alliance to Teratosphaeriaceae, Capnodiales.

    PubMed

    Wäli, Pauliina P; Huhtinen, Seppo; Pino-Bodas, Raquel; Stenroos, Soili

    2014-12-01

    Bryophilous ascomycetes are an overlooked and poorly known fungal group. In this study, the extreme and small-sized niche of Polytrichum piliferum hyaline leaf tips was screened for the presence of these fungi in Finland. Three closely related species were found. Bryochiton perpusillus and Bryochiton monascus were identified from several samples, and DNA isolations revealed a third closely related species, Bryochiton sp. In addition, melanised hyphae, typical to the Bryochiton species, were present in all the samples. According to phylogenetic analyses consisting of combined small subunit (SSU), large subunit (LSU), and 5.8S rDNA sequences, and internal transcribed spacer (ITS) rDNA sequences, the species showed affinity with Teratosphaeriaceae within Capnodiales, and especially with black, meristematic species often inhabiting rock substrate in extreme environments. The connection was supported by meristematic growth of the Bryochiton species in culture. Bryochiton is the second sexual genus associated within the family Teratosphaeriaceae, and B. perpusillus, and B. monascus constitute examples of teleomorphs within a group of meristematic anamorphs. These findings emphasize the multiform diversity underlying poorly researched fungal groups, such as the bryophilous fungi.

  20. Research of 3D display using anamorphic optics

    NASA Astrophysics Data System (ADS)

    Matsumoto, Kenji; Honda, Toshio

    1997-05-01

    This paper describes the auto-stereoscopic display which can reconstruct more reality and viewer friendly 3-D image by increasing the number of parallaxes and giving motion parallax horizontally. It is difficult to increase number of parallaxes to give motion parallax to the 3-D image without reducing the resolution, because the resolution of display device is insufficient. The magnification and the image formation position can be selected independently in horizontal direction and the vertical direction by projecting between the display device and the 3-D image with the anamorphic optics. The anamorphic optics is an optics system with different magnification in horizontal direction and the vertical direction. It consists of the combination of cylindrical lenses with different focal length. By using this optics, even if we use a dynamic display such as liquid crystal display (LCD), it is possible to display the realistic 3-D image having motion parallax. Motion parallax is obtained by assuming width of the single parallax at the viewing position to be about the same size as the pupil diameter of viewer. In addition, because the focus depth of the 3-D image is deep in this method, conflict of accommodation and convergence is small, and natural 3-D image can be displayed.

  1. Dual Double-Wedge Pseudo-Depolarizer with Anamorphic PSF

    NASA Technical Reports Server (NTRS)

    Hill, Peter; Thompson, Patrick

    2012-01-01

    A polarized scene, which may occur at oblique illumination angles, creates a radiometric signal that varies as a function of viewing angle. One common optical component that is used to minimize such an effect is a polarization scrambler or depolarizer. As part of the CLARREO mission, the SOLARIS instrument project at Goddard Space Flight Center has developed a new class of polarization scramblers using a dual double-wedge pseudo-depolarizer that produces an anamorphic point spread function (PSF). The SOLARIS instrument uses two Wollaston type scramblers in series, each with a distinct wedge angle, to image a pseudo-depolarized scene that is free of eigenstates. Since each wedge is distinct, the scrambler is able to produce an anamorphic PSF that maintains high spatial resolution in one dimension by sacrificing the spatial resolution in the other dimension. This scrambler geometry is ideal for 1-D imagers, such as pushbroom slit spectrometers, which require high spectral resolution, high spatial resolution, and low sensitivity to polarized light. Moreover, the geometry is applicable to a wide range of scientific instruments that require both high SNR (signal-to-noise ratio) and low sensitivity to polarized scenes

  2. Emulation of anamorphic imaging on the SHARP extreme ultraviolet mask microscope

    NASA Astrophysics Data System (ADS)

    Benk, Markus P.; Wojdyla, Antoine; Chao, Weilun; Salmassi, Farhad; Oh, Sharon; Wang, Yow-Gwo; Miyakawa, Ryan H.; Naulleau, Patrick P.; Goldberg, Kenneth A.

    2016-07-01

    The SHARP high-numerical aperture actinic reticle review project is a synchrotron-based, extreme ultraviolet (EUV) microscope dedicated to photomask research. SHARP emulates the illumination and imaging conditions of current EUV lithography scanners and those several generations into the future. An anamorphic imaging optic with increased mask-side numerical aperture (NA) in the horizontal and increased demagnification in the vertical direction has been proposed to overcome limitations of current multilayer coatings and extend EUV lithography beyond 0.33 NA. Zoneplate lenses with an anamorphic 4×/8× NA of 0.55 are fabricated and installed in the SHARP microscope to emulate anamorphic imaging. SHARP's Fourier synthesis illuminator with a range of angles exceeding the collected solid angle of the newly designed elliptical zoneplates can produce arbitrary angular source spectra matched to anamorphic imaging. A target with anamorphic dense features down to 50-nm critical dimension is fabricated using 40 nm of nickel as the absorber. In a demonstration experiment, anamorphic imaging at 0.55 4×/8× NA and 6 deg central ray angle (CRA) is compared with conventional imaging at 0.5 4× NA and 8 deg CRA. A significant contrast loss in horizontal features is observed in the conventional images. The anamorphic images show the same image quality in the horizontal and vertical directions.

  3. Taxonomy, nomenclature and phylogeny of three cladosporium-like hyphomycetes, Sorocybe resinae, Seifertia azaleae and the Hormoconis anamorph of Amorphotheca resinae

    PubMed Central

    Seifert, K.A.; Hughes, S.J.; Boulay, H.; Louis-Seize, G.

    2007-01-01

    Using morphological characters, cultural characters, large subunit and internal transcribed spacer rDNA (ITS) sequences, and provisions of the International Code of Botanical Nomenclature, this paper attempts to resolve the taxonomic and nomenclatural confusion surrounding three species of cladosporium-like hyphomycetes. The type specimen of Hormodendrum resinae, the basis for the use of the epithet resinae for the creosote fungus {either as Hormoconis resinae or Cladosporium resinae) represents the mononematous synanamorph of the synnematous, resinicolous fungus Sorocybe resinae. The phylogenetic relationships of the creosote fungus, which is the anamorph of Amorphotheca resinae, are with the family Myxotrichaceae, whereas S. resinae is related to Capronia (Chaetothyriales, Herpotrichiellaceae). Our data support the segregation of Pycnostysanus azaleae, the cause of bud blast of rhododendrons, in the recently described anamorph genus Seifertia, distinct from Sorocybe; this species is related to the Dothideomycetes but its exact phylogenetic placement is uncertain. To formally stabilize the name of the anamorph of the creosote fungus, conservation of Hormodendrum resinae with a new holotype should be considered. The paraphyly of the family Myxotrichaceae with the Amorphothecaceae suggested by ITS sequences should be confirmed with additional genes. PMID:18491002

  4. Extracellular synthesis of mycogenic silver nanoparticles by Cylindrocladium floridanum and its homogeneous catalytic degradation of 4-nitrophenol.

    PubMed

    Narayanan, Kannan Badri; Park, Hyun Ho; Sakthivel, Natarajan

    2013-12-01

    Green synthesis of extracellular mycogenic silver nanoparticles using the fungus, Cylindrocladium floridanum is reported. The synthesized mycogenic silver nanoparticles were characterized using UV-Vis absorption spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), and transmission electron microscopy (TEM) techniques. The nanoparticles exhibit fcc structure with Bragg's reflections of (111), (200), (220) and (311) was evidenced by XRD pattern, high-resolution TEM lattice fringes and circular rings in selected-area electron diffraction (SAED) pattern. The morphology of nanoparticles was roughly spherical in shape with an average size of ca. 25 nm. From FTIR spectrum, it was found that the biomolecules with amide I and II band were involved in the stabilization of nanoparticles. These mycogenic silver nanoparticles exhibited the homogeneous catalytic potential in the reduction of pollutant, 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) using sodium borohydride, which followed a pseudo-first-order kinetic model. Thus, the synthesis of metal nanoparticles using sustainable microbial approach opens up possibilities in the usage of mycogenic metal nanoparticles as catalysts in various chemical reactions.

  5. Extracellular synthesis of mycogenic silver nanoparticles by Cylindrocladium floridanum and its homogeneous catalytic degradation of 4-nitrophenol

    NASA Astrophysics Data System (ADS)

    Narayanan, Kannan Badri; Park, Hyun Ho; Sakthivel, Natarajan

    2013-12-01

    Green synthesis of extracellular mycogenic silver nanoparticles using the fungus, Cylindrocladium floridanum is reported. The synthesized mycogenic silver nanoparticles were characterized using UV-Vis absorption spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), and transmission electron microscopy (TEM) techniques. The nanoparticles exhibit fcc structure with Bragg's reflections of (1 1 1), (2 0 0), (2 2 0) and (3 1 1) was evidenced by XRD pattern, high-resolution TEM lattice fringes and circular rings in selected-area electron diffraction (SAED) pattern. The morphology of nanoparticles was roughly spherical in shape with an average size of ca. 25 nm. From FTIR spectrum, it was found that the biomolecules with amide I and II band were involved in the stabilization of nanoparticles. These mycogenic silver nanoparticles exhibited the homogeneous catalytic potential in the reduction of pollutant, 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) using sodium borohydride, which followed a pseudo-first-order kinetic model. Thus, the synthesis of metal nanoparticles using sustainable microbial approach opens up possibilities in the usage of mycogenic metal nanoparticles as catalysts in various chemical reactions.

  6. Molecular taxonomy of bambusicolous fungi: Tetraplosphaeriaceae, a new pleosporalean family with Tetraploa-like anamorphs

    PubMed Central

    Tanaka, K.; Hirayama, K.; Yonezawa, H.; Hatakeyama, S.; Harada, Y.; Sano, T.; Shirouzu, T.; Hosoya, T.

    2009-01-01

    A new pleosporalean family Tetraplosphaeriaceae is established to accommodate five new genera; 1) Tetraplosphaeria with small ascomata and anamorphs belonging to Tetraploa s. str., 2) Triplosphaeria characterised by hemispherical ascomata with rim-like side walls and anamorphs similar to Tetraploa but with three conidial setose appendages, 3) Polyplosphaeria with large ascomata surrounded by brown hyphae and anamorphs producing globose conidia with several setose appendages, 4) Pseudotetraploa, an anamorphic genus, having obpyriform conidia with pseudosepta and four to eight setose appendages, and 5) Quadricrura, an anamorphic genus, having globose conidia with one or two long setose appendages at the apex and four to five short setose appendages at the base. Fifteen new taxa in these genera mostly collected from bamboo are described and illustrated. They are linked by their Tetraploa s. l. anamorphs. To infer phylogenetic placement in the Pleosporales, analyses based on a combined dataset of small- and large-subunit nuclear ribosomal DNA (SSU+LSU nrDNA) was carried out. Tetraplosphaeriaceae, however, is basal to the main pleosporalean clade and therefore its relationship with other existing families was not completely resolved. To evaluate the validity of each taxon and to clarify the phylogenetic relationships within this family, further analyses using sequences from ITS-5.8S nrDNA (ITS), transcription elongation factor 1-α (TEF), and β-tubulin (BT), were also conducted. Monophyly of the family and that of each genus were strongly supported by analyses based on a combined dataset of the three regions (ITS+TEF+BT). Our results also suggest that Tetraplosphaeria (anamorph: Tetraploa s. str.) is an ancestral lineage within this family. Taxonomic placement of the bambusicolous fungi in Astrosphaeriella, Kalmusia, Katumotoa, Massarina, Ophiosphaerella, Phaeosphaeria, Roussoella, Roussoellopsis, and Versicolorisporium, are also discussed based on the SSU

  7. AFLP fingerprinting for identification of infra-species groups of Rhizoctonia solani and Waitea circinata

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Patch diseases caused by Thanatephorus cucumeris and Waitea circinata varieties (anamorphs: Rhizoctonia species) pose a serious threat to successful maintenance of several important turfgrass species. Reliance on field symptoms to identify Rhizoctonia causal agents can be difficult and misleading. D...

  8. Deep fungal dermatitis caused by the Chrysosporium anamorph of Nannizziopsis vriesii in captive coastal bearded dragons (Pogona barbata).

    PubMed

    Johnson, R S P; Sangster, C R; Sigler, L; Hambleton, S; Paré, J A

    2011-12-01

    Deep fungal dermatitis caused by the Chrysosporium anamorph of Nannizziopsis vriesii (CANV) was diagnosed in a group of coastal bearded dragons (Pogona barbata). The outbreak extended over a 6-month period, with four of six lizards from the same zoological outdoor enclosure succumbing to infection. A fifth case of dermatomycosis was identified in a pet lizard originally sourced from the wild. Diagnosis of infection with the CANV was based on similar clinical signs and histopathology in all animals and confirmed by culture and sequencing of the fungus from one animal. This is the first report of the CANV causing disease in a terrestrial reptile species in Australia and the first in the coastal bearded dragon.

  9. Cyanonectria, a new genus for “Nectria” cyanostoma and its Fusarium anamorph

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The new genus Cyanonectria is proposed for Nectria cyanostoma (= Cyanonectria cyanostoma comb. nov.). This genus is characterized by Nectria-like, red perithecia that have a bluish-purple papilla and a Fusarium anamorph. DNA sequences (large subunit and internal transcribed spacers of the nuclear rD...

  10. Nonminimally coupled inflation with initial conditions from a preinflation anamorphic contracting era

    NASA Astrophysics Data System (ADS)

    McDonald, John

    2016-08-01

    Inflation due to a nonminimally coupled scalar field, as first proposed by Salopek, Bardeen and Bond (SBB), is in good agreement with the observed value of the spectral index and constraints on the tensor-to-scalar ratio. Here we explore the possibility that SBB inflation represents the late stage of a Universe which emerges from an early contracting era. We present a model in which the Universe smoothly transitions from an anamorphic contracting era to late-time SBB inflation without encountering a singular bounce. This corresponds to a continuous expansion in the Einstein frame throughout. We show that the anamorphic contracting era is able to provide the smooth superhorizon initial conditions necessary for subsequent SBB inflation to occur. The model predicts corrections to the nonminimal coupling, kinetic term and potential of SBB inflation which can observably increase the spectral index relative to its SBB prediction.

  11. Characterization of the anamorphic and frequency dependent phenomenon in Liquid Crystal on Silicon displays

    NASA Astrophysics Data System (ADS)

    Lobato, L.; Lizana, A.; Márquez, A.; Moreno, I.; Iemmi, C.; Campos, J.; Yzuel, M. J.

    2011-04-01

    The diffractive efficiency of Liquid Crystal on Silicon (LCoS) displays can be greatly diminished by the appearance of temporal phase fluctuations in the reflected beam, depolarization effects and also because of phase modulation depths smaller than 2π. In order to maximize the efficiency of the Diffractive Optical Elements (DOEs) implemented in the LCoS device, the Minimum Euclidean Distance principle can be applied. However, not all the diffractive elements can be corrected in the same way due to the anamorphic and frequency dependent phenomenon, which is related to the LCoS response, largely dependending on the period and the spatial orientation of the generated DOE. Experimental evidence for the anamorphic and frequency dependent phenomenon is provided in this paper, as well as a comparative study between the efficiency obtained for binary gratings of different periods

  12. Development of Nested PCR, Multiplex PCR, and Loop-Mediated Isothermal Amplification Assays for Rapid Detection of Cylindrocladium scoparium on Eucalyptus

    PubMed Central

    Qiao, Tian-Min; Zhang, Jing; Li, Shu-Jiang; Han, Shan; Zhu, Tian-Hui

    2016-01-01

    Eucalyptus dieback disease, caused by Cylindrocladium scoparium, has occurred in last few years in large Eucalyptus planting areas in China and other countries. Rapid, simple, and reliable diagnostic techniques are desired for the early detection of Eucalyptus dieback of C. scoparium prior to formulation of efficient control plan. For this purpose, three PCR-based methods of nested PCR, multiplex PCR, loop-mediated isothermal amplification (LAMP) were developed for detection of C. scoparium based on factor 1-alpha (tef1) and beta-tubulin gene in this study. All of the three methods showed highly specific to C. scoparium. The sensitivities of the nested PCR and LAMP were much higher than the multiplex PCR. The sensitivity of multiplex PCR was also higher than regular PCR. C. scoparium could be detected within 60 min from infected Eucalyptus plants by LAMP, while at least 2 h was needed by the rest two methods. Using different Eucalyptus tissues as samples for C. scoparium detection, all of the three PCR-based methods showed much better detection results than regular PCR. Base on the results from this study, we concluded that any of the three PCR-based methods could be used as diagnostic technology for the development of efficient strategies of Eucalyptus dieback disease control. Particularly, LAMP was the most practical method in field application because of its one-step and rapid reaction, simple operation, single-tube utilization, and simple visualization of amplification products. PMID:27721691

  13. Development of Nested PCR, Multiplex PCR, and Loop-Mediated Isothermal Amplification Assays for Rapid Detection of Cylindrocladium scoparium on Eucalyptus.

    PubMed

    Qiao, Tian-Min; Zhang, Jing; Li, Shu-Jiang; Han, Shan; Zhu, Tian-Hui

    2016-10-01

    Eucalyptus dieback disease, caused by Cylindrocladium scoparium, has occurred in last few years in large Eucalyptus planting areas in China and other countries. Rapid, simple, and reliable diagnostic techniques are desired for the early detection of Eucalyptus dieback of C. scoparium prior to formulation of efficient control plan. For this purpose, three PCR-based methods of nested PCR, multiplex PCR, loop-mediated isothermal amplification (LAMP) were developed for detection of C. scoparium based on factor 1-alpha (tef1) and beta-tubulin gene in this study. All of the three methods showed highly specific to C. scoparium. The sensitivities of the nested PCR and LAMP were much higher than the multiplex PCR. The sensitivity of multiplex PCR was also higher than regular PCR. C. scoparium could be detected within 60 min from infected Eucalyptus plants by LAMP, while at least 2 h was needed by the rest two methods. Using different Eucalyptus tissues as samples for C. scoparium detection, all of the three PCR-based methods showed much better detection results than regular PCR. Base on the results from this study, we concluded that any of the three PCR-based methods could be used as diagnostic technology for the development of efficient strategies of Eucalyptus dieback disease control. Particularly, LAMP was the most practical method in field application because of its one-step and rapid reaction, simple operation, single-tube utilization, and simple visualization of amplification products.

  14. Deep fungal dermatitis in three inland bearded dragons (Pogona vitticeps) caused by the Chrysosporium anamorph of Nannizziopsis vriesii.

    PubMed

    Bowman, Michelle R; Paré, Jean A; Sigler, Lynne; Naeser, John P; Sladky, Kurt K; Hanley, Chris S; Helmer, Peter; Phillips, Lynette A; Brower, Alexandra; Porter, Robert

    2007-06-01

    The Chrysosporium anamorph of Nannizziopsis vriesii (CANV), a keratinophilic fungus that naturally and experimentally causes severe and often fatal dermatitis in multiple reptile species, was isolated in pure culture from skin samples of three inland bearded dragons (Pogona vitticeps) with deep granulomatous dermatomycosis. The first animal presented with a focal maxillary swelling involving the skin and gingiva. This lizard died while undergoing itraconazole and topical miconazole therapy. The second presented with focally extensive discoloration and thickening of the skin of the ventrum and was euthanized after 10 weeks of itraconazole therapy. A third lizard presented with hyperkeratotic exudative dermatitis on a markedly swollen forelimb. Amputation and itraconazole therapy resulted in a clinical cure. Histopathology of tissue biopsies in all cases demonstrated granulomatous dermatitis with intralesional hyphae morphologically consistent with those produced by the CANV. The second lizard also had granulomatous hepatitis with intralesional hyphae. Evidence in this report suggests that the CANV is the etiologic agent of an emerging condition in captive bearded dragons that has been called 'yellow fungus disease'.

  15. Endomelanconiopsis, a new anamorph genus in the Botryosphaeriaceae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The new species Endomelanconium endphyticum was common among endophytes isolated from healthy leaves of Theobroma cacao (cacao, Malvaceae) and Heisteria concinna (Oleaceae) in Panama. A total of fifteen endophytic cultures representing both hosts were selected for sequencing and morphological chara...

  16. Design of anamorphic magnification high-numerical aperture objective for extreme ultraviolet lithography by curvatures combination method.

    PubMed

    Liu, Yan; Li, Yanqiu; Cao, Zhen

    2016-06-20

    An anamorphic magnification extreme ultraviolet (EUV) lithographic objective could increase the size of the exposure field at a wafer in the orthogonal scanning direction to improve the throughput of the lithographic system. In this paper, we present a curvatures combination method for an anamorphic magnification EUV lithographic objective with high numerical aperture (NA). This method achieves an anamorphic magnification initial structure by use of the double-curvature surfaces, which are formed by combining the curvatures of the corresponding surfaces into two coaxial spherical systems. A series of control measures is taken to design the two coaxial spherical systems for ensuring the rationalities of the initial structure and the surfaces after combining. The image quality of the anamorphic initial structure is optimized by a gradual optimization process. Finally, as an example, we design an Mx1/4 and My1/8 anamorphic magnification EUV lithographic objective with the presented design method. This objective achieves 0.5 NA and a 26  mm×16.5  mm exposure field at the wafer. The wavefront error RMS reaches 0.06λ (λ=13.5  nm), and the distortion is less than 2.8 nm. The design result proves the availability of the curvatures combination method.

  17. Hypocrea britdaniae and H. foliicola: two remarkable new European species

    PubMed Central

    Jaklitsch, Walter M.; Voglmayr, Hermann

    2014-01-01

    Two new species of Hypocrea are added here to the European funga. Hypocrea britdaniae, a fungus with unknown anamorph and large, conspicuous stromata resembling basidiomata of a corticiaceous fungus, is a sister species to the Longibrachiatum clade, while H. foliicola, a leaf-dwelling species that forms pulvinate stromata, is recognized as an additional member of the pachybasium core group. Hypocrea foliicola sporulates in culture in a reduced verticillium-like manner, while it produces a white, typical pachybasium-like anamorph in nature. Ecologically H. foliicola is remarkable in inhabiting leaves, a substrate rarely recorded for Hypocrea. All relevant morphological teleomorphic and anamorphic traits are given. The phylogenetic placement of the new species within Hypocrea/Trichoderma was determined with combined analyses of rpb2 and tef1 exon sequences. PMID:22505436

  18. Chrysosporium anamorph Nannizziopsis vriesii: an emerging fungal pathogen of captive and wild reptiles.

    PubMed

    Mitchell, Mark A; Walden, Michael R

    2013-09-01

    Chrysosporium anamorph Nannizziopsis vriesii is a recent pathogen associated with infections in lizards, snakes, and crocodilians. It seems to be an obligate pathogen. It has been isolated from wild reptiles in addition to captive animals. Affected animals often present with aggressive, pyogranulomatous lesions that can affect the integument and musculoskeletal systems. Diagnosis can be done using culture, histopathology, and polymerase chain reaction assay. Ancillary diagnostic tests can be useful in characterizing the health status of the affected reptile and aid in planning supportive care and therapy. Treatment using antifungals has shown mixed results.

  19. Synthesis and characterization of nano-gold composite using Cylindrocladium floridanum and its heterogeneous catalysis in the degradation of 4-nitrophenol.

    PubMed

    Narayanan, Kannan Badri; Sakthivel, Natarajan

    2011-05-15

    Greener synthesis of nanogold-biocomposite by fungus, Cylindrocladium floridanum was reported in this study. Results revealed that when cultured in static condition for a period of 7d, the fungus accumulated gold nanoparticles on the surface of the mycelia. Bionanocomposites with Au nanocrystals were characterized by UV-Vis spectroscopy, XRD, SEM, EDX and high-resolution TEM. The SPR band of UV-Vis spectrum at 540 nm confirmed the presence of gold nanoparticles on the surface of the fungal mycelia. The fcc (111)-oriented crystalline nature of particles was identified by XRD pattern. The synthesized particles are spherical in shape as evidenced by TEM image. The biocomposites with Au nanoparticles function as an efficient heterogeneous catalyst in the degradation of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP), in the presence of reducing agent, sodium borohydride which was reflected by UV-Vis spectra of the catalytic reaction kinetics. The reduction of 4-nitrophenol follows pseudo-first-order kinetic model with the reaction rate constant of 2.67 × 10(-2)min(-1) with 5.07 × 10(-6)mol/dm(3) of gold at ca. 25 nm. The rate of the reaction was increased by increasing the concentration of gold nanoparticles from 2.54 × 10(-6) to 12.67 × 10(-6)mol/dm(3) (∼ 25 nm) and with reduced size from 53.2 to 18.9 nm respectively. This is the first report on fungal-matrixed gold(0) nanocomposites heterogeneously catalyzing the reduction of the toxic organic pollutant, 4-nitrophenol that enable the recovery and recycling of AuNPs catalysts.

  20. Image slicing with a twist: spatial and spectral Nyquist sampling without anamorphic optics

    NASA Astrophysics Data System (ADS)

    Tecza, Matthias

    2014-07-01

    Integral field spectrographs have become mainstream instruments at modern telescopes because of their efficient way of collecting data-cubes. Image slicer based integral field spectrographs achieve the highest fill-factor on the detector, but due to the need to Nyquist-sample the spectra, their spatial sampling on the sky is rectangular. Using anamorphic pre-optics before the image slicer overcomes this effect further maximising the fill-factor, but introduces optical aberrations, throughput losses, and additional alignment and calibration requirements, compromising overall instrument performance. In this paper I present a concept for an image-slicer that achieves both spatial and spectral Nyquist-sampling without anamorphic pre-optics. Rotating each slitlet by 45° with respect to the dispersion direction, and arranging them into a saw-tooth pseudo-slit, leads to a lozenge shaped sampling element on the sky, however, the centres of the lozenges lie on a regular and square grid, satisfying the Nyquist sampling criterion in both spatial directions.

  1. Isaria takamizusanensis is the anamorph of Cordyceps ryogamimontana, warranting a new combination, Purpureocillium takamizusanense comb. nov.

    PubMed

    Ban, Sayaka; Azuma, Yuta; Sato, Hiroki; Suzuki, Ken-Ichiro; Nakagiri, Akira

    2015-08-01

    The entomogenous anamorphic fungus Isaria takamizusanensis has not been resolved clearly in its teleomorphic state. We succeeded in inducing ascostroma formation by incubating conidiomata of I. takamizusanensis on cicada adults in a moist chamber. We observed the ascostroma and conducted a phylogenetic analysis based on ITS rDNA and EF-1α genes. The morphology of the ascostroma was identical to that of Cordyceps ryogamimontana. In the phylogenetic tree inferred from EF-1α, the isolate from the partspores grouped with nine strains derived from conidia of I. takamizusanensis, which was distinct from a clade including Purpureocillium lilacinum. Moreover, a conidial structure identical to that of I. takamizusanensis was rediscovered on the holotype specimen of C. ryogamimontana. As a result, we propose a new name, Purpureocillium takamizusanense, which is a combination of the teleomorph-anamorph connection of C. ryogamimontana-I. takamizusanensis, in accordance with the 'one fungus, one name' concept of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN).

  2. A monograph of Allantonectria, Nectria, and Pleonectria (Nectriaceae, Hypocreales, Ascomycota) and their pycnidial, sporodochial, and synnematous anamorphs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although Nectria is the type genus of Nectriaceae (Hypocreales, Sordariomycetes, Pezizomycotina, Ascomycota), the systematics of the teleomorphic and anamorphic state of Nectria sensu Rossman has not been studied in detail. The objectives of this study were to 1) provide a phylogenetic overview to d...

  3. Orthonormal aberration polynomials for anamorphic optical imaging systems with circular pupils.

    PubMed

    Mahajan, Virendra N

    2012-06-20

    In a recent paper, we considered the classical aberrations of an anamorphic optical imaging system with a rectangular pupil, representing the terms of a power series expansion of its aberration function. These aberrations are inherently separable in the Cartesian coordinates (x,y) of a point on the pupil. Accordingly, there is x-defocus and x-coma, y-defocus and y-coma, and so on. We showed that the aberration polynomials orthonormal over the pupil and representing balanced aberrations for such a system are represented by the products of two Legendre polynomials, one for each of the two Cartesian coordinates of the pupil point; for example, L(l)(x)L(m)(y), where l and m are positive integers (including zero) and L(l)(x), for example, represents an orthonormal Legendre polynomial of degree l in x. The compound two-dimensional (2D) Legendre polynomials, like the classical aberrations, are thus also inherently separable in the Cartesian coordinates of the pupil point. Moreover, for every orthonormal polynomial L(l)(x)L(m)(y), there is a corresponding orthonormal polynomial L(l)(y)L(m)(x) obtained by interchanging x and y. These polynomials are different from the corresponding orthogonal polynomials for a system with rotational symmetry but a rectangular pupil. In this paper, we show that the orthonormal aberration polynomials for an anamorphic system with a circular pupil, obtained by the Gram-Schmidt orthogonalization of the 2D Legendre polynomials, are not separable in the two coordinates. Moreover, for a given polynomial in x and y, there is no corresponding polynomial obtained by interchanging x and y. For example, there are polynomials representing x-defocus, balanced x-coma, and balanced x-spherical aberration, but no corresponding y-aberration polynomials. The missing y-aberration terms are contained in other polynomials. We emphasize that the Zernike circle polynomials, although orthogonal over a circular pupil, are not suitable for an anamorphic system as

  4. Free-forms optics into astronomical use: the case of an all-mirror anamorphic collimator

    NASA Astrophysics Data System (ADS)

    Spanò, Paolo

    2008-07-01

    Up to now, optical design of astronomical instrumentation has been based onto "classical" surfaces, i.e. plano surfaces, spherical surfaces, and some classes of aspheric surfaces. More complex surfaces (like cylinders), are used from time to time to correct for aberrations. A new class of more general surfaces, i.e. non-rotationally symmetrical and completely "free-form" surfaces have been recently introduced. Their use in astronomy, however, has not widely used so far. We propose a new layout for an anamorphic collimator based onto two "free-form" cylinder surfaces, giving diffraction limited images. This collimator can be used to create an elliptical pupil, and allows reducing size of optical systems, too. Two interesting cases of application in astronomy are shown: a very-high resolution spectrograph for large telescopes, and an interferometer cavity to test large plano optics.

  5. Dermatitis and cellulitis in leopard geckos (Eublepharis macularius) caused by the Chrysosporium anamorph of Nannizziopsis vriesii.

    PubMed

    Toplon, D E; Terrell, S P; Sigler, L; Jacobson, E R

    2013-07-01

    An epizootic of ulcerative to nodular ventral dermatitis was observed in a large breeding colony of 8-month to 5-year-old leopard geckos (Eublepharis macularius) of both sexes. Two representative mature male geckos were euthanized for diagnostic necropsy. The Chrysosporium anamorph of Nannizziopsis vriesii (CANV) was isolated from the skin lesions, and identification was confirmed by sequencing of the internal transcribed spacer region of the rRNA gene. Histopathology revealed multifocal to coalescing dermal and subcutaneous heterophilic granulomas that contained septate fungal hyphae. There was also multifocal epidermal hyperplasia with hyperkeratosis, and similar hyphae were present within the stratum corneum, occasionally with terminal chains of arthroconidia consistent with the CANV. In one case, there was focal extension of granulomatous inflammation into the underlying masseter muscle. This is the first report of dermatitis and cellulitis due to the CANV in leopard geckos.

  6. Molecular Characterization of Reptile Pathogens Currently Known as Members of the Chrysosporium Anamorph of Nannizziopsis vriesii Complex and Relationship with Some Human-Associated Isolates

    PubMed Central

    Hambleton, Sarah; Paré, Jean A.

    2013-01-01

    In recent years, the Chrysosporium anamorph of Nannizziopsis vriesii (CANV), Chrysosporium guarroi, Chrysosporium ophiodiicola, and Chrysosporium species have been reported as the causes of dermal or deep lesions in reptiles. These infections are contagious and often fatal and affect both captive and wild animals. Forty-nine CANV isolates from reptiles and six isolates from human sources were compared with N. vriesii based on their cultural characteristics and DNA sequence data. Analyses of the sequences of the internal transcribed spacer and small subunit of the nuclear ribosomal gene revealed that the reptile pathogens and human isolates belong in well-supported clades corresponding to three lineages that are distinct from all other taxa within the family Onygenaceae of the order Onygenales. One lineage represents the genus Nannizziopsis and comprises N. vriesii, N. guarroi, and six additional species encompassing isolates from chameleons and geckos, crocodiles, agamid and iguanid lizards, and humans. Two other lineages comprise the genus Ophidiomyces, with the species Ophidiomyces ophiodiicola occurring only in snakes, and Paranannizziopsis gen. nov., with three new species infecting squamates and tuataras. The newly described species are Nannizziopsis dermatitidis, Nannizziopsis crocodili, Nannizziopsis barbata, Nannizziopsis infrequens, Nannizziopsis hominis, Nannizziopsis obscura, Paranannizziopsis australasiensis, Paranannizziopsis californiensis, and Paranannizziopsis crustacea. Chrysosporium longisporum has been reclassified as Paranannizziopsis longispora. N. guarroi causes yellow fungus disease, a common infection in bearded dragons and green iguanas, and O. ophiodiicola is an emerging pathogen of captive and wild snakes. Human-associated species were not recovered from reptiles, and reptile-associated species were recovered only from reptiles, thereby mitigating concerns related to zoonosis. PMID:23926168

  7. Molecular characterization of reptile pathogens currently known as members of the chrysosporium anamorph of Nannizziopsis vriesii complex and relationship with some human-associated isolates.

    PubMed

    Sigler, Lynne; Hambleton, Sarah; Paré, Jean A

    2013-10-01

    In recent years, the Chrysosporium anamorph of Nannizziopsis vriesii (CANV), Chrysosporium guarroi, Chrysosporium ophiodiicola, and Chrysosporium species have been reported as the causes of dermal or deep lesions in reptiles. These infections are contagious and often fatal and affect both captive and wild animals. Forty-nine CANV isolates from reptiles and six isolates from human sources were compared with N. vriesii based on their cultural characteristics and DNA sequence data. Analyses of the sequences of the internal transcribed spacer and small subunit of the nuclear ribosomal gene revealed that the reptile pathogens and human isolates belong in well-supported clades corresponding to three lineages that are distinct from all other taxa within the family Onygenaceae of the order Onygenales. One lineage represents the genus Nannizziopsis and comprises N. vriesii, N. guarroi, and six additional species encompassing isolates from chameleons and geckos, crocodiles, agamid and iguanid lizards, and humans. Two other lineages comprise the genus Ophidiomyces, with the species Ophidiomyces ophiodiicola occurring only in snakes, and Paranannizziopsis gen. nov., with three new species infecting squamates and tuataras. The newly described species are Nannizziopsis dermatitidis, Nannizziopsis crocodili, Nannizziopsis barbata, Nannizziopsis infrequens, Nannizziopsis hominis, Nannizziopsis obscura, Paranannizziopsis australasiensis, Paranannizziopsis californiensis, and Paranannizziopsis crustacea. Chrysosporium longisporum has been reclassified as Paranannizziopsis longispora. N. guarroi causes yellow fungus disease, a common infection in bearded dragons and green iguanas, and O. ophiodiicola is an emerging pathogen of captive and wild snakes. Human-associated species were not recovered from reptiles, and reptile-associated species were recovered only from reptiles, thereby mitigating concerns related to zoonosis.

  8. Anamorphic imaging at high-NA EUV: mask error factor and interaction between demagnification and lithographic metrics

    NASA Astrophysics Data System (ADS)

    Bottiglieri, Gerardo; Last, Thorsten; Colina, Alberto; van Setten, Eelco; Rispens, Gijsbert; van Schoot, Jan; van Ingen Schenau, Koen

    2016-10-01

    This paper presents some of the main imaging properties introduced with the design of a possible new EUV High-NA (NA > 0.5) exposure system with anamorphic projection lens, a concept not new in optics but applied for the first time in semiconductor lithography. The system is projected to use a demagnification of 4 in the X-direction and of 8 in the Y-direction. We show that a new definition of the Mask Error Factor needs to be used in order to describe correctly the property introduced by the anamorphic optics. Moreover, for both 1-Dimensional (1D) and 2-Dimensional (2D) features the reticle writing error in the low demagnification direction X is more critical than the error in high demagnification direction Y. The effects of the change in demagnification on imaging are described on an elementary case, and are ultimately linked to the basic physical phenomenon of diffraction.

  9. Nomenclatural realignment of Neotyphodium species with genus Epichloe

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nomenclatural rule changes in the International Code of Nomenclature for algae, fungi and plants made at the 18th International Botanical Congress in Melbourne, Australia in 2011 require that a single name is used for all fungi. Since the anamorphic stages of Epichloë species have been classified i...

  10. Observations on Neobarya, including new species and new combinations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New combinations and new species are proposed in Neobarya: N. aurantiaca comb. nov., N. byssicola comb. nov., N. lichenicola comb. nov., N. lutea sp. nov., N. peltigerae sp. nov., N. xylariicola sp. nov. Neobarya agaricicola, and N. parasitica are redescribed. Anamorphs associated with N. agaricico...

  11. Mycosphaerella species associated with Eucalyptus in south-western Australia: new species, new records and a key.

    PubMed

    Maxwell, Aaron; Dell, Bernie; Neumeister-Kemp, Heike G; St J Hardy, Giles E

    2003-03-01

    Mycosphaerella ambiphylla sp. nov. (anamorph: Phaeophleospora) and Mycosphaerella aurantia sp. nov., are described from diseased Eucalyptus globulus leaves. In addition, a new fungal record in Australia, M. mexicana, and two new records for Western Australia, M. gregaria and M. parva, are discussed. A key is provided to Mycosphaerella species on E. globulus in Western Australia.

  12. Yamadazyma barbieri f.a. sp. nov., an ascomycetous anamorphic yeast isolated from a Mid-Atlantic Ridge hydrothermal site (-2300 m) and marine coastal waters.

    PubMed

    Burgaud, Gaëtan; Coton, Monika; Jacques, Noémie; Debaets, Stella; Maciel, Natália O P; Rosa, Carlos A; Gadanho, Mário; Sampaio, José Paulo; Casaregola, Serge

    2016-09-01

    Two yeast strains that are members of the same species were isolated from different marine habitats, i.e. one from Mid-Atlantic Ridge ocean water samples located in the direct vicinity of black smokers near the Rainbow deep-sea hydrothermal vent and one from Brazilian marine water samples off the Ipanema beach. Strains CLIB 1964T and CLIB 1965 are anamorphic ascomycetous yeasts affiliated to the Yamadazyma clade of Saccharomycetales. Interestingly, these strains were phylogenetically and distinctly positioned into a group of species comprising all species of the genus Yamadazyma isolated from marine habitats including deep-sea hydrothermal vents, i.e.Candida atmosphaerica,C. spencermartinsiae,C. atlantica,C. oceani and C. taylorii. These strains differed significantly in their D1/D2 domain sequences of the LSU rRNA gene from the closely related species mentioned above, by 2.6, 3.0, 3.4, 3.8 and 6.0 %, respectively. Internal transcribed spacer region sequence divergence was also significant and corresponded to 4.6, 4.7, 4.7, 12.0 and 24.7 % with C. atlantica,C. atmosphaerica, C. spencermartinsiae,C. oceani and C. taylorii, respectively. Phenotypically, strains CLIB 1964T and CLIB 1965 could be distinguished from closely related species by their inability to assimilate l-sorbose. CLIB 1964T (=CBS 14301T=UBOCC-A-214001T) is the designated type strain for Yamadazyma barbieri sp. nov. The MycoBank number is MB 815884.

  13. A new species of Hydropisphaera, H. bambusicola, is the sexual state of Gliomastix fusigera

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new species of Hydropisphaera, H. bambusicola sp. nov., is described and illustrated based on a collection from Bambusa vulgaris in Martinique. The asexual state was obtained in culture and identified as Gliomastix fusigera. Gliomastix fusigera is an anamorph species that occurs on members of the ...

  14. Ghost reflections of Gaussian beams in anamorphic optical systems with an application to Michelson interferometer.

    PubMed

    Abd El-Maksoud, Rania H

    2016-02-20

    In this paper, a methodology is developed to model and analyze the effect of undesired (ghost) reflections of Gaussian beams that are produced by anamorphic optical systems. The superposition of these beams with the nominal beam modulates the nominal power distribution at the recording plane. This modulation may cause contrast reduction, veiling parts of the nominal image, and/or the formation of spurious interference fringes. The developed methodology is based on synthesizing the beam optical paths into nominal and ghost optical beam paths. Similar to the nominal beam, we present the concept that each ghost beam is characterized by a beam size, wavefront radius of curvature, and Gouy phase in the paraxial regime. The nominal and ghost beams are sequentially traced through the system and formulas for estimating the electric field magnitude and phase of each ghost beam at the recording plane are presented. The effective electric field is the addition of the individual nominal and ghost electric fields. Formulas for estimating Gouy phase, the shape of the interference fringes, and the central interference order are introduced. As an application, the theory of the formation of the interference fringes by Michelson interferometer is presented. This theory takes into consideration the ghost reflections that are formed by the beam splitter. To illustrate the theory and to show its wide applicability, simulation examples that include a Mangin mirror, a Michelson interferometer, and a black box optical system are provided.

  15. Implications of Planck2015 for inflationary, ekpyrotic and anamorphic bouncing cosmologies

    NASA Astrophysics Data System (ADS)

    Ijjas, Anna; Steinhardt, Paul J.

    2016-02-01

    The results from Planck2015, when combined with earlier observations from the Wilkinson Microwave Anisotropy Probe, Atacama Cosmology Telescope, South Pole Telescope and other experiments, were the first observations to disfavor the ‘classic’ inflationary paradigm. To satisfy the observational constraints, inflationary theorists have been forced to consider plateau-like inflaton potentials that introduce more parameters and more fine-tuning, problematic initial conditions, multiverse-unpredictability issues, and a new ‘unlikeliness problem’. Some propose turning instead to a ‘postmodern’ inflationary paradigm in which the cosmological properties in our observable Universe are only locally valid and set randomly, with completely different properties (and perhaps even different physical laws) existing in most regions outside our horizon. By contrast, the new results are consistent with the simplest versions of ekpyrotic cyclic models in which the Universe is smoothed and flattened during a period of slow contraction followed by a bounce, and another promising bouncing theory, anamorphic cosmology, has been proposed that can produce distinctive predictions.

  16. Anamorphic preclinical SPECT imaging with high-resolution silicon double-sided strip detectors

    NASA Astrophysics Data System (ADS)

    Durko, Heather L.

    Preclinical single-photon emission computed tomography (SPECT) is an essential tool for studying progression, response to treatment, and physiological changes in small animal models of human disease. The wide range of imaging applications is often limited by the static design of many preclinical SPECT systems. We have developed a prototype imaging system that replaces the standard static pinhole aperture with two sets of movable, keel-edged copper-tungsten blades configured as crossed (skewed) slits. These apertures can be positioned independently between the object and detector, producing an anamorphic image in which the axial and transaxial magnications are not constrained to be equal. We incorporated a 60 mm x 60 mm, millimeter-thick megapixel silicon double-sided strip detector that permits ultrahigh-resolution imaging. While the stopping power of silicon is low for many common clinical radioisotopes, its performance is sufficient in the range of 20-60 keV to allow practical imaging experiments. The low-energy emissions of 125I fall within this energy window, and the 60-day half life provides an advantage for longitudinal studies. The flexible nature of this system allows the future application of adaptive imaging techniques. We have demonstrated ˜225-mum axial and ˜175-mum transaxial resolution across a 2.65 cm3 cylindrical field of view, as well as the capability for simultaneous multi-isotope acquisitions. We describe the key advancements that have made this system operational, including bringing up a new detector readout ASIC, development of detector control software and data-processing algorithms, and characterization of operating characteristics. We describe design and fabrication of the adjustable slit aperture platform, as well as the development of an accurate imaging forward model and its application in a novel geometric calibration technique and a GPU-based ultrahigh-resolution reconstruction code.

  17. European species of Hypocrea Part I. The green-spored species

    PubMed Central

    Jaklitsch, Walter M.

    2009-01-01

    At present 75 species of Hypocrea have been identified in temperate Europe. Nineteen green-spored species and their Trichoderma asexual states are here described in detail. Extensive searches for Hypocrea teleomorphs in 14 European countries, with emphasis on Central Europe, yielded more than 620 specimens within five years. The morphology of fresh and dry stromata was studied. In addition, available types of species described from Europe were examined. Cultures were prepared from ascospores and used to study the morphology of cultures and anamorphs, to determine growth rates, and to extract DNA that was used for amplification and sequencing of three genetic markers. ITS was used for identification, while RNA polymerase II subunit b (rpb2) and translation elongation factor 1 alpha (tef1) were analyzed for phylogenetic reconstruction of the genus. Several unexpected findings resulted from this project: 1) The previous view that only a small number of Trichoderma species form a teleomorph is erroneous. 2) All expectations concerning the number of species in Europe are by far exceeded. Seventy-five species of Hypocrea, two species of Protocrea, and Arachnocrea stipata, are herein identified in temperate Europe, based on the ITS identification routine using fresh material, on species described earlier without molecular data and on species recently described but not collected during this project. 3) Current data suggest that the biodiversity of Hypocrea / Trichoderma above soil exceeds the number of species isolated from soil. 4) The number of Trichoderma species forming hyaline conidia has been considered a small fraction. In Europe, 26 species of those forming teleomorphs produce hyaline conidia, while 42 green-conidial species are known. Three of the detected Hypocrea species do not form an anamorph in culture, while the anamorph is unknown in four species, because they have never been cultured. This work is a preliminary account of Hypocrea and their Trichoderma

  18. Anthracnose disease of centipedegrass turf caused by Colletotrichum eremochloae, a new fungal species closely related to Colletotrichum sublineola

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Colletotrichum is a cosmopolitan anamorphic fungal genus responsible for anthracnose disease in hundreds of plant species worldwide, including members of the grass family Poaceae. Anthracnose disease of the widely planted, non-native, warm-season lawn grass, Eremochloa ophiuroides (centipedegrass),...

  19. Anthraquinone dyes decolorization capacity of anamorphic Bjerkandera adusta CCBAS 930 strain and its HRP-like negative mutants.

    PubMed

    Korniłłowicz-Kowalska, Teresa; Rybczyńska, Kamila

    2014-06-01

    Cultures of the anamorphic fungus Bjerkandera adusta CCBAS 930 decolorizing, in stationary cultures, 0.01 % solutions of carminic acid and Poly R-478, were characterised by a strong increase in the activity of the horseradish peroxidase (HRP-like) and manganese-dependent peroxidase (MnP) at a low activity of lignin peroxidase. Genotypically modified mutants of B. adusta CCBAS 930: 930-5 and 930-14, with total or partial loss of decolorization capabilities relative to anthraquinonic dyes, showed inhibition of the activity of HRP-like peroxidase and MnP. Whereas, compared to the parental strain, in the mutant cultures there was an increase in the activity of lignin peroxidase and laccase. The paper presents a discussion of the role of the studied enzymatic activities in the process of decolorization of anthraquinonic dyes by the strain B. adusta CCBAS 930.

  20. An anamorph of the white-rot fungus Bjerkandera adusta capable of colonizing and degrading compact disc components.

    PubMed

    Romero, Elvira; Speranza, Mariela; García-Guinea, Javier; Martínez, Angel T; Martínez, María Jesús

    2007-10-01

    A Geotrichum-like fungus isolated from a biodeteriorated compact disc (CD) was able to degrade in vitro the components of different CD types. The fungal hyphae inside the CD fragments grew through the aluminium layer and produced the solubilization of this metal. Furthermore, examination of CDs by scanning electron microscopy showed that the fungus was able to destroy the pits and lands structures grooved in the polycarbonate layer, confirming degradation of this aromatic polymer. The fungus secretes aryl-alcohol oxidase and Mn2+-oxidizing peroxidase, two kinds of oxidoreductases characteristic of ligninolytic basidiomycetes. Analysis of the ITS region of ribosomal DNA, as well as the morphological characteristics, the lack of sexual forms and the profile of enzymes secreted in liquid medium identified the fungus as a Geotrichum-like anamorph of Bjerkandera adusta (Willd.) P. Karst.

  1. Vertical viewing angle enhancement for the 360  degree integral-floating display using an anamorphic optic system.

    PubMed

    Erdenebat, Munkh-Uchral; Kwon, Ki-Chul; Yoo, Kwan-Hee; Baasantseren, Ganbat; Park, Jae-Hyeung; Kim, Eun-Soo; Kim, Nam

    2014-04-15

    We propose a 360 degree integral-floating display with an enhanced vertical viewing angle. The system projects two-dimensional elemental image arrays via a high-speed digital micromirror device projector and reconstructs them into 3D perspectives with a lens array. Double floating lenses relate initial 3D perspectives to the center of a vertically curved convex mirror. The anamorphic optic system tailors the initial 3D perspectives horizontally and vertically disperse light rays more widely. By the proposed method, the entire 3D image provides both monocular and binocular depth cues, a full-parallax demonstration with high-angular ray density and an enhanced vertical viewing angle.

  2. Description of Martiniozyma gen. nov. and transfer of seven Candida species to Saturnispora as new combinations.

    PubMed

    Kurtzman, Cletus P

    2015-10-01

    DNA sequence analysis has shown Candida abiesophila (NRRL Y-11514(T), CBS 5366(T)) and Candida asiatica (NRRL Y-63747(T), CBS 10863(T)) to be members of a small clade that is phylogenetically separate from other yeasts. In view of their isolation from neighboring genera, such as Pichia and Saturnispora, the two anamorphic species are proposed for transfer to Martiniozyma gen. nov. (MycoBank MB 812061) with Martiniozyma abiesophila designated as type species (MycoBank MB 812062). In keeping with the International Code of Nomenclature for algae, fungi, and plants, which specifies that related anamorphic and teleomorphic species can be assigned to the same genus, the following Candida species are transferred to Saturnispora to conform with their phylogenetic placement: Candida diversa (NRRL Y-5713(T)), Candida halmiae (CBS 11009(T)), Candida sanitii (CBS 10864(T)), Candida sekii (CBS 10931(T)), Candida siamensis (CBS 11022(T)), Candida silvae (NRRL Y-6725(T)) and Candida suwanaritii (CBS 11021(T)).

  3. Voriconazole, a safe alternative for treating infections caused by the Chrysosporium anamorph of Nannizziopsis vriesii in bearded dragons (Pogona vitticeps).

    PubMed

    Van Waeyenberghe, L; Baert, K; Pasmans, F; van Rooij, P; Hellebuyck, T; Beernaert, L; de Backer, P; Haesebrouck, F; Martel, A

    2010-09-01

    Dermal and systemic infections caused by the Chrysosporium anamorph of Nannizziopsis vriesii (CANV) are highly prevalent in reptiles and may result in severe disease and high mortality. Due to the high incidence of therapeutic failures, optimizing treatment is required. We first determined in this study the minimal inhibitory concentrations (MIC) of itraconazole, voriconazole, amphotericin B and terbinafine against 32 CANV isolates. For voriconazole, amphotericin B and terbinafine a monomodal MIC distribution was seen, whereas a bimodal MIC distribution was present for itraconazole, indicating acquired resistance in one isolate. Fourteen naturally-infected bearded dragons (Pogona vitticeps), from the same owner, were treated orally with either itraconazole (5 mg/kg q24h) or voriconazole (10 mg/kg q24h). The clinical condition, drug plasma concentrations and the presence of CANV in skin samples were followed. The animals were treated until complete clearance of the fungus. The plasma concentrations of voriconazole and itraconazole exceeded the minimal inhibitory concentrations of the CANV isolates. Elimination of CANV was achieved on average after 27 and 47 days of treatment with itraconazole and voriconazole, respectively. Whereas only 2 out of 7 survived after itraconazole treatment, only a single animal died in the voriconazole treated group. In conclusion, based on a limited number of animals, voriconazole applied at a regimen of 10 mg/kg bodyweight (BW) q24h seems to be a safe and effective antimycotic drug to eliminate CANV infections in bearded dragons.

  4. Description of Kuraishia piskuri f.a., sp. nov., a new methanol assimilating yeast and transfer of phylogenetically related Candida species to the genera Kuraishia and Nakazawaea as new combinations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The new anamorphic yeast Kuraishia piskuri, f.a., sp. nov. is described for three strains that were isolated from insect frass from trees growing in Florida, USA (type strain, NRRL YB-2544, CBS 13714). Species placement was based on phylogenetic analysis of nuclear gene sequences for the D1/D2 domai...

  5. Fungal infection of mantis shrimp (Oratosquilla oratoria) caused by two anamorphic fungi found in Japan.

    PubMed

    Duc, Pham Minh; Hatai, Kishio; Kurata, Osamu; Tensha, Kozue; Yoshitaka, Uchida; Yaguchi, Takashi; Udagawa, Shun-ichi

    2009-05-01

    Two fungal pathogens of the mantis shrimp (Oratosquilla oratoria) in Yamaguchi and Aichi Prefectures, Japan are described as the new species Plectosporium oratosquillae and Acremonium sp. (a member of the Emericellopsis marine clade). Both fungi infect the gills of the mantis shrimp, which become brown or black due to melanization. The former species is characterized by its slow growth on artificial seawater yeast extract peptone glucose (PYGS) agar, pale yellow to pale orange or grayish yellow colonies, short cylindrical solitary phialides with a wavy tip, and one-celled ellipsoidal conidia. Although lacking the two-celled conidia demonstrated by the type species Plectosporium tabacinum, the taxonomic placement of the new species was confirmed by DNA sequence analysis of the internal transcribed spacer (ITS) region of ribosomal DNA (ITS1, 5.8S rDNA and ITS2). Acremonium sp., the other causal pathogen, differs from P. oratosquillae by its fast growth on PYGS agar, pale orange to salmon-colored colonies, long, slender conidiophores consisting of solitary phialides with tips lacking an undulate outline, and typically cylindrical conidia. Analysis of ITS and beta-tubulin gene sequences placed this fungus within the phylogenetically distinct Emericellopsis (anam. Acremonium) marine clade. Various physiological characteristics of both pathogens were also investigated. This is the first report of a fungal infection found on the mantis shrimp in Japan.

  6. Cryptococcus terrestris sp. nov., a tremellaceous, anamorphic yeast phylogenetically related to Cryptococcus flavescens.

    PubMed

    Crestani, Juliana; Fontes Landell, Melissa; Faganello, Josiane; Henning Vainstein, Marilene; Simpson Vishniac, Helen; Valente, Patrícia

    2009-03-01

    Cryptococcus terrestris sp. nov. (Basidiomycota, Agaricomycotina, Tremellomycetes, Tremellales) is typified by CJDX4 Y23(T) (=CBS 10810(T) =NRRL Y-48451(T)), isolated from forest soil in Oklahoma, USA. This species is most readily identified by the sequence of the D1/D2 domain region of the 26S rDNA and ITS (internal transcribed spacer) region. Additional strains from Oklahoma (C107DX4 Y11 =CBS 10813 =NRRL Y-48452) and Brazil (Ep11c =CBS 10812 =NRRL Y-48454; 56e =CBS 10811 =NRRL Y-48453) either had identical sequences or differed minimally. C. terrestris differs physiologically from the most closely related species, Cryptococcus flavescens, by the weak or delayed assimilation of ribose and salicin, and differs from Cryptococcus aureus by the utilization of nitrate and nitrite and growth in vitamin-free medium.

  7. Species concepts and biodiversity in Trichoderma and Hypocrea: from aggregate species to species clusters?*

    PubMed Central

    Druzhinina, Irina; Kubicek, Christian P

    2005-01-01

    Trichoderma/Hypocrea is a genus of soil-borne or wood-decaying fungi containing members important to mankind as producers of industrial enzymes and biocontrol agents against plant pathogens, but also as opportunistic pathogens of immunocompromised humans. Species identification, while essential in view of the controversial properties of taxa of this genus, has been problematic by traditional methods. Here we will present a critical survey of the various identification methods in use. In addition, we will present an update on the taxonomy and phylogeny of the 88 taxa (which occur as 14 holomorphs, 49 teleomorphs and 25 anamorphs in nature) of Trichoderma/Hypocrea that have been confirmed by a combination of morphological, physiological and genetic approaches. PMID:15633245

  8. Diversity and potential impact of Calonectria species in Eucalyptus plantations in Brazil

    PubMed Central

    Alfenas, R.F.; Lombard, L.; Pereira, O.L.; Alfenas, A.C.; Crous, P.W.

    2015-01-01

    Species in the genus Calonectria (Hypocreales) represent an important group of plant pathogenic fungi that cause serious losses to plant crops in tropical and subtropical climates. Calonectria leaf blight is currently one of the main impediments to Eucalyptus cultivation in Brazil, and various species of Calonectria have been associated with this disease. Since most previous identifications were solely based on morphological characters, much of the published literature needs to be re-evaluated. The aim of this study was thus to identify and determine the phylogenetic relationships among species that occur in the Eucalyptus growing regions of Brazil by using partial sequences of the β-tubulin, calmodulin, translation elongation factor 1-α and histone H3 gene regions. Based on extensive collections from soil and infected eucalypt leaf samples from plantations, phylogenetic inference revealed the Ca. pteridis complex to be the most common species complex present in Eucalyptus plantations in Brazil. By elucidating taxa in the Ca. pteridis, Ca. cylindrospora and Ca. candelabra species complexes, 20 novel Calonectria species were identified, and a new name in Calonectria provided for Cylindrocladium macrosporum as Ca. pseudopteridis. PMID:26955192

  9. The Trichoderma koningii aggregate species

    PubMed Central

    Samuels, Gary J.; Dodd, Sarah L.; Lu, Bing-Sheng; Petrini, Orlando; Schroers, Hans-Josef; Druzhinina, Irina S.

    2006-01-01

    The morphological concept of Trichoderma koningii is found to include several species that differ from each other in details of phenotype (including conidium morphology, growth rate) and biogeography. Phylogenetic analysis utilizing partial sequences of the translation-elongation factor 1 alpha (tef1), as well as fragments of actin and calmodulin genes, indicate that phenotypic characters typical of T. koningii evolved independently in three well-separated main lineages. Combined molecular and phenotype data lead to the development of a taxonomy with the recognition of twelve taxonomic species and one variety within the three lineages. These lineages include: (1) T. koningii and T. ovalisporum and the new species T. caribbaeum var. caribbaeum, T. caribbaeum var. aequatoriale, T. dorotheae, T. dingleyae, T. intricatum, T. koningiopsis, T. petersenii and T. taiwanense; (2) the new species T. rogersonii and T. austrokoningii, and (3) the new anamorph T. stilbohypoxyli. Trichoderma koningii s. str. is an uncommon species restricted to Europe and eastern North America; T. caribbaeum var. aequatoriale, T. koningiopsis, and T. ovalisporum were isolated as endophytes of trunks of Theobroma species in tropical America, and T. ovalisporum from the woody liana Banisteropsis caapi in Ecuador; T. koningiopsis is common in tropical America but was isolated also from natural substrata in East Africa, Europe and Canada, and from ascospores in eastern North America, and as an endophyte in Theobroma species; T. stilbohypoxyli, originally described as a parasite of Stilbohypoxylon species in Puerto Rico, is found to be more common in the tropics, besides an endophytic isolate from Fagus in U.K. The additional new species are known almost exclusively from their teleomorphs. Isolates of T. ovalisporum and T. koningiopsis may have biological control potential. A morphophenetic key and a set of tools for molecular species identification were developed. PMID:18490990

  10. Hypocrea rufa/Trichoderma viride: a reassessment, and description of five closely related species with and without warted conidia

    PubMed Central

    Jaklitsch, Walter M.; Samuels, Gary J.; Dodd, Sarah L.; Lu, Bing-Sheng; Druzhinina, Irina S.

    2006-01-01

    The type species of the genus Hypocrea (Hypocreaceae, Hypocreales, Ascomycota, Fungi), H. rufa, is re-defined and epitypified using a combination of phenotype (morphology of teleomorphs and anamorphs, and characteristics in culture) and phylogenetic analyses of the translation-elongation factor 1α gene. Its anamorph, T. viride, the type species of Trichoderma, is re-described and epitypified. Eidamia viridescens is combined as Trichoderma viridescens and is recognised as one of the most morphologically and phylogenetically similar relatives of T. viride. Its teleomorph is newly described as Hypocrea viridescens. Contrary to frequent citations of H. rufa and T. viride in the literature, this species is relatively rare. Although both T. viride and T. viridescens have a wide geographic distribution, their greatest genetic diversity appears to be in Europe and North America. Hypocrea vinosa is characterised and its anamorph, T. vinosum sp. nov., is described. Conidia of T. vinosum are subglobose and warted. The new species T. gamsii is proposed. It shares eidamia-like morphology of conidiophores with T. viridescens, but it has smooth, ellipsoidal conidia that have the longest L/W ratio that we have seen in Trichoderma. Trichoderma scalesiae, an endophyte of trunks of Scalesia pedunculata in the Galapagos Islands, is described as new. It only produces conidia on a low-nutrient agar to which filter paper has been added. Additional phylogenetically distinct clades are recognised and provisionally delimited from the species here described. Trichoderma neokoningii, a T. koningii-like species, is described from a collection made in Peru on a fruit of Theobroma cacao infected with Moniliophthora roreri. PMID:18490991

  11. Two new anamorphic yeasts, Candida thailandica sp. nov. and Candida lignicola sp. nov., isolated from insect frass in Thailand.

    PubMed

    Jindamorakot, Sasitorn; Limtong, Savitree; Yongmanitchai, Wichien; Tuntirungkij, Manee; Potacharoen, Wanchern; Kawasaki, Hiroko; Nakase, Takashi

    2007-12-01

    Two new yeast strains of the genus Candida were isolated from insect frass collected in Khao-Yai National Park, Nakhonrachasima, Thailand. Based on the morphological, physiological and chemotaxonomic characteristics, and sequence analysis of the D1/D2 domain of 26S rRNA gene, these two strains were found to represent two distinct undescribed species and were named Candida thailandica sp. nov. (ST-17 = BCC 7717(T) = NBRC 102562(T)=CBS 10 610) and Candida lignicola sp. nov. (ST-33 = BCC 7733(T) = NBRC 102564(T) = CBS 10612). In the D1/D2 domain of 26S rRNA gene, C. thailandica (GeneBank accession no. AY228491) differs from Candida tsuchiyae, the nearest species, in 66 nucleotide substitutions (10%) and C. lignicola (GeneBank accession no. AY845350) differs from Candida coipomoensis, the nearest species, in nine nucleotides (1.6%). These two new species are clearly distinguished from their closest species by the assimilation of several carbon compounds.

  12. Molecular and morphological description of two new species of Stemphylium from China and France.

    PubMed

    Wang, Yong; Geng, Yun; Pei, Yun-Fei; Zhang, Xiu-Guo

    2010-01-01

    Two new species of Stemphylium (anamorphic Pleospora) are described on the basis of morphological characters and molecular phylogenetic analyses. Stemphylium phaseolina and S. variabilis were isolated respectively from diseased leaves of Phaseolus vulgaris L. in Hebei Province, China, and from diseased leaves of Allium sativum L. in Angres, France. The two species exhibit characteristic Stemphylium morphology but are distinct from similar species based on the morphology and development of conidia. The internal transcribed spacer (ITS) nuclear rDNA region and glyceraldehyde-3-phosphate dehydrogenase (gpd) genes were sequenced. The results of maximum parsimony (MP) and maximum likelihood (ML) phylogenetic analyses of the combined DNA sequences of these two gene regions supported S. phaseolina and S. variabilis as two distinct phylogenetic species. The taxonomic descriptions of the new species and their comparison with related species are presented, together with the phylogenetic analysis based on combined DNA sequences of ITS and gpd gene regions.

  13. The genus Chaetomium in Iran, a phylogenetic study including six new species.

    PubMed

    Asgari, Bita; Zare, Rasoul

    2011-01-01

    Twenty-one species of Chaetomium known from Iran were compared on the basis of morphological and molecular characters. Six new species are recognized, five isolated from cereals and one from nematode cysts. A combined sequence dataset of the ITS region, partial LSU rDNA, and β-tubulin gene sufficiently resolved five species groups of Chaetomium that are largely concordant with combined features of peridium structure, ascospore shape and germ pore position. Among the new species C. undulatulum is a close relative of C. globosum, C. rectangulare is close to C. elatum, C. interruptum and C. grande are close to C. megalocarpum, altogether forming the C. globosum species group. Chaetomium iranianum and C. truncatulum are members of the C. carinthiacum species group, characterized by spirally coiled ascomatal hairs and fusiform ascospores. A chrysosporium-like anamorph is newly described for C. acropullum.

  14. The Trichoderma harzianum demon: complex speciation history resulting in coexistence of hypothetical biological species, recent agamospecies and numerous relict lineages

    PubMed Central

    2010-01-01

    Background The mitosporic fungus Trichoderma harzianum (Hypocrea, Ascomycota, Hypocreales, Hypocreaceae) is an ubiquitous species in the environment with some strains commercially exploited for the biological control of plant pathogenic fungi. Although T. harzianum is asexual (or anamorphic), its sexual stage (or teleomorph) has been described as Hypocrea lixii. Since recombination would be an important issue for the efficacy of an agent of the biological control in the field, we investigated the phylogenetic structure of the species. Results Using DNA sequence data from three unlinked loci for each of 93 strains collected worldwide, we detected a complex speciation process revealing overlapping reproductively isolated biological species, recent agamospecies and numerous relict lineages with unresolved phylogenetic positions. Genealogical concordance and recombination analyses confirm the existence of two genetically isolated agamospecies including T. harzianum sensu stricto and two hypothetical holomorphic species related to but different from H. lixii. The exact phylogenetic position of the majority of strains was not resolved and therefore attributed to a diverse network of recombining strains conventionally called 'pseudoharzianum matrix'. Since H. lixii and T. harzianum are evidently genetically isolated, the anamorph - teleomorph combination comprising H. lixii/T. harzianum in one holomorph must be rejected in favor of two separate species. Conclusions Our data illustrate a complex speciation within H. lixii - T. harzianum species group, which is based on coexistence and interaction of organisms with different evolutionary histories and on the absence of strict genetic borders between them. PMID:20359347

  15. Geotrichum bryndzae sp. nov., a novel asexual arthroconidial yeast species related to the genus Galactomyces.

    PubMed

    Sulo, Pavol; Laurencík, Michal; Poláková, Silvia; Minárik, Gabriel; Sláviková, Elena

    2009-09-01

    Ten strains of an asexual arthroconidial yeast species were isolated from Bryndza, a traditional Slovak artisanal sheep cheese, which was manufactured from raw milk during a 4-month summer production period at two Slovakian sites (the northern RuZomberok and the central-southern Tisovec areas). Sequence comparison of the D1/D2 domains of the large-subunit rRNA gene revealed that this yeast represents a novel species of the genus Geotrichum, which contains anamorphs of the ascogenous genus Galactomyces, for which the name Geotrichum bryndzae sp. nov. is proposed (type culture CCY 16-2-1T=NRRL Y-48450T=CBS 11176T). The novel species is most closely related to Geotrichum silvicola NRRL Y-27641T, although yeasts with identical or very similar sequences have been found throughout the world.

  16. Candida cabralensis sp. nov., a yeast species isolated from traditional Spanish blue-veined Cabrales cheese.

    PubMed

    Flórez, Ana Belén; Belloch, Carmela; Alvarez-Martín, Pablo; Querol, Amparo; Mayo, Baltasar

    2010-11-01

    Three yeast strains, 1AD8(T), 3AD15 and 3AD23, belonging to a previously unknown yeast species were isolated from two independent batches of the Spanish blue-veined Cabrales cheese, a traditional cheese manufactured without the addition of starter and mould cultures. Physiological characterization revealed that the unknown yeast is not fermentative and does not assimilate lactose; rather it assimilates dl-lactic acid and ethanol, major end products of lactic acid bacteria metabolism in cheese. The novel yeast is anamorphic. Phylogenetic tree reconstruction based on nucleotide sequence comparison of the D1/D2 region of the 26S rRNA gene showed that Pichia terricola and Pichia fermentans are the closest relatives of the unknown species. The name Candida cabralensis sp. nov. is proposed, and the isolate 1AD8(T) (=CECT 13027(T) =CBS 11679(T)) is the type strain of this novel taxon.

  17. Candida middelhoveniana sp. nov., a new yeast species found on the rhizoplane of organically cultivated sugarcane.

    PubMed

    Ribeiro, José R de A; Carvalho, Patrícia M B de; Cabral, Anderson de S; Macrae, Andrew; Mendonça-Hagler, Leda C S; Berbara, Ricardo L L; Hagler, Allen N

    2011-10-01

    A novel yeast species within the Metschnikowiaceae is described based on a strain from the sugarcane (Saccharum sp.) rhizoplane of an organically managed farm in Rio de Janeiro, Brazil. The D1/D2 domain of the large subunit ribosomal RNA gene sequence analysis showed that the closest related species were Candida tsuchiyae with 86.2% and Candida thailandica with 86.7% of sequence identity. All three are anamorphs in the Clavispora opuntiae clade. The name Candida middelhoveniana sp. nov. is proposed to accommodate this highly divergent organism with the type strain Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (IMUFRJ) 51965(T) (=Centraalbureau voor Schimmelcultures (CBS) 12306(T), Universidade Federal de Minas Gerais (UFMG)-70(T), DBVPG 8031(T)) and the GenBank/EMBL/DDBJ accession number for the D1/D2 domain LSU rDNA sequence is FN428871. The Mycobank deposit number is MB 519801.

  18. Fumonisin production by Gibberella fujikuroi strains from Pinus species.

    PubMed

    Mirete, S; Patiño, B; Vázquez, C; Jiménez, M; Hinojo, M J; Soldevilla, C; González-Jaén, M T

    2003-12-31

    Fumonisins are important mycotoxins basically produced by strains from the Gibberella fujikuroi species complex (with anamorphs in Fusarium genus) which contaminate food and feed products representing a risk to human and animal health. In this work, we report for the first time the fumonisin production of Fusarium moniliforme Sheldon strains associated to edible pine nuts of Pinus pinea. P. pinea is an important and widely distributed Pinus species in the Mediterranean area where their pine nuts are consumed raw or slightly processed in diverse food products. In this work, characterization and further identification of those strains were performed by polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) of the intergenic spacer region of the rDNA (IGS) with the aid of the eight mating populations (A-H) described for G. fujikuroi species complex. The method was powerful to detect polymorphism, allowing discrimination between individuals and could be used to study the genetic relationships among them and within the G. fujikuroi species complex. Fusarium strains associated to Pinus radiata were also included in the present study. These strains did not produce fumonisins and showed no close relation with the strains isolated from P. pinea. The approach used in this work was rapid and proved to be efficient to assist identification and to characterize and analyse relatedness of new isolates within the G. fujikuroi species complex.

  19. Identification of Geotrichum candidum at the species and strain level: proposal for a standardized protocol.

    PubMed

    Gente, S; Sohier, D; Coton, E; Duhamel, C; Gueguen, M

    2006-12-01

    In this study, the M13 primer was used to distinguish Geotrichum candidum from the anamorphic and teleomorphic forms of other arthrospore-forming species (discriminatory power = 0.99). For intraspecific characterization, the GATA4 primer showed the highest level of discrimination for G. candidum among the 20 microsatellite primers tested. A molecular typing protocol (DNA concentration, hybridization temperature and type of PCR machine) was optimized through a series of intra- and interlaboratory trials. This protocol was validated using 75 strains of G. candidum, one strain of G. capitatum and one strain of G. fragrans, and exhibited a discrimination score of 0.87. This method could therefore be used in the agro-food industries to identify and to evaluate biodiversity and trace strains of G. candidum. The results show that the GATA4 primer might be used to differentiate strains according to their ecological niche.

  20. Gibberella musae (Fusarium musae) sp. nov., a recently discovered species from banana is sister to F. verticillioides.

    PubMed

    Van Hove, François; Waalwijk, Cees; Logrieco, Antonio; Munaut, Françoise; Moretti, Antonio

    2011-01-01

    Several strains of Fusarium isolated from banana were identified previously as F. verticillioides (Sacc.) Nirenberg but described as unable to produce fumonisin. Here we report biochemical and morphological evidence, as well as multilocus phylogenetic analyses based on elongation factor (EF-1α), calmodulin, β-tubulin, and the second largest subunit of RNA polymerase II (RPB2) sequences, indicating that these isolates represent a unique lineage in the Gibberella fujikuroi species complex related to but distinct from F. verticillioides. Together with previous results of molecular studies, as well as with results of metabolite analyses, crossing experiments, pathogenicity tests and morphological characterization, these new data indicate that these strains isolated from banana represent a new species, Gibberella musae Van Hove et al. sp. nov. (anamorph: Fusarium musae Van Hove et al. sp. nov.), which is described herein.

  1. Molecular Phylogeny of the Pseudallescheria boydii Species Complex: Proposal of Two New Species†

    PubMed Central

    Gilgado, Felix; Cano, Josep; Gené, Josepa; Guarro, Josep

    2005-01-01

    Pseudallescheria boydii (anamorph Scedosporium apiospermum) is the species responsible for human scedosporiosis, a fungal infection with a high mortality rate and which is difficult to treat. Recently, it has been demonstrated that high genetic variation exists within this species. We have performed a morphological and molecular study involving numerous strains of clinical or environmental origins and from different countries. The analysis of partial sequences of the β-tubulin (two loci) and calmodulin genes and the internal transcribed spacer region of the rRNA gene has demonstrated that P. boydii is a species complex. The combined analysis of the sequences of the four loci of 60 strains has showed the presence of 44 haplotypes in the ingroup. Three species morphologically related to P. boydii sensu stricto, i.e., Pseudallescheria angusta, Pseudallescheria ellipsoidea, and Pseudallescheria fusoidea, which had previously been considered synonyms, could be differentiated genetically from P. boydii in our study. It is relevant that two of the three strains now included in P. ellipsoidea have caused invasive infections. The species Pseudallescheria minutispora and Scedosporium aurantiacum are clearly phylogenetically separated from the other species studied and are here proposed as new. Morphological features support this proposal. All the strains included in S. aurantiacum species have a clinical origin, while those included in P. minutispora are environmental. Further studies are needed to demonstrate whether all the species included in the P. boydii complex have different clinical spectra and antifungal susceptibility. PMID:16207945

  2. Using human sera to identify a 52-kDa exoantigen of Penicillium chrysogenum and implications of polyphasic taxonomy of anamorphic ascomycetes in the study of antigenic proteins.

    PubMed

    Wilson, Aaron M; Luo, Wen; Miller, J David

    2009-11-01

    We are interested in isolating and identifying antigenic fungal proteins from species that grow on damp building materials. The indoor clade of Penicillium chrysogenum, the so-called Fleming clade, is the most common species of Penicillium on moldy building materials. We have identified a 52-kDa marker protein for the indoor clade of P. chrysogenum not present in a taxonomically diverse selection of fungi. It is found in high concentrations in protein extracted from the fungus grown on paper-faced gypsum wallboard. During this process, we illuminated the variability in response to patient sera and of strains of the fungus collected over a wide geographic area. From a collection of sera from all over the USA, 25 of the 48 patients reacted to the 52-kDa protein from this prescreened collection of sera. Most strain/antibody combinations had proportionate ELISA response associated with the presence of the target. However, approximately 25% of the strain/patient serum combinations included people who responded to many common allergens from the Penicillia. All the P. chrysogenum strains tested produced the target protein. However, there was considerable variability in patient IgG response to 32-, 30-, and 18-kDa antigens and in their production by the various clade 4 strains. The target protein was not found in spores or culture extracts of a wide selection of relevant fungi. It appears that the previous studies have been conducted on strains of the fungus from the three clades not those associated with the built environment.

  3. Two new species of the genus Candida in the Zygoascus clade, Candida lundiana sp. nov. and Candida suthepensis sp. nov., isolated from raw honey in Thailand.

    PubMed

    Saksinchai, Sujinan; Suzuki, Motofumi; Lumyong, Saisamorn; Ohkuma, Moriya; Chantawannakul, Panuwan

    2012-03-01

    During a survey of yeasts associated with raw honey collected in Thailand, two strains of the Zygoascus clade were isolated from the Asian cavity-nesting honeybee Apis cerana and the stingless bee Homotrigona fimbriata. Phylogeny based on 26S rDNA D1/D2 sequences placed these yeasts as members of a clade including Candida bituminiphila, Candida patagonica and Candida polysorbophila. The strains of the two novel species, CBS 12271(T) and CBS 12270(T), respectively, could be unquestionably distinguished from their relatives by rDNA sequences and other taxonomic characteristics. Therefore, the novel anamorphic species, Candida lundiana sp. nov. (type strain CBS 12271(T) = JCM 16823(T)) and Candida suthepensis sp. nov. (type strain CBS 12270(T) = JCM 16822(T)) are described.

  4. DNA fingerprinting and anastomosis grouping reveal similar genetic diversity in Rhizoctonia species infecting turfgrasses in the transition zone of USA.

    PubMed

    Amaradasa, B S; Horvath, B J; Lakshman, D K; Warnke, S E

    2013-01-01

    Rhizoctonia blight is a common and serious disease of many turfgrass species. The most widespread causal agent, Thanatephorus cucumeris (anamorph: R. solani), consists of several genetically different subpopulations. In addition, Waitea circinata varieties zeae, oryzae and circinata (anamorph: Rhizoctonia spp.) also can cause the disease. Accurate identification of the causal pathogen is important for effective management of the disease. It is challenging to distinguish the specific causal pathogen based on disease symptoms or macroscopic and microscopic morphology. Traditional methods such as anastomosis reactions with tester isolates are time consuming and sometimes difficult to interpret. In the present study universally primed PCR (UP-PCR) fingerprinting was used to assess genetic diversity of Rhizoctonia spp. infecting turfgrasses. Eighty-four Rhizoctonia isolates were sampled from diseased turfgrass leaves from seven distinct geographic areas in Virginia and Maryland. Rhizoctonia isolates were characterized by ribosomal DNA internal transcribed spacer (rDNA-ITS) region and UP-PCR. The isolates formed seven clusters based on ITS sequences analysis and unweighted pair group method with arithmetic mean (UPGMA) clustering of UP-PCR markers, which corresponded well with anastomosis groups (AGs) of the isolates. Isolates of R. solani AG 1-IB (n = 18), AG 2-2IIIB (n = 30) and AG 5 (n = 1) clustered separately. Waitea circinata var. zeae (n = 9) and var. circinata (n = 4) grouped separately. A cluster of six isolates of Waitea (UWC) did not fall into any known Waitea variety. The binucleate Rhizoctonia-like fungi (BNR) (n = 16) clustered into two groups. Rhizoctonia solani AG 2-2IIIB was the most dominant pathogen in this study, followed by AG 1-IB. There was no relationship between the geographic origin of the isolates and clustering of isolates based on the genetic associations. To our knowledge this is the first time UP-PCR was used to characterize Rhizoctonia

  5. New species from the Fusarium solani species complex derived from perithecia and soil in the old World tropics.

    PubMed

    Nalim, F Ameena; Samuels, Gary J; Wijesundera, Ravi L; Geiser, David M

    2011-01-01

    A large collection of strains belonging to the Fusarium solani species complex (FSSC) was isolated from soil and perithecia in primary forests in Sri Lanka (from fallen tree bark) and tropical Australia (Queensland, from fallen tree fruits and nuts). Portions of the translation elongation factor 1-alpha (tef1) gene, the nuclear large subunit (NLSU) and internal transcribed spacer regions (ITS) of the nuclear ribosomal RNA genes were sequenced in 52 isolates from soil and perithecia. The FSSC was divided previously into three clades with some biogeographic structure, termed Clades 1, 2 and 3. All Sri Lankan and Australian soil isolates were found to be members of Clade 3, most grouping with the cosmopolitan soil-associated species F. falciforme. All but two Sri Lankan perithecial isolates were associated with a set of five divergent phylogenetic lineages that were associated with Clade 2. Australian perithecial isolates resided in a subclade of Clade 3 where most of the previously defined mating populations of the FSSC reside. Isolates from perithecia and those cultured from soil were always members of different species lineages, even when derived from proximal locations. The previous biogeographic assignment of Clade 2 to South America is now expanded to the worldwide tropics. Sri Lanka appears to be an important center of diversity for the FSSC. Nectria haematococca is epitypified with a collection from the type locality in Sri Lanka; its anamorph is described as a new species, Fusarium haematococcum. Neocosmospora E.F. Smith is adopted as the correct genus for Nectria haematococca. These new species are described: F. kurunegalense/Neo. kurunegalensis, F. rectiphorus/Neo. rectiphora/, F. mahasenii/Neo. mahasenii/, F. kelerajum/Neo. keleraja.

  6. Entomopathogens of Amazonian stick insects and locusts are members of the Beauveria species complex (Cordyceps sensu stricto).

    PubMed

    Sanjuan, Tatiana; Tabima, Javier; Restrepo, Silvia; Læssøe, Thomas; Spatafora, Joseph W; Franco-Molano, Ana Esperanza

    2014-01-01

    In the Amazon the only described species of Cordyceps sensu stricto (Hypocreales, Cordycipitaceae) that parasitize insects of Orthopterida (orders Orthoptera and Phasmida) are Cordyceps locustiphila and C. uleana. However, the type specimens for both taxa have been lost and the concepts of these species are uncertain. To achieve a more comprehensive understanding of the systematics of these species, collections of Cordyceps from the Amazon regions of Colombia, Ecuador and Guyana were subjected to morphological, ecological and molecular phylogenetic studies. Phylogenetic analyses were conducted on partial sequences of SSU, LSU, TEF, RPB1 and RPB2 nuclear loci. Two new species are proposed including C. diapheromeriphila, a parasite of Phasmida, and C. acridophila, a parasite of the superfamily Acridomorpha (Orthoptera), which is broadly distributed across the Amazon. For C. locustiphila a lectotypification and an epitypification are made. Cordyceps locustiphila is host specific with Colpolopha (Acridomorpha: Romaleidae), and its distribution coincides with that of its host. The phylogenetic placement of these three species was resolved with strong support in the Beauveria clade of Cordyceps s. str. (Cordycipitaceae). This relationship and the morphological similarity of their yellow stromata with known teleomorphs of the clade, suggest that the holomorphs of these species may include Beauveria or Beauveria-like anamorphs. The varying host specificity of the beauverioid Cordyceps species suggest the potential importance of identifying the natural host taxon before future consideration of strains for use in biological control of pest locusts.

  7. Diffusion studies of anamorphic GRIN lenses

    NASA Astrophysics Data System (ADS)

    Sekh, Md. Asraful; SoodBiswas, Nisha; Sarkar, Samir; Basuray, Amitabha

    2016-12-01

    The present paper reports the diffusion study of cylindrical GRIN rod with elliptical cross section, developed by ion exchange process. The diffusion equation takes the form of Mathieu equations when transform into elliptic coordinate system and the solutions are derived in terms of angular and radial Mathieu functions. Computations of eigenvalues and expansion coefficients as well as angular and radial Mathieu functions are made which shows good agreement with the existing results. Simpler expression for ionic concentration is derived using asymptotic formulae of the functions which are used for final computation of ionic concentration of diffusing cations in elliptic GRIN. The plot of change in concentration versus diffusion depth along different directions approximately correlates with the results obtained by an earlier experimental study.

  8. Species concepts and species delimitation.

    PubMed

    De Queiroz, Kevin

    2007-12-01

    The issue of species delimitation has long been confused with that of species conceptualization, leading to a half century of controversy concerning both the definition of the species category and methods for inferring the boundaries and numbers of species. Alternative species concepts agree in treating existence as a separately evolving metapopulation lineage as the primary defining property of the species category, but they disagree in adopting different properties acquired by lineages during the course of divergence (e.g., intrinsic reproductive isolation, diagnosability, monophyly) as secondary defining properties (secondary species criteria). A unified species concept can be achieved by treating existence as a separately evolving metapopulation lineage as the only necessary property of species and the former secondary species criteria as different lines of evidence (operational criteria) relevant to assessing lineage separation. This unified concept of species has several consequences for species delimitation, including the following: First, the issues of species conceptualization and species delimitation are clearly separated; the former secondary species criteria are no longer considered relevant to species conceptualization but only to species delimitation. Second, all of the properties formerly treated as secondary species criteria are relevant to species delimitation to the extent that they provide evidence of lineage separation. Third, the presence of any one of the properties (if appropriately interpreted) is evidence for the existence of a species, though more properties and thus more lines of evidence are associated with a higher degree of corroboration. Fourth, and perhaps most significantly, a unified species concept shifts emphasis away from the traditional species criteria, encouraging biologists to develop new methods of species delimitation that are not tied to those properties.

  9. Invasive Species

    EPA Pesticide Factsheets

    Invasive species have significantly changed the Great Lakes ecosystem. An invasive species is a plant or animal that is not native to an ecosystem, and whose introduction is likely to cause economic, human health, or environmental damage.

  10. A morphological and phylogenetic revision of the Nectria cinnabarina species complex

    PubMed Central

    Hirooka, Y.; Rossman, A.Y.; Chaverri, P.

    2011-01-01

    The genus Nectria is typified by N. cinnabarina, a wood-inhabiting fungus common in temperate regions of the Northern Hemisphere. To determine the diversity within N. cinnabarina, specimens and cultures from Asia, Europe, and North America were obtained and examined. Their phylogeny was determined using sequences of multiple loci, specifically act, ITS, LSU, rpb1, tef1, and tub. Based on these observations, four species are recognised within the N. cinnabarina complex. Each species is delimited based on DNA sequence analyses and described and illustrated from specimens and cultures. The basionym for N. cinnabarina, Sphaeria cinnabarina, is lectotypified based on an illustration that is part of the protologue, and an epitype specimen is designated. Nectria cinnabarina s. str. is recircumscribed as having 2-septate ascospores and long stipitate sporodochia. Nectria dematiosa, previously considered a synonym of N. cinnabarina, has up to 2-septate ascospores and sessile sporodochia or no anamorph on the natural substrate. A third species, Nectria nigrescens, has up to 3-septate ascospores and short to long stipitate sporodochia. One newly described species, Nectria asiatica with a distribution restricted to Asia, has (0–)1-septate ascospores and short stipitate sporodochia. Young and mature conidia developing on SNA were observed for each species. Mature conidia of N. asiatica, N. cinnabarina, and N. nigrescens but not N. dematiosa bud when the mature conidia are crowded. On PDA the optimal temperature for growth for N. dematiosa is 20 °C, while for the other three species it is 25 °C. Based on our phylogenetic analyses, three subclades are evident within N. dematiosa. Although subtle culture and geographical differences exist, these subclades are not recognised as distinct species because the number of samples is small and the few specimens are insufficient to determine if morphological differences exist in the natural environment. PMID:21523188

  11. Blue pigment in Hypocrea caerulescens sp. nov. and two additional new species in sect. Trichoderma

    PubMed Central

    Jaklitsch, Walter M.; Stadler, Marc; Voglmayr, Hermann

    2012-01-01

    Three new species of Hypocrea/Trichoderma sect. Trichoderma (Hypocreaceae, Hypocreales, Ascomycota, Fungi) are described from recent collections in southern Europe and the Canary Islands. They have been characterized by morphological and molecular methods, including microscopic examination of the teleomorph in thin sections, the anamorph, growth rate experiments and phylogenetic analyses based on a part of the translation elongation factor 1-alpha encoding gene (tef1) containing the two last introns and a part of the rpb2 gene, encoding the second largest RNA polymerase subunit. Analyses involving tef1 did not unequivocally resolve the sister clade relationship of Hypocrea caerulescens relative to the Koningii and Viride clades, while analyses based on rpb2 clearly suggest a close relationship with the former, although the phenotype of H. caerulescens is similar to H. viridescens, particularly by its warted conidia and a coconut-like odor in CMD culture. Hypocrea hispanica and T. samuelsii however are clearly related to the Viride clade by both phylogenetic markers, despite their morphological similarity to H. koningii and its relatives. An apparently specific blue pigment is formed in CMD cultures by Hypocrea caerulescens but could not be obtained by extraction with organic solvents. PMID:22453122

  12. Identification and pathogenicity of Botryosphaeriaceae species associated with coast live oak (Quercus agrifolia) decline in southern California.

    PubMed

    Lynch, Shannon C; Eskalen, Akif; Zambino, Paul J; Mayorquin, Joey S; Wang, Danny H

    2013-01-01

    Symptoms of decline have been observed on dying coast live oak (Quercus agrifolia) trees in areas throughout southern California that are both infested and uninfested by the gold-spotted oak borer (GSOB). The purpose of this study was to identify and assess the pathogenicity of several anamorph species of the Botryosphaeriaceae, including Diplodia corticola, Dothiorella iberica and Diplodia agrifolia sp. nov., that were recovered consistently from symptomatic tissues. Species were identified morphologically and by phylogenetic analyses of the complete sequence of the internal transcribed spacer (ITS) of the rDNA and partial sequences of β-tubulin and elongation factor (EF1-α) genes. Results from morphological assessments and phylogenetic analyses support the erection of a new species closely related to D. mutila, described herein as Diplodia agrifolia sp. nov. Pathogenicity of all species was verified by wound inoculation of 1 y old coast live oak seedlings under controlled conditions. Isolates of D. corticola were the most aggressive tested, and isolates of D. agrifolia were the second most aggressive. Both species caused bleeding symptoms on inoculated seedlings. Seedlings inoculated with D. corticola died within 4 wk, with the pathogen progressing up and down through the xylem in advance of living phloem and moving throughout the taproot in 70% of inoculated seedlings. Colonization and re-isolation was successful for all species. All three fungal species represent newly recorded fungal pathogens of coast live oak in California. Results from the pathogenicity test suggest that these fungi play a role in the decline of coast live oaks throughout southern California.

  13. Systematic reappraisal of Coniella and Pilidiella, with specific reference to species occurring on Eucalyptus and Vitis in South Africa.

    PubMed

    Van Niekerk, Jan M; Groenewald, J Z Ewald; Verkley, Gerard J M; Fourie, Paul H; Wingfield, Michael J; Crous, Pedro W

    2004-03-01

    The genus Pilidiella, including its teleomorphs in Schizoparme, has a cosmopolitan distribution and is associated with disease symptoms on many plants. In the past, conidial pigmentation has been used as a character to separate Pilidiella (hyaline to pale brown conidia) from Coniella (dark brown conidia). In recent years, however, the two genera have been regarded as synonymous, the older name Coniella having priority. To address the generic question, sequences of the internal transcribed spacer region (ITS1, ITS2), 5.8S gene, large subunit (LSU) and elongation factor 1-alpha gene (EF 1-alpha) were analysed to compare the type species of Pilidiella and Coniella. All three gene regions supported the separation of Coniella from Pilidiella, with the majority of taxa residing in Pilidiella. Pilidiella is characterised by having species with hyaline to pale brown conidia (avg. length:width > 1.5), in contrast to the dark brown conidia of Coniella (avg. length:width < or = 1.5). Pilidiella diplodiella, which is a pathogen associated with white rot of grapevines, was shown to be an older name for C. petrakii. To delineate species in the P. diplodiella species complex, isolates were also compared based on histone (H3) gene sequences. Analyses derived from these sequence data separated P. diplodiella from a newly described species, P. diplodiopsis. The new species P. eucalyptorum sp. nov. is proposed for isolates formerly treated as C. fragariae and associated with leaf spots of Eucalyptus spp. This species clustered basal to Pilidiella, and may represent yet a third genus within this complex. Pilidiella destruens sp. nov. is newly described as anamorph of Schizoparme destruens, which is associated with twig dieback of Eucalyptus spp. in Hawaii. A key based on morphological characteristics is provided to separate the taxa treated in this study.

  14. A new species of Harpophora (Magnaporthaceae) recovered from healthy wild rice (Oryza granulata) roots, representing a novel member of a beneficial dark septate endophyte.

    PubMed

    Yuan, Zhi-Lin; Lin, Fu-Cheng; Zhang, Chu-Long; Kubicek, Christian P

    2010-06-01

    A survey of the endophytic fungal community of wild rice (Oryza granulata) in China was conducted. Two isolates recovered from healthy roots are assumed to be dark septate endophytes (DSEs). They are morphologically similar to species from the genus Harpophora and are identified as a new species, Harpophora oryzae, based on the molecular phylogeny and morphological characteristics. A neighbor-joining tree constructed from ITS-5.8S rRNA gene regions reveals that H. oryzae forms a distinctive subclade within the genus Harpophora, and is not genetically close to other species of Harpophora. Harpophora oryzae exhibits a moderate growth rate, with a frequent production of rope-like strands. It sporulates readily on artificial medium. Phialides are usually flask or bottle shaped and occur singly along hyphae or laterally and terminally on branched, hyaline to brown conidiophores, and also form whorls on metulae. Conidiophores are mostly branched with a slightly thickened wall, varying in dimensions. Conidia are one-celled and hyaline, most of them being falcate and strongly curved. The morphological differences between Harpophora spp. and Harpophora-like anamorphs representing different orders are also discussed. An in vitro inoculation test showed that H. oryzae may contribute towards improving rice (Oryza sativa L.) growth. Microscopic inspection of roots and phylogenetic placement of isolates further confirmed that H. oryzae represents a novel member of DSEs.

  15. Hydrogen species

    NASA Technical Reports Server (NTRS)

    Schiff, H. I.; Burnett, C.; Carli, B.; Dezafra, R.; Evans, W. F. J.; Guthrie, P. D.; Hampson, R. F.; Heaps, W.; Jones, R.; Kley, D.

    1985-01-01

    Measurements of the members of the HO(x) family (OH, HO2, and H2O2) and their major source gases, H2O, and CH4 are discussed. Emphasis is placed on measurements which were made since the 1982 World Meteorologic Organization (WMO) report. Measurement techniques, available data, an assessment of data reliability, and a comparison of the data with theoretical distributions of stratospheric HO(x) species predicted from one and two dimensional photochemical models are discussed.

  16. Characterisation and classification of phylloplane yeasts from Portugal related to the genus Taphrina and description of five novel Lalaria species.

    PubMed

    Inácio, João; Rodrigues, Manuel G; Sobral, Patrícia; Fonseca, Alvaro

    2004-01-01

    Taphrina Fries is a genus of dimorphic ascomycetes comprising more than 90 species distinguished by the specific infections they produce on different vascular plants. Their filamentous states are restricted to parasitised plant tissue whereas the yeast states are saprobic and can be grown on artificial media. The latter coincide with the anamorphic phases and have been given separate nomenclatural status by the erection of the genus Lalaria R.T. Moore. In its original circumscription Lalaria included only 23 yeast states of known species of Taphrina and its creation was then redundant. Here we describe five novel species in the genus Lalaria to accommodate a total of 44 yeast isolates obtained mainly from leaf surfaces (phylloplane) of different plants in Portugal: Lalaria arrabidae sp. nov. (one strain), L. carpini sp. nov. (one strain), L. inositophila sp. nov. (37 strains), L. kurtzmanii sp. nov. (one strain) and L. veronaerambellii sp. nov. (four strains). L. inositophila was notable for its widespread occurrence since it was recovered during two consecutive years from the leaves of miscellaneous plant species. In the absence of sexual states and of unequivocal associations to particular host plants, the taxonomic relationship of the novel species to the yeast states of Taphrina available from culture collections was verified by the comparative analysis of physiological and molecular characteristics. The latter included PCR fingerprinting using single primers for microsatellite regions, sequencing of the 5' end of the 26S rRNA (LSU) gene (D1/D2 domains) and of the ITS1 and ITS2 rDNA spacer regions, and DNA-DNA hybridisation experiments. An emended description of the genus Lalaria is provided.

  17. Description of Cryptosporiopsis kienholzii and species profiles of Neofabraea in major pome fruit growing districts in the Pacific Northwest USA.

    PubMed

    Spotts, Robert A; Seifert, Keith A; Wallis, Kelly M; Sugar, David; Xiao, Chang Lin; Serdani, Maryna; Henriquez, Jose L

    2009-11-01

    The objectives of this study were i) to give a taxonomic description of a fungus phylogenetically related to Neofabraea and assign the name Cryptosporiopsis kienholzii to this fungus, ii) to expand previous Neofabraea species profiles from infected apple and pear fruit collected from major pome fruit production districts in Oregon and Washington, and iii) to determine the sensitivity of Neofabraea alba, Neofabraea malicorticis, Neofabraea perennans, and C. kienholzii to a range of fungicides. A name is given herein to the anamorph of the fungus previously called 'Neofabraea sp. nov.' in the literature, and the fungus is designated as C. kienholzii. The teleomorph of this fungus has never been observed in vivo or in vitro. N. alba, N. perennans, and C. kienholzii accounted for 61.3, 35.6, and 3.1 %, respectively, of 608 isolates obtained from pear fruit and 6.0, 81.3, and 12.7 % of 150 isolates from apple fruit. N. alba was the most common species in Oregon and N. perennans was most common in Washington. N. malicorticis was not found in any of the districts and may be limited to the wet climates west of the Cascade mountain range. C. kienholzii occurs in pome fruit orchards from southern Oregon to North Central Washington, and this is the first report of C. kienholzii in the state of Washington. The four most effective fungicides for control of bull's-eye rot caused by all species were thiabendazole, thiophanate-methyl, pyrimethanil, and pyraclostrobin+boscalid. Other fungicides gave acceptable control of some species of Neofabraea but not others. There was good agreement of the microbioassay with fungicide evaluations using wound-inoculated pear fruit for five of seven fungicides, but the microbioassay was not consistent enough for determination of the sensitivity of Neofabraea species to new fungicides.

  18. Phylogeny and taxonomic revision of Thelonectria discophora (Ascomycota, Hypocreales, Nectriaceae) species complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thelonectria discophora (Thelonectria, Nectriaceae, Hypocreales) is a conspicuous group of saprobic fungi on decaying plant material, characterized by red perithecia each with a broad mammiform (nipple-like) apex. The anamorphic state is characterized by a cylindrocarpon-like morphology, with 3–5 se...

  19. New species of Ophiostomatales from Scolytinae and Platypodinae beetles in the Cape Floristic Region, including the discovery of the sexual state of Raffaelea.

    PubMed

    Musvuugwa, Tendai; de Beer, Z Wilhelm; Duong, Tuan A; Dreyer, Léanne L; Oberlander, Kenneth C; Roets, Francois

    2015-10-01

    Olea capensis and Rapanea melanophloeos are important canopy trees in South African Afromontane forests. Dying or recently dead individuals of these trees are often infested by Scolytinae and Platypodinae (Curculionidae) beetles. Fungi were isolated from the surfaces of beetles emerging from wood samples and their galleries. Based on micro-morphological and phylogenetic analyses, four fungal species in the Ophiostomatales were isolated. These were Sporothrix pallida and three taxa here newly described as Sporothrix aemulophila sp. nov., Raffaelea vaginata sp. nov. and Raffaelea rapaneae sp. nov. This study represents the first collection of S. pallida, a species known from many environmental samples from across the world, from Scolytinae beetles. S. aemulophila sp. nov. is an associate of the ambrosia beetle Xyleborinus aemulus. R. rapaneae sp. nov. and R. vaginata sp. nov. were associated with a Lanurgus sp. and Platypodinae beetle, respectively, and represent the first Raffaelea spp. reported from the Cape Floristic Region. Of significance is that R. vaginata produced a sexual state analogous with those of Ophiostoma seticolle and O. deltoideosporum that also grouped in our analyses in Raffaelea s. str., to date considered an asexual genus. The morphology of the ossiform ascospores and anamorphs of the three species corresponded and the generic circumscription of Raffaelea is thus emended to accommodate sexual states. The two known species are provided with new combinations, namely Raffaelea seticollis (R.W. Davidson) Z.W. de Beer and T.A. Duong comb. nov. and Raffaelea deltoideospora (Olchow. and J. Reid) Z.W. de Beer and T.A. Duong comb. nov.

  20. Phylogenetic lineages in the Botryosphaeriaceae

    PubMed Central

    Crous, Pedro W.; Slippers, Bernard; Wingfield, Michael J.; Rheeder, John; Marasas, Walter F.O.; Philips, Alan J.L.; Alves, Artur; Burgess, Treena; Barber, Paul; Groenewald, Johannes Z.

    2006-01-01

    Botryosphaeria is a species-rich genus with a cosmopolitan distribution, commonly associated with dieback and cankers of woody plants. As many as 18 anamorph genera have been associated with Botryosphaeria, most of which have been reduced to synonymy under Diplodia (conidia mostly ovoid, pigmented, thick-walled), or Fusicoccum (conidia mostly fusoid, hyaline, thin-walled). However, there are numerous conidial anamorphs having morphological characteristics intermediate between Diplodia and Fusicoccum, and there are several records of species outside the Botryosphaeriaceae that have anamorphs apparently typical of Botryosphaeria s.str. Recent studies have also linked Botryosphaeria to species with pigmented, septate ascospores, and Dothiorella anamorphs, or Fusicoccum anamorphs with Dichomera synanamorphs. The aim of this study was to employ DNA sequence data of the 28S rDNA to resolve apparent lineages within the Botryosphaeriaceae. From these data, 12 clades are recognised. Two of these lineages clustered outside the Botryosphaeriaceae, namely Diplodia-like anamorphs occurring on maize, which are best accommodated in Stenocarpella (Diaporthales), as well as an unresolved clade including species of Camarosporium/Microdiplodia. We recognise 10 lineages within the Botryosphaeriaceae, including an unresolved clade (Diplodia/Lasiodiplodia/Tiarosporella), Botryosphaeria s.str. (Fusicoccum anamorphs), Macrophomina, Neoscytalidium gen. nov., Dothidotthia (Dothiorella anamorphs), Neofusicoccum gen. nov. (Botryosphaeria-like teleomorphs, Dichomera-like synanamorphs), Pseudofusicoccum gen. nov., Saccharata (Fusicoccum- and Diplodia-like synanamorphs), “Botryosphaeria” quercuum (Diplodia-like anamorph), and Guignardia (Phyllosticta anamorphs). Separate teleomorph and anamorph names are not provided for newly introduced genera, even where both morphs are known. The taxonomy of some clades and isolates (e.g. B. mamane) remains unresolved due to the absence of ex

  1. Bi-fluorescence imaging for estimating accurately the nuclear condition of Rhizoctonia spp.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the absence of perfect state, the number of nuclei in their vegetative hyphae is one of the anamorphic features that separate Rhizoctonia solani from other Rhizoctonia-like fungi. Anamorphs of Rhizoctonia solani are typically multinucleate while the other Rhizoctonia species are binucleate. Howev...

  2. Endangered species: Deciding which species to save

    NASA Astrophysics Data System (ADS)

    Thibodeau, Francis R.

    1983-03-01

    Many species face extinction because preservation organizations do not have the resources to mount all of the interventions that are needed. Decision analysis provides techniques that can help managers of these organizations to make judgments about which species they will attempt to rescue. A formal analysis of the choices available to the US Fish and Wildlife Services' endangered species program with regard to Isotria medeoloides illustrates how the difficulties of making preservation decisions can be lessened. I. medeoloides is perhaps the rarest orchid in the United States. Little is known of the species' biology and less about effective management. Yet unless a preservation effort is mounted, the species will continue to be threatened by habitat destruction and botanical collecting. The analysis employs formal probabalistic techniques to weigh the utility of possible intervention strategies, that is, their likelihood of achieving different amounts of increase in the longevity of the species, and to balance these gains against their costs. If similar decision analyses are performed on other endangered species, the technique can be used to choose among them, as well as among strategies for individual species.

  3. A PCA-based hyperspectral approach to detect infections by mycophilic fungi on dried porcini mushrooms (boletus edulis and allied species).

    PubMed

    Bagnasco, Lucia; Zotti, Mirca; Sitta, Nicola; Oliveri, Paolo

    2015-11-01

    Mycophilic fungi of anamorphic genus Sepedonium (telomorphs in Hypomyces, Hypocreales, Ascomycota) infect and parasitize sporomata of boletes. The obligated hosts such as Boletus edulis and allied species (known as "porcini mushrooms") are among the most valued and prized edible wild mushrooms in the world. Sepedonium infections have a great morphological variability: at the initial state, contaminated mushrooms present a white coating covering tubes and pores; at the final state, Sepedonium forms a deep and thick hyphal layer that eventually leads to the total necrosis of the host. Up to date, Sepedonium infections in porcini mushrooms have been evaluated only through macroscopic and microscopic visual analysis. In this study, in order to implement the infection evaluation as a routine methodology for industrial purposes, the potential application of Hyperspectral Imaging (HSI) and Principal Component Analysis (PCA) for detection of Sepedonium presence on sliced and dried B. edulis and allied species was investigated. Hyperspectral images were obtained using a pushbroom line-scanning HSI instrument, operating in the wavelength range between 400 and 1000 nm with 5 nm resolution. PCA was applied on normal and contaminated samples. To reduce the spectral variability caused by factors unrelated to Sepedonium infection, such as scattering effects and differences in sample height, different spectral pre-treatments were applied. A supervised rule was then developed to assign spectra recorded on new test samples to each of the two classes, based on the PC scores. This allowed to visualize directly - within false-color images of test samples - which points of the samples were contaminated. The results achieved may lead to the development of a non-destructive monitoring system for a rapid on-line screening of contaminated mushrooms.

  4. Endangered Species Protection Bulletins

    EPA Pesticide Factsheets

    Endangered Species Protection Bulletins set forth geographically specific pesticide use limitations for the protection of threatened and endangered (listed) species and their designated critical habitat. Find out how to get and use Bulletins.

  5. The Earth's Vanishing Species.

    ERIC Educational Resources Information Center

    USA Today, 1981

    1981-01-01

    Elaborates on the problem of expanding human activity to the world's plant and animal species. Concludes that preserving an individual species is largely a waste of time and effort and that the best way to protect the most species of plants and animals is to save their environments over large tracts of land. (DB)

  6. Defining an invasive species.

    PubMed

    Moutou, F; Pastoret, P P

    2010-04-01

    The definition of an invasive species will depend on the viewpoint of the observer, who in some cases may be responsible for introducing the species. History has taught us that humans are the species that has invaded the largest surface area of the planet. So, before going on to propose a few definitions, this article describes three different examples or types of example in which domestic animal species, wild animal species and microorganisms (for biological pest control) have been transported intentionally. By doing so, this paper uses a variety of situations to support the definitions. A contemporary argument would counter a strictly biogeographical definition with a more ecological definition. The two are probably complementary. In any case, these definitions should remain practical. The consequences of species movements vary. However, their health impacts should not be underestimated.

  7. Plasmids in diatom species.

    PubMed Central

    Hildebrand, M; Corey, D K; Ludwig, J R; Kukel, A; Feng, T Y; Volcani, B E

    1991-01-01

    We have discovered plasmids in 5 of 18 diatom species surveyed. In several species, more than one type of plasmid is present. Several of the plasmids show similarity by hybridization previously characterized plasmids in Cylindrotheca fusiformis (J. D. Jacobs et al., unpublished data). Additionally, there is similarity between the plasmids found in C. fusiformis and chloroplast DNA in three diatom species. These results add to the evidence that the plasmids have features of mobile genetic elements. Images PMID:1885558

  8. Species and paleoanthropology.

    PubMed

    Tattersall, Ian; Mowbray, Kenneth

    2005-04-01

    The biotic world is self-evidently "packaged" into units, of which the most basic is the species. It is necessary to develop an accurate understanding of what species are and how they are to be identified before we can proceed to more complex analyses of the evolutionary histories and relationships of extinct and extant taxa at all levels of the systematic hierarchy. In this article, we review the major species concepts current today among paleoanthropologists, and examine the limitations of their applicability to practical studies of extant and extinct faunas. The primary such limitation for paleoanthropologists is the fact that all major species definitions stress reproductive continuity (whether by exclusionary or inclusionary mechanisms), a quality that is inferential at best among forms known only as fossils (and, in many cases, in the extant fauna as well). The only reliable signal as to species status in the fossil record is morphology, yet speciation carries with it no specifiable quantity of morphological innovation. Some groups with autapomorphies are not species, and some species do not bear autapomorphies. How, then, are we to recognize species in the hominid and other fossil records? Noting that osteodental differences among congeneric primate species tend to be subtle, and that when consistent identifiable "morphs" can be found at least as many species are present, we recommend equating morphs based on several characters with species-realizing that only one or two distinctive characters may not make a morph. In this way, our views of the phylogenetic histories of higher taxa may be oversimplified, but their essential patterns will not be distorted.

  9. Splitting of asphaltene species

    SciTech Connect

    Galimov, R.A.; Yusupova, T.N.; Abushaeva, V.V.

    1994-05-10

    The extent of splitting of asphaltene species under the action of solvents correlates with their nature, and primarily with their electron- and proton-donor properties. According to the data of thermal analysis asphaltene species being retained after the action of solvents differ in the weight ratio of peripheral substituents to condensed part and in the fraction of labile bonds. 12 refs., 4 tabs.

  10. Delimitating species in paleoanthropology.

    PubMed

    White, Tim D

    2014-01-01

    Evolutionary biologists created a large twentieth-century literature about delimiting biological species. Paleontologists contributed the unique complications of deep time. Toward century's end, one participant wrote: "In all probability more paper has been consumed on the questions of the nature and definition of the species than any other subject in evolutionary and systematic biology."

  11. Barbaloin in aloe species.

    PubMed

    Groom, Q J; Reynolds, T

    1987-08-01

    Barbaloin levels in the exudates from the leaves of 68 species of ALOE in the Kew collection have been determined by light absorption at 375 nm following separation by HPLC. The exudates from most species contained between 10-20% although a few concentrations of around 30% were found. The level in the leaf was usually around 1% of thedry weight in plants grown in glasshouses at Kew although some species were found to contain up to 5%. The highest concentrations of barbaloin were found in exudates from young mature leaves just below the apex and the level decreased in older leaves towards the base of the plant. Species in the natural groupings of the genus, Section ANGUIALOE and Group 4, all had appreciable concentrations of barbaloin in the leaf exudates. Species containing barbaloinwere distributed throughout the large heterogeneous Sections EUALOE and PACHYDENDRON with no apparent taxonomic significance.

  12. Biofilms of Clostridium species.

    PubMed

    Pantaléon, Véronique; Bouttier, Sylvie; Soavelomandroso, Anna Philibertine; Janoir, Claire; Candela, Thomas

    2014-12-01

    The biofilm is a microbial community embedded in a synthesized matrix and is the main bacterial way of life. A biofilm adheres on surfaces or is found on interfaces. It protects bacteria from the environment, toxic molecules and may have a role in virulence. Clostridium species are spread throughout both environments and hosts, but their biofilms have not been extensively described in comparison with other bacterial species. In this review we describe all biofilms formed by Clostridium species during both industrial processes and in mammals where biofilms may be formed either during infections or associated to microbiota in the gut. We have specifically focussed on Clostridium difficile and Clostridium perfringens biofilms, which have been studied in vitro. Regulatory processes including sporulation and germination highlight how these Clostridium species live in biofilms. Furthermore, biofilms may have a role in the survival and spreading of Clostridium species.

  13. How reticulated are species?

    PubMed Central

    Besansky, Nora; Hahn, Matthew W.

    2015-01-01

    Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree‐like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control. PMID:26709836

  14. Endangered Species: Pesticide Restrictions

    EPA Pesticide Factsheets

    Our goal is to protect threatened and endangered species and their habitats, without placing unnecessary burden on agriculture and pesticide users. Pesticide limitations are developed to ensure safe use of pesticides in order to meet this goal.

  15. Beyond Single Species Interpretation.

    ERIC Educational Resources Information Center

    Richie, Deborah

    1995-01-01

    Species diversity, learning about wildlife in its natural habitats and conservation goals are integral to Watchable Wildlife programs. Examines the role of wildlife observation in spreading the message of biodiversity importance. Twenty-three references cited. (LZ)

  16. Theoretical ecology without species

    NASA Astrophysics Data System (ADS)

    Tikhonov, Mikhail

    The sequencing-driven revolution in microbial ecology demonstrated that discrete ``species'' are an inadequate description of the vast majority of life on our planet. Developing a novel theoretical language that, unlike classical ecology, would not require postulating the existence of species, is a challenge of tremendous medical and environmental significance, and an exciting direction for theoretical physics. Here, it is proposed that community dynamics can be described in a naturally hierarchical way in terms of population fluctuation eigenmodes. The approach is applied to a simple model of division of labor in a multi-species community. In one regime, effective species with a core and accessory genome are shown to naturally appear as emergent concepts. However, the same model allows a transition into a regime where the species formalism becomes inadequate, but the eigenmode description remains well-defined. Treating a community as a black box that expresses enzymes in response to resources reveals mathematically exact parallels between a community and a single coherent organism with its own fitness function. This coherence is a generic consequence of division of labor, requires no cooperative interactions, and can be expected to be widespread in microbial ecosystems. Harvard Center of Mathematical Sciences and Applications;John A. Paulson School of Engineering and Applied Sciences.

  17. Development of SCAR markers and UP-PCR cross-hybridization method for specific detection of four major subgroups of Rhizoctonia from infected turfgrasses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several species and hyphal anastomosis groups (AG) of Rhizoctonia solani (sensu lato) cause brown patch diseases of turfgrasses. Conventional methods of identification of Rhizoctonia pathogens are time consuming and often inaccurate. A rapid identification assay for Waitea circinata (anamorph: Rhizo...

  18. Bounding Species Distribution Models

    NASA Technical Reports Server (NTRS)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  19. Aquatic Nuisance Species Locator

    EPA Pesticide Factsheets

    Data in this map has been collected by the United States Geological Survey's Nonindigenous Aquatic Species program located in Gainesville, Florida (http://nas.er.usgs.gov/default.aspx). This dataset may have some inaccuracies and is only current to June 15, 2012. The species identified in this dataset are not inclusive of all aquatic nuisance species, but rather a subset identified to be at risk for transport by recreational activities such as boating and angling. Additionally, the locations where organisims have been identified are also not inclusive and should be treated as a guide. Organisms are limited to the following: American bullfrog, Asian clam, Asian shore crab, Asian tunicate, Australian spotted jellyfish, Chinese mitten crab, New Zealand mudsnail, Colonial sea squirt, Alewife, Bighead carp, Black carp, Flathead catfish, Grass carp, Green crab, Lionfish, Northern snakehead, Quagga mussel, Round Goby, Ruffe, Rusty crayfish, Sea lamprey, Silver carp, Spiny water flea, Veined rapa whelk, Zebra mussel

  20. Genomic definition of species

    SciTech Connect

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  1. Bounding species distribution models

    USGS Publications Warehouse

    Stohlgren, T.J.; Jarnevich, C.S.; Esaias, W.E.; Morisette, J.T.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used. ?? 2011 Current Zoology.

  2. Endangered Species: Wild & Rare.

    ERIC Educational Resources Information Center

    Braus, Judy, Ed.

    1987-01-01

    Ranger Rick's NatureScope is a creative education series dedicated to inspiring in children an understanding and appreciation of the natural world while developing the skills they will need to make responsible decisions about the environment. The topic of this issue is "Endangered Species: Wild and Rare." Contents are organized into the…

  3. Endangered Species. Teacher's Guide.

    ERIC Educational Resources Information Center

    Brown, Mark; And Others

    This unit is intended to examine the causes of the endangerment of Florida's plant and animal species with a detailed look at varied ecological systems. Individual lessons are designed to be used either by individual students progressing at their own rate or by small groups. Units may be modified for use by large groups. (Author/RE)

  4. Three sensitive species

    SciTech Connect

    Calix, R.E.; Diener, D.

    1995-12-31

    MEC Analytical Systems, Inc., has conducted marine monitoring of a large ocean wastewater outfall since 1985. This EPA mandated monitoring program was designed to measure the spatial and temporal variability of the biological communities and assess the impact associated with the discharge. The ostracod Euphilomedes carcarodonta, has shown enhanced abundances centered at the outfall since the late 70`s. While flow rates continue to increase the concentration of solids and contaminants has been decreasing with improve treatment levels. However the abundance and spatial distribution of this species has remain relatively unchanged. It is hypothesized that this species feeds on the small organic particles. In contrast, the abundance of the polychaete Capitella capitata, an indicator of disturbed habitat and organic enrichment, has decreased significantly. This decrease correlates with decreasing concentrations of wastewater solids and decreasing sediment organic carbon concentrations. The brittle star, Amphiodia urtica, has been found to be one of the most sensitive species to wastewater discharges and its abundance was significantly decreased over a large area in the 70`s. Since 1985 this species has shown a steady recovery of abundance to areas near the discharge. This recovery correlates with lower sediment contaminant levels and decreased solid concentrations, and indicates that the environmental quality near the discharge is similar to reference areas.

  5. Translating Dyslexia across Species

    ERIC Educational Resources Information Center

    Gabel, Lisa A.; Manglani, Monica; Escalona, Nicholas; Cysner, Jessica; Hamilton, Rachel; Pfaffmann, Jeffrey; Johnson, Evelyn

    2016-01-01

    Direct relationships between induced mutation in the "DCDC2" candidate dyslexia susceptibility gene in mice and changes in behavioral measures of visual spatial learning have been reported. We were interested in determining whether performance on a visual-spatial learning and memory task could be translated across species (study 1) and…

  6. Man as a Species.

    ERIC Educational Resources Information Center

    Solem, Alan; And Others

    Written in 1964, the document represents experimental material of the Anthropology Curriculum Study Project. The objectives of the project were to discuss the evolution of man as distinguished from the evolution of other species and as related to culture, and to emphasize human diversity. Three brief essays are presented. The first, "The…

  7. Invasive species in agriculture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Agricultural production of food, feed, fiber or fuel is a local human activity with global ecological impacts, including the potential to foster invasions. Agriculture plays an unusual role in biological invasions, in that it is both a source of non-indigenous invasive species (NIS) and especially s...

  8. Endangered Species. Issue Pac.

    ERIC Educational Resources Information Center

    Fish and Wildlife Service (Dept. of Interior), Washington, DC.

    The materials in this educational packet are designed for use with students in grades 4 through 7. They consist of an overview, three lesson plans and student data sheets, and a poster. The overview presents the history, causes, and present state of species endangerment and a review of legislation by Congress designed to protect threatened or…

  9. Coniolariella hispanica sp. nov. and other additions to Coniolariella.

    PubMed

    Checa, Julia; Arenal, Francisco; Blanco, Natividad; Rogers, Jack D

    2008-07-01

    Coniolariella hispanica, isolated as an endophyte from leaves of Eryngium campestre on the Iberian Peninsula, is established as a new cleistocarpous species. The perithecial species Rosellinia limoniispora is transferred to Coniolariella on morphological and molecular evidence. R. australis is transferred to Coniolariella as a variety of C. limoniispora. The type species of Coniolariella, C. gamsii, is considered to be a variety of C. limoniispora. The taxa discussed here have soft stromata, deliquescent asci that lack an iodine-positive apical ring, and more or less symmetrical ascospores. They lack subicula in natural conditions. C. hispanica and C. limoniispora var. limoniispora have Sporothrix- or Geniculosporium-like anamorphs associated with stromata at different stages of development, but anamorphs are not usually evident in cultures. Coniolariella limoniispora var. gamsii produces the anamorph abundantly in culture. It is not known whether or not C. limoniispora var. australis possesses an anamorph. An emendation of the description of Coniolariella is necessitated by these changes.

  10. Identification of Malassezia species.

    PubMed

    Kindo, A J; Sophia, S K C; Kalyani, J; Anandan, S

    2004-01-01

    Malassezia spp. are lipophilic unipolar yeasts recognized as commensals of skin that may be pathogenic under certain conditions. The genus Malassezia now comprises of seven species. This study was aimed at using a simple practical approach to speciate Malassezia yeasts from clinical material. Seventy skin scrapings from patients with pityriasis versicolor infection, positive in 10% potassium hydroxide (KOH), were cultured onto modified Dixon's agar (mDixon's agar) and Sabouraud dextrose agar (SDA) and incubated at 32 degrees C. Speciation was done on the basis of Gram stain morphology, catalase test, and utilization of Tweens. Out of 70 scrapings 48 (68.75%) showed growth on mDixon's agar. The commonest isolate was M. sympodialis (28, 58%) followed by M. globosa (19, 40%) and one isolate was (2%) of M. restricta. M. sympodialis was the commonest species affecting our population and there was no isolation of M. obtusa, M. slooffiae, M. pachydermatis and M. furfur.

  11. Introduced Terrestrial Species Richness

    EPA Pesticide Factsheets

    These data represent predicted current distributions of all introduced mammals, birds, reptiles, amphibians and butterflies in the Middle-Atlantic region. These data are available for both 8-digit HUCs and EMAP hexagons. The data are species counts for each spatial unit. More information about these resources, including the variables used in this study, may be found here: https://edg.epa.gov/data/Public/ORD/NERL/ReVA/ReVA_Data.zip.

  12. Temperature sensing across species

    PubMed Central

    2010-01-01

    The ability to detect changes in temperature is a fundamental sensory mechanism for every species and provides organisms with a detailed view of the environment. This review focuses on what is known of the neuronal and molecular substrates for thermosensation across species, focusing on the three robust model systems extensively used to study sensory signaling, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the laboratory mouse. Nematodes migrate to thermal climes that are amenable to their survival, a behavior that is regulated primarily through a single sensory neuron. Additionally, nematodes “learn” to seek out this temperate zone based upon their prior experience, a robust model of learning and memory. Drosophila larvae also prefer select thermal zones that are optimal for growth and have also developed vigorous mechanisms to avoid unfavorable conditions. In mammals, the transduction mechanisms for thermosensation have been identified primarily due to the fact that naturally occurring plant products evoke distinct psychophysical sensation of temperature change. More remarkably, the elucidation of the molecular sensors in mammals, along with those in Drosophila, has demonstrated conservation in the molecular mediators of temperature sensation across diverse species. PMID:17219191

  13. Electrophoretic study of Clostridium species.

    PubMed Central

    Cato, E P; Hash, D E; Holdeman, L V; Moore, W E

    1982-01-01

    Polyacrylamide gel electrophoretic analysis of soluble cellular proteins (without sodium dodecyl sulfate) of 70 Clostridium species indicated that the procedure was readily applicable to the differentiation of species in the genus. The protein patterns correlated well with the available DNA homology data and with most accepted differential tests. Results indicated that several earlier names for species were synonyms of those of accepted species and that two accepted species may be synonymous. Images PMID:6175658

  14. Estimating Effects of Species Interactions on Populations of Endangered Species.

    PubMed

    Roth, Tobias; Bühler, Christoph; Amrhein, Valentin

    2016-04-01

    Global change causes community composition to change considerably through time, with ever-new combinations of interacting species. To study the consequences of newly established species interactions, one available source of data could be observational surveys from biodiversity monitoring. However, approaches using observational data would need to account for niche differences between species and for imperfect detection of individuals. To estimate population sizes of interacting species, we extended N-mixture models that were developed to estimate true population sizes in single species. Simulations revealed that our model is able to disentangle direct effects of dominant on subordinate species from indirect effects of dominant species on detection probability of subordinate species. For illustration, we applied our model to data from a Swiss amphibian monitoring program and showed that sizes of expanding water frog populations were negatively related to population sizes of endangered yellow-bellied toads and common midwife toads and partly of natterjack toads. Unlike other studies that analyzed presence and absence of species, our model suggests that the spread of water frogs in Central Europe is one of the reasons for the decline of endangered toad species. Thus, studying population impacts of dominant species on population sizes of endangered species using data from biodiversity monitoring programs should help to inform conservation policy and to decide whether competing species should be subject to population management.

  15. Flavonoids in Sophora Species

    NASA Astrophysics Data System (ADS)

    Shirataki, Yoshiaki; Motohashi, Noboru

    Sophora species of Leguminosae are abundantly present in the natural kingdom. Today, among Sophora plants, the flavonoids of the plant phenols occupy a remarkable position. For a very long time flavonoids have been used as natural pigments and dyes. Some of the colorful anthocyanins of the glucosides are used for color and flavor in foodstuffs. Therefore, these flavonoids are beneficial to daily human life. Herein we concentrate on flavonoids in Sophora plants, and the relationship between their chemical structures and nutraceutical effect. For this purpose, soy-based infant formulas, osteoporosis, antitumor activity, antimicrobial activity, anti-HIV activity, radical generation and O2 - scavenging activity, and enzyme inhibitory activity have been described.

  16. Genetically Altered Plant Species

    NASA Technical Reports Server (NTRS)

    2003-01-01

    Researchers in Robert Ferl's lab at the University of Florida in Gainesville, genetically altered this Arabdopsis Thaliana (a brassica species) plant to learn how extreme environments, such as the low atmospheric pressure on Mars, affect plant genes. They inserted green fluorescent protein (GFP) near the on/off switches for anoxia and drought genes. When those genes were turned on after exposure to reduced atmospheric pressure, GFP was turned on as well, causing cells expressing those genes to glow green under a blue light. The natural fluorescence of chlorophyll accounts for the red glow.

  17. Genomics of Bacillus Species

    NASA Astrophysics Data System (ADS)

    Økstad, Ole Andreas; Kolstø, Anne-Brit

    Members of the genus Bacillus are rod-shaped spore-forming bacteria belonging to the Firmicutes, the low G+C gram-positive bacteria. The Bacillus genus was first described and classified by Ferdinand Cohn in Cohn (1872), and Bacillus subtilis was defined as the type species (Soule, 1932). Several Bacilli may be linked to opportunistic infections. However, pathogenicity among Bacillus spp. is mainly a feature of bacteria belonging to the Bacillus cereus group, including B. cereus, Bacillus anthracis, and Bacillus thuringiensis. Here we review the genomics of B. cereus group bacteria in relation to their roles as etiological agents of two food poisoning syndromes (emetic and diarrhoeal).

  18. Aquatic species program

    SciTech Connect

    Bollmeier, W.S.; Sprague, S.

    1989-09-01

    Researchers have learned that many species of aquatic microalgae produce lipids, or oils, when stimulated by environmental stress. These oils can then be processed into diesel fuel or gasoline. Scientists in the Department of Energy (DOE)/Solar Energy Research Institute (SERI) Aquatics Species Program have collected and screened more than 3,000 strains of microalgae from desert and saline environments. The most promising of these strains are maintained in a culture collection at SERI, and research is now focusing on applying genetic techniques to enhance lipid production of microalgae. Researchers are also studying ways to optimize microalgae lipid production by growing the microalgae in intensive cultures of large outdoor ponds. Because microalgae require large amounts of carbon dioxide as a nutrient, these microalgae facilities could be coupled with a power plant or other source of carbon dioxide. Thus, this technology offers not only the potential of producing renewable liquid fuels, but a possible way to improve the environment at the same time. 135 refs., 25 figs., 29 tabs.

  19. Save Our Species: Protecting Endangered Species from Pesticides.

    ERIC Educational Resources Information Center

    Environmental Protection Agency, Washington, DC.

    This full-size poster profiles 11 wildlife species that are endangered. Color illustrations of animals and plants are accompanied by narrative describing their habitats and reasons for endangerment. The reverse side of the poster contains information on the Endangered Species Act, why protecting endangered and threatened species is important, how…

  20. Indicators: Wetland Vegetation (Introduced Species)

    EPA Pesticide Factsheets

    Introduced plants are indicators of the ecological integrity of waters and evidence of increased human-caused disturbance in the watershed. Introduced species that cause economic or environmental harm, or harm to human health, are called invasive species.

  1. Does climate limit species richness by limiting individual species' ranges?

    PubMed

    Boucher-Lalonde, Véronique; Kerr, Jeremy T; Currie, David J

    2014-02-07

    Broad-scale geographical variation in species richness is strongly correlated with climate, yet the mechanisms underlying this correlation are still unclear. We test two broad classes of hypotheses to explain this pattern. Bottom-up hypotheses propose that the environment determines individual species' ranges. Ranges then sum up to yield species richness patterns. Top-down hypotheses propose that the environment limits the number of species that occur in a region, but not which ones. We test these two classes of hypotheses using a natural experiment: seasonal changes in environmental variables and seasonal range shifts of 625 migratory birds in the Americas. We show that richness seasonally tracks the environment. By contrast, individual species' geographical distributions do not. Rather, species occupy different sets of environmental conditions in two seasons. Our results are inconsistent with extant bottom-up hypotheses. Instead, a top-down mechanism appears to constrain the number of species that can occur in a given region.

  2. Timeless standards for species delimitation.

    PubMed

    Amorim, Dalton S; Santos, Charles Morphy D; Krell, Frank-Thorsten; Dubois, Alain; Nihei, Silvio S; Oliveira, Otto M P; Pont, Adrian; Song, Hojun; Verdade, Vanessa K; Fachin, Diego A; Klassa, Bruna; Lamas, Carlos José E; Oliveira, Sarah S; Carvalho, Claudio J B De; Mello-Patiu, Cátia A; Hajdu, Eduardo; Couri, Márcia S; Silva, Vera C; Capellari, Renato S; Falaschi, Rafaela L; Feitosa, Rodrigo M; Prendini, Lorenzo; Pombal, José P Jr; Fernández, Fernando; Rocha, Rosana M; Lattke, John E; Caramaschi, Ulisses; Duarte, Marcelo; Marques, Antonio Carlos; Reis, Roberto E; Kurina, Olavi; Takiya, Daniela M; Tavares, Marcos; Fernandes, Daniel Silva; Franco, Francisco Luís; Cuezzo, Fabiana; Paulson, Dennis; Guénard, Benoit; Schlick-Steiner, Birgit C; Arthofer, Wolfgang; Steiner, Florian M; Fisher, Brian L; Johnson, Robert A; Delsinne, Thibaut Dominique; Donoso, David A; Mulieri, Pablo Ricardo; Patitucci, Luciano Damián; Carpenter, James M; Herman, Lee; Grimaldi, David

    2016-07-08

    Recently a new species of bombyliid fly, Marleyimyia xylocopae, was described by Marshall & Evenhuis (2015) based on two photographs taken during fieldwork in the Republic of South Africa. This species has no preserved holotype. The paper generated some buzz, especially among dipterists, because in most cases photographs taken in the field provide insufficient information for properly diagnosing and documenting species of Diptera.

  3. California Endangered Species Resource Guide.

    ERIC Educational Resources Information Center

    California State Dept. of Education, Los Angeles.

    This document was developed in response to California Senate Bill No. 885, "The Endangered Species Education Project," that called for a statewide program in which schools adopt a local endangered species, research past and current efforts to preserve the species' habitat, develop and implement an action plan to educate the community…

  4. 75 FR 78974 - Endangered Species

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-17

    ... National Oceanic and Atmospheric Administration RIN 0648-XA086 Endangered Species AGENCY: National Marine.... 10022-01 is requested under the authority of the Endangered Species Act of 1973, as amended (16 U.S.C... Comment'' from the Features box on the Applications and Permits for Protected Species (APPS) home...

  5. 76 FR 1405 - Endangered Species

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-10

    ... National Oceanic and Atmospheric Administration RIN 0648-XA128 Endangered Species AGENCY: National Marine... issued under the authority of the Endangered Species Act of 1973, as amended (ESA; 16 U.S.C. 1531 et seq... not operate to the disadvantage of such endangered or threatened species, and (3) is consistent...

  6. 76 FR 2348 - Endangered Species

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-13

    ... National Oceanic and Atmospheric Administration RIN 0648-XA140 Endangered Species AGENCY: National Marine... Fort Fisher. The requested permit has been issued under the authority of the Endangered Species Act of... exporting of endangered and threatened species (50 CFR parts 222-226). The North Carolina Aquarium at...

  7. Diversity and Biological Activities of Endophytic Fungi Associated with Micropropagated Medicinal Plant Echinacea purpurea (L.) Moench

    DTIC Science & Technology

    2012-08-01

    symbionts associated with orchids [23] and angiosperms [5]. An interesting isolate found in E. purpurea was the phylotype M. indicus, a tropical to...cosmopolitan being found as saprotrophic, pathogenic and as part of an orchid endomycorrhizal group [27]. Ceratorhiza is the anamorphic genus Cer...atobasidium, its species are common endophytes associ- ated with orchids [27]. Glomerella (Ascomycota) is the anamorphic genus Colletotrichum which includes

  8. Introduced species as evolutionary traps

    USGS Publications Warehouse

    Schlaepfer, Martin A.; Sherman, P.W.; Blossey, B.; Runge, M.C.

    2005-01-01

    Invasive species can alter environments in such a way that normal behavioural decision-making rules of native species are no longer adaptive. The evolutionary trap concept provides a useful framework for predicting and managing the impact of harmful invasive species. We discuss how native species can respond to changes in their selective regime via evolution or learning. We also propose novel management strategies to promote the long-term co-existence of native and introduced species in cases where the eradication of the latter is either economically or biologically unrealistic.

  9. The Species Delimitation Uncertainty Principle

    PubMed Central

    Adams, Byron J.

    2001-01-01

    If, as Einstein said, "it is the theory which decides what we can observe," then "the species problem" could be solved by simply improving our theoretical definition of what a species is. However, because delimiting species entails predicting the historical fate of evolutionary lineages, species appear to behave according to the Heisenberg Uncertainty Principle, which states that the most philosophically satisfying definitions of species are the least operational, and as species concepts are modified to become more operational they tend to lose their philosophical integrity. Can species be delimited operationally without losing their philosophical rigor? To mitigate the contingent properties of species that tend to make them difficult for us to delimit, I advocate a set of operations that takes into account the prospective nature of delimiting species. Given the fundamental role of species in studies of evolution and biodiversity, I also suggest that species delimitation proceed within the context of explicit hypothesis testing, like other scientific endeavors. The real challenge is not so much the inherent fallibility of predicting the future but rather adequately sampling and interpreting the evidence available to us in the present. PMID:19265874

  10. Rare species occupy uncommon niches

    PubMed Central

    Markham, John

    2014-01-01

    The fact that temperate grasslands often contain upwards of 30 vascular plant species per m2 yet these species seem to have relatively similar life histories and resource requirements has made explaining species coexistence in these communities a major focus of research. While the reduction of competition by disturbance has been a popular explanation for species coexistence, in tallgrass prairies any level of disturbance either has no effect, or decreases diversity, since it favors the dominant plants. Although there has long been speculation that grassland species could coexist by niche partitioning the concept received renewed interest when it was shown that soil hydrology could explain species coexistence. One aspect of community structure that has not been explained by niche partitioning is the rareness and commonness of species within communities. There are three classes of explanations for rareness: narrow habitat requirements, low competitive ability combined with frequency dependent fitness and, dispersal ability. However, evidence for these explanations tend to be anecdotal, focusing on particular species. Here I show that in tallgrass prairies common and rare species consistently occupy different parts of niche space, with rare species being restricted by the cover of common species and occupying the rare available niches. PMID:25110113

  11. Rare species occupy uncommon niches

    NASA Astrophysics Data System (ADS)

    Markham, John

    2014-08-01

    The fact that temperate grasslands often contain upwards of 30 vascular plant species per m2 yet these species seem to have relatively similar life histories and resource requirements has made explaining species coexistence in these communities a major focus of research. While the reduction of competition by disturbance has been a popular explanation for species coexistence, in tallgrass prairies any level of disturbance either has no effect, or decreases diversity, since it favors the dominant plants. Although there has long been speculation that grassland species could coexist by niche partitioning the concept received renewed interest when it was shown that soil hydrology could explain species coexistence. One aspect of community structure that has not been explained by niche partitioning is the rareness and commonness of species within communities. There are three classes of explanations for rareness: narrow habitat requirements, low competitive ability combined with frequency dependent fitness and, dispersal ability. However, evidence for these explanations tend to be anecdotal, focusing on particular species. Here I show that in tallgrass prairies common and rare species consistently occupy different parts of niche space, with rare species being restricted by the cover of common species and occupying the rare available niches.

  12. Seed dormancy in alpine species

    PubMed Central

    Schwienbacher, Erich; Navarro-Cano, Jose Antonio; Neuner, Gilbert; Erschbamer, Brigitta

    2011-01-01

    In alpine species the classification of the various mechanisms underlying seed dormancy has been rather questionable and controversial. Thus, we investigated 28 alpine species to evaluate the prevailing types of dormancy. Embryo type and water impermeability of seed coats gave an indication of the potential seed dormancy class. To ascertain the actual dormancy class and level, we performed germination experiments comparing the behavior of seeds without storage, after cold-dry storage, after cold-wet storage, and scarification. We also tested the light requirement for germination in some species. Germination behavior was characterized using the final germination percentage and the mean germination time. Considering the effects of the pretreatments, a refined classification of the prevailing dormancy types was constructed based on the results of our pretreatments. Only two out of the 28 species that we evaluated had predominantly non-dormant seeds. Physiological dormancy was prevalent in 20 species, with deep physiological dormancy being the most abundant, followed by non-deep and intermediate physiological dormancy. Seeds of four species with underdeveloped embryos were assigned to the morphophysiologial dormancy class. An impermeable seed coat was identified in two species, with no additional physiological germination block. We defined these species as having physical dormancy. Light promoted the germination of seeds without storage in all but one species with physiological dormancy. In species with physical dormancy, light responses were of minor importance. We discuss our new classification in the context of former germination studies and draw implications for the timing of germination in the field. PMID:24415831

  13. Management of marine species

    NASA Astrophysics Data System (ADS)

    Korringa, P.

    1980-03-01

    Marine fish and shellfish constitute important natural resources. Provided they are wisely exploited, they are not liable to exhaustion but continue to renew themselves. Wise exploitation requires sound management, and for such management one should be well informed about the factors governing the fluctuations in the stocks and about the costs of exploitation. A century of scientific fisheries research provided a wealth of information on reproduction, migration and growth of commercially important species of fish and shellfish and about the losses the stocks suffer through natural causes such as predation, diseases and parasites, and through the fishery itself. Such information is available for areas which are intensively fished. In fertile waters, the approximate growth increase of fish stocks is some 15 % by weight year-1. If one were to harvest this 15 % only, to be considered as interest on this natural capital, and to leave the capital itself untouched, one could go on fishing for ever. There would be no overfishing or stock depletion. For sound management we need not only ecological data but also information on economic fishery aspects, e. g. on size and power of the fleet, type of fish-finding apparatus installed, costs of netting and wages, fuel required per fishing trip, and on the capital invested. Further we need statistical information on the landings and on the proceeds. Such information is available in countries which participate intensively in fishing. Therefore, one would assume that governments which are well informed by their fishery biologists about fluctuations in stocks of fish and shellfish and by their economists on various aspects of the exploitation would apply sound management to ensure that fishing may continue for many years to come without depletion. A number of examples related to the North East Atlantic area, where intensive fishing is carried out and from where a wealth of scientific information is available, makes clear that cases

  14. DNA barcoding Australia's fish species

    PubMed Central

    Ward, Robert D; Zemlak, Tyler S; Innes, Bronwyn H; Last, Peter R; Hebert, Paul D.N

    2005-01-01

    Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups—dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus—were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or ‘barcoding’, can be used to identify fish species. PMID:16214743

  15. The Politics of Endangered Species.

    ERIC Educational Resources Information Center

    Lipscomb, Fran

    1982-01-01

    Presents background information and teaching suggestions about endangered species for social studies teachers. Discusses political processes, economics, current events, and ethics. Lists resource information. (DC)

  16. Previously unknown species of Aspergillus.

    PubMed

    Gautier, M; Normand, A-C; Ranque, S

    2016-08-01

    The use of multi-locus DNA sequence analysis has led to the description of previously unknown 'cryptic' Aspergillus species, whereas classical morphology-based identification of Aspergillus remains limited to the section or species-complex level. The current literature highlights two main features concerning these 'cryptic' Aspergillus species. First, the prevalence of such species in clinical samples is relatively high compared with emergent filamentous fungal taxa such as Mucorales, Scedosporium or Fusarium. Second, it is clearly important to identify these species in the clinical laboratory because of the high frequency of antifungal drug-resistant isolates of such Aspergillus species. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been shown to enable the identification of filamentous fungi with an accuracy similar to that of DNA sequence-based methods. As MALDI-TOF MS is well suited to the routine clinical laboratory workflow, it facilitates the identification of these 'cryptic' Aspergillus species at the routine mycology bench. The rapid establishment of enhanced filamentous fungi identification facilities will lead to a better understanding of the epidemiology and clinical importance of these emerging Aspergillus species. Based on routine MALDI-TOF MS-based identification results, we provide original insights into the key interpretation issues of a positive Aspergillus culture from a clinical sample. Which ubiquitous species that are frequently isolated from air samples are rarely involved in human invasive disease? Can both the species and the type of biological sample indicate Aspergillus carriage, colonization or infection in a patient? Highly accurate routine filamentous fungi identification is central to enhance the understanding of these previously unknown Aspergillus species, with a vital impact on further improved patient care.

  17. Common Pyraloidea species of Dominica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Forty-six adult crambid moths of the superfamily Pyraloidea from Dominica are illustrated and identified. These images are a tool for the identification of large, common species in the Caribbean. The Caribbean is a common entry and pathway of invasive species to southeastern United States....

  18. A NEW SPECIES OF MEMNONIELLA

    EPA Science Inventory

    A new species, Stachybotrys longistipitata sp. nov is described and illustrated. This fungus was originally isolated from forest soil in Japan and deposited as Memnoniella subsimplex.

    Introduction

    Four species have been described in the mitosporic genus Memnoniella ...

  19. 75 FR 78974 - Endangered Species

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-17

    ... National Oceanic and Atmospheric Administration RIN 0648-XA087 Endangered Species AGENCY: National Marine... under the authority of the Endangered Species Act of 1973, as amended (ESA; 16 U.S.C. 1531 et seq.) and the regulations governing the taking, importing, and exporting of endangered and threatened...

  20. 76 FR 74778 - Endangered Species

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-01

    ... National Oceanic and Atmospheric Administration RIN 0648-XA850 Endangered Species AGENCY: National Marine... has been issued under the authority of the Endangered Species Act of 1973, as amended (ESA; 16 U.S.C. 1531 et seq.) and the regulations governing the taking, importing, and exporting of endangered...

  1. Teaching an Endangered Species Unit.

    ERIC Educational Resources Information Center

    Quilty, Joan; And Others

    1986-01-01

    Describes how a student speech activity can serve as a culminating exercise in a unit on endangered species. Offers suggestions and guidelines for researching, formatting, and delivering the speech. A table is also included explaining the causes and prevention of species endangerment. (ML)

  2. Antifungal compounds from Piper species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Piper is a big genus of the plant family Piperaceae, with more than 700 species widely distributed in the tropical and subtropical regions of the world. Some species are used in folk medicine as analgesics, antiseptics, insecticides, and antimicrobials or for the treatment of toothache, haemorrhoid...

  3. Species listing under Canada's Species at Risk Act.

    PubMed

    Findlay, C Scott; Elgie, Stewart; Giles, Brian; Burr, Linda

    2009-12-01

    In a preliminary analysis of listing decisions under Canada's Species at Risk Act (SARA), Mooers et al. (2007)demonstrated an apparent bias against marine and northern species. As a follow-up, we expanded the set of potential explanatory variables, including information on jurisdictional and administrative elements of the listing process, and considered an additional 16 species recommended for listing by SARA's scientific advisory committee as of 15 August 2006. Logistic model selection based on Akaike differences suggested that species were less likely to be listed if they were harvested or had commercial or subsistence harvesting as an explicitly identified threat; had Department of Fisheries and Oceans (DFO) as a responsible authority (RA); were located in Canada's north generally, and especially in Nunavut; or were found mostly or entirely within Canada. Subsequent model validation with an independent set of 50 species for which a listing decision was handed down in December 2007 showed an overall misclassification rate of <0.10, indicating reasonable predictive power. In light of these results, we recommend that RAs under SARA adopt a two-track listing approach to address problems of delays arising from extended consultations and the inconsistent use by the RAs of socioeconomic analysis; consider revising SARA so that socioeconomic analysis occurs during decisions about protecting species and their habitats rather than at the listing stage; and maintain an integrated database with information on species' biology, threats, and agency actions to enable future evaluation of SARA's impact.

  4. Lethal Amanita species in China.

    PubMed

    Cai, Qing; Cui, Yang-Yang; Yang, Zhu L

    2016-09-01

    Lethal amanitas (Amanita sect. Phalloideae) cause many casualties worldwide. Recent molecular phylogenetic studies revealed diverse lethal Amanita spp. in China. Here a 5-gene phylogeny (nuc rDNA region encompassing the internal transcribed spacers 1 and 2 with the 5.8S rDNA, the D1-D3 domains of nuc 28S rDNA, and partial RNA polymerase II second largest subunit, translation elongation factor 1-α and β-tubulin genes) is used to investigate the phylogenetic lineages and species delimitation in this section. Thirteen species are recognized, including four new species, namely A. griseorosea, A. molliuscula, A. parviexitialis, and A. subfuliginea They are documented with morphological, multigene phylogenetic, and ecological evidence, line drawings, and photographs and compared with similar species. A key to the Chinese lethal Amanita species is provided.

  5. Species Delimitation and Global Biosecurity

    PubMed Central

    Boykin, Laura M.; Armstrong, Karen F.; Kubatko, Laura; De Barro, Paul

    2012-01-01

    Species delimitation directly impacts on global biosecurity. It is a critical element in the decisions made by national governments in regard to the flow of trade and to the biosecurity measures imposed to protect countries from the threat of invasive species. Here we outline a novel approach to species delimitation, “tip to root”, for two highly invasive insect pests, Bemisia tabaci (sweetpotato whitefly) and Lymantria dispar (Asian gypsy moth). Both species are of concern to biosecurity, but illustrate the extremes of phylogenetic resolution that present the most complex delimitation issues for biosecurity; B. tabaci having extremely high intra-specific genetic variability and L. dispar composed of relatively indistinct subspecies. This study tests a series of analytical options to determine their applicability as tools to provide more rigorous species delimitation measures and consequently more defensible species assignments and identification of unknowns for biosecurity. Data from established DNA barcode datasets (COI), which are becoming increasingly considered for adoption in biosecurity, were used here as an example. The analytical approaches included the commonly used Kimura two-parameter (K2P) inter-species distance plus four more stringent measures of taxon distinctiveness, (1) Rosenberg’s reciprocal monophyly, (P(AB)),1 (2) Rodrigo’s (P(randomly distinct)),2 (3) genealogical sorting index, (gsi),3 and (4) General mixed Yule-coalescent (GMYC).4,5 For both insect datasets, a comparative analysis of the methods revealed that the K2P distance method does not capture the same level of species distinctiveness revealed by the other three measures; in B. tabaci there are more distinct groups than previously identified using the K2P distances and for L. dipsar far less variation is apparent within the predefined subspecies. A consensus for the results from P(AB), P(randomly distinct) and gsi offers greater statistical confidence as to where genetic limits

  6. Species-barrier-independent prion replication in apparently resistant species

    NASA Astrophysics Data System (ADS)

    Hill, Andrew F.; Joiner, Susan; Linehan, Jackie; Desbruslais, Melanie; Lantos, Peter L.; Collinge, John

    2000-08-01

    Transmission of prions between mammalian species is thought to be limited by a "species barrier," which depends on differences in the primary structure of prion proteins in the infecting inoculum and the host. Here we demonstrate that a strain of hamster prions thought to be nonpathogenic for conventional mice leads to prion replication to high levels in such mice but without causing clinical disease. Prions pathogenic in both mice and hamsters are produced. These results demonstrate the existence of subclinical forms of prion infection with important public health implications, both with respect to iatrogenic transmission from apparently healthy humans and dietary exposure to cattle and other species exposed to bovine spongiform encephalopathy prions. Current definitions of the species barrier, which have been based on clinical end-points, need to be fundamentally reassessed.

  7. Species of colletotrichum on agavaceae.

    PubMed

    Farr, David F; Aime, M Catherine; Rossman, Amy Y; Palm, Mary E

    2006-12-01

    Species of Colletotrichum cause diseases on a wide range of hosts, frequently infecting plants in the Agavaceae (monocotyledons: Liliales). Three species of Colletotrichum restricted to the Agavaceae were detected through morphological studies of specimens and molecular sequence analyses of the LSU of the nu-rDNA and the ITS region of the nu-rDNA from cultures. Colletotrichum agaves on Agave is fully described and illustrated. Colletotrichum dracaenophilum is described as a new species for isolates having long conidia and occurring on Dracaena sanderiana from China. Colletotrichum phormii and Glomerella phormii are determined to be the correct scientific names for the asexual and sexual states, respectively, of a species commonly referred to as C. rhodocyclum and G. phacidiomorpha occurring mainly on Phormium. In addition, C. gloeosporioides and C. boninense were isolated from plants in the Agavaceae. All species of Colletotrichum described on Agavaceae were evaluated based on type specimens. A key to the five species of Colletotrichum on Agavaceae is included. This paper includes one new species, Colletotrichum dracaenophilum, and three new combinations, Colletotrichum phormii, Glomerella phormii, and Phaeosphaeriopsis phacidiomorpha.

  8. Intraspecific variation and species coexistence.

    PubMed

    Lichstein, Jeremy W; Dushoff, Jonathan; Levin, Simon A; Pacala, Stephen W

    2007-12-01

    We use a two-species model of plant competition to explore the effect of intraspecific variation on community dynamics. The competitive ability ("performance") of each individual is assigned by an independent random draw from a species-specific probability distribution. If the density of individuals competing for open space is high (e.g., because fecundity is high), species with high maximum (or large variance in) performance are favored, while if density is low, species with high typical (e.g., mean) performance are favored. If there is an interspecific mean-variance performance trade-off, stable coexistence can occur across a limited range of intermediate densities, but the stabilizing effect of this trade-off appears to be weak. In the absence of this trade-off, one species is superior. In this case, intraspecific variation can blur interspecific differences (i.e., shift the dynamics toward what would be expected in the neutral case), but the strength of this effect diminishes as competitor density increases. If density is sufficiently high, the inferior species is driven to extinction just as rapidly as in the case where there is no overlap in performance between species. Intraspecific variation can facilitate coexistence, but this may be relatively unimportant in maintaining diversity in most real communities.

  9. Evolution of mutualism between species

    SciTech Connect

    Post, W.M.; Travis, C.C.; DeAngelis, D.L.

    1980-01-01

    Recent theoretical work on mutualism, the interaction between species populations that is mutually beneficial, is reviewed. Several ecological facts that should be addressed in the construction of dynamic models for mutualism are examined. Basic terminology is clarified. (PSB)

  10. Some species tolerate ocean acidification

    NASA Astrophysics Data System (ADS)

    Balcerak, Ernie

    2011-12-01

    Increasing carbon dioxide levels lead to rising ocean acidity, which can harm corals and many other species of ocean life. Acidification causes calcium carbonate, which corals usually need to build skeletons, to dissolve. “Every day, ocean acidification is taking up the weight of 6 million midsize cars' worth of carbon, said Nina Keul, a graduate student at the Alfred Wegener Institute for Polar and Marine Research in Germany during a 7 December press conference at the AGU Fall Meeting. Somewhat surprising, though, is that some species are more tolerant of acidic conditions than scientists had expected. For instance, Keul exposed a species of foraminifera, Ammonia tepida, to seawater with varying acidity and varying carbonate ion concentrations. Previous studies had found that foraminifera growth declined with decreasing carbonate levels, but Keul's foraminifera continued to grow in the acidic conditions. She said that the mechanism that allows this species to tolerate the low carbonate conditions is as yet unknown.

  11. Species Typing in Dermal Leishmaniasis

    PubMed Central

    Dujardin, Jean-Claude

    2015-01-01

    SUMMARY Leishmania is an infectious protozoan parasite related to African and American trypanosomes. All Leishmania species that are pathogenic to humans can cause dermal disease. When one is confronted with cutaneous leishmaniasis, identification of the causative species is relevant in both clinical and epidemiological studies, case management, and control. This review gives an overview of the currently existing and most used assays for species discrimination, with a critical appraisal of the limitations of each technique. The consensus taxonomy for the genus is outlined, including debatable species designations. Finally, a numerical literature analysis is presented that describes which methods are most used in various countries and regions in the world, and for which purposes. PMID:25672782

  12. Written Research: An Endangered Species?

    ERIC Educational Resources Information Center

    Hill, Bonnie Campbell

    1989-01-01

    Describes how an integrated unit on endangered species brings research alive for second through sixth graders. Presents lessons involving pre-writing, modeling, guided practice, independent practice, revision, and publication of student papers. (KEH)

  13. Western Shield Threatened Species Program.

    ERIC Educational Resources Information Center

    Moore, Elizabeth

    2001-01-01

    Outlines strategies used to involve the teaching community in a program of native wildlife recovery. Through involvement, teachers and students learn how to contribute to protecting threatened species and maintaining biodiversity. (DDR)

  14. Collective behaviour across animal species

    NASA Astrophysics Data System (ADS)

    Delellis, Pietro; Polverino, Giovanni; Ustuner, Gozde; Abaid, Nicole; Macrì, Simone; Bollt, Erik M.; Porfiri, Maurizio

    2014-01-01

    We posit a new geometric perspective to define, detect, and classify inherent patterns of collective behaviour across a variety of animal species. We show that machine learning techniques, and specifically the isometric mapping algorithm, allow the identification and interpretation of different types of collective behaviour in five social animal species. These results offer a first glimpse at the transformative potential of machine learning for ethology, similar to its impact on robotics, where it enabled robots to recognize objects and navigate the environment.

  15. Collective behaviour across animal species.

    PubMed

    DeLellis, Pietro; Polverino, Giovanni; Ustuner, Gozde; Abaid, Nicole; Macrì, Simone; Bollt, Erik M; Porfiri, Maurizio

    2014-01-16

    We posit a new geometric perspective to define, detect, and classify inherent patterns of collective behaviour across a variety of animal species. We show that machine learning techniques, and specifically the isometric mapping algorithm, allow the identification and interpretation of different types of collective behaviour in five social animal species. These results offer a first glimpse at the transformative potential of machine learning for ethology, similar to its impact on robotics, where it enabled robots to recognize objects and navigate the environment.

  16. The nature of plant species

    PubMed Central

    Rieseberg, Loren H.; Wood, Troy E.; Baack, Eric J.

    2008-01-01

    Many botanists doubt the existence of plant species1–5, viewing them as arbitrary constructs of the human mind, as opposed to discrete, objective entities that represent reproductively independent lineages or ‘units of evolution’. However, the discreteness of plant species and their correspondence with reproductive communities have not been tested quantitatively, allowing zoologists to argue that botanists have been overly influenced by a few ‘botanical horror stories’, such as dandelions, blackberries and oaks6,7. Here we analyse phenetic and/or crossing relationships in over 400 genera of plants and animals. We show that although discrete phenotypic clusters exist in most genera (>80%), the correspondence of taxonomic species to these clusters is poor (<60%) and no different between plants and animals. Lack of congruence is caused by polyploidy, asexual reproduction and over-differentiation by taxonomists, but not by contemporary hybridization. Nonetheless, crossability data indicate that 70% of taxonomic species and 75% of phenotypic clusters in plants correspond to reproductively independent lineages (as measured by postmating isolation), and thus represent biologically real entities. Contrary to conventional wisdom8, plant species are more likely than animal species to represent reproductively independent lineages. PMID:16554818

  17. Thromboelastography in Selected Avian Species.

    PubMed

    Strindberg, Sophie; Nielsen, Tenna W; Ribeiro, Ângela M; Wiinberg, Bo; Kristensen, Annemarie T; Bertelsen, Mads F

    2015-12-01

    Currently available assay methods and reagents are not optimized for evaluating avian hemostasis; therefore, assessing avian coagulopathies is challenging. Recently, thromboelastography (TEG), which measures the viscoelastic properties of blood, has been used clinically in mammalian species to diagnose and characterize hemostatic disorders. To evaluate TEG in healthy individuals of 6 avian species, we modified existing mammalian TEG protocols to allow analysis of citrated, avian whole-blood samples collected from scarlet ibis (Eudocimus ruber) (n = 13), American flamingos ( Phoenicopterus ruber ) (n = 13), helmeted Guinea fowl ( Numida meleagris ) (n = 12), Amazon parrots (Amazona species) (n = 9), Humboldt penguins ( Spheniscus humboldti ) (n = 6), and domestic chickens (n = 16). Activated partial thromboplastin time, prothrombin time, and fibrinogen were measured as a means of comparison. Regardless of the mode of activation, clot formation in the species studied was markedly delayed compared with mammals. Because of prolonged reaction time (14.7-52.7 minutes) with kaolin and diluted tissue factor, undiluted human tissue factor was used in all avian samples because it provided the shortest reaction time. Species differed significantly in reaction time (P = .007), clotting rate (P < .001), rate of clot formation (α angle; P < .001), and maximum amplitude (P < .001) values, indicating that species-specific reference intervals are necessary. Based on these results, TEG with specific reference intervals could prove useful in evaluating avian hemostatic disorders.

  18. Keystone species and food webs

    PubMed Central

    Jordán, Ferenc

    2009-01-01

    Different species are of different importance in maintaining ecosystem functions in natural communities. Quantitative approaches are needed to identify unusually important or influential, ‘keystone’ species particularly for conservation purposes. Since the importance of some species may largely be the consequence of their rich interaction structure, one possible quantitative approach to identify the most influential species is to study their position in the network of interspecific interactions. In this paper, I discuss the role of network analysis (and centrality indices in particular) in this process and present a new and simple approach to characterizing the interaction structures of each species in a complex network. Understanding the linkage between structure and dynamics is a condition to test the results of topological studies, I briefly overview our current knowledge on this issue. The study of key nodes in networks has become an increasingly general interest in several disciplines: I will discuss some parallels. Finally, I will argue that conservation biology needs to devote more attention to identify and conserve keystone species and relatively less attention to rarity. PMID:19451124

  19. The Colletotrichum gloeosporioides species complex

    PubMed Central

    Weir, B.S.; Johnston, P.R.; Damm, U.

    2012-01-01

    The limit of the Colletotrichum gloeosporioides species complex is defined genetically, based on a strongly supported clade within the Colletotrichum ITS gene tree. All taxa accepted within this clade are morphologically more or less typical of the broadly defined C. gloeosporioides, as it has been applied in the literature for the past 50 years. We accept 22 species plus one subspecies within the C. gloeosporioides complex. These include C. asianum, C. cordylinicola, C. fructicola, C. gloeosporioides, C. horii, C. kahawae subsp. kahawae, C. musae, C. nupharicola, C. psidii, C. siamense, C. theobromicola, C. tropicale, and C. xanthorrhoeae, along with the taxa described here as new, C. aenigma, C. aeschynomenes, C. alatae, C. alienum, C. aotearoa, C. clidemiae, C. kahawae subsp. ciggaro, C. salsolae, and C. ti, plus the nom. nov. C. queenslandicum (for C. gloeosporioides var. minus). All of the taxa are defined genetically on the basis of multi-gene phylogenies. Brief morphological descriptions are provided for species where no modern description is available. Many of the species are unable to be reliably distinguished using ITS, the official barcoding gene for fungi. Particularly problematic are a set of species genetically close to C. musae and another set of species genetically close to C. kahawae, referred to here as the Musae clade and the Kahawae clade, respectively. Each clade contains several species that are phylogenetically well supported in multi-gene analyses, but within the clades branch lengths are short because of the small number of phylogenetically informative characters, and in a few cases individual gene trees are incongruent. Some single genes or combinations of genes, such as glyceraldehyde-3-phosphate dehydrogenase and glutamine synthetase, can be used to reliably distinguish most taxa and will need to be developed as secondary barcodes for species level identification, which is important because many of these fungi are of biosecurity

  20. Molecular Epidemiology of Fonsecaea Species

    PubMed Central

    Najafzadeh, Mohammad Javad; Sun, Jiufeng; Vicente, Vania A.; Klaassen, Corne H.W.; Bonifaz, Alexandro; van den Ende, A.H.G. Gerrits; Menken, Steph B.J.

    2011-01-01

    To assess population diversities among 81 strains of fungi in the genus Fonsecaea that had been identified down to species level, we applied amplified fragment-length polymorphism (AFLP) technology and sequenced the internal transcribed spacer regions and the partial cell division cycle, β-tubulin, and actin genes. Many species of the genus Fonsecaea cause human chromoblastomycosis. Strains originated from a global sampling of clinical and environmental sources in the Western Hemisphere, Asia, Africa, and Europe. According to AFLP fingerprinting, Fonsecaea isolates clustered in 5 groups corresponding with F. pedrosoi, F. monophora, and F. nubica: the latter 2 species each comprised 2 groups, and F. pedrosoi appeared to be of monophyletic origin. F. pedrosoi was found nearly exclusively in Central and South America. F. monophora and F. nubica were distributed worldwide, but both showed substantial geographic structuring. Clinical cases outside areas where Fonsecaea is endemic were probably distributed by human migration. PMID:21392438

  1. Molecular epidemiology of Fonsecaea species.

    PubMed

    Najafzadeh, Mohammad Javad; Sun, Jiufeng; Vicente, Vania A; Klaassen, Corne H W; Bonifaz, Alexandro; Gerrits van den Ende, A H G; Menken, Steph B J; de Hoog, G Sybren

    2011-03-01

    To assess population diversities among 81 strains of fungi in the genus Fonsecaea that had been identified down to species level, we applied amplified fragment-length polymorphism (AFLP) technology and sequenced the internal transcribed spacer regions and the partial cell division cycle, beta-tubulin, and actin genes. Many species of the genus Fonsecaea cause human chromoblastomycosis. Strains originated from a global sampling of clinical and environmental sources in the Western Hemisphere, Asia, Africa, and Europe. According to AFLP fingerprinting, Fonsecaea isolates clustered in 5 groups corresponding with F. pedrosoi, F. monophora, and F. nubica: the latter 2 species each comprised 2 groups, and F. pedrosoi appeared to be of monophyletic origin. F. pedrosoi was found nearly exclusively in Central and South America. F. monophora and F. nubica were distributed worldwide, but both showed substantial geographic structuring. Clinical cases outside areas where Fonsecaea is endemic were probably distributed by human migration.

  2. Species interaction mechanisms maintain grassland plant species diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Theory has outpaced empirical research in pursuit of identifying mechanisms maintaining species diversity. Here we demonstrate how data from diversity-ecosystem functioning experiments can be used to test maintenance of diversity theory. We predict that grassland plant diversity can be maintained by...

  3. Genomics of Pathogenic Vibrio Species

    NASA Astrophysics Data System (ADS)

    Dziejman, Michelle; Yildiz, Fitnat H.

    Members of the heterotrophic bacterial family Vibrionaceae are native inhabitants of aquatic environments worldwide, constituting a diverse and abundant component of marine microbial organisms. Over 60 species of the genus Vibrio have been identified (Thompson et al., 2004) and their phenotypic heterogeneity is well documented. The ecology of the genus remains less well understood, however, despite reports that vibrios are the dominant microorganisms inhabiting the superficial water layer and colonizing the chitinous exoskeleton of zooplankton (e.g., copepods, Thompson et al., 2004). Although some species were originally isolated from seawater as free living organisms, most were isolated in association with marine life such as bivalves, fish, eels, or shrimp.

  4. The Colletotrichum boninense species complex

    PubMed Central

    Damm, U.; Cannon, P.F.; Woudenberg, J.H.C.; Johnston, P.R.; Weir, B.S.; Tan, Y.P.; Shivas, R.G.; Crous, P.W.

    2012-01-01

    Although only recently described, Colletotrichum boninense is well established in literature as an anthracnose pathogen or endophyte of a diverse range of host plants worldwide. It is especially prominent on members of Amaryllidaceae, Orchidaceae, Proteaceae and Solanaceae. Reports from literature and preliminary studies using ITS sequence data indicated that C. boninense represents a species complex. A multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3, CAL) of 86 strains previously identified as C. boninense and other related strains revealed 18 clades. These clades are recognised here as separate species, including C. boninense s. str., C. hippeastri, C. karstii and 12 previously undescribed species, C. annellatum, C. beeveri, C. brassicicola, C. brasiliense, C. colombiense, C. constrictum, C. cymbidiicola, C. dacrycarpi, C. novae-zelandiae, C. oncidii, C. parsonsiae and C. torulosum. Seven of the new species are only known from New Zealand, perhaps reflecting a sampling bias. The new combination C. phyllanthi was made, and C. dracaenae Petch was epitypified and the name replaced with C. petchii. Typical for species of the C. boninense species complex are the conidiogenous cells with rather prominent periclinal thickening that also sometimes extend to form a new conidiogenous locus or annellations as well as conidia that have a prominent basal scar. Many species in the C. boninense complex form teleomorphs in culture. Taxonomic novelties: New combination - Colletotrichum phyllanthi (H. Surendranath Pai) Damm, P.F. Cannon & Crous. Name replacement - C. petchii Damm, P.F. Cannon & Crous. New species - C. annellatum Damm, P.F. Cannon & Crous, C. beeveri Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. brassicicola Damm, P.F. Cannon & Crous, C. brasiliense Damm, P.F. Cannon, Crous & Massola, C. colombiense Damm, P.F. Cannon, Crous, C. constrictum Damm, P.F. Cannon, Crous, P.R. Johnst. & B. Weir, C. cymbidiicola Damm, P.F. Cannon

  5. Collective behaviour across animal species

    PubMed Central

    DeLellis, Pietro; Polverino, Giovanni; Ustuner, Gozde; Abaid, Nicole; Macrì, Simone; Bollt, Erik M.; Porfiri, Maurizio

    2014-01-01

    We posit a new geometric perspective to define, detect, and classify inherent patterns of collective behaviour across a variety of animal species. We show that machine learning techniques, and specifically the isometric mapping algorithm, allow the identification and interpretation of different types of collective behaviour in five social animal species. These results offer a first glimpse at the transformative potential of machine learning for ethology, similar to its impact on robotics, where it enabled robots to recognize objects and navigate the environment. PMID:24430561

  6. The Colletotrichum acutatum species complex

    PubMed Central

    Damm, U.; Cannon, P.F.; Woudenberg, J.H.C.; Crous, P.W.

    2012-01-01

    Colletotrichum acutatum is known as an important anthracnose pathogen of a wide range of host plants worldwide. Numerous studies have reported subgroups within the C. acutatum species complex. Multilocus molecular phylogenetic analysis (ITS, ACT, TUB2, CHS-1, GAPDH, HIS3) of 331 strains previously identified as C. acutatum and other related taxa, including strains from numerous hosts with wide geographic distributions, confirmed the molecular groups previously recognised and identified a series of novel taxa. Thirty-one species are accepted, of which 21 have not previously been recognised. Colletotrichum orchidophilum clusters basal to the C. acutatum species complex. There is a high phenotypic diversity within this complex, and some of the species appear to have preferences to specific hosts or geographical regions. Others appear to be plurivorous and are present in multiple regions. In this study, only C. salicis and C. rhombiforme formed sexual morphs in culture, although sexual morphs have been described from other taxa (especially as laboratory crosses), and there is evidence of hybridisation between different species. One species with similar morphology to C. acutatum but not belonging to this species complex was also described here as new, namely C. pseudoacutatum. Taxonomic novelties: New combinations - Colletotrichum limetticola (R.E. Clausen) Damm, P.F. Cannon & Crous, C. lupini (Bondar) Damm, P.F. Cannon & Crous, C. salicis (Fuckel) Damm, P.F. Cannon & Crous. New species - C. acerbum Damm, P.F. Cannon & Crous, C. australe Damm, P.F. Cannon & Crous, C. brisbanense Damm, P.F. Cannon & Crous, C. cosmi Damm, P.F. Cannon & Crous, C. costaricense Damm, P.F. Cannon & Crous, C. cuscutae Damm, P.F. Cannon & Crous, C. guajavae Damm, P.F. Cannon & Crous, C. indonesiense Damm, P.F. Cannon & Crous, C. johnstonii Damm, P.F. Cannon & Crous, C. kinghornii Damm, P.F. Cannon & Crous, C. laticiphilum Damm, P.F. Cannon & Crous, C. melonis Damm, P.F. Cannon & Crous, C

  7. Genetic relatedness among Filobasidiella species.

    PubMed

    Sivakumaran, Swarna; Bridge, Paul; Roberts, Peter

    2002-01-01

    The three accepted species of Filobasidiella, F. neoformans, F. depauperata, and F. lutea, are compared morphologically and by molecular analysis. Sequences of the internally transcribed spacer (ITS) and the small subunit (SSU) gene of the ribosomal RNA (rRNA) gene cluster were obtained, and analysed by Neighbor-joining and Maximum parsimony methods. The three species of Filobsidiella are shown to form a single monophyletic clade, rooted by Tremella mesenterica. F. lutea was recovered as a distinct, but closely related taxon with the Filobasidiella clade. This is the first report of DNA sequences from herbarium specimens of F. lutea.

  8. Detection of toxic monofluoroacetate in Palicourea species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Numerous plant species worldwide including some Palicourea (Rubiaceae), Tanaecium (Bignoniaceae), and Amorimia (Malpighiaceae) species in Brazil cause sudden death and are known to contain monofluoroacetate (MFA). Two species of Palicourea, P. aenofusca and P. marcgravii, cause sudden death and are...

  9. Evolution: a new cat species emerges.

    PubMed

    O'Brien, Stephen J; Koepfli, Klaus-Peter

    2013-12-16

    The complex ongoing process of species development is highlighted by the description of a new felid species, Leopardus guttulus, from Brazil. Broad molecular genetic assessments affirm reproductive isolation and separation in nature, the hallmark of species recognition.

  10. Would species richness estimators change the observed species area relationship?

    NASA Astrophysics Data System (ADS)

    Borges, Paulo A. V.; Hortal, Joaquín; Gabriel, Rosalina; Homem, Nídia

    2009-01-01

    We evaluate whether the description of the species area relationship (SAR) can be improved by using richness estimates instead of observed richness values. To do this, we use three independent datasets gathered with standardized survey methods from the native laurisilva forest of the Azorean archipelago, encompassing different distributional extent and biological groups: soil epigean arthropods at eight forest fragments in Terceira Island, canopy arthropods inhabiting Juniperus brevifolia at 16 forest fragments of six different islands, and bryophytes of seven forest fragments from Terceira and Pico islands. Species richness values were estimated for each forest fragment using seven non-parametric estimators (ACE, ICE, Chao1, Chao2, Jackknife1, Jackknife2 and Bootstrap; five in the case of bryophytes). These estimates were fitted to classical log-log species-area curves and the intercept, slope and goodness of fit of these curves were compared with those obtained from the observed species richness values to determine if significant differences appear in these parameters. We hypothesized that the intercepts would be higher in the estimated data sets compared with the observed data, as estimated richness values are typically higher than observed values. We found partial support for the hypothesis - intercepts of the SAR obtained from estimated richness values were significantly higher in the case of epigean arthropods and bryophyte datasets. In contrast, the slope and goodness of fit obtained with estimated values were not significantly different from those obtained from observed species richness in all groups, although a few small differences appeared. We conclude that, although little is gained using these estimators if data come from standardized surveys, their estimations could be used to analyze macroecological relationships with non-standardized observed data, provided that survey incompleteness and/or unevenness are also taken into account.

  11. The Encounter of the Emblematic Tradition with Optics. The Anamorphic Elephant of Simon Vouet.

    PubMed

    Gómez López, Susana

    2016-01-01

    In his excellent work Anamorphoses ou perspectives curieuses (1955), Baltrusaitis concluded the chapter on catoptric anamorphosis with an allusion to the small engraving by Hans Tröschel (1585-1628) after Simon Vouet's drawing Eight satyrs observing an elephant reflected on a cylinder, the first known representation of a cylindrical anamorphosis made in Europe. This paper explores the Baroque intellectual and artistic context in which Vouet made his drawing, attempting to answer two central sets of questions. Firstly, why did Vouet make this image? For what purpose did he ideate such a curious image? Was it commissioned or did Vouet intend to offer it to someone? And if so, to whom? A reconstruction of this story leads me to conclude that the cylindrical anamorphosis was conceived as an emblem for Prince Maurice of Savoy. Secondly, how did what was originally the project for a sophisticated emblem give rise in Paris, after the return of Vouet from Italy in 1627, to the geometrical study of catoptrical anamorphosis? Through the study of this case, I hope to show that in early modern science the emblematic tradition was not only linked to natural history, but that insofar as it was a central feature of Baroque culture, it seeped into other branches of scientific inquiry, in this case the development of catoptrical anamorphosis. Vouet's image is also a good example of how the visual and artistic poetics of the baroque were closely linked--to the point of being inseparable--with the scientific developments of the period.

  12. Phylogenetic relationships among Maloideae species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Maloideae is a highly diverse sub-family of the Rosaceae containing several agronomically important species (Malus sp. and Pyrus sp.) and their wild relatives. Previous phylogenetic work within the group has revealed extensive intergeneric hybridization and polyploidization. In order to develop...

  13. Endangered Species and Human Survival.

    ERIC Educational Resources Information Center

    Regenstein, Lewis

    1984-01-01

    In wiping out the natural heritage over which we were given dominion and stewardship responsibilities, we are sowing the seeds of our own destruction. With the advent of the Reagan administration, the government's endangered species program has all but ceased to function. (RM)

  14. Endangered Species: An Educator's Handbook.

    ERIC Educational Resources Information Center

    Smith, Jean, M., Comp.

    Presented are two articles, an annotated bibliography, and other information useful in teaching about endangered species, especially those found in Florida. The articles provide an ethical rationale, teaching suggestions, and a discussion of the value of wildlife. Descriptions of over 100 pertinent books, periodicals, movies, and filmstrips are in…

  15. Human Infections with Sarcocystis Species

    PubMed Central

    Esposito, Douglas H.; Dubey, Jitender P.

    2015-01-01

    SUMMARY Recurrent outbreaks of muscular sarcocystosis among tourists visiting islands in Malaysia have focused international attention on sarcocystosis, a disease once considered rare in humans. Sarcocystis species require two hosts, definitive and intermediate, to complete their life cycle. Humans can serve as definitive hosts, with intestinal sarcocystosis for two species acquired from eating undercooked meat: Sarcocystis hominis, from beef, and Sarcocystis suihominis, from pork. Symptoms such as nausea, stomachache, and diarrhea vary widely depending on the number of cysts ingested but appear more severe with pork than with beef. Humans serve as intermediate hosts for Sarcocystis nesbitti, a species with a reptilian definitive host, and possibly other unidentified species, acquired by ingesting sporocysts from feces-contaminated food or water and the environment; infections have an early phase of development in vascular endothelium, with illness that is difficult to diagnose; clinical signs include fever, headache, and myalgia. Subsequent development of intramuscular cysts is characterized by myositis. Presumptive diagnosis based on travel history to tropical regions, elevated serum enzyme levels, and eosinophilia is confirmed by finding sarcocysts in muscle biopsy specimens. There is no vaccine or confirmed effective antiparasitic drug for muscular sarcocystosis, but anti-inflammatory drugs may reduce symptoms. Prevention strategies are also discussed. PMID:25715644

  16. Man...An Endangered Species?

    ERIC Educational Resources Information Center

    Department of the Interior, Washington, DC.

    The general theme of this 1968 yearbook is that man is a threatened species, facing overpopulation and unbridled technology - both self induced. The presentation is broad, relating to many aspects of conservation and natural resources in the United States in a descriptive, non-technical style. The yearbook is divided into major topics: Land…

  17. New Pyrenochaeta Species Causing Keratitis▿

    PubMed Central

    Ferrer, Consuelo; Pérez-Santonja, Juan J.; Rodríguez, Alejandra E.; Colom, M. Francisca; Gené, Josepa; Alio, Jorge L.; Verkley, Gerard J. M.; Guarro, Josep

    2009-01-01

    We report a new fungus as an agent of fungal keratitis in a diabetic woman. The fungal etiology was established by classic microbiology and PCR following 3 months of antibacterial therapy. The morphological features of the isolate and sequence analysis of the internal transcribed spacer region indicate a new species of Pyrenochaeta (Coelomycetes). PMID:19297598

  18. Chromosome synteny in cucumis species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cucumber, Cucumis sativus L. (2n = 2x = 14) and melon, C. melo L. (2n = 2x = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae). Two inter-fertile botanical varieties with 14 chromosomes, the cultivated C. sativus var. sativus L. and the wild C. sativus var. hardwick...

  19. Influenza vaccines for avian species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beginning in Southeast Asia, in 2003, a multi-national epizootic outbreak of H5N1 highly pathogenic avian influenza (HPAI) was identified in commercial poultry and wild bird species. This lineage, originally identified in Southern China in 1996 and then Hong Kong in 1997, caused severe morbidity an...

  20. Spread dynamics of invasive species

    PubMed Central

    Arim, Matías; Abades, Sebastián R.; Neill, Paula E.; Lima, Mauricio; Marquet, Pablo A.

    2006-01-01

    Species invasions are a principal component of global change, causing large losses in biodiversity as well as economic damage. Invasion theory attempts to understand and predict invasion success and patterns of spread. However, there is no consensus regarding which species or community attributes enhance invader success or explain spread dynamics. Experimental and theoretical studies suggest that regulation of spread dynamics is possible; however, the conditions for its existence have not yet been empirically demonstrated. If invasion spread is a regulated process, the structure that accounts for this regulation will be a main determinant of invasion dynamics. Here we explore the existence of regulation underlying changes in the rate of new site colonization. We employ concepts and analytical tools from the study of abundance dynamics and show that spread dynamics are, in fact, regulated processes and that the regulation structure is notably consistent among invasions occurring in widely different contexts. We base our conclusions on the analysis of the spread dynamics of 30 species invasions, including birds, amphibians, fish, invertebrates, plants, and a virus, all of which exhibited similar regulation structures. In contrast to current beliefs that species invasions are idiosyncratic phenomena, here we provide evidence that general patterns do indeed exist. PMID:16387862

  1. Human infections with Sarcocystis species.

    PubMed

    Fayer, Ronald; Esposito, Douglas H; Dubey, Jitender P

    2015-04-01

    Recurrent outbreaks of muscular sarcocystosis among tourists visiting islands in Malaysia have focused international attention on sarcocystosis, a disease once considered rare in humans. Sarcocystis species require two hosts, definitive and intermediate, to complete their life cycle. Humans can serve as definitive hosts, with intestinal sarcocystosis for two species acquired from eating undercooked meat: Sarcocystis hominis, from beef, and Sarcocystis suihominis, from pork. Symptoms such as nausea, stomachache, and diarrhea vary widely depending on the number of cysts ingested but appear more severe with pork than with beef. Humans serve as intermediate hosts for Sarcocystis nesbitti, a species with a reptilian definitive host, and possibly other unidentified species, acquired by ingesting sporocysts from feces-contaminated food or water and the environment; infections have an early phase of development in vascular endothelium, with illness that is difficult to diagnose; clinical signs include fever, headache, and myalgia. Subsequent development of intramuscular cysts is characterized by myositis. Presumptive diagnosis based on travel history to tropical regions, elevated serum enzyme levels, and eosinophilia is confirmed by finding sarcocysts in muscle biopsy specimens. There is no vaccine or confirmed effective antiparasitic drug for muscular sarcocystosis, but anti-inflammatory drugs may reduce symptoms. Prevention strategies are also discussed.

  2. Species identification through DNA "barcodes".

    PubMed

    Ferri, Gianmarco; Alù, Milena; Corradini, Beatrice; Licata, Manuela; Beduschi, Giovanni

    2009-06-01

    Conventional methods for forensic species identification are mainly based on immunological procedures, which have limited applications for old and degraded specimens. The mitochondrial cytochrome b gene sequence has emerged in forensics among molecular methods. Recent investigations in the taxonomic field have suggested that a DNA-based identification system may aid the resolution of animal diversity and classification using sequence analysis and phylogenetic links. Selected gene sequences can be viewed as a genetic "barcode," which is enclosed in every cell, and barcoding is a standardized approach for characterizing species using short DNA sequences as a diagnostic biomarker for organisms. The aim of this study was to evaluate the potential of barcode mitochondrial genes, such as the cytochrome c oxidase sub 1 (COI) and the 16S rRNA gene, as a forensic tool. We developed a new approach for species testing and identification with a singleplex PCR amplification that will be useful not only in criminal casework but also in biosecurity, food authentication, investigation against poaching or illegal trade of endangered species, and wildlife enforcement. Seven fragments ranging from 157 to 541 bp (base pairs) in humans were selected from COI and 16S rRNA genes by different redesigned sets of primers suitable for forensic purposes. The specificity of each primer pair was evaluated with a single PCR reaction on different substrates, and the diversity values were calculated by statistical tests to select a set of markers that could be useful in different caseworks. A case example of forensic species identification is also presented.

  3. Optimal Conservation of Migratory Species

    PubMed Central

    Martin, Tara G.; Chadès, Iadine; Arcese, Peter; Marra, Peter P.; Possingham, Hugh P.; Norris, D. Ryan

    2007-01-01

    Background Migratory animals comprise a significant portion of biodiversity worldwide with annual investment for their conservation exceeding several billion dollars. Designing effective conservation plans presents enormous challenges. Migratory species are influenced by multiple events across land and sea–regions that are often separated by thousands of kilometres and span international borders. To date, conservation strategies for migratory species fail to take into account how migratory animals are spatially connected between different periods of the annual cycle (i.e. migratory connectivity) bringing into question the utility and efficiency of current conservation efforts. Methodology/Principal Findings Here, we report the first framework for determining an optimal conservation strategy for a migratory species. Employing a decision theoretic approach using dynamic optimization, we address the problem of how to allocate resources for habitat conservation for a Neotropical-Nearctic migratory bird, the American redstart Setophaga ruticilla, whose winter habitat is under threat. Our first conservation strategy used the acquisition of winter habitat based on land cost, relative bird density, and the rate of habitat loss to maximize the abundance of birds on the wintering grounds. Our second strategy maximized bird abundance across the entire range of the species by adding the constraint of maintaining a minimum percentage of birds within each breeding region in North America using information on migratory connectivity as estimated from stable-hydrogen isotopes in feathers. We show that failure to take into account migratory connectivity may doom some regional populations to extinction, whereas including information on migratory connectivity results in the protection of the species across its entire range. Conclusions/Significance We demonstrate that conservation strategies for migratory animals depend critically upon two factors: knowledge of migratory

  4. Modeling species-abundance relationships in multi-species collections

    USGS Publications Warehouse

    Peng, S.; Yin, Z.; Ren, H.; Guo, Q.

    2003-01-01

    Species-abundance relationship is one of the most fundamental aspects of community ecology. Since Motomura first developed the geometric series model to describe the feature of community structure, ecologists have developed many other models to fit the species-abundance data in communities. These models can be classified into empirical and theoretical ones, including (1) statistical models, i.e., negative binomial distribution (and its extension), log-series distribution (and its extension), geometric distribution, lognormal distribution, Poisson-lognormal distribution, (2) niche models, i.e., geometric series, broken stick, overlapping niche, particulate niche, random assortment, dominance pre-emption, dominance decay, random fraction, weighted random fraction, composite niche, Zipf or Zipf-Mandelbrot model, and (3) dynamic models describing community dynamics and restrictive function of environment on community. These models have different characteristics and fit species-abundance data in various communities or collections. Among them, log-series distribution, lognormal distribution, geometric series, and broken stick model have been most widely used.

  5. Tensor species and symmetric functions.

    PubMed Central

    Méndez, M

    1991-01-01

    An equivariant representation of the symmetric group Sn (equivariant representation from here on) is defined as a particular type of tensor species. For any tensor species R the characteristic generating function of R is defined in a way that generalizes the Frobenius characters of representations of the symmetric groups. If R is an equivariant representation, then the characteristic is a homogeneous symmetric function. The combinatorial operations on equivariant representations correspond to formal operations on the respective characteristic functions. In particular, substitution of equivariant representations corresponds to plethysm of symmetric functions. Equivariant representations are constructed that have as characteristic the elementary, complete, and Schur functions. Bijective proofs are given for the formulas that connect them with the monomial symmetric functions. PMID:11607233

  6. Ranking species in mutualistic networks

    NASA Astrophysics Data System (ADS)

    Domínguez-García, Virginia; Muñoz, Miguel A.

    2015-02-01

    Understanding the architectural subtleties of ecological networks, believed to confer them enhanced stability and robustness, is a subject of outmost relevance. Mutualistic interactions have been profusely studied and their corresponding bipartite networks, such as plant-pollinator networks, have been reported to exhibit a characteristic ``nested'' structure. Assessing the importance of any given species in mutualistic networks is a key task when evaluating extinction risks and possible cascade effects. Inspired in a recently introduced algorithm -similar in spirit to Google's PageRank but with a built-in non-linearity- here we propose a method which -by exploiting their nested architecture- allows us to derive a sound ranking of species importance in mutualistic networks. This method clearly outperforms other existing ranking schemes and can become very useful for ecosystem management and biodiversity preservation, where decisions on what aspects of ecosystems to explicitly protect need to be made.

  7. Ranking species in mutualistic networks

    PubMed Central

    Domínguez-García, Virginia; Muñoz, Miguel A.

    2015-01-01

    Understanding the architectural subtleties of ecological networks, believed to confer them enhanced stability and robustness, is a subject of outmost relevance. Mutualistic interactions have been profusely studied and their corresponding bipartite networks, such as plant-pollinator networks, have been reported to exhibit a characteristic “nested” structure. Assessing the importance of any given species in mutualistic networks is a key task when evaluating extinction risks and possible cascade effects. Inspired in a recently introduced algorithm –similar in spirit to Google's PageRank but with a built-in non-linearity– here we propose a method which –by exploiting their nested architecture– allows us to derive a sound ranking of species importance in mutualistic networks. This method clearly outperforms other existing ranking schemes and can become very useful for ecosystem management and biodiversity preservation, where decisions on what aspects of ecosystems to explicitly protect need to be made. PMID:25640575

  8. Ranking species in mutualistic networks.

    PubMed

    Domínguez-García, Virginia; Muñoz, Miguel A

    2015-02-02

    Understanding the architectural subtleties of ecological networks, believed to confer them enhanced stability and robustness, is a subject of outmost relevance. Mutualistic interactions have been profusely studied and their corresponding bipartite networks, such as plant-pollinator networks, have been reported to exhibit a characteristic "nested" structure. Assessing the importance of any given species in mutualistic networks is a key task when evaluating extinction risks and possible cascade effects. Inspired in a recently introduced algorithm--similar in spirit to Google's PageRank but with a built-in non-linearity--here we propose a method which--by exploiting their nested architecture--allows us to derive a sound ranking of species importance in mutualistic networks. This method clearly outperforms other existing ranking schemes and can become very useful for ecosystem management and biodiversity preservation, where decisions on what aspects of ecosystems to explicitly protect need to be made.

  9. Protein secretion in Bacillus species.

    PubMed Central

    Simonen, M; Palva, I

    1993-01-01

    Bacilli secrete numerous proteins into the environment. Many of the secretory proteins, their export signals, and their processing steps during secretion have been characterized in detail. In contrast, the molecular mechanisms of protein secretion have been relatively poorly characterized. However, several components of the protein secretion machinery have been identified and cloned recently, which is likely to lead to rapid expansion of the knowledge of the protein secretion mechanism in Bacillus species. Comparison of the presently known export components of Bacillus species with those of Escherichia coli suggests that the mechanism of protein translocation across the cytoplasmic membrane is conserved among gram-negative and gram-positive bacteria differences are found in steps preceding and following the translocation process. Many of the secretory proteins of bacilli are produced industrially, but several problems have been encountered in the production of Bacillus heterologous secretory proteins. In the final section we discuss these problems and point out some possibilities to overcome them. PMID:8464403

  10. Native Terrestrial Animal Species Richness

    EPA Pesticide Factsheets

    These data represent predicted current distributions of all native mammals, birds, reptiles, amphibians and butterflies in the Middle-Atlantic region. The data are available for both 8-digit HUCs and EMAP hexagons and represent total species counts for each spatial unit. More information about these resources, including the variables used in this study, may be found here: https://edg.epa.gov/data/Public/ORD/NERL/ReVA/ReVA_Data.zip.

  11. Influenza viruses: transmission between species.

    PubMed

    Webster, R G; Hinshaw, V S; Bean, W J; Sriram, G

    1980-02-25

    The only direct evidence for transmission of influenza viruses between species comes from studies on swine influenza viruses. Antigenically and genetically identical Hsw1N1 influenza viruses were isolated from pigs and man on the same farm in Wisconsin, U.S.A. The isolation of H3N2 influenza viruses from a wide range of lower animals and birds suggests that influenza viruses of man can spread to the lower orders. Under some conditions the H3N2 viruses can persist for a number of years in some species. The isolation, from aquatic birds, of a large number of influenza A viruses that possess surface proteins antigenically similar to the viruses isolated from man, pigs and horses provides indirect evidence for inter-species transmission. There is now a considerable body of evidence which suggests that influenza viruses of lower animals and birds may play a role in the origin of some of the pandemic strains of influenza A viruses. There is no direct evidence that the influenza viruses in aquatic birds are transmitted to man, but they may serve as a genetic pool from which some genes may be introduced into humans by recombination. Preliminary evidence suggests that the molecular basis of host range and virulence may be related to the RNA segments coding for one of the polymerase proteins (P3) and for the nucleoprotein (NP).

  12. Automated species identification: why not?

    PubMed Central

    Gaston, Kevin J; O'Neill, Mark A

    2004-01-01

    Where possible, automation has been a common response of humankind to many activities that have to be repeated numerous times. The routine identification of specimens of previously described species has many of the characteristics of other activities that have been automated, and poses a major constraint on studies in many areas of both pure and applied biology. In this paper, we consider some of the reasons why automated species identification has not become widely employed, and whether it is a realistic option, addressing the notions that it is too difficult, too threatening, too different or too costly. Although recognizing that there are some very real technical obstacles yet to be overcome, we argue that progress in the development of automated species identification is extremely encouraging that such an approach has the potential to make a valuable contribution to reducing the burden of routine identifications. Vision and enterprise are perhaps more limiting at present than practical constraints on what might possibly be achieved. PMID:15253351

  13. Infections caused by Propionibacterium species.

    PubMed

    Brook, I; Frazier, E H

    1991-01-01

    Eight hundred and sixteen isolates of Propionibacterium species (725 of which were Propionibacterium acnes) were isolated from 3,971 specimens submitted for the identification of anaerobic bacteria over the course of 10 years. A total of 94 Propionibacterium isolates (12%) identified in 92 patients were considered to cause infection. The rest of the isolates were determined to be contaminants or of uncertain pathogenic significance. Significant infections caused by Propionibacterium species were associated with the blood in 15 patients, central nervous system in 11, lymph glands in 10, abscesses in eight, joints in seven, wounds in seven, cysts in six, and sinuses in five. Predisposing or underlying conditions were noted in 66 patients (70%). The most common conditions were the presence of foreign bodies (29 patients), diabetes (12), previous surgery (10), trauma (seven), malignancy (seven), immunodeficiency (seven), and steroid therapy (four). Antimicrobial therapy was administered to 83 patients; for 47 patients this therapy was given in conjunction with surgical drainage or correction. Surgical drainage alone was performed in nine patients. Five patients (5%) died. These data illustrate that although Propionibacterium species are rarely associated with infections, these organisms can occasionally cause serious infections.

  14. 77 FR 40375 - Receipt of Applications for Endangered Species Permits

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-09

    ... the following species of freshwater mussels: Fat threeridge--Amblema neislerii Shinyrayed pocketbook... species, 14 fish species, 34 fresh-water mussel species, 2 snail species, 1 insect species, and 2...

  15. 78 FR 24432 - Receipt of Applications for Endangered Species Permits

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-25

    ... mussels, 12 species of freshwater snails, and 3 species of terrestrial snails throughout Arkansas..., tag, release) 56 freshwater mussel species, 5 snail species, 7 fish species, and 1 species of...

  16. Ribosomal DNA sequence divergence and group I introns within the Leucostoma species L. cinctum, L. persoonii, and L. parapersoonii sp. nov., ascomycetes that cause Cytospora canker of fruit trees.

    PubMed

    Adams, Gerard C; Surve-Iyer, Rupa S; Iezzoni, Amy F

    2002-01-01

    Leucostoma species that are the causal agents of Cytospora canker of stone and pome fruit trees were studied in detail. DNA sequence of the internal transcribed spacer regions and the 5.8S of the nuclear ribosomal DNA operon (ITS rDNA) supplied sufficient characters to assess the phylogenetic relationships among species of Leucostoma, Valsa, Valsella, and related anamorphs in Cytospora. Parsimony analysis of the aligned sequence divided Cytospora isolates from fruit trees into clades that generally agreed with the morphological species concepts, and with some of the phenetic groupings (PG 1-6) identified previously by isozyme analysis and cultural characteristics. Phylogenetic analysis inferred that isolates of L. persoonii formed two well-resolved clades distinct from isolates of L. cinctum. Phylogenetic analysis of the ITS rDNA, isozyme analysis, and cultural characteristics supported the inference that L. persoonii groups PG 2 and PG 3 were populations of a new species apparently more genetically different from L. persoonii PG 1 than from isolates representative of L. massariana, L. niveum, L. translucens, and Valsella melastoma. The new species, L. parapersoonii, was described. A diverse collection of isolates of L. cinctum, L. persoonii, and L. parapersoonii were examined for genetic variation using restriction fragment length polymorphism (RFLP) analysis of the ITS rDNA and the five prime end of the large subunit of the rDNA (LSU rDNA). HinfI and HpaII endonucleases were each useful in dividing the Leucostoma isolates into RFLP profiles corresponding to the isozyme phenetic groups, PG 1-6. RFLP analysis was more effective than isozyme analysis in uncovering variation among isolates of L. persoonii PG 1, but less effective within L. cinctum populations. Isolates representative of seven of the L. persoonii formae speciales proposed by G. Défago in 1935 were found to be genetically diverse isolates of PG 1. Two large insertions, 415 and 309 nucleotides long, in

  17. Natural Constraints to Species Diversification

    PubMed Central

    Lewitus, Eric; Morlon, Hélène

    2016-01-01

    Identifying modes of species diversification is fundamental to our understanding of how biodiversity changes over evolutionary time. Diversification modes are captured in species phylogenies, but characterizing the landscape of diversification has been limited by the analytical tools available for directly comparing phylogenetic trees of groups of organisms. Here, we use a novel, non-parametric approach and 214 family-level phylogenies of vertebrates representing over 500 million years of evolution to identify major diversification modes, to characterize phylogenetic space, and to evaluate the bounds and central tendencies of species diversification. We identify five principal patterns of diversification to which all vertebrate families hold. These patterns, mapped onto multidimensional space, constitute a phylogenetic space with distinct properties. Firstly, phylogenetic space occupies only a portion of all possible tree space, showing family-level phylogenies to be constrained to a limited range of diversification patterns. Secondly, the geometry of phylogenetic space is delimited by quantifiable trade-offs in tree size and the heterogeneity and stem-to-tip distribution of branching events. These trade-offs are indicative of the instability of certain diversification patterns and effectively bound speciation rates (for successful clades) within upper and lower limits. Finally, both the constrained range and geometry of phylogenetic space are established by the differential effects of macroevolutionary processes on patterns of diversification. Given these properties, we show that the average path through phylogenetic space over evolutionary time traverses several diversification stages, each of which is defined by a different principal pattern of diversification and directed by a different macroevolutionary process. The identification of universal patterns and natural constraints to diversification provides a foundation for understanding the deep-time evolution of

  18. The Invasive Species Forecasting System

    NASA Technical Reports Server (NTRS)

    Schnase, John; Most, Neal; Gill, Roger; Ma, Peter

    2011-01-01

    The Invasive Species Forecasting System (ISFS) provides computational support for the generic work processes found in many regional-scale ecosystem modeling applications. Decision support tools built using ISFS allow a user to load point occurrence field sample data for a plant species of interest and quickly generate habitat suitability maps for geographic regions of management concern, such as a national park, monument, forest, or refuge. This type of decision product helps resource managers plan invasive species protection, monitoring, and control strategies for the lands they manage. Until now, scientists and resource managers have lacked the data-assembly and computing capabilities to produce these maps quickly and cost efficiently. ISFS focuses on regional-scale habitat suitability modeling for invasive terrestrial plants. ISFS s component architecture emphasizes simplicity and adaptability. Its core services can be easily adapted to produce model-based decision support tools tailored to particular parks, monuments, forests, refuges, and related management units. ISFS can be used to build standalone run-time tools that require no connection to the Internet, as well as fully Internet-based decision support applications. ISFS provides the core data structures, operating system interfaces, network interfaces, and inter-component constraints comprising the canonical workflow for habitat suitability modeling. The predictors, analysis methods, and geographic extents involved in any particular model run are elements of the user space and arbitrarily configurable by the user. ISFS provides small, lightweight, readily hardened core components of general utility. These components can be adapted to unanticipated uses, are tailorable, and require at most a loosely coupled, nonproprietary connection to the Web. Users can invoke capabilities from a command line; programmers can integrate ISFS's core components into more complex systems and services. Taken together, these

  19. VIDAS Listeria species Xpress (LSX).

    PubMed

    Johnson, Ronald; Mills, John

    2013-01-01

    The AOAC GovVal study compared the VIDAS Listeria species Xpress (LSX) to the Health Products and Food Branch MFHPB-30 reference method for detection of Listeria on stainless steel. The LSX method utilizes a novel and proprietary enrichment media, Listeria Xpress broth, enabling detection of Listeria species in environmental samples with the automated VIDAS in a minimum of 26 h. The LSX method also includes the use of the chromogenic media, chromID Ottaviani Agosti Agar (OAA) and chromID Lmono for confirmation of LSX presumptive results. In previous AOAC validation studies comparing VIDAS LSX to the U.S. Food and Drug Administration's Bacteriological Analytical Manual (FDA-BAM) and the U.S. Department of Agriculture-Food Safety and Inspection Service (USDA-FSIS) reference methods, the LSX method was approved as AOAC Official Method 2010.02 for the detection of Listeria species in dairy products, vegetables, seafood, raw meats and poultry, and processed meats and poultry, and as AOAC Performance Tested Method 100501 in a variety of foods and on environmental surfaces. The GovVal comparative study included 20 replicate test portions each at two contamination levels for stainless steel where fractionally positive results (5-15 positive results/20 replicate portions tested) were obtained by at least one method at one level. Five uncontaminated controls were included. In the stainless steel artificially contaminated surface study, there were 25 confirmed positives by the VIDAS LSX assay and 22 confirmed positives by the standard culture methods. Chi-square analysis indicated no statistical differences between the VIDAS LSX method and the MFHPB-30 standard methods at the 5% level of significance. Confirmation of presumptive LSX results with the chromogenic OAA and Lmono media was shown to be equivalent to the appropriate reference method agars. The data in this study demonstrate that the VIDAS LSX method is an acceptable alternative method to the MFHPB-30 standard

  20. Georgia Species at Risk Project

    DTIC Science & Technology

    2009-06-01

    This G2G3S2S3 plant is known on Robins Air Force Base from a wet depressional meadow just to the south of Scout Lake . Habitat for this species...reptile is known from two areas in the headwaters of Lake Walter F. George reservoir on the southwestern end of Fort Benning, on the Alabama side...1.18 Successional shrub/scrub (clearcut) 6927.53 2.29 Unconsolidated shore ( lake /river/pond) 7.34 0.00 Quarry/strip mine/gravel pit 2482.42 0.82

  1. A New Species from Athous (Orthathous) acutangulus Species Group from Turkey

    PubMed Central

    Kabalak, Mahmut; Sert, Osman

    2012-01-01

    A new Elateridae species, Athous (Orthathous) cagatayae n. sp., is presented from Ankara, Turkey. The morphology of the new species is described. Photographs of imago and aedeagus, aedeagi drawings of the new species, and identification key are given. The new species is discussed with species of acutangulus group, with a differential diagnosis. PMID:23448209

  2. Reactive oxygen species in periodontitis

    PubMed Central

    Dahiya, Parveen; Kamal, Reet; Gupta, Rajan; Bhardwaj, Rohit; Chaudhary, Karun; Kaur, Simerpreet

    2013-01-01

    Recent epidemiological studies reveal that more than two-third of the world's population suffers from one of the chronic forms of periodontal disease. The primary etiological agent of this inflammatory disease is a polymicrobial complex, predominantly Gram negative anaerobic or facultative bacteria within the sub-gingival biofilm. These bacterial species initiate the production of various cytokines such as interleukin-8 and TNF-α, further causing an increase in number and activity of polymorphonucleocytes (PMN) along with these cytokines, PMNs also produce reactive oxygen species (ROS) superoxide via the respiratory burst mechanism as the part of the defence response to infection. ROS just like the interleukins have deleterious effects on tissue cells when produced in excess. To counter the harmful effects of ROS, human body has its own defence mechanisms to eliminate them as soon as they are formed. The aim of this review is to focus on the role of different free radicals, ROS, and antioxidants in the pathophysiology of periodontal tissue destruction. PMID:24174716

  3. Two new Pediopsis species and a new Ruandopsis species (Hemiptera: Cicadellidae: Macropsinae) from Madagascar.

    PubMed

    Yang, Liyuan; Dietrich, Christopher H; Zhang, Yalin

    2016-10-04

    Three new species, Pediopsis tripartita, P. subtilis and Ruandopsis elongata spp. nov., from Madagascar are described. These species represent the first records of their respective genera in Madagascar. Images of adults and genitalia of the three species are provided.

  4. 75 FR 29359 - Invasive Species Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-25

    .../coastal environments in the world, with over 50 invasive species that threaten the Bay's vibrant economy... within invasive species efforts, ballast water related issues, and the development of state...

  5. Endangered species toxicity extrapolation using ICE models

    EPA Science Inventory

    The National Research Council’s (NRC) report on assessing pesticide risks to threatened and endangered species (T&E) included the recommendation of using interspecies correlation models (ICE) as an alternative to general safety factors for extrapolating across species. ...

  6. Species pool and dynamics of marine paleocommunities.

    PubMed

    Buzas, M A; Culver, S J

    1994-06-03

    Foraminiferal communities in the Cenozoic shelf deposits of the North American Atlantic Coastal Plain exhibit little unity during almost 55 million years of successive transgressions and regressions. Transgression communities are composed of a dynamic mixture of immigrants and newly evolved species. During regressions, species within these communities either became extinct or emigrated. Some emigrants returned during subsequent transgressions, but many did not. The neritic species of the Atlantic and Gulf continental margins constitute a species pool. Immigrants and emigrants transferred into and out of the species pool, while extinctions and originations repeatedly altered its species composition. While the results indicate a lack of local community unity, at the same time they demonstrate the necessity of a species pool to sustain species diversity.

  7. Assessing Pesticides under the Endangered Species Act

    EPA Pesticide Factsheets

    EPA’s pesticide risk assessment and regulatory processes ensure that protections are in place for all populations of non-target species. We have developed risk assessment procedures to determine potential for harm to individuals of a listed species.

  8. About the Endangered Species Protection Program

    EPA Pesticide Factsheets

    The goal of EPA's Endangered Species Protection Program is to carry out EPA’s FIFRA responsibilities in compliance with the Endangered Species Act, without placing unnecessary burden on agriculture and other pesticide users. Read an overview of the ESPP.

  9. 75 FR 69698 - Invasive Species Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-15

    .... The full ISAC will also consider a white paper entitled, Invasive Species and Climate Change, as drafted by the ISAC Task Team on Climate Change. DATES: Meeting of the Invasive Species Advisory...

  10. Genome size differences in Hyalella cryptic species.

    PubMed

    Vergilino, Roland; Dionne, Kaven; Nozais, Christian; Dufresne, France; Belzile, Claude

    2012-02-01

    The Hyalella azteca (Saussure) complex includes numerous amphipod cryptic species in freshwater habitats in America as revealed by DNA barcoding surveys. Two ecomorphs (small and large) have evolved numerous times in this complex. Few phenotypic criteria have been found to differentiate between the numerous species of this complex. The present study aims to explore genome size differences between some species of the H. azteca complex co-occurring in a Canadian boreal lake using flow cytometry. Nuclear DNA content was estimated for 50 individuals belonging to six COI haplotypes corresponding to four provisional species of the H. azteca complex. Species from the large ecomorph had C-values significantly larger than species from the small ecomorph, whereas slight differences were found among species of the small ecomorph. These differences in genome sizes might be linked to ecological and physiological differences among species of the H. azteca complex.

  11. New enchytraeid species (Enchytraeidae, Oligochaeta) from Korea.

    PubMed

    Dózsa-Farkas, Klára; Felföldi, Tamás; Hong, Yong

    2015-08-21

    We give descriptions of five new enchytraeid species (Enchytraeidae, Oligochaeta) from Korea: Henlea magnaampullacea sp. n., Fridericia sphaerica sp. n., F. cusanicaformis sp. n., F. granulocyta sp. n. and Mesenchytraeus calyx sp. n., with morphological and molecular (mitochondrial cytochrome c oxidase subunit I, nuclear histone 3 genes and nuclear ribosomal ITS region sequences) data. In total, 19 enchytraeid species belonging to seven genera have been found in the studied woodland and agronomical soil samples. Apart from the five new species, three further species are new for the Korean enchytraeid fauna, Enchytraeus christenseni, E. dichaetus, and Achaeta cf. brevivasa. Molecular taxonomical analyses show that the Korean species resembling H. ventriculosa is not identical with the European species, furthermore sequence analysis of individuals morphologically identified as F. seoraksani indicate the possibility of species-complexity and the presence of cryptic species.

  12. The systematic relevance of conidiogenesis modes in the gilled Agaricales.

    PubMed

    Walther, Grit; Garnica, Sigisfredo; Weiss, Michael

    2005-05-01

    Dikaryotic and haploid mycelia of more than 150 gilled species of euagarics were studied morphologically and by molecular phylogenetic methods. The morphological investigations revealed anamorphs in more than 90 species that were often specific at the genus or family level. Thallic conidiogenesis dominated and varied from fragmentation of normally branched hyphae to the formation of differentiated sympodially branched conidiophores. Secession modes, coiling of the conidiogenous hyphae or the swelling of the conidia were additional distinguishing features. Phylogenetic analysis of the D1-D3 domains of the nuclear gene for the ribosomal large subunit using a Bayesian Markov chain Monte Carlo approach resulted in several well-supported groups that are consistent with anamorph morphology. These results indicate that the anamorphs provide valuable characters for a natural classification of the Agaricales.

  13. Mycosphaerella is polyphyletic

    PubMed Central

    Crous, P.W.; Braun, U.; Groenewald, J.Z.

    2007-01-01

    Mycosphaerella, one of the largest genera of ascomycetes, encompasses several thousand species and has anamorphs residing in more than 30 form genera. Although previous phylogenetic studies based on the ITS rDNA locus supported the monophyly of the genus, DNA sequence data derived from the LSU gene distinguish several clades and families in what has hitherto been considered to represent the Mycosphaerellaceae. Several important leaf spotting and extremotolerant species need to be disposed to the genus Teratosphaeria, for which a new family, the Teratosphaeriaceae, is introduced. Other distinct clades represent the Schizothyriaceae, Davidiellaceae, Capnodiaceae, and the Mycosphaerellaceae. Within the two major clades, namely Teratosphaeriaceae and Mycosphaerellaceae, most anamorph genera are polyphyletic, and new anamorph concepts need to be derived to cope with dual nomenclature within the Mycosphaerella complex. PMID:18490994

  14. Council Coordination of Federal Invasive Species Efforts

    DTIC Science & Technology

    2004-08-01

    Chris Dionigi, Assistant Director, Domestic Policy National Invasive Species Council Coordination of Federal Invasive Species Efforts Report...REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE CouncilCoordination of Federal Invasive Species Efforts 5a. CONTRACT NUMBER 5b...ADDRESS(ES) National Invasive Species Council (NISC) 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS

  15. NOAA Lists 20 Coral Species as Threatened

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2014-09-01

    Twenty coral species have been listed as threatened under the U.S. Endangered Species Act (ESA), the National Oceanic and Atmospheric Administration (NOAA) announced on 27 August. This is NOAA's largest ESA rule making. The coral species include 15 found in the Indo-Pacific region and 5 that are located in the Caribbean. They join two other Caribbean coral species that NOAA listed as threatened in 2006.

  16. Eight new species in the genus Alphabaculovirus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This taxonomic proposal recommends the addition of eight new species to the genus Alphabaculovirus of the family Baculoviridae. Placement of these new species within genus Alphabaculovirus is based on the following criteria: host species of the insect order Lepidoptera; circular double-stranded DNA...

  17. Discovery of a novel species of Bordetella

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bordetella species are Gram-negative coccobacilli. There are currently nine described species that constitute the genus Bordetella. Historically, this genus is subdivided into two groups of species: the “classical” and “non-classical” Bordetella. The classical Bordetella are the most studied group r...

  18. 78 FR 70317 - Invasive Species Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-25

    ... Office of the Secretary Invasive Species Advisory Committee AGENCY: Office of the Secretary, Interior. ACTION: Notice of Public Meeting (via Teleconference) of the Invasive Species Advisory Committee. SUMMARY... Invasive Species Advisory Committee. The purpose of the Advisory Committee is to provide advice to...

  19. 78 FR 11899 - Invasive Species Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-20

    ... Office of the Secretary Invasive Species Advisory Committee AGENCY: Office of the Secretary, Interior... Invasive Species Advisory Committee. The document contained incorrect dates. This document corrects those.... Meeting of the Invasive Species Advisory Committee (OPEN): Thursday, March 7, 2013 through Friday, March...

  20. 76 FR 68776 - Invasive Species Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-07

    ...] [FR Doc No: 2011-28743] DEPARTMENT OF THE INTERIOR Office of the Secretary Invasive Species Advisory..., notice is hereby given of meetings of the Invasive Species Advisory Committee (ISAC). Comprised of 29 nonfederal invasive species experts and stakeholders from across the nation, the purpose of the...

  1. 22 CFR 216.5 - Endangered species.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 22 Foreign Relations 1 2013-04-01 2013-04-01 false Endangered species. 216.5 Section 216.5 Foreign Relations AGENCY FOR INTERNATIONAL DEVELOPMENT ENVIRONMENTAL PROCEDURES § 216.5 Endangered species. It is A... endangered or threatened species and their critical habitats. The Initial Environmental Examination for...

  2. 22 CFR 216.5 - Endangered species.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 22 Foreign Relations 1 2014-04-01 2014-04-01 false Endangered species. 216.5 Section 216.5 Foreign Relations AGENCY FOR INTERNATIONAL DEVELOPMENT ENVIRONMENTAL PROCEDURES § 216.5 Endangered species. It is A... endangered or threatened species and their critical habitats. The Initial Environmental Examination for...

  3. 3 CFR - The Endangered Species Act

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 3 The President 1 2010-01-01 2010-01-01 false The Endangered Species Act Presidential Documents Other Presidential Documents Memorandum of March 3, 2009 The Endangered Species Act Memorandum for the Heads of Executive Departments and Agencies The Endangered Species Act (ESA), 16 U.S.C. 1531 et...

  4. 22 CFR 216.5 - Endangered species.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 22 Foreign Relations 1 2012-04-01 2012-04-01 false Endangered species. 216.5 Section 216.5 Foreign Relations AGENCY FOR INTERNATIONAL DEVELOPMENT ENVIRONMENTAL PROCEDURES § 216.5 Endangered species. It is A... endangered or threatened species and their critical habitats. The Initial Environmental Examination for...

  5. 22 CFR 216.5 - Endangered species.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 22 Foreign Relations 1 2011-04-01 2011-04-01 false Endangered species. 216.5 Section 216.5 Foreign Relations AGENCY FOR INTERNATIONAL DEVELOPMENT ENVIRONMENTAL PROCEDURES § 216.5 Endangered species. It is A... endangered or threatened species and their critical habitats. The Initial Environmental Examination for...

  6. 22 CFR 216.5 - Endangered species.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Endangered species. 216.5 Section 216.5 Foreign Relations AGENCY FOR INTERNATIONAL DEVELOPMENT ENVIRONMENTAL PROCEDURES § 216.5 Endangered species. It is A... endangered or threatened species and their critical habitats. The Initial Environmental Examination for...

  7. Multiplex PCR for four Sclerotinia species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sclerotinia homeocarpa, S. minor, S. sclerotiorum, and S. trifoliorum are common species within the genus Sclerotinia, where the morphological identification is challenging, especially when one crop hosts multiple species. The objective of this study was to design species specific primers compatibl...

  8. Endangered Species & Biodiversity: A Classroom Project & Theme

    ERIC Educational Resources Information Center

    Lauro, Brook

    2012-01-01

    Students discover the factors contributing to species losses worldwide by conducting a project about endangered species as a component of a larger classroom theme of biodiversity. Groups conduct research using online endangered- species databases and present results to the class using PowerPoint. Students will improve computer research abilities…

  9. Distinguishing Glyceria Species of Western North America

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There are seven North American and three introduced European Glyceria species growing in western North America, yet distinguihsing among the species is challenging. As contaminants in annual ryegrass grass seed lots, the introduced species G. declinata and G. fluitans are undesirable domestically, ...

  10. Biology, speciation, and utilization of peanut species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Arachis has a large number of highly diverse species. Large collections of cultivated peanut exist at multiple locations and several hundreds of wild species are maintained in germplasm banks. Many of the species have been characterized for agronomic traits, but much of the germplasm colle...

  11. Developmental shifts and species selection in gastropods

    PubMed Central

    Duda, Thomas F.; Palumbi, Stephen R.

    1999-01-01

    The fossil record of marine gastropods has been used as evidence to support the operation of species selection; namely, that species with limited dispersal differentially increase in numbers because they are more likely to speciate than widely dispersing species. This conclusion is based on a tacit phylogenetic assumption that increases in species with limited dispersal are solely the result of speciation within monophyletic groups with low dispersal. To test this assumption, we reconstructed a phylogeny from nuclear sequence data for 70 species of the marine gastropod genus Conus and used it to map the evolution of developmental mode. All eight species without planktonic life history phases recently and independently evolved this characteristic from ancestors with planktonic larval phases, showing that transitions in developmental mode are common in this group. A simple model of species diversification shows that such shifts can control the relative numbers of species with and without dispersing larval stages, leading to apparent species selection. Such results challenge the conclusion that increases in the number of nonplanktonic species relative to species with planktonic larvae over geologic time is necessarily a result of higher rates of speciation of nonplanktonic lineages and show that demonstration of species selection requires a phylogenetic framework. PMID:10468598

  12. Satellite tracking of threatened species

    USGS Publications Warehouse

    Williams, M.; Lunsford, A.; Ellis, D.; Robinson, J.; Coronado, P.; Campbell, W.

    1998-01-01

    In 1990, a joint effort of two U.S. federal agencies, NASA Goddard Space Flight Center (GSFC) and the Patuxent Wildlife Research Center, began. We initially joined forces in a project that used satellite telemetry to discover the winter home of a tiny dwindling population of Siberian Cranes. Since then several projects have emerged, and a web site was created to follow some of these activities. This web site is called the Satellite Tracking of Threatened Species and its location is http://sdcd.gsfc.nasa.gov/ISTO/satellite_tracking. It describes the overall program, and links you to three subsections that describe the projects in more detail: Satellite Direct Readout, Birdtracks, and Birdworld.

  13. Multilocus species delimitation in the Crotalus triseriatus species group (Serpentes: Viperidae: Crotalinae), with the description of two new species.

    PubMed

    Bryson, Robert W; Linkem, Charles W; Dorcas, Michael E; Lathrop, Amy; Jones, Jason M; Alvarado-Díaz, Javier; Grünwald, Christoph I; Murphy, Robert W

    2014-07-01

    Members of the Crotalus triseriatus species group of montane rattlesnakes are widely distributed across the highlands of Mexico and southwestern USA. Although five species are currently recognized within the group, species limits remain to be tested. Genetic studies suggest that species may be paraphyletic and that at least one cryptic species may be present. We generate 3,346 base pairs of DNA sequence data from seven nuclear loci to test competing models of species delimitation in the C. triseriatus group using Bayes factor delimitation. We also examine museum specimens from the Trans-Mexican Volcanic Belt for evidence of cryptic species. We find strong support for a nine-species model and genetic and morphological evidence for recognizing two new species within the group, which we formally describe here. Our results suggest that the current taxonomy of the C. triseriatus species group does not reflect evolutionary history. We suggest several conservative taxonomic changes to the group, but future studies are needed to better clarify relationships among species and examine genetic patterns and structure within wide-ranging lineages.

  14. Reconsideration of Protocrea (Hypocreales, Hypocreaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Protocrea is re-defined, based on holotype and fresh specimens of its type species P. farinosa, using morphology of teleomorph and anamorph and phylogenetic analyses of rpb2 sequences. Data based on currently available specimens suggest the existence of six species. Apart from the type, P....

  15. Glucosylation and other biotransformations of T-2 toxin by yeasts of the Trichomonascus clade

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Twenty-five yeasts assigned to the Trichomonascus clade (Saccharomycotina, Ascomycota), including three Trichomonascus species and 22 anamorphic species presently classified in Blastobotrys, were tested for their ability to convert T-2 toxin, a Fusarium trichothecene mycotoxin, to less toxic product...

  16. 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

  17. Core-satellite species hypothesis and native versus exotic species in secondary succession

    USGS Publications Warehouse

    Martinez, Kelsey A.; Gibson, David J.; Middleton, Beth A.

    2015-01-01

    A number of hypotheses exist to explain species’ distributions in a landscape, but these hypotheses are not frequently utilized to explain the differences in native and exotic species distributions. The core-satellite species (CSS) hypothesis predicts species occupancy will be bimodally distributed, i.e., many species will be common and many species will be rare, but does not explicitly consider exotic species distributions. The parallel dynamics (PD) hypothesis predicts that regional occurrence patterns of exotic species will be similar to native species. Together, the CSS and PD hypotheses may increase our understanding of exotic species’ distribution relative to natives. We selected an old field undergoing secondary succession to study the CSS and PD hypotheses in conjunction with each other. The ratio of exotic to native species (richness and abundance) was observed through 17 years of secondary succession. We predicted species would be bimodally distributed and that exotic:native species ratios would remain steady or decrease through time under frequent disturbance. In contrast to the CSS and PD hypotheses, native species occupancies were not bimodally distributed at the site, but exotic species were. The exotic:native species ratios for both richness (E:Nrichness) and abundance (E:Ncover) generally decreased or remained constant throughout supporting the PD hypothesis. Our results suggest exotic species exhibit metapopulation structure in old field landscapes, but that metapopulation structures of native species are disrupted, perhaps because these species are dispersal limited in the fragmented landscape.

  18. Ecological impacts of non-native species

    USGS Publications Warehouse

    Wilkinson, John W.

    2012-01-01

    Non-native species are considered one of the greatest threats to freshwater biodiversity worldwide (Drake et al. 1989; Allen and Flecker 1993; Dudgeon et al. 2005). Some of the first hypotheses proposed to explain global patterns of amphibian declines included the effects of non-native species (Barinaga 1990; Blaustein and Wake 1990; Wake and Morowitz 1991). Evidence for the impact of non-native species on amphibians stems (1) from correlative research that relates the distribution or abundance of a species to that of a putative non-native species, and (2) from experimental tests of the effects of a non-native species on survival, growth, development or behaviour of a target species (Kats and Ferrer 2003). Over the past two decades, research on the effects of non-native species on amphibians has mostly focused on introduced aquatic predators, particularly fish. Recent research has shifted to more complex ecological relationships such as influences of sub-lethal stressors (e.g. contaminants) on the effects of non-native species (Linder et al. 2003; Sih et al. 2004), non-native species as vectors of disease (Daszak et al. 2004; Garner et al. 2006), hybridization between non-natives and native congeners (Riley et al. 2003; Storfer et al. 2004), and the alteration of food-webs by non-native species (Nystrom et al. 2001). Other research has examined the interaction of non-native species in terms of facilitation (i.e. one non-native enabling another to become established or spread) or the synergistic effects of multiple non-native species on native amphibians, the so-called invasional meltdown hypothesis (Simerloff and Von Holle 1999). Although there is evidence that some non-native species may interact (Ricciardi 2001), there has yet to be convincing evidence that such interactions have led to an accelerated increase in the number of non-native species and cumulative impacts are still uncertain (Simberloff 2006). Applied research on the control, eradication, and

  19. Dynamics and topology of species networks

    NASA Astrophysics Data System (ADS)

    Bastolla, Ugo; Laessig, Michael; Manrubia, Susanna C.; Valleriani, Angelo

    We study communities formed by a large number of species, which are an example of dynamical networks in biology. Interactions between species, such as prey-predator relationships and mutual competition, define the links of these networks. They also govern the dynamics of their population sizes. This dynamics acts as a selection mechanism, which can lead to the extinction of species. Adaptive changes of the interactions or the generation of new species involve random mutations as well as selection. We show how this dynamics determines key topological characteristics of species networks. The results are in agreement with observations.

  20. The nuclear question: rethinking species importance in multi-species animal groups.

    PubMed

    Srinivasan, Umesh; Raza, Rashid Hasnain; Quader, Suhel

    2010-09-01

    1. Animals group for various benefits, and may form either simple single-species groups, or more complex multi-species associations. Multi-species groups are thought to provide anti-predator and foraging benefits to participant individuals. 2. Despite detailed studies on multi-species animal groups, the importance of species in group initiation and maintenance is still rated qualitatively as 'nuclear' (maintaining groups) or 'attendant' (species following nuclear species) based on species-specific traits. This overly simplifies and limits understanding of inherently complex associations, and is biologically unrealistic, because species roles in multi-species groups are: (i) likely to be context-specific and not simply a fixed species property, and (ii) much more variable than this dichotomy indicates. 3. We propose a new view of species importance (measured as number of inter-species associations), along a continuum from 'most nuclear' to 'least nuclear'. Using mixed-species bird flocks from a tropical rainforest in India as an example, we derive inter-species association measures from randomizations on bird species abundance data (which takes into account species 'availability') and data on 86 mixed-species flocks from two different flock types. Our results show that the number and average strength of inter-species associations covary positively, and we argue that species with many, strong associations are the most nuclear. 4. From our data, group size and foraging method are ecological and behavioural traits of species that best explain nuclearity in mixed-species bird flocks. Parallels have been observed in multi-species fish shoals, in which group size and foraging method, as well as diet, have been shown to correlate with nuclearity. Further, the context in which multi-species groups occur, in conjunction with species-specific traits, influences the role played by a species in a multi-species group, and this highlights the importance of extrinsic factors in

  1. Multispecies coalescent delimits structure, not species.

    PubMed

    Sukumaran, Jeet; Knowles, L Lacey

    2017-02-14

    The multispecies coalescent model underlies many approaches used for species delimitation. In previous work assessing the performance of species delimitation under this model, speciation was treated as an instantaneous event rather than as an extended process involving distinct phases of speciation initiation (structuring) and completion. Here, we use data under simulations that explicitly model speciation as an extended process rather than an instantaneous event and carry out species delimitation inference on these data under the multispecies coalescent. We show that the multispecies coalescent diagnoses genetic structure, not species, and that it does not statistically distinguish structure associated with population isolation vs. species boundaries. Because of the misidentification of population structure as putative species, our work raises questions about the practice of genome-based species discovery, with cascading consequences in other fields. Specifically, all fields that rely on species as units of analysis, from conservation biology to studies of macroevolutionary dynamics, will be impacted by inflated estimates of the number of species, especially as genomic resources provide unprecedented power for detecting increasingly finer-scaled genetic structure under the multispecies coalescent. As such, our work also represents a general call for systematic study to reconsider a reliance on genomic data alone. Until new methods are developed that can discriminate between structure due to population-level processes and that due to species boundaries, genomic-based results should only be considered a hypothesis that requires validation of delimited species with multiple data types, such as phenotypic and ecological information.

  2. Locally rare species influence grassland ecosystem multifunctionality.

    PubMed

    Soliveres, Santiago; Manning, Peter; Prati, Daniel; Gossner, Martin M; Alt, Fabian; Arndt, Hartmut; Baumgartner, Vanessa; Binkenstein, Julia; Birkhofer, Klaus; Blaser, Stefan; Blüthgen, Nico; Boch, Steffen; Böhm, Stefan; Börschig, Carmen; Buscot, Francois; Diekötter, Tim; Heinze, Johannes; Hölzel, Norbert; Jung, Kirsten; Klaus, Valentin H; Klein, Alexandra-Maria; Kleinebecker, Till; Klemmer, Sandra; Krauss, Jochen; Lange, Markus; Morris, E Kathryn; Müller, Jörg; Oelmann, Yvonne; Overmann, Jörg; Pašalić, Esther; Renner, Swen C; Rillig, Matthias C; Schaefer, H Martin; Schloter, Michael; Schmitt, Barbara; Schöning, Ingo; Schrumpf, Marion; Sikorski, Johannes; Socher, Stephanie A; Solly, Emily F; Sonnemann, Ilja; Sorkau, Elisabeth; Steckel, Juliane; Steffan-Dewenter, Ingolf; Stempfhuber, Barbara; Tschapka, Marco; Türke, Manfred; Venter, Paul; Weiner, Christiane N; Weisser, Wolfgang W; Werner, Michael; Westphal, Catrin; Wilcke, Wolfgang; Wolters, Volkmar; Wubet, Tesfaye; Wurst, Susanne; Fischer, Markus; Allan, Eric

    2016-05-19

    Species diversity promotes the delivery of multiple ecosystem functions (multifunctionality). However, the relative functional importance of rare and common species in driving the biodiversity-multifunctionality relationship remains unknown. We studied the relationship between the diversity of rare and common species (according to their local abundances and across nine different trophic groups), and multifunctionality indices derived from 14 ecosystem functions on 150 grasslands across a land-use intensity (LUI) gradient. The diversity of above- and below-ground rare species had opposite effects, with rare above-ground species being associated with high levels of multifunctionality, probably because their effects on different functions did not trade off against each other. Conversely, common species were only related to average, not high, levels of multifunctionality, and their functional effects declined with LUI. Apart from the community-level effects of diversity, we found significant positive associations between the abundance of individual species and multifunctionality in 6% of the species tested. Species-specific functional effects were best predicted by their response to LUI: species that declined in abundance with land use intensification were those associated with higher levels of multifunctionality. Our results highlight the importance of rare species for ecosystem multifunctionality and help guiding future conservation priorities.

  3. Petal anatomy of four Justicia (Acanthaceae) species

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    Comparative anatomical study on flower petals was studied in four selected Justicia species from Peninsular Malaysia, i.e. J. comata (L.) Lam., J. carnea Lindl. J. betonica Linn. and J. procumbens L with the objective to provide useful data for species identification and differentiation within the genus of Justicia. Methods used in this study are mechanical scrapping on the leaf surfaces and observation under light microscope. Finding in this study has shown that all species are sharing similar type of anticlinal walls pattern, which is sinuous pattern. Two or more type of trichomes is present in all species studied and this character can be used to differentiate Justicia species. Simple multicellular trichomes are found to be present in all species studied. Justicia betonica can be isolated from other species by the existence of cyclo-paracytic stomata on the petal surfaces.

  4. Genomic definition of species. Revision 1

    SciTech Connect

    Crkvenjakov, R.; Dramanac, R.

    1992-06-01

    A genome is the sum total of the DNA sequences in the cells of an individual organism. The common usage that species possess genomes comes naturally to biochemists, who have shown that all protein and nucleic acid molecules are at the same time species and individual-specific, with minor individual variations being superimposed on a consensus sequence that is constant for a species. By extension, this property is attributed to the common features of DNA in the chromosomes of members of a given species and is called (species) genome. The definition of species based on chromosomes, genes, or genome common to its member organisms has been implied or mentioned in passing numerous times. Some population biologists think that members of species have similar ``homeostatic genotypes,`` which are to a degree resistant to mutation or environmental change in the production of a basic phenotype.

  5. Microbial species delineation using whole genome sequences

    SciTech Connect

    Kyrpides, Nikos; Mukherjee, Supratim; Ivanova, Natalia; Mavrommatics, Kostas; Pati, Amrita; Konstantinidis, Konstantinos

    2014-10-20

    Species assignments in prokaryotes use a manual, poly-phasic approach utilizing both phenotypic traits and sequence information of phylogenetic marker genes. With thousands of genomes being sequenced every year, an automated, uniform and scalable approach exploiting the rich genomic information in whole genome sequences is desired, at least for the initial assignment of species to an organism. We have evaluated pairwise genome-wide Average Nucleotide Identity (gANI) values and alignment fractions (AFs) for nearly 13,000 genomes using our fast implementation of the computation, identifying robust and widely applicable hard cut-offs for species assignments based on AF and gANI. Using these cutoffs, we generated stable species-level clusters of organisms, which enabled the identification of several species mis-assignments and facilitated the assignment of species for organisms without species definitions.

  6. Genomic definition of species. Revision 2

    SciTech Connect

    Crkvenjakov, R.; Drmanac, R.

    1993-03-01

    A genome is the sum total of the DNA sequences in the cells of an individual organism. The common usage that species possess genomes comes naturally to biochemists, who have shown that all protein and nucleic acid molecules are at the same time species- and individual-specific, with minor individual variations being superimposed on a consensus sequence that is constant for a species. By extension, this property is attributed to the common features of DNA in the chromosomes of members of a given species and is called species genome. Our proposal for the definition of a biological species is as follows: A species comprises a group of actual and potential biological organisms built according to a unique genome program that is recorded, and at least in part expressed, in the structures of their genomic nucleic acid molecule(s), having intragroup sequence differences which can be fully interconverted in the process of organismal reproduction.

  7. STRAW: Species TRee Analysis Web server

    PubMed Central

    Shaw, Timothy I.; Ruan, Zheng; Glenn, Travis C.; Liu, Liang

    2013-01-01

    The coalescent methods for species tree reconstruction are increasingly popular because they can accommodate coalescence and multilocus data sets. Herein, we present STRAW, a web server that offers workflows for reconstruction of phylogenies of species using three species tree methods—MP-EST, STAR and NJst. The input data are a collection of rooted gene trees (for STAR and MP-EST methods) or unrooted gene trees (for NJst). The output includes the estimated species tree, modified Robinson-Foulds distances between gene trees and the estimated species tree and visualization of trees to compare gene trees with the estimated species tree. The web sever is available at http://bioinformatics.publichealth.uga.edu/SpeciesTreeAnalysis/. PMID:23661681

  8. Assemblage and diversity of fungi on wood and seaweed litter of seven northwest portuguese beaches.

    PubMed

    Sridhar, K R; Karamchand, K S; Pascoal, C; Cássio, F

    2012-01-01

    Three hundred and fifty woody litter and one hundred and forty seaweed litter sampled from seven beaches of Northwest Portugal were assessed for the filamentous fungal assemblage and diversity. The woody litter was screened for fungi up to 42 months using damp chamber incubation. They consisted of 36 taxa (ascomycetes, 21; basidiomycetes, 3; anamorphic taxa, 12) comprising 10 core group taxa (≥10%) (ascomycetes, 8; basidiomycete, 1; anamorphic taxa, 1). The total fungal isolates ranged between 150 and 243, while the number of fungal taxa per wood ranged between 3 and 4.9. The seaweed litter was screened up to four months in damp chamber incubation. They encompassed 29 taxa (ascomycetes, 16; basidiomycetes, 2; anamorphic taxa, 11) comprising 15 core group taxa (ascomycetes, 9; basidiomycete, 1; anamorphic taxa, 5). Total fungal isolates ranged between 56 and 120, while the number of fungal taxa per seaweed segment ranged between 4.8 and 6.3. Fifteen taxa of ascomycetes, two of basidiomycetes, and four anamorphic taxa were common to wood and seaweed litter. On both the substrates, two arenicolous fungi Arenariomyces trifurcates and Corollospora maritima were the predominant fungi (72.6-85.9%). The species abundance curves showed higher frequency of occurrence of fungal taxa in seaweed than woody litter. Our study revealed rich assemblage and diversity of marine fungi on wood and seaweed litter of Northwest Portugal beaches. The fungal composition and diversity of this survey have been compared with earlier investigations on marine fungi of Portugal coast.

  9. Effect of species pool size on species occurrence frequencies: Musical chairs on islands

    PubMed Central

    Diamond, Jared

    1982-01-01

    If species interactions affect species distributions, then species occurrence frequencies (νi), defined as the fraction of an archipelago's islands that species i inhabits, should vary with species pool size. A “natural experiment” approximating this test is provided by the Bismarck, Solomon, and New Hebrides archipelagoes, whose bird species pools decrease in that order, the species of each archipelago being mostly a subset of those of the next richer archipelago. The average ν for an archipelago's species decreases with archipelago pool size. In the archipelago with the largest pool, most species are on few islands and few species are on most islands, whereas the reverse is true in the archipelago with the smallest pool. For species shared between two or more archipelagoes, νi decreases with pool size or number of species in the same guild. These interarchipelagal differences in νi or average ν reflect differences in level of interspecific competition, which reduces νs in species-rich archipelagoes in two ways: usually, by reducing a species' incidence on small islands and restricting the species to larger islands; less often (for so-called supertramps), by restricting a species to small islands. PMID:16578762

  10. Two new species of the Stenochinus amplus species-group from China (Coleoptera, Tenebrionidae, Stenochiini)

    PubMed Central

    Yuan, Cai-Xia; Ren, Guo-Dong

    2014-01-01

    Abstract Two new species of the Stenochinus amplus species-group are described, S. apiciconcavus sp. n. (CHINA: Shaanxi) and S. xinyicus sp. n. (CHINA: Guangdong). Also, some new distribution data are provided for S. cylindricus (Gebien, 1914), and a key to the seven species of the S. amplus species-group from China is given. PMID:25061347

  11. Bacillus cereus and related species.

    PubMed Central

    Drobniewski, F A

    1993-01-01

    Bacillus cereus is a gram-positive aerobic or facultatively anaerobic spore-forming rod. It is a cause of food poisoning, which is frequently associated with the consumption of rice-based dishes. The organism produces an emetic or diarrheal syndrome induced by an emetic toxin and enterotoxin, respectively. Other toxins are produced during growth, including phospholipases, proteases, and hemolysins, one of which, cereolysin, is a thiol-activated hemolysin. These toxins may contribute to the pathogenicity of B. cereus in nongastrointestinal disease. B. cereus isolated from clinical material other than feces or vomitus was commonly dismissed as a contaminant, but increasingly it is being recognized as a species with pathogenic potential. It is now recognized as an infrequent cause of serious nongastrointestinal infection, particularly in drug addicts, the immunosuppressed, neonates, and postsurgical patients, especially when prosthetic implants such as ventricular shunts are inserted. Ocular infections are the commonest types of severe infection, including endophthalmitis, panophthalmitis, and keratitis, usually with the characteristic formation of corneal ring abscesses. Even with prompt surgical and antimicrobial agent treatment, enucleation of the eye and blindness are common sequelae. Septicemia, meningitis, endocarditis, osteomyelitis, and surgical and traumatic wound infections are other manifestations of severe disease. B. cereus produces beta-lactamases, unlike Bacillus anthracis, and so is resistant to beta-lactam antibiotics; it is usually susceptible to treatment with clindamycin, vancomycin, gentamicin, chloramphenicol, and erythromycin. Simultaneous therapy via multiple routes may be required. PMID:8269390

  12. Antiviral effects of Glycyrrhiza species.

    PubMed

    Fiore, Cristina; Eisenhut, Michael; Krausse, Rea; Ragazzi, Eugenio; Pellati, Donatella; Armanini, Decio; Bielenberg, Jens

    2008-02-01

    Historical sources for the use of Glycyrrhiza species include ancient manuscripts from China, India and Greece. They all mention its use for symptoms of viral respiratory tract infections and hepatitis. Randomized controlled trials confirmed that the Glycyrrhiza glabra derived compound glycyrrhizin and its derivatives reduced hepatocellular damage in chronic hepatitis B and C. In hepatitis C virus-induced cirrhosis the risk of hepatocellular carcinoma was reduced. Animal studies demonstrated a reduction of mortality and viral activity in herpes simplex virus encephalitis and influenza A virus pneumonia. In vitro studies revealed antiviral activity against HIV-1, SARS related coronavirus, respiratory syncytial virus, arboviruses, vaccinia virus and vesicular stomatitis virus. Mechanisms for antiviral activity of Glycyrrhiza spp. include reduced transport to the membrane and sialylation of hepatitis B virus surface antigen, reduction of membrane fluidity leading to inhibition of fusion of the viral membrane of HIV-1 with the cell, induction of interferon gamma in T-cells, inhibition of phosphorylating enzymes in vesicular stomatitis virus infection and reduction of viral latency. Future research needs to explore the potency of compounds derived from licorice in prevention and treatment of influenza A virus pneumonia and as an adjuvant treatment in patients infected with HIV resistant to antiretroviral drugs.

  13. Malassezia species and seborrheic dermatitis.

    PubMed

    Zisova, Lilia G

    2009-01-01

    Malassezia spp. are medically important dimorphic, lipophilic yeasts that form part of the normal cutaneous microflora of human. Seborrheic dermatitis is a multifactor disease that needs endogenous and exogenous predisposing factors for its development. Presence of these factors leads to reproduction of the saprophytic opportunistic pathogen Malassezia spp. and development of a disease. The inflammatory reaction against the yeast Malassezia is considered basic in the etiology of the seborrheic dermatitis. The pathogenesis and exact mechanisms via which these yeasts cause inflammation are still not fully elucidated. They are rather complex and subject of controversy in literature. Most probably Malassezia spp. cause seborrheic dermatitis by involving and combining both nonummune and immune mechanisms (nonspecific and specific). Which of these mechanisms will dominate in any single case depends on the number and virulence of the yeasts as well as on the microorganism reactivity. In the recent years a great interest have been aroused by the epidemiological investigations. Depending on the geographical place of the countries different Malassezia species in seborrheic dermatitis dominate in the different countries. In view of the etiology and pathogenesis of the seborrheic dermatitis comprehensive antifungal preparations have been recently introduced and are nowadays the basic therapeutic resource in the treatment of this disease.

  14. Antibiotic resistance in Burkholderia species.

    PubMed

    Rhodes, Katherine A; Schweizer, Herbert P

    2016-09-01

    The genus Burkholderia comprises metabolically diverse and adaptable Gram-negative bacteria, which thrive in often adversarial environments. A few members of the genus are prominent opportunistic pathogens. These include Burkholderia mallei and Burkholderia pseudomallei of the B. pseudomallei complex, which cause glanders and melioidosis, respectively. Burkholderia cenocepacia, Burkholderia multivorans, and Burkholderia vietnamiensis belong to the Burkholderia cepacia complex and affect mostly cystic fibrosis patients. Infections caused by these bacteria are difficult to treat because of significant antibiotic resistance. The first line of defense against antimicrobials in Burkholderia species is the outer membrane penetration barrier. Most Burkholderia contain a modified lipopolysaccharide that causes intrinsic polymyxin resistance. Contributing to reduced drug penetration are restrictive porin proteins. Efflux pumps of the resistance nodulation cell division family are major players in Burkholderia multidrug resistance. Third and fourth generation β-lactam antibiotics are seminal for treatment of Burkholderia infections, but therapeutic efficacy is compromised by expression of several β-lactamases and ceftazidime target mutations. Altered DNA gyrase and dihydrofolate reductase targets cause fluoroquinolone and trimethoprim resistance, respectively. Although antibiotic resistance hampers therapy of Burkholderia infections, the characterization of resistance mechanisms lags behind other non-enteric Gram-negative pathogens, especially ESKAPE bacteria such as Acinetobacter baumannii, Klebsiella pneumoniae and Pseudomonas aeruginosa.

  15. Bacillus cereus and related species.

    PubMed

    Drobniewski, F A

    1993-10-01

    Bacillus cereus is a gram-positive aerobic or facultatively anaerobic spore-forming rod. It is a cause of food poisoning, which is frequently associated with the consumption of rice-based dishes. The organism produces an emetic or diarrheal syndrome induced by an emetic toxin and enterotoxin, respectively. Other toxins are produced during growth, including phospholipases, proteases, and hemolysins, one of which, cereolysin, is a thiol-activated hemolysin. These toxins may contribute to the pathogenicity of B. cereus in nongastrointestinal disease. B. cereus isolated from clinical material other than feces or vomitus was commonly dismissed as a contaminant, but increasingly it is being recognized as a species with pathogenic potential. It is now recognized as an infrequent cause of serious nongastrointestinal infection, particularly in drug addicts, the immunosuppressed, neonates, and postsurgical patients, especially when prosthetic implants such as ventricular shunts are inserted. Ocular infections are the commonest types of severe infection, including endophthalmitis, panophthalmitis, and keratitis, usually with the characteristic formation of corneal ring abscesses. Even with prompt surgical and antimicrobial agent treatment, enucleation of the eye and blindness are common sequelae. Septicemia, meningitis, endocarditis, osteomyelitis, and surgical and traumatic wound infections are other manifestations of severe disease. B. cereus produces beta-lactamases, unlike Bacillus anthracis, and so is resistant to beta-lactam antibiotics; it is usually susceptible to treatment with clindamycin, vancomycin, gentamicin, chloramphenicol, and erythromycin. Simultaneous therapy via multiple routes may be required.

  16. [Pharmacognosy study of Verbascum species].

    PubMed

    Török, Tamás; Varga, Erzsébet

    2015-01-01

    The mullein (Verbascum phlomoides L., V thapsus L., V. thapsiforme Schrad., V. speciosum L.) is a medicinal herb known and used for a long time, especially in traditional Turkish medicine. The aims of our study were to identify the species and study the plant's major active substances both qualitatively and quantitatively, comparing it to data found in scientific literature. The plants were identified as probable hybrids of V. phlomoides and V. thapsiforme. Microscopic analysis of the flowers showed no major difference between the specimens. The diameter of both stomata and pollen we observed was around 15-20 μm. Important flavonoids like rutin and quercetin were identified. Dosage resulted in a 0.135% total flavonoid aglycone content. (expressed as hypericin) and a 1.3% total flavonoid glycoside content (expressed as rutoside). Thin layer chromatography from saponines revealed two spots. A hemolytic index of 13095 was also determined. Repeating the dosage experiment a year later resulted in significantly lower flavonoid aglycone and glycoside content (0.006% and 0.95% respectively) as well as a hemolytic index of approximately 4000.

  17. Proctolaelaps species (Acari: Mesostigmata: Melicharidae) from Egypt, with description of a new species and complementary descriptions of other five species.

    PubMed

    Abo-Shnaf, Reham I A; Moraes, Gilberto J De

    2016-09-12

    The objective of this paper is to provide a taxonomic appraisal of the melicharids from Egypt, based on specimens previously collected by different authors and on specimens newly collected by the first author of this paper, all belonging to the genus Proctolaelaps Berlese. A new species, Proctolaelaps gizaensis n. sp., is described, thus raising to six the number of Proctolaelaps species recorded from Egypt. Complementary descriptions of the following species are also provided: Proctolaelaps aegyptiacus Nasr, 1986; Proctolaelaps holoventris Moraes, Britto, Mineiro & Halliday, 2016; Proctolaelaps pygmaeus (Müller, 1859); Proctolaelaps drosophilae Karg, Baker & Jenkinson, 1995 and Proctolaelaps regalis De Leon, 1963. The latter two species were not found in Egypt, but they are related to the new species described here. They were re-described based on the type specimens from Europe and North America. A dichotomous key is given to help the separation of the Proctolaelaps species concluded to be found in Egypt.

  18. Can natural selection favour altruism between species?

    PubMed

    Wyatt, G A K; West, S A; Gardner, A

    2013-09-01

    Darwin suggested that the discovery of altruism between species would annihilate his theory of natural selection. However, it has not been formally shown whether between-species altruism can evolve by natural selection, or why this could never happen. Here, we develop a spatial population genetic model of two interacting species, showing that indiscriminate between species helping can be favoured by natural selection. We then ask if this helping behaviour constitutes altruism between species, using a linear-regression analysis to separate the total action of natural selection into its direct and indirect (kin selected) components. We show that our model can be interpreted in two ways, as either altruism within species, or altruism between species. This ambiguity arises depending on whether or not we treat genes in the other species as predictors of an individual's fitness, which is equivalent to treating these individuals as agents (actors or recipients). Our formal analysis, which focuses upon evolutionary dynamics rather than agents and their agendas, cannot resolve which is the better approach. Nonetheless, because a within-species altruism interpretation is always possible, our analysis supports Darwin's suggestion that natural selection does not favour traits that provide benefits exclusively to individuals of other species.

  19. Species longevity in North American fossil mammals.

    PubMed

    Prothero, Donald R

    2014-08-01

    Species longevity in the fossil record is related to many paleoecological variables and is important to macroevolutionary studies, yet there are very few reliable data on average species durations in Cenozoic fossil mammals. Many of the online databases (such as the Paleobiology Database) use only genera of North American Cenozoic mammals and there are severe problems because key groups (e.g. camels, oreodonts, pronghorns and proboscideans) have no reliable updated taxonomy, with many invalid genera and species and/or many undescribed genera and species. Most of the published datasets yield species duration estimates of approximately 2.3-4.3 Myr for larger mammals, with small mammals tending to have shorter species durations. My own compilation of all the valid species durations in families with updated taxonomy (39 families, containing 431 genera and 998 species, averaging 2.3 species per genus) yields a mean duration of 3.21 Myr for larger mammals. This breaks down to 4.10-4.39 Myr for artiodactyls, 3.14-3.31 Myr for perissodactyls and 2.63-2.95 Myr for carnivorous mammals (carnivorans plus creodonts). These averages are based on a much larger, more robust dataset than most previous estimates, so they should be more reliable for any studies that need species longevity to be accurately estimated.

  20. The myth of plant species saturation

    USGS Publications Warehouse

    Stohlgren, Thomas J.; Barnett, David T.; Jarnevich, Catherine S.; Flather, Curtis; Kartesz, John

    2008-01-01

    Plant species assemblages, communities or regional floras might be termed ‘saturated’ when additional immigrant species are unsuccessful at establishing due to competitive exclusion or other inter-specific interactions, or when the immigration of species is off-set by extirpation of species. This is clearly not the case for state, regional or national floras in the USA where colonization (i.e. invasion by exotic species) exceeds extirpation by roughly a 24 to 1 margin. We report an alarming temporal trend in plant invasions in the Pacific Northwest over the past 100 years whereby counties highest in native species richness appear increasingly invaded over time. Despite the possibility of some increased awareness and reporting of native and exotic plant species in recent decades, historical records show a significant, consistent long-term increase in exotic species (number and frequency) at county, state and regional scales in the Pacific Northwest. Here, as in other regions of the country, colonization rates by exotic species are high and extirpation rates are negligible. The rates of species accumulation in space in multi-scale vegetation plots may provide some clues to the mechanisms of the invasion process from local to national scales.

  1. Two new species of Herina (Diptera: Ulidiidae) from the Mediterranean region, with key to species groups.

    PubMed

    Morgulis, E; Freidberg, A; Kameneva, E P

    2013-01-01

    Herina dimorphica n. sp. (type locality Israel) and H. sicula n. sp. (type locality Sicily, Italy) are described and illustrated, and a new species group (the Herina dimorphica species group) is established for both species. H. dimorphica is characterized by a sexually-dimorphic wing pattern and venation. H. sicula is similar albeit not sexually-dimorphic. Almost all known Herina species are assigned to one of nine species groups, which are keyed.

  2. A new species of Calogalesus Kieffer from China (Hymenoptera, Diapriidae) with a key to World species

    PubMed Central

    Feng, Jun; Notton, David; Xu, Zai-fu

    2016-01-01

    Abstract A new species of Calogalesus Kieffer, 1912, Calogalesus sinicus sp. n., is described and illustrated, collected from a Chinese prickly ash (Zanthoxylum bungeanum Maxim.) orchard in Yunnan province of China. This is the third described species of the genus in the World. The new species can be distinguished from the other two described Calogalesus species by the head profile, proportions of the antennal segments, tridentate mandible, and mandible length. A key to World species of the genus is provided. PMID:27833433

  3. Bovine Eimeria species in Austria.

    PubMed

    Koutny, H; Joachim, A; Tichy, A; Baumgartner, W

    2012-05-01

    Bovine eimeriosis is considered to be of considerable importance for the productivity and health of cattle worldwide. Despite the importance of cattle farming in Austria, little is known in this country about the abundance and distribution of bovine Eimeria spp. The objective of this study was to obtain detailed information about the occurrence of different Eimeria spp. on Austrian dairy farms. Fecal samples from individual calves (n = 868) from 296 farms all over Austria (82 districts) were collected. Additionally, each farmer was questioned about the occurrence of calf diarrhea, and about the knowledge on coccidiosis and possible control measures. On 97.97% of the investigated farms, calves excreted Eimeria oocysts, and 83.67% of the individual samples were positive. After sporulation of positive samples pooled from each farm, 11 Eimeria species were found, with E. bovis (in 65.54% of the samples and 27.74% of the farms), E.zuernii (63.85%/13.86%), E. auburnensis (56.76%/13.41%) and E. ellipsoidalis (54.05%/14.38%) being the most prevalent, followed by E. alabamensis (45.61%/11.56%), E. subspherica (35.14%/5.5.05%), E. cylindrica (33.11%/7.00%), and E. canadensis (31.08%/7.74%). E. wyomingensis, E. pellita and E. bukidnonensis were only found sporadically (3.04-4.73% of the samples and 0.16-0.59% of the farms). Mixed infections were present on all farms (2-9 Eimeria species/farm). Prevalences by state provinces were high throughout with 77.1-87.9% of the samples and 93.8-100% of the farms. Lower Austria had the highest percentage of positive farms, and Vorarlberg the lowest. Individual OPG (oocysts per gram of feces) values were generally low; 75% of the samples had an OPG of 1,000 or less. The highest detected OPG was 72,400. The mean OPG was 2,525 with above average numbers in Tirol, Carinthia, and Lower Austria. The mean OPG values were significantly positively correlated with the cattle density in the different districts. The majority of the samples were from

  4. Thresholds for impaired species recovery

    PubMed Central

    Hutchings, Jeffrey A.

    2015-01-01

    Studies on small and declining populations dominate research in conservation biology. This emphasis reflects two overarching frameworks: the small-population paradigm focuses on correlates of increased extinction probability; the declining-population paradigm directs attention to the causes and consequences of depletion. Neither, however, particularly informs research on the determinants, rate or uncertainty of population increase. By contrast, Allee effects (positive associations between population size and realized per capita population growth rate, rrealized, a metric of average individual fitness) offer a theoretical and empirical basis for identifying numerical and temporal thresholds at which recovery is unlikely or uncertain. Following a critique of studies on Allee effects, I quantify population-size minima and subsequent trajectories of marine fishes that have and have not recovered following threat mitigation. The data suggest that threat amelioration, albeit necessary, can be insufficient to effect recovery for populations depleted to less than 10% of maximum abundance (Nmax), especially when they remain depleted for lengthy periods of time. Comparing terrestrial and aquatic vertebrates, life-history analyses suggest that population-size thresholds for impaired recovery are likely to be comparatively low for marine fishes but high for marine mammals. Articulation of a ‘recovering population paradigm’ would seem warranted. It might stimulate concerted efforts to identify generic impaired recovery thresholds across species. It might also serve to reduce the confusion of terminology, and the conflation of causes and consequences with patterns currently evident in the literature on Allee effects, thus strengthening communication among researchers and enhancing the practical utility of recovery-oriented research to conservation practitioners and resource managers. PMID:26213739

  5. On the failure of modern species concepts.

    PubMed

    Hey, Jody

    2006-08-01

    The modern age of species concepts began in 1942, when Ernst Mayr gave concept names to several different approaches to species identification. A long list of species concepts then followed, as well as a complex literature on their merits, motivations and uses. Some of these complexities arose as a consequence of the semantic shift that Mayr introduced, in which procedures for identifying species were elevated to concepts. Much of the debate in recent decades over concepts, and over pluralism versus monism, can be seen as an unnecessary consequence of treating species identification criteria as if they were more fundamental concepts. Recently, biologists have begun to recognize both the shortcomings of a lexicon of multiple species concepts and a common evolutionary idea that underlies them.

  6. Tree species richness of upper Amazonian forests

    PubMed Central

    Gentry, Alwyn H.

    1988-01-01

    Upper Amazonian data for tree species richness in 1-hectare plots are reported. All plants ≥10 cm diameter were censused and identified in six plots in Amazonian Peru and one on the Venezuela-Brazil border. The two plots from the everwet forests near Iquitos, Peru, are the most species-rich in the world, with ≈300 species ≥10 cm diameter in single hectares; all of the Peruvian plots are among the most species-rich ever reported. Contrary to accepted opinion, upper Amazonian forest, and perhaps Central African ones, have as many or more tree species as comparable Asian forests. Very high tree species richness seems to be a general property of mature lowland evergreen forests on fertile to moderately infertile soils on all three continents. PMID:16578826

  7. Inter-species comparisons of carcinogenicity.

    PubMed Central

    Purchase, I. F.

    1980-01-01

    The carcinogenicity of 250 chemicals in 2 species, usually the rat and the mouse, was obtained from the published literature through 3 independent sources. Of the 250 compounds listed, 38% were non-carcinogenic in both rats and mice, and 44% were carcinogenic in both species. A total of 43 compounds had different results in the two species, 21 (8%) being carcinogenic in mice only, 17 (7%) in rats only and 5 (2%) having differing results from other species. A comparison of the major target organs affected by chemicals carcinogenic in both species revealed that 64% of the chemicals studied produced cancer at the same site. This comparison of carcinogenic activity in 2 species suggests that extrapolation from results in a single-animal study to man may be subject to substantial errors. PMID:7387835

  8. Weighted species richness outperforms species richness as predictor of biotic resistance.

    PubMed

    Henriksson, Anna; Yu, Jun; Wardle, David A; Trygg, Johan; Englund, Göran

    2016-01-01

    The species richness hypothesis, which predicts that species-rich communities should be better at resisting invasions than species-poor communities, has been empirically tested many times and is often poorly supported. In this study, we contrast the species richness hypothesis with four alternative hypotheses with the aim of finding better descriptors of invasion resistance. These alternative hypotheses state that resistance to invasions is determined by abiotic conditions, community saturation (i.e., the number of resident species relative to the maximum number of species that can be supported), presence/absence of key species, or weighted species richness. Weighted species richness is a weighted sum of the number of species, where each species' weight describes its contribution to resistance. We tested these hypotheses using data on the success of 571 introductions of four freshwater fish species into lakes throughout Sweden, i.e., Arctic char (Salvelinus alpinus), tench (Tinca tinca), zander (Sander lucioperca), and whitefish (Coregonus lavaretus). We found that weighted species richness best predicted invasion success. The weights describing the contribution of each resident species to community resistance varied considerably in both strength and sign. Positive resistance weights, which indicate that species repel invaders, were as common as negative resistance weights, which indicate facilitative interactions. This result can be contrasted with the implicit assumption of the original species richness hypothesis, that all resident species have negative effects on invader success. We argue that this assumption is unlikely to be true in natural communities, and thus that we expect that weighted species richness is a better predictor of invader success than the actual number of resident species.

  9. Molecular species identification boosts bat diversity

    PubMed Central

    Mayer, Frieder; Dietz, Christian; Kiefer, Andreas

    2007-01-01

    The lack of obvious morphological differences between species impedes the identification of species in many groups of organisms. Meanwhile, DNA-based approaches are increasingly used to survey biological diversity. In this study we show that sequencing the mitochondrial protein-coding gene NADH dehydrogenase, subunit 1 (nd1) from 534 bats of the Western Palaearctic region corroborates the promise of DNA barcodes in two major respects. First, species described with classical taxonomic tools can be genetically identified with only a few exceptions. Second, substantial sequence divergence suggests an unexpected high number of undiscovered species. PMID:17295921

  10. Epigenetics and Developmental Plasticity Across Species

    PubMed Central

    Champagne, Frances A.

    2012-01-01

    Plasticity is a typical feature of development and can lead to divergent phenotypes. There is increasing evidence that epigenetic mechanisms, such as DNA methylation, are present across species, are modifiable by the environment, and are involved in developmental plasticity. Thus, in the context of the concept of developmental homology, epigenetic mechanisms may serve to create a process homology between species by providing a common molecular pathway through which environmental experiences shape development, ultimately leading to phenotypic diversity. This article will highlight evidence derived from across-species investigations of epigenetics, development, and plasticity which may contribute to our understanding of the homology that exists between species and between ancestors and descendants. PMID:22711291

  11. Time Resolved Studies Of Adsorbed Species

    NASA Astrophysics Data System (ADS)

    Howard, J.; Nicol, J. M.

    1985-12-01

    A time-resolved Fourier transform IR study of ethyne adsorbed on ZnNaA zeolite yields results very different from those reported for related systems. Initially two species (A and B) are formed by the interaction of C2H2 with the cations. Whereas species A (π-bonded C2H2) was found to be removed immediately on evacuation, species B (probably Zn-acetylide) was not fully removed after 60 mins evacuation. In the presence of the gas phase, bands due to Species A decreased slowly in intensity as new bands due to adsorbed ethanal were observed.

  12. Effects of land use on threatened species.

    PubMed

    Lenzen, Manfred; Lane, Amanda; Widmer-Cooper, Asaph; Williams, Moira

    2009-04-01

    There is widespread agreement that biodiversity loss must be reduced, yet to alleviate threats to plant and animal species, the forces driving these losses need to be better understood. We searched for explanatory variables for threatened-species data at the country level through land-use information instead of previously used socioeconomic and demographic variables. To explain the number of threatened species in one country, we used information on land-use patterns in all neighboring countries and on the extent of the country's sea border. We carried out multiple regressions of the numbers of threatened species as a function of land-use patterns, and we tested various specifications of this function, including spatial autocorrelation. Most cross-border land-use patterns had a significant influence on the number of threatened species, and land-use patterns explained the number of threatened species better than less proximate socioeconomic variables. More specifically, our overall results showed a highly adverse influence of plantations and permanent cropland, a weaker negative influence of permanent pasture, and, for the most part, a beneficial influence of nonarable lands and natural forest. Surprisingly, built-up land also showed a conserving influence on threatened species. The adverse influences extended to distances between about 250 km (plants) and 2000 km (birds and mammals) away from where the species threat was recorded, depending on the species. Our results highlight that legislation affecting biodiversity should look beyond national boundaries.

  13. Species coexistence in a lattice-structured habitat: effects of species dispersal and interactions.

    PubMed

    Ying, Zhixia; Liao, Jinbao; Wang, Shichang; Lu, Hui; Liu, Yongjie; Ma, Liang; Li, Zhenqing

    2014-10-21

    Opinions differ on how the spatial distribution of species over space affects species coexistence. Here, we constructed both mean-field and pair approximation (PA) models to explore the effects of interspecific and intraspecific interactions and dispersal modes on species coexistence. We found that spatial structure resulting from species dispersal traits and neighboring interactions in PA model did not promote coexistence if two species had the same traits, though it might intensify the contact frequency of intraspecific competition. If two species adopt different dispersal modes, the spatial structure in PA would make the coexistence or founder control less likely since it alters the species effective birth rate. This suggests that the spatial distribution caused by neighboring interactions and local dispersal does not affect species coexistence unless it adequately alters the effective birth rate for two species. Besides, we modeled how the initial densities and patterns affected population dynamics and revealed how the final spatial pattern was generated.

  14. Use of species-specific PCR for the identification of 10 sea cucumber species

    NASA Astrophysics Data System (ADS)

    Wen, Jing; Zeng, Ling

    2014-11-01

    We developed a species-specific PCR method to identify species among dehydrated products of 10 sea cucumber species. Ten reverse species-specific primers designed from the 16S rRNA gene, in combination with one forward universal primer, generated PCR fragments of ca. 270 bp length for each species. The specificity of the PCR assay was tested with DNA of samples of 21 sea cucumber species. Amplification was observed in specific species only. The species-specific PCR method we developed was successfully applied to authenticate species of commercial products of dehydrated sea cucumber, and was proven to be a useful, rapid, and low-cost technique to identify the origin of the sea cucumber product.

  15. 78 FR 48898 - Receipt of Applications for Endangered Species Permits

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-12

    ... species of freshwater crayfish, 2 species of freshwater snails, and 43 species of freshwater mussels for... (Percina antesella), Conasauga logperch (Percina jenkinsi), snail darter (Percina tanasi), blackside...

  16. Development and Evaluation of Species-Specific PCR for Detection of Nine Acinetobacter Species.

    PubMed

    Li, Xue Min; Choi, Ji Ae; Choi, In Sun; Kook, Joong Ki; Chang, Young-Hyo; Park, Geon; Jang, Sook Jin; Kang, Seong Ho; Moon, Dae Soo

    2016-05-01

    Molecular methods have the potential to improve the speed and accuracy of Acinetobacter species identification in clinical settings. The goal of this study is to develop species-specific PCR assays based on differences in the RNA polymerase beta-subunit gene (rpoB) to detect nine commonly isolated Acinetobacter species including Acinetobacter baumannii, Acinetobacter calcoaceticus, Acinetobacter pittii, Acinetobacter nosocomialis, Acinetobacter lwoffii, Acinetobacter ursingii, Acinetobacter bereziniae, Acinetobacter haemolyticus, and Acinetobacter schindleri. The sensitivity and specificity of these nine assays were measured using genomic DNA templates from 55 reference strains and from 474 Acinetobacter clinical isolates. The sensitivity of A. baumannii-specific PCR assay was 98.9%, and the sensitivity of species-specific PCR assays for all other species was 100%. The specificities of A. lwoffii- and A. schindleri-specific PCR were 97.8 and 98.9%, respectively. The specificity of species-specific PCR for all other tested Acinetobacter species was 100%. The lower limit of detection for the nine species-specific PCR assays developed in this study was 20 or 200 pg of genomic DNA from type strains of each species. The Acinetobacter species-specific PCR assay would be useful to determine the correct species among suggested candidate Acinetobacter species when conventional methods including MALDI-TOF MS identify Acinetobacter only to the genus level. The species-specific assay can be used to screen large numbers of clinical and environmental samples obtained for epidemiologic study of Acinetobacter for the presence of target species.

  17. Estimating species richness and accumulation by modeling species occurrence and detectability

    USGS Publications Warehouse

    Dorazio, R.M.; Royle, J. Andrew; Soderstrom, B.; Glimskarc, A.

    2006-01-01

    A statistical model is developed for estimating species richness and accumulation by formulating these community-level attributes as functions of model-based estimators of species occurrence while accounting for imperfect detection of individual species. The model requires a sampling protocol wherein repeated observations are made at a collection of sample locations selected to be representative of the community. This temporal replication provides the data needed to resolve the ambiguity between species absence and nondetection when species are unobserved at sample locations. Estimates of species richness and accumulation are computed for two communities, an avian community and a butterfly community. Our model-based estimates suggest that detection failures in many bird species were attributed to low rates of occurrence, as opposed to simply low rates of detection. We estimate that the avian community contains a substantial number of uncommon species and that species richness greatly exceeds the number of species actually observed in the sample. In fact, predictions of species accumulation suggest that even doubling the number of sample locations would not have revealed all of the species in the community. In contrast, our analysis of the butterfly community suggests that many species are relatively common and that the estimated richness of species in the community is nearly equal to the number of species actually detected in the sample. Our predictions of species accumulation suggest that the number of sample locations actually used in the butterfly survey could have been cut in half and the asymptotic richness of species still would have been attained. Our approach of developing occurrence-based summaries of communities while allowing for imperfect detection of species is broadly applicable and should prove useful in the design and analysis of surveys of biodiversity.

  18. Relating species abundance distributions to species-area curves in two Mediterranean-type shrublands

    USGS Publications Warehouse

    Keeley, Jon E.

    2003-01-01

    Based on both theoretical and empirical studies there is evidence that different species abundance distributions underlie different species-area relationships. Here I show that Australian and Californian shrubland communities (at the scale from 1 to 1000 m2) exhibit different species-area relationships and different species abundance patterns. The species-area relationship in Australian heathlands best fits an exponential model and species abundance (based on both density and cover) follows a narrow log normal distribution. In contrast, the species-area relationship in Californian shrublands is best fit with the power model and, although species abundance appears to fit a log normal distribution, the distribution is much broader than in Australian heathlands. I hypothesize that the primary driver of these differences is the abundance of small-stature annual species in California and the lack of annuals in Australian heathlands. Species-area is best fit by an exponential model in Australian heathlands because the bulk of the species are common and thus the species-area curves initially rise rapidly between 1 and 100 m2. Annuals in Californian shrublands generate very broad species abundance distributions with many uncommon or rare species. The power function is a better model in these communities because richness increases slowly from 1 to 100 m2 but more rapidly between 100 and 1000 m2due to the abundance of rare or uncommon species that are more likely to be encountered at coarser spatial scales. The implications of this study are that both the exponential and power function models are legitimate representations of species-area relationships in different plant communities. Also, structural differences in community organization, arising from different species abundance distributions, may lead to different species-area curves, and this may be tied to patterns of life form distribution.

  19. A New Species of the Agriotes nuceus Species Group from Turkey

    PubMed Central

    Kabalak, Mahmut; Sert, Osman; Özgen, İnanç; Platia, Giuseppe

    2013-01-01

    A new Elateridae species, Agriotes longipronotum n. sp. (Coleoptera: Elateridae: Elaterinae: Agriotini), is described from Siirt province, Turkey. Photographs of the imago and the aedeagus, and drawings of the aedeagus of the new species, A. sameki, A. bulgaricus, and A. rahmei are given. A rearranged diagnostic key of all Turkish species of nuceus-group is given. The new species is discussed in relation with closely related species. The species of the Agriotes nuceus-group from Turkey are listed, and their distributions are given. PMID:23885925

  20. Clonal growth and plant species abundance

    PubMed Central

    Herben, Tomáš; Nováková, Zuzana; Klimešová, Jitka

    2014-01-01

    Background and Aims Both regional and local plant abundances are driven by species' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf–height–seed) traits and by actual performance in the botanical garden. Methods Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area – height – seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates. Key Results After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level. Conclusions Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially

  1. DNA barcoding of endangered Indian Paphiopedilum species.

    PubMed

    Parveen, Iffat; Singh, Hemant K; Raghuvanshi, Saurabh; Pradhan, Udai C; Babbar, Shashi B

    2012-01-01

    The indiscriminate collections of Paphiopedilum species from the wild for their exotic ornamental flowers have rendered these plants endangered. Although the trade of these endangered species from the wild is strictly forbidden, it continues unabated in one or other forms that elude the current identification methods. DNA barcoding that offers identification of a species even if only a small fragment of the organism at any stage of development is available could be of great utility in scrutinizing the illegal trade of both endangered plant and animal species. Therefore, this study was undertaken to develop DNA barcodes of Indian species of Paphiopedilum along with their three natural hybrids using loci from both the chloroplast and nuclear genomes. The five loci tested for their potential as effective barcodes were RNA polymerase-β subunit (rpoB), RNA polymerase-β' subunit (rpoC1), Rubisco large subunit (rbcL) and maturase K (matK) from the chloroplast genome and nuclear ribosomal internal transcribed spacer (nrITS) from the nuclear genome. The intra- and inter-specific divergence values and species discrimination rates were calculated by Kimura 2 parameter (K2P) method using mega 4.0. The matK with 0.9% average inter-specific divergence value yielded 100% species resolution, thus could distinguish all the eight species of Paphiopedilum unequivocally. The species identification capability of these sequences was further confirmed as each of the matK sequences was found to be unique for the species when a blast analysis of these sequences was carried out on NCBI. nrITS, although had 4.4% average inter-specific divergence value, afforded only 50% species resolution. DNA barcodes of the three hybrids also reflected their parentage.

  2. Evaluating species richness: biased ecological inference results from spatial heterogeneity in species detection probabilities

    USGS Publications Warehouse

    McNew, Lance B.; Handel, Colleen M.

    2015-01-01

    Accurate estimates of species richness are necessary to test predictions of ecological theory and evaluate biodiversity for conservation purposes. However, species richness is difficult to measure in the field because some species will almost always be overlooked due to their cryptic nature or the observer's failure to perceive their cues. Common measures of species richness that assume consistent observability across species are inviting because they may require only single counts of species at survey sites. Single-visit estimation methods ignore spatial and temporal variation in species detection probabilities related to survey or site conditions that may confound estimates of species richness. We used simulated and empirical data to evaluate the bias and precision of raw species counts, the limiting forms of jackknife and Chao estimators, and multi-species occupancy models when estimating species richness to evaluate whether the choice of estimator can affect inferences about the relationships between environmental conditions and community size under variable detection processes. Four simulated scenarios with realistic and variable detection processes were considered. Results of simulations indicated that (1) raw species counts were always biased low, (2) single-visit jackknife and Chao estimators were significantly biased regardless of detection process, (3) multispecies occupancy models were more precise and generally less biased than the jackknife and Chao estimators, and (4) spatial heterogeneity resulting from the effects of a site covariate on species detection probabilities had significant impacts on the inferred relationships between species richness and a spatially explicit environmental condition. For a real dataset of bird observations in northwestern Alaska, the four estimation methods produced different estimates of local species richness, which severely affected inferences about the effects of shrubs on local avian richness. Overall, our results

  3. An empirical test of stable species coexistence in an amphipod species complex.

    PubMed

    Cothran, Rickey D; Noyes, Patrick; Relyea, Rick A

    2015-07-01

    The ability of phenotypically similar species to coexist at local scales is paradoxical given that species that closely resemble each other should compete strongly for resources and thus be subject to competitive exclusion. Although theory has identified the key requirements for species to stably coexist, empirical tests of coexistence have rarely been conducted. We explored a key requirement for species to stably coexist: a species can invade a community when it is initially rare. We also assessed whether primary productivity (manipulated using phosphorus availability) affected invasion success by increasing the amount of resources available. Using two mesocosm experiments and an assemblage of phenotypically similar amphipod species in the genus Hyalella, we found no evidence for invasion success among the three Hyalella species. Further, patterns of species exclusions differed among the species, which suggests that one species is an especially poor competitor. Finally, these patterns were consistent regardless of whether mesocosms were fertilized with low or high levels of phosphorus. Our results, suggest that species differences in resource competition and predator avoidance ability found in previous studies using these Hyalella species may not be sufficient to allow for coexistence. Moreover, our study demonstrates the importance of using a variety of empirical approaches to test species coexistence theory.

  4. Predicting total global species richness using rates of species description and estimates of taxonomic effort.

    PubMed

    Costello, Mark J; Wilson, Simon; Houlding, Brett

    2012-10-01

    We found that trends in the rate of description of 580,000 marine and terrestrial species, in the taxonomically authoritative World Register of Marine Species and Catalogue of Life databases, were similar until the 1950s. Since then, the relative number of marine to terrestrial species described per year has increased, reflecting the less explored nature of the oceans. From the mid-19th century, the cumulative number of species described has been linear, with the highest number of species described in the decade of 1900, and fewer species described and fewer authors active during the World Wars. There were more authors describing species since the 1960s, indicating greater taxonomic effort. There were fewer species described per author since the 1920s, suggesting it has become more difficult to discover new species. There was no evidence of any change in individual effort by taxonomists. Using a nonhomogeneous renewal process model we predicted that 24-31% to 21-29% more marine and terrestrial species remain to be discovered, respectively. We discuss why we consider that marine species comprise only 16% of all species on Earth although the oceans contain a greater phylogenetic diversity than occurs on land. We predict that there may be 1.8-2.0 million species on Earth, of which about 0.3 million are marine, significantly less than some previous estimates.

  5. Selecting focal species as surrogates for imperiled species using relative sensitivities derived from occupancy analysis

    USGS Publications Warehouse

    Silvano, Amy; Guyer, Craig; Steury, Todd; Grand, James B.

    2017-01-01

    Most imperiled species are rare or elusive and difficult to detect, which makes gathering data to estimate their response to habitat restoration a challenge. We used a repeatable, systematic method for selecting focal species using relative sensitivities derived from occupancy analysis. Our objective was to select suites of focal species that would be useful as surrogates when predicting effects of restoration of habitat characteristics preferred by imperiled species. We developed 27 habitat profiles that represent general habitat relationships for 118 imperiled species. We identified 23 regularly encountered species that were sensitive to important aspects of those profiles. We validated our approach by examining the correlation between estimated probabilities of occupancy for species of concern and focal species selected using our method. Occupancy rates of focal species were more related to occupancy rates of imperiled species when they were sensitive to more of the parameters appearing in profiles of imperiled species. We suggest that this approach can be an effective means of predicting responses by imperiled species to proposed management actions. However, adequate monitoring will be required to determine the effectiveness of using focal species to guide management actions.

  6. SELECTING PLANT SPECIES FOR PESTICIDE REGISTRATION TESTS

    EPA Science Inventory

    Current test protocols used by the US EPA for the registration of pesticides examines plant responses of 10 crop species but may not examine regionally important native plants or crops. In order to test the efficiency of current test protocols we selected six native plant species...

  7. The role of taxonomy in species conservation.

    PubMed Central

    Mace, Georgina M

    2004-01-01

    Taxonomy and species conservation are often assumed to be completely interdependent activities. However, a shortage of taxonomic information and skills, and confusion over where the limits to 'species' should be set, both cause problems for conservationists. There is no simple solution because species lists used for conservation planning (e.g. threatened species, species richness estimates, species covered by legislation) are often also used to determine which units should be the focus of conservation actions; this despite the fact that the two processes have such different goals and information needs. Species conservation needs two kinds of taxonomic solution: (i) a set of practical rules to standardize the species units included on lists; and (ii) an approach to the units chosen for conservation recovery planning which recognizes the dynamic nature of natural systems and the differences from the units in listing processes that result. These solutions are well within our grasp but require a new kind of collaboration among conservation biologists, taxonomists and legislators, as well as an increased resource of taxonomists with relevant and high-quality skills. PMID:15253356

  8. Caveats for correlative species distribution modeling

    USGS Publications Warehouse

    Jarnevich, Catherine S.; Stohlgren, Thomas J.; Kumar, Sunil; Morisette, Jeffrey T.; Holcombe, Tracy R.

    2015-01-01

    Correlative species distribution models are becoming commonplace in the scientific literature and public outreach products, displaying locations, abundance, or suitable environmental conditions for harmful invasive species, threatened and endangered species, or species of special concern. Accurate species distribution models are useful for efficient and adaptive management and conservation, research, and ecological forecasting. Yet, these models are often presented without fully examining or explaining the caveats for their proper use and interpretation and are often implemented without understanding the limitations and assumptions of the model being used. We describe common pitfalls, assumptions, and caveats of correlative species distribution models to help novice users and end users better interpret these models. Four primary caveats corresponding to different phases of the modeling process, each with supporting documentation and examples, include: (1) all sampling data are incomplete and potentially biased; (2) predictor variables must capture distribution constraints; (3) no single model works best for all species, in all areas, at all spatial scales, and over time; and (4) the results of species distribution models should be treated like a hypothesis to be tested and validated with additional sampling and modeling in an iterative process.

  9. Fatal attraction: rare species in the spotlight

    PubMed Central

    Angulo, Elena; Deves, Anne-Laure; Saint Jalmes, Michel; Courchamp, Franck

    2009-01-01

    The exploitation of rare and endangered species can end in the species's extinction because the increased value people associate with rarity increases the economic incentive to exploit the last individuals, creating a positive feedback loop. This recently proposed concept, called the anthropogenic Allee effect (AAE), relies on the assumption that people do value rarity, but this remains to be established. Moreover, it also remains to be determined whether attraction to rarity is a trait confined to a minority of hobbyists (e.g. wildlife collectors, exotic pet owners) or characteristic of the general public. We estimated how much the general public valued rare species compared with common ones, using five different metrics related to personal investment: time spent, physical effort, unpleasantness, economic investment and risk. We surveyed the visitors of a zoo. To see the rare species, the visitors to the zoo invested more time in searching and contemplation, they were ready to expend more physical effort, they tolerated more unpleasant conditions, they were willing to pay more and, finally, they risked more to obtain (steal) a rare species. Our results provide substantial evidence of how the general public places more value on rare species, compared with common species. This confirms the AAE as an actual process, which in addition concerns a large part of the population. This has important consequences for the conservation of species that are rare now, or that could become so in the future. PMID:19141425

  10. Divergence in codon usage of Lactobacillus species.

    PubMed Central

    Pouwels, P H; Leunissen, J A

    1994-01-01

    We have analyzed codon usage patterns of 70 sequenced genes from different Lactobacillus species. Codon usage in lactobacilli is highly biased. Both inter-species and intra-species heterogeneity of codon usage bias was observed. Codon usage in L. acidophilus is similar to that in L. helveticus, but dissimilar to that in L. bulgaricus, L. casei, L. pentosus and L. plantarum. Codon usage in the latter three organisms is not significantly different, but is different from that in L. bulgaricus. Inter-species differences in codon usage can, at least in part, be explained by differences in mutational drift. L. bulgaricus shows GC drift, whereas all other species show AT drift. L. acidophilus and L. helveticus rarely use NNG in family-box (a set of synonymous) codons, in contrast to all other species. This result may be explained by assuming that L. acidophilus and L. helveticus, but not other species examined, use a single tRNA species for translation of family-box codons. Differences in expression level of genes are positively correlated with codon usage bias. Highly expressed genes show highly biased codon usage, whereas weakly expressed genes show much less biased codon usage. Codon usage patterns at the 5'-end of Lactobacillus genes is not significantly different from that of entire genes. The GC content of codons 2-6 is significantly reduced compared with that of the remainder of the gene. The possible implications of a reduced GC content for the control of translation efficiency are discussed. PMID:8152923

  11. The Pangean origin of 'Candidatus Liberibacter' species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There are six currently recognized “Candidatus Liberibacter” species. Three are associated with Huanglongbing of citrus, and one with Zebra Chip and Psyllid Yellows in Solanaceous crops and Yellows Decline in carrots. Another is an apparently asymptomatic infection of apple, pear and related specie...

  12. Calcineurin signaling: lessons from Candida species.

    PubMed

    Yu, Shang-Jie; Chang, Ya-Lin; Chen, Ying-Lien

    2015-06-01

    Human fungal infections have significantly increased in recent years due to the emergence of immunocompromised patients with AIDS and cancer. Among them, Candida species are frequently isolated and associated with high mortality if not appropriately treated. Current antifungal drugs (azoles, echinocandins and polyenes) are not sufficient to combat Candida species particularly those that are drug resistant. Calcineurin, a calcium/calmodulin-dependent protein phosphatase, is an attractive antifungal drug target, and its inhibitor (FK506 or cyclosporin A) can be combined with azoles or echinocandins for use against multidrug-resistant Candida species. The role of calcineurin in the hyphal growth of Candida albicans is controversial, but its roles in C. dubliniensis, C. tropicalis and C. lusitaniae can be demonstrated. In addition, calcineurin is required for virulence of Candida species in murine systemic, ocular or urinary infection models. However, the requirement for calcineurin substrate Crz1 in these infection models varies in Candida species, suggesting that Crz1 has diverse functions in different Candida species. Besides being critical for growth in serum of Candida species, calcineurin is critical for plasma membrane integrity and growth at body temperature (37°C) uniquely in C. glabrata, suggesting that Candida calcineurin controls pathogenesis via various novel mechanisms. In this review, we summarize studies of calcineurin signaling and hyphal growth, virulence and its relationship with drug tolerance in Candida species, focusing on the divergent and conserved functions.

  13. Mining wild species elleles from introgressed genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tomato (Solanum Section Lycopersicon) is composed of one cultivated (S. lycopersicum) and 12 wild species. Because the species are closely related to each other, introgression breeding has been extensive and released cultivars have been improved for many more traits using wild alleles than has any o...

  14. Ensemble habitat mapping of invasive plant species.

    PubMed

    Stohlgren, Thomas J; Ma, Peter; Kumar, Sunil; Rocca, Monique; Morisette, Jeffrey T; Jarnevich, Catherine S; Benson, Nate

    2010-02-01

    Ensemble species distribution models combine the strengths of several species environmental matching models, while minimizing the weakness of any one model. Ensemble models may be particularly useful in risk analysis of recently arrived, harmful invasive species because species may not yet have spread to all suitable habitats, leaving species-environment relationships difficult to determine. We tested five individual models (logistic regression, boosted regression trees, random forest, multivariate adaptive regression splines (MARS), and maximum entropy model or Maxent) and ensemble modeling for selected nonnative plant species in Yellowstone and Grand Teton National Parks, Wyoming; Sequoia and Kings Canyon National Parks, California, and areas of interior Alaska. The models are based on field data provided by the park staffs, combined with topographic, climatic, and vegetation predictors derived from satellite data. For the four invasive plant species tested, ensemble models were the only models that ranked in the top three models for both field validation and test data. Ensemble models may be more robust than individual species-environment matching models for risk analysis.

  15. Territorial battles between fiddler crab species

    PubMed Central

    Backwell, P. R. Y.

    2017-01-01

    Many species worldwide are impacted by habitat loss. This may result in increased competition both within species and between species. Many studies have demonstrated that when two previously non-overlapping species are forced to compete over a resource, one species is likely to become dominant over the other. This study explores the impact a larger species of fiddler crab (Tabuca elegans—previously known as Uca elegans) has when invading an area previously used solely by a smaller species (Austruca mjoebergi—previously known as Uca mjoebergi). Here we show that, while there are some detrimental effects of living next to a heterospecific, they are relatively minor. New heterospecific neighbours fight more regularly with resident crabs, but each fight is no longer or more escalated than those between the resident and a new conspecific male. The residents are not specifically targeted by intruding heterospecifics, thus, given the large advantage of having a heterospecific neighbour in terms of lowered competition for females, the overall impact of species mixing is probably not as negative as might have been predicted. PMID:28280560

  16. Toward reassessing data-deficient species.

    PubMed

    Bland, Lucie M; Bielby, Jon; Kearney, Stephen; Orme, C David L; Watson, James E M; Collen, Ben

    2016-10-03

    One in 6 species (13,465 species) on the International Union for Conservation of Nature (IUCN) Red List is classified as data deficient due to lack of information on their taxonomy, population status, or impact of threats. Despite the chance that many are at high risk of extinction, data-deficient species are typically excluded from global and local conservation priorities, as well as funding schemes. The number of data-deficient species will greatly increase as the IUCN Red List becomes more inclusive of poorly known and speciose groups. A strategic approach is urgently needed to enhance the conservation value of data-deficient assessments. To develop this, we reviewed 2879 data-deficient assessments in 6 animal groups and identified 8 main justifications for assigning data-deficient status (type series, few records, old records, uncertain provenance, uncertain population status or distribution, uncertain threats, taxonomic uncertainty, and new species). Assigning a consistent set of justification tags (i.e., consistent assignment to assessment justifications) to species classified as data deficient is a simple way to achieve more strategic assessments. Such tags would clarify the causes of data deficiency; facilitate the prediction of extinction risk; facilitate comparisons of data deficiency among taxonomic groups; and help prioritize species for reassessment. With renewed efforts, it could be straightforward to prevent thousands of data-deficient species slipping unnoticed toward extinction.

  17. SERI Aquatic Species Program: 1983 Annual Report

    SciTech Connect

    Not Available

    1984-03-01

    During 1983 research was carried out under three tasks: biological, engineering, and analysis. Biological research was aimed at screening for promising species of microalgae, macroalgae, and emergent plants that could be cultivated for energy products. Promising species were studied further to improve yields.

  18. A natural species concept for prokaryotes

    NASA Technical Reports Server (NTRS)

    Ward, D. M.

    1998-01-01

    Direct molecular analyses of natural microbial populations reveal patterns that should compel microbiologists to adopt a more natural species concept that has been known to biologists for decades. The species debate can be exploited to address a larger issue - microbiologists need, in general, to take a more natural view of the organisms they study.

  19. 76 FR 30955 - Invasive Species Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-27

    ... Office of the Secretary Invasive Species Advisory Committee AGENCY: Office of the Secretary, Interior. ACTION: Notice of public meetings of the Invasive Species Advisory Committee. SUMMARY: Pursuant to the provisions of the Federal Advisory Committee Act, notice is hereby given of meetings of the Invasive...

  20. The Invasive Plant Species Education Guide

    ERIC Educational Resources Information Center

    Mason, Kevin; James, Krista; Carlson, Kitrina; D'Angelo, Jean

    2010-01-01

    To help high school students gain a solid understanding of invasive plant species, university faculty and students from the University of Wisconsin-Stout (UW-Stout) and a local high school teacher worked together to develop the Invasive Plant Species (IPS) Education Guide. The IPS Education Guide includes nine lessons that give students an…

  1. ENDANGERED SPECIES SENSITIVITY AND ECOLOGICAL RISK ASSESSMENT

    EPA Science Inventory

    he U.S. Environmental Protection Agency (EPA), U.S. Fish & Wildlife Service, and National Marine Fisheries Service share a common responsibility for the protection of our nation's aquatic species under the Endangered Species Act (ESA) of 1973. The EPA, under the Federal Insectici...

  2. Introduced species and their missing parasites

    USGS Publications Warehouse

    Torchin, Mark E.; Lafferty, Kevin D.; Dobson, Andrew P.; McKenzie, Valerie J.; Kuris, Armand M.

    2003-01-01

    Damage caused by introduced species results from the high population densities and large body sizes that they attain in their new location. Escape from the effects of natural enemies is a frequent explanation given for the success of introduced species. Because some parasites can reduce host density and decrease body size, an invader that leaves parasites behind and encounters few new parasites can experience a demographic release and become a pest. To test whether introduced species are less parasitized, we have compared the parasites of exotic species in their native and introduced ranges, using 26 host species of molluscs, crustaceans, fishes, birds, mammals, amphibians and reptiles. Here we report that the number of parasite species found in native populations is twice that found in exotic populations. In addition, introduced populations are less heavily parasitized (in terms of percentage infected) than are native populations. Reduced parasitization of introduced species has several causes, including reduced probability of the introduction of parasites with exotic species (or early extinction after host establishment), absence of other required hosts in the new location, and the host-specific limitations of native parasites adapting to new hosts.

  3. Endangered Species in the Pacific Northwest.

    ERIC Educational Resources Information Center

    Clearing: Nature and Learning in the Pacific Northwest, 1985

    1985-01-01

    Suggests that students can learn how society works by studying threatened and endangered plant and animal species which occur in the local environments. Pictures, descriptions, habitats, and niche information are given for 21 threatened or endangered species of the Pacific Northwest. (DH)

  4. Endangered Species (Plants). LC Science Tracer Bullet.

    ERIC Educational Resources Information Center

    Niskern, Diana, Comp.

    This guide is intended for those who wish to study the literature dealing with various aspects of endangered plant species. This document includes the following sections, some of which are bibliographies: (1) "Introductions to the Topic"; (2) "Subject Headings" (for endangered species of plants used by the Library of Congress); (3) "General…

  5. Endangered Species: Real Life in Two Dimensions

    ERIC Educational Resources Information Center

    Henderson, Lynette K.

    2012-01-01

    The focus of "Endangered Species: Real Life in Two Dimensions" is to create awareness about a critical environmental issue. There is a special urgency to this project because large numbers of animal species are currently endangered or on the brink of extinction. In addition to being enlightened about this important topic through research, students…

  6. CONSERVATION PROGRAMS THAT PROMOTE INVASIVE SPECIES

    EPA Science Inventory

    Invasive plant species are degrading the structure and function of ecosystems throughout the world. Although most state and federal conservation agencies in the U.S. attempt to reduce the impact of invasive species, some agency activities can contribute to the spread of invasive...

  7. Morphological and genetic variation among sphaeralcea species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The herbaceous perennial species in the genus Sphaeralcea have desirable drought tolerance and aesthetics with potential for low-water use landscapes. However, taxonomy of these species is ambiguous, which leads to decreased consumer's confidence in the native plant industry. The goal of this stud...

  8. Discrimination among Panax species using spectral fingerprinting

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spectral fingerprints of samples of three Panax species (P. quinquefolius L., P. ginseng, and P. notoginseng) were acquired using UV, NIR, and MS spectrometry. With principal components analysis (PCA), all three methods allowed visual discrimination between all three species. All three methods wer...

  9. Comparison of Brassicaceae species for phytotoxicity testing

    EPA Science Inventory

    We compared four Brassicaceae species for potential use as test species in the EPAs Series 850 vegetative vigor test and other phytotoxicity tests to determine effects of chemicals on non-target plants. Arabidopsis thaliana var. Columbia is commonly used in plant molecular and p...

  10. Territorial battles between fiddler crab species.

    PubMed

    Clark, H L; Backwell, P R Y

    2017-01-01

    Many species worldwide are impacted by habitat loss. This may result in increased competition both within species and between species. Many studies have demonstrated that when two previously non-overlapping species are forced to compete over a resource, one species is likely to become dominant over the other. This study explores the impact a larger species of fiddler crab (Tabuca elegans-previously known as Uca elegans) has when invading an area previously used solely by a smaller species (Austruca mjoebergi-previously known as Uca mjoebergi). Here we show that, while there are some detrimental effects of living next to a heterospecific, they are relatively minor. New heterospecific neighbours fight more regularly with resident crabs, but each fight is no longer or more escalated than those between the resident and a new conspecific male. The residents are not specifically targeted by intruding heterospecifics, thus, given the large advantage of having a heterospecific neighbour in terms of lowered competition for females, the overall impact of species mixing is probably not as negative as might have been predicted.

  11. Historical species losses in bumblebee evolution.

    PubMed

    Condamine, Fabien L; Hines, Heather M

    2015-03-01

    Investigating how species coped with past environmental changes informs how modern species might face human-induced global changes, notably via the study of historical extinction, a dominant feature that has shaped current biodiversity patterns. The genus Bombus, which comprises 250 mostly cold-adapted species, is an iconic insect group sensitive to current global changes. Through a combination of habitat loss, pathogens and climate change, bumblebees have experienced major population declines, and several species are threatened with extinction. Using a time-calibrated tree of Bombus, we analyse their diversification dynamics and test hypotheses about the role of extinction during major environmental changes in their evolutionary history. These analyses support a history of fluctuating species dynamics with two periods of historical species loss in bumblebees. Dating estimates gauge that one of these events started after the middle Miocene climatic optimum and one during the early Pliocene. Both periods are coincident with global climate change that may have extirpated Bombus species. Interestingly, bumblebees experienced high diversification rates during the Plio-Pleistocene glaciations. We also found evidence for a major species loss in the past one million years that may be continuing today.

  12. Ensemble habitat mapping of invasive plant species

    USGS Publications Warehouse

    Stohlgren, T.J.; Ma, P.; Kumar, S.; Rocca, M.; Morisette, J.T.; Jarnevich, C.S.; Benson, N.

    2010-01-01

    Ensemble species distribution models combine the strengths of several species environmental matching models, while minimizing the weakness of any one model. Ensemble models may be particularly useful in risk analysis of recently arrived, harmful invasive species because species may not yet have spread to all suitable habitats, leaving species-environment relationships difficult to determine. We tested five individual models (logistic regression, boosted regression trees, random forest, multivariate adaptive regression splines (MARS), and maximum entropy model or Maxent) and ensemble modeling for selected nonnative plant species in Yellowstone and Grand Teton National Parks, Wyoming; Sequoia and Kings Canyon National Parks, California, and areas of interior Alaska. The models are based on field data provided by the park staffs, combined with topographic, climatic, and vegetation predictors derived from satellite data. For the four invasive plant species tested, ensemble models were the only models that ranked in the top three models for both field validation and test data. Ensemble models may be more robust than individual species-environment matching models for risk analysis. ?? 2010 Society for Risk Analysis.

  13. Species diversity of Trichoderma in Poland

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fifteen species of Trichoderma were identified from among 118 strains originating from different regions and ecological niches in Poland. This low number indicates low species diversity of Trichoderma in this Central European region. Using the ITS1-ITS2 regions, 64 strains were positively identified...

  14. COMPUTATIONAL RESOURCES FOR BIOFUEL FEEDSTOCK SPECIES

    SciTech Connect

    Buell, Carol Robin; Childs, Kevin L

    2013-05-07

    While current production of ethanol as a biofuel relies on starch and sugar inputs, it is anticipated that sustainable production of ethanol for biofuel use will utilize lignocellulosic feedstocks. Candidate plant species to be used for lignocellulosic ethanol production include a large number of species within the Grass, Pine and Birch plant families. For these biofuel feedstock species, there are variable amounts of genome sequence resources available, ranging from complete genome sequences (e.g. sorghum, poplar) to transcriptome data sets (e.g. switchgrass, pine). These data sets are not only dispersed in location but also disparate in content. It will be essential to leverage and improve these genomic data sets for the improvement of biofuel feedstock production. The objectives of this project were to provide computational tools and resources for data-mining genome sequence/annotation and large-scale functional genomic datasets available for biofuel feedstock species. We have created a Bioenergy Feedstock Genomics Resource that provides a web-based portal or clearing house for genomic data for plant species relevant to biofuel feedstock production. Sequence data from a total of 54 plant species are included in the Bioenergy Feedstock Genomics Resource including model plant species that permit leveraging of knowledge across taxa to biofuel feedstock species.We have generated additional computational analyses of these data, including uniform annotation, to facilitate genomic approaches to improved biofuel feedstock production. These data have been centralized in the publicly available Bioenergy Feedstock Genomics Resource (http://bfgr.plantbiology.msu.edu/).

  15. Species occurrence data for the nation

    USGS Publications Warehouse

    ,

    2015-09-28

    BISON's size is unprecedented, including records for most living species found in the U.S. and encompassing the efforts of more than a million professional and citizen scientists. And the vast majority of BISON's species occurrence records are specific locations, not just county or state records.

  16. Multiplexed microsatellite markers for seven Metarhizium species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cross-species transferability of 41 previously published simple sequence repeat (SSR) markers was assessed for 11 species of the entomopathogenic fungus Metarhizium. A collection of 65 Metarhizium isolates including all 54 used in a recent phylogenetic revision of the genus were characterized. Betwe...

  17. Grain Unloading Of Arsenic Species In Rice

    EPA Science Inventory

    Rice (Oryza sativa) is the staple food for over half the world's population yet may represent a significant dietary source of inorganic arsenic (As), a nonthreshold, class 1 human carcinogen. Rice grain As is dominated by the inorganic species, and the organic species dim...

  18. Highlighting Astyanax Species Diversity through DNA Barcoding

    PubMed Central

    Oliveira, Carlos Alexandre Miranda; de Melo, Filipe Augusto Gonçalves; Bertaco, Vinicius de Araújo; de Astarloa, Juan M. Díaz; Rosso, Juan J.; Foresti, Fausto; Oliveira, Claudio

    2016-01-01

    DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions. PMID:27992537

  19. Multi-species mating disruption in cranberries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cranberries in Wisconsin are often attacked by three moth species, known commonly as Sparganothis fruitworm, cranberry fruitworm, and black-headed fireworm. These moth species require multiple insecticide applications each season in Wisconsin. With the loss of certain broad-spectrum insecticides and...

  20. New Neotropical species of Chimarra (Trichoptera, Philopotamidae)

    PubMed Central

    Blahnik, Roger J.; Holzenthal, Ralph W.

    2012-01-01

    Abstract Ten new Neotropical species of Chimarra are described in the subgenera Chimarra, Chimarrita, and Otarrha. New species in the subgenus Chimarra include, in the Chimarra ortiziana group: Chimarra calori sp. n. (southeastern Brazil) and Chimarra onchyrhina sp. n. (Venezuela); in the Chimarra picea group: Chimarra inchoata sp. n. (Venezuela), Chimarra nicehuh sp. n. (Venezuela), and Chimarra sunima sp. n. (Colombia); and in the Chimarra poolei group: Chimarra cauca sp. n. (Colombia) and Chimarra desirae sp. n. (Bolivia). New species in the subgenus Chimarrita include, in the Chimarra simpliciforma group: Chimarra curvipenis sp. n. (SE Brazil) and Chimarra latiforceps sp. n. (SE Brazil). A single new species in the subgenus Otarrha is also described: Chimarra soroa sp. n. (Cuba). Males and females for all of the new species are illustrated, except for Chimarra desirae, for which female specimens were unavailable. Additionally, the female of Chimarra (Chimarrita) camella, which was previously unknown, is illustrated. PMID:22573949

  1. Dissolved mineral species precipitation during coal flotation

    SciTech Connect

    Somasundaran, P.; Liu, D.

    1995-12-31

    Beneficiation by froth flotation, which exploits the difference in surface properties of minerals, has been a promising method for coal cleaning.However, dissolved mineral species present in coal flotation systems can interact with particles and other species leading to drastic effects on flotation. Particularly, precipitation or adsorption of such species on the particles can alter their surface properties and thus influence the efficiency of coal cleaning. In this work, the bulk and surface precipitation of the dissolved mineral species present in Pittsburgh No. 8 coal was investigated under controlled experimental conditions. Changes in the surface properties of coal due to the precipitation were monitored by following zeta potential. Solution potential data were used to elucidate the mechanism of the precipitation. The effect of the precipitation of the dissolved species on the floatability of coal was found to be marked.

  2. The Drosophila flavopilosa species group (Diptera, Drosophilidae)

    PubMed Central

    Robe, Lizandra J.; De Ré, Francine Cenzi; Ludwig, Adriana; Loreto, Elgion L.S.

    2013-01-01

    The D. flavopilosa group encompasses an ecologically restricted set of species strictly adapted to hosting flowers of Cestrum (Solanaceae). This group presents potential to be used as a model to the study of different questions regarding ecologically restricted species macro and microevolutionary responses, geographical vs. ecological speciation and intra and interspecific competition. This review aims to revisit and reanalyze the patterns and processes that are subjacent to the interesting ecological and evolutionary properties of these species. Biotic and abiotic niche properties of some species were reanalyzed in face of ecological niche modeling approaches in order to get some insights into their ecological evolution. A test of the potential of DNA-Barcoding provided evidences that this technology may be a way of overcoming difficulties related to cryptic species differentiation. The new focus replenishes the scenario with new questions, presenting a case where neither geographical nor ecological speciation may be as yet suggested. PMID:23459119

  3. Predicting unknown species numbers using discovery curves

    PubMed Central

    Bebber, Daniel P; Marriott, Francis H.C; Gaston, Kevin J; Harris, Stephen A; Scotland, Robert W

    2007-01-01

    A common approach to estimating the total number of extant species in a taxonomic group is to extrapolate from the temporal pattern of known species descriptions. A formal statistical approach to this problem is provided. The approach is applied to a number of global datasets for birds, ants, mosses, lycophytes, monilophytes (ferns and horsetails), gymnosperms and also to New World grasses and UK flowering plants. Overall, our results suggest that unless the inventory of a group is nearly complete, estimating the total number of species is associated with very large margins of error. The strong influence of unpredictable variations in the discovery process on species accumulation curves makes these data unreliable in estimating total species numbers. PMID:17456460

  4. Organoarsenical species contents in cooked seafood.

    PubMed

    Devesa, V; Súñer, M A; Algora, S; Vélez, D; Montoro, R; Jalón, M; Urieta, I; Macho, M L

    2005-11-02

    The organoarsenical species arsenobetaine (AB), arsenocholine (AC), tetramethylarsonium ion (TMA+), dimethylarsinic acid (DMA), and monomethylarsonic acid (MMA) were determined in 64 cooked seafood products (fish, bivalves, squid, crustaceans) included in a Total Diet Study carried out in the Basque Country (Spain). For cooking, various treatments were employed (grilling, roasting, baking, stewing, boiling, steaming, microwaving). The results obtained show that in cooked seafood AB is the major species, followed by DMA and TMA+. AC and MMA are minor species. The results in cooked seafood were compared with the arsenic species contents obtained for the same product raw. After cooking there was an increase in DMA for sardines and bivalves and an increase or appearance of TMA+ for meagrim, anchovy, Atlantic horse mackerel, and sardine. The data provided add to the very scant information available about organoarsenical species contents in cooked seafood.

  5. The National Nonindigenous Aquatic Species Program

    USGS Publications Warehouse

    Pawlitz, Rachel J.; David, Kayla D.

    2012-01-01

    The U.S. Geological Survey (USGS) Nonindigenous Aquatic Species (NAS) Program monitors, analyzes, and records sightings of non-native (introduced) aquatic species throughout the United States. The program is based at the USGS Southeast Ecological Science Center in Gainesville, Florida. The initiative to maintain scientific information on nationwide occurrences of non-native aquatic species began with the Aquatic Nuisance Species Task Force, a group created by Congress in 1990 to address the need for this type of information by natural resource managers. Since then, the NAS program has maintained the database as a clearinghouse of information for confirmed sightings of non-native aquatic species throughout the Nation. The program also produces email alerts, maps, summary graphs, publications, and other information products to support natural resource managers.

  6. Reactive nitrogen species in cellular signaling

    PubMed Central

    Adams, Levi; Franco, Maria C

    2015-01-01

    The transduction of cellular signals occurs through the modification of target molecules. Most of these modifications are transitory, thus the signal transduction pathways can be tightly regulated. Reactive nitrogen species are a group of compounds with different properties and reactivity. Some reactive nitrogen species are highly reactive and their interaction with macromolecules can lead to permanent modifications, which suggested they were lacking the specificity needed to participate in cell signaling events. However, the perception of reactive nitrogen species as oxidizers of macromolecules leading to general oxidative damage has recently evolved. The concept of redox signaling is now well established for a number of reactive oxygen and nitrogen species. In this context, the post-translational modifications introduced by reactive nitrogen species can be very specific and are active participants in signal transduction pathways. This review addresses the role of these oxidative modifications in the regulation of cell signaling events. PMID:25888647

  7. 75 FR 33633 - Endangered Species Recovery Permit Applications

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-14

    ... Fish and Wildlife Service Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife... conduct certain activities with endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such...

  8. 76 FR 14424 - Endangered Species Recovery Permit Applications

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-16

    ... Fish and Wildlife Service Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife... conduct certain activities with endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows such...

  9. 77 FR 37700 - Endangered Species Recovery Permit Applications

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-22

    ... Fish and Wildlife Service Endangered Species Recovery Permit Applications AGENCY: Fish and Wildlife... conduct certain activities with ] endangered species. With some exceptions, the Endangered Species Act (Act) prohibits activities with endangered and threatened species unless a Federal permit allows...

  10. 77 FR 70456 - Receipt of Applications for Endangered Species Permits

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-26

    ...) bat species, one(1) freshwater fish species, twelve (12) fresh-water mussel species, one (1) snake... authorization to conduct presence/absence surveys for the following freshwater fish species: Etowah...

  11. 76 FR 12990 - Endangered Species Receipt of Applications for Permit

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-09

    ... Fish and Wildlife Service Endangered Species Receipt of Applications for Permit AGENCY: Fish and... certain activities with endangered species. With some exceptions, the Endangered Species Act (ESA.... Background To help us carry out our conservation responsibilities for affected species, the...

  12. ALIEN SPECIES: THEIR ROLE IN AMPHIBIAN POPULATION DECLINES AND RESTORATION

    EPA Science Inventory

    Alien species (also referred to as exotic, invasive, introduced, or normative species) have been implicated as causal agents in population declines of many amphibian species. Herein, we evaluate the relative contributions of alien species and other factors in adversely affecting ...

  13. Abundance of common species, not species richness, drives delivery of a real-world ecosystem service.

    PubMed

    Winfree, Rachael; Fox, Jeremy W; Williams, Neal M; Reilly, James R; Cariveau, Daniel P

    2015-07-01

    Biodiversity-ecosystem functioning experiments have established that species richness and composition are both important determinants of ecosystem function in an experimental context. Determining whether this result holds for real-world ecosystem services has remained elusive, however, largely due to the lack of analytical methods appropriate for large-scale, associational data. Here, we use a novel analytical approach, the Price equation, to partition the contribution to ecosystem services made by species richness, composition and abundance in four large-scale data sets on crop pollination by native bees. We found that abundance fluctuations of dominant species drove ecosystem service delivery, whereas richness changes were relatively unimportant because they primarily involved rare species that contributed little to function. Thus, the mechanism behind our results was the skewed species-abundance distribution. Our finding that a few common species, not species richness, drive ecosystem service delivery could have broad generality given the ubiquity of skewed species-abundance distributions in nature.

  14. 75 FR 38069 - Injurious Wildlife Species; Listing the Boa Constrictor, Four Python Species, and Four Anaconda...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-01

    ... Constrictor, Four Python Species, and Four Anaconda Species as Injurious Reptiles AGENCY: Fish and Wildlife... regulations to add Indian python (Python molurus, including Burmese python Python molurus bivittatus), reticulated python (Broghammerus reticulatus or Python reticulatus), Northern African python (Python...

  15. Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Diaporthe comprises pathogenic, endophytic and saprobic species with both temperate and tropical distributions. Cryptic diversification, phenotypic plasticity and extensive host associations have long complicated accurate identifications of species in this genus. The delimitation of the ge...

  16. Immigration and extinction probabilities for individual species: relation to incidence functions and species colonization curves.

    PubMed Central

    Gilpin, M E; Diamond, J M

    1981-01-01

    We develop a dynamic model of island biogeography based on immigration and extinction probabilities of individual species rather than on the usual biogeographic parameters of the number of species immigrating or going extinct per unit time. In the real world, these probabilities vary enormously among species, and three field studies suggest lognormal distributions. Based on such distributions of individual probabilities, our model proceeds by calculating the conditional probability of species occurrence--the likelihood that a given species will occur on a given island--as a function of total species number on the island. The model succeeds in predicting two observed features of species communities; (i) staggered, sigmoidally-shaped incidence functions ("differing area requirements of different species") and (ii) concave immigration and extinction curves. PMID:6941254

  17. How to assess species richness along single environmental gradients? Implications of potential versus realized species distributions.

    PubMed

    van Goethem, Thomas M W J; Huijbregts, Mark A J; Wamelink, G W Wieger; Schipper, Aafke M

    2015-05-01

    Quantifying relationships between species richness and single environmental factors is challenging as species richness typically depends on multiple environmental factors. Recently, various methods have been proposed to tackle this challenge. Using a dataset comprising field observations of grassland vegetation and measured pH values, we compared three methods for deriving species richness response curves. One of the methods estimates species richness close to the maximum species richness observed at the sites, whereas the other two provide estimates of the potential species richness along the environmental gradient. Our response curves suggest that potential species richness of grasslands is slightly more sensitive to acidification than realized plant species richness. However, differences in corresponding environmental quality standards (EQS) for acidification were small compared to intrinsic spatial differences in natural soil pH, indicating that natural background values are more important to consider in the derivation of EQS for pH than methodological differences between the three approaches.

  18. Spatial complementarity and the coexistence of species.

    PubMed

    Velázquez, Jorge; Garrahan, Juan P; Eichhorn, Markus P

    2014-01-01

    Coexistence of apparently similar species remains an enduring paradox in ecology. Spatial structure has been predicted to enable coexistence even when population-level models predict competitive exclusion if it causes each species to limit its own population more than that of its competitor. Nevertheless, existing hypotheses conflict with regard to whether clustering favours or precludes coexistence. The spatial segregation hypothesis predicts that in clustered populations the frequency of intra-specific interactions will be increased, causing each species to be self-limiting. Alternatively, individuals of the same species might compete over greater distances, known as heteromyopia, breaking down clusters and opening space for a second species to invade. In this study we create an individual-based model in homogeneous two-dimensional space for two putative sessile species differing only in their demographic rates and the range and strength of their competitive interactions. We fully characterise the parameter space within which coexistence occurs beyond population-level predictions, thereby revealing a region of coexistence generated by a previously-unrecognised process which we term the triadic mechanism. Here coexistence occurs due to the ability of a second generation of offspring of the rarer species to escape competition from their ancestors. We diagnose the conditions under which each of three spatial coexistence mechanisms operates and their characteristic spatial signatures. Deriving insights from a novel metric - ecological pressure - we demonstrate that coexistence is not solely determined by features of the numerically-dominant species. This results in a common framework for predicting, given any pair of species and knowledge of the relevant parameters, whether they will coexist, the mechanism by which they will do so, and the resultant spatial pattern of the community. Spatial coexistence arises from complementary combinations of traits in each species

  19. Pseudoabsence Generation Strategies for Species Distribution Models

    PubMed Central

    Hanberry, Brice B.; He, Hong S.; Palik, Brian J.

    2012-01-01

    Background Species distribution models require selection of species, study extent and spatial unit, statistical methods, variables, and assessment metrics. If absence data are not available, another important consideration is pseudoabsence generation. Different strategies for pseudoabsence generation can produce varying spatial representation of species. Methodology We considered model outcomes from four different strategies for generating pseudoabsences. We generating pseudoabsences randomly by 1) selection from the entire study extent, 2) a two-step process of selection first from the entire study extent, followed by selection for pseudoabsences from areas with predicted probability <25%, 3) selection from plots surveyed without detection of species presence, 4) a two-step process of selection first for pseudoabsences from plots surveyed without detection of species presence, followed by selection for pseudoabsences from the areas with predicted probability <25%. We used Random Forests as our statistical method and sixteen predictor variables to model tree species with at least 150 records from Forest Inventory and Analysis surveys in the Laurentian Mixed Forest province of Minnesota. Conclusions Pseudoabsence generation strategy completely affected the area predicted as present for species distribution models and may be one of the most influential determinants of models. All the pseudoabsence strategies produced mean AUC values of at least 0.87. More importantly than accuracy metrics, the two-step strategies over-predicted species presence, due to too much environmental distance between the pseudoabsences and recorded presences, whereas models based on random pseudoabsences under-predicted species presence, due to too little environmental distance between the pseudoabsences and recorded presences. Models using pseudoabsences from surveyed plots produced a balance between areas with high and low predicted probabilities and the strongest relationship between

  20. Spatial Complementarity and the Coexistence of Species

    PubMed Central

    Velázquez, Jorge; Garrahan, Juan P.; Eichhorn, Markus P.

    2014-01-01

    Coexistence of apparently similar species remains an enduring paradox in ecology. Spatial structure has been predicted to enable coexistence even when population-level models predict competitive exclusion if it causes each species to limit its own population more than that of its competitor. Nevertheless, existing hypotheses conflict with regard to whether clustering favours or precludes coexistence. The spatial segregation hypothesis predicts that in clustered populations the frequency of intra-specific interactions will be increased, causing each species to be self-limiting. Alternatively, individuals of the same species might compete over greater distances, known as heteromyopia, breaking down clusters and opening space for a second species to invade. In this study we create an individual-based model in homogeneous two-dimensional space for two putative sessile species differing only in their demographic rates and the range and strength of their competitive interactions. We fully characterise the parameter space within which coexistence occurs beyond population-level predictions, thereby revealing a region of coexistence generated by a previously-unrecognised process which we term the triadic mechanism. Here coexistence occurs due to the ability of a second generation of offspring of the rarer species to escape competition from their ancestors. We diagnose the conditions under which each of three spatial coexistence mechanisms operates and their characteristic spatial signatures. Deriving insights from a novel metric — ecological pressure — we demonstrate that coexistence is not solely determined by features of the numerically-dominant species. This results in a common framework for predicting, given any pair of species and knowledge of the relevant parameters, whether they will coexist, the mechanism by which they will do so, and the resultant spatial pattern of the community. Spatial coexistence arises from complementary combinations of traits in each

  1. Eight known species of Aphelenchoides nematodes with description of a new species from Manipur, India.

    PubMed

    Chanu, L Bina; Mohilal, N; Victoria, L; Shah, M Manjur

    2015-06-01

    Study of Aphelenchoides nematodes from different localities of Manipur were conducted for their documentation. During the study eight known and a new species were identified. Aphelenchoides aerialis sp. nov. differed from all other species of Aphelenchoides in having a tail without bifurcation and strong ventral mucro with single ventrosublateral caudal papillae in male. The known species along with the new species are described in the present study.

  2. Managing aquatic species of conservation concern in the face of climate change and invasive species.

    PubMed

    Rahel, Frank J; Bierwagen, Britta; Taniguchi, Yoshinori

    2008-06-01

    The difficult task of managing species of conservation concern is likely to become even more challenging due to the interaction of climate change and invasive species. In addition to direct effects on habitat quality, climate change will foster the expansion of invasive species into new areas and magnify the effects of invasive species already present by altering competitive dominance, increasing predation rates, and enhancing the virulence of diseases. In some cases parapatric species may expand into new habitats and have detrimental effects that are similar to those of invading non-native species. The traditional strategy of isolating imperiled species in reserves may not be adequate if habitat conditions change beyond historic ranges or in ways that favor invasive species. The consequences of climate change will require a more active management paradigm that includes implementing habitat improvements that reduce the effects of climate change and creating migration barriers that prevent an influx of invasive species. Other management actions that should be considered include providing dispersal corridors that allow species to track environmental changes, translocating species to newly suitable habitats where migration is not possible, and developing action plans for the early detection and eradication of new invasive species.

  3. Protectiveness of Species Sensitivity Distribution Hazard Concentrations for Acute Toxicity Used in Endangered Species Risk Assessment

    EPA Science Inventory

    A primary objective of threatened and endangered species conservation is to ensure that chemical contaminants and other stressors do not adversely affect listed species. Assessments of the ecological risks of chemical exposures to listed species often rely on the use of surrogate...

  4. The Species Problem and the Value of Teaching and the Complexities of Species

    ERIC Educational Resources Information Center

    Chung, Carl

    2004-01-01

    Discussions on species taxa directly refer to a range of complex biological phenomena. Given these phenomena, biologists have developed and continue to appeal to a series of species concepts and do not have a clear definition for it as each species concept tells us part of the story or helps the biologists to explain and understand a subset of…

  5. Rare species contribute disproportionately to the functional structure of species assemblages.

    PubMed

    Leitão, Rafael P; Zuanon, Jansen; Villéger, Sébastien; Williams, Stephen E; Baraloto, Christopher; Fortunel, Claire; Mendonça, Fernando P; Mouillot, David

    2016-04-13

    There is broad consensus that the diversity of functional traits within species assemblages drives several ecological processes. It is also widely recognized that rare species are the first to become extinct following human-induced disturbances. Surprisingly, however, the functional importance of rare species is still poorly understood, particularly in tropical species-rich assemblages where the majority of species are rare, and the rate of species extinction can be high. Here, we investigated the consequences of local and regional extinctions on the functional structure of species assemblages. We used three extensive datasets (stream fish from the Brazilian Amazon, rainforest trees from French Guiana, and birds from the Australian Wet Tropics) and built an integrative measure of species rarity versus commonness, combining local abundance, geographical range, and habitat breadth. Using different scenarios of species loss, we found a disproportionate impact of rare species extinction for the three groups, with significant reductions in levels of functional richness, specialization, and originality of assemblages, which may severely undermine the integrity of ecological processes. The whole breadth of functional abilities within species assemblages, which is disproportionately supported by rare species, is certainly critical in maintaining ecosystems particularly under the ongoing rapid environmental transitions.

  6. 78 FR 52123 - Atlantic Highly Migratory Species; 2006 Consolidated Highly Migratory Species Fishery Management...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-22

    ... Species; 2006 Consolidated Highly Migratory Species Fishery Management Plan; Amendment 7 AGENCY: National... 7 to the 2006 Consolidated Highly Migratory Species (HMS) Fishery Management Plan (FMP) to control... quota categories utilize quota. In this notice, NMFS announces the dates and logistics for 10...

  7. Phylogenetic species recognition and hybridisation in Lasiodiplodia: A case study on species from baobabs.

    PubMed

    Cruywagen, Elsie M; Slippers, Bernard; Roux, Jolanda; Wingfield, Michael J

    2017-04-01

    Lasiodiplodia species (Botryosphaeriaceae, Ascomycota) infect a wide range of typically woody plants on which they are associated with many different disease symptoms. In this study, we determined the identity of Lasiodiplodia isolates obtained from baobab (Adansonia species) trees in Africa and reviewed the molecular markers used to describe Lasiodiplodia species. Publicly available and newly produced sequence data for some of the type strains of Lasiodiplodia species showed incongruence amongst phylogenies of five nuclear loci. We conclude that several of the previously described Lasiodiplodia species are hybrids of other species. Isolates from baobab trees in Africa included nine species of Lasiodiplodia and two hybrid species. Inoculation trials with the most common Lasiodiplodia species collected from these trees produced significant lesions on young baobab trees. There was also variation in aggressiveness amongst isolates from the same species. The apparently widespread tendency of Lasiodiplodia species to hybridise demands that phylogenies from multiple loci (more than two and preferably four or more) are compared for congruence prior to new species being described. This will avoid hybrids being incorrectly described as new taxa, as has clearly occurred in the past.

  8. New species and records of Cactopinus Schwarz with a key to species (Coleoptera, Curculionidae, Scolytinae)

    PubMed Central

    H. Atkinson, Thomas

    2010-01-01

    Abstract Three new species in the genus Cactopinus Schwarz are described from Mexico and the U.S., bringing the total of known species to 21. New host and distribution records and a new key to species are included. PMID:21594169

  9. Monitoring two native Spodoptera species using an exotic pheromone lure developed for an exotic species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The pheromone lure for the exotic species Spodoptera exempta was successful at attracting two native species, S. latifascia and S. albula. Trapping was conducted in north-central Florida and in southern Texas. Large numbers of both native species were collected throughout the season....

  10. Invading species in the Eel River, California: Successes, failures, and relationships with resident species

    USGS Publications Warehouse

    Brown, L.R.; Moyle, P.B.

    1997-01-01

    We examined invasions of non-native fishes into the Eel River, California. At least 16 species of fish have been introduced into the drainage which originally supported 12-14 fish species. Our study was prompted by the unauthorized introduction in 1979 of Sacramento squawfish, Ptychocheilus grandis, a large predatory cyprinid. From 1986 to 1990, we conducted growth and diet studies of squaw fish, conducted intensive surveys of the distribution and habitat associations of both native and introduced species, and examined the nature of species-habitat and interspecies relationships. We found no evidence for increased growth or expanded feeding habits, compared to native populations, of Sacramento squawfish as they invaded the Eel River drainage. Ten of the introduced species were well established, with four species limited to a reservoir and six species established in streams. The success or failure of introductions of stream species appeared to be a function of the ability of a species to survive the fluctuating, highly seasonal, flow regime. The present mixture of native and exotic species has not formed stable fish assemblages but it seems likely that four habitat-associated assemblages will develop. The overall effect of the successful species introductions has been to assemble a group of species, with some exceptions, that are native to and occur together in many California streams. The assemblages now forming are similar to those found in other California streams. The assemblage characterized by squawfish and suckers is likely to be resistant to invasion, in the absence of human caused habitat modifications.

  11. Revision of Microplitis species from China with description of a new species.

    PubMed

    Zhang, Wangzhen; Song, Dongbao; Chen, Jiahua

    2017-02-09

    Microplitis bicoloratus Chen 2004 is a synonym of Microplitis prodeniae Rao & Kurian 1950, and is also the junior homonym of Microplitis bicoloratus Xu & He 2003. A new species, Microplitis fujianica sp. nov. is described and illustrated. The new species is compared with its related species from the Oriental region.

  12. Two New Species of Nocturnal Bees of the Genus Megalopta (Hymenoptera: Halictidae) with Keys to Species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two new species of the nocturnal bee genus Megalopta are described: M. (Megalopta) tetewana, n. sp., from Mexico and M. (Noctoraptor) huaoranii, n. sp., from Ecuador. Identification keys to the Mesoamerican species of Megalopta s. str. and the species of the cleptoparasitic subgenus Noctoraptor ar...

  13. Conservation status of Chinese species: (2) Invertebrates.

    PubMed

    Xie, Yan; Wang, Sung

    2007-06-01

    A total of 2441 invertebrate species were evaluated using the IUCN Red List Criteria and Regional Guidelines. Approximately 30 experts were involved in this project, which covered a wide range of species, including jellyfish, corals, planarians, snails, mollusks, bivalves, decapods, benthic crustaceans, arachnids (spiders, scorpions), butterflies, moths, beetles, sea cucumbers, sea urchins, sea stars, acorn worms and lancelets. In general, invertebrate species in China were found to be severely threatened, with 0.9% being critically endangered, 13.44% endangered and 20.63% vulnerable. All species of hermatypic corals and planarians are threatened. More than 80% of evaluated species face serious threat due to habitat destruction by coral collection, logging, non-woody vegetation collection, timber plantations, non-timber plantations, extraction and/or livestock. Other threats are intrinsic factors, harvesting by humans, alien invasive species and pollution. The main intrinsic factors contributing to the high levels of threat are limited dispersal and restricted range. No conservation measures have been taken for 70% of the threatened invertebrates evaluated. Existing conservation measures include: strengthening of national and international legislation (Convention on International Trade in Endangered Species of Wild Fauna and Flora), increasing public awareness, studying population trends/monitoring, and establishment of protected areas. The major conservation measure employed is strengthening of policies. Relative to the situation worldwide (2006 IUCN Red List), there is little information available about invertebrate extinctions in China.

  14. How variation between individuals affects species coexistence.

    PubMed

    Hart, Simon P; Schreiber, Sebastian J; Levine, Jonathan M

    2016-08-01

    Although the effects of variation between individuals within species are traditionally ignored in studies of species coexistence, the magnitude of intraspecific variation in nature is forcing ecologists to reconsider. Compelling intuitive arguments suggest that individual variation may provide a previously unrecognised route to diversity maintenance by blurring species-level competitive differences or substituting for species-level niche differences. These arguments, which are motivating a large body of empirical work, have rarely been evaluated with quantitative theory. Here we incorporate intraspecific variation into a common model of competition and identify three pathways by which this variation affects coexistence: (1) changes in competitive dynamics because of nonlinear averaging, (2) changes in species' mean interaction strengths because of variation in underlying traits (also via nonlinear averaging) and (3) effects on stochastic demography. As a consequence of the first two mechanisms, we find that intraspecific variation in competitive ability increases the dominance of superior competitors, and intraspecific niche variation reduces species-level niche differentiation, both of which make coexistence more difficult. In addition, individual variation can exacerbate the effects of demographic stochasticity, and this further destabilises coexistence. Our work provides a theoretical foundation for emerging empirical interests in the effects of intraspecific variation on species diversity.

  15. Extinction risks of Amazonian plant species.

    PubMed

    Feeley, Kenneth J; Silman, Miles R

    2009-07-28

    Estimates of the number, and preferably the identity, of species that will be threatened by land-use change and habitat loss are an invaluable tool for setting conservation priorities. Here, we use collections data and ecoregion maps to generate spatially explicit distributions for more than 40,000 vascular plant species from the Amazon basin (representing more than 80% of the estimated Amazonian plant diversity). Using the distribution maps, we then estimate the rates of habitat loss and associated extinction probabilities due to land-use changes as modeled under 2 disturbance scenarios. We predict that by 2050, human land-use practices will have reduced the habitat available to Amazonian plant species by approximately 12-24%, resulting in 5-9% of species becoming "committed to extinction," significantly fewer than other recent estimates. Contrary to previous studies, we find that the primary determinant of habitat loss and extinction risk is not the size of a species' range, but rather its location. The resulting extinction risk estimates are a valuable conservation tool because they indicate not only the total percentage of Amazonian plant species threatened with extinction but also the degree to which individual species and habitats will be affected by current and future land-use changes.

  16. Pushing the Pace of Tree Species Migration

    PubMed Central

    Lazarus, Eli D.; McGill, Brian J.

    2014-01-01

    Plants and animals have responded to past climate changes by migrating with habitable environments, sometimes shifting the boundaries of their geographic ranges by tens of kilometers per year or more. Species migrating in response to present climate conditions, however, must contend with landscapes fragmented by anthropogenic disturbance. We consider this problem in the context of wind-dispersed tree species. Mechanisms of long-distance seed dispersal make these species capable of rapid migration rates. Models of species-front migration suggest that even tree species with the capacity for long-distance dispersal will be unable to keep pace with future spatial changes in temperature gradients, exclusive of habitat fragmentation effects. Here we present a numerical model that captures the salient dynamics of migration by long-distance dispersal for a generic tree species. We then use the model to explore the possible effects of assisted colonization within a fragmented landscape under a simulated tree-planting scheme. Our results suggest that an assisted-colonization program could accelerate species-front migration rates enough to match the speed of climate change, but such a program would involve an environmental-sustainability intervention at a massive scale. PMID:25162663

  17. Species identification of Papaver by metabolite profiling.

    PubMed

    Choe, Sanggil; Kim, Suncheun; Lee, Chul; Yang, Wonkyung; Park, Yuran; Choi, Hwakyung; Chung, Heesun; Lee, Dongho; Hwang, Bang Yeon

    2011-09-10

    Papaver somniferum L. and Papaver setigerum D.C. are controlled as opium poppy in Korea because they contain narcotic substances such as morphine and codeine. It is one of the critical issues whether the plants similar to opium poppy in shape are controlled plants or not. There are more than 110 species in the genus Papaver worldwide and about 10 species in Korea. As the morphological features of some species are very similar and the alkaloid contents and the ratios among the major alkaloids vary even within the same species, it is often difficult to identify the exact species by the morphological features and/or major alkaloids analysis. To develop a new method that uses metabolite profiling for species discrimination between P. somniferum, Papaver rhoeas and P. setigerum, the gas chromatography/mass spectrometry (GC-MS) data of the alkaline extract were processed with in-house Microsoft Visual Basic(®) modules and the chemical information was analyzed through multivariate statistical analyses such as Hierarchical cluster analysis (HCA), principal component analysis (PCA) and discriminant analysis (DA). The GC-MS results combined with multivariate analysis demonstrated that the metabolite profiling was an efficient technique for the classification and this method will provide a powerful tool for the identification of Korean Papaver species.

  18. Energetic Constraints on Species Coexistence in Birds

    PubMed Central

    Pigot, Alexander L.

    2016-01-01

    The association between species richness and ecosystem energy availability is one of the major geographic trends in biodiversity. It is often explained in terms of energetic constraints, such that coexistence among competing species is limited in low productivity environments. However, it has proven challenging to reject alternative views, including the null hypothesis that species richness has simply had more time to accumulate in productive regions, and thus the role of energetic constraints in limiting coexistence remains largely unknown. We use the phylogenetic relationships and geographic ranges of sister species (pairs of lineages who are each other’s closest extant relatives) to examine the association between energy availability and coexistence across an entire vertebrate class (Aves). We show that the incidence of coexistence among sister species increases with overall species richness and is elevated in more productive ecosystems, even when accounting for differences in the evolutionary time available for coexistence to occur. Our results indicate that energy availability promotes species coexistence in closely related lineages, providing a key step toward a more mechanistic understanding of the productivity–richness relationship underlying global gradients in biodiversity. PMID:26974194

  19. Species coexistence in a changing world

    PubMed Central

    Valladares, Fernando; Bastias, Cristina C.; Godoy, Oscar; Granda, Elena; Escudero, Adrián

    2015-01-01

    The consequences of global change for the maintenance of species diversity will depend on the sum of each species responses to the environment and on the interactions among them. A wide ecological literature supports that these species-specific responses can arise from factors related to life strategies, evolutionary history and intraspecific variation, and also from environmental variation in space and time. In the light of recent advances from coexistence theory combined with mechanistic explanations of diversity maintenance, we discuss how global change drivers can influence species coexistence. We revise the importance of both competition and facilitation for understanding coexistence in different ecosystems, address the influence of phylogenetic relatedness, functional traits, phenotypic plasticity and intraspecific variability, and discuss lessons learnt from invasion ecology. While most previous studies have focused their efforts on disentangling the mechanisms that maintain the biological diversity in species-rich ecosystems such as tropical forests, grasslands and coral reefs, we argue that much can be learnt from pauci-specific communities where functional variability within each species, together with demographic and stochastic processes becomes key to understand species interactions and eventually community responses to global change. PMID:26528323

  20. Species ages in neutral biodiversity models.

    PubMed

    Chisholm, Ryan A; O'Dwyer, James P

    2014-05-01

    Biogeography seeks to understand the mechanisms that drive biodiversity across long temporal and large spatial scales. Theoretical models of biogeography can be tested by comparing their predictions of quantities such as species ages against empirical estimates. It has previously been claimed that the neutral theory of biodiversity and biogeography predicts species ages that are unrealistically long. Any improved theory of biodiversity must rectify this problem, but first it is necessary to quantify the problem precisely. Here we provide analytical expressions for species ages in neutral biodiversity communities. We analyse a spatially implicit metacommunity model and solve for both the zero-sum and non-zero-sum cases. We explain why our new expressions are, in the context of biodiversity, usually more appropriate than those previously imported from neutral molecular evolution. Because of the time symmetry of the spatially implicit neutral model, our expressions also lead directly to formulas for species persistence times and species lifetimes. We use our new expressions to estimate species ages of forest trees under a neutral model and find that they are about an order of magnitude shorter than those predicted previously but still unrealistically long. In light of our results, we discuss different models of biogeography that may solve the problem of species ages.

  1. Isoprene emission from tropical tree species.

    PubMed

    Padhy, P K; Varshney, C K

    2005-05-01

    Foliar emission of isoprene was measured in nine commonly growing tree species of Delhi, India. Dynamic flow enclosure technique was used and gas samples were collected onto Tenax-GC/Carboseive cartridges, which were then attached to the sample injection system in the gas chromatograph (GC). Eluting compounds were analysed using a flame ionisation detector (FID). Out of the nine tree species, isoprene emission was found in six species (Eucalyptus sp., Ficus benghalensis, Ficus religiosa, Mangifera indica, Melia azedarach, and Syzygium jambolanum), whereas, in the remaining three tree species (Alstonia scholaris, Azadirachta indica, and Cassia fistula) no isoprene emission was detected or the levels of emission were negligible or below the detection limit (BDL). Among six tree species, the highest hourly emission (10.2 +/- 6.8 microg g(-1) leaf dry weight, average of five seasons) was observed in Ficus religiosa, while minimum emission was from Melia azedarach (2.2 +/- 4.9 microg g(-1) leaf dry weight, average of five seasons). Isoprene emission (average of six species), over five seasons, was found to vary between 3.9 and 8.5 microg g(-1) leaf dry weight during the rainy season. In addition, significant diurnal variation in isoprene emission was observed in each species. The preliminary estimate made in this study on the annual biogenic VOC emission from India may probably be the first of its kind from this part of the world.

  2. Fort Collins Science Center: Invasive Species Science

    USGS Publications Warehouse

    Stohlgren, Tom

    2004-01-01

    FORT is also the administrative home of the National Institute of Invasive Species Science, a growing consortium of partnerships between government and private organizations established by the U.S. Geological Survey (USGS) and its many cooperators. The Institute was formed to develop cooperative approaches for invasive species science that meet the urgent needs of land managers and the public. Its mission is to work with others to coordinate data and research from many sources to predict and reduce the effects of harmful nonnative plants, animals, and diseases in natural areas and throughout the United States, with a strategic approach to information management, research, modeling, technical assistance, and outreach. The Institute research team will develop local-, regional-, and national- scale maps of invasive species and identify priority invasive species, vulnerable habitats, and pathways of invasion. County-level and point data on occurrence will be linked to plot-level and site-level information on species abundance and spread. FORT scientists and Institute partners are working to integrate remote sensing data and GIS-based predictive models to track the spread of invasive species across the country. This information will be linked to control and restoration efforts to evaluate their cost-effectiveness. Understanding both successes and failures will advance the science of invasive species containment and control as well as restoration of habitats and native biodiversity.

  3. Biological and ecological traits of marine species.

    PubMed

    Costello, Mark John; Claus, Simon; Dekeyzer, Stefanie; Vandepitte, Leen; Tuama, Éamonn Ó; Lear, Dan; Tyler-Walters, Harvey

    2015-01-01

    This paper reviews the utility and availability of biological and ecological traits for marine species so as to prioritise the development of a world database on marine species traits. In addition, the 'status' of species for conservation, that is, whether they are introduced or invasive, of fishery or aquaculture interest, harmful, or used as an ecological indicator, were reviewed because these attributes are of particular interest to society. Whereas traits are an enduring characteristic of a species and/or population, a species status may vary geographically and over time. Criteria for selecting traits were that they could be applied to most taxa, were easily available, and their inclusion would result in new research and/or management applications. Numerical traits were favoured over categorical. Habitat was excluded as it can be derived from a selection of these traits. Ten traits were prioritized for inclusion in the most comprehensive open access database on marine species (World Register of Marine Species), namely taxonomic classification, environment, geography, depth, substratum, mobility, skeleton, diet, body size and reproduction. These traits and statuses are being added to the database and new use cases may further subdivide and expand upon them.

  4. Biological and ecological traits of marine species

    PubMed Central

    Claus, Simon; Dekeyzer, Stefanie; Vandepitte, Leen; Tuama, Éamonn Ó; Lear, Dan; Tyler-Walters, Harvey

    2015-01-01

    This paper reviews the utility and availability of biological and ecological traits for marine species so as to prioritise the development of a world database on marine species traits. In addition, the ‘status’ of species for conservation, that is, whether they are introduced or invasive, of fishery or aquaculture interest, harmful, or used as an ecological indicator, were reviewed because these attributes are of particular interest to society. Whereas traits are an enduring characteristic of a species and/or population, a species status may vary geographically and over time. Criteria for selecting traits were that they could be applied to most taxa, were easily available, and their inclusion would result in new research and/or management applications. Numerical traits were favoured over categorical. Habitat was excluded as it can be derived from a selection of these traits. Ten traits were prioritized for inclusion in the most comprehensive open access database on marine species (World Register of Marine Species), namely taxonomic classification, environment, geography, depth, substratum, mobility, skeleton, diet, body size and reproduction. These traits and statuses are being added to the database and new use cases may further subdivide and expand upon them. PMID:26312188

  5. Resistance of polychaete species and trait patterns to simulated species loss in coastal lagoons

    NASA Astrophysics Data System (ADS)

    Faulwetter, Sarah; Papageorgiou, Nafsika; Koulouri, Panayota; Fanini, Lucia; Chatzinikolaou, Eva; Markantonatou, Vasiliki; Pavloudi, Christina; Chatzigeorgiou, Georgios; Keklikoglou, Kleoniki; Vasileiadou, Katerina; Basset, Alberto; Pinna, Maurizio; Rosati, Ilaria; Reizopoulou, Sofia; Nicolaidou, Artemis; Arvanitidis, Christos

    2015-04-01

    The loss of species is known to have negative impacts on the integrity of ecosystems, but the details of this relationship are still far from being fully understood. This study investigates how the distribution patterns of polychaete species and their associated biological trait patterns in six Mediterranean coastal lagoons change under computationally simulated scenarios of random species loss. Species were progressively removed from the full polychaete assemblage and the similarity between the full assemblage and the reduced matrices of both species and trait patterns was calculated. The results indicate the magnitude of changes that might follow species loss in the real world, and allow consideration of the resistance of the system's functional capacity to loss of species, expressed through the species' biological traits as an approximation to functioning. Comparisons were made between the changes in the distribution of species and of traits, as well as between the six different lagoons. While the change of species and trait patterns was strongly correlated within most lagoons, different lagoons showed distinctly different patterns. In disturbed lagoons, the dominance of one or few species was the major driver for the observed patterns and the loss of these species caused extreme changes. Less disturbed lagoons were less susceptible to extreme changes and had a greater resistance towards species loss. Species richness appears to be less important for the ability of the lagoons to buffer changes, instead the initial composition of the assemblage and the identity of the lost species determine the response of the system and our ability to predict changes of the assemblage's functional potential.

  6. Use of RAD sequencing for delimiting species

    PubMed Central

    Pante, E; Abdelkrim, J; Viricel, A; Gey, D; France, S C; Boisselier, M C; Samadi, S

    2015-01-01

    RAD-tag sequencing is a promising method for conducting genome-wide evolutionary studies. However, to date, only a handful of studies empirically tested its applicability above the species level. In this communication, we use RAD tags to contribute to the delimitation of species within a diverse genus of deep-sea octocorals, Chrysogorgia, for which few classical genetic markers have proved informative. Previous studies have hypothesized that single mitochondrial haplotypes can be used to delimit Chrysogorgia species. On the basis of two lanes of Illumina sequencing, we inferred phylogenetic relationships among 12 putative species that were delimited using mitochondrial data, comparing two RAD analysis pipelines (Stacks and PyRAD). The number of homologous RAD loci decreased dramatically with increasing divergence, as >70% of loci are lost when comparing specimens separated by two mutations on the 700-nt long mitochondrial phylogeny. Species delimitation hypotheses based on the mitochondrial mtMutS gene are largely supported, as six out of nine putative species represented by more than one colony were recovered as discrete, well-supported clades. Significant genetic structure (correlating with geography) was detected within one putative species, suggesting that individuals characterized by the same mtMutS haplotype may belong to distinct species. Conversely, three mtMutS haplotypes formed one well-supported clade within which no population structure was detected, also suggesting that intraspecific variation exists at mtMutS in Chrysogorgia. Despite an impressive decrease in the number of homologous loci across clades, RAD data helped us to fine-tune our interpretations of classical mitochondrial markers used in octocoral species delimitation, and discover previously undetected diversity. PMID:25407078

  7. Genus Paracoccidioides: Species Recognition and Biogeographic Aspects

    PubMed Central

    Theodoro, Raquel Cordeiro; Teixeira, Marcus de Melo; Felipe, Maria Sueli Soares; Paduan, Karina dos Santos; Ribolla, Paulo Martins; San-Blas, Gioconda; Bagagli, Eduardo

    2012-01-01

    Background Paracoccidioidomycosis is a systemic mycosis caused by Paracoccidioides brasiliensis (species S1, PS2, PS3), and Paracoccidioides lutzii. This work aimed to differentiate species within the genus Paracoccidioides, without applying multilocus sequencing, as well as to obtain knowledge of the possible speciation processes. Methodology/Principal Findings Single nucleotide polymorphism analysis on GP43, ARF and PRP8 intein genes successfully distinguished isolates into four different species. Morphological evaluation indicated that elongated conidia were observed exclusively in P. lutzii isolates, while all other species (S1, PS2 and PS3) were indistinguishable. To evaluate the biogeographic events that led to the current geographic distribution of Paracoccidioides species and their sister species, Nested Clade and Likelihood Analysis of Geographic Range Evolution (LAGRANGE) analyses were applied. The radiation of Paracoccidioides started in northwest South America, around 11–32 million years ago, as calculated on the basis of ARF substitution rate, in the BEAST program. Vicariance was responsible for the divergence among S1, PS2 and P. lutzii and a recent dispersal generated the PS3 species, restricted to Colombia. Taking into account the ancestral areas revealed by the LAGRANGE analysis and the major geographic distribution of L. loboi in the Amazon basin, a region strongly affected by the Andes uplift and marine incursions in the Cenozoic era, we also speculate about the effect of these geological events on the vicariance between Paracoccidioides and L. loboi. Conclusions/Significance The use of at least 3 SNPs, but not morphological criteria, as markers allows us to distinguish among the four cryptic species of the genus Paracoccidioides. The work also presents a biogeographic study speculating on how these species might have diverged in South America, thus contributing to elucidating evolutionary aspects of the genus Paracoccidioides. PMID:22666382

  8. Blastobotrys von Klopotek (1967)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter describes the anamorphic ascomycete genus Blastobotrys and is to be published in The Yeasts, a Taxonomic Study, 5th edition. The genus Blastobotrys, which represents the asexual state of the genus Trichomonascus, has been phylogenetically defined and has 21 assigned species. Blastobot...

  9. Description of Groenewaldozyma gen. nov. for placement of Candida auringiensis, Candida salmanticensis and Candida tartarivorans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA sequence analyses have demonstrated that species of the polyphyletic anamorphic ascomycete genus Candida may be members of described teleomorphic genera, members of the Candida tropicalis clade upon which the genus Candida is circumscribed, or members of isolated clades that represent undescribe...

  10. The population dynamics of aflatoxigenic aspergilli

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the early eighteenth century, P.A. Micheli characterized the genus Aspergillus as an asexually reproducing species. Nearly a century later the first teleomorph was discovered and identified. Though other teleomorphs have been identified since Eurotium herbariorum (anamorph = A. glaucus), the ge...

  11. Hybrid incompatibility "snowballs" between Solanum species.

    PubMed

    Moyle, Leonie C; Nakazato, Takuya

    2010-09-17

    Among the reproductive barriers that can isolate species, hybrid sterility is frequently due to dysfunctional interactions between loci that accumulate between differentiating lineages. Theory describing the evolution of these incompatibilities has generated the prediction, still empirically untested, that loci underlying hybrid incompatibility should accumulate faster than linearly with time--the "snowball effect." We evaluated the accumulation of quantitative trait loci (QTL) between species in the plant group Solanum and found evidence for a faster-than-linear accumulation of hybrid seed sterility QTL, thus empirically evaluating and confirming this theoretical prediction. In comparison, loci underlying traits unrelated to hybrid sterility show no evidence for an accelerating rate of accumulation between species.

  12. Automatic identification of species with neural networks

    PubMed Central

    Jiménez-Segura, Luz Fernanda

    2014-01-01

    A new automatic identification system using photographic images has been designed to recognize fish, plant, and butterfly species from Europe and South America. The automatic classification system integrates multiple image processing tools to extract the geometry, morphology, and texture of the images. Artificial neural networks (ANNs) were used as the pattern recognition method. We tested a data set that included 740 species and 11,198 individuals. Our results show that the system performed with high accuracy, reaching 91.65% of true positive fish identifications, 92.87% of plants and 93.25% of butterflies. Our results highlight how the neural networks are complementary to species identification. PMID:25392749

  13. Reservoirs of Non-baumannii Acinetobacter Species

    PubMed Central

    Al Atrouni, Ahmad; Joly-Guillou, Marie-Laure; Hamze, Monzer; Kempf, Marie

    2016-01-01

    Acinetobacter spp. are ubiquitous gram negative and non-fermenting coccobacilli that have the ability to occupy several ecological niches including environment, animals and human. Among the different species, Acinetobacter baumannii has evolved as global pathogen causing wide range of infection. Since the implementation of molecular techniques, the habitat and the role of non-baumannii Acinetobacter in human infection have been elucidated. In addition, several new species have been described. In the present review, we summarize the recent data about the natural reservoir of non-baumannii Acinetobacter including the novel species that have been described for the first time from environmental sources and reported during the last years. PMID:26870013

  14. How many species of giraffe are there?

    PubMed

    Bercovitch, Fred B; Berry, Philip S M; Dagg, Anne; Deacon, Francois; Doherty, John B; Lee, Derek E; Mineur, Frédéric; Muller, Zoe; Ogden, Rob; Seymour, Russell; Shorrocks, Bryan; Tutchings, Andy

    2017-02-20

    In a recent paper in Current Biology, Fennessy and colleagues [1] conclude that there are four species of giraffe and that their numbers are declining in Africa. Giraffes (Giraffa camelopardalis) are presently classified as one species, with nine subspecies, which are considered 'Vulnerable' on the IUCN Red List [2]. The present consensus of one species divided into nine subspecies has previously been questioned (Supplemental information), and Fennessy and colleagues [1] provide another viewpoint on giraffe taxonomy. The fundamental reason for different taxonomic interpretations is that they are based upon different datasets that adopt different statistical techniques and follow different criteria for nomenclature.

  15. Plant responses to climatic extremes: within-species variation equals among-species variation.

    PubMed

    Malyshev, Andrey V; Arfin Khan, Mohammed A S; Beierkuhnlein, Carl; Steinbauer, Manuel J; Henry, Hugh A L; Jentsch, Anke; Dengler, Jürgen; Willner, Evelin; Kreyling, Juergen

    2016-01-01

    Within-species and among-species differences in growth responses to a changing climate have been well documented, yet the relative magnitude of within-species vs. among-species variation has remained largely unexplored. This missing comparison impedes our ability to make general predictions of biodiversity change and to project future species distributions using models. We present a direct comparison of among- versus within-species variation in response to three of the main stresses anticipated with climate change: drought, warming, and frost. Two earlier experiments had experimentally induced (i) summer drought and (ii) spring frost for four common European grass species and their ecotypes from across Europe. To supplement existing data, a third experiment was carried out, to compare variation among species from different functional groups to within-species variation. Here, we simulated (iii) winter warming plus frost for four grasses, two nonleguminous, and two leguminous forbs, in addition to eleven European ecotypes of the widespread grass Arrhenatherum elatius. For each experiment, we measured: (i) C/N ratio and biomass, (ii) chlorophyll content and biomass, and (iii) plant greenness, root (15) N uptake, and live and dead tissue mass. Using coefficients of variation (CVs) for each experiment and response parameter, a total of 156 within- vs. among-species comparisons were conducted, comparing within-species variation in each of four species with among-species variation for each seed origin (five countries). Of the six significant differences, within-species CVs were higher than among-species CVs in four cases. Partitioning of variance within each treatment in two of the three experiments showed that within-species variability (ecotypes) could explain an additional 9% of response variation after accounting for the among-species variation. Our observation that within-species variation was generally as high as among-species variation emphasizes the importance of

  16. Revision of the Urophora xanthippe species group, with description of new species (Diptera: Tephritidae).

    PubMed

    Namin, Saeed Mohamadzade; Nozari, Jamasb

    2015-07-23

    The xanthippe group of species of the genus Urophora Robineau-Desvoidy, 1830 is revised and keyed. It contains seven species with a yellow area on the scutum medial to the notopleuron: Urophora bakhtiari new species (from flowerheads of Cousinia archibaldii), Urophora dirlbeki new species (from flowerheads of Onopordum acanthium), U. iani Korneyev & Merz 1998, U. impicta (Hering 1942) (= Urophora hermonis Freidberg 1974, new synonym), U. kasachstanica (Richter 1964), U. stalker Korneyev 1985, and U. xanthippe (Munro 1934). All the species are described, illustrated and keyed.

  17. A new species of the Callophrys paulae Pfeiffer, 1932 species group from Afghanistan (Lepidoptera, Lycaenidae).

    PubMed

    Krupitsky, Anatoly V; Pljushtch, Igor G; Pak, Oleg V

    2015-10-02

    A new species from the Callophrys paulae Pfeiffer, 1932 species group--C. succuba sp. n.--is described from the mountains of Central Afghanistan, Bamyan Province. The new species differs from the geographically close C. p. jomuda Nekrutenko & Tshikolovets in morphology of the male and female genitalia along with the distinct wavy shape of the postdiscal white line on the hindwing underside. Discovery of the new species from C. paulae species group extends known distribution range of the group to the eastern part of the Iranian Plateau in Central Afghanistan.

  18. An updated checklist of mosquito species (Diptera: Culicidae) from Madagascar.

    PubMed

    Tantely, Michaël Luciano; Le Goff, Gilbert; Boyer, Sébastien; Fontenille, Didier

    2016-01-01

    An updated checklist of 235 mosquito species from Madagascar is presented. The number of species has increased considerably compared to previous checklists, particularly the last published in 2003 (178 species). This annotated checklist provides concise information on endemism, taxonomic position, developmental stages, larval habitats, distribution, behavior, and vector-borne diseases potentially transmitted. The 235 species belong to 14 genera: Aedeomyia (3 species), Aedes (35 species), Anopheles (26 species), Coquillettidia (3 species), Culex (at least 50 species), Eretmapodites (4 species), Ficalbia (2 species), Hodgesia (at least one species), Lutzia (one species), Mansonia (2 species), Mimomyia (22 species), Orthopodomyia (8 species), Toxorhynchites (6 species), and Uranotaenia (73 species). Due to non-deciphered species complexes, several species remain undescribed. The main remarkable characteristic of Malagasy mosquito fauna is the high biodiversity with 138 endemic species (59%). Presence and abundance of species, and their association, in a given location could be a bio-indicator of environmental particularities such as urban, rural, forested, deforested, and mountainous habitats. Finally, taking into account that Malagasy culicidian fauna includes 64 species (27%) with a known medical or veterinary interest in the world, knowledge of their biology and host preference summarized in this paper improves understanding of their involvement in pathogen transmission in Madagascar.

  19. An updated checklist of mosquito species (Diptera: Culicidae) from Madagascar

    PubMed Central

    Tantely, Michaël Luciano; Le Goff, Gilbert; Boyer, Sébastien; Fontenille, Didier

    2016-01-01

    An updated checklist of 235 mosquito species from Madagascar is presented. The number of species has increased considerably compared to previous checklists, particularly the last published in 2003 (178 species). This annotated checklist provides concise information on endemism, taxonomic position, developmental stages, larval habitats, distribution, behavior, and vector-borne diseases potentially transmitted. The 235 species belong to 14 genera: Aedeomyia (3 species), Aedes (35 species), Anopheles (26 species), Coquillettidia (3 species), Culex (at least 50 species), Eretmapodites (4 species), Ficalbia (2 species), Hodgesia (at least one species), Lutzia (one species), Mansonia (2 species), Mimomyia (22 species), Orthopodomyia (8 species), Toxorhynchites (6 species), and Uranotaenia (73 species). Due to non-deciphered species complexes, several species remain undescribed. The main remarkable characteristic of Malagasy mosquito fauna is the high biodiversity with 138 endemic species (59%). Presence and abundance of species, and their association, in a given location could be a bio-indicator of environmental particularities such as urban, rural, forested, deforested, and mountainous habitats. Finally, taking into account that Malagasy culicidian fauna includes 64 species (27%) with a known medical or veterinary interest in the world, knowledge of their biology and host preference summarized in this paper improves understanding of their involvement in pathogen transmission in Madagascar. PMID:27101839

  20. Recovery of imperiled species under the Endangered Species Act: The need for a new approach

    USGS Publications Warehouse

    Scott, J.M.; Goble, D.D.; Wiens, J.A.; Wilcove, D.S.; Bean, M.; Male, T.

    2005-01-01

    The recovery (delisting) of a threatened or endangered species is often accompanied by the expectation that conservation management of the species will no longer be necessary. However, the magnitude and pace of human impacts on the environment make it unlikely that substantial progress will be made in delisting many species unless the definition of "recovery" includes some form of active management. Preventing delisted species from again being at risk of extinction may require continuing, species-specific management actions. We characterize such species as "conservation-reliant", and suggest that viewing "recovery" as a continuum of states rather than as a simple "recovered/not recovered" dichotomy may enhance our ability to manage such species within the framework of the Endangered Species Act. With ongoing loss of habitat, disruption of natural disturbance regimes, and the increasing impacts of non-native invasive species, it is probable that the number of conservation-reliant species will increase. We propose the development of "recovery management agreements", with legally and biologically defensible contracts that would provide for continu-ing conservation management following delisting. The use of such formalized agreements will facilitate shared management responsibilities between federal wildlife agencies and other federal agencies, and with state, local, and tribal governments, as well as with private entities that have demonstrated the capability to meet the needs of conservation-reliant species. ?? The Ecological Society of America.

  1. Phenotypic differentiation within a foundation grass species correlates with species richness in a subalpine community.

    PubMed

    Al Hayek, Patrick; Touzard, Blaise; Le Bagousse-Pinguet, Yoann; Michalet, Richard

    2014-10-01

    Few studies have examined consequences of ecotypic differentiation within alpine foundation species for community diversity and their feedbacks for the foundation species' fitness. Additionally, no study has quantified ecotypic differences in competitive effects in the field and in controlled conditions to disentangle genetic from plasticity effects in foundation/subordinate species interactions. We focused on a subalpine community of the French Pyrenees including two phenotypes of a cushion-forming species, Festuca gautieri: tight cushions in dry convex outcrops, and loose cushions (exhibiting high subordinate species richness) in wet concave slopes. We assessed, with field and shadehouse experiments, the genetic vs. plasticity basis of differences in: (1) cushion traits and (2) competitive effects on subordinates, and (3) quantified community feedbacks on foundation species' fitness. We found that trait differences across habitats had both genetic and plasticity bases, with stronger contribution of the latter. Field results showed higher competition within loose than tight phenotypes. In contrast, shadehouse results showed higher competitive ability for tight phenotypes. However, as changes in interactions across habitats were due to environmental effects without changes in cushion effects, we argue that heritable and plastic changes in competitive effects maintain high subordinate species diversity through decreasing competition. We showed high reproduction cost for loose cushions when hosting subordinates highlighting the occurrence of community feedbacks. These results suggest that phenotypic differentiation within foundation species may cascade on subordinate species diversity through heritable and plastic changes in the foundation species' competitive effects, and that community feedbacks may affect foundation species' fitness.

  2. Can conservation of single surrogate species protect co-occurring species?

    PubMed

    Kang, Dongwei; Yang, Hongwei; Li, Junqing; Chen, Youping

    2013-09-01

    Conservation of surrogate species is expected to benefit co-occurring species with similar distributions that share the same habitat, yet the usefulness of this approach to protect nontarget species has been extensively challenged. In this study, we aimed to assess whether co-occurring species could be afforded protection under the conservation of two proposed surrogate species, the giant panda and the takin. We undertook a thorough study on the habitat requirements of these two endangered species, based on the analysis of their habitat preferences. The results revealed that the giant panda exhibits more specialized habitat preferences than does the takin and that habitat separation between these species mainly reflected differences in their dietary requirements and preferences. We suggest that these differences might facilitate their coexistence in sympatric areas. Meanwhile, results of a discriminant function analysis showed that protection of giant pandas would protect 82.1 % of the panda's habitat, but only 25.4 % of the takin's habitat and just 57.0 % of the joint habitats of these species. Importantly, our results also showed that a joint surrogate species approach to conservation would protect 86.9 % of the panda's habitat, 53.7 % of the takin's habitat, and 72.2 % of the joint habitats of these species. This is a higher degree of habitat protection than the single surrogate conservation of pandas. We conclude that the joint surrogate species approach should be adopted to improve biodiversity conservation.

  3. Corroborating molecular species discovery: Four new pine-feeding species of Chionaspis (Hemiptera, Diaspididae)

    PubMed Central

    Vea, Isabelle M.; Gwiazdowski, Rodger A.; Normark, Benjamin B.

    2013-01-01

    Abstract The genus Chionaspis (Hemiptera, Diaspididae) includes two North American species of armored scale insects feeding on Pinaceae: Chionaspis heterophyllae Cooley, and Chionaspis pinifoliae (Fitch). Despite the economic impact of conifer-feeding Chionaspis on horticulture, the species diversity in this group has only recently been systematically investigated using samples from across the group’s geographic and host range. This paper provides morphological recognition characters for four new species that were recently hypothesized to exist on the basis of molecular evidence. The new species, here described, are Chionaspis brachycephalon Vea sp. n., Chionaspis caudata Vea sp. n., Chionaspis sonorae Vea sp. n. and Chionaspis torreyanae Vea sp. n.  One of the new species, Chionaspis caudata Vea, has a gland spine at the apex of the pygidium, between the median lobes, unlike any other species of Chionaspis. An identification key to the species of Chionaspis feeding on pine in North America is provided. PMID:23717184

  4. Genetic diversity in widespread species is not congruent with species richness in alpine plant communities.

    PubMed

    Taberlet, Pierre; Zimmermann, Niklaus E; Englisch, Thorsten; Tribsch, Andreas; Holderegger, Rolf; Alvarez, Nadir; Niklfeld, Harald; Coldea, Gheorghe; Mirek, Zbigniew; Moilanen, Atte; Ahlmer, Wolfgang; Marsan, Paolo Ajmone; Bona, Enzo; Bovio, Maurizio; Choler, Philippe; Cieślak, Elżbieta; Colli, Licia; Cristea, Vasile; Dalmas, Jean-Pierre; Frajman, Božo; Garraud, Luc; Gaudeul, Myriam; Gielly, Ludovic; Gutermann, Walter; Jogan, Nejc; Kagalo, Alexander A; Korbecka, Grażyna; Küpfer, Philippe; Lequette, Benoît; Letz, Dominik Roman; Manel, Stéphanie; Mansion, Guilhem; Marhold, Karol; Martini, Fabrizio; Negrini, Riccardo; Niño, Fernando; Paun, Ovidiu; Pellecchia, Marco; Perico, Giovanni; Piękoś-Mirkowa, Halina; Prosser, Filippo; Puşcaş, Mihai; Ronikier, Michał; Scheuerer, Martin; Schneeweiss, Gerald M; Schönswetter, Peter; Schratt-Ehrendorfer, Luise; Schüpfer, Fanny; Selvaggi, Alberto; Steinmann, Katharina; Thiel-Egenter, Conny; van Loo, Marcela; Winkler, Manuela; Wohlgemuth, Thomas; Wraber, Tone; Gugerli, Felix; Vellend, Mark

    2012-12-01

    The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, that is, ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesised to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning, though their relationship has not been properly evaluated. We tested whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach. We chose the high-mountain flora of the Alps and the Carpathians as study systems and demonstrate that species richness and genetic diversity are not correlated. Species richness thus cannot act as a surrogate for genetic diversity. Our results have important consequences for implementing the CBD when designing conservation strategies.

  5. Fingerprinting the Asterid Species Using Subtracted Diversity Array Reveals Novel Species-Specific Sequences

    PubMed Central

    Mantri, Nitin; Olarte, Alexandra; Li, Chun Guang; Xue, Charlie; Pang, Edwin C. K.

    2012-01-01

    Background Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade. Methodology/Principal Findings Pooled genomic DNA of 104 non-asterid angiosperm and non-angiosperm species was subtracted from pooled genomic DNA of 67 asterid species. Subsequently, 283 subtracted DNA fragments were used to construct an Asterid-specific array. The validation of Asterid-specific array revealed a high (99.5%) subtraction efficiency. Twenty-five Asterid species (mostly medicinal) representing 20 families and 9 orders within the clade were hybridized onto the array to reveal its level of species discrimination. All these species could be successfully differentiated using their hybridization patterns. A number of species-specific probes were identified for commercially important species like tea, coffee, dandelion, yarrow, motherwort, Japanese honeysuckle, valerian, wild celery, and yerba mate. Thirty-seven polymorphic probes were characterized by sequencing. A large number of probes were novel species-specific probes whilst some of them were from chloroplast region including genes like atpB, rpoB, and ndh that have extensively been used for fingerprinting and phylogenetic analysis of plants. Conclusions/Significance Subtracted Diversity Array technique is highly efficient in fingerprinting species with little or no genomic information. The Asterid-specific array could fingerprint all 25 species assessed including three species that were not used in constructing the array. This study validates the use of chloroplast genes for bar-coding (fingerprinting) plant species. In addition, this method allowed detection of several new loci that can be explored to solve

  6. Predicting fish species distribution in estuaries: Influence of species' ecology in model accuracy

    NASA Astrophysics Data System (ADS)

    França, Susana; Cabral, Henrique N.

    2016-10-01

    Current threats to biodiversity, combined with limited data availability, have made for species distribution models (SDMs) to be increasingly used due to their ability to predict species' potential distribution, by relating species occurrence with environmental estimates. Often used in ecology, conservation biology and environmental management, SDMs have been informing conservation strategies, and thus it is becoming crucial to understand how trustworthy their predictions are. Uncertainty in model predictions is expected, but knowing the origin of prediction errors may help reducing it. Indeed, uncertainty may be related not only with data quality and the modelling algorithm used, but also with species ecological characteristics. To investigate whether the performance of SDM's may vary with species' ecological characteristics, distribution models for 21 fish species occurring in estuaries from the Portuguese coast were examined. These models were built at two distinct spatial resolutions and seven environmental explanatory variables were used as predictors. SDMs' accuracy was assessed with the area under the curve (AUC) of receiver operating characteristics (ROC) plots, sensitivity and specificity. Relationships between each measure of accuracy and species ecological characteristics were then examined. SDMs of the fish species presented small differences between the considered scales, and predictors as latitude, temperature and salinity were often selected at both scales. Measures of model accuracy presented differences between species and scales, but generally higher accuracy was obtained at smaller spatial scales. Among the ecological traits tested, species feeding mode and estuarine use functional groups were the most influential on the performance of distribution models. Habitat tolerance (number of habitat types frequented), species abundance, body size and spawning period also showed some effect. This analyses will contribute to distinguish, based on species

  7. Chemotaxis of Azospirillum species to aromatic compounds

    SciTech Connect

    Lopez-de-Victoria, G.; Lovell, C.R. )

    1993-09-01

    Azospirillum sspeciesare free-living nitrogen fixing bacteria commonly found in soils and in association with plant roots, including important agricultural crops. Rhizosphere colonization my Azospirillum species has been shown to stimulate growth of a variety of plant species. Chemotaxis is one of the properties which may contribute to survival, rhizosphere colonization and the initiation of mutualistic interactions by Azospirillum species. This study evaluates the chemotactic responses of three Azospirillum stains to a variety of aromatic compounds:benzoate, catechol, 4-HB, and PCA. Results indicate that the same aromatic substance can elicit different chemotactic responses from different Azospirillum species, and that Azospirillum can detect aromatic substrates at concentrations similar to those they encounter naturally. 36 refs., 1 fig., 6 tabs.

  8. Differentiating pollen from four species of Gossypium

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cotton, Gossypium (Malvaceae), has been spun, woven, and dyed since prehistoric times. Four cotton species are economically important, Gossypium arboreum (tree cotton), G. barbadense (American pima cotton), G. herbaceum (levant cotton), and G. hirsutum (American upland cotton). Previous research h...

  9. New trends in species distribution modelling

    USGS Publications Warehouse

    Zimmermann, Niklaus E.; Edwards, Thomas C.; Graham, Catherine H.; Pearman, Peter B.; Svenning, Jens-Christian

    2010-01-01

    Species distribution modelling has its origin in the late 1970s when computing capacity was limited. Early work in the field concentrated mostly on the development of methods to model effectively the shape of a species' response to environmental gradients (Austin 1987, Austin et al. 1990). The methodology and its framework were summarized in reviews 10–15 yr ago (Franklin 1995, Guisan and Zimmermann 2000), and these syntheses are still widely used as reference landmarks in the current distribution modelling literature. However, enormous advancements have occurred over the last decade, with hundreds – if not thousands – of publications on species distribution model (SDM) methodologies and their application to a broad set of conservation, ecological and evolutionary questions. With this special issue, originating from the third of a set of specialized SDM workshops (2008 Riederalp) entitled 'The Utility of Species Distribution Models as Tools for Conservation Ecology', we reflect on current trends and the progress achieved over the last decade.

  10. 77 FR 23740 - Invasive Species Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-20

    ..., ecological, and human health impacts that invasive species cause. The Council is co-chaired by the Secretary... the Pacific Northwest. A ``systems thinking'' approach to this meeting in both ecological...

  11. Climate change and invasive species: double jeopardy.

    PubMed

    Mainka, Susan A; Howard, Geoffrey W

    2010-06-01

    Two of the key drivers of biodiversity loss today are climate change and invasive species. Climate change is already having a measurable impact on species distributions, reproduction and behavior, and all evidence suggests that things will get worse even if we act tomorrow to mitigate any future increases in greenhouse gas emissions: temperature will increase, precipitation will change, sea level will rise and ocean chemistry will change. At the same time, biological invasions remain an important threat to biodiversity, causing species loss, changes in distribution and habitat degradation. Acting together, the impacts of each of these drivers of change are compounded and interactions between these two threats present even greater challenges to field conservationists as well as policymakers. Similarly, the social and economic impacts of climate change and invasive species, already substantial, will be magnified. Awareness of the links between the two should underpin all biodiversity management planning and policy.

  12. Lunar Gene Bank for Endangered Species

    NASA Astrophysics Data System (ADS)

    Swain, R. K.; Behera, D.; Sahoo, P. K.; Swain, S. K.; Sasmal, A.

    2012-03-01

    In the face of failure of conservation programs, a Gene Bank in the lunar PSR, preferably the Shoemaker crater incorporating natural cryopreservation will provide permanent preservation of germplasms to protect endangered species from extinction.

  13. Endangered Species Litigation and Associated Pesticide Limitations

    EPA Pesticide Factsheets

    EPA has been subject to several citizen suits. As a result we have conducted scientific assessments and made effects determinations for various pesticide products as related to specific species of concern.

  14. Provisional Models for Endangered Species Pesticide Assessments

    EPA Pesticide Factsheets

    The tools and models on this web page were developed for use in the Steps 1 and 2 analyses of national level assessments of the risks of chlorpyrifos, diazinon and malathion to endangered and threatened species and designated critical habitat.

  15. The Grolier World Encyclopedia of Endangered Species.

    ERIC Educational Resources Information Center

    Martin, Ron

    1994-01-01

    Reviews "The Grolier World Encyclopedia of Endangered Species" and describes a lesson plan for grades five and six that includes library media skills objectives, science objectives, resources, instructional roles, activity and procedure for completion, evaluation, and follow-up. (LRW)

  16. Bioeconomic analysis supports the endangered species act.

    PubMed

    Salau, Kehinde R; Fenichel, Eli P

    2015-10-01

    The United States Endangered Species Act (ESA) was enacted to protect and restore declining fish, wildlife, and plant populations. The ESA mandates endangered species protection irrespective of costs. This translates to the restriction of activities that harm endangered populations. We discuss criticisms of the ESA in the context of public land management and examine under what circumstance banning non-conservation activity on multiple use federal lands can be socially optimal. We develop a bioeconomic model to frame the species management problem under the ESA and identify scenarios where ESA-imposed regulations emerge as optimal strategies. Results suggest that banning harmful activities is a preferred strategy when valued endangered species are in decline or exposed to poor habitat quality. However, it is not optimal to sustain such a strategy in perpetuity. An optimal plan involves a switch to land-use practices characteristic of habitat conservation plans.

  17. Detection of Campylobacter species using monoclonal antibodies

    NASA Astrophysics Data System (ADS)

    Young, Colin R.; Lee, Alice; Stanker, Larry H.

    1999-01-01

    A panel of species specific monoclonal antibodies were raised to Campylobacter coli, Campylobacter jejuni and Campylobacter lari. The isotypes, and cross-reactivity profiles of each monoclonal antibody against an extensive panel of micro- organisms, were determined.

  18. Molecular characterization of Eimeria species in macropods.

    PubMed

    Yang, Rongchang; Fenwick, Stan; Potter, Abbey; Elliot, Aileen; Power, Michelle; Beveridge, Ian; Ryan, Una

    2012-10-01

    A total of 597 faecal samples were collected from western grey kangaroos (Macropus fuliginosus), Euros (M. robustus), red kangaroos (M. rufus) in Western Australia and Eastern Grey Kangaroos (M. giganteus) from Victoria and screened for the presence of Eimeria by PCR at the 18S ribosomal RNA (rRNA) locus. The overall prevalence was 24.3% (145/597). At the 18S rRNA locus, sequences were obtained for 25 of the 145 positives. Phylogenetic analysis indicated that all the macropod-derived Eimeria species grouped in a separate marsupial clade that included Eimeria trichosuri from brushtail possums. At least 6 different clades were identified within the marsupial isolates and many of the genotypes identified are likely to be valid species, however morphological and biological data need to be collected to match sequences to previously characterized Eimeria species or identify if they are new species.

  19. Eradication of bacterial species via photosensitization

    NASA Astrophysics Data System (ADS)

    Golding, Paul S.; Maddocks, L.; King, Terence A.; Drucker, D. B.

    1999-02-01

    Photosensitization and inactivation efficacy of three bacterial species: Prevotella nigrescens, Staphylococcus aureus and Escherichia coli have been investigated. Samples of Staphylococcus aureus and Escherichia coli were treated with the triphenylmethane dye malachite green isothiocyanate and exposed to light from a variety of continuous and pulsed light sauces at a wavelength of approximately 630 nm. Inactivation of the Gram-positive species Staphylococcus aureus was found to increase with radiation dose, whilst Gram-negative Escherichia coli was resistant to such treatment. Samples of the pigmented species Prevotella nigrescens were found to be inactivated by exposure to light alone. The mechanism of photosensitization and inactivation of Staphylococcus aureus with malachite green isothiocyanate is addressed. The possible roles of the excited triplet state of the photosensitizer, the involvement of molecular oxygen, and the bacterial cell wall are discussed. Photosensitization may provide a way of eliminating naturally pigmented species responsible for a variety of infections, including oral diseases such as gingivitis and periodontitis.

  20. Local adaptation within a hybrid species.

    PubMed

    Eroukhmanoff, F; Hermansen, J S; Bailey, R I; Sæther, S A; Sætre, G-P

    2013-10-01

    Ecological divergence among populations may be strongly influenced by their genetic background. For instance, genetic admixture through introgressive hybridization or hybrid speciation is likely to affect the genetic variation and evolvability of phenotypic traits. We studied geographic variation in two beak dimensions and three other phenotypic traits of the Italian sparrow (Passer italiae), a young hybrid species formed through interbreeding between house sparrows (P. domesticus) and Spanish sparrows (P. hispaniolensis). We found that beak morphology was strongly influenced by precipitation regimes and that it appeared to be the target of divergent selection within Italian sparrows. Interestingly, however, the degree of parental genetic contribution in the hybrid species had no effect on phenotypic beak variation. Moreover, beak height divergence may mediate genetic differentiation between populations, consistent with isolation-by-adaptation within this hybrid species. The study illustrates how hybrid species may be relatively unconstrained by their admixed genetic background, allowing them to adapt rapidly to environmental variation.

  1. 50 CFR 622.33 - Prohibited species.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ..., DEPARTMENT OF COMMERCE FISHERIES OF THE CARIBBEAN, GULF OF MEXICO, AND SOUTH ATLANTIC Reef Fish Resources of the Gulf of Mexico § 622.33 Prohibited species. (a) General. The harvest and possession...

  2. Ethnobotany of Apocynaceae species in Kenya.

    PubMed

    Omino, E A; Kokwaro, J O

    1993-12-01

    The study of Apocynaceae species used in traditional medicine reveals that 25 species in 16 genera are of ethnobotanical interest. Nineteen species are medicinal, sixteen of which fall under the subfamily Plumerioideae which usually has indole alkaloids. The most common category of diseases treated is skin and ectoparasitic diseases followed by abdominal diseases, diseases of the head, female conditions and venereal diseases. The root is the most commonly used part of the plant and it is possible that the alkaloids play an important role in the medicinal value of the plants. Many species are used for non-medicinal purposes as fruit (Saba comorensis), edible roots (Carissa edulis), poisons (Acokanthera schimperi), fodder (Strophanthus mirabilis), wood (Funtumia africana), birdlime (Tabernaemontana pachysiphon), ornamentals (Adenium obesum), dye (Carissa edulis) and perfume (Wrightia demartiniana).

  3. Functional Diversification within a Predatory Species Flock

    PubMed Central

    Burress, Edward D.; Duarte, Alejandro; Serra, Wilson S.; Loueiro, Marcelo; Gangloff, Michael M.; Siefferman, Lynn

    2013-01-01

    Ecological speciation is well-known from adaptive radiations in cichlid fishes inhabiting lentic ecosystems throughout the African rift valley and Central America. Here, we investigate the ecological and morphological diversification of a recently discovered lotic predatory Neotropical cichlid species flock in subtropical South America. We document morphological and functional diversification using geometric morphometrics, stable C and N isotopes, stomach contents and character evolution. This species flock displays species-specific diets and skull and pharyngeal jaw morphology. Moreover, this lineage appears to have independently evolved away from piscivory multiple times and derived forms are highly specialized morphologically and functionally relative to ancestral states. Ecological speciation played a fundamental role in this radiation and our data reveal novel conditions of ecological speciation including a species flock that evolved: 1) in a piscivorous lineage, 2) under lotic conditions and 3) with pronounced morphological novelties, including hypertrophied lips that appear to have evolved rapidly. PMID:24278349

  4. Spore Size Comparison Between Several Bacillus Species

    DTIC Science & Technology

    2005-10-01

    Spore Size Comparison Between Several Bacillus Species Ruben O. Zandomeni1, Joseph E. Fitzgibbon2, Monica Carrera1, Edward Stuebing2, James E...OCT 2005 2. REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE Spore Size Comparison Between Several Bacillus Species 5a. CONTRACT...Systematic comparison of the size of B.anthracis spores to size of other Bacillus spores (simulants/surrogates) - all spores produced under the same

  5. The ethics of reviving long extinct species.

    PubMed

    Sandler, Ronald

    2014-04-01

    There now appears to be a plausible pathway for reviving species that have been extinct for several decades, centuries, or even millennia. I conducted an ethical analysis of de-extinction of long extinct species. I assessed several possible ethical considerations in favor of pursuing de-extinction: that it is a matter of justice; that it would reestablish lost value; that it would create new value; and that society needs it as a conservation last resort. I also assessed several possible ethical arguments against pursuing de-extinction: that it is unnatural; that it could cause animal suffering; that it could be ecologically problematic or detrimental to human health; and that it is hubristic. There are reasons in favor of reviving long extinct species, and it can be ethically acceptable to do so. However, the reasons in favor of pursuing de-extinction do not have to do with its usefulness in species conservation; rather, they concern the status of revived species as scientific and technological achievements, and it would be ethically problematic to promote de-extinction as a significant conservation strategy, because it does not prevent species extinctions, does not address the causes of extinction, and could be detrimental to some species conservation efforts. Moreover, humanity does not have a responsibility or obligation to pursue de-extinction of long extinct species, and reviving them does not address any urgent problem. Therefore, legitimate ecological, political, animal welfare, legal, or human health concerns associated with a de-extinction (and reintroduction) must be thoroughly addressed for it to be ethically acceptable.

  6. Invasive Species - A Threat to the Homeland?

    DTIC Science & Technology

    2003-04-07

    continent in the 14th century and killed a large portion of the European population or the current problem with leafy spurge , an invasive plant that causes an...and difficult to mitigate. While trying to re-establish native prairie grass and forbs, it was very difficult to eradicate the non-native species and...north it may spread. Total eradication of the species is no longer feasible at this point of its spread and establishment. Government agencies

  7. Defining viral species: making taxonomy useful.

    PubMed

    Peterson, A Townsend

    2014-07-23

    Virus taxonomy at present is best characterized as a categorization of convenience, without a firm basis in the principles of evolutionary biology. Specifically, virus species definitions appear to depend more on tradition and popular opinion among virologists than on firm, quantitative biological evidence. I suggest a series of changes to underlying species concepts that would shift the field from one that simply files viruses away in taxonomic boxes to one that can learn important biological lessons from its taxonomy.

  8. Transvalued species in an African forest.

    PubMed

    Remis, Melissa J; Hardin, Rebecca

    2009-12-01

    We combined ethnographic investigations with repeated ecological transect surveys in the Dzanga-Sangha Dense Forest Reserve (RDS), Central African Republic, to elucidate consequences of intensifying mixed use of forests. We devised a framework for transvaluation of wildlife species, which means the valuing of species on the basis of their ecological, economic, and symbolic roles in human lives. We measured responses to hunting, tourism, and conservation of two transvalued species in RDS: elephants (Loxodonta cyclotis) and gorillas (Gorilla gorilla). Our methods included collecting data on encounter rates and habitat use on line transects. We recorded cross-cultural variation in ideas about and interactions with these species during participant observation of hunting and tourism encounters and ethnographic interviews with hunters, conservation staff, researchers, and tourists. Ecologically, gorillas used human-modified landscapes successfully, and elephants were more vulnerable than gorillas to hunting. Economically, tourism and encounters with elephants and gorillas generated revenues and other benefits for local participants. Symbolically, transvaluation of species seemed to undergird competing institutions of forest management that could prove unsustainable. Nevertheless, transvaluation may also offer alternatives to existing social hierarchies, thereby integrating local and transnational support for conservation measures. The study of transvaluation requires attention to transnational flows of ideas and resources because they influence transspecies interactions. Cross-disciplinary in nature, transvalution of species addresses the political and economic challenges to conservation because it recognizes the varied human communities that shape the survival of wildlife in a given site. Transvaluation of species could foster more socially inclusive management and monitoring approaches attuned to competing economic demands, specific species behaviors, and human

  9. Species sensitivities and prediction of teratogenic potential.

    PubMed Central

    Schardein, J L; Schwetz, B A; Kenel, M F

    1985-01-01

    Many chemicals shown to be teratogenic in laboratory animals are not known to be teratogenic in humans. However, it remains to be determined if the unresponsiveness of humans is due to lessened sensitivity, to generally subteratogenic exposure levels, or to the lack of an appropriate means of identifying human teratogens. On the other hand, with the exception of the coumarin anticoagulant drugs, those agents well accepted as human teratogens have been shown to be teratogenic in one or more laboratory species. Yet, no single species has clearly distinguished itself as being more advantageous in the detection of human teratogens over any other. Among the species used for testing, the rat and mouse most successfully model the human reaction, but the rabbit is less likely than other species to give a false positive finding. Among species less commonly used for testing, primates offered a higher level of predicability than others. Regarding concordance of target malformations, the mouse and rat produced the greatest number of concordant defects, but they also were responsible for the most noncorcordant responses as well. Since no other species is clearly more predictive of the human response, it is concluded that safety decisions should be based on all reproductive and developmental toxicity data in light of the agent's known pharmacokinetic, metabolic and toxicologic parameters. PMID:3905381

  10. Species-specific beaked whale echolocation signals.

    PubMed

    Baumann-Pickering, Simone; McDonald, Mark A; Simonis, Anne E; Solsona Berga, Alba; Merkens, Karlina P B; Oleson, Erin M; Roch, Marie A; Wiggins, Sean M; Rankin, Shannon; Yack, Tina M; Hildebrand, John A

    2013-09-01

    Beaked whale echolocation signals are mostly frequency-modulated (FM) upsweep pulses and appear to be species specific. Evolutionary processes of niche separation may have driven differentiation of beaked whale signals used for spatial orientation and foraging. FM pulses of eight species of beaked whales were identified, as well as five distinct pulse types of unknown species, but presumed to be from beaked whales. Current evidence suggests these five distinct but unidentified FM pulse types are also species-specific and are each produced by a separate species. There may be a relationship between adult body length and center frequency with smaller whales producing higher frequency signals. This could be due to anatomical and physiological restraints or it could be an evolutionary adaption for detection of smaller prey for smaller whales with higher resolution using higher frequencies. The disadvantage of higher frequencies is a shorter detection range. Whales echolocating with the highest frequencies, or broadband, likely lower source level signals also use a higher repetition rate, which might compensate for the shorter detection range. Habitat modeling with acoustic detections should give further insights into how niches and prey may have shaped species-specific FM pulse types.

  11. Historical Biogeography Using Species Geographical Ranges

    PubMed Central

    Quintero, Ignacio; Keil, Petr; Jetz, Walter; Crawford, Forrest W.

    2015-01-01

    Spatial variation in biodiversity is the result of complex interactions between evolutionary history and ecological factors. Methods in historical biogeography combine phylogenetic information with current species locations to infer the evolutionary history of a clade through space and time. A major limitation of most methods for historical biogeographic inference is the requirement of single locations for terminal lineages, reducing contemporary species geographical ranges to a point in two-dimensional space. In reality, geographic ranges usually show complex geographic patterns, irregular shapes, or discontinuities. In this article, we describe a method for phylogeographic analysis using polygonal species geographic ranges of arbitrary complexity. By integrating the geographic diversification process across species ranges, we provide a method to infer the geographic location of ancestors in a Bayesian framework. By modeling migration conditioned on a phylogenetic tree, this approach permits reconstructing the geographic location of ancestors through time. We apply this new method to the diversification of two neotropical bird genera, Trumpeters (Psophia) and Cinclodes ovenbirds. We demonstrate the usefulness of our method (called rase) in phylogeographic reconstruction of species ancestral locations and contrast our results with previous methods that compel researchers to reduce the distribution of species to one point in space. We discuss model extensions to enable a more general, spatially explicit framework for historical biogeographic analysis. PMID:26254671

  12. Global threat to agriculture from invasive species.

    PubMed

    Paini, Dean R; Sheppard, Andy W; Cook, David C; De Barro, Paul J; Worner, Susan P; Thomas, Matthew B

    2016-07-05

    Invasive species present significant threats to global agriculture, although how the magnitude and distribution of the threats vary between countries and regions remains unclear. Here, we present an analysis of almost 1,300 known invasive insect pests and pathogens, calculating the total potential cost of these species invading each of 124 countries of the world, as well as determining which countries present the greatest threat to the rest of the world given their trading partners and incumbent pool of invasive species. We find that countries vary in terms of potential threat from invasive species and also their role as potential sources, with apparently similar countries sometimes varying markedly depending on specifics of agricultural commodities and trade patterns. Overall, the biggest agricultural producers (China and the United States) could experience the greatest absolute cost from further species invasions. However, developing countries, in particular, Sub-Saharan African countries, appear most vulnerable in relative terms. Furthermore, China and the United States represent the greatest potential sources of invasive species for the rest of the world. The analysis reveals considerable scope for ongoing redistribution of known invasive pests and highlights the need for international cooperation to slow their spread.

  13. Historical Biogeography Using Species Geographical Ranges.

    PubMed

    Quintero, Ignacio; Keil, Petr; Jetz, Walter; Crawford, Forrest W

    2015-11-01

    Spatial variation in biodiversity is the result of complex interactions between evolutionary history and ecological factors. Methods in historical biogeography combine phylogenetic information with current species locations to infer the evolutionary history of a clade through space and time. A major limitation of most methods for historical biogeographic inference is the requirement of single locations for terminal lineages, reducing contemporary species geographical ranges to a point in two-dimensional space. In reality, geographic ranges usually show complex geographic patterns, irregular shapes, or discontinuities. In this article, we describe a method for phylogeographic analysis using polygonal species geographic ranges of arbitrary complexity. By integrating the geographic diversification process across species ranges, we provide a method to infer the geographic location of ancestors in a Bayesian framework. By modeling migration conditioned on a phylogenetic tree, this approach permits reconstructing the geographic location of ancestors through time. We apply this new method to the diversification of two neotropical bird genera, Trumpeters (Psophia) and Cinclodes ovenbirds. We demonstrate the usefulness of our method (called rase) in phylogeographic reconstruction of species ancestral locations and contrast our results with previous methods that compel researchers to reduce the distribution of species to one point in space. We discuss model extensions to enable a more general, spatially explicit framework for historical biogeographic analysis.

  14. Phytate, reactive oxygen species and colorectal cancer.

    PubMed

    Owen, R W; Spiegelhalder, B; Bartsch, H

    1998-05-01

    Reproducible high-performance liquid chromatography methods have been developed and validated which allow an accurate quantification of phytic acid in faeces and food and reactive oxygen species in an in vitro model system and in faecal specimens. When applied to the evaluation of reactive oxygen species generation by faeces, this method has shown that 1:100 dilutions of matrix obtained from stool samples of adenoma patients are capable of generating significant quantities of reactive oxygen species as evinced by the production of diphenols from salicylic acid. Moreover, it has been shown that the major product of HO. attack on salicylic acid is 2,5-dihydroxy benzoic acid and not 2, 3-dihydroxy benzoic acid as previously reported. In the presence of the antioxidant ascorbic acid the inhibitory capacity of phytic acid on the generation of reactive oxygen species is completely subverted. Therefore, the kinetics of reactive oxygen species production by faeces is currently under further investigation by high-performance liquid chromatography and chemiluminescence in various patient groups and may give an insight into the role of reactive oxygen species in the aetiology of colorectal cancer.

  15. Global threat to agriculture from invasive species

    PubMed Central

    Paini, Dean R.; Sheppard, Andy W.; Cook, David C.; De Barro, Paul J.; Worner, Susan P.; Thomas, Matthew B.

    2016-01-01

    Invasive species present significant threats to global agriculture, although how the magnitude and distribution of the threats vary between countries and regions remains unclear. Here, we present an analysis of almost 1,300 known invasive insect pests and pathogens, calculating the total potential cost of these species invading each of 124 countries of the world, as well as determining which countries present the greatest threat to the rest of the world given their trading partners and incumbent pool of invasive species. We find that countries vary in terms of potential threat from invasive species and also their role as potential sources, with apparently similar countries sometimes varying markedly depending on specifics of agricultural commodities and trade patterns. Overall, the biggest agricultural producers (China and the United States) could experience the greatest absolute cost from further species invasions. However, developing countries, in particular, Sub-Saharan African countries, appear most vulnerable in relative terms. Furthermore, China and the United States represent the greatest potential sources of invasive species for the rest of the world. The analysis reveals considerable scope for ongoing redistribution of known invasive pests and highlights the need for international cooperation to slow their spread. PMID:27325781

  16. Consideration of species community composition in statistical ...

    EPA Pesticide Factsheets

    Diseases are increasing in marine ecosystems, and these increases have been attributed to a number of environmental factors including climate change, pollution, and overfishing. However, many studies pool disease prevalence into taxonomic groups, disregarding host species composition when comparing sites or assessing environmental impacts on patterns of disease presence. We used simulated data under a known environmental effect to assess the ability of standard statistical methods (binomial and linear regression, ANOVA) to detect a significant environmental effect on pooled disease prevalence with varying species abundance distributions and relative susceptibilities to disease. When one species was more susceptible to a disease and both species only partially overlapped in their distributions, models tended to produce a greater number of false positives (Type I error). Differences in disease risk between regions or along an environmental gradient tended to be underestimated, or even in the wrong direction, when highly susceptible taxa had reduced abundances in impacted sites, a situation likely to be common in nature. Including relative abundance as an additional variable in regressions improved model accuracy, but tended to be conservative, producing more false negatives (Type II error) when species abundance was strongly correlated with the environmental effect. Investigators should be cautious of underlying assumptions of species similarity in susceptib

  17. Response of tree growth and species coexistence to density and species evenness in a young forest plantation with two competing species

    PubMed Central

    Collet, Catherine; Ningre, François; Barbeito, Ignacio; Arnaud, Anthony; Piboule, Alexandre

    2014-01-01

    Background and Aims There is considerable evidence for the presence of positive species diversity–productivity relationships in plant populations, but the population parameters determining the type and strength of the relationship are poorly defined. Relationships between species evenness and tree survival or species coexistence are not well established. The objective of this study was to quantify the joint effects of density and species evenness on tree productivity and species coexistence. Methods A 12-year-old experimental tree plantation mixing two species according to a double gradient of density and species proportion was used. A neighbourhood approach was employed and descriptors of local competition were used to model individual tree growth. Fagus sylvatica and Acer pseudoplatanus were used as model species, as they can be considered as ecologically equivalent in their young stages. Key Results Density and tree size were primary factors determining individual growth and stand productivity. Species identity had a significant, but less pronounced, role. Stand productivity was highest when species evenness was close to 1 and slightly lower in uneven mixtures. The reduction in stand productivity when species evenness decreased was of similar magnitude irrespective of which species became dominant, indicating symmetric effects for the two species. When examining individual tree growth in response to species proportion for each species separately, it was observed for both species that individual trees exhibited greater growth in uneven mixtures in which the other species was more frequent. Conclusions The results suggest that mixtures of these two functionally similar species have the highest production at maximum evenness, indicating a complementary effect between them. The presence of a mixture combines both stabilizing mechanisms (individuals from both species show higher growth when surrounded by individuals from the other species) and equalizing mechanisms

  18. Species delimitation and biogeography of two fir species (Abies) in central China: cytoplasmic DNA variation

    PubMed Central

    Wang, J; Abbott, R J; Peng, Y L; Du, F K; Liu, J-Q

    2011-01-01

    It remains unclear how speciation history might contribute to species-specific variation and affect species delimitation. We examined concordance between cytoplasmic genetic variation and morphological taxonomy in two fir species, Abies chensiensis and A. fargesii, with overlapping distributions in central China. Range-wide genetic variation was investigated using mitochondrial (mt) and plastid (pt) DNA sequences, which contrast in their rates of gene flow. Four mtDNA haplotypes were recovered and showed no obvious species' bias in terms of relative frequency. In contrast, a high level of ptDNA variation was recorded in both species with 3 common ptDNA haplotypes shared between them and 21 rare ptDNA haplotypes specific to one or other species. We argue that the lack of concordance between morphological and molecular variation between the two fir species most likely reflects extensive ancestral polymorphism sharing for both forms of cytoplasmic DNA variation. It is feasible that a relatively fast mutation rate for ptDNA contributed to the production of many species-specific ptDNA haplotypes, which remained rare due to insufficient time passing for their spread and fixation in either species, despite high levels of intraspecific ptDNA gene flow. Our phylogeographic analyses further suggest that polymorphisms in both organelle genomes most likely originated during and following glacial intervals preceding the last glacial maximum, when species distributions became fragmented into several refugia and then expanded in range across central China. PMID:21448232

  19. Local coexistence and genetic isolation of three pollinator species on the same fig tree species.

    PubMed

    Sutton, T L; DeGabriel, J L; Riegler, M; Cook, J M

    2017-01-11

    Molecular tools increasingly reveal cryptic lineages and species that were previously unnoticed by traditional taxonomy. The discovery of cryptic species in sympatry prompts the question of how they coexist in the apparent absence of ecological divergence. However, this assumes first that the molecular taxonomy used to identify cryptic lineages delimits species boundaries accurately. This issue is important, because many diversity studies rely heavily or solely on data from mitochondrial DNA sequences for species delimitation, and several factors may lead to poor identification of species boundaries. We used a multilocus population genetics approach to show that three mtDNA-defined cryptic lineages of the fig wasp Pleistodontes imperialis Saunders, which pollinate Port Jackson figs (Ficus rubiginosa) in north-eastern Australia, represent reproductively isolated species. These species coexist locally, with about 13% of figs (where mating occurs) containing wasps from two or three species. However, there was no evidence for gene flow between them. Confirmed cases of coexisting cryptic species provide excellent opportunities for future studies of the ecological and evolutionary forces shaping both species coexistence and fig/pollinator coevolution.Heredity advance online publication, 11 January 2017; doi:10.1038/hdy.2016.125.

  20. Species concepts and malaria parasites: detecting a cryptic species of Plasmodium.

    PubMed Central

    Perkins, S L

    2000-01-01

    Species of malaria parasite (phylum Apicomplexa: genus Plasmodium) have traditionally been described using the similarity species concept (based primarily on differences in morphological or life-history characteristics). The biological species concept (reproductive isolation) and phylogenetic species concept (based on monophyly) have not been used before in defining species of Plasmodium. Plasmodium azurophilum, described from Anolis lizards in the eastern Caribbean, is actually a two-species cryptic complex. The parasites were studied from eight islands, from Puerto Rico in the north to Grenada in the south. Morphology of the two species is very similar (differences are indistinguishable to the eye), but one infects only erythrocytes and the other only white blood cells. Molecular data for the cytochrome b gene reveal that the two forms are reproductively isolated; distinct haplotypes are present on each island and are never shared between the erythrocyte-infecting and leucocyte-infecting species. Each forms a monophyletic lineage indicating that they diverged before becoming established in the anoles of the eastern Caribbean. This comparison of the similarity, biological and phylogenetic species concepts for malaria parasites reveals the limited value of using only similarity measures in defining protozoan species. PMID:11413654

  1. Multi-gene phylogenies define Ceratocystiopsis and Grosmannia distinct from Ophiostoma

    PubMed Central

    Zipfel, Renate D.; de Beer, Z. Wilhelm; Jacobs, Karin; Wingfield, Brenda D.; Wingfield, Michael J.

    2006-01-01

    Ophiostoma species have diverse morphological features and are found in a large variety of ecological niches. Many different classification schemes have been applied to these fungi in the past based on teleomorph and anamorph features. More recently, studies based on DNA sequence comparisions have shown that Ophiostoma consists of different phylogenetic groups, but the data have not been sufficient to define clear monophyletic lineages represented by practical taxonomic units. We used DNA sequence data from combined partial nuclear LSU and β-tubulin genes to consider the phylogenetic relationships of 50 Ophiostoma species, representing all the major morphological groups in the genus. Our data showed three well-supported, monophyletic lineages in Ophiostoma. Species with Leptographium anamorphs grouped together and to accommodate these species the teleomorph-genus Grosmannia (type species G. penicillata), including 27 species and 24 new combinations, is re-instated. Another well-defined lineage includes species that are cycloheximide-sensitive with short perithecial necks, falcate ascospores and Hyalorhinocladiella anamorphs. For these species, the teleomorph-genus Ceratocystiopsis (type species O. minuta), including 11 species and three new combinations, is re-instated. A third group of species with either Sporothrix or Pesotum anamorphs includes species from various ecological niches such as Protea infructescences in South Africa. This group also includes O. piliferum, the type species of Ophiostoma, and these species are retained in that genus. Ophiostoma is redefined to reflect the changes resulting from new combinations in Grosmannia and Ceratocystiopsis. Our data have revealed additional lineages in Ophiostoma linked to morphological characters. However, these species are retained in Ophiostoma until further data for a larger number of species can be obtained to confirm monophyly of the apparent lineages. PMID:18490973

  2. Extrapolation of acute toxicity across bee species.

    PubMed

    Thompson, Helen

    2016-10-01

    In applying cross-species extrapolation safety factors from honeybees to other bee species, some basic principles of toxicity have not been included, for example, the importance of body mass in determining a toxic dose. The present study re-analyzed published toxicity data, taking into account the reported mass of the individuals in the identified species. The analysis demonstrated a shift to the left in the distribution of sensitivity of honeybees relative to 20 other bee species when body size is taken into account, with the 95(th) percentile for contact and oral toxicity reducing from 10.7 (based on μg/individual bee) to 5.0 (based on μg/g bodyweight). Such an approach results in the real drivers of species differences in sensitivity-such as variability in absorption, distribution, metabolism, and excretion in and target-receptor binding-being more realistically reflected in the revised safety factor. Body mass can also be used to underpin the other parameter of first-tier risk assessment, that is, exposure. However, the key exposure factors that cannot be predicted from bodyweight are the effects of ecology and behavior of the different species on exposure to a treated crop. Further data are required to understand the biology of species associated with agricultural crops and the potential consequences of effects on individuals at the levels of the colony or bee populations. This information will allow the development of appropriate higher-tier refinement of risk assessments and testing strategies rather than extensive additional toxicity testing at Tier 1. Integr Environ Assess Manag 2016;12:622-626. © 2015 SETAC.

  3. Phylogeny of Fomitopsis pinicola: a species complex.

    PubMed

    Haight, John-Erich; Laursen, Gary A; Glaeser, Jessie A; Taylor, D Lee

    2016-09-01

    Fungal species with a broad distribution may exhibit considerable genetic variation over their geographic ranges. Variation may develop among populations based on geographic isolation, lack of migration, and genetic drift, though this genetic variation may not always be evident when examining phenotypic characters. Fomitopsis pinicola is an abundant saprotrophic fungus found on decaying logs throughout temperate regions of the Northern Hemisphere. Phylogenetic studies have addressed the relationship of F. pinicola to other wood-rotting fungi, but pan-continental variation within F. pinicola has not been addressed using molecular data. While forms found growing on hardwood and softwood hosts exhibit variation in habit and appearance, it is unknown if these forms are genetically distinct. In this study, we generated DNA sequences of the nuc rDNA internal transcribed spacers (ITS), the TEF1 gene encoding translation elongation factor 1-α, and the RPB2 gene encoding the second largest subunit of RNA polymerase II for collections across all major geographic regions where this fungus occurs, with a primary focus on North America. We used Bayesian and maximum likelihood analyses and evaluated the gene trees within the species tree using coalescent methods to elucidate evolutionarily independent lineages. We find that F. pinicola sensu lato encompasses four well-supported, congruent clades: a European clade, southwestern US clade, and two sympatric northern North American clades. Each clade represents distinct species according to phylogenetic and population-genetic species concepts. Morphological data currently available for F. pinicola do not delimit these species, and three of the species are not specific to either hardwood or softwood trees. Originally described from Europe, F. pinicola appears to be restricted to Eurasia. Based on DNA data obtained from an isotype, one well-defined and widespread clade found only in North America represents the recently described

  4. Phylogeny of Fomitopsis pinicola: a species complex.

    PubMed

    Haight, John-Erich; Laursen, Gary A; Glaeser, Jessie; Taylor, Lee

    2016-08-22

    Fungal species with a broad distribution may exhibit considerable genetic variation over their geographic ranges. Variation may develop among populations based on geographic isolation, lack of migration, and genetic drift, though this genetic variation may not always be evident when examining phenotypic characters. Fomitopsis pinicola is an abundant saprotrophic fungus found on decaying logs throughout temperate regions of the Northern Hemisphere. Phylogenetic studies have addressed the relationship of F. pinicola to other wood-rotting fungi, but pan-continental variation within F. pinicola has not been addressed using molecular data. While forms found growing on hardwood and softwood hosts exhibit variation in habit and appearance, it is unknown if these forms are genetically distinct. In this study, we generated DNA sequences of the nuc rDNA internal transcribed spacers (ITS), the TEF1 gene encoding translation elongation factor 1-α, and the RPB2 gene encoding the second largest subunit of RNA polymerase II for collections across all major geographic regions where this fungus occurs, with a primary focus on North America. We used Bayesian and maximum likelihood analyses and evaluated the gene trees within the species tree using coalescent methods to elucidate evolutionarily independent lineages. We find that F. pinicola sensu lato encompasses four well-supported, congruent clades: a European clade, southwestern US clade, and two sympatric northern North American clades. Each clade represents distinct species according to phylogenetic and population-genetic species concepts. Morphological data currently available for F. pinicola do not delimit these species, and three of the species are not specific to either hardwood or softwood trees. Originally described from Europe, F. pinicola appears to be restricted to Eurasia. Based on DNA data obtained from an isotype, one well-defined and widespread clade found only in North America represents the recently described

  5. Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex.

    PubMed

    Hagen, Ferry; Khayhan, Kantarawee; Theelen, Bart; Kolecka, Anna; Polacheck, Itzhack; Sionov, Edward; Falk, Rama; Parnmen, Sittiporn; Lumbsch, H Thorsten; Boekhout, Teun

    2015-05-01

    Phylogenetic analysis of 11 genetic loci and results from many genotyping studies revealed significant genetic diversity with the pathogenic Cryptococcus gattii/Cryptococcus neoformans species complex. Genealogical concordance, coalescence-based, and species tree approaches supported the presence of distinct and concordant lineages within the complex. Consequently, we propose to recognize the current C. neoformans var. grubii and C. neoformans var. neoformans as separate species, and five species within C. gattii. The type strain of C. neoformans CBS132 represents a serotype AD hybrid and is replaced. The newly delimited species differ in aspects of pathogenicity, prevalence for patient groups, as well as biochemical and physiological aspects, such as susceptibility to antifungals. MALDI-TOF mass spectrometry readily distinguishes the newly recognized species.

  6. Patterns of species description and species richness of geometrid moths (lepidoptera: geometridae) on the Korean peninsula.

    PubMed

    Choi, Sei-Woong

    2006-02-01

    The diversity and pattern of species description among geometrid moths in Korea from 1883 to 2004 were assessed. A total of 647 geometrid species have been described: Ennominae (275 species, 43%), Larentiinae (227 spp., 35%), Geometrinae (68 spp., 11%), Sterrhinae (67 spp., 11%), Oenochrominae (9 spp., 2%), and Archiearinae (1 sp., <1%). Fourteen authors described more than 80% of geometrid species. The cumulative curve of the number of geometrid species described showed three high-rate peaks of description, around the 1900s, 1950s, and 2000s. The cumulative curves of five subfamilies (Ennominae, Larentiinae, Geometrinae, Sterrhinae, and Oenochrominae) fluctuated equally, and none has clearly reached an asymptote. The localities where a species was first recorded in Korea are mostly in the northern and central parts of the peninsula. The utility of larentiines, which are predominant in mountainous habitats and high latitudes, as a bioindicator for global warming is briefly discussed.

  7. Molecular approaches to identify cryptic species and polymorphic species within a complex community of fig wasps.

    PubMed

    Xiao, Jin-Hua; Wang, Ning-Xin; Li, Yan-Wei; Murphy, Robert W; Wan, Dong-Guang; Niu, Li-Ming; Hu, Hao-Yuan; Fu, Yue-Guan; Huang, Da-Wei

    2010-11-29

    Cryptic and polymorphic species can complicate traditional taxonomic research and both of these concerns are common in fig wasp communities. Species identification is very difficult, despite great effort and the ecological importance of fig wasps. Herein, we try to identify all chalcidoid wasp species hosted by one species of fig, using both morphological and molecular methods. We compare the efficiency of four different DNA regions and find that ITS2 is highly effective for species identification, while mitochondrial COI and Cytb regions appear less reliable, possibly due to the interference signals from either nuclear copies of mtDNA, i.e. NUMTs, or the effects of Wolbachia infections. The analyses suggest that combining multiple markers is the best choice for inferring species identifications as any one marker may be unsuitable in a given case.

  8. Environmental responses, not species interactions, determine synchrony of dominant species in semiarid grasslands.

    PubMed

    Tredennick, Andrew T; de Mazancourt, Claire; Loreau, Michel; Adler, Peter B

    2017-02-01

    Temporal asynchrony among species helps diversity to stabilize ecosystem functioning, but identifying the mechanisms that determine synchrony remains a challenge. Here, we refine and test theory showing that synchrony depends on three factors: species responses to environmental variation, interspecific interactions, and demographic stochasticity. We then conduct simulation experiments with empirical population models to quantify the relative influence of these factors on the synchrony of dominant species in five semiarid grasslands. We found that the average synchrony of per capita growth rates, which can range from 0 (perfect asynchrony) to 1 (perfect synchrony), was higher when environmental variation was present (0.62) rather than absent (0.43). Removing interspecific interactions and demographic stochasticity had small effects on synchrony. For the dominant species in these plant communities, where species interactions and demographic stochasticity have little influence, synchrony reflects the covariance in species responses to the environment. This article is protected by copyright. All rights reserved.

  9. Microsatellite markers for the New Zealand endemic Myosotis pygmaea species group (Boraginaceae) amplify across species1

    PubMed Central

    Prebble, Jessica M.; Tate, Jennifer A.; Meudt, Heidi M.; Symonds, V. Vaughan

    2015-01-01

    Premise of the study: Microsatellite loci were developed as polymorphic markers for the New Zealand endemic Myosotis pygmaea species group (Boraginaceae) for use in species delimitation and population and conservation genetic studies. Methods and Results: Illumina MiSeq sequencing was performed on genomic DNA from seedlings of M. drucei. From trimmed paired-end sequences >400 bp, 484 microsatellite loci were identified. Twelve of 48 microsatellite loci tested were found to be polymorphic and consistently scorable when screened on 53 individuals from four populations representing the geographic range of M. drucei. They also amplify in all other species in the M. pygmaea species group, i.e., M. antarctica, M. brevis, M. glauca, and M. pygmaea, as well as 18 other Myosotis species. Conclusions: These 12 polymorphic microsatellite markers establish an important resource for research and conservation of the M. pygmaea species group and potentially other Southern Hemisphere Myosotis. PMID:26082880

  10. Invasive Species: Federal and Selected State Funding to Address Harmful, Nonnative Species

    DTIC Science & Technology

    2000-08-01

    Invasive species -harmful nonnative plants, animals, and microorganisms - pose a serious threat to U.S. agriculture and the environment, with...estimated damages exceeding billions of dollars annually. Invasive species are found in all 50 states, with some states, such as Florida and Hawaii, more...seriously affected than others. Examples of well-known invasive species include the zebra mussel (a mollusk that clogs water intake pipes and filtration

  11. New species of Graphocaecilius Enderlein (Psocodea: 'Psocoptera': Lachesillidae) from Colombia.

    PubMed

    Arango, Stephania Sandoval; Obando, Ranulfo González; Aldrete, Alfonso Neri García

    2016-08-05

    Three new species of Graphocaecilius Enderlein are here described and illustrated; the species were found in the Colombian departments of Valle del Cauca and Risaralda, raising to five the number of species of this genus in Colombia, making it the most species rich country for Graphocaecilius in South America. A key to the species in the genus is included.

  12. New species and checklist of Turkish Eupithecia Curtis (Geometridae: Larentiinae).

    PubMed

    Mironov, Vladimir

    2013-01-01

    Four new species of Eupithecia are described from Turkey; seven species are added as new for the fauna of Turkey; two taxa are raised from subspecies rank and restored from synonymy to species rank; one species is downgraded to subspecies rank; five other species names are synonymized; an updated checklist of the genus Eupithecia in Turkey is provided.

  13. Two new species of South American Glaresidae (Coleoptera: Scarabaeoidea).

    PubMed

    Paulsen, M J

    2016-08-24

    Two new species of South American Glaresidae (Coleoptera: Scarabaeoidea) are described: Glaresis smithi Paulsen, new species from Argentina, and Glaresis mondacai Paulsen, new species from Chile and Peru. The species are compared to their closest congener, Glaresis fritzi Martínez et al., and a key is provided for the known South American species of the genus Glaresis Erichson.

  14. 76 FR 54480 - Endangered Species; Receipt of Applications for Permit

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-01

    ... Fish and Wildlife Service Endangered Species; Receipt of Applications for Permit AGENCY: Fish and... certain activities with endangered species. With some exceptions, the Endangered Species Act (ESA... responsibilities for affected species, section 10(a)(1)(A) of the Endangered Species Act of 1973, as amended (16...

  15. Competition with wind-pollinated plant species alters floral traits of insect-pollinated plant species

    PubMed Central

    Flacher, Floriane; Raynaud, Xavier; Hansart, Amandine; Motard, Eric; Dajoz, Isabelle

    2015-01-01

    Plant traits related to attractiveness to pollinators (e.g. flowers and nectar) can be sensitive to abiotic or biotic conditions. Soil nutrient availability, as well as interactions among insect-pollinated plants species, can induce changes in flower and nectar production. However, further investigations are needed to determine the impact of interactions between insect-pollinated species and abiotically pollinated species on such floral traits, especially floral rewards. We carried out a pot experiment in which three insect-pollinated plant species were grown in binary mixtures with four wind-pollinated plant species, differing in their competitive ability. Along the flowering period, we measured floral traits of the insect-pollinated species involved in attractiveness to pollinators (i.e. floral display size, flower size, daily and total 1) flower production, 2) nectar volume, 3) amount of sucrose allocated to nectar). Final plant biomass was measured to quantify competitive interactions. For two out of three insect-pollinated species, we found that the presence of a wind-pollinated species can negatively impact floral traits involved in attractiveness to pollinators. This effect was stronger with wind-pollinated species that induced stronger competitive interactions. These results stress the importance of studying the whole plant community (and not just the insect-pollinated plant community) when working on plant-pollinator interactions. PMID:26335409

  16. The Puccinia species of Berkheya (Asteraceae) with description of four new species from South Africa.

    PubMed

    Berndt, Reinhard

    2010-01-01

    Puccinia species (rust fungi, Pucciniales, formerly Uredinales) occurring on Berkheya (syn. Stobaea) of Asteraceae are critically evaluated. Puccinia berkheyicola, P. stobaeae var. stobaeae and P. stobaeae var. woodii are recognized as valid species and varieties, while P. berkheyae is relegated to a synonym of P. stobaeae var. stobaeae. Lectotypes are selected for P. stobaeae var. stobaeae and P. stobaeae var. woodii. P. clanwilliamensis, P. garstfonteinii and P. monsfontium are proposed as new species for three rust fungi previously assigned to P. stobaeae; P. berkheyaephila is described as new on B. bipinnatifida. A key to the accepted species is presented.

  17. Are Introduced Species Better Dispersers Than Native Species? A Global Comparative Study of Seed Dispersal Distance

    PubMed Central

    Flores-Moreno, Habacuc; Thomson, Fiona J.; Warton, David I.; Moles, Angela T.

    2013-01-01

    We provide the first global test of the idea that introduced species have greater seed dispersal distances than do native species, using data for 51 introduced and 360 native species from the global literature. Counter to our expectations, there was no significant difference in mean or maximum dispersal distance between introduced and native species. Next, we asked whether differences in dispersal distance might have been obscured by differences in seed mass, plant height and dispersal syndrome, all traits that affect dispersal distance and which can differ between native and introduced species. When we included all three variables in the model, there was no clear difference in dispersal distance between introduced and native species. These results remained consistent when we performed analyses including a random effect for site. Analyses also showed that the lack of a significant difference in dispersal distance was not due to differences in biome, taxonomic composition, growth form, nitrogen fixation, our inclusion of non-invasive introduced species, or our exclusion of species with human-assisted dispersal. Thus, if introduced species do have higher spread rates, it seems likely that these are driven by differences in post-dispersal processes such as germination, seedling survival, and survival to reproduction. PMID:23818991

  18. Onychiurid species from Wanda Mountains in China, with descriptions of two new species (Collembola, Onychiuridae).

    PubMed

    Sun, Xin; Wu, Donghui

    2014-01-01

    A checklist of onychiurid species from the Wanda Mountains in China is presented. Eighteen species belonging to twelve genera have been found, including two new species. Bionychiurus qinglongensis sp. n. can be easily distinguished from other known species of the genus by the absence of pseudocelli on Th. I tergum and fewer number of vesicles in postantennal organ. Onychiurus heilongjiangensis sp. n. is diagnosed by pseudocellar formulae as 32/133/33352 dorsally and 3/011/31120 ventrally, parapseudocellar formula as 0/000/111001+1(m), ratio of anal spine/unguis as 0.6, unguiculus without inner basal lamella, and male ventral organ absent.

  19. Are introduced species better dispersers than native species? A global comparative study of seed dispersal distance.

    PubMed

    Flores-Moreno, Habacuc; Thomson, Fiona J; Warton, David I; Moles, Angela T

    2013-01-01

    We provide the first global test of the idea that introduced species have greater seed dispersal distances than do native species, using data for 51 introduced and 360 native species from the global literature. Counter to our expectations, there was no significant difference in mean or maximum dispersal distance between introduced and native species. Next, we asked whether differences in dispersal distance might have been obscured by differences in seed mass, plant height and dispersal syndrome, all traits that affect dispersal distance and which can differ between native and introduced species. When we included all three variables in the model, there was no clear difference in dispersal distance between introduced and native species. These results remained consistent when we performed analyses including a random effect for site. Analyses also showed that the lack of a significant difference in dispersal distance was not due to differences in biome, taxonomic composition, growth form, nitrogen fixation, our inclusion of non-invasive introduced species, or our exclusion of species with human-assisted dispersal. Thus, if introduced species do have higher spread rates, it seems likely that these are driven by differences in post-dispersal processes such as germination, seedling survival, and survival to reproduction.

  20. Seasonal species interactions minimize the impact of species turnover on the likelihood of community persistence.

    PubMed

    Saavedra, Serguei; Rohr, Rudolf P; Fortuna, Miguel A; Selva, Nuria; Bascompte, Jordi

    2016-04-01

    Many of the observed species interactions embedded in ecological communities are not permanent, but are characterized by temporal changes that are observed along with abiotic and biotic variations. While work has been done describing and quantifying these changes, little is known about their consequences for species coexistence. Here, we investigate the extent to which changes of species composition impact the likelihood of persistence of the predator-prey community in the highly seasonal Białowieza Primeval Forest (northeast Poland), and the extent to which seasonal changes of species interactions (predator diet) modulate the expected impact. This likelihood is estimated extending recent developments on the study of structural stability in ecological communities. We find that the observed species turnover strongly varies the likelihood of community persistence between summer and winter. Importantly, we demonstrate that the observed seasonal interaction changes minimize the variation in the likelihood of persistence associated with species turnover across the year. We find that these community dynamics can be explained as the coupling of individual species to their environment by minimizing both the variation in persistence conditions and the interaction changes between seasons. Our results provide a homeostatic explanation for seasonal species interactions and suggest that monitoring the association of interactions changes with the level of variation in community dynamics can provide a good indicator of the response of species to environmental pressures.

  1. Historical Species Distribution Models Predict Species Limits in Western Plethodon Salamanders.

    PubMed

    Pelletier, Tara A; Crisafulli, Charlie; Wagner, Steve; Zellmer, Amanda J; Carstens, Bryan C

    2015-11-01

    Allopatry is commonly used to predict boundaries in species delimitation investigations under the assumption that currently allopatric distributions are indicative of reproductive isolation; however, species ranges are known to change over time. Incorporating a temporal perspective of geographic distributions should improve species delimitation; to explore this, we investigate three species of western Plethodon salamanders that have shifted their ranges since the end of the Pleistocene. We generate species distribution models (SDM) of the current range, hindcast these models onto a climatic model 21 Ka, and use three molecular approaches to delimit species in an integrated fashion. In contrast to expectations based on the current distribution, we detect no independent lineages in species with allopatric and patchy distributions (Plethodon vandykei and Plethodon larselli). The SDMs indicate that probable habitat is more expansive than their current range, especially during the last glacial maximum (LGM) (21 Ka). However, with a contiguous distribution, two independent lineages were detected in Plethodon idahoensis, possibly due to isolation in multiple glacial refugia. Results indicate that historical SDMs are a better predictor of species boundaries than current distributions, and strongly imply that researchers should incorporate SDM and hindcasting into their investigations and the development of species hypotheses.

  2. Socially-parasitic Myrmica species (Hymenoptera, Formicidae) of Himalaya, with the description of a new species

    PubMed Central

    Bharti, Himender; Radchenko, Alexander; Sasi, Sishal

    2016-01-01

    Abstract A new socially-parasitic species, Myrmica latra sp. n. is described based on a queen and male from Indian Himalaya. Its queen differs from other species by the distinctly narrower petiole and postpetiole, blunt and non-divergent propodeal spines, and a darker body colour. The taxonomic position of the three known Himalayan socially-parasitic Myrmica species is discussed, and Myrmica ereptrix Bolton 1988 is transferred to the smythiesii species-group. It is supposed that Myrmica nefaria Bharti 2012 is a temporary social parasite, but Myrmica ereptrix and Myrmica latra sp. n. are permanent social parasites, and a key for their identification is provided. PMID:27551216

  3. Helminth parasite species richness in rodents from Southeast Asia: role of host species and habitat.

    PubMed

    Palmeirim, Marta; Bordes, Frédéric; Chaisiri, Kittipong; Siribat, Praphaiphat; Ribas, Alexis; Morand, Serge

    2014-10-01

    Southeast Asia is a biodiversity hotspot that harbours many species of rodents, including some that live in close contact with humans. They host helminth parasites, some of which are of zoonotic importance. It is therefore important to understand the factors that influence the richness of the helminths parasitizing rodents. The specific objectives of this study were to evaluate rodent species as a factor determining helminth richness in rodent assemblages, to identify the major rodent helminth reservoir species and to explore the influence of habitat on helminth richness. We estimated helminth species richness using a large dataset of 18 rodent species (1,651 individuals) originating from Southeast Asia and screened for helminth parasites. The use of an unbiased estimator shows that the helminth species richness varies substantially among rodent species and across habitats. We confirmed this pattern by investigating the number of helminth species per individual rodent in all rodent species, and specifically in the two mitochondrial lineages Rattus tanezumi and R. tanezumi R3, which were captured in all habitats.

  4. Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae)

    PubMed Central

    Ačanski, Jelena; Vujić, Ante; Ståhls, Gunilla; Radenković, Snežana; Milić, Dubravka; Obreht Vidaković, Dragana; Đan, Mihajla

    2016-01-01

    The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods). PMID:27532618

  5. How context dependent are species interactions?

    PubMed

    Chamberlain, Scott A; Bronstein, Judith L; Rudgers, Jennifer A

    2014-07-01

    The net effects of interspecific species interactions on individuals and populations vary in both sign (-, 0, +) and magnitude (strong to weak). Interaction outcomes are context-dependent when the sign and/or magnitude change as a function of the biotic or abiotic context. While context dependency appears to be common, its distribution in nature is poorly described. Here, we used meta-analysis to quantify variation in species interaction outcomes (competition, mutualism, or predation) for 247 published articles. Contrary to our expectations, variation in the magnitude of effect sizes did not differ among species interactions, and while mutualism was most likely to change sign across contexts (and predation least likely), mutualism did not strongly differ from competition. Both the magnitude and sign of species interactions varied the most along spatial and abiotic gradients, and least as a function of the presence/absence of a third species. However, the degree of context dependency across these context types was not consistent among mutualism, competition and predation studies. Surprisingly, study location and ecosystem type varied in the degree of context dependency, with laboratory studies showing the highest variation in outcomes. We urge that studying context dependency per se, rather than focusing only on mean outcomes, can provide a general method for describing patterns of variation in nature.

  6. Alternaria Species and Their Associated Mycotoxins.

    PubMed

    Pinto, Virginia Elena Fernández; Patriarca, Andrea

    2017-01-01

    The genus Alternaria includes more than 250 species. The traditional methods for identification of Alternaria species are based on morphological characteristics of the reproductive structures and sporulation patterns under controlled culture conditions. Cladistics analyses of "housekeeping genes" commonly used for other genera, failed to discriminate among the small-spored Alternaria species. The development of molecular methods achieving a better agreement with morphological differences is still needed. The production of secondary metabolites has also been used as a means of classification and identification. Alternaria spp. can produce a wide variety of toxic metabolites. These metabolites belong principally to three different structural groups: (1) the dibenzopyrone derivatives, alternariol (AOH), alternariol monomethyl ether (AME), and altenuene (ALT); (2) the perylene derivative altertoxins (ATX-I, ATX-II, and ATX II); and (3) the tetramic acid derivative, tenuazonic acid (TeA). TeA, AOH, AME, ALT, and ATX-I are the main. Certain species in the genus Alternaria produce host-specific toxins (HSTs) that contribute to their pathogenicity and virulence. Alternaria species are plant pathogens that cause spoilage of agricultural commodities with consequent mycotoxin accumulation and economic losses. Vegetable foods infected by Alternaria rot could introduce high amounts of these toxins to the human diet. More investigations on the toxic potential of these toxins and their hazard for human consumption are needed to make a reliable risk assessment of dietary exposure.

  7. SERI Aquatic Species Program 1984 annual report

    SciTech Connect

    Not Available

    1985-03-01

    The purpose of this program is to improve the productivity, conversion to fuels, and cost efficiency of aquatic plant species cultivated for energy. The emphasis of the program is on developing oil-yielding microalgae that will grow in the saline waters of the desert in the American Southwest. During 1984 research was carried out under three tasks: biological, engineering, and analysis. Biological research was aimed at improving photosynthetic efficiencies and lipid yield of species that can be cultivated using mass culture technologies operated in the American Southwest. Emphasis has been placed on screening for productive species, developing culture and management techniques for growing desirable species, and understanding photosynthetic and lipid physiology as it applies to increasing yields. Engineering research focused on the development and analysis of harvesting schemes applicable to species of microalgae that grow in saline waters. Three system designs and analyses were initiated in 1984, and these designs will be completed in 1985. The analysis task is designed to support technology development through the determination of cost goals, assessment of resources, and evaluation of emerging technologies. A comprehensive technical and economic evaluation was completed during 1984. This analysis and assessment provided insights into where program emphasis should be placed for the next ten years. 6 refs., 36 figs., 19 tabs.

  8. Invasive species management and research using GIS

    USGS Publications Warehouse

    Holcombe, Tracy R.; Stohlgren, Thomas J.; Jarnevich, Catherine S.

    2007-01-01

    Geographical Information Systems (GIS) are powerful tools in the field of invasive species management. GIS can be used to create potential distribution maps for all manner of taxa, including plants, animals, and diseases. GIS also performs well in the early detection and rapid assessment of invasive species. Here, we used GIS applications to investigate species richness and invasion patterns in fish in the United States (US) at the 6-digit Hydrologic Unit Code (HUC) level. We also created maps of potential spread of the cane toad (Bufo marinus) in the southeastern US at the 8-digit HUC level using regression and environmental envelope techniques. Equipped with this potential map, resource managers can target their field surveys to areas most vulnerable to invasion. Advances in GIS technology, maps, data, and many of these techniques can be found on websites such as the National Institute of Invasive Species Science (www.NIISS.org). Such websites provide a forum for data sharing and analysis that is an invaluable service to the invasive species community.

  9. Measurement of reactive species for plasma medicine

    NASA Astrophysics Data System (ADS)

    Ono, Ryo

    2015-09-01

    Plasma medicine has been intensively studied over the last decade. Reactive oxygen and nitrogen species are responsible for the therapeutic effects in plasma medicine. To examine the therapeutic effects of reactive species, the densities of OH, O, and NO were measured using laser-induced fluorescence (LIF). A helium atmospheric-pressure plasma jet (10 kV, 10 kHz of 40 μs pulses) and a nanosecond streamer discharge (24 kV, 8 ns, 30 Hz) were utilized to treat mouse melanoma cells in a culture medium. Correlation between the dose of reactive species and deactivation rate of melanoma cells was measured with the aid of LIF. The results showed that the rate of cell death correlates with OH density, but not with O and NO densities. Next, a method to supply a specific reactive species to living organisms was developed. It utilizes photolysis of helium-buffered H2O and O2 by vacuum ultraviolet (VUV) light to produce reactive species. The VUV method was utilized to sterilize Bacillus atrophaeus on agar plate. With the VUV method, it was succeeded to show sterilization only by OH radicals. A 30 s treatment with approximately 0.1 ppm OH radicals caused visible sterilization.

  10. A spectacular new species of seadragon (Syngnathidae)

    PubMed Central

    Stiller, Josefin; Wilson, Nerida G.; Rouse, Greg W.

    2015-01-01

    The exploration of Earth's biodiversity is an exciting and ongoing endeavour. Here, we report a new species of seadragon from Western Australia with substantial morphological and genetic differences to the only two other known species. We describe it as Phyllopteryx dewysea n. sp. Although the leafy seadragon (Phycodurus eques) and the common seadragon (Phyllopteryx taeniolatus) occur along Australia's southern coast, generally among relatively shallow macroalgal reefs, the new species was found more offshore in slightly deeper waters. The holotype was trawled east of the remote Recherche Archipelago in 51 m; additional specimens extend the distribution west to Perth in 72 m. Molecular sequence data show clear divergence from the other seadragons (7.4–13.1% uncorrected divergence in mitochondrial DNA) and support a placement as the sister-species to the common seadragon. Radiographs and micro-computed tomography were used on the holotype of the new species and revealed unique features, in addition to its unusual red coloration. The discovery provides a spectacular example of the surprises still hidden in our oceans, even in relatively shallow waters. PMID:26064603

  11. Zoonotic Chlamydiaceae Species Associated with Trachoma, Nepal

    PubMed Central

    Rothschild, James; Ruettger, Anke; Kandel, Ram Prasad; Sachse, Konrad

    2013-01-01

    Trachoma is the leading cause of preventable blindness. Commercial assays do not discriminate among all Chlamydiaceae species that might be involved in trachoma. We investigated whether a commercial Micro-ArrayTube could discriminate Chlamydiaceae species in DNA extracted directly from conjunctival samples from 101 trachoma patients in Nepal. To evaluate organism viability, we extracted RNA, reverse transcribed it, and subjected it to quantitative real-time PCR. We found that 71 (70.3%) villagers were infected. ArrayTube sensitivity was 91.7% and specificity was 100% compared with that of real-time PCR. Concordance between genotypes detected by microarray and ompA genotyping was 100%. Species distribution included 54 (76%) single infections with Chlamydia trachomatis, C. psittaci, C. suis, or C. pecorum, and 17 (24%) mixed infections that includied C. pneumoniae. Ocular infections were caused by 5 Chlamydiaceae species. Additional studies of trachoma pathogenesis involving Chlamydiaceae species other than C. trachomatis and their zoonotic origins are needed. PMID:24274654

  12. Egyptian plant species as new ozone indicators.

    PubMed

    Madkour, Samia A; Laurence, J A

    2002-01-01

    The aim of this study was to test and select one or more highly sensitive, specific and environmentally successful Egyptian bioindicator plants for ozone (O3). For that purpose more than 30 Egyptian species and cultivars were subjected to extensive screening studies under controlled environmental and pollutant exposure conditions to mimic the Egyptian environmental conditions and O3 levels in urban and rural sites. Four plant species were found to be more sensitive to O3 than the universally used O3-bioindicator, tobacco Bel W3, under the Egyptian environmental conditions used. These plant species, jute (Corchorus olitorius c.v. local), clover (Trifolium alexandrinum L. c.v. Masry), garden rocket (Eruca sativa c.v. local) and alfalfa (Medicago sativa L. c.v. local), ranked in order of decreasing sensitivity, exhibited typical O3 injury symptoms faster and at lower 03 concentrations than Bel W3. Three variables were tested in search of a reliable tool for the diagnosis and prediction of O3 response prior to the appearance of visible foliar symptoms: pigment degradation, stomatal conductance (g(s)) and net photosynthetic CO2 assimilation (Pnet). Pigment degradation was found to be unreliable in predicting species sensitivity to O3. Evidence supporting stomatal conductance involvement in 03 tolerance was found only in tolerant species. A good correlation was found between g(s), restriction of O3 and CO2 influx into the mesophyll tissues, and Pnet. Changes in Pnet seemed to depend largely on fluctuations in g(s).

  13. New Potential Pharmaceutical Applications of Hypericum Species.

    PubMed

    Marrelli, Mariangela; Statti, Giancarlo; Conforti, Filomena; Menichini, Francesco

    2016-01-01

    The genus Hypericum includes more than 450 species distributed in Europe, North America, North Africa and West Asia. These plants are widely used in folk medicine for the treatment of inflammation, bacterial and viral infections, burns and gastric disorders. The use for alleviating inflammation and promoting wound healing is well known for H. Perforatum L. (St. John's wort) and other species. Because of its pharmacological activity, H. perforatum L. is one of the most important species of this genus. This plant has been largely utilized for its efficacy in the treatment of mild to moderate depression. However, some other species have been utilized in traditional medicine and have been studied for their phytochemical composition and for their biological activities to date. Hypericum species contain biologically active secondary metabolites belonging to at least ten different classes, with prevalence of naphthodianthrones (hypericin and pseudohypericin), phloroglucinols (hyperforin), flavonoids (rutin, hyperoside, isoquercitrin, quercitrin, quercetin, amentoflavone) and phenylpropanoids (chlorogenic acid). However, great variations in contents have been reported for wild populations worldwide. The purpose of this review is to provide an overview of most recent studies about potential pharmaceutical applications of plants belonging to Hypericum genus. The most interesting isolated active principles and both in vitro and in vivo effects of Hypericum extracts are presented and discussed.

  14. Dynamics of genome change among Legionella species

    PubMed Central

    Joseph, Sandeep J.; Cox, Daniel; Wolff, Bernard; Morrison, Shatavia S.; Kozak-Muiznieks, Natalia A.; Frace, Michael; Didelot, Xavier; Castillo-Ramirez, Santiago; Winchell, Jonas; Read, Timothy D.; Dean, Deborah

    2016-01-01

    Legionella species inhabit freshwater and soil ecosystems where they parasitize protozoa. L. pneumonphila (LP) serogroup-1 (Lp1) is the major cause of Legionnaires’ Disease (LD), a life-threatening pulmonary infection that can spread systemically. The increased global frequency of LD caused by Lp and non-Lp species underscores the need to expand our knowledge of evolutionary forces underlying disease pathogenesis. Whole genome analyses of 43 strains, including all known Lp serogroups 1–17 and 17 emergent LD-causing Legionella species (of which 33 were sequenced in this study) in addition to 10 publicly available genomes, resolved the strains into four phylogenetic clades along host virulence demarcations. Clade-specific genes were distinct for genetic exchange and signal-transduction, indicating adaptation to specific cellular and/or environmental niches. CRISPR spacer comparisons hinted at larger pools of accessory DNA sequences in Lp than predicted by the pan-genome analyses. While recombination within Lp was frequent and has been reported previously, population structure analysis identified surprisingly few DNA admixture events between species. In summary, diverse Legionella LD–causing species share a conserved core-genome, are genetically isolated from each other, and selectively acquire genes with potential for enhanced virulence. PMID:27633769

  15. Malaria vector species in Colombia - A review

    PubMed Central

    Montoya-Lerma, James; Solarte, Yezid A; Giraldo-Calderón, Gloria Isabel; Quiñones, Martha L; Ruiz-López, Freddy; Wilkerson, Richard C; González, Ranulfo

    2016-01-01

    Here we present a comprehensive review of the literature on the vectorial importance of the major Anopheles malaria vectors in Colombia. We provide basic information on the geographical distribution, altitudinal range, immature habitats, adult behaviour, feeding preferences and anthropophily, endophily and infectivity rates. We additionally review information on the life cycle, longevity and population fluctuation of Colombian Anopheles species. Emphasis was placed on the primary vectors that have been epidemiologically incriminated in malaria transmission: Anopheles darlingi, Anopheles albimanus and Anopheles nuneztovari. The role of a selection of local, regional or secondary vectors (e.g., Anopheles pseudopunctipennis and Anopheles neivai) is also discussed. We highlight the importance of combining biological, morphological and molecular data for the correct taxonomical determination of a given species, particularly for members of the species complexes. We likewise emphasise the importance of studying the bionomics of primary and secondary vectors along with an examination of the local conditions affecting the transmission of malaria. The presence and spread of the major vectors and the emergence of secondary species capable of transmitting human Plasmodia are of great interest. When selecting control measures, the anopheline diversity in the region must be considered. Variation in macroclimate conditions over a species’ geographical range must be well understood and targeted to plan effective control measures based on the population dynamics of the local Anopheles species. PMID:21881778

  16. Symbiotic two-species contact process

    NASA Astrophysics Data System (ADS)

    de Oliveira, Marcelo Martins; Dos Santos, Renato Vieira; Dickman, Ronald

    2012-07-01

    We study a contact process (CP) with two species that interact in a symbiotic manner. In our model, each site of a lattice may be vacant or host individuals of species A and/or B; multiple occupancy by the same species is prohibited. Symbiosis is represented by a reduced death rate μ<1 for individuals at sites with both species present. Otherwise, the dynamics is that of the basic CP, with creation (at vacant neighbor sites) at rate λ and death of (isolated) individuals at a rate of unity. Mean-field theory and Monte Carlo simulation show that the critical creation rate λc(μ) is a decreasing function of μ, even though a single-species population must go extinct for λ<λc(1), the critical point of the basic CP. Extensive simulations yield results for critical behavior that are compatible with the directed percolation (DP) universality class, but with unusually strong corrections to scaling. A field-theoretic argument supports the conclusion of DP critical behavior. We obtain similar results for a CP with creation at second-neighbor sites and enhanced survival at first neighbors in the form of an annihilation rate that decreases with the number of occupied first neighbors.

  17. Species interactions differ in their genetic robustness

    DOE PAGES

    Chubiz, Lon M.; Granger, Brian R.; Segre, Daniel; ...

    2015-04-14

    Conflict and cooperation between bacterial species drive the composition and function of microbial communities. Stability of these emergent properties will be influenced by the degree to which species' interactions are robust to genetic perturbations. We use genome-scale metabolic modeling to computationally analyze the impact of genetic changes when Escherichia coli and Salmonella enterica compete, or cooperate. We systematically knocked out in silico each reaction in the metabolic network of E. coli to construct all 2583 mutant stoichiometric models. Then, using a recently developed multi-scale computational framework, we simulated the growth of each mutant E. coli in the presence of S.more » enterica. The type of interaction between species was set by modulating the initial metabolites present in the environment. We found that the community was most robust to genetic perturbations when the organisms were cooperating. Species ratios were more stable in the cooperative community, and community biomass had equal variance in the two contexts. Additionally, the number of mutations that have a substantial effect is lower when the species cooperate than when they are competing. In contrast, when mutations were added to the S. enterica network the system was more robust when the bacteria were competing. These results highlight the utility of connecting metabolic mechanisms and studies of ecological stability. Cooperation and conflict alter the connection between genetic changes and properties that emerge at higher levels of biological organization.« less

  18. The dissimilarity of species interaction networks.

    PubMed

    Poisot, Timothée; Canard, Elsa; Mouillot, David; Mouquet, Nicolas; Gravel, Dominique

    2012-12-01

    In a context of global changes, and amidst the perpetual modification of community structure undergone by most natural ecosystems, it is more important than ever to understand how species interactions vary through space and time. The integration of biogeography and network theory will yield important results and further our understanding of species interactions. It has, however, been hampered so far by the difficulty to quantify variation among interaction networks. Here, we propose a general framework to study the dissimilarity of species interaction networks over time, space or environments, allowing both the use of quantitative and qualitative data. We decompose network dissimilarity into interactions and species turnover components, so that it is immediately comparable to common measures of β-diversity. We emphasise that scaling up β-diversity of community composition to the β-diversity of interactions requires only a small methodological step, which we foresee will help empiricists adopt this method. We illustrate the framework with a large dataset of hosts and parasites interactions and highlight other possible usages. We discuss a research agenda towards a biogeographical theory of species interactions.

  19. Exploring similarities among many species distributions

    USGS Publications Warehouse

    Simmerman, Scott; Wang, Jingyuan; Osborne, James; Shook, Kimberly; Huang, Jian; Godsoe, William; Simons, Theodore R.

    2012-01-01

    Collecting species presence data and then building models to predict species distribution has been long practiced in the field of ecology for the purpose of improving our understanding of species relationships with each other and with the environment. Due to limitations of computing power as well as limited means of using modeling software on HPC facilities, past species distribution studies have been unable to fully explore diverse data sets. We build a system that can, for the first time to our knowledge, leverage HPC to support effective exploration of species similarities in distribution as well as their dependencies on common environmental conditions. Our system can also compute and reveal uncertainties in the modeling results enabling domain experts to make informed judgments about the data. Our work was motivated by and centered around data collection efforts within the Great Smoky Mountains National Park that date back to the 1940s. Our findings present new research opportunities in ecology and produce actionable field-work items for biodiversity management personnel to include in their planning of daily management activities.

  20. Babesia species in questing Ixodes ricinus, Sweden.

    PubMed

    Karlsson, Maria E; Andersson, Martin O

    2016-02-01

    Babesiosis is an emerging tick-transmitted zoonosis in large parts of the world. In Sweden, the occurrence and diversity of Babesia species is largely unknown. In order to estimate the exposure to Babesia from infected ticks, we collected questing Ixodes ricinus from several sites across southern Sweden during two consecutive field seasons and investigated the occurrence of Babesia species. We report for the first time the occurrence of the zoonotic species Babesia venatorum in Swedish ticks, with a prevalence of 1%. We also detected B. microti (prevalence 3.2%) and B. divergens (prevalence 0.2%). The incidence of Babesia in questing ticks is substantially lower than that of several other tick-borne diseases in Sweden. Nevertheless, babesiosis should not be neglected as a possible diagnosis following tick bites in humans and animals in Sweden.