Science.gov

Sample records for cylindrocladium anamorphs species

  1. 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…

  2. On the reclassification of species assigned to Candida and other anamorphic ascomycetous yeast genera based on phylogenetic circumscription.

    PubMed

    Daniel, Heide-Marie; Lachance, Marc-André; Kurtzman, Cletus P

    2014-07-01

    Multigene phylogenies have been instrumental in revising the classification of ascosporic (teleomorph) yeasts in a natural system based on lines of descent. Although many taxonomic changes have already been implemented for teleomorph taxa, this is not yet the case for the large genus Candida and smaller anascosporic (anamorph) genera. In view of the recently introduced requirement that a fungal species or higher taxon be assigned only a single valid name under the new International Code of Nomenclature for algae, fungi, and plants (Melbourne Code), the current species of Candida and other anamorph yeast genera must undergo revision to make genus membership consistent with phylogenetic affinities. A review of existing data and analyses shows that certain Candida species may be assigned to teleomorph genera with high confidence using multigene phylogenies. Candida species that form well-circumscribed phylogenetic clades without any teleomorph member justify the creation of new genera. However, a considerable number of Candida species sit at the end of isolated and often long branches, and hence cannot be assigned to larger species groups. They should be maintained in Candida sensu lato until studied by multigene analyses in datasets with comprehensive taxon sampling. The principle of name stability has to be honoured to the largest extent compatible with a natural classification of Candida species. PMID:24748333

  3. Wickerhamomyces mori sp. nov., an anamorphic yeast species found in the guts of wood-boring insect larvae.

    PubMed

    Hui, Feng-Li; Chen, Liang; Chu, Xue-Ying; Niu, Qiu-Hong; Ke, Tao

    2013-03-01

    A novel anamorphic yeast species is described to accommodate three isolates recovered from the guts of three different wood-boring insect larvae collected in Henan, central China. On the basis of sequence analyses of the D1/D2 domains of the large-subunit rRNA gene and the internal transcribed spacer regions, the three strains are assigned to a novel species of the genus Wickerhamomyces, although the formation of ascospores was not observed. These strains also exhibited a number of distinct morphological and physiological characteristics that clearly differentiated them from Wickerhamomyces mucosus, Candida odintsovae and Wickerhamomyces rabaulensis, the most closely related species. In view of the phenotypic differences and unique rRNA gene sequences, we consider that these three isolates represent a novel species of the genus Wickerhamomyces, Wickerhamomyces mori sp. nov. The type strain is NYNU 1216(T) ( = CICC 1983(T)  = CBS 12678(T)).

  4. 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. PMID:23360973

  5. Starmerella caucasica sp. nov., a novel anamorphic yeast species isolated from flowers in the Caucasus.

    PubMed

    Sipiczki, Matthias

    2013-01-01

    Taxonomic analysis of budding yeast strains isolated from flowers of Wisteria sinensis (Fabales, Fabaceae) abundantly visited by flying insects, mainly bees in city parks of Baku is described. The isolates forming slightly pink colonies and propagating by budding represent a hitherto unknown yeast species for which the name Starmerella caucasica is proposed. The sequences of the D1/D2 domains of the large subunit rRNA genes and the ITS1-5.8S-ITS2 regions were highly similar in the isolates and indicated a close relationship with Candida kuoi and Starmerella bombicola in the phylogenetic analysis. S. caucasica can be separated from these species by its growth on glucosamine and D-tryptophan, in vitamin-free medium and at 37°C, and its inability to grow on citrate, ethylamine, cadaverine and in media supplemented with 0.01% of cycloheximide. The type strain is 11-1071.1(T). It has been deposited in Centralbureau voor Schimmelcultures (Utrecht, the Netherlands) as CBS 12650(T), the National Collection of Agricultural and Industrial Microorganisms (Budapest, Hungary) as NCAIM Y.02030(T) and the Culture Collection of Yeasts (Bratislava, Slovakia) as CCY 90-1-1(T). The GenBank accession numbers for nucleotide sequences of S. caucasica are JX112043 (D1/D2 domain of the 26S rRNA gene) and JX112044 (ITS1-5.8S-ITS2). Mycobank: MB 800536.

  6. Starmerella caucasica sp. nov., a novel anamorphic yeast species isolated from flowers in the Caucasus.

    PubMed

    Sipiczki, Matthias

    2013-01-01

    Taxonomic analysis of budding yeast strains isolated from flowers of Wisteria sinensis (Fabales, Fabaceae) abundantly visited by flying insects, mainly bees in city parks of Baku is described. The isolates forming slightly pink colonies and propagating by budding represent a hitherto unknown yeast species for which the name Starmerella caucasica is proposed. The sequences of the D1/D2 domains of the large subunit rRNA genes and the ITS1-5.8S-ITS2 regions were highly similar in the isolates and indicated a close relationship with Candida kuoi and Starmerella bombicola in the phylogenetic analysis. S. caucasica can be separated from these species by its growth on glucosamine and D-tryptophan, in vitamin-free medium and at 37°C, and its inability to grow on citrate, ethylamine, cadaverine and in media supplemented with 0.01% of cycloheximide. The type strain is 11-1071.1(T). It has been deposited in Centralbureau voor Schimmelcultures (Utrecht, the Netherlands) as CBS 12650(T), the National Collection of Agricultural and Industrial Microorganisms (Budapest, Hungary) as NCAIM Y.02030(T) and the Culture Collection of Yeasts (Bratislava, Slovakia) as CCY 90-1-1(T). The GenBank accession numbers for nucleotide sequences of S. caucasica are JX112043 (D1/D2 domain of the 26S rRNA gene) and JX112044 (ITS1-5.8S-ITS2). Mycobank: MB 800536. PMID:23518520

  7. 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.

  8. 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.

  9. 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...

  10. 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.

  11. 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.

  12. Gibberella xylarioides (anamorph: Fusarium xylarioides), a causative agent of coffee wilt disease in Africa, is a previously unrecognized member of the G. fujikuroi species complex.

    PubMed

    Geiser, David M; Ivey, Melanie L Lewis; Hakiza, Georgina; Juba, Jean H; Miller, Sally A

    2005-01-01

    Tracheomycosis or coffee wilt has emerged as a major disease of robusta coffee in Uganda in the past 10 years. Coffee wilt historically has been associated with Fusarium xylarioides Steyaert (teleomorph Gibberella xylarioides Heim and Sacc.), a species that has been classified as a member of Fusarium section Lateritium. We investigated the molecular phylogenetics of fusarial coffee wilt isolates by generating partial DNA sequences from two protein coding regions, translation elongation factor 1-alpha and beta-tubulin, in 36 isolates previously identified as F. xylarioides and related fusaria from coffee and other woody hosts, as well as from 12 isolates associated with a current coffee wilt outbreak in Uganda. These isolates fell into two morphologically and phylogenetically distinct groups. The first group was found to represent previously unidentified members of the Gibberella fujikuroi species complex (GFC), a clade that replaces the artificial Fusarium section Liseola. This group of isolates fit the original description of F. xylarioides, thus connecting it to the GFC. The second group, which was diverse in its morphology and DNA sequences, comprised four distinct lineages related to Fusarium lateritium. Our finding of unrelated species associated with coffee wilt disease has important implications regarding its epidemiology, etiology and control. PMID:16389971

  13. New anamorphic yeast species: Candida infanticola sp. nov., Candida polysorbophila sp. nov., Candida transvaalensis sp. nov. and Trigonopsis californica sp. nov.

    PubMed

    Kurtzman, Cletus P

    2007-08-01

    Three new species of Candida and a new species of Trigonopsis are described based on their recognition from phylogenetic analysis of gene sequences from large subunit ribosomal RNA, ITS1/ITS2 rRNA, mitochondrial small subunit rRNA and cytochrome oxidase II. Candida infanticola sp. nov. (type strain NRRL Y-17858, CBS 7922) was isolated from the ear of an infant in Germany and is closely related to Candida sorbophila. Candida polysorbophila sp. nov. (type strain NRRL Y-27161, CBS 7317) is a member of the Zygoascus clade and was isolated in South Africa as a contaminant from an emulsion of white oil and polysorbate. Candida transvaalensis sp. nov. (type strain NRRL Y-27140, CBS 6663) was obtained from forest litter, the Transvaal, South Africa, and forms an isolated clade with Candida santjacobensis. Trigonopsis californica sp. nov. (type strain NRRL Y-27307, CBS 10351) represents a contaminant from wine in California, and forms a well-supported clade with Trigonopsis cantarellii, Trigonopsis variabilis and Trigonopsis vinaria.

  14. Anamorphic Imaging with Three Mirrors: A Survey

    NASA Technical Reports Server (NTRS)

    Howard, Joseph M.; Stone, Bryan D.

    2010-01-01

    Design methods are described for unobstructed, plane-symmetric, anamorphic systems composed of three mirrors. Low order imaging constraints are used to reduce the dimensionality of the configuration space. Examples are presented from a specific class of systems with fixed packaging constraints.

  15. Anamorphic high-NA EUV lithography optics

    NASA Astrophysics Data System (ADS)

    Migura, Sascha; Kneer, Bernhard; Neumann, Jens Timo; Kaiser, Winfried; van Schoot, Jan

    2015-09-01

    EUV lithography (EUVL) for a limit resolution below 8 nm requires the numerical aperture (NA) of the projection optics to be larger than 0.50. For such a high-NA optics a configuration of 4x magnification, full field size of 26 x 33 mm² and 6'' mask is not feasible anymore. The increased chief ray angle and higher NA at reticle lead to non-acceptable mask shadowing effects. These shadowing effects can only be controlled by increasing the magnification, hence reducing the system productivity or demanding larger mask sizes. We demonstrate that the best compromise in imaging, productivity and field split is a so-called anamorphic magnification and a half field of 26 x 16.5 mm² but utilizing existing 6'' mask infrastructure. We discuss the optical solutions for such anamorphic high-NA EUVL.

  16. 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.

  17. Phylogeny and systematics of the anamorphic, entomopathogenic genus Beauveria.

    PubMed

    Rehner, Stephen A; Minnis, Andrew M; Sung, Gi-Ho; Luangsa-ard, J Jennifer; Devotto, Luis; Humber, Richard A

    2011-01-01

    Beauveria is a cosmopolitan anamorphic genus of arthropod pathogens that includes the agronomically important species, B. bassiana and B. brongniartii, which are used as mycoinsecticides for the biological control of pest insects. Recent phylogenetic evidence demonstrates that Beauveria is monophyletic within the Cordycipitaceae (Hypocreales), and both B. bassiana and B. brongniartii have been linked developmentally and phylogenetically to Cordyceps species. Despite recent interest in the genetic diversity and molecular ecology of Beauveria, particularly as it relates to their role as pathogens of insects in natural and agricultural environments, the genus has not received critical taxonomic review for several decades. A multilocus phylogeny of Beauveria based on partial sequences of RPB1, RPB2, TEF and the nuclear intergenic region, Bloc, is presented and used to assess diversity within the genus and to evaluate species concepts and their taxonomic status. B. bassiana and B. brongniartii, both which represent species complexes and which heretofore have lacked type specimens, are redescribed and types are proposed. In addition six new species are described including B. varroae and B. kipukae, which form a biphyletic, morphologically cryptic sister lineage to B. bassiana, B. pseudobassiana, which also is morphologically similar to but phylogenetically distant from B. bassiana, B. asiatica and B. australis, which are sister lineages to B. brongniartii, and B. sungii, an Asian species that is linked to an undetermined species of Cordyceps. The combination B. amorpha is validly published and an epitype is designated. PMID:21482632

  18. 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

  19. Emulation of anamorphic imaging on the SHARP EUV 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.

    2016-03-01

    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 several generations into the future. An anamorphic imaging optic with increased mask side-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.1 Zoneplate lenses with an anamorphic 4x/8x 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 4x/8xNA and 6° central ray angle is compared to conventional imaging at 0.5 4xNA and 8° central ray angle. 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.

  20. 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

  1. Climatic mapping to identify high-risk areas for Cylindrocladium quinqueseptatum leaf blight on eucalypts in mainland South East Asia and around the world.

    PubMed

    Booth, T H; Jovanovic, T; Old, K M; Dudzinski, M J

    2000-06-01

    Cylindrocladium quinqueseptatum is a pathogen on a wide range of hosts. It affects at least 20 species of eucalypts and is an important causal agent of leaf blight of Eucalyptus camaldulensis in central and southern Vietnam. Results from previous studies and observations of broadscale infection patterns in mainland South East Asia were used to derive simple rules (i.e. mean minimum temperature of coldest month > or =16 degrees C and mean annual precipitation > or =1400 mm) to identify locations which are likely to have a high risk of C. quinqueseptatum leaf blight (CqLB). Climatic mapping programs, which include interpolated climatic data estimated for numerous locations, were used to map these high risk areas in Africa, Australia and Latin America as well as in South East Asia. The predicted high-risk areas included several regions where CqLB has already been reported and the maps generated suggested other areas which may be at risk under present climatic conditions given the presence of C. quinqueseptatum and susceptible hosts. Some simple climate change scenarios were also used to suggest areas in mainland South East Asia which may become vulnerable to CqLB over the next 50 years. It is concluded that climatic mapping programs can assist the broadscale evaluation of risk of CqLB infections, although it is recognised that more detailed models and survey information are also needed. PMID:15092931

  2. 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

  3. 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

  4. 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

  5. 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.

  6. Phylogenetic placement of the lichenicolous, anamorphic genus Lichenodiplis and its connection to Muellerella-like teleomorphs.

    PubMed

    Muggia, Lucia; Kopun, Theodora; Ertz, Damien

    2015-11-01

    Lichenicolous fungi are a specialized group of taxa which inhabit lichens and develop diverse degrees of specificity and parasitic behaviour towards their hosts. They are recognized only by their phenotypic symptoms and sexual or asexual spore-producing structures on the lichen thalli. Only recently, molecular data and culture dependent approaches have helped in uncovering the species diversity and in verifying the phylogenetic position and anamorph-teleomorph relationships of some taxa. Here, we studied the phylogenetic placement of representative taxa of two lichenicolous genera, the coelomycete Lichenodiplis and the ascomycete Muellerella. We obtained molecular data for three nuclear and mitochondrial loci (28S, 18S, and 16S), both from fresh collected specimens and culture isolates. Our multilocus phylogeny places Lichenodiplis and Muellerella samples in one monophyletic, fully supported clade, sister to Epibryon (Epibryaceae) in Chaetothyriales (Eurotiomycetes). Morphological analyses of axenically cultured fungi show the formation of conidiomata and conidiospores in both Lichenodiplis and Muellerella isolates. We suggest that the species Lichenodiplis lecanorae and Muellerella atricola represent, respectively, the anamorphic and teleomorphic stages of the same fungus and discuss their relationships with the other fungal families in Chaetothyriomycetidae. PMID:26466884

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

    PubMed

    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

  8. Taxonomy and phylogeny of the ascomycetous yeast genus Zygoascus, with proposal of Zygoascus meyerae sp. nov. and related anamorphic varieties.

    PubMed

    Smith, Maudy Th; Robert, V; Poot, G A; Epping, Wendy; de Cock, A W A M

    2005-05-01

    Physiological characters, mating compatibility, PCR-RAPD fingerprints, mol% G + C content, DNA-DNA relatedness, and large-subunit and internal transcribed spacer rRNA gene sequences of strains assigned to the genus Zygoascus were re-examined. On the basis of those data, and after phylogenetic analyses, an emendation of Zygoascus hellenicus (type material is a cross of CBS 6736(T) x CBS 5839(T)) is proposed, comprising two novel anamorphic varieties, Candida steatolytica var. steatolytica (CBS 6736(T)) and C. steatolytica var. inositophila (CBS 5839(T)). A novel teleomorphic species, Zygoascus meyerae sp. nov. (type material is a cross of CBS 4099(T) x CBS 7521(T)) is described, together with two novel anamorphic varieties corresponding to it, Candida hellenica var. hellenica (CBS 4099(T)) and C. hellenica var. acidophila (CBS 7115(T)).

  9. Phialide arrangement and character evolution in the helotialean anamorph genera Cadophora and Phialocephala.

    PubMed

    Day, Melissa J; Hall, Jocelyn C; Currah, Randolph S

    2012-01-01

    The dematiaceous hyphomycete genera Cadophora and Phialocephala are anamorphs associated with mollisioid inoperculate discomycetes (Helotiales) and are delineated based on the complexity of the phialide arrangement with members of Cadophora producing solitary phialides and species of Phialocephala producing complex heads of multiple phialides. A third phylogenetically related taxon, Leptodontidium orchidicola, produces mostly indehiscent conidia that may represent non-functional phialides. Morphological characteristics of both sexual and asexual states of these and other fungi in a focal group of helotialean taxa were re-examined, in light of relationships shown by molecular phylogenetic analyses of rDNA ITS sequences, to determine the evolutionary significance of phialide arrangement. The focal species of Phialocephala formed a monophyletic clade, while five of six species of Cadophora including the type were in a separate clade along with L. orchidicola. C. finlandica was placed in a third clade with species of Meliniomyces and Rhizoscyphus. We hypothesized that the ancestral state for species in Cadophora and Phialocephala is the production of sclerotium-like heads of multiple phialides, which has been retained in most species assignable to Phialocephala. A reduction to solitary phialides occurred in the lineage leading to the clade containing most of the Cadophora species. Two possible reductions to non-functional phialides were identified: one in the Meliniomyces-C. finlandica-Chloridium paucisporum clade and another in the L. orchidicola and Mollisia "rhizophila": clade. A reversion to increased phialide complexity might have occurred in the clade containing C. finlandica and Ch. paucisporum. Our data and analyses also show a previously unrecognized relationship between teleomorph and anamorph morphology in that Mollisia species with smaller asci would be expected to have Phialocephala states while those with larger asci would be expected to have Cadophora

  10. 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

  11. The anamorphic genus Monotosporella (Ascomycota) from Eocene amber and from modern Agathis resin.

    PubMed

    Sadowski, Eva-Maria; Beimforde, Christina; Gube, Matthias; Rikkinen, Jouko; Singh, Hukam; Seyfullah, Leyla J; Heinrichs, Jochen; Nascimbene, Paul C; Reitner, Joachim; Schmidt, Alexander R

    2012-10-01

    The anamorphic fungal genus Monotosporella (Ascomycota, Sordariomycetes) has been reco-vered from a piece of Early Eocene Indian amber, as well as from the surface of extant resin flows in New Caledonia. The fossil fungus was obtained from the Tarkeshwar Lignite Mine of Gujarat State, western India, and was part of the biota of an early tropical angiosperm rainforest. The amber inclusion represents the second fossil record of Sordariomycetes, as well as the first fossil of its particular order (either Savoryellales or Chaetosphaeriales). The fossil fungus is distinguished from extant representatives by possessing both short conidiophores and small two-septate pyriform conidia, and is described as Monotosporella doerfeltii sp. nov. Inside the amber, the anamorph is attached to its substrate, which is likely the degraded thallus of a cladoniform lichen. The extant New Caledonian species is assigned to Monotosporella setosa. It was found growing on semi-solidified resin flows of Agathis ovata (Araucariaceae), and is the first record of Monotosporella from modern resin substrates. PMID:23063189

  12. 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.

  13. 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.

  14. 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.

  15. Mrakiella cryoconiti gen. nov., sp. nov., a psychrophilic, anamorphic, basidiomycetous yeast from alpine and arctic habitats.

    PubMed

    Margesin, Rosa; Fell, Jack W

    2008-12-01

    A novel psychrophilic basidiomycetous species is described in a new anamorphic genus as Mrakiella cryoconiti gen. nov., sp. nov.; the type strain of Mrakiella cryoconiti is strain A15(T) (=CBS 10834(T) =DSM 21094(T)). Two representatives were isolated from alpine glacier cryoconite and from northern Siberian sediment. Physiological and biochemical properties are similar to characteristics shared by members of the genus Mrakia, although sexual reproduction is absent. Mrakiella cryoconiti strains are psychrophilic and produce cold-active pectate lyase. Sequence analyses of the ITS and 26S rRNA D1/D2 regions indicated that these strains represent a distinct taxon within the Mrakia clade of the order Cystofilobasidiales, class Tremellomycetes and phylum Basidiomycota. On the basis of phenotypic and genotypic characteristics, Cryptococcus aquaticus (a member of the Mrakia clade) is transferred to the newly described genus as Mrakiella aquatica comb. nov.

  16. First isolation of the anamorphic basidiomycetous yeast Trichosporon faecale in Germany, from the skin of a patient with tinea pedis.

    PubMed

    Hahner, Désirée; Kirschner, Roland; Piepenbring, Meike; Schöfer, Helmut

    2008-03-01

    Mycoses due to yeasts belonging to other genera than Candida have become common in the last years especially in immuno-compromised patients. Species of the anamorphic basidiomycetous yeast genus Trichosporon are such opportunistic human pathogenic yeasts which cause several diseases. In this study, Trichosporon faecale is reported in Germany for the first time. The isolate was taken from a human foot, where it was associated with a tinea pedis. The fungal isolate was identified by investigating the morphology, physiology by a commercial API 32 C-set and molecular data of SSU and LSU rDNA as well as the ITS region.

  17. 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

  18. 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. PMID:25457943

  19. Anamorphic transformation and its application to time-bandwidth compression.

    PubMed

    Asghari, Mohammad H; Jalali, Bahram

    2013-09-20

    A general method for compressing the modulation time-bandwidth product of analog signals is introduced. As one of its applications, this physics-based signal grooming, performed in the analog domain, allows a conventional digitizer to sample and digitize the analog signal with variable resolution. The net result is that frequency components that were beyond the digitizer bandwidth can now be captured and, at the same time, the total digital data size is reduced. This compression is lossless and is achieved through a feature selective reshaping of the signal's complex field, performed in the analog domain prior to sampling. Our method is inspired by operation of Fovea centralis in the human eye and by anamorphic transformation in visual arts. The proposed transform can also be performed in the digital domain as a data compression algorithm to alleviate the storage and transmission bottlenecks associated with "big data."

  20. Active scale changer for anamorphic, distortion free, telecentric zoom system

    NASA Astrophysics Data System (ADS)

    Wang, Xin; Hugot, Emmanuel; Bernard, Anaïs.; Madec, Fabrice; Lemared, Sabri

    2014-07-01

    We present the conception of an anamorphic and telecentric scale changer with no distortion, able to provide magnifications in the range of 2 to 30 without any interchangeable optics, dedicated to ground or space applications. Several optical designs are investigated and the final configuration is based on off-axis five mirrors system with no moving elements. Four active mirrors are adapted to four different zoom configurations. A specific mechanical profile with variable thickness distribution is simulated and optimized on each mirror to allow using a minimal number of actuators. An opto-mechanical design will be presented, showing the implementation of actuators on the system. This work is done in the frame of the ANR project OASIX and will produce a lab prototype in 2015.

  1. Anamorphic transformation and its application to time-bandwidth compression.

    PubMed

    Asghari, Mohammad H; Jalali, Bahram

    2013-09-20

    A general method for compressing the modulation time-bandwidth product of analog signals is introduced. As one of its applications, this physics-based signal grooming, performed in the analog domain, allows a conventional digitizer to sample and digitize the analog signal with variable resolution. The net result is that frequency components that were beyond the digitizer bandwidth can now be captured and, at the same time, the total digital data size is reduced. This compression is lossless and is achieved through a feature selective reshaping of the signal's complex field, performed in the analog domain prior to sampling. Our method is inspired by operation of Fovea centralis in the human eye and by anamorphic transformation in visual arts. The proposed transform can also be performed in the digital domain as a data compression algorithm to alleviate the storage and transmission bottlenecks associated with "big data." PMID:24085172

  2. 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

  3. Evolution and Ecophysiology of the Industrial Producer Hypocrea jecorina (Anamorph Trichoderma reesei) and a New Sympatric Agamospecies Related to It

    PubMed Central

    Druzhinina, Irina S.; Komoń-Zelazowska, Monika; Atanasova, Lea; Seidl, Verena; Kubicek, Christian P.

    2010-01-01

    Background Trichoderma reesei, a mitosporic green mould, was recognized during the WW II based on a single isolate from the Solomon Islands and since then used in industry for production of cellulases. It is believed to be an anamorph (asexual stage) of the common pantropical ascomycete Hypocrea jecorina. Methodology/Principal Findings We combined molecular evolutionary analysis and multiple methods of phenotype profiling in order to reveal the genetic relationship of T. reesei to H. jecorina. The resulting data show that the isolates which were previously identified as H. jecorina by means of morphophysiology and ITS1 and 2 (rRNA gene cluster) barcode in fact comprise several species: i) H. jecorina/T. reesei sensu stricto which contains most of the teleomorphs (sexual stages) found on dead wood and the wild-type strain of T. reesei QM 6a; ii) T. parareesei nom. prov., which contains all strains isolated as anamorphs from soil; iii) and two other hypothetical new species for which only one or two isolates are available. In silico tests for recombination and in vitro mating experiments revealed a history of sexual reproduction for H. jecorina and confirmed clonality for T. parareesei nom. prov. Isolates of both species were consistently found worldwide in pantropical climatic zone. Ecophysiological comparison of H. jecorina and T. parareesei nom. prov. revealed striking differences in carbon source utilization, conidiation intensity, photosensitivity and mycoparasitism, thus suggesting adaptation to different ecological niches with the high opportunistic potential for T. parareesei nom. prov. Conclusions Our data prove that T. reesei belongs to a holomorph H. jecorina and displays a history of worldwide gene flow. We also show that its nearest genetic neighbour - T. parareesei nom. prov., is a cryptic phylogenetic agamospecies which inhabits the same biogeographic zone. These two species thus provide a so far rare example of sympatric speciation within saprotrophic

  4. The Visual Journal as an Image Sphere: Interpreting Artworks with an Anamorphic Perspective

    ERIC Educational Resources Information Center

    Sinner, Anita

    2011-01-01

    During a 1-year study, the visual journal of a preservice teacher was explored as an image sphere, or "bildraum", in relation to teacher culture. Artworks created in the visual journal offered an anamorphic perspective on the materiality of teacher culture, tracing the lived experiences of a student of art in the process of becoming an art teacher…

  5. 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

  6. 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...

  7. 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.

  8. Cytological Characterization of Anamorphic Fungus Lecanicillium pui and Its Relationship with Chinese Caterpillar Mushroom, Ophiocordyceps sinensis (Ascomycetes).

    PubMed

    Lei, Wei; Zhang, Guren; Wu, Guangguo; Liu, Xin

    2016-01-01

    Ophiocordyceps sinensis (syn. Cordyceps sinensis), one of the most valuable medicinal mushrooms, has great economic importance on the Tibetan Plateau. We isolated an anamorphic fungus Lecanicillium pui from natural O. sinensis specimens and found that the optimal temperature for its culture on potato dextrose agar media was 25°C. Cell ultrastructure in L. pui hyphae and spores was characterized by transmission electron microscopy, and it was observed that some primary organelles showed the typical fungal features. Five chemical elements were determined in this fungus and niobium was discovered for the first time even with trace amounts. A species-specific method, nested polymerase chain reaction, was established to investigate the colonization of this fungus. Thus, the extensive distribution of L. pui on O. sinensis, in the shape of hyphae or mycelia, suggested that it may have subtle and chronic effects on the growth of the O. sinensis teleomorphic stage. These findings provide a potential reference, in the view of microbial ecology, for the study on the occurrence and mechanism of development of O. sinensis. PMID:27279447

  9. 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. PMID:27409118

  10. Neosartorya fischeri var fischeri (Wehmer) Malloch and Cain 1972 (anamorph: Aspergillus fischerianus Samson and Gams 1985) as a cause of mycotic keratitis.

    PubMed

    Coriglione, G; Stella, G; Gafa, L; Spata, G; Oliveri, S; Padhye, A A; Ajello, L

    1990-12-01

    The first case of mycotic keratitis caused by Neosartorya fischeri var. fischeri the teleomorph of Aspergillus fischerianus, is described. The patient, a 62-year-old man, had no history of trauma to his infected left eye. The infection progressed despite treatment with ketoconazole and the eye had to be eviscerated. Histological studies revealed the presence of hyaline, septate mycelium in the eye tissue. Cultures gave rise to a thermotolerant mould that developed both its asexual and sexual forms. The isolate was identified on the basis of the morphologic features of its anamorphic and teleomorphic states. In the literature only seven other species of Aspergillus have been unequivocally reported as causing mycotic keratitis. PMID:2091938

  11. 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.

  12. 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.

  13. Stray light characterization of an InGaAs anamorphic hyperspectral imager.

    PubMed

    Lin, Mike; Swanson, Rand; Moon, Thomas; Smith, Casey; Kehoe, Michael; Brown, Steven W; Lykke, Keith R

    2010-08-01

    Compact hyperspectral sensors potentially have a wide range of applications, including machine vision, quality control, and surveillance from small Unmanned Aerial Vehicles (UAVs). With the development of Indium Gallium Arsenide (InGaAs) focal plane arrays, much of the Short Wave Infra-Red (SWIR) spectral regime can be accessed with a small hyperspectral imaging system, thereby substantially expanding hyperspectral sensing capabilities. To fully realize this potential, system performance must be well-understood. Here, stray light characterization of a recently-developed push-broom hyperspectral sensor sensitive in the 1 microm -1.7 microm spectral regime is described. The sensor utilizes anamorphic fore-optics that partially decouple image formation along the spatial and spectral axes of the instrument. This design benefits from a reduction in complexity over standard high-performance spectrometer optical designs while maintaining excellent aberration control and spatial and spectral distortion characteristics. The stray light performance characteristics of the anamorphic imaging spectrometer were measured using the spectral irradiance and radiance responsivity calibrations using uniform sources (SIRCUS) facility at the National Institute of Standards and Technology (NIST). A description of the measurements and results are presented. Additionally, a stray-light matrix was assembled for the instrument to improve the instrument's spectral accuracy. Transmittance of a silicon wafer was measured to validate this approach.

  14. Cryptococcus randhawai sp. nov., a novel anamorphic basidiomycetous yeast isolated from tree trunk hollow of Ficus religiosa (peepal tree) from New Delhi, India.

    PubMed

    Khan, Zia U; Ahmad, Suhail; Hagen, Ferry; Fell, Jack W; Kowshik, Tusharantak; Chandy, Rachel; Boekhout, Teun

    2010-03-01

    A novel anamorphic Cryptococcus species is described, which was isolated in New Delhi (India) from decaying wood of a tree trunk hollow of Ficus religiosa. On the basis of sequence analysis of the D1/D2 domains of the 26S rRNA gene and the internally transcribed spacer (ITS)-1 and ITS-2 region sequences, the isolate belonged to the Cryptococcus albidus cluster (Filobasidiales, Tremellomycetes) and was closely related to Cryptococcus saitoi, Cryptococcus cerealis and Cryptococcus friedmannii with 98% sequence identity. Phenotypically, the species differed from C. saitoi with respect to growth temperature (up to 37degrees C), presence of a thin capsule, ability to grow in the absence of vitamins, and inability to assimilate citrate and ethylamine. With respect to C. friedmannii, it differed in growth temperature, ability to assimilate lactose, raffinose, L: -rhamnose, myo-inositol, and inability to utilize citrate. Furthermore, our isolate also differed from C. cerealis in growth temperature, presence of capsule and inability to assimilate L: -sorbose. In view of the above phenotypic differences and unique rDNA sequences, we consider that our isolate represents a new species of Cryptococcus, and therefore, a new species, Cryptococcus randhawai is proposed for this taxon. The type strain J11/2002 has been deposited in the culture collection of the Centraalbureau voor Schimmelcultures (CBS10160) and CABI Biosciences (IMI 393306). PMID:20091225

  15. Fusarium species from nepalese rice and production of mycotoxins and gibberellic acid by selected species.

    PubMed

    Desjardins, A E; Manandhar, H K; Plattner, R D; Manandhar, G G; Poling, S M; Maragos, C M

    2000-03-01

    Infection of cereal grains with Fusarium species can cause contamination with mycotoxins that affect human and animal health. To determine the potential for mycotoxin contamination, we isolated Fusarium species from samples of rice seeds that were collected in 1997 on farms in the foothills of the Nepal Himalaya. The predominant Fusarium species in surface-disinfested seeds with husks were species of the Gibberella fujikuroi complex, including G. fujikuroi mating population A (anamorph, Fusarium verticillioides), G. fujikuroi mating population C (anamorph, Fusarium fujikuroi), and G. fujikuroi mating population D (anamorph, Fusarium proliferatum). The widespread occurrence of mating population D suggests that its role in the complex symptoms of bakanae disease of rice may be significant. Other common species were Gibberella zeae (anamorph, Fusarium graminearum) and Fusarium semitectum, with Fusarium acuminatum, Fusarium anguioides, Fusarium avenaceum, Fusarium chlamydosporum, Fusarium equiseti, and Fusarium oxysporum occasionally present. Strains of mating population C produced beauvericin, moniliformin, and gibberellic acid, but little or no fumonisin, whereas strains of mating population D produced beauvericin, fumonisin, and, usually, moniliformin, but no gibberellic acid. Some strains of G. zeae produced the 8-ketotrichothecene nivalenol, whereas others produced deoxynivalenol. Despite the occurrence of fumonisin-producing strains of mating population D, and of 8-ketotrichothecene-producing strains of G. zeae, Nepalese rice showed no detectable contamination with these mycotoxins. Effective traditional practices for grain drying and storage may prevent contamination of Nepalese rice with Fusarium mycotoxins.

  16. 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

  17. 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.

  18. 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. PMID:26906582

  19. 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.

  20. 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.

  1. 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...

  2. Taxonomy and Phylogeny of the Fusarium dimerum Species Group

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The morphospecies Fusarium dimerum, known only from its anamorph, comprises at least 12 phylogenetically distinct species. Analyses of the large subunit ribosomal DNA (LSU rDNA) show they are taxa of the Nectriaceae (Hypocreales) and form a phylogenetically distinct clade within Fusarium. Accordin...

  3. 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...

  4. Species diversity and polymorphism in the Exophiala spinifera clade containing opportunistic black yeast-like fungi.

    PubMed

    de Hoog, G S; Vicente, V; Caligiorne, R B; Kantarcioglu, S; Tintelnot, K; Gerrits van den Ende, A H G; Haase, G

    2003-10-01

    A monophyletic group of black yeast-like fungi containing opportunistic pathogens around Exophiala spinifera is analyzed using sequences of the small-subunit (SSU) and internal transcribed spacer (ITS) domains of ribosomal DNA. The group contains yeast-like and annellidic species (anamorph genus Exophiala) in addition to sympodial taxa (anamorph genera Ramichloridium and Rhinocladiella). The new species Exophiala oligosperma, Ramichloridium basitonum, and Rhinocladiella similis are introduced and compared with their morphologically similar counterparts at larger phylogenetic distances outside the E. spinifera clade. Exophiala jeanselmei is redefined. New combinations are proposed in EXOPHIALA: Exophiala exophialae for Phaeococcomyces exophialae and Exophiala heteromorpha for E. jeanselmei var. heteromorpha. PMID:14532218

  5. Species Diversity and Polymorphism in the Exophiala spinifera Clade Containing Opportunistic Black Yeast-Like Fungi

    PubMed Central

    de Hoog, G. S.; Vicente, V.; Caligiorne, R. B.; Kantarcioglu, S.; Tintelnot, K.; Gerrits van den Ende, A. H. G.; Haase, G.

    2003-01-01

    A monophyletic group of black yeast-like fungi containing opportunistic pathogens around Exophiala spinifera is analyzed using sequences of the small-subunit (SSU) and internal transcribed spacer (ITS) domains of ribosomal DNA. The group contains yeast-like and annellidic species (anamorph genus Exophiala) in addition to sympodial taxa (anamorph genera Ramichloridium and Rhinocladiella). The new species Exophiala oligosperma, Ramichloridium basitonum, and Rhinocladiella similis are introduced and compared with their morphologically similar counterparts at larger phylogenetic distances outside the E. spinifera clade. Exophiala jeanselmei is redefined. New combinations are proposed in Exophiala: Exophiala exophialae for Phaeococcomyces exophialae and Exophiala heteromorpha for E. jeanselmei var. heteromorpha. PMID:14532218

  6. 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. PMID:24415463

  7. Tropical species of Cladobotryum and Hypomyces producing red pigments

    PubMed Central

    Põldmaa, Kadri

    2011-01-01

    Twelve species of Hypomyces/Cladobotryum producing red pigments are reported growing in various tropical areas of the world. Ten of these are described as new, including teleomorphs for two previously known anamorphic species. In two species the teleomorph has been found in nature and in three others it was obtained in culture; only anamorphs are known for the rest. None of the studied tropical collections belongs to the common temperate species H. rosellus and H. odoratus to which the tropical teleomorphic collections had previously been assigned. Instead, taxa encountered in the tropics are genetically and morphologically distinct from the nine species of Hypomyces/Cladobotryum producing red pigments known from temperate regions. Besides observed host preferences, anamorphs of several species can spread fast on soft ephemeral agaricoid basidiomata but the slower developing teleomorphs are mostly found on polyporoid basidiomata or bark. While a majority of previous records from the tropics involve collections from Central America, this paper also reports the diversity of these fungi in the Paleotropics. Africa appears to hold a variety of taxa as five of the new species include material collected in scattered localities of this mostly unexplored continent. In examining distribution patterns, most of the taxa do not appear to be pantropical. Some species are known only from the Western Hemisphere, while others have a geographic range from southeastern Asia to Africa or Australia. The use of various morphological characters of anamorphs and teleomorphs as well as culture characteristics in species delimitation is evaluated. For detecting genetic segregation, partial sequences of the two largest subunits of the ribosomal polymerase perform the best in terms of providing informative sites and the number of well-supported groups recognised in the phylogenies. These are followed by the sequence data of the translation-elongation factor 1-alpha, while the ribosomal DNA

  8. 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

  9. 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),...

  10. Analysis of expressed sequence tags from the anamorphic basidiomycetous yeast, Pseudozyma antarctica, which produces glycolipid biosurfactants, mannosylerythritol lipids.

    PubMed

    Morita, Tomotake; Konishi, Masaaki; Fukuoka, Tokuma; Imura, Tomohiro; Kitamoto, Dai

    2006-07-15

    Pseudozyma antarctica T-34 secretes a large amount of biosurfactants (BS), mannosylerythritol lipids (MEL), from different carbon sources such as hydrocarbons and vegetable oils. The detailed biosynthetic pathway of MEL remained unknown due to lack of genetic information on the anamorphic basidiomycetous yeasts, including the genus Pseudozyma. Here, in order to obtain genetic information on P. antarctica T-34, we constructed a cDNA library from yeast cells producing MEL from soybean oil and identified the genes expressed through the creation of an expressed sequence tags (EST) library. We generated 398 ESTs, assembled into 146 contiguous sequences. Based upon a BLAST search similarity cut-off of E

  11. 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. PMID:19169846

  12. Candida theae sp. nov., a new anamorphic beverage-associated member of the Lodderomyces clade.

    PubMed

    Chang, Chin-Feng; Lin, Yu-Ching; Chen, Shan-Fu; Carvajal Barriga, Enrique Javier; Carvaja Barriga, Enrique Javier; Barahona, Patricia Portero; James, Stephen A; Bond, Christopher J; Roberts, Ian N; Lee, Ching-Fu

    2012-02-01

    Four strains representing a novel yeast species belonging to the genus Candida were independently isolated in Taiwan and Ecuador. Two strains (G17(T) and G31) were isolated in Taiwan, by pellet precipitation from plastic-bottled tea drinks produced in Indonesia, while two additional strains (CLQCA 10-049 and CLQCA 10-062) were recovered from ancient chicha fermentation vessels found in tombs in Quito, Ecuador. These four strains were morphologically, and phylogenetically identical to each other. No sexual reproduction was observed on common sporulation media. Large-subunit (LSU) rRNA gene sequence analysis revealed the four strains to belong to the Lodderomyces clade, closely related to members of the Candida parapsilosis species complex. The four strains, which have identical LSU D1/D2 sequences, differ from their closest phylogenetic neighbors, Candida orthopsilosis and Candida parapsilosis, by 6-9 nt substitutions, respectively. Physiologically, the four strains are similar to Candida parapsilosis, although they can be distinguished from their closest relative by the assimilation of arbutin, nitrite, and creatine. The Indonesian and Ecuadorian strain sets can also be distinguished from one another based on ITS sequencing, differing by 4 substitutions in ITS1 and 1 single nucleotide indel in ITS2. Collectively, the results indicate that the four strains represent a previously unrecognized species of Candida. The name Candida theae sp. nov. is proposed to accommodate these strains, with G-17(T) (BCRC 23242(T)=CBS 12239(T)=ATCC MYA-4746(T)) designated as the type strain.

  13. Candida theae sp. nov., a new anamorphic beverage-associated member of the Lodderomyces clade.

    PubMed

    Chang, Chin-Feng; Lin, Yu-Ching; Chen, Shan-Fu; Carvajal Barriga, Enrique Javier; Carvaja Barriga, Enrique Javier; Barahona, Patricia Portero; James, Stephen A; Bond, Christopher J; Roberts, Ian N; Lee, Ching-Fu

    2012-02-01

    Four strains representing a novel yeast species belonging to the genus Candida were independently isolated in Taiwan and Ecuador. Two strains (G17(T) and G31) were isolated in Taiwan, by pellet precipitation from plastic-bottled tea drinks produced in Indonesia, while two additional strains (CLQCA 10-049 and CLQCA 10-062) were recovered from ancient chicha fermentation vessels found in tombs in Quito, Ecuador. These four strains were morphologically, and phylogenetically identical to each other. No sexual reproduction was observed on common sporulation media. Large-subunit (LSU) rRNA gene sequence analysis revealed the four strains to belong to the Lodderomyces clade, closely related to members of the Candida parapsilosis species complex. The four strains, which have identical LSU D1/D2 sequences, differ from their closest phylogenetic neighbors, Candida orthopsilosis and Candida parapsilosis, by 6-9 nt substitutions, respectively. Physiologically, the four strains are similar to Candida parapsilosis, although they can be distinguished from their closest relative by the assimilation of arbutin, nitrite, and creatine. The Indonesian and Ecuadorian strain sets can also be distinguished from one another based on ITS sequencing, differing by 4 substitutions in ITS1 and 1 single nucleotide indel in ITS2. Collectively, the results indicate that the four strains represent a previously unrecognized species of Candida. The name Candida theae sp. nov. is proposed to accommodate these strains, with G-17(T) (BCRC 23242(T)=CBS 12239(T)=ATCC MYA-4746(T)) designated as the type strain. PMID:22088606

  14. 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...

  15. [Keratinophilic fungal flora isolated from small wild mammals and rabbit-warren in France. Discussion on the fungal species found].

    PubMed

    Chabasse, D; Guiguen, C; Couatarmanac'h, A; Launay, H; Reecht, V; de Bièvre, C

    1987-01-01

    The occurrence of dermatophytes and other keratinophilic fungi was investigated in 237 small wild mammals and 125 european rabbit. The purpose of the investigation was to determine what were the species of fungi present in the these animals. Four species of dermatophytes were isolated: Trichophyton ajelloi, Trichophyton terrestre, Trichophyton mentagrophytes, Microsporum persicolor. Trichophyton terrestre was the most frequently isolated and it occurred more frequently than its presence could be explained by the contamination from soil. Members of the genus Chrysosporium were found in many animals: Chrysosporium keratinophilum, Chrysosporium tropicum, Chrysosporium multifidum, Chrysosporium pannorum, Chrysosporium georgii, Chrysosporium merdarium, Chrysosporium anamorph of Arthroderma curreyi, Chrysosporium anamorph of Arthroderma cuniculi, Anixiopsis stercoraria, Chrysosporium parvum. Wild small mammals and european rabbits in France, not only act as carrier of keratinophilic fungi and allied dermatophytes but also provide a suitable habitat for their survival as saprophytes. The recurrence of numerous species present on the coat, isolated fort the first time in France was remarkable.

  16. Cryptic species related to Daldinia concentrica and D. eschscholzii, with notes on D. bakeri.

    PubMed

    Stadler, Marc; Wollweber, Hartmund; Jäger, Wolfgang; Briegert, Manuela; Venturella, Giuseppe; Castro, Juan M; Tichy, Hans-Volker

    2004-03-01

    Daldinia macaronesica (from the Canary Islands and Madeira), D. palmensis (from the Canary Islands), D. martinii and D. raimundi (from Sicily), and D. vanderguchtiae (from Jersey, Channel Islands) spp. nov., are described, based on new combinations of teleomorphic and anamorphic characters. They all resemble the pantropical D. eschscholzii and/or the European D. concentrica with regard to teleomorphic characters and secondary metabolite profiles generated by analytical HPLC. The status of the newly described taxa was established by SEM of ascospores and microscopic studies of their anamorphs in comparison with various materials of the aforementioned known species. HPLC and SEM studies on the holotype of D. bakeri confirmed its relationships to D. fissa and D. loculata. Yellowish pigments contained in the type specimen of D. bakeri are probably artificial. PMID:15185977

  17. 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

  18. A fissitunicate ascus mechanism in the Calosphaeriaceae, and novel species of Jattaea and Calosphaeria on Prunus wood.

    PubMed

    Damm, U; Crous, P W; Fourie, P H

    2008-06-01

    During a survey of Prunus wood from South Africa, isolations were made of three presumably Calosphaerialean fungi that formed hyphomycetous, phialidic anamorphs in culture. In order to reveal the phylogenetic relationship of these fungi, they were characterised on a morphological and molecular (LSU and ITS rDNA) basis. Two isolates that formed a teleomorph in culture are newly described as Calosphaeria africana sp. nov. Although asci of Calosphaeria are characterised by having non-amyloid apical rings, two functional wall layers were observed in asci of C. africana, which has hitherto not been observed in any member of the Calosphaeriaceae. However, Calosphaeriaceae (Calosphaeriales, Sordariomycetes) are not closely related to other bitunicate fungi like Dothideomycetes, Chaetothyriales and bitunicate lichens. Possession of two separating wall layers is considered to be a result of both inherited abilities and convergent evolution under a strong selection pressure of the environmental conditions that favour an extension of the ascus. The other two species represented a separate lineage within Calosphaeriaceae, and formed phialophora-like anamorphs. By obtaining the teleomorph in culture, one of them could be identified as a species of Jattaea, described here as Jattaea prunicola sp. nov., while the second, which only produced the anamorph, is named as Jattaea mookgoponga sp. nov. These findings suggest that some species of Jattaea are true members of the Calosphaeriaceae, though the phylogenetic relation of the type, J. algeriensis, remains unknown. Furthermore, it also represents the first report of Jattaea on Prunus wood, and from South Africa.

  19. Heat tolerant fungi and applied research: Addition to the previously treated group of strictly thermotolerant species.

    PubMed

    Mouchacca, Jean

    2007-12-01

    Heat tolerant fungi are organisms that may perform bioconversion processes and produce industrially important metabolites. They may either be obligate thermophiles or simple thermotolerants. The present document is the continuation of a critical note on thermotolerant fungi erroneously reported in the literature as possessing thermophilic attributes. Fifty strictly thermotolerant taxa are here considered. Some of their binomials have only recently been introduced in the scientific literature. The reported thermotolerant species are grouped according to broad taxonomic categories. The nomenclature of zygomycetous taxa and anamorphic fungi is straightforward, as usually only one binomial is available or only one state is produced in culture respectively. For Ascomycetes regularly producing in culture a conidial state, the name of the sexual state (teleomorph) should be used to designate the organism even when a binomial is available for the anamorph; this prevents the practice of interchangeably using the name of either states of the same fungus. When ascomycetous taxa produce the anamorph regularly and the teleomorph only under specific cultural conditions, the name of the anamorph could be preferentially selected. The goal is to introduce uniformity in name citations of fungi, particularly in the literature of applied research. Each species is reported under its taxonomically correct name, either the original binomial or the latest combined binomial after generic transfer(s). Known synonyms are also specified. Maximum efforts were undertaken to trace updated information on the taxonomic position of these fifty strict thermotolerant species. For each, information on the type material, morphological features distinguishing it from related members of the genus (and when necessary a generic taxonomic assessment) and, finally, salient ecological features including heat tolerance levels are given. For some information on their biotechnological use is also provided

  20. Amplistroma gen. nov. and its relation to Wallrothiella, two genera with globose ascospores and acrodontium-like anamorphs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Amplistroma is described as a new genus for A. caroliniana, A. diminuspora, A. guianensis, A. hallingii, A. rava, A. tartarea, and A. xylarioides. Species of Amplistroma are distinguished by large stromata of textura intricata with polystichous ascomata and long necks that are either erumpent from t...

  1. Coniochaeta polymorpha, a new species from endotracheal aspirate of a preterm neonate, and transfer of Lecythophora species to Coniochaeta.

    PubMed

    Khan, Ziauddin; Gené, Josepa; Ahmad, Suhail; Cano, Josep; Al-Sweih, Noura; Joseph, Leena; Chandy, Rachel; Guarro, Josep

    2013-08-01

    A new species of Coniochaeta from endotracheal secretion of a preterm neonate, Coniochaeta polymorpha, is described. This anamorphic species is characterized by development of dark brown colonies after 1 week of incubation on culture medium, formation of abundant yeast-like cells and sclerotium-like structures producing discrete, brown, nearly globose phialidic conidiogenous cells and absence of chlamydospores. A combined sequence dataset of the ITS region, partial LSU rDNA, actin and β-tubulin genes sufficiently resolved the unique phylogenetic status of this species. In response to recent changes in the nomenclature for pleomorphic fungi, we transfer the Lecythophora species to Coniochaeta, and propose the following new combinations: Coniochaeta canina, Coniochaeta cateniformis, Coniochaeta decumbens, Coniochaeta fasciculata, Coniochaeta hoffmannii, Coniochaeta lignicola, Coniochaeta luteorubra, Coniochaeta luteoviridis and Coniochaeta mutabilis. PMID:23748934

  2. 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

  3. 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

  4. Scytalidium parasiticum sp. nov., a New Species Parasitizing on Ganoderma boninense Isolated from Oil Palm in Peninsular Malaysia

    PubMed Central

    Goh, Teik Khiang; Marzuki, Nurul Fadhilah; Tung, Hun Jiat; Goh, You Keng; Goh, Kah Joo

    2015-01-01

    A mycoparasite, Scytalidium parasiticum sp. nov., isolated from the basidiomata of Ganoderma boninense causing basal stem rot of oil palm in Johor, Malaysia, is described and illustrated. It is distinct from other Scytalidium species in having smaller asci and ascospores (teleomorphic stage), longer arthroconidia (anamorphic stage), hyaline to yellowish chlamydospores, and producing a fluorescent pigment. The phylogenetic position of S. parasiticum was determined by sequence analyses of the internal transcribed spacers and the small-subunit ribosomal RNA gene regions. A key to identify Scytalidium species with teleomorphic stage is provided. PMID:26190917

  5. 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

  6. Nutritional physiology and taxonomy of human-pathogenic Cladosporium-Xylohypha species.

    PubMed

    de Hoog, G S; Guého, E; Masclaux, F; Gerrits van den Ende, A H; Kwon-Chung, K J; McGinnis, M R

    1995-01-01

    Physiological profiles of type, authentic and some additional isolates of Cladosporium-Xylohypha species of purported herpotrichiellaceous relationship are established. This group comprises melanized catenate hyphomycetes which are prevalently found on the human host. The species are excluded from the genus Cladosporium and are classified in the genus Cladophialophora. Taeniolella boppii is also transferred to this genus. Cladosporium bantianum (= Xylohypha emmonsii) and C. trichoides are considered conspecific and are now referred to as Cladophialophora bantiana. Meso-erythritol, L-arabinitol, ethanol and growth at 40 degrees C are found to be the most useful criteria for species distinction. The species Cladosporium carrionii is found to be heterogeneous. The anamorph of the saprophytic ascomycete Capronia pilosella is morphologically similar to an authentic strain of Cladosporium carrionii, but physiologically distinct. A diagnostic key for the recognized Cladophialophora species and to morphologically similar taxa is provided.

  7. A six-gene phylogeny reveals the evolution of mode of infection in the rice blast fungus and allied species.

    PubMed

    Zhang, Ning; Zhao, Shuang; Shen, Qirong

    2011-01-01

    The family Magnaporthaceae contains devastating fungal cereal and grass pathogens, such as Magnaporthe oryzae (rice blast fungus, formerly known as M. grisea), M. poae (summer patch pathogen of turf grasses) and Gaeumannomyces graminis (take-all fungus of various cereals and grasses), which are popular model organisms in fungal biology and host-pathogen interaction studies. Despite their ecological and economic importance, the phylogenetic relationships among the constituent species remain ambiguous due to the lack of convincing morphological characters and paucity of molecular data for the majority of the non-model species in the family. In this study our multilocus phylogeny suggests that both Magnaporthe and Gaeumannomyces are polyphyletic genera. The phylogeny also provides insights into fungal biology and pathogenesis. Magnaporthe oryzae formed a basal clade, while M. poae and M. rhizophila formed another well supported clade with G. incrustans and G. graminis. The basal species infect both root and aerial parts of the plant host, while the aerial infection capacity seems to be lost in the taxa of the latter clade. The phylogeny is corroborated by evolution of the anamorphs and a cAMP-dependent protein kinase (CPKA) gene. Magnaporthe oryzae produces Pyricularia, while taxa in the latter clade all produce Phialophora-like anamorphs. CPKA is present in animals and many fungal lineages with various functions. In M. oryzae CPKA is essential for the formation of functional appressoria for leaf penetration. In root-infecting G. graminis var. tritici and M. poae however only non-functional CPKA homologous pseudogenes were found in their genomes. The study indicates that anamorphic and ecological features are more informative than the teleomorphic characters in defining monophyletic groups among these taxa. PMID:21642347

  8. Leptographium longiclavatum sp. nov., a new species associated with the mountain pine beetle, Dendroctonus ponderosae.

    PubMed

    Lee, Sangwon; Kim, Jae-Jin; Breuil, Colette

    2005-10-01

    The mountain pine beetle, Dendroctonus ponderosae, and its fungal associates are devastating the lodgepole pine forests in British Columbia, Canada. During our fungal survey, an unknown Leptographium species has been consistently isolated from both D. ponderosae and infested lodgepole pine (Pinus contorta var. latifolia). This Leptographium species has similar morphology with the Leptographium anamorph of Ophiostoma clavigerum whose association with the D. ponderosae is well known. However, thorough morphological comparisons showed that this fungus is distinct from all the other Leptographium species described in the literature, and especially from O. clavigerum. Comparison of DNA sequences of multiple loci and the profiles by the PCR-RFLP marker also confirmed that this Leptographium species represents an undescribed taxon. Based on its distinct morphological, physiological characteristics and phylogenetic position, we describe it as L. longiclavatum sp. nov.

  9. A phylogenetic study on galactose-containing Candida species based on 18S ribosomal DNA sequences.

    PubMed

    Suzuki, Motofumi; Suh, Sung-Oui; Sugita, Takashi; Nakase, Takashi

    1999-10-01

    Phylogenetic relationships of 33 Candida species containing galactose in the cells were investigated by using 18S ribosomal DNA sequence analysis. Galactose-containing Candida species and galactose-containing species from nine ascomycetous genera were a heterogeneous assemblage. They were divided into three clusters (II, III, and IV) which were phylogenetically distant from cluster I, comprising 9 galactose-lacking Candida species, C. glabrata, C. holmii, C. krusei, C. tropicalis (the type species of Candida), C. albicans, C. viswanathii, C. maltosa, C. parapsilosis, C. guilliermondii, and C. lusitaniae, and 17 related ascomycetous yeasts. These three clusters were also phylogenetically distant from Schizosaccharomyces pombe, which contains galactomannan in its cell wall. Cluster II comprised C. magnoliae, C. vaccinii, C. apis, C. gropengiesseri, C. etchellsii, C. floricola, C. lactiscondensi, Wickerhamiella domercqiae, C. versatilis, C. azyma, C. vanderwaltii, C. pararugosa, C. sorbophila, C. spandovensis, C. galacta, C. ingens, C. incommunis, Yarrowia lipolytica, Galactomyces geotrichum, and Dipodascus albidus. Cluster III comprised C. tepae, C. antillancae and its synonym C. bondarzewiae, C. ancudensis, C. petrohuensis, C. santjacobensis, C. ciferrii (anamorph of Stephanoascus ciferrii), Arxula terrestris, C. castrensis, C. valdiviana, C. paludigena, C. blankii, C. salmanticensis, C. auringiensis, C. bertae, and its synonym C. bertae var. chiloensis, C. edax (anamorph of Stephanoascus smithiae), Arxula adeninivorans, and C. steatolytica (synonym of Zygoascus hellenicus). Cluster IV comprised C. cantarellii, C. vinaria, Dipodascopsis uninucleata, and Lipomyces lipofer. Two galactose-lacking and Q-8-forming species, C. stellata and Pichia pastoris, and 5 galactose-lacking and Q-9-forming species, C. apicola, C. bombi, C. bombicola, C. geochares, and C. insectalens, were included in Cluster II. Two galactose-lacking and Q-9-forming species, C. drimydis and C

  10. Phylogenetic utility of indels within ribosomal DNA and beta-tubulin sequences from fungi in the Rhizoctonia solani species complex.

    PubMed

    González, Dolores; Cubeta, Marc A; Vilgalys, Rytas

    2006-08-01

    The genus Rhizoctonia consists of a diverse assemblage of anamorphic fungi frequently associated with plants and soil throughout the world. Some anamorphs are related with teleomorphs (sexual stage) in different taxonomic classes, orders, and families. The fungus may exist as pathogen, saprophyte, or mycorrhizal symbiont and shows extensive variation in characteristics such as geographic location, morphology, host specificity, and pathogenicity. In this study, phylogenetic analyses were performed in the Rhizoctonia solani species complex with individual and combined data sets from three gene partitions (ITS, LSU rDNA, and beta-tubulin). To explore whether indels were a source of phylogenetically informative characters, single-site indels were treated as a new state, while indels greater than one contiguous nucleotide were analyzed by including them as ambiguous data (Coding A); excluding them from the analyses (Coding B), and with three distinct codes: multistate for different sequence (Coding C); multistate for different length (Coding D) and different characters for each distinct sequence (Coding E). Results suggest that indels in noncoding regions contain phylogenetic information and support the fact that the R. solani species complex is not monophyletic. Six clades within R. solani (teleomorph=Thanatephorus) representing distinct anastomosis groups and five clades within binucleate Rhizoctonia (teleomorph=Ceratobasidium) were well supported in all analyses. The data suggest that clades with representatives of R. solani fungi belonging to anastomosis groups 1, 4, 6, and 8 should be recognized as phylogenetic species.

  11. Ergot species of the Claviceps purpurea group from South Africa.

    PubMed

    van der Linde, Elna J; Pešicová, Kamila; Pažoutová, Sylvie; Stodůlková, Eva; Flieger, Miroslav; Kolařík, Miroslav

    2016-08-01

    Results of a survey and study of the Claviceps purpurea group of species in South Africa are being presented and five new species are described. Morphological descriptions are based on the anamorphs and four nuclear genetic loci. Claviceps fimbristylidis sp. nov. on Fimbristylis complanata was discovered wide-spread across five provinces of the country associated with water and represents the fourth Claviceps species recorded from the Cyperaceae. Claviceps monticola sp. nov. is described from Brachypodium flexum growing in mountain forests in Mpumalanga Province, as well as the northern Drakensberg southwards into the Eastern Cape Province. Claviceps pazoutovae sp. nov. is recorded from Stipa dregeana var. dregeana and Ehrharta erecta var. erecta, also associated with these mountain ranges. Claviceps macroura sp. nov. is recorded from Cenchrus macrourus from the Eastern Cape and Claviceps capensis sp. nov. from Ehrharta villosa var. villosa is recorded from the Western Cape Province. Claviceps cyperi, only recorded from South Africa is included in the study. Ergot alkaloid profiles of all species are provided and showed similarity to C. purpurea. Only C. cyperi and in lesser degree C. capensis, C. macroura, and C. pazoutovae produced ergot alkaloids in clinically significant amounts. Several reported species infect invasive grass species, native to South Africa, and thus represent potentially invasive species. PMID:27521625

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

    PubMed

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

    2010-01-01

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

  13. Opportunistic, human-pathogenic species in the Herpotrichiellaceae are phenotypically similar to saprobic or phytopathogenic species in the Venturiaceae

    PubMed Central

    Crous, P.W.; Schubert, K.; Braun, U.; de Hoog, G.S.; Hocking, A.D.; Shin, H.-D.; Groenewald, J.Z.

    2007-01-01

    Although morphologically similar, species of Cladophialophora (Herpotrichiellaceae) were shown to be phylogenetically distinct from Pseudocladosporium (Venturiaceae), which was revealed to be synonymous with the older genus, Fusicladium. Other than being associated with human disorders, species of Cladophialophora were found to also be phytopathogenic, or to occur as saprobes on organic material, or in water, fruit juices, or sports drinks, along with species of Exophiala. Caproventuria and Metacoleroa were confirmed to be synonyms of Venturia, which has Fusicladium (= Pseudocladosporium) anamorphs. Apiosporina, based on A. collinsii, clustered basal to the Venturia clade, and appears to represent a further synonym. Several species with a pseudocladosporium-like morphology in vitro represent a sister clade to the Venturia clade, and are unrelated to Polyscytalum. These taxa are newly described in Fusicladium, which is morphologically close to Anungitea, a heterogeneous genus with unknown phylogenetic affinity. In contrast to the Herpotrichiellaceae, which were shown to produce numerous synanamorphs in culture, species of the Venturiaceae were morphologically and phylogenetically more uniform. Several new species and new combinations were introduced in Cladophialophora, Cyphellophora (Herpotrichiellaceae), Exophiala, Fusicladium, Venturia (Venturiaceae), and Cylindrosympodium (incertae sedis). PMID:18491000

  14. 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.

  15. Liberomyces gen. nov. with two new species of endophytic coelomycetes from broadleaf trees.

    PubMed

    Pazoutová, Sylvie; Srutka, Petr; Holusa, Jaroslav; Chudícková, Milada; Kubátová, Alena; Kolarík, Miroslav

    2012-01-01

    During a study of endophytic and saprotrophic fungi in the sapwood and phloem of broadleaf trees (Salix alba, Quercus robur, Ulmus laevis, Alnus glutinosa, Betula pendula) fungi belonging to an anamorphic coelomycetous genus not attributable to a described taxon were detected and isolated in pure culture. The new genus, Liberomyces, with two species, L. saliciphilus and L. macrosporus, is described. Both species have subglobose conidiomata containing holoblastic sympodial conidiogenous cells. The conidiomata dehisce irregularly or by ostiole and secrete a slimy suspension of conidia. The conidia are hyaline, narrowly allantoid with a typically curved distal end. In L. macrosporus simultaneous production of synanamorph with thin filamentous conidia was observed occasionally. The genus has no known teleomorph. Related sequences in the public databases belong to endophytes of angiosperms. Phylogenetic analysis revealed a position close to the Xylariales (Sordariomycetes), but family and order affiliation remained unclear.

  16. Molecular identification of Aspergillus and Eurotium species isolated from rice and their toxin-producing ability.

    PubMed

    Yazdani, D; Zainal Abidin, M A; Tan, Y H; Kamaruzaman, S

    2011-01-01

    Thirty milled rice samples were collected from retailers in 4 provinces of Malaysia. These samples were evaluated for Aspergillus spp. infection by direct plating on malt extract salt agar (MESA). All Aspergillus holomorphs were isolated and identified using nucleotide sequences of ITS 1 and ITS 2 of rDNA. Five anamorphs (Aspergillus flavus, A. oryzae, A. tamarii, A. fumigatus and A. niger) and 5 teleomorphs (Eurotium rubrum, E. amstelodami, E. chevalieri, E. cristatum and E. tonophilum) were identified. The PCR-sequencing based technique for sequences of ITS 1 and ITS 2 is a fast technique for identification of Aspergillus and Eurotium species, although it doesn't work flawlessly for differentiation of Eurotium species. All Aspergillus and Eurotium isolates were screened for their ability to produce aflatoxin and ochratoxin A (OTA) by HPLC and TLC techniques. Only A. flavus isolate UPM 89 was able to produce aflatoxins B1 and B2. PMID:22168015

  17. Novel Phaeoacremonium species associated with necrotic wood of Prunus trees.

    PubMed

    Damm, U; Mostert, L; Crous, P W; Fourie, P H

    2008-06-01

    The genus Phaeoacremonium is associated with opportunistic human infections, as well as stunted growth and die-back of various woody hosts, especially grapevines. In this study, Phaeoacremonium species were isolated from necrotic woody tissue of Prunus spp. (plum, peach, nectarine and apricot) from different stone fruit growing areas in South Africa. Morphological and cultural characteristics as well as DNA sequence data (5.8S rDNA, ITS1, ITS2, beta-tubulin, actin and 18S rDNA) were used to identify known, and describe novel species. From the total number of wood samples collected (257), 42 Phaeoacremonium isolates were obtained, from which 14 species were identified. Phaeoacremonium scolyti was most frequently isolated, and present on all Prunus species sampled, followed by Togninia minima (anamorph: Pm. aleophilum) and Pm. australiense. Almost all taxa isolated represent new records on Prunus. Furthermore, Pm. australiense,Pm. iranianum, T. fraxinopennsylvanica and Pm. griseorubrum represent new records for South Africa, while Pm. griseorubrum, hitherto only known from humans, is newly reported from a plant host. Five species are newly described, two of which produce a Togninia sexual state. Togninia africana, T. griseo-olivacea and Pm. pallidum are newly described from Prunus armeniaca, while Pm. prunicolum and Pm. fuscum are described from Prunus salicina.

  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. 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

  20. A multi-gene phylogeny for species of Mycosphaerella occurring on Eucalyptus leaves.

    PubMed

    Hunter, Gavin C; Wingfield, Brenda D; Crous, Pedro W; Wingfield, Michael J

    2006-01-01

    Species of the ascomycete genus Mycosphaerella are regarded as some of the most destructive leaf pathogens of a large number of economically important crop plants. Amongst these, approximately 60 Mycosphaerella spp. have been identified from various Eucalyptus spp. where they cause leaf diseases collectively known as Mycosphaerella Leaf Disease (MLD). Species concepts for this group of fungi remain confused, and hence their species identification is notoriously difficult. Thus, the introduction of DNA sequence comparisons has become the definitive characteristic used to distinguish species of Mycosphaerella. Sequences of the Internal Transcribed Spacer (ITS) region of the ribosomal RNA operon have most commonly been used to consider species boundaries in Mycosphaerella. However, sequences for this gene region do not always provide sufficient resolution for cryptic taxa. The aim of this study was, therefore, to use DNA sequences for three loci, ITS, Elongation factor 1-alpha (EF-1alpha) and Actin (ACT) to reconsider species boundaries for Mycosphaerella spp. from Eucalyptus. A further aim was to study the anamorph concepts and resolve the deeper nodes of Mycosphaerella, for which part of the Large Subunit (LSU) of the nuclear rRNA operon was sequenced. The ITS and EF-1alpha gene regions were found to be useful, but the ACT gene region did not provide species-level resolution in Mycosphaerella. A phylogeny of the combined DNA datasets showed that species of Mycosphaerella from Eucalyptus cluster in two distinct groups, which might ultimately represent discrete genera. PMID:18490976

  1. DNA barcoding of Mycosphaerella species of quarantine importance to Europe.

    PubMed

    Quaedvlieg, W; Groenewald, J Z; de Jesús Yáñez-Morales, M; Crous, P W

    2012-12-01

    The EU 7th Framework Program provided funds for Quarantine Barcoding of Life (QBOL) to develop a quick, reliable and accurate DNA barcode-based diagnostic tool for selected species on the European and Mediterranean Plant Protection Organization (EPPO) A1/A2 quarantine lists. Seven nuclear genomic loci were evaluated to determine those best suited for identifying species of Mycosphaerella and/or its associated anamorphs. These genes included β-tubulin (Btub), internal transcribed spacer regions of the nrDNA operon (ITS), 28S nrDNA (LSU), Actin (Act), Calmodulin (Cal), Translation elongation factor 1-alpha (EF-1α) and RNA polymerase II second largest subunit (RPB2). Loci were tested on their Kimura-2-parameter-based inter- and intraspecific variation, PCR amplification success rate and ability to distinguish between quarantine species and closely related taxa. Results showed that none of these loci was solely suited as a reliable barcoding locus for the tested fungi. A combination of a primary and secondary barcoding locus was found to compensate for individual weaknesses and provide reliable identification. A combination of ITS with either EF-1α or Btub was reliable as barcoding loci for EPPO A1/A2-listed Mycosphaerella species. Furthermore, Lecanosticta acicola was shown to represent a species complex, revealing two novel species described here, namely L. brevispora sp. nov. on Pinus sp. from Mexico and L. guatemalensis sp. nov. on Pinus oocarpa from Guatemala. Epitypes were also designated for L. acicola and L. longispora to resolve the genetic application of these names. PMID:23606768

  2. 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

  3. Coniochaeta (Lecythophora), Collophora gen. nov. and Phaeomoniella species associated with wood necroses of Prunus trees.

    PubMed

    Damm, U; Fourie, P H; Crous, P W

    2010-06-01

    Species of the genus Coniochaeta (anamorph: Lecythophora) are known as pathogens of woody hosts, but can also cause opportunistic human infections. Several fungi with conidial stages resembling Lecythophora were isolated from necrotic wood samples of Prunus trees in South Africa. In order to reveal their phylogenetic relationships, these fungi were studied on a morphological and molecular (5.8S nrDNA, ITS-1, ITS-2, GAPDH, EF-1alpha, 28S nrDNA, 18S nrDNA) basis. Some of the isolates were identified as Coniochaeta (Sordariomycetes), including C. velutina and two new species, C. africana and C. prunicola. The majority of the isolates, however, formed pycnidial or pseudopycnidial synanamorphs and were not closely related to Coniochaeta. According to their 28S nrDNA phylogeny, they formed two distinct groups, one of which was closely related to Helotiales (Leotiomycetes). The new genus Collophora is proposed, comprising five species that frequently occur in necrotic peach and nectarine wood, namely Co. africana, Co. capensis, Co. paarla, Co. pallida and Co. rubra. The second group was closely related to Phaeomoniella chlamydospora (Eurotiomycetes), occurring mainly in plum wood. Besides P. zymoides occurring on Prunus salicina, four new species are described, namely P. dura, P. effusa, P. prunicola and P. tardicola. In a preliminary inoculation study, pathogenicity was confirmed for some of the new species on apricot, peach or plum wood.

  4. Two Trichosporon species isolated from Central-European mygalomorph spiders (Araneae: Mygalomorphae).

    PubMed

    Heneberg, Petr; Řezáč, Milan

    2013-04-01

    Trichosporon (Dikarya: Basidiomycota) is a genus of anamorphic yeasts typically associated with soil and water, although many species are causative agents of diseases in animals and man. Here we provide the first compelling evidence that spiders can be occasionally colonized by at least two Trichosporon species. Trichosporon dulcitum (Berkhout) Weijman 1979 was isolated from the exoskeleton of purse-web spider Atypus piceus, while Trichosporon porosum (Stautz) Middelhoven, Scorzetti & Fell 2001 was isolated from the exoskeleton of purse-web spider Atypus affinis. Both of the species were identified based on DNA sequence analysis of the host specimens displaying macroscopic signs of the superficial white mycosis on their exoskeleton. Only two specimens with macroscopic signs of superficial yeast growth were identified among the 125 individuals of A. affinis, A. piceus and Atypus muralis examined that were collected at various sites throughout the Czech Republic. The consistent burrow microclimate, uninterrupted occupancy of the single burrow for several subsequent years, and presence of prey remnants in the burrow below the purse-web may play a role in the course of infection of the mygalomorphs examined. The phylogenetic relationships of Trichosporon species are analyzed, concluding that association with invertebrates clusters predominantly among four groups of closely related species in independent Trichosporon clades.

  5. 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. PMID:24782494

  6. Occultifur tropicalis f.a., sp. nov., a novel cystobasidiomycetous yeast species isolated from tropical regions.

    PubMed

    Khunnamwong, Pannida; Surussawadee, Janjira; Jindamorakot, Sasitorn; Ribeiro, José R A; Hagler, Allen N; Limtong, Savitree

    2015-05-01

    Five strains representing a single novel anamorphic yeast species were isolated from sugar cane. Two strains were from tissue (DMKU-SE38, DMKU-SE59(T)) and two from the external surface (DMKU-SP385, DMKU-SP403) of leaves collected in Thailand and the fifth (IMUFRJ 52020) from the rhizoplane of sugar cane in an organically cultivated field in Brazil. On the basis of sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, they were classified as representing a single species of the genus Occultifur. The sequences of the D1/D2 region of the LSU rRNA genes and the ITS regions of the five strains were either identical or differed from each other by only one nucleotide substitution. The novel species was related most closely to Occultifur brasiliensis f.a. CBS 12687(T) but with 0.7-1.0% nucleotide substitutions (4-6 nt) in the D1/D2 region of the LSU rRNA gene and 2.5-2.7% nucleotide substitutions (14-15 nt) in the ITS region. The name Occultifur tropicalis f.a., sp. nov. is proposed. The type strain is DMKU-SE59(T) ( =BCC 61184(T) =NBRC 109696(T) =CBS 13389 (T)).

  7. Occultifur tropicalis f.a., sp. nov., a novel cystobasidiomycetous yeast species isolated from tropical regions.

    PubMed

    Khunnamwong, Pannida; Surussawadee, Janjira; Jindamorakot, Sasitorn; Ribeiro, José R A; Hagler, Allen N; Limtong, Savitree

    2015-05-01

    Five strains representing a single novel anamorphic yeast species were isolated from sugar cane. Two strains were from tissue (DMKU-SE38, DMKU-SE59(T)) and two from the external surface (DMKU-SP385, DMKU-SP403) of leaves collected in Thailand and the fifth (IMUFRJ 52020) from the rhizoplane of sugar cane in an organically cultivated field in Brazil. On the basis of sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, they were classified as representing a single species of the genus Occultifur. The sequences of the D1/D2 region of the LSU rRNA genes and the ITS regions of the five strains were either identical or differed from each other by only one nucleotide substitution. The novel species was related most closely to Occultifur brasiliensis f.a. CBS 12687(T) but with 0.7-1.0% nucleotide substitutions (4-6 nt) in the D1/D2 region of the LSU rRNA gene and 2.5-2.7% nucleotide substitutions (14-15 nt) in the ITS region. The name Occultifur tropicalis f.a., sp. nov. is proposed. The type strain is DMKU-SE59(T) ( =BCC 61184(T) =NBRC 109696(T) =CBS 13389 (T)). PMID:25713048

  8. Ceratocystis larium sp. nov., a new species from Styrax benzoin wounds associated with incense harvesting in Indonesia.

    PubMed

    van Wyk, M; Wingfield, B D; Clegg, P A; Wingfield, M J

    2009-06-01

    Styrax benzoin trees, native to the island Sumatra, Indonesia are wounded to produce resin that is collected and burned as incense. These wounds on trees commonly develop into expanding cankers that lead to tree death. The aim of this study was to consider whether Ophiostomatoid fungi, typically associated with wounds on trees might be associated with resin harvesting on S. benzoin. Samples were collected from the edges of artificially induced wounds, and particularly where cankers and staining of the vascular tissue was evident. Tissue samples were incubated in moist chambers and carrot baiting was also used to detect the presence of Ceratocystis spp. Fruiting structures with morphology typical of species in the C. fimbriata s.l. species complex and species in the anamorph genus Thielaviopsis were found, on both the incubated wood and the carrot baits. DNA sequences were generated for the Internal Transcribed Spacer regions 1 and 2 including the 5.8S rRNA gene, part of the beta-tubulin and the Transcription Elongation Factor 1-alpha gene regions. These data were compared with those of other species in the C. fimbriata s.l. species complex and Thielaviopsis using phylogenetic analysis. Morphology of the isolates in culture as well as phylogenetic inference showed that the Thielaviopsis sp. present on the wounds was T. basicola. The Ceratocystis sp. from S. benzoin represents a new taxon in the C. fimbriata s.l. complex described here as C. larium sp. nov.

  9. The genus Cryptosphaeria in the western United States: taxonomy, multilocus phylogeny and a new species, C. multicontinentalis.

    PubMed

    Trouillas, Florent P; Hand, Francesca Peduto; Inderbitzin, Patrik; Gubler, Walter D

    2015-01-01

    This study investigates the diversity and taxonomy of Cryptosphaeria species occurring in the western United States on the basis of morphological characters and multilocus phylogenetic analyses of the ribosomal internal transcribed spacer region, parts of a β-tubulin gene, the DNA-dependent RNA polymerase II second-largest subunit gene and the nuclear ribosomal large subunit gene. Cryptosphaeria multicontinentalis sp. nov is described from the Sierra Nevada and central coast of California on Populus tremuloides, P. balsamifera subsp. trichocarpa and P. fremontii. Cryptosphaeria pullmanensis is reported from a wide geographic area in the western United States on the main host, P. fremontii. The pathogen C. lignyota is reported for the first time from the Sierra Nevada of California on P. tremuloides. The phylogenetic analyses showed that C. multicontinentalis is a sister species to C. lignyota. Both species were closely related to C. subcutanea and more distantly related to C. pullmanensis. Characteristics of both teleomorph and anamorph of the newly introduced species C. multicontinentalis are described and illustrated.

  10. Clonal Species Trichoderma parareesei sp. nov. Likely Resembles the Ancestor of the Cellulase Producer Hypocrea jecorina/T. reesei▿ †

    PubMed Central

    Atanasova, Lea; Jaklitsch, Walter M.; Komoń-Zelazowska, Monika; Kubicek, Christian P.; Druzhinina, Irina S.

    2010-01-01

    We have previously reported that the prominent industrial enzyme producer Trichoderma reesei (teleomorph Hypocrea jecorina; Hypocreales, Ascomycota, Dikarya) has a genetically isolated, sympatric sister species devoid of sexual reproduction and which is constituted by the majority of anamorphic strains previously attributed to H. jecorina/T. reesei. In this paper we present the formal taxonomic description of this new species, T. parareesei, complemented by multivariate phenotype profiling and molecular evolutionary examination. A phylogenetic analysis of relatively conserved loci, such as coding fragments of the RNA polymerase B subunit II (rpb2) and GH18 chitinase (chi18-5), showed that T. parareesei is genetically invariable and likely resembles the ancestor which gave raise to H. jecorina. This and the fact that at least one mating type gene of T. parareesei has previously been found to be essentially altered compared to the sequence of H. jecorina/T. reesei indicate that divergence probably occurred due to the impaired functionality of the mating system in the hypothetical ancestor of both species. In contrast, we show that the sexually reproducing and correspondingly more polymorphic H. jecorina/T. reesei is essentially evolutionarily derived. Phenotype microarray analyses performed at seven temperature regimens support our previous speculations that T. parareesei possesses a relatively high opportunistic potential, which probably ensured the survival of this species in ancient and sustainable environment such as tropical forests. PMID:20817800

  11. Subcutaneous Phaeohyphomycosis Caused by Phaeoacremonium Species in a Kidney Transplant Patient: The First Case in Korea

    PubMed Central

    Choi, Jonghyeon; Lee, Yangsoon; Chung, Hae-Sun; Koo, Ja-Seung; Kim, Yu Sun; Lee, Kyungwon; Chong, Yunsop

    2011-01-01

    Phaeohyphomycosis is a subcutaneous infection caused by dark pigmented fungi, including fungi of the species Phaeoacremonium, Alternaria, Exophiala, and Pyrenochaeta. In August 2005, a 54-yr-old man who had received a renal transplant 5 yr ago was admitted to our hospital with a subcutaneous mass on the third finger of the right hand; the mass had been present for several months. He had been receiving immunosuppressive agents for several years. He underwent excision of the mass, which was followed by aspiration of the wound for bacterial and fungal cultures. Many fungal hyphae were observed on the histology slide treated with periodic acid-Schiff stain. A few white waxy colonies with a woolly texture grew on the Sabouraud dextrose agar at 30℃ and changed to dark brown in color. Nucleotide sequencing of internal transcribed spacer regions revealed 100% homology to the Phaeoacremonium aleophilum anamorph and Togninia minima teleomorph (514 bp/514 bp). The patient completely recovered after wide surgical excision. Here, we report the first case of phaeohyphomycosis caused by Phaeoacremonium species in a kidney transplant patient in Korea. PMID:21779196

  12. A Phylogenetic Analysis of Greek Isolates of Aspergillus Species Based on Morphology and Nuclear and Mitochondrial Gene Sequences

    PubMed Central

    Krimitzas, Antonios; Kouvelis, Vassili N.; Kapsanaki-Gotsi, Evangelia; Typas, Milton A.

    2013-01-01

    Aspergillus species originating from Greece were examined by morphological and molecular criteria to explore the diversity of this genus. The phylogenetic relationships of these species were determined using sequences from the ITS and IGS region of the nuclear rRNA gene complex, two nuclear genes (β-tubulin (benA) and RNA polymerase II second largest subunit (rpb2)) and two mitochondrial genes (small rRNA subunit (rns) and cytochrome oxidase subunit I (cox1)) and, where available, related sequences from databases. The morphological characters of the anamorphs and teleomorphs, and the single gene phylogenetic trees, differentiated and placed the species examined in the well-supported sections of Aenei, Aspergillus, Bispori, Candidi, Circumdati, Clavati, Cremei, Flavi, Flavipedes, Fumigati, Nidulantes, Nigri, Restricti, Terrei, Usti, and Zonati, with few uncertainties. The combined use of the three commonly employed nuclear genes (benA, rpb2, and ITS), the IGS region, and two less often used mitochondrial gene sequences (rns and cox1) as a single unit resolved several taxonomic ambiguities. A phylogenetic tree was inferred using Neighbour-Joining, Maximum Parsimony, and Bayesian methods. The strains examined formed seven well-supported clades within the genus Aspergillus. Altogether, the concatenated nuclear and mitochondrial sequences offer additional tools for an improved understanding of phylogenetic relationships within this genus. PMID:23762830

  13. Isolation of Pseudozyma churashimaensis sp. nov., a novel ustilaginomycetous yeast species as a producer of glycolipid biosurfactants, mannosylerythritol lipids.

    PubMed

    Morita, Tomotake; Ogura, Yuki; Takashima, Masako; Hirose, Naoto; Fukuoka, Tokuma; Imura, Tomohiro; Kondo, Yukishige; Kitamoto, Dai

    2011-08-01

    An ustilaginomycetous anamorphic yeast species isolated from the leaves of Saccharum officinarum (sugarcane) in Okinawa, Japan, was identified as a novel Pseudozyma species based on morphological and physiological aspects and molecular taxonomic analysis using the D1/D2 domains of the large subunit (26S) rRNA gene and the internal transcribed spacer 1 (ITS1)-5.8S-ITS2 regions. The name Pseudozyma churashimaensis sp. nov. was proposed for the novel species, with JCM 16988(T) as the type strain. Interestingly, P. churashimaensis was found to produce glycolipid biosurfactants, a mixture of mannosylerythritol lipids (MELs), including a novel tri-acetylated derivative (MEL-A2), from glucose. The observed critical micelle concentration (CMC) and the surface tension at CMC of MEL-A2 were 1.7 × 10⁻⁶ M and 29.2 mN/m, respectively. Moreover, on a water-penetration scan, MEL-A2 efficiently formed different lyotropic liquid crystalline phases, including the lamella phase at a wide range of concentrations, indicating its excellent surface-active and self-assembling properties. The novel strain of the genus Pseudozyma should thus facilitate the application of glycolipid biosurfactants in combination with other MEL producers. PMID:21606002

  14. 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

  15. Genome-wide comparative analysis of pogo-like transposable elements in different Fusarium species.

    PubMed

    Dufresne, Marie; Lespinet, Olivier; Daboussi, Marie-Josée; Hua-Van, Aurélie

    2011-10-01

    The recent availability of genome sequences of four different Fusarium species offers the opportunity to perform extensive comparative analyses, in particular of repeated sequences. In a recent work, the overall content of such sequences in the genomes of three phylogenetically related Fusarium species, F. graminearum, F. verticillioides, and F. oxysporum f. sp. lycopersici has been estimated. In this study, we present an exhaustive characterization of pogo-like elements, named Fots, in four Fusarium genomes. Overall 10 Fot and two Fot-related miniature inverted-repeat transposable element families were identified, revealing a diversification of multiple lineages of pogo-like elements, some of which accompanied by a gain of introns. This analysis also showed that such elements are present in an unusual high proportion in the genomes of F. oxysporum f. sp. lycopersici and Nectria haematococca (anamorph F. solani f. sp. pisi) in contrast with most other fungal genomes in which retroelements are the most represented. Interestingly, our analysis showed that the most numerous Fot families all contain potentially active or mobilisable copies, thus conferring a mutagenic potential of these transposable elements and consequently a role in strain adaptation and genome evolution. This role is strongly reinforced when examining their genomic distribution which is clearly biased with a high proportion (more than 80%) located on strain- or species-specific regions enriched in genes involved in pathogenicity and/or adaptation. Finally, the different reproductive characteristics of the four Fusarium species allowed us to investigate the impact of the process of repeat-induced point mutations on the expansion and diversification of Fot elements.

  16. Nitrogen species

    NASA Technical Reports Server (NTRS)

    Harries, J. E.; Brasseur, G.; Coffey, M. T.; Fischer, H.; Gille, J.; Jones, R.; Louisnard, N.; Mccormick, M. P.; Noxon, J.; Owens, A. J.

    1985-01-01

    Total odd nitrogen, NO(y), may be defined as the sum of all active nitrogen species that interchange photochemically with one another on a time scale of the order of weeks or less. As noted, NO + NO2 reactions dominate the processes controlling the ozone balance in the contemporary stratosphere. The observational data from non-satellite platforms are reviewed. The growth in available satellite data in the past four years is considered. Some of the most important scientific issues are discussed, taking into account new results from atmospheric models (mainly 2-D). The model results are compared with the observational data.

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

    PubMed

    Crouch, Jo Anne; Tomaso-Peterson, Maria

    2012-01-01

    Colletotrichum is a cosmopolitan, anamorphic fungal genus responsible for anthracnose disease in hundreds of plant species worldwide, including members of the Poaceae. Anthracnose disease of the widely planted, non-native, warm-season lawn grass, Eremochloae ophiuroides (centipedegrass), is commonly encountered in the southern United States, but the causal agent has never been identified. We use DNA sequence data from modern cultures and archival fungarium specimens in this study to determine the identity of the fungus responsible for centipedegrass anthracnose disease and provide experimental confirmation of pathogenicity. C. eremochloae sp. nov., a pathogen of centipedegrass, is proposed based on phylogenetic evidence from four sequence markers (Apn2, Apn2/ Mat1, Sod2, ITS). C. eremochloae isolates from centipedegrass shared common morphology and phenotype with C. sublineola, a destructive pathogen of cultivated sorghum and Johnsongrass weeds (Sorghum halepense, S. vulgaris). Molecular phylogenetic analysis identified C. eremochloae and C. sublineola as closely related sister taxa, but genealogical concordance supported their distinction as unique phylogenetic species. Fixed nucleotide differences between C. eremochloae and C. sublineola were observed from collections of these fungi spanning 105 y, including the 1904 lectotype specimen of C. sublineola. C. eremochloae was identified from a fungarium specimen of centipedegrass intercepted at a USA port from a 1923 Chinese shipment; the multilocus sequence from this specimen was identical to modern samples of the fungus. Thus, it appears that the fungus might have migrated to the USA around the same time that centipedegrass first was introduced to the USA in 1916 from China, where the grass is indigenous. The new species C. eremochloae is described and illustrated, along with a description and discussion of C. sublineola based on the lectotype and newly designated epitype.

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

    PubMed

    Crouch, Jo Anne; Tomaso-Peterson, Maria

    2012-01-01

    Colletotrichum is a cosmopolitan, anamorphic fungal genus responsible for anthracnose disease in hundreds of plant species worldwide, including members of the Poaceae. Anthracnose disease of the widely planted, non-native, warm-season lawn grass, Eremochloae ophiuroides (centipedegrass), is commonly encountered in the southern United States, but the causal agent has never been identified. We use DNA sequence data from modern cultures and archival fungarium specimens in this study to determine the identity of the fungus responsible for centipedegrass anthracnose disease and provide experimental confirmation of pathogenicity. C. eremochloae sp. nov., a pathogen of centipedegrass, is proposed based on phylogenetic evidence from four sequence markers (Apn2, Apn2/ Mat1, Sod2, ITS). C. eremochloae isolates from centipedegrass shared common morphology and phenotype with C. sublineola, a destructive pathogen of cultivated sorghum and Johnsongrass weeds (Sorghum halepense, S. vulgaris). Molecular phylogenetic analysis identified C. eremochloae and C. sublineola as closely related sister taxa, but genealogical concordance supported their distinction as unique phylogenetic species. Fixed nucleotide differences between C. eremochloae and C. sublineola were observed from collections of these fungi spanning 105 y, including the 1904 lectotype specimen of C. sublineola. C. eremochloae was identified from a fungarium specimen of centipedegrass intercepted at a USA port from a 1923 Chinese shipment; the multilocus sequence from this specimen was identical to modern samples of the fungus. Thus, it appears that the fungus might have migrated to the USA around the same time that centipedegrass first was introduced to the USA in 1916 from China, where the grass is indigenous. The new species C. eremochloae is described and illustrated, along with a description and discussion of C. sublineola based on the lectotype and newly designated epitype. PMID:22492402

  19. Aflavinines and other antiinsectan metabolites from the ascostromata of Eupenicillium crustaceum and related species.

    PubMed

    Wang, H J; Gloer, J B; Wicklow, D T; Dowd, P F

    1995-12-01

    This report describes the distribution of antiinsectan metabolites present in sclerotioid ascostromata produced by representative strains of Eupenicillium crustaceum and fungal taxa that are considered to be closely related. The hexane and chloroform extracts of E. crustaceum NRRL 3332 displayed significant antiinsectan activity in assays against the corn earworm, Helicoverpa zea. The major metabolite accounting for this antiinsectan activity was a known aflavinine analog, 10,23-dihydro-24,25-dehydroaflavinine, occurring at approximately 2.8 mg/g of dry ascostromata. In dietary assays at ca. 3,000 ppm, a 79% reduction in weight gain and a 42% reduction in feeding rate were observed in H. zea and Carpophilus hemipterus larvae, respectively. A new aflavinine analog, 10,23,24,25-tetrahydro-24-hydroxyaflavinine, was also identified. These aflavinine compounds are the first to be reported from a fungal genus other than Aspergillus. New macrophorin-type metabolites accounted for the antiinsectan activity of ascostromata produced by E. crustaceum NRRL 22307, which produced no aflavinines, while Eupenicillium molle NRRL 13062 produced both aflavinines and macrophorins. Sclerotia produced by Penicillium gladioli NRRL 938, NRRL 939, and QM 2743, a fungus reported to be conspecific with the anamorph of E. crustaceum, produced neither aflavinines nor macrophorins. Eupenicillium reticulisporum NRRL 3446 produced the aflavinine analog 10,23-dihydro-24,25-dehydroaflavinine and an unrelated compound called pyripyropene A, a potent inhibitor of acyl-coenzyme A-cholesterol acyltransferase. Eupenicillium abidjanum NRRL 5809, reported to be conspecific with E. reticulisporum, produced neither of these compounds. The Eupenicillium species that produced aflavinines are also known for their ability to grow rapidly with reduced water activity. PMID:8534106

  20. Aflavinines and other antiinsectan metabolites from the ascostromata of Eupenicillium crustaceum and related species.

    PubMed Central

    Wang, H J; Gloer, J B; Wicklow, D T; Dowd, P F

    1995-01-01

    This report describes the distribution of antiinsectan metabolites present in sclerotioid ascostromata produced by representative strains of Eupenicillium crustaceum and fungal taxa that are considered to be closely related. The hexane and chloroform extracts of E. crustaceum NRRL 3332 displayed significant antiinsectan activity in assays against the corn earworm, Helicoverpa zea. The major metabolite accounting for this antiinsectan activity was a known aflavinine analog, 10,23-dihydro-24,25-dehydroaflavinine, occurring at approximately 2.8 mg/g of dry ascostromata. In dietary assays at ca. 3,000 ppm, a 79% reduction in weight gain and a 42% reduction in feeding rate were observed in H. zea and Carpophilus hemipterus larvae, respectively. A new aflavinine analog, 10,23,24,25-tetrahydro-24-hydroxyaflavinine, was also identified. These aflavinine compounds are the first to be reported from a fungal genus other than Aspergillus. New macrophorin-type metabolites accounted for the antiinsectan activity of ascostromata produced by E. crustaceum NRRL 22307, which produced no aflavinines, while Eupenicillium molle NRRL 13062 produced both aflavinines and macrophorins. Sclerotia produced by Penicillium gladioli NRRL 938, NRRL 939, and QM 2743, a fungus reported to be conspecific with the anamorph of E. crustaceum, produced neither aflavinines nor macrophorins. Eupenicillium reticulisporum NRRL 3446 produced the aflavinine analog 10,23-dihydro-24,25-dehydroaflavinine and an unrelated compound called pyripyropene A, a potent inhibitor of acyl-coenzyme A-cholesterol acyltransferase. Eupenicillium abidjanum NRRL 5809, reported to be conspecific with E. reticulisporum, produced neither of these compounds. The Eupenicillium species that produced aflavinines are also known for their ability to grow rapidly with reduced water activity. PMID:8534106

  1. 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...

  2. In defense of species.

    PubMed

    LaPorte, Joseph

    2007-03-01

    In this paper, I address the charge that the category species should be abandoned in biological work. The widespread appeal to species in scientific discourse provides a presumption in favor of the category's usefulness, but a defeasible presumption. Widely acknowledged troubles attend species: these troubles might render the concept unusable by showing that 'species' is equivocal or meaningless or in some similar way fatally flawed. Further, there might be better alternatives to species. I argue that the presumption in favor of species is not defeated on these scores. Troubles attending species, which arise on account of contextual variation attending the use of 'species', do not indicate that the concept is unusable. And alternatives to the use of 'species', which have been proposed in connection with rank-free systematics and in connection with conservation efforts, fail to provide a proper replacement for species.

  3. 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.

  4. Phylogenetic lineages in the Botryosphaeriaceae.

    PubMed

    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-type cultures

  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. Aquatic invasive species

    USGS Publications Warehouse

    Thorsteinson, Lyman

    2005-01-01

    Invasive species are plants or animals that are present in an ecosystem beyond their native range. They may have few natural controls in their new environment and proliferate. They can threaten native species and interfere with human activities. The Western Fisheries Research Center (WFRC) has been conducting research to understand how non-native species invade and affect ecosystems, thus aiding management efforts.

  7. 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.

  8. Crossing species boundaries.

    PubMed

    Robert, Jason Scott; Baylis, Françoise

    2003-01-01

    This paper critically examines the biology of species identity and the morality of crossing species boundaries in the context of emerging research that involves combining human and nonhuman animals at the genetic or cellular level. We begin with the notion of species identity, particularly focusing on the ostensible fixity of species boundaries, and we explore the general biological and philosophical problem of defining species. Against this backdrop, we survey and criticize earlier attempts to forbid crossing species boundaries in the creation of novel beings. We do not attempt to establish the immorality of crossing species boundaries, but we conclude with some thoughts about such crossings, alluding to the notion of moral confusion regarding social and ethical obligations to novel interspecies beings.

  9. Darwin's species category realism.

    PubMed

    Stamos, D N

    1999-01-01

    Ever since Charles Darwin's On the Origin of Species was published, the received view has been that Darwin literally thought of species as not extra-mentally real. In 1969 Michael Ghiselin upset the received view by interpreting Darwin to mean that species taxa are indeed real but not the species category. In 1985 John Beatty took Ghiselin's thesis a step further by providing a strategy theory to explain why Darwin would say one thing (his repeated nominalistic definition of species) and do another (hold that species taxa are real). In the present paper I attempt to take this line of interpretation to a new level. Guided by the principle of charity, I provide and analyze a considerable amount of evidence from Darwin's mature writings (both private and published) to show that (contra Ghiselin and Beatty) Darwin did not simply accept the species delimitations of his fellow naturalists but actually employed, repeatedly and consistently, a species concept in a thoroughly modern sense, albeit with an implicit definition, a concept uniquely his own and fully in accord with his theory of evolution by natural selection. This implicit concept and definition is carefully reconstructed in the present paper. A new strategy theory is then provided to account for why Darwin would define species (both taxa and category) nominalistically on the one hand but delimit species realistically on the other.

  10. 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.

  11. Fusarium species and fumonisins associated with maize kernels produced in Rio Grande do Sul State for the 2008/09 and 2009/10 growing seasons

    PubMed Central

    Stumpf, R.; dos Santos, J.; Gomes, L.B.; Silva, C.N.; Tessmann, D.J.; Ferreira, F.D.; Machinski, M.; Del Ponte, E.M.

    2013-01-01

    Ear rots caused by Fusarium spp. are among the main fungal diseases that contribute to poor quality and the contamination of maize grains with mycotoxins. This study aimed to determine the visual incidence of fungal-damaged kernels (FDKs), the incidence of two main Gibberella (a teleomorph of Fusarium) complexes (G. fujikuroi and G. zeae) associated with maize using a seed health blotter test, and the fumonisin levels, using high performance liquid chromatography, in samples of maize grains grown across 23 municipalities during the 2008/09 and 2009/10 growing seasons. Additionally, 104 strains that were representative of all of the analysed samples were identified to species using PCR assays. The mean FDK was seven per cent, and only six of the samples had levels greater than six per cent. Fusarium spp. of the G. fujikuroi complex were present in 96% of the samples, and G. zeae was present in 18% of the samples (5/27). The mean incidence of G. fujikuroi was 58%, and the incidence of G. zeae varied from 2 to 6%. FB1 was found in 58.6%, FB2 in 37.9%, and both toxins in 37.9% of the samples. The FB1 and FB2 levels were below the quantification limits for 41.3% of the samples, and the mean FB1 levels (0.66 μg/g) were higher than the mean FB2 levels (0.42 μg/g). The PCR identification separated the 104 isolates into three of the G. fujikuroi complex: F. verticillioides (76%), F. subglutinans (4%) and F. proliferatum (2%); and G. zeae (anamorph = F. graminearum) (18%). Our results confirmed the dominance of F. verticillioides, similar to other regions of Brazil, but they differed due to the relatively higher incidence of F. graminearum. Total fumonisin levels were below the maximum limit determined by current Brazilian regulations. PMID:24159288

  12. Fusarium species and fumonisins associated with maize kernels produced in Rio Grande do Sul State for the 2008/09 and 2009/10 growing seasons.

    PubMed

    Stumpf, R; Dos Santos, J; Gomes, L B; Silva, C N; Tessmann, D J; Ferreira, F D; Machinski, M; Del Ponte, E M

    2013-05-31

    Ear rots caused by Fusarium spp. are among the main fungal diseases that contribute to poor quality and the contamination of maize grains with mycotoxins. This study aimed to determine the visual incidence of fungal-damaged kernels (FDKs), the incidence of two main Gibberella (a teleomorph of Fusarium) complexes (G. fujikuroi and G. zeae) associated with maize using a seed health blotter test, and the fumonisin levels, using high performance liquid chromatography, in samples of maize grains grown across 23 municipalities during the 2008/09 and 2009/10 growing seasons. Additionally, 104 strains that were representative of all of the analysed samples were identified to species using PCR assays. The mean FDK was seven per cent, and only six of the samples had levels greater than six per cent. Fusarium spp. of the G. fujikuroi complex were present in 96% of the samples, and G. zeae was present in 18% of the samples (5/27). The mean incidence of G. fujikuroi was 58%, and the incidence of G. zeae varied from 2 to 6%. FB1 was found in 58.6%, FB2 in 37.9%, and both toxins in 37.9% of the samples. The FB1 and FB2 levels were below the quantification limits for 41.3% of the samples, and the mean FB1 levels (0.66 μg/g) were higher than the mean FB2 levels (0.42 μg/g). The PCR identification separated the 104 isolates into three of the G. fujikuroi complex: F. verticillioides (76%), F. subglutinans (4%) and F. proliferatum (2%); and G. zeae (anamorph = F. graminearum) (18%). Our results confirmed the dominance of F. verticillioides, similar to other regions of Brazil, but they differed due to the relatively higher incidence of F. graminearum. Total fumonisin levels were below the maximum limit determined by current Brazilian regulations.

  13. The species in primatology.

    PubMed

    Groves, Colin

    2014-01-01

    Biologists of the late eighteenth and early nineteenth centuries all bandied about the term "species," but very rarely actually said what they meant by it. Often, however, one can get inside their thinking by piecing together some of their remarks. One of the most nearly explicit-appropriately, for the man who wrote a book called The Origin of Species - was Charles Darwin: "Practically, when a naturalist can unite two forms together by others having intermediate characters, he treats the one as a variety of the other… He later translated this into evolutionary terms: "Hereafter, we shall be compelled to acknowledge that the only distinction between species and well-marked varieties is, that the latter are known, or believed, to be connected at the present day by intermediate gradations, whereas species were formerly thus connected"(1:484-5.) PMID:24591131

  14. How reticulated are species?

    PubMed

    Mallet, James; Besansky, Nora; Hahn, Matthew W

    2016-02-01

    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.

  15. The species in primatology.

    PubMed

    Groves, Colin

    2014-01-01

    Biologists of the late eighteenth and early nineteenth centuries all bandied about the term "species," but very rarely actually said what they meant by it. Often, however, one can get inside their thinking by piecing together some of their remarks. One of the most nearly explicit-appropriately, for the man who wrote a book called The Origin of Species - was Charles Darwin: "Practically, when a naturalist can unite two forms together by others having intermediate characters, he treats the one as a variety of the other… He later translated this into evolutionary terms: "Hereafter, we shall be compelled to acknowledge that the only distinction between species and well-marked varieties is, that the latter are known, or believed, to be connected at the present day by intermediate gradations, whereas species were formerly thus connected"(1:484-5.)

  16. 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)

  17. How reticulated are species?

    PubMed

    Mallet, James; Besansky, Nora; Hahn, Matthew W

    2016-02-01

    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

  18. 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

  19. USGS invasive species solutions

    USGS Publications Warehouse

    Simpson, Annie

    2011-01-01

    Land managers must meet the invasive species challenge every day, starting with identification of problem species, then the collection of best practices for their control, and finally the implementation of a plan to remove the problem. At each step of the process, the availability of reliable information is essential to success. The U.S. Geological Survey (USGS) has developed a suite of resources for early detection and rapid response, along with data management and sharing.

  20. Species integrity in trees.

    PubMed

    Ortiz-Barrientos, Daniel; Baack, Eric J

    2014-09-01

    From California sequoia, to Australian eucalyptus, to the outstanding diversity of Amazonian forests, trees are fundamental to many processes in ecology and evolution. Trees define the communities that they inhabit, are host to a multiplicity of other organisms and can determine the ecological dynamics of other plants and animals. Trees are also at the heart of major patterns of biodiversity such as the latitudinal gradient of species diversity and thus are important systems for studying the origin of new plant species. Although the role of trees in community assembly and ecological succession is partially understood, the origin of tree diversity remains largely opaque. For instance, the relative importance of differing habitats and phenologies as barriers to hybridization between closely related species is still largely uncharacterized in trees. Consequently, we know very little about the origin of trees species and their integrity. Similarly, studies on the interplay between speciation and tree community assembly are in their infancy and so are studies on how processes like forest maturation modifies the context in which reproductive isolation evolves. In this issue of Molecular Ecology, Lindtke et al. (2014) and Lagache et al. (2014) overcome some traditional difficulties in studying mating systems and sexual isolation in the iconic oaks and poplars, providing novel insights about the integrity of tree species and on how ecology leads to variation in selection on reproductive isolation over time and space. PMID:25155715

  1. 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.

  2. 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.

  3. 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].

  4. 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.

  5. Bioterrorism and invasive species.

    PubMed

    Chomel, B B; Sun, B

    2010-08-01

    The risk of dispersing invasive species, especially human pathogens, through acts of bioterrorism, cannot be neglected. However, that risk appears quite low in comparison with the risk of dispersing animal pathogens that could dramatically burden the agricultural economy of food animal producing countries, such as Australia and countries in Europe and North and South America. Although it is not directly related to bioterrorism, the intentional release of non-native species, particularly undesired companion animals or wildlife, may also have a major economic impact on the environment and, possibly, on animal and human health, in the case of accidental release of zoonotic agents.

  6. Dual Species NMR Oscillator

    NASA Astrophysics Data System (ADS)

    Weber, Joshua; Korver, Anna; Thrasher, Daniel; Walker, Thad

    2016-05-01

    We present progress towards a dual species nuclear magnetic oscillator using synchronous spin exchange optical pumping. By applying the bias field as a sequence of alkali 2 π pulses, we generate alkali polarization transverse to the bias field. The alkali polarization is then modulated at the noble gas resonance so that through spin exchange collisions the noble gas becomes polarized. This novel method of NMR suppresses the alkali field frequency shift by at least a factor of 2500 as compared to longitudinal NMR. We will present details of the apparatus and measurements of dual species co-magnetometry using this method. Research supported by the NSF and Northrop-Grumman Corp.

  7. 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)

  8. 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 following…

  9. 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 Species…

  10. 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…

  11. 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...

  12. 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

  13. Estimating species richness: The importance of heterogeneity in species detectability

    USGS Publications Warehouse

    Boulinier, T.; Nichols, J.D.; Sauer, J.R.; Hines, J.E.; Pollock, K.H.

    1998-01-01

    Estimating species richness (i.e. the actual number of species present in a given area) is a basic objective of many field studies carried out in community ecology and is also of crucial concern when dealing with the conservation and management of biodiversity. In most studies, the total number of species recorded in an area at a given time is taken as a measure of species richness. Here we use a capture-recapture approach to species richness estimation with North American Breeding Bird Survey (BBS) data in order to estimate species detectability and thus gain insight about its importance. We carried out analyses on all survey routes of four states, Arizona, Maryland, North Dakota, and Wisconsin, in two years, 1970 and 1990. These states were chosen to provide contrasting habitats, bird species composition and survey quality. We investigated the effect of state, year and observer ability on the proportions of different models selected, and on estimates of detectability and species richness. Our results indicate that model Mh, which assumes heterogeneous detection probability among species, is frequently appropriate for estimating species richness from BBS data. Species detectability varied among states and was higher for the more skilled observers. These results emphasize the need to take into account potential heterogeneities in detectability among species in studies of factors affecting species richness.

  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. PMID:27028074

  15. 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.

  16. 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).

  17. 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.

  18. 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.

  19. Nutrition of aquaculture species.

    PubMed

    Lovell, R T

    1991-10-01

    Dietary requirements for amino acids and fatty acids have been reported for channel catfish (Ictalurus punctatus), salmonids (Oncorhynchus spp.), common carp (Cyprinus carpio), tilapias (Oreochromis spp.), and eel (Anguilla japonicus). Most of the vitamin and mineral requirements are available for channel catfish and salmonids, and some are available for common carp, tilapia, eel, and other finfish and crustaceans. From this available information, cost-effective feeds can be formulated for the major commercial aquaculture species. Major differences in nutrient requirements between fish and mammals or birds are as follows: fish have a lower digestible energy:protein ratio (8 to 10 kcal of DE/g of CP for fish vs 15 to 20 kcal of DE/g of CP for livestock); fish require n-3 fatty acids and land animals require n-6; fish can absorb minerals from the water, which negates the need for some minerals in the diet; and fish have limited ability to synthesize vitamin C and must depend on a dietary source. Areas for further research include 1) refinement of nutrient requirements of the major culture species considering effects of fish size, temperature, and management; 2) nutrient requirements of crustaceans; 3) effects of nutrition on fish health and product quality; and 4) feeding technology. PMID:1778835

  20. ULTRASTRUCTURE OF MYCOPLASMA SPECIES

    PubMed Central

    Domermuth, C. H.; Nielsen, M. H.; Freundt, E. A.; Birch-Andersen, A.

    1964-01-01

    Domermuth, C. H. (Statens Seruminstitut, Copenhagen, Denmark), M. H. Nielsen, E. A. Freundt, and A. Birch-Andersen. Ultrastructure of Mycoplasma species. J. Bacteriol. 88:727–744. 1964.—The ultrastructure of 19 strains (15 species) of Mycoplasmatales grown on solid medium was studied with the aid of an electron microscope. The cells possessed a triple-layered limiting membrane 75 to 100 A thick. This membrane appeared to be symmetrical in some strains and asymmetrical in others. An electron-dense material found in close contact with the cell surface was tentatively interpreted to be a capsular substance. Ribosomes and strands of nuclear material were observed in the cytoplasm of cells of all strains. Ribosomes observed in the JA strain of M. gallisepticum were frequently arranged in a regular geometric pattern of characteristic appearance. Dense inclusions sometimes limited by triple-layered membranes (possibly developing elementary bodies), as well as membrane-surrounded vesicles, were observed in the cytoplasm of cells of some strains. Images PMID:14208513

  1. 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…

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

    PubMed

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

    2014-02-01

    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.

  3. Invasive species and climate change

    USGS Publications Warehouse

    Middleton, Beth A.

    2006-01-01

    Invasive species challenge managers in their work of conserving and managing natural areas and are one of the most serious problems these managers face. Because invasive species are likely to spread in response to changes in climate, managers may need to change their approaches to invasive species management accordingly.

  4. 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...

  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. 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 about the…

  7. Ubiquitous dispersal of microbial species

    NASA Astrophysics Data System (ADS)

    Finlay, Bland J.; Clarke, Ken J.

    1999-08-01

    The biosphere supports astronomical numbers of free-living microorganisms that belong to an indeterminate number of species. One view is that the abundance of microorganisms drives their dispersal, making them ubiquitous and resulting in a moderate global richness of species. But ubiquity is hard to demonstrate, not only because active species have a rapid turnover, but also because most species in a habitat at any moment in time are relatively rare or in some cryptic state. Here we use microbes that leave traces of their recent population growth in the form of siliceous scale structures to show that all species in the chrysomonad flagellate genus Paraphysomonas are probably ubiquitous.

  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. Importance of species traits for species distribution in fragmented landscapes.

    PubMed

    Tremlová, Katerina; Münzbergová, Zuzana

    2007-04-01

    Knowledge of the relationship between species traits and species distribution in fragmented landscapes is important for understanding current distribution patterns and as background information for predictive models of the effect of future landscape changes. The existing studies on the topic suffer from several drawbacks. First, they usually consider only traits related to dispersal ability and not growth. Furthermore, they do not apply phylogenetic corrections, and we thus do not know how considerations of phylogenetic relationships can alter the conclusions. Finally, they usually apply only one technique to calculate habitat isolation, and we do not know how other isolation measures would change the results. We studied the issues using 30 species forming congeneric pairs occurring in fragmented dry grasslands. We measured traits related to dispersal, survival, and growth in the species and recorded distribution of the species in 215 grassland fragments. We show many strong relationships between species traits related to both dispersal and growth and species distribution in the landscape, such as the positive relationship between habitat occupancy and anemochory and negative relationships between habitat occupancy and seed dormancy. The directions of these relationships, however, often change after application of phylogenetic correction. For example, more isolated habitats host species with smaller seeds. After phylogenetic correction, however, they turn out to host species with larger seeds. The conclusions also partly change depending on how we calculate habitat isolation. Specifically, habitat isolation calculated from occupied habitats only has the highest predictive power. This indicates slow dynamics of the species. All the results support the expectation that species traits have a high potential to explain patterns of species distribution in the landscape and that they can be used to build predictive models of species distribution. The specific conclusions

  11. Eighteen new oleaginous yeast species.

    PubMed

    Garay, Luis A; Sitepu, Irnayuli R; Cajka, Tomas; Chandra, Idelia; Shi, Sandy; Lin, Ting; German, J Bruce; Fiehn, Oliver; Boundy-Mills, Kyria L

    2016-07-01

    Of 1600 known species of yeasts, about 70 are known to be oleaginous, defined as being able to accumulate over 20 % intracellular lipids. These yeasts have value for fundamental and applied research. A survey of yeasts from the Phaff Yeast Culture Collection, University of California Davis was performed to identify additional oleaginous species within the Basidiomycota phylum. Fifty-nine strains belonging to 34 species were grown in lipid inducing media, and total cell mass, lipid yield and triacylglycerol profiles were determined. Thirty-two species accumulated at least 20 % lipid and 25 species accumulated over 40 % lipid by dry weight. Eighteen of these species were not previously reported to be oleaginous. Triacylglycerol profiles were suitable for biodiesel production. These results greatly expand the number of known oleaginous yeast species, and reveal the wealth of natural diversity of triacylglycerol profiles within wild-type oleaginous Basidiomycetes.

  12. Eighteen new oleaginous yeast species.

    PubMed

    Garay, Luis A; Sitepu, Irnayuli R; Cajka, Tomas; Chandra, Idelia; Shi, Sandy; Lin, Ting; German, J Bruce; Fiehn, Oliver; Boundy-Mills, Kyria L

    2016-07-01

    Of 1600 known species of yeasts, about 70 are known to be oleaginous, defined as being able to accumulate over 20 % intracellular lipids. These yeasts have value for fundamental and applied research. A survey of yeasts from the Phaff Yeast Culture Collection, University of California Davis was performed to identify additional oleaginous species within the Basidiomycota phylum. Fifty-nine strains belonging to 34 species were grown in lipid inducing media, and total cell mass, lipid yield and triacylglycerol profiles were determined. Thirty-two species accumulated at least 20 % lipid and 25 species accumulated over 40 % lipid by dry weight. Eighteen of these species were not previously reported to be oleaginous. Triacylglycerol profiles were suitable for biodiesel production. These results greatly expand the number of known oleaginous yeast species, and reveal the wealth of natural diversity of triacylglycerol profiles within wild-type oleaginous Basidiomycetes. PMID:27072563

  13. 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

  14. Confronting species distribution model predictions with species functional traits.

    PubMed

    Wittmann, Marion E; Barnes, Matthew A; Jerde, Christopher L; Jones, Lisa A; Lodge, David M

    2016-02-01

    Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

  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. Cryptic species in Stachybotrys chartarum.

    PubMed

    Cruse, Michael; Telerant, Robin; Gallagher, Thomas; Lee, Thomas; Taylor, John W

    2002-01-01

    Stachybotrys chartarum has received much attention as a possible cause of sick-building syndrome. Because morphological species recognition in fungi can hide diversity, we applied a phylogenetic approach to search for cryptic species. We examined 23 isolates from the San Francisco Bay Area, and another seven from around the US. Using markers we developed for three polymorphic protein coding loci (chitin synthase 1, beta-tubulin 2, and trichodiene synthase 5), we infer that two distinct phylogenetic species exist within the single described morphological species. We have found no correlation between genetic isolation and geographic distance. PMID:21156555

  17. 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. PMID:27356338

  18. 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.

  19. 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. PMID:27263029

  20. Ring species as demonstrations of the continuum of species formation.

    PubMed

    Pereira, Ricardo J; Wake, David B

    2015-11-01

    In the mid-20th century, Ernst Mayr (1942) and Theodosius Dobzhansky (1958) championed the significance of 'circular overlaps' or 'ring species' as the perfect demonstration of the gradual nature of species formation. As an ancestral species expands its range, wrapping around a geographic barrier, derived taxa within the ring display interactions typical of populations, such as genetic and morphological intergradation, while overlapping taxa at the terminus of the ring behave largely as sympatric, reproductively isolated species. Are ring species extremely rare or are they just difficult to detect? What conditions favour their formation? Modelling studies have attempted to address these knowledge gaps by estimating the biological parameters that result in stable ring species (Martins et al. 2013), and determining the necessary topographic parameters of the barriers encircled (Monahan et al. 2012). However, any generalization is undermined by a major limitation: only a handful of ring species are known to exist in nature. In addition, many of them have been broken into multiple species presumed to be evolving independently, usually obscuring the evolutionary dynamics that generate diversity. A paper in this issue of Molecular Ecology by Fuchs et al. (2015), focused on the entire genealogy of a bulbul (Alophoixus) species complex, offers key insights into the evolutionary processes underlying diversification of this Indo-Malayan bird. Their findings fulfil most of the criteria that can be expected for ring species (Fig. ): an ancestor has colonized the mainland from Sundaland, expanded along the forested habitat wrapping around Thailand's lowlands, adjacent taxa intergrade around the ring distribution, and terminal taxa overlap at the ring closure. Although it remains unclear whether ring divergence has resulted in restrictive gene flow relative to that observed around the ring, their results suggest that circular overlaps might be more common in nature than

  1. 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....

  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. 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 ...

  4. 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...

  5. 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..., notice was published in the Federal Register (76 FR 33703) that a request for a scientific...

  6. 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)

  7. Chironomids' Relationship with Aeromonas Species.

    PubMed

    Laviad, Sivan; Halpern, Malka

    2016-01-01

    Chironomids (Diptera: Chironomidae), also known as non-biting midges, are one of the most abundant groups of insects in aquatic habitats. They undergo a complete metamorphosis of four life stages of which three are aquatic (egg, larva, and pupa), and the adult emerges into the air. Chironomids serve as a natural reservoir of Aeromonas and Vibrio cholerae species. Here, we review existing knowledge about the mutual relations between Aeromonas species and chironomids. Using 454-pyrosequencing of the 16S rRNA gene, we found that the prevalence of Aeromonas species in the insects' egg masses and larvae was 1.6 and 3.3% of the insects' endogenous microbiota, respectively. Aeromonas abundance per egg mass remained stable during a 6-month period of bacterial monitoring. Different Aeromonas species were isolated and some demonstrated the ability to degrade the insect's egg masses and to prevent eggs hatching. Chitinase was identified as the enzyme responsible for the egg mass degradation. Different Aeromonas species isolated from chironomids demonstrated the potential to protect their host from toxic metals. Aeromonas is a causative agent of fish infections. Fish are frequently recorded as feeding on chironomids. Thus, fish might be infected with Aeromonas species via chironomid consumption. Aeromonas strains are also responsible for causing gastroenteritis and wound infections in humans. Different virulence genes were identified in Aeromonas species isolated from chironomids. Chironomids may infest drinking water reservoirs, hence be the source of pathogenic Aeromonas strains in drinking water. Chironomids and Aeromonas species have a complicated mutual relationship. PMID:27242751

  8. Conservation of tropical plant species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This book is designed to provide a review of the methods and current status of conservation of many tropical plant species. Future perspectives of conservation of tropical species will also be discussed. The section on methods covers the range of conservation techniques, in situ, seed banking, in vi...

  9. Humans as a Hyperkeystone Species.

    PubMed

    Worm, Boris; Paine, Robert T

    2016-08-01

    Ecologists have identified numerous keystone species, defined as organisms that have outsized ecological impacts relative to their biomass. Here we identify human beings as a higher-order or 'hyperkeystone' species that drives complex interaction chains by affecting other keystone actors across different habitats. Strong indirect effects and a global reach further characterize these interactions and amplify the impacts of human activities on diverse ecosystems, from oceans to forests. We require better understanding of hyperkeystone interaction chains most urgently, especially for marine species and terrestrial large carnivores, which experience relatively higher exploitation rates than other species. This requires innovative approaches that integrate the study of human behavior with food-web theory, and which might provide surprising new insights into the complex ecology of our own species. PMID:27312777

  10. Interference competition and species coexistence.

    PubMed Central

    Amarasekare, Priyanga

    2002-01-01

    Interference competition is ubiquitous in nature. Yet its effects on resource exploitation remain largely unexplored for species that compete for dynamic resources. Here, I present a model of exploitative and interference competition with explicit resource dynamics. The model incorporates both biotic and abiotic resources. It considers interference competition both in the classical sense (i.e. each species suffers a net reduction in per capita growth rate via interference from, and interference on, the other species) and in the broad sense (i.e. each species suffers a net reduction in per capita growth rate via interference from, but can experience an increase in growth rate via interference on, the other species). Coexistence cannot occur under classical interference competition even when the species inferior at resource exploitation is superior at interference. Such a trade-off can, however, change the mechanism of competitive exclusion from dominance by the superior resource exploiter to a priority effect. Now the inferior resource exploiter can exclude the superior resource exploiter provided it has a higher initial abundance. By contrast, when interference is beneficial to the interacting species, coexistence is possible via a trade-off between exploitation and interference. These results hold regardless of whether the resource is biotic or abiotic, indicating that the outcome of exploitative and interference competition does not depend on the exact nature of resource dynamics. The model makes two key predictions. First, species that engage in costly interference mechanisms (e.g. territoriality, overgrowth or undercutting, allelopathy and other forms of chemical competition) should not be able to coexist unless they also engage in beneficial interference mechanisms (e.g. predation or parasitism). Second, exotic invasive species that displace native biota should be superior resource exploiters that have strong interference effects on native species with little

  11. 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

  12. 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.

  13. Are most species small? Not within species-level phylogenies.

    PubMed

    Orme, C David L; Isaac, Nick J B; Purvis, Andy

    2002-06-22

    The robust macro-ecological observation that there are more small-bodied species implies that small-bodied organisms have experienced elevated net rates of diversification. We investigate the role of body size in creating non-random differences in rates of cladogenesis using a set of 38 species-level phylogenies drawn from a range of animal groups. We use independent contrasts to explore the relationship between body size and species richness within individual phylogenies and across related sets of phylogenies. We also carry out a meta-analysis looking for associations between body size and species richness across the taxa. We find little evidence for increased cladogenesis among small-bodied organisms within taxa, and no evidence for any consistent differences between taxa. We explore possible explanations for the inconsistency of our findings with macro-ecological patterns.

  14. Molecular characterisation of Brucella species.

    PubMed

    Scholz, H C; Vergnaud, G

    2013-04-01

    The genus Brucella (Mayer and Shaw, 1920) currently consists often species with validly published names. Within most species further differentiation into biovars exists. Genetically, all Brucella species are highly related to each other, exhibiting sequence similarity values of 98% to 100% in aligned regions (core genome). The population structure is clonal. Despite this close genetic relatedness, the various species can be clearly distinguished from each other by application of high-resolution molecular typing tools, in addition to assessment of phenotype and host preference. Accurate species delineation can be achieved by conventional multiplex polymerase chain reaction (PCR), single nucleotide polymorphism (SNP) analysis and multilocus sequence typing (MLST) or multilocus sequence analysis (MLSA). The last is also suitable for phylogenetic reconstructions, owing to the highly clonal evolution of the different species. Highly discriminatory multilocus variable number of tandem repeats (VNTR) analysis (MLVA) allows both species delineation and differentiation of individual isolates and thus represents a perfect first-line toolfor molecular epidemiological studies within outbreak investigations. More recently,whole genome sequencing (WGS)and the resulting global genome-wide SNP analysis have become available. These novel approaches should help in further understanding the evolution, host specificity and pathogenicity of the genus Brucella.

  15. Species names in phylogenetic nomenclature.

    PubMed

    Cantino, P D; Bryant, H N; de Queiroz, K; Donoghue, M J; Eriksson, T; Hillis, D M; Lee, M S

    1999-12-01

    Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names; their capacity to convey phylogenetic information; and the distinguishability of species names that are governed by a code of phylogenetic nomenclature both from clade names and from species names governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons for each. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials. PMID:12066299

  16. Species interactions and plant polyploidy.

    PubMed

    Segraves, Kari A; Anneberg, Thomas J

    2016-07-01

    Polyploidy is a common mode of speciation that can have far-reaching consequences for plant ecology and evolution. Because polyploidy can induce an array of phenotypic changes, there can be cascading effects on interactions with other species. These interactions, in turn, can have reciprocal effects on polyploid plants, potentially impacting their establishment and persistence. Although there is a wealth of information on the genetic and phenotypic effects of polyploidy, the study of species interactions in polyploid plants remains a comparatively young field. Here we reviewed the available evidence for how polyploidy may impact many types of species interactions that range from mutualism to antagonism. Specifically, we focused on three main questions: (1) Does polyploidy directly cause the formation of novel interactions not experienced by diploids, or does it create an opportunity for natural selection to then form novel interactions? (2) Does polyploidy cause consistent, predictable changes in species interactions vs. the evolution of idiosyncratic differences? (3) Does polyploidy lead to greater evolvability in species interactions? From the scarce evidence available, we found that novel interactions are rare but that polyploidy can induce changes in pollinator, herbivore, and pathogen interactions. Although further tests are needed, it is likely that selection following whole-genome duplication is important in all types of species interaction and that there are circumstances in which polyploidy can enhance the evolvability of interactions with other species. PMID:27370313

  17. 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.

  18. 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)

  19. [Phylogenetic analysis of Pleurotus species].

    PubMed

    Shnyreva, A A; Shnyreva, A V

    2015-02-01

    We performed phylogenetic analysis for ten Pleurotus species, based on internal transcribed spacer (ITS) sequences of rDNA. A phylogenetic tree was constructed on the basis of 31 oyster fungi strains of different origin and 10 reference sequences from GenBank. Our analysis demonstrates that the tested Pleurotus species are of monophyletic origin. We evaluated the evolutionary distances between these species. Classic genetic analysis of sexual compatibility based on monocaryon (mon)-mon crosses showed no reproductive barriers within the P. cornucopiae-P. euosmus species complex. Thus, despite the divergence (subclustering) between commercial strains and natural isolates of P. ostreatus revealed by phylogenetic analysis, there is no reproductive isolation between these groups. A common allele of the matB locus was identified for the commercial strains Sommer and L/4, supporting the common origin of these strains. PMID:25966583

  20. 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)

  1. 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

  2. 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)

  3. The Candida Pathogenic Species Complex

    PubMed Central

    Turner, Siobhán A.; Butler, Geraldine

    2014-01-01

    Candida species are the most common causes of fungal infection. Approximately 90% of infections are caused by five species: Candida albicans, Candida glabrata, Candida tropicalis, Candida parapsilosis, and Candida krusei. Three (C. albicans, C. tropicalis, and C. parapsilosis) belong to the CTG clade, in which the CTG codon is translated as serine and not leucine. C. albicans remains the most commonly isolated but is decreasing relative to the other species. The increasing incidence of C. glabrata is related to its reduced susceptibility to azole drugs. Genome analysis suggests that virulence in the CTG clade is associated with expansion of gene families, particularly of cell wall genes. Similar independent processes took place in the C. glabrata species group. Gene loss and expansion in an ancestor of C. glabrata may have resulted in preadaptations that enabled pathogenicity. PMID:25183855

  4. Earth Day: All Species Projects.

    ERIC Educational Resources Information Center

    Kraft, Marty

    1994-01-01

    Describes the All Species Project, an interdisciplinary program that attempts to build a sense of community and understanding of the natural world by integrating ideas from art, science, anthropology, counseling, theater, and any other area deemed applicable. (MDH)

  5. Chironomids’ Relationship with Aeromonas Species

    PubMed Central

    Laviad, Sivan; Halpern, Malka

    2016-01-01

    Chironomids (Diptera: Chironomidae), also known as non-biting midges, are one of the most abundant groups of insects in aquatic habitats. They undergo a complete metamorphosis of four life stages of which three are aquatic (egg, larva, and pupa), and the adult emerges into the air. Chironomids serve as a natural reservoir of Aeromonas and Vibrio cholerae species. Here, we review existing knowledge about the mutual relations between Aeromonas species and chironomids. Using 454-pyrosequencing of the 16S rRNA gene, we found that the prevalence of Aeromonas species in the insects’ egg masses and larvae was 1.6 and 3.3% of the insects’ endogenous microbiota, respectively. Aeromonas abundance per egg mass remained stable during a 6-month period of bacterial monitoring. Different Aeromonas species were isolated and some demonstrated the ability to degrade the insect’s egg masses and to prevent eggs hatching. Chitinase was identified as the enzyme responsible for the egg mass degradation. Different Aeromonas species isolated from chironomids demonstrated the potential to protect their host from toxic metals. Aeromonas is a causative agent of fish infections. Fish are frequently recorded as feeding on chironomids. Thus, fish might be infected with Aeromonas species via chironomid consumption. Aeromonas strains are also responsible for causing gastroenteritis and wound infections in humans. Different virulence genes were identified in Aeromonas species isolated from chironomids. Chironomids may infest drinking water reservoirs, hence be the source of pathogenic Aeromonas strains in drinking water. Chironomids and Aeromonas species have a complicated mutual relationship. PMID:27242751

  6. 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.

  7. Olfactory sensitivity in mammalian species.

    PubMed

    Wackermannová, M; Pinc, L; Jebavý, L

    2016-07-18

    Olfaction enables most mammalian species to detect and discriminate vast numbers of chemical structures called odorants and pheromones. The perception of such chemical compounds is mediated via two major olfactory systems, the main olfactory system and the vomeronasal system, as well as minor systems, such as the septal organ and the Grueneberg ganglion. Distinct differences exist not only among species but also among individuals in terms of their olfactory sensitivity; however, little is known about the mechanisms that determine these differences. In research on the olfactory sensitivity of mammals, scientists thus depend in most cases on behavioral testing. In this article, we reviewed scientific studies performed on various mammalian species using different methodologies and target chemical substances. Human and non-human primates as well as rodents and dogs are the most frequently studied species. Olfactory threshold studies on other species do not exist with the exception of domestic pigs. Olfactory testing performed on seals, elephants, and bats focused more on discriminative abilities than on sensitivity. An overview of olfactory sensitivity studies as well as olfactory detection ability in most studied mammalian species is presented here, focusing on comparable olfactory detection thresholds. The basics of olfactory perception and olfactory sensitivity factors are also described. PMID:27070753

  8. 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.

  9. 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. PMID:26771317

  10. 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

  11. New Helicobacter species in humans.

    PubMed

    Andersen, L P

    2001-01-01

    During the last decade several new Helicobacter species have been isolated from human gastric mucosa, fecal samples, liver, and gallbladder. Gastric corkscrew-shaped Helicobacter species: H. heilmannii is usually seen in the gastric foveolae in 0.2-0.6% of histological sections from the gastric mucosa of patients with dyspepsia in Western Europe, but it has only been cultured once. It is genetically and morphologically closely related to H. bizzozeronii and H. salmonis which are common in dogs and cats. It causes constantly active chronic gastritis and is regularly associated with peptic ulcer. Intestinal Helicobacter species: H. cinaedi, H. fennelliae, H. pullorum, H. westmeadii, H. canadensis, and 'H. rappini' have been isolated from patients with enteritis and proctitis. H. fennelliae, H. cinaedi, H. westmeadii, and 'H. rappini' have been isolated also from patients with septicemia. Studies indicate that H. cinaedi is transmitted from hamsters and that H. pullorum is common in chickens. 'H. rappini' has been isolated from sheep, dogs, and mice, whereas no animal reservoir has been found for H. fennelliae. Except for the cases of septicemia, none of these Helicobacter species have yet been proven to cause human disease, but they are suspected to play a role in inflammatory bowel diseases. Hepatobiliary Helicobacter species include several Helicobacter species isolated from bile and liver of animals, but only H. bilis has been isolated from the human gallbladder and H. pylori from the human liver. H. bilis has been isolated from dogs, cats, mice, and rats. Nonpylori Helicobacter species are usually difficult to culture and may be more frequently causes of human disease than realized today.

  12. Xiphinema krugi, Species Complex or Complex of Cryptic Species?

    PubMed

    Oliveira, Claudio M G; Ferraz, Luiz C C B; Neilson, Roy

    2006-12-01

    Fourteen morphologically putative populations of X. krugi were clearly separated into four different profiles by RFLP analysis (Alu I and Hinf I), sequencing of the ITS-1 region, and subsequent Maximum Likelihood phylogenetic analyses. These four profiles were further supported by a principal component analysis of morphometric characters that yielded four taxonomic clusters matching those produced by the molecular data. Sequence homology was greater amongst populations that represented the same RFLP profile than between profiles and similar both between representative populations of the RFLP profiles and putative closely related Xiphinema species. This study suggests that X. krugi is a potential species complex comprised of at least four distinct genotypes.

  13. Species-specific optical lattices

    SciTech Connect

    LeBlanc, L. J.; Thywissen, J. H.

    2007-05-15

    We examine single-frequency optical schemes for species-selective trapping of ultracold alkali-metal atoms. Independently addressing the elements of a binary mixture enables the creation of an optical lattice for one atomic species with little or no effect on the other. We analyze a 'tune-in' scheme, using near-resonant detuning to create a strong potential for one specific element. A 'tune-out' scheme is also developed, in which the trapping wavelength is chosen to lie between two strong transitions of an alkali-metal atom such that the induced dipole moment is zero for that species but is nonzero for any other. We compare these schemes by examining the trap depths and heating rates associated with both. We find that the tune-in scheme is preferable for Li-Na, Li-K, and K-Na mixtures, while the tune-out scheme is preferable for Li-Cs, K-Rb, Rb-Cs, K-Cs, and {sup 39}K-{sup 40}K mixtures. Several applications of species-selective optical lattices are explored, including the creation of a lattice for a single species in the presence of a phononlike background, the tuning of relative effective mass, and the isothermal increase of phase-space density.

  14. Experimental Evolution of Species Recognition.

    PubMed

    Rogers, David W; Denton, Jai A; McConnell, Ellen; Greig, Duncan

    2015-06-29

    Sex with another species can be disastrous, especially for organisms that mate only once, like yeast. Courtship signals, including pheromones, often differ between species and can provide a basis for distinguishing between reproductively compatible and incompatible partners. Remarkably, we show that the baker's yeast Saccharomyces cerevisiae does not reject mates engineered to produce pheromones from highly diverged species, including species that have been reproductively isolated for up to 100 million years. To determine whether effective discrimination against mates producing pheromones from other species is possible, we experimentally evolved pheromone receptors under conditions that imposed high fitness costs on mating with cells producing diverged pheromones. Evolved receptors allowed both efficient mating with cells producing the S. cerevisiae pheromone and near-perfect discrimination against cells producing diverged pheromones. Sequencing evolved receptors revealed that each contained multiple mutations that altered the amino acid sequence. By isolating individual mutations, we identified specific amino acid changes that dramatically improved discrimination. However, the improved discrimination conferred by these individual mutations came at the cost of reduced mating efficiency with cells producing the S. cerevisiae pheromone, resulting in low fitness. This tradeoff could be overcome by simultaneous introduction of separate mutations that improved mating efficiency alongside those that improved discrimination. Thus, if mutations occur sequentially, the shape of the fitness landscape may prevent evolution of the optimal phenotype--offering a possible explanation for the poor discrimination of receptors found in nature.

  15. Tripartite genome of all species.

    PubMed

    Long, MengPing; Hu, TaoBo

    2016-01-01

    Neutral theory has dominated the molecular evolution field for more than half a century, but it has been severely challenged by the recently emerged Maximum Genetic Diversity (MGD) theory. However, based on our recent work of tripartite human genome architecture, we found that MGD theory may have overlooked the regulatory but variable genomic regions that increase with species complexity. Here we propose a new molecular evolution theory named Increasing Functional Variation (IFV) hypothesis. According to the IFV hypothesis, the genome of all species is divided into three regions that are 'functional and invariable', 'functional and variable' and 'non-functional and variable'. While the 'non-functional and variable' region decreases as species become more complex, the other two regions increase. PMID:27366319

  16. Tripartite genome of all species

    PubMed Central

    2016-01-01

    Neutral theory has dominated the molecular evolution field for more than half a century, but it has been severely challenged by the recently emerged Maximum Genetic Diversity (MGD) theory. However, based on our recent work of tripartite human genome architecture, we found that MGD theory may have overlooked the regulatory but variable genomic regions that increase with species complexity. Here we propose a new molecular evolution theory named Increasing Functional Variation (IFV) hypothesis. According to the IFV hypothesis, the genome of all species is divided into three regions that are ‘functional and invariable’, ‘functional and variable’ and ‘non-functional and variable’. While the ‘non-functional and variable’ region decreases as species become more complex, the other two regions increase. PMID:27366319

  17. 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

  18. 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.

  19. Collective behaviour across animal species.

    PubMed

    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

  20. 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

  1. 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

  2. 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.

  3. 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

  4. 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...

  5. 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. PMID:24355788

  6. 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.

  7. 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

  8. Micropropagation of endangered plant species.

    PubMed

    Liao, Zhihua; Chen, Min; Sun, Xiaofen; Tang, Kexuan

    2006-01-01

    This chapter describes the multiple-shoot-based methods of micropropagation for endangered plant species. Taxus and aloe are used here as examples. For Taxus, the process of micropropagation includes initiating multiple shoots, elongating shoots, rooting shoots, and transplanting plantlets. For aloe, the process of micropropagation includes initiating multiple shoots, rooting shoots, and transplanting plantlets.

  9. 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…

  10. 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)

  11. 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…

  12. 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...

  13. 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

  14. 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. PMID:25715644

  15. Quaternary alkaloids of tinospora species.

    PubMed

    Bisset, N G; Nwaiwu, J

    1983-08-01

    The occurrence of quaternary alkaloids in TINOSPORA (and PARABAENA) species (Menispermaceae) has been studied. The main components were generally the protoberberine bases berberine and palmatine, with jatrorrhizine an occasional minor constituent, and the aporphine base magnoflorine. Choline was also often present. Only magnoflorine was detected in the PARABAENA material examined. PMID:17404996

  16. 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

  17. 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.

  18. Why the phylogenetic species concept?-Elementary.

    PubMed

    Wheeler, Q D

    1999-06-01

    Although species play a number of unique and necessary roles in biology, none are more important than as the elements of phylogeny, nomenclature, and biodiversity study. Species are not divisible into any smaller units among which shared derived characters can be recognized with fidelity. Biodiversity inventory, assessment, and conservation are dependent upon a uniformly applicable species concept. Species are the fundamental units in formal Linnaean classification and zoological nomenclature. The Biological Species Concept, long given nominal support by most zoologists, forced an essentialy taxonomic problem (what are species?) into a population genetics framework (why are there species?). Early efforts at a phylogenetic species concept focused on correcting problems in the Biological Species Concept associated with ancestral populations, then applying phylogenetic logic to species themselves. Subsequently, Eldredge and Cracraft, and Nelson and Platnick, each proposed essentially identical and truly phylogenetic species concepts that permitted the rigorous recognition of species prior to and for the purposes of phylogenetic analysis, yet maintained the integrity of the Phylogenetic Species Concept outside of cladistic analysis. Such phylogenetic elements have many benefits, including giving to biology a unit species concept applicable across all kinds of living things including sexual and asexual forms. This is possible because the Phylogenetic Species Concept is based on patterns of character distributions and is therefore consistent with the full range of possible evolutionary processes that contribute to species formation, including both biotic and abiotic (even random) factors. PMID:19270883

  19. Fifteen new species of Penicillium.

    PubMed

    Visagie, C M; Renaud, J B; Burgess, K M N; Malloch, D W; Clark, D; Ketch, L; Urb, M; Louis-Seize, G; Assabgui, R; Sumarah, M W; Seifert, K A

    2016-06-01

    We introduce 15 new species of Penicillium isolated from a diverse range of locations, including Canada, Costa Rica, Germany, Italy, New Zealand, Tanzania, USA and the Dry Valleys of Antarctica, from a variety of habitats, including leaf surfaces in tropical rain forests, soil eaten by chimpanzees, infrabuccal pockets of carpenter ants, intestinal contents of caterpillars and soil. The new species are classified in sections Aspergilloides (1), Canescentia (2), Charlesia (1), Exilicaulis (3), Lanata-Divaricata (7) and Stolkia (1). Each is characterised and described using classical morphology, LC-MS based extrolite analyses and multigene phylogenies based on ITS, BenA and CaM. Significant extrolites detected include andrastin, pulvilloric acid, penitrem A and citrinin amongst many others. PMID:27616792

  20. Fifteen new species of Penicillium.

    PubMed

    Visagie, C M; Renaud, J B; Burgess, K M N; Malloch, D W; Clark, D; Ketch, L; Urb, M; Louis-Seize, G; Assabgui, R; Sumarah, M W; Seifert, K A

    2016-06-01

    We introduce 15 new species of Penicillium isolated from a diverse range of locations, including Canada, Costa Rica, Germany, Italy, New Zealand, Tanzania, USA and the Dry Valleys of Antarctica, from a variety of habitats, including leaf surfaces in tropical rain forests, soil eaten by chimpanzees, infrabuccal pockets of carpenter ants, intestinal contents of caterpillars and soil. The new species are classified in sections Aspergilloides (1), Canescentia (2), Charlesia (1), Exilicaulis (3), Lanata-Divaricata (7) and Stolkia (1). Each is characterised and described using classical morphology, LC-MS based extrolite analyses and multigene phylogenies based on ITS, BenA and CaM. Significant extrolites detected include andrastin, pulvilloric acid, penitrem A and citrinin amongst many others.

  1. The Hirudo medicinalis species complex

    NASA Astrophysics Data System (ADS)

    Kutschera, U.

    2012-05-01

    Recently, Hildebrandt and Lemke (Naturwissenschaften 98:995-1008, 2011) argued that the taxonomic status of the three European medicinal leeches, Hirudo medicinalis Linnaeus 1758, Hirudo verbana Carena 1820, and Hirudo orientalis Utevsky and Trontelj (Parasitol Res 98:61-66, 2005) is "questionable" since "all three species interbreed in the laboratory". This statement is in conflict with data published by Elliott and Kutschera (Freshwater Reviews 4:21-41, 2011), indicating that these leeches, which are reciprocally copulating hermaphrodites, represent reproductively isolated biospecies. Here, I summarize evidence indicating that these three European taxa, plus the North African "dragon leech" ( Hirudo troctina Johnson 1816), must be interpreted as a complex of closely related species, and that the economically most important taxon H. verbana is polymorphic.

  2. 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.

  3. 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.

  4. 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

  5. Comparative genomics of Listeria species.

    PubMed

    Glaser, P; Frangeul, L; Buchrieser, C; Rusniok, C; Amend, A; Baquero, F; Berche, P; Bloecker, H; Brandt, P; Chakraborty, T; Charbit, A; Chetouani, F; Couvé, E; de Daruvar, A; Dehoux, P; Domann, E; Domínguez-Bernal, G; Duchaud, E; Durant, L; Dussurget, O; Entian, K D; Fsihi, H; García-del Portillo, F; Garrido, P; Gautier, L; Goebel, W; Gómez-López, N; Hain, T; Hauf, J; Jackson, D; Jones, L M; Kaerst, U; Kreft, J; Kuhn, M; Kunst, F; Kurapkat, G; Madueno, E; Maitournam, A; Vicente, J M; Ng, E; Nedjari, H; Nordsiek, G; Novella, S; de Pablos, B; Pérez-Diaz, J C; Purcell, R; Remmel, B; Rose, M; Schlueter, T; Simoes, N; Tierrez, A; Vázquez-Boland, J A; Voss, H; Wehland, J; Cossart, P

    2001-10-26

    Listeria monocytogenes is a food-borne pathogen with a high mortality rate that has also emerged as a paradigm for intracellular parasitism. We present and compare the genome sequences of L. monocytogenes (2,944,528 base pairs) and a nonpathogenic species, L. innocua (3,011,209 base pairs). We found a large number of predicted genes encoding surface and secreted proteins, transporters, and transcriptional regulators, consistent with the ability of both species to adapt to diverse environments. The presence of 270 L. monocytogenes and 149 L. innocua strain-specific genes (clustered in 100 and 63 islets, respectively) suggests that virulence in Listeria results from multiple gene acquisition and deletion events.

  6. Allopatric origins of microbial species

    PubMed Central

    Whitaker, Rachel J

    2006-01-01

    Although allopatric divergence is a well-accepted mechanism of speciation for eukaryotic macro-organisms, the importance of geographical barriers to divergence in microbial populations is a subject of great debate. Do geographically separated populations of micro-organisms diverge independently, or does their structure fit the often quoted Bass-Becking description ‘everything is everywhere; the environment selects’? Aided by high-resolution genetic and genomic tools, the search for ‘microbial marsupials’ has revealed that in fact both are true; some species of micro-organisms demonstrate allopatric divergence, while others do not. This discovery opens the door for comparative analyses, where questions about the differences in evolutionary and ecological mechanisms that drive divergence and speciation in different microbial species can begin to be explored. Investigating these differences in evolutionary mechanisms will greatly enhance interest in, and understanding of, the dynamic processes that create and maintain the vast diversity of the microbial world. PMID:17062415

  7. Recognizing species, present and past.

    PubMed

    Tattersall, Ian

    2014-01-01

    Nobody disputes that nature is meaningfully "packaged" in some way. But debate persists over exactly how (and even whether) the boundaries dividing taxa should (can) be drawn. At one end of the scale, some zealots abstrusely deny real existence to higher taxa.(1) At the other, laborers at the taxonomic rock-face confront genuine challenges in recognizing and delineating the species that systematists agree constitute the most fundamental unit of taxonomic analysis.

  8. 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

  9. Molecular Phylogenetic Analysis of the Amiota taurusata Species Group within the Chinese Species, with Descriptions of Two New Species

    PubMed Central

    Shao, Zhen-fang; Li, Tong; Jiang, Jian-jun; Lu, Jin-ming; Chen, Hong-wei

    2014-01-01

    The relationships among six species of the Amiota taurusata Takada, Beppu, & Toda (Diptera: Drosophilidae) species group were investigated based on DNA sequence data of the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene, using three species of the genus Amiota as outgroups. A mitochondrial gene, cytochrome c oxidase I (COI), can be used to discriminate between species of the taurusata group. Two new species are described from South China: A. protuberantis Shao et Chen, sp. nov. and A. shennongi Shao et Chen, sp. nov. A key to all the species of the taurusata group based on morphological characters is provided. PMID:25373180

  10. Natural Constraints to Species Diversification.

    PubMed

    Lewitus, Eric; Morlon, Hélène

    2016-08-01

    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

  11. 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

  12. 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

  13. Natural Constraints to Species Diversification.

    PubMed

    Lewitus, Eric; Morlon, Hélène

    2016-08-01

    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

  14. 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

  15. Dicer Functions in Aquatic Species

    PubMed Central

    Kitagishi, Yasuko; Okumura, Naoko; Yoshida, Hitomi; Tateishi, Chika; Nishimura, Yuri; Matsuda, Satoru

    2011-01-01

    Dicer is an RNase III enzyme with two catalytic subunits, which catalyzes the cleavage of double-stranded RNA to small interfering RNAs and micro-RNAs, which are mainly involved in invasive nucleic acid defense and endogenous genes regulation. Dicer is abundantly expressed in embryos, indicating the importance of the protein in early embryonic development. In addition, Dicer is thought to be involved in defense mechanism against foreign nucleic acids such as viruses. This paper will mainly focus on the recent progress of Dicer-related research and discuss potential RNA interference pathways in aquatic species. PMID:22312469

  16. Clinical hematology of rodent species.

    PubMed

    Pilny, Anthony A

    2008-09-01

    Pet rodents, such as rats, guinea pigs, and chinchillas, differ from more traditional companion animal species in many aspects of their hematologic parameters. Animals within this order have much diversity in size, anatomy, methods of restraint, and blood collection technique. Appropriate sample collection is often the most challenging aspect of the diagnostic protocol, and inappropriate restraint may cause a stress response that interferes with blood test results. For many of these patients, sedation is required and can also affect results as well. In most cases, however, obtaining a standard database is necessary and very possible when providing medical care for this popular group of pets. PMID:18675732

  17. The eclipse of species ranges.

    PubMed

    Hemerik, Lia; Hengeveld, Rob; Lippe, Ernst

    2006-01-01

    This paper distinguishes four recognisably different geographical processes in principle causing species to die out. One of these processes, the one we dub "range eclipse", holds that one range expands at the expense of another one, thereby usurping it. Channell and Lomolino (2000a, Journal of Biogeography 27: 169-179; 2000b, Nature 403: 84-87; see also Lomolino and Channell, 1995, Journal of Mammalogy 76: 335-347) measured the course of this process in terms of the proportion of the total range remaining in its original centre, thereby essentially assuming a homogeneous distribution of animals over the range. However, part of their measure seems mistaken. By giving a general, analytical formulation of eclipsing ranges, we estimate the exact course of this process. Also, our formulation does not partition a range into two spatially equal parts, its core and its edge, but it assumes continuity. For applying this model to data on the time evolution of species, individual time series should be available for each of them. For practical purposes we give an alternative way of plotting and interpreting such time series. Our approach, being more sensitive than Channell and Lomolino's, gives a less optimistic indication of range eclipses than theirs once these have started. PMID:17318329

  18. Renal biomarkers in domestic species.

    PubMed

    Hokamp, Jessica A; Nabity, Mary B

    2016-03-01

    Current conventional tests of kidney damage and function in blood (serum creatinine and urea nitrogen) and urine (urine protein creatinine ratio and urine specific gravity) are widely used for diagnosis and monitoring of kidney disease. However, they all have important limitations, and additional markers of glomerular filtration rate and glomerular and tubular damage are desirable, particularly for earlier detection of renal disease when therapy is most effective. Additionally, urinary markers of kidney damage and function may help localize damage to the affected portion of the kidney. In general, the presence of high- and intermediate-molecular weight proteins in the urine are indicative of glomerular damage, while low-molecular weight proteins and enzymes in the urine suggest tubular damage due to decreased reabsorption of proteins, direct tubular damage, or both. This review aims to discuss many of these new blood and urinary biomarkers in domestic veterinary species, focusing primarily on dogs and cats, how they may be used for diagnosis of renal disease, and their limitations. Additionally, a brief discussion of serum creatinine is presented, highlighting its limitations and important considerations for its improved interpretation in domestic species based on past literature and recent studies. PMID:26918420

  19. Thermochemistry of small iodine species

    NASA Astrophysics Data System (ADS)

    Šulková, K.; Federič, J.; Louis, F.; Cantrel, L.; Demovič, L.; Černušák, I.

    2013-11-01

    We present a systematic study of the thermochemistry for a set of iodine species relevant to atmospheric chemistry. The reactions include H, O and I atoms and H2, OH, HI, I2, iodine monoxide, hypoiodous acid (HOI) and H2O species. The calculations presented were performed using completely renormalized coupled cluster theory including single, double and non-iterative triple substitutions in conjunction with the ANO-RCC basis sets developed for scalar relativistic calculations. The second-order spin-free Douglas-Kroll-Hess Hamiltonian was used to account for the scalar relativistic effects. The calculations also included spin-orbit corrections and semi-core correlation contributions. The resulting reaction enthalpies and Gibbs energies at 298 K have been compared with the experimental data. On the basis of a set of selected reactions we suggest an updated value for Δ f H298K° of HOI based on the set of isogyric reactions: -69.0 ± 3.7 kJ mol-1.

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

    PubMed

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

    2015-01-01

    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. PMID:26623764

  1. 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. ...

  2. Ecology: is speciation driven by species diversity?

    PubMed

    Cadena, Carlos Daniel; Ricklefs, Robert E; Jiménez, Iván; Bermingham, Eldredge

    2005-11-01

    Emerson and Kolm show that the proportion of species endemic to an island is positively related to its species richness and, assuming that endemism indexes speciation rate, they infer that greater species diversity accelerates diversification. Here we demonstrate that the same correlation between species richness and percentage endemism can arise even if within-island speciation is negligible, particularly when both endemism and species richness depend on attributes of islands (such as area) that influence the average age of resident populations. Island biogeography theory indicates that, where the average time to extinction is relatively long, diversity increases through colonization, irrespective of whether new species are formed; at the same time, islands on which populations persist for longer accumulate more endemic species as local populations differentiate and populations on neighbouring islands become extinct. We therefore suggest that species richness and endemism are correlated fortuitously owing to their mutual dependence on the life spans of populations on islands, which is unrelated to speciation itself.

  3. Species richness changes lag behind climate change.

    PubMed

    Menéndez, Rosa; Megías, Adela González; Hill, Jane K; Braschler, Brigitte; Willis, Stephen G; Collingham, Yvonne; Fox, Richard; Roy, David B; Thomas, Chris D

    2006-06-22

    Species-energy theory indicates that recent climate warming should have driven increases in species richness in cool and species-poor parts of the Northern Hemisphere. We confirm that the average species richness of British butterflies has increased since 1970-82, but much more slowly than predicted from changes of climate: on average, only one-third of the predicted increase has taken place. The resultant species assemblages are increasingly dominated by generalist species that were able to respond quickly. The time lag is confirmed by the successful introduction of many species to climatically suitable areas beyond their ranges. Our results imply that it may be decades or centuries before the species richness and composition of biological communities adjusts to the current climate. PMID:16777739

  4. The Neotropical species of Atractodes (Hymenoptera, Ichneumonidae, Cryptinae), II: the A. pleuripunctatus species-group.

    PubMed

    Bordera, Santiago; Mazón, Marina; Sääksjärvi, Ilari E

    2016-09-06

    We describe three new species of parasitoid wasps of the genus Atractodes (Ichneumonidae: Cryptinae) from South America: A. colchaguensis sp. nov. from Chile, and A. pleuripunctatus sp. nov. and A. saragurensis sp. nov. from Ecuador. These species are all characterized by a densely and strongly punctate mesopleuron. The Atractodes pleuripunctatus species-group is defined to accommodate the new species. In addition, the second part of the key to species of the Neotropical Atractodes including this species-group is given.

  5. The Neotropical species of Atractodes (Hymenoptera, Ichneumonidae, Cryptinae), II: the A. pleuripunctatus species-group.

    PubMed

    Bordera, Santiago; Mazón, Marina; Sääksjärvi, Ilari E

    2016-01-01

    We describe three new species of parasitoid wasps of the genus Atractodes (Ichneumonidae: Cryptinae) from South America: A. colchaguensis sp. nov. from Chile, and A. pleuripunctatus sp. nov. and A. saragurensis sp. nov. from Ecuador. These species are all characterized by a densely and strongly punctate mesopleuron. The Atractodes pleuripunctatus species-group is defined to accommodate the new species. In addition, the second part of the key to species of the Neotropical Atractodes including this species-group is given. PMID:27615943

  6. SNP Arrays for Species Identification in Salmonids.

    PubMed

    Wenne, Roman; Drywa, Agata; Kent, Matthew; Sundsaasen, Kristil Kindem; Lien, Sigbjørn

    2016-01-01

    The use of SNP genotyping microarrays, developed in one species to analyze a closely related species for which genomic sequence information is scarce, enables the rapid development of a genomic resource (SNP information) without the need to develop new species-specific markers. Using large numbers of microarray SNPs offers the best chance to detect informative markers in nontarget species, markers that can very often be assayed using a lower throughput platform as is described in this paper. PMID:27460372

  7. The genetics of Neisseria species.

    PubMed

    Rotman, Ella; Seifert, H Steven

    2014-01-01

    Neisseria gonorrhoeae and Neisseria meningitidis are closely related organisms that cause the sexually transmitted infection gonorrhea and serious bacterial meningitis and septicemia, respectively. Both species possess multiple mechanisms to alter the expression of surface-exposed proteins through the processes of phase and antigenic variation. This potential for wide variability in surface-exposed structures allows the organisms to always have subpopulations of divergent antigenic types to avoid immune surveillance and to contribute to functional variation. Additionally, the Neisseria are naturally competent for DNA transformation, which is their main means of genetic exchange. Although bacteriophages and plasmids are present in this genus, they are not as effective as DNA transformation for horizontal genetic exchange. There are barriers to genetic transfer, such as restriction-modification systems and CRISPR loci, that limit particular types of exchange. These host-restricted pathogens illustrate the rich complexity of genetics that can help define the similarities and differences of closely related organisms.

  8. 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.

  9. 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...

  10. 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...

  11. 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…

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. Evolutionary speed of species invasions.

    PubMed

    García-Ramos, Gisela; Rodríguez, Diego

    2002-04-01

    Successful invasion may depend of the capacity of a species to adjust genetically to a spatially varying environment. This research modeled a species invasion by examining the interaction between a quantitative genetic trait and population density. It assumed: (I) a quantitative genetic trait describes the adaptation of an individual to its local ecological conditions; (2) populations far from the local optimum grow more slowly than those near the optimum; and (3) the evolution of a trait depends on local population density, because differences in local population densities cause asymmetrical gene flow. This genetics-density interaction determined the propagation speed of populations. Numerical simulations showed that populations spread by advancing as two synchronic traveling waves, one for population density and one for trait adaptation. The form of the density wave was a step front that advances homogenizing populations at their carrying capacity; the adaptation wave was a curve with finite slope that homogenizes populations at full adaptation. The largest speed of population expansion, for a dimensionless analysis, corresponded to an almost homogeneous spatial environment when this model approached an ecological description such as the Fisher-Skellam's model. A large genetic response also favored faster speeds. Evolutionary speeds, in a natural scale, showed a wide range of rates that were also slower compared to models that only consider demographics. This evolutionary speed increased with high heritability, strong stabilizing selection, and high intrinsic growth rate. It decreased for steeper environmental gradients. Also indicated was an optimal dispersal rate over which evolutionary speed declined. This is expected because dispersal moves individuals further, but homogenizes populations genetically, making them maladapted. The evolutionary speed was compared to observed data. Furthermore, a moderate increase in the speed of expansion was predicted for

  2. 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.

  3. Cluster Analysis of Longidorus Species (Nematoda: Longidoridae), a New Approach in Species Identification

    PubMed Central

    Ye, Weimin; Robbins, R. T.

    2004-01-01

    Hierarchical cluster analysis based on female morphometric character means including body length, distance from vulva opening to anterior end, head width, odontostyle length, esophagus length, body width, tail length, and tail width were used to examine the morphometric relationships and create dendrograms for (i) 62 populations belonging to 9 Longidorus species from Arkansas, (ii) 137 published Longidorus species, and (iii) 137 published Longidorus species plus 86 populations of 16 Longidorus species from Arkansas and various other locations by using JMP 4.02 software (SAS Institute, Cary, NC). Cluster analysis dendograms visually illustrated the grouping and morphometric relationships of the species and populations. It provided a computerized statistical approach to assist by helping to identify and distinguish species, by indicating morphometric relationships among species, and by assisting with new species diagnosis. The preliminary species identification can be accomplished by running cluster analysis for unknown species together with the data matrix of known published Longidorus species. PMID:19262809

  4. 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.

  5. Barcoding markers for Pneumocystis species in wildlife.

    PubMed

    Danesi, Patrizia; da Rold, Graziana; Rizzoli, Annapaola; Hauffe, Heidi C; Marangon, Stefano; Samerpitak, Kittipan; Demanche, Cristine; Guillot, Jacques; Capelli, Gioia; de Hoog, Sybren G

    2016-02-01

    Lung specimens (n = 216) from six wildlife species were examined for occurrence of Pneumocystis species in pulmonary tissues. Among small mammals the shrew Sorex antinorii (80 %) were most frequently colonized. In contrast, foxes and badgers did not yield positive amplification. Host-specificity was noted, at least at the level of the host genus. Phylogenetic trees based on partial mtLSU and mtSSU showed high diversity of species corresponding to animal host diversity. Nuclear rDNA ITS data confirmed unambiguous separation of species. In conclusion, ITS is an excellent marker to distinguish species of the genus Pneumocystis. PMID:26781376

  6. The problem with the species problem.

    PubMed

    Ellis, Mark W

    2011-01-01

    When Charles Darwin convinced the scientific community that species evolve, the long-held essentialist view of each species as fixed was rejected and a clear conceptual understanding of the term was lost. For the next century, a real species problem existed that became culturally entrenched within the scientific community. Although largely solved decades ago, the species problem remains entrenched today due to a suite of factors. Most of the factors that help maintain its perceived intractability have been revealed and logically dismissed; yet this is not widely known so those factors continue to be influential. It is time to recognize this false foundation and relegate the species problem to history.

  7. Species Conservation and Management: Case Studies

    USGS Publications Warehouse

    Akcakaya, H.R.; Burgman, M.A.; Kindvall, O.; Wood, C.C.; Sjogren-Gulve, P.; Hatfield, J.S.; McCarthy, M.A.

    2004-01-01

    This edited volume is a collection of population and metapopulation models for a wide variety of species, including plants, invertebrates, fishes, amphibians, reptiles, birds, and mammals. Each chapter of the book describes the application of RAMAS GIS 4.0 to one species, with the aim of demonstrating how various life history characteristics of the species are incorporated into the model, and how the results of the model has been or can be used in conservation and management of the species. The book comes with a CD that includes a demo version of the program, and the data files for each species.

  8. 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

  9. 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

  10. 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. PMID:27114572

  11. Microbial species delineation using whole genome sequences

    PubMed Central

    Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T.; Mavrommatis, Kostas; Kyrpides, Nikos C.; Pati, Amrita

    2015-01-01

    Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required. PMID:26150420

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. STRAW: Species TRee Analysis Web server.

    PubMed

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

    2013-07-01

    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/.

  17. 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

  18. Hypocrea peltata: a mycological Dr Jekyll and Mr Hyde?

    PubMed

    Samuels, Gary J; Ismaiel, Adnan

    2011-01-01

    Hypocrea peltata (Pezizomycotina, Hypocreales, Hypocreaceae) is a common, widespread essentially subtropical species, with an uncharacteristically large stroma and asci containing four large and four small bicellular ascospores. Its only anamorph consists of indehiscent aleuriospores; it does not form a Trichoderma anamorph, which is typical of most Trichoderma/Hypocrea species. Hypocrea peltata grows very well at 37 C. The large stromata and failure to form a Trichoderma anamorph could lead one to doubt its generic placement. However sequences of the internal transcribed spacer region (ITS), 28S nuclear large subunit (LSU) of rDNA and RNA polymerase subunit II (rpb2) regions indicate that it represents a unique lineage within Trichoderma/Hypocrea. ITS and rbp2 sequences derived from cultures of H. peltata are identical to the "unidentified Hypocreaceae" reported in the literature as being isolated from lung of a patient with non-fatal pulmonary fibrosis. PMID:21262986

  19. 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

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

    PubMed

    Diamond, J

    1982-04-01

    If species interactions affect species distributions, then species occurrence frequencies (nu(i)), 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 nu 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, nu(i) decreases with pool size or number of species in the same guild. These interarchipelagal differences in nu(i) or average nu reflect differences in level of interspecific competition, which reduces nus 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

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

    PubMed

    Diamond, J

    1982-04-01

    If species interactions affect species distributions, then species occurrence frequencies (nu(i)), 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 nu 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, nu(i) decreases with pool size or number of species in the same guild. These interarchipelagal differences in nu(i) or average nu reflect differences in level of interspecific competition, which reduces nus 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.

  2. Zygoascus hellenicus gen. nov., sp. nov., the teleomorph of Candida hellenica (= C. inositophila = C. steatolytica).

    PubMed

    Smith, M T

    1986-01-01

    The anamorphic yeast species Candida hellenica, C. inositophila and C. steatolytica were found to constitute haploid mating types of an undescribed, filamentous heterothallic Endomycete. The new genus Zygoascus is proposed for the teleomorph. Descriptions are given of the genus and type species, Z. hellenicus.

  3. 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.

  4. 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. PMID:27620956

  5. Secondary metabolites from Rubiaceae species.

    PubMed

    Martins, Daiane; Nunez, Cecilia Veronica

    2015-07-22

    This study describes some characteristics of the Rubiaceae family pertaining to the occurrence and distribution of secondary metabolites in the main genera of this family. It reports the review of phytochemical studies addressing all species of Rubiaceae, published between 1990 and 2014. Iridoids, anthraquinones, triterpenes, indole alkaloids as well as other varying alkaloid subclasses, have shown to be the most common. These compounds have been mostly isolated from the genera Uncaria, Psychotria, Hedyotis, Ophiorrhiza and Morinda. The occurrence and distribution of iridoids, alkaloids and anthraquinones point out their chemotaxonomic correlation among tribes and subfamilies. From an evolutionary point of view, Rubioideae is the most ancient subfamily, followed by Ixoroideae and finally Cinchonoideae. The chemical biosynthetic pathway, which is not so specific in Rubioideae, can explain this and large amounts of both iridoids and indole alkaloids are produced. In Ixoroideae, the most active biosysthetic pathway is the one that produces iridoids; while in Cinchonoideae, it produces indole alkaloids together with other alkaloids. The chemical biosynthetic pathway now supports this botanical conclusion.

  6. 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

  7. 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. PMID:17886224

  8. [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.

  9. 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

    2016-01-01

    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. PMID:27615986

  10. 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.

  11. 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.

  12. 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.

  13. Illuminating geographical patterns in species' range shifts.

    PubMed

    Grenouillet, Gaël; Comte, Lise

    2014-10-01

    Species' range shifts in response to ongoing climate change have been widely documented, but although complex spatial patterns in species' responses are expected to be common, comprehensive comparisons of species' ranges over time have undergone little investigation. Here, we outline a modeling framework based on historical and current species distribution records for disentangling different drivers (i.e. climatic vs. nonclimatic) and assessing distinct facets (i.e. colonization, extirpation, persistence, and lags) of species' range shifts. We used extensive monitoring data for stream fish assemblages throughout France to assess range shifts for 32 fish species between an initial period (1980-1992) and a contemporary one (2003-2009). Our results provide strong evidence that the responses of individual species varied considerably and exhibited complex mosaics of spatial rearrangements. By dissociating range shifts in climatically suitable and unsuitable habitats, we demonstrated that patterns in climate-driven colonization and extirpation were less marked than those attributed to nonclimatic drivers, although this situation could rapidly shift in the near future. We also found evidence that range shifts could be related to some species' traits and that the traits involved varied depending on the facet of range shift considered. The persistence of populations in climatically unsuitable areas was greater for short-lived species, whereas the extent of the lag behind climate change was greater for long-lived, restricted-range, and low-elevation species. We further demonstrated that nonclimatic extirpations were primarily related to the size of the species' range, whereas climate-driven extirpations were better explained by thermal tolerance. Thus, the proposed framework demonstrated its potential for markedly improving our understanding of the key processes involved in range shifting and also offers a template for informing management decisions. Conservation strategies

  14. Illuminating geographical patterns in species' range shifts.

    PubMed

    Grenouillet, Gaël; Comte, Lise

    2014-10-01

    Species' range shifts in response to ongoing climate change have been widely documented, but although complex spatial patterns in species' responses are expected to be common, comprehensive comparisons of species' ranges over time have undergone little investigation. Here, we outline a modeling framework based on historical and current species distribution records for disentangling different drivers (i.e. climatic vs. nonclimatic) and assessing distinct facets (i.e. colonization, extirpation, persistence, and lags) of species' range shifts. We used extensive monitoring data for stream fish assemblages throughout France to assess range shifts for 32 fish species between an initial period (1980-1992) and a contemporary one (2003-2009). Our results provide strong evidence that the responses of individual species varied considerably and exhibited complex mosaics of spatial rearrangements. By dissociating range shifts in climatically suitable and unsuitable habitats, we demonstrated that patterns in climate-driven colonization and extirpation were less marked than those attributed to nonclimatic drivers, although this situation could rapidly shift in the near future. We also found evidence that range shifts could be related to some species' traits and that the traits involved varied depending on the facet of range shift considered. The persistence of populations in climatically unsuitable areas was greater for short-lived species, whereas the extent of the lag behind climate change was greater for long-lived, restricted-range, and low-elevation species. We further demonstrated that nonclimatic extirpations were primarily related to the size of the species' range, whereas climate-driven extirpations were better explained by thermal tolerance. Thus, the proposed framework demonstrated its potential for markedly improving our understanding of the key processes involved in range shifting and also offers a template for informing management decisions. Conservation strategies

  15. Species of Thripinae (Thysanoptera) from bamboo in Malaysia, with one new species and six new records.

    PubMed

    Ng, Y F; Mound, L A

    2015-01-01

    Nine species of Thripinae that inhabit bamboo are recorded from Malaysia. Clypeothrips idrisi sp.n. is described as a second species in the genus, and Trichromothrips bruncurrum Reyes is considered a syn.n. of Neocorynothrips asiaticus Ramakrishna & Margabandhu. Six species are newly recorded from Malaysia: N. asiaticus, Okajimaella tubercula, Simulothrips banpoti, Stenchaetothrips bambusicola, S. bambusae and S. spinalis. Seven species of Stenchaetothrips are now known from Malaysia. Illustrations and descriptions of each species are provided.

  16. The taxonomy of the Tarentola mauritanica species complex (Gekkota: Phyllodactylidae): Bayesian species delimitation supports six candidate species.

    PubMed

    Rato, Catarina; Harris, David James; Carranza, Salvador; Machado, Luís; Perera, Ana

    2016-01-01

    The lack of morphological diagnosable characters typical of cryptic species, poses a particular problem to taxonomists. This is especially true when taxa are closely related, sharing considerable amounts of ancestral polymorphism. Phylogenetic studies on the Moorish gecko species-complex, Tarentola mauritanica, uncovered extremely high levels of mtDNA diversity with six identified clades, including one from the Canary Islands identified as T. angustimentalis. Because of the conserved morphology of this species and its paraphyletic status with respect to T. angustimentalis, it was suggested that T. mauritanica is a cryptic species complex. Nevertheless, none of the nuclear loci used were reciprocally monophyletic regarding the mitochondrial lineages due to retention of ancestral polymorphism. In this study, we added three new intron markers to the already available dataset and used additional tools, namely phylogenetic gene trees, species tree and species limits within a Bayesian coalescent framework to confirm the support of the main lineages. Bayesian clustering analysis supports all six mtDNA lineages as independent groups, despite showing signs of ancestral polymorphism or possibly gene flow between the Maghreb/South Iberia and Central Morocco clades. The species tree recovered two major groups; one clustering taxa from Europe and Northern Maghreb and another one encompassing the lineages from Central/Southern Morocco, Central Morocco and Canary Islands, indicating that the ancestor of T. angustimentalis came from the Central/Southern Morocco region. Finally, Bayesian coalescent species delimitation analysis supports all six mitochondrial clades as "unconfirmed candidate species", pending morphological data to define them. PMID:26391222

  17. The taxonomy of the Tarentola mauritanica species complex (Gekkota: Phyllodactylidae): Bayesian species delimitation supports six candidate species.

    PubMed

    Rato, Catarina; Harris, David James; Carranza, Salvador; Machado, Luís; Perera, Ana

    2016-01-01

    The lack of morphological diagnosable characters typical of cryptic species, poses a particular problem to taxonomists. This is especially true when taxa are closely related, sharing considerable amounts of ancestral polymorphism. Phylogenetic studies on the Moorish gecko species-complex, Tarentola mauritanica, uncovered extremely high levels of mtDNA diversity with six identified clades, including one from the Canary Islands identified as T. angustimentalis. Because of the conserved morphology of this species and its paraphyletic status with respect to T. angustimentalis, it was suggested that T. mauritanica is a cryptic species complex. Nevertheless, none of the nuclear loci used were reciprocally monophyletic regarding the mitochondrial lineages due to retention of ancestral polymorphism. In this study, we added three new intron markers to the already available dataset and used additional tools, namely phylogenetic gene trees, species tree and species limits within a Bayesian coalescent framework to confirm the support of the main lineages. Bayesian clustering analysis supports all six mtDNA lineages as independent groups, despite showing signs of ancestral polymorphism or possibly gene flow between the Maghreb/South Iberia and Central Morocco clades. The species tree recovered two major groups; one clustering taxa from Europe and Northern Maghreb and another one encompassing the lineages from Central/Southern Morocco, Central Morocco and Canary Islands, indicating that the ancestor of T. angustimentalis came from the Central/Southern Morocco region. Finally, Bayesian coalescent species delimitation analysis supports all six mitochondrial clades as "unconfirmed candidate species", pending morphological data to define them.

  18. 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

  19. Thresholds for impaired species recovery.

    PubMed

    Hutchings, Jeffrey A

    2015-06-22

    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, r(realized), 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 (N(max)), 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

  20. Luminescent Mycena: new and noteworthy species.

    PubMed

    Desjardin, Dennis E; Perry, Brian A; Lodge, D Jean; Stevani, Cassius V; Nagasawa, Eiji

    2010-01-01

    Seven species of Mycena are reported as luminescent, representing specimens collected in Belize, Brazil, Dominican Republic, Jamaica, Japan (Bonin Islands), Malaysia (Borneo) and Puerto Rico. Four of them represent new species (Mycena luxaeterna, M. luxarboricola, M. luxperpetua, M. silvaelucens) and three represent new reports of luminescence in previously described species (M. aff. abieticola, M. aspratilis, M. margarita). Mycena subepipterygia is synonymized with M. margarita, and M. chlorinosma is proposed as a possible synonym. Comprehensive descriptions, illustrations, photographs and comparisons with phenetically similar species are provided. A redescription of M. chlorophos, based on analyses of type specimens and recently collected topotypical material, is provided. The addition of these seven new or newly reported luminescent species of Mycena brings the total to 71 known bioluminescent species of fungi.

  1. Self-localized states in species competition

    NASA Astrophysics Data System (ADS)

    Paulau, Pavel V.; Gomila, DamiÃ; López, Cristóbal; Hernández-García, Emilio

    2014-03-01

    We study the conditions under which species interaction, as described by continuous versions of the competitive Lotka-Volterra model (namely the nonlocal Kolmogorov-Fisher model, and its differential approximation), can support the existence of localized states, i.e., patches of species with enhanced population surrounded in niche space by species at smaller densities. These states would arise from species interaction, and not by any preferred niche location or better fitness. In contrast to previous works we include only quadratic nonlinearities, so that the localized patches appear on a background of homogeneously distributed species coexistence, instead of on top of the no-species empty state. For the differential model we find and describe in detail the stable localized states. For the full nonlocal model, however, competitive interactions alone do not allow the conditions for the observation of self-localized states, and we show how the inclusion of additional facilitative interactions leads to the appearance of them.

  2. Self-localized states in species competition.

    PubMed

    Paulau, Pavel V; Gomila, Damià; López, Cristóbal; Hernández-García, Emilio

    2014-03-01

    We study the conditions under which species interaction, as described by continuous versions of the competitive Lotka-Volterra model (namely the nonlocal Kolmogorov-Fisher model, and its differential approximation), can support the existence of localized states, i.e., patches of species with enhanced population surrounded in niche space by species at smaller densities. These states would arise from species interaction, and not by any preferred niche location or better fitness. In contrast to previous works we include only quadratic nonlinearities, so that the localized patches appear on a background of homogeneously distributed species coexistence, instead of on top of the no-species empty state. For the differential model we find and describe in detail the stable localized states. For the full nonlocal model, however, competitive interactions alone do not allow the conditions for the observation of self-localized states, and we show how the inclusion of additional facilitative interactions leads to the appearance of them. PMID:24730891

  3. The Species Problem in Myxomycetes Revisited.

    PubMed

    Walker, Laura M; Stephenson, Steven L

    2016-08-01

    Species identification in the myxomycetes (plasmodial slime molds or myxogastrids) poses particular challenges to researchers as a result of their morphological plasticity and frequent alteration between sexual and asexual life strategies. Traditionally, myxomycete morphology has been used as the primary method of species delimitation. However, with the increasing availability of genetic information, traditional myxomycete taxonomy is being increasingly challenged, and new hypotheses continue to emerge. Due to conflicts that sometimes occur between traditional and more modern species concepts that are based largely on molecular data, there is a pressing need to revisit the discussion surrounding the species concept used for myxomycetes. Biological diversity is being increasingly studied with molecular methods and data accumulates at ever-faster rates, making resolution of this matter urgent. In this review, currently used and potentially useful species concepts (biological, morphological, phylogenetic and ecological) are reviewed, and an integrated approach to resolve the myxomycete species problem is discussed. PMID:27351595

  4. 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.

  5. The local introduction of strongly interacting species and the loss of geographic variation in species and species interactions.

    PubMed

    Benkman, Craig W; Siepielski, Adam M; Parchman, Thomas L

    2008-01-01

    Species introductions into nearby communities may seem innocuous, however, these introductions, like long-distance introductions (e.g. trans- and intercontinental), can cause extinctions and alter the evolutionary trajectories of remaining community members. These 'local introductions' can also more cryptically homogenize formerly distinct populations within a species. We focus on several characteristics and the potential consequences of local introductions. First, local introductions are commonly successful because the species being introduced is compatible with existing abiotic and biotic conditions; many nearby communities differ because of historical factors and the absence of certain species is simply the result of barriers to dispersal. Moreover, the species with which they interact most strongly (e.g. prey) may have, for example, lost defences making the establishment even more likely. The loss or absence of defences is especially likely when the absent species is a strongly interacting species, which we argue often includes mammals in terrestrial communities. Second, the effects of the introduction may be difficult to detect because the community is likely to converge onto nearby communities that naturally have the introduced species (hence the perceived innocuousness). This homogenization of formerly distinct populations eliminates the geographic diversity of species interactions and the geographic potential for speciation, and reduces regional species diversity. We illustrate these ideas by focusing on the introduction of tree squirrels into formerly squirrel-less forest patches. Such introductions have eliminated incipient species of crossbills (Loxia spp.) co-evolving in arms races with conifers and will likely have considerable impacts on community structure and ecosystem processes. PMID:18173508

  6. Why does phenology drive species distribution?

    PubMed

    Chuine, Isabelle

    2010-10-12

    Despite the numerous studies which have been conducted during the past decade on species ranges and their relationship to the environment, our understanding of how environmental conditions shape species distribution is still far from complete. Yet, some process-based species distribution models have been able to simulate plants and insects distribution at a global scale. These models strongly rely on the completion of the annual cycle of the species and therefore on their accomplished phenology. In particular, they have shown that the northern limit of species' ranges appears to be caused mainly by the inability to undergo full fruit maturation, while the southern limit appears to be caused by the inability to flower or unfold leaves owing to a lack of chilling temperatures that are necessary to break bud dormancy. I discuss here why phenology is a key adaptive trait in shaping species distribution using mostly examples from plant species, which have been the most documented. After discussing how phenology is involved in fitness and why it is an adaptive trait susceptible to evolve quickly in changing climate conditions, I describe how phenology is related to fitness in species distribution process-based models and discuss the fate of species under climate change scenarios using model projections and experimental or field studies from the literature.

  7. Protected areas facilitate species' range expansions.

    PubMed

    Thomas, Chris D; Gillingham, Phillipa K; Bradbury, Richard B; Roy, David B; Anderson, Barbara J; Baxter, John M; Bourn, Nigel A D; Crick, Humphrey Q P; Findon, Richard A; Fox, Richard; Hodgson, Jenny A; Holt, Alison R; Morecroft, Mike D; O'Hanlon, Nina J; Oliver, Tom H; Pearce-Higgins, James W; Procter, Deborah A; Thomas, Jeremy A; Walker, Kevin J; Walmsley, Clive A; Wilson, Robert J; Hill, Jane K

    2012-08-28

    The benefits of protected areas (PAs) for biodiversity have been questioned in the context of climate change because PAs are static, whereas the distributions of species are dynamic. Current PAs may, however, continue to be important if they provide suitable locations for species to colonize at their leading-edge range boundaries, thereby enabling spread into new regions. Here, we present an empirical assessment of the role of PAs as targets for colonization during recent range expansions. Records from intensive surveys revealed that seven bird and butterfly species have colonized PAs 4.2 (median) times more frequently than expected from the availability of PAs in the landscapes colonized. Records of an additional 256 invertebrate species with less-intensive surveys supported these findings and showed that 98% of species are disproportionately associated with PAs in newly colonized parts of their ranges. Although colonizing species favor PAs in general, species vary greatly in their reliance on PAs, reflecting differences in the dependence of individual species on particular habitats and other conditions that are available only in PAs. These findings highlight the importance of current PAs for facilitating range expansions and show that a small subset of the landscape receives a high proportion of colonizations by range-expanding species. PMID:22893689

  8. A Five-Species Jungle Game.

    PubMed

    Kang, Yibin; Pan, Qiuhui; Wang, Xueting; He, Mingfeng

    2016-01-01

    In this paper, we investigate the five-species Jungle game in the framework of evolutionary game theory. We address the coexistence and biodiversity of the system using mean-field theory and Monte Carlo simulations. Then, we find that the inhibition from the bottom-level species to the top-level species can be critical factors that affect biodiversity, no matter how it is distributed, whether homogeneously well mixed or structured. We also find that predators' different preferences for food affect species' coexistence. PMID:27332995

  9. How species respond to multiple extinction threats.

    PubMed Central

    Isaac, Nick J. B.; Cowlishaw, Guy

    2004-01-01

    It is well established that different species vary in their vulnerability to extinction risk and that species biology can underpin much of this variation. By contrast, very little is known about how the same species responds to different threat processes. The purpose of this paper is therefore twofold: to examine the extent to which a species' vulnerability to different types of threat might covary and to explore the biological traits that are associated with threat-specific responses. We use an objective and quantitative measure of local extinction risk to show that vulnerability to local population decline in primates varies substantially among species and between threat types. Our results show that a species' response to one threat type does not predict its response to others. Multivariate analyses also suggest that different mechanisms of decline are associated with each type of threat, since different biological traits are correlated with each threat-specific response. Primate species at risk from forestry tend to exhibit low ecological flexibility, while those species vulnerable to agriculture tend to live in the canopy and eat low-fruit diets; in further contrast, primates at risk from hunting tend to exhibit large body size. Our analyses therefore indicate that a species' vulnerability to local extinction can be highly variable and is likely to depend on both threat type and biology. PMID:15306363

  10. Applying the species concept to plant viruses.

    PubMed

    Van Regenmortel, M H

    1989-01-01

    Plant virologists who maintain that the concept of species cannot be applied to viruses argue their case in terms of an obsolete concept of biological species defined by gene pools and reproductive isolation and applicable only to sexually reproducing organisms. In fact, various species concepts have been used by biologists and some of them are applicable to asexual organisms. The rationale for applying the species concept in virology is that viruses are biological entities and not chemicals: they possess genes, replicate, specialize, evolve and occupy specific ecological niches. The following definition is proposed: a virus species is a polythetic class of viruses constituting a replicating lineage and occupying a particular ecological niche. Such a definition of the species category does not and cannot provide a list of diagnostic properties for recognizing members of a particular virus species. It should also be stressed that a single property such as an arbitrary level of genome homology or the extent of serological relationship always fails to establish membership in a polythetic class. A binomial system of nomenclature is advocated in which the vernacular English name of the plant virus is adopted as the species name and the group name is assimilated to the level of genus. Adoption of this system would ensure that a universal classification system based on the classical categories of species, genus, and family becomes possible for all viruses. PMID:2647059

  11. Why does phenology drive species distribution?

    PubMed Central

    Chuine, Isabelle

    2010-01-01

    Despite the numerous studies which have been conducted during the past decade on species ranges and their relationship to the environment, our understanding of how environmental conditions shape species distribution is still far from complete. Yet, some process-based species distribution models have been able to simulate plants and insects distribution at a global scale. These models strongly rely on the completion of the annual cycle of the species and therefore on their accomplished phenology. In particular, they have shown that the northern limit of species' ranges appears to be caused mainly by the inability to undergo full fruit maturation, while the southern limit appears to be caused by the inability to flower or unfold leaves owing to a lack of chilling temperatures that are necessary to break bud dormancy. I discuss here why phenology is a key adaptive trait in shaping species distribution using mostly examples from plant species, which have been the most documented. After discussing how phenology is involved in fitness and why it is an adaptive trait susceptible to evolve quickly in changing climate conditions, I describe how phenology is related to fitness in species distribution process-based models and discuss the fate of species under climate change scenarios using model projections and experimental or field studies from the literature. PMID:20819809

  12. National Institute of Invasive Species Science (NIISS)

    USGS Publications Warehouse

    Stohlgren, Tom

    2006-01-01

    The National Institute of Invasive Species Science (www.NIISS.org) is a consortium of governmental and nongovernmental partners, led by the U.S. Geological Survey (USGS), whose aim is to provide reliable information and advanced decision support tools for documenting, understanding, predicting, assessing, and addressing the threat of invasive species in the United States. The Institute coordinates the National Aeronautical and Space Administrationa??s (NASAa??s) Invasive Species National Application activities for the Department of the Interior and has al lead role in developing NASA-derived remote sensing and landscape-scale predictive modeling capabilities for the invasive species community.

  13. 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. PMID:19183200

  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. 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.

  16. Estimation of species extinction: what are the consequences when total species number is unknown?

    PubMed

    Chen, Youhua

    2014-12-01

    The species-area relationship (SAR) is known to overestimate species extinction but the underlying mechanisms remain unclear to a great extent. Here, I show that when total species number in an area is unknown, the SAR model exaggerates the estimation of species extinction. It is proposed that to accurately estimate species extinction caused by habitat destruction, one of the principal prerequisites is to accurately total the species numbers presented in the whole study area. One can better evaluate and compare alternative theoretical SAR models on the accurate estimation of species loss only when the exact total species number for the whole area is clear. This presents an opportunity for ecologists to simulate more research on accurately estimating Whittaker's gamma diversity for the purpose of better predicting species loss.

  17. 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... crypticus), palezone shiner (Notropis albizonatus), ring pink mussel (Obovaria retusa), Nashville...

  18. 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.

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

    USGS Publications Warehouse

    Keeley, J.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 m2 due 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.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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

  5. On the estimation of species richness based on the accumulation of previously unrecorded species

    USGS Publications Warehouse

    Cam, E.; Nichols, J.D.; Sauer, J.R.; Hines, J.E.

    2002-01-01

    Estimation of species richness of local communities has become an important topic in community ecology and monitoring. Investigators can seldom enumerate all the species present in the area of interest during sampling sessions. If the location of interest is sampled repeatedly within a short time period, the number of new species recorded is typically largest in the initial sample and decreases as sampling proceeds, but new species may be detected if sampling sessions are added. The question is how to estimate the total number of species. The data collected by sampling the area of interest repeatedly can be used to build species-accumulation curves: the cumulative number of species recorded as a function of the number of sampling sessions (which we refer to as ?species-accumulation data?). A classic approach used to compute total species richness is to fit curves to the data on species accumulation with sampling effort. This approach does not rest on direct estimation of the probability of detecting species during sampling sessions and has no underlying basis regarding the sampling process that gave rise to the data. Here we recommend a probabilistic, nonparametric estimator for species richness for use with species-accumulation data. We use estimators of population size that were developed for capture-recapture data, but that can be used to estimate the size of species assemblages using species-accumulation data. Models of detection probability account for the underlying sampling process. They permit variation in detection probability among species. We illustrate this approach using data from the North American Breeding Bird Survey (BBS). We describe other situations where species accumulation data are collected under different designs (e.g., over longer periods of time, or over spatial replicates) and that lend themselves to use of capture-recapture models for estimating the size of the community of interest. We discuss the assumptions and interpretations

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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...

  11. 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...

  12. 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...

  13. Emergent neutrality drives phytoplankton species coexistence

    PubMed Central

    Segura, Angel M.; Calliari, Danilo; Kruk, Carla; Conde, Daniel; Bonilla, Sylvia; Fort, Hugo

    2011-01-01

    The mechanisms that drive species coexistence and community dynamics have long puzzled ecologists. Here, we explain species coexistence, size structure and diversity patterns in a phytoplankton community using a combination of four fundamental factors: organism traits, size-based constraints, hydrology and species competition. Using a ‘microscopic’ Lotka–Volterra competition (MLVC) model (i.e. with explicit recipes to compute its parameters), we provide a mechanistic explanation of species coexistence along a niche axis (i.e. organismic volume). We based our model on empirically measured quantities, minimal ecological assumptions and stochastic processes. In nature, we found aggregated patterns of species biovolume (i.e. clumps) along the volume axis and a peak in species richness. Both patterns were reproduced by the MLVC model. Observed clumps corresponded to niche zones (volumes) where species fitness was highest, or where fitness was equal among competing species. The latter implies the action of equalizing processes, which would suggest emergent neutrality as a plausible mechanism to explain community patterns. PMID:21177680

  14. 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.

  15. Increased competition may promote species coexistence.

    PubMed

    Vandermeer, J; Evans, M A; Foster, P; Höök, T; Reiskind, M; Wund, M

    2002-06-25

    It is a mainstay of community ecology that local exclusion of species will result if competitive pressures become too large. The pattern of exclusion may be complicated, but the qualitative orthodoxy has changed little since the pioneering work of Lotka, Volterra, and Gause--no two species can occupy the same niche. Stated in a more precise form, the higher the intensity of interspecific competition in an assemblage of species, the fewer the number of species that can coexist in perpetuity. We suggest that this orthodoxy results from "linear" thinking, and that if the classical equations are formulated more realistically with attendant nonlinearities, the orthodoxy breaks down and higher levels of competition may actually increase the likelihood that species will avoid competitive exclusion. Furthermore, this increased probability of coexistence at higher levels of competition is accompanied by characteristic dynamic patterns: (i) at lower levels of competition, after all extinction events have occurred, remaining species follow irregular chaotic patterns; (ii) at higher levels of competition, when most species coexist, all species are entrained in a single large limit cycle; (iii) the transient behavior appears to correspond to a special case of chaos, uniform phase chaotic amplitude.

  16. 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.

  17. 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.

  18. 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.

  19. 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...

  20. 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.

  1. 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/).

  2. Estimating species richness using environmental DNA.

    PubMed

    Olds, Brett P; Jerde, Christopher L; Renshaw, Mark A; Li, Yiyuan; Evans, Nathan T; Turner, Cameron R; Deiner, Kristy; Mahon, Andrew R; Brueseke, Michael A; Shirey, Patrick D; Pfrender, Michael E; Lodge, David M; Lamberti, Gary A

    2016-06-01

    The foundation for any ecological study and for the effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion-based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that eDNA provides an alternative means of determining species richness and species identities for a natural ecosystem. In a northern Indiana stream, electrofishing yielded a direct estimate of 12 species and a mean estimated richness (Chao II estimator) of 16.6 species with a 95% confidence interval from 12.8 to 42.2. eDNA sampling detected an additional four species, congruent with the mean Chao II estimate from electrofishing. This increased detection rate for fish species between methods suggests that eDNA sampling can enhance estimation of fish fauna in flowing waters while having minimal sampling impacts on fish and their habitat. Modern genetic approaches therefore have the potential to transform our ability to build a more complete list of species for ecological investigations and inform management of aquatic ecosystems. PMID:27516876

  3. Three New Species of the Genus Ochroconis.

    PubMed

    Samerpitak, K; Gerrits van den Ende, A H G; Menken, S B J; de Hoog, G S

    2015-08-01

    Ochroconis bacilliformis, O. phaeophora and O. robusta, three novel species of the melanized genus Ochroconis (Sympoventuriaceae, Venturiales), are described, illustrated and distinguished phenotypically and molecularly from previously described species in the genus Ochroconis. Their potential significance for infection of cold-blooded vertebrates is discussed. PMID:26093392

  4. Species-specific proteins in fossils

    NASA Astrophysics Data System (ADS)

    Lowenstein, Jerold M.

    1980-07-01

    With a solid-phase radioimmunoassay it has been possible to detect species-specific collagen and albumin in fossils as old as 1.9 million years. This technique may provide new data on the genetic relations of fossil species to each other and to living forms.

  5. 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…

  6. 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. PMID:25878052

  7. Estimating species richness using environmental DNA.

    PubMed

    Olds, Brett P; Jerde, Christopher L; Renshaw, Mark A; Li, Yiyuan; Evans, Nathan T; Turner, Cameron R; Deiner, Kristy; Mahon, Andrew R; Brueseke, Michael A; Shirey, Patrick D; Pfrender, Michael E; Lodge, David M; Lamberti, Gary A

    2016-06-01

    The foundation for any ecological study and for the effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion-based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that eDNA provides an alternative means of determining species richness and species identities for a natural ecosystem. In a northern Indiana stream, electrofishing yielded a direct estimate of 12 species and a mean estimated richness (Chao II estimator) of 16.6 species with a 95% confidence interval from 12.8 to 42.2. eDNA sampling detected an additional four species, congruent with the mean Chao II estimate from electrofishing. This increased detection rate for fish species between methods suggests that eDNA sampling can enhance estimation of fish fauna in flowing waters while having minimal sampling impacts on fish and their habitat. Modern genetic approaches therefore have the potential to transform our ability to build a more complete list of species for ecological investigations and inform management of aquatic ecosystems.

  8. 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…

  9. 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)

  10. 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…

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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.

  16. How to fail at species delimitation.

    PubMed

    Carstens, Bryan C; Pelletier, Tara A; Reid, Noah M; Satler, Jordan D

    2013-09-01

    Species delimitation is the act of identifying species-level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimiting species. However, most recent investigations only utilize a handful (i.e. 2-3) of the available methods, often for unstated reasons. Because the parameter space that is potentially relevant to species delimitation far exceeds the parameterization of any existing method, a given method necessarily makes a number of simplifying assumptions, any one of which could be violated in a particular system. We suggest that researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods. Incongruence across the results from different methods is evidence of either a difference in the power to detect cryptic lineages across one or more of the approaches used to delimit species and could indicate that assumptions of one or more of the methods have been violated. In either case, the inferences drawn from species delimitation studies should be conservative, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.

  17. 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...

  18. 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. PMID:20136746

  19. 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...

  20. System and method for ultrafast optical signal detecting via a synchronously coupled anamorphic light pulse encoded laterally

    DOEpatents

    Heebner, John E.

    2010-08-03

    In one general embodiment, a method for ultrafast optical signal detecting is provided. In operation, a first optical input signal is propagated through a first wave guiding layer of a waveguide. Additionally, a second optical input signal is propagated through a second wave guiding layer of the waveguide. Furthermore, an optical control signal is applied to a top of the waveguide, the optical control signal being oriented diagonally relative to the top of the waveguide such that the application is used to influence at least a portion of the first optical input signal propagating through the first wave guiding layer of the waveguide. In addition, the first and the second optical input signals output from the waveguide are combined. Further, the combined optical signals output from the waveguide are detected. In another general embodiment, a system for ultrafast optical signal recording is provided comprising a waveguide including a plurality of wave guiding layers, an optical control source positioned to propagate an optical control signal towards the waveguide in a diagonal orientation relative to a top of the waveguide, at least one optical input source positioned to input an optical input signal into at least a first and a second wave guiding layer of the waveguide, and a detector for detecting at least one interference pattern output from the waveguide, where at least one of the interference patterns results from a combination of the optical input signals input into the first and the second wave guiding layer. Furthermore, propagation of the optical control signal is used to influence at least a portion of the optical input signal propagating through the first wave guiding layer of the waveguide.

  1. The Porphyra species of Helgoland (Bangiales, Rhodophyta)

    NASA Astrophysics Data System (ADS)

    Kornmann, P.; Sahling, P.-H.

    1991-03-01

    This revision of seven Porphyra species of Helgoland was based on a study of the structure of their fertile thalli and the behaviour of their spores. Regarding the reproductive organization the species may be arranged in two groups. P. leucosticta and P. purpureo-violacea are obligate monoecious species. Asexual thalli have never been observed in the field. The other five species are generally dioecious. Isomorphic sexual thalli and asexually propagating ones are mixed in uniform populations. Carpospores originating from sexual fusion develop into the diploid Conchocelis phase. Sporangia of asexual plants, though homologous in formation, produce spores of different kinds: aplanospores that give rise to the vegetative thallus directly (in P. umbilicalis, P. insolita n. sp. and P. ochotensis) and spores that develop into haploid Conchocelis (in P. laciniata and in P. linearis). P. laciniata — formerly considered synonymous with P. purpurea — is an independent species.

  2. Actinomyces Species Isolated from Breast Infections.

    PubMed

    Bing, A U; Loh, S F; Morris, T; Hughes, H; Dixon, J M; Helgason, K O

    2015-10-01

    Actinomycosis is a chronic infection caused by Actinomyces species characterized by abscess formation, tissue fibrosis, and draining sinuses. The spectrum of infections caused by Actinomyces species ranges from classical invasive actinomycosis to a less invasive form of superficial skin and soft tissue infection. We present a review detailing all Actinomyces species isolated from breast infections in NHS Lothian between 2005 and 2013, Actinomyces species isolated from breast infections referred to the United Kingdom Anaerobe Reference Unit between 1988 and 2014, and cases describing Actinomyces breast infections published in the medical literature since 1994. Actinomyces species are fastidious organisms which can be difficult to identify and are likely to be underascertained as a cause of breast infections. Due to improved diagnostic methods, they are increasingly associated with chronic, recurrent breast infections and may play a more significant role in these infections than has previously been appreciated.

  3. 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

  4. 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

  5. Region effects influence local tree species diversity

    PubMed Central

    Ricklefs, Robert E.; He, Fangliang

    2016-01-01

    Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species. PMID:26733680

  6. Region effects influence local tree species diversity.

    PubMed

    Ricklefs, Robert E; He, Fangliang

    2016-01-19

    Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species. PMID:26733680

  7. Biodiversity hotspots house most undiscovered plant species.

    PubMed

    Joppa, Lucas N; Roberts, David L; Myers, Norman; Pimm, Stuart L

    2011-08-01

    For most organisms, the number of described species considerably underestimates how many exist. This is itself a problem and causes secondary complications given present high rates of species extinction. Known numbers of flowering plants form the basis of biodiversity "hotspots"--places where high levels of endemism and habitat loss coincide to produce high extinction rates. How different would conservation priorities be if the catalog were complete? Approximately 15% more species of flowering plant are likely still undiscovered. They are almost certainly rare, and depending on where they live, suffer high risks of extinction from habitat loss and global climate disruption. By using a model that incorporates taxonomic effort over time, regions predicted to contain large numbers of undiscovered species are already conservation priorities. Our results leave global conservation priorities more or less intact, but suggest considerably higher levels of species imperilment than previously acknowledged.

  8. Species classification problems in virus taxonomy.

    PubMed

    Kingsbury, D W

    1985-01-01

    Although the species is the fundamental unit of taxonomy, virologists only recently have begun to classify virus species in a systematic way under the leadership of the International Committee on Taxonomy of Viruses. Progress has been slow and uneven for several reasons: (i) Attempts to sort species are hampered even when the distinction between classification and nomenclature is blurred. Classifying is based on observation and involves deductive reasoning, whereas naming can be as arbitrary as desired, even to the point of dispensing with the traditional Latin binomial form. (ii) Some virologists deny the possibility of applying the species concept to asexual organisms, such as viruses. Those persons are influenced by an obsolete definition of biological species which rests on observed or inferred barriers to sexual reproduction. (iii) New taxonomic tools, such as mathematical (numerical) taxonomy, might be applied profitably to virus classification, but are unfamiliar to many virologists. PMID:4055308

  9. Actinomyces Species Isolated from Breast Infections

    PubMed Central

    Loh, S. F.; Morris, T.; Hughes, H.; Dixon, J. M.

    2015-01-01

    Actinomycosis is a chronic infection caused by Actinomyces species characterized by abscess formation, tissue fibrosis, and draining sinuses. The spectrum of infections caused by Actinomyces species ranges from classical invasive actinomycosis to a less invasive form of superficial skin and soft tissue infection. We present a review detailing all Actinomyces species isolated from breast infections in NHS Lothian between 2005 and 2013, Actinomyces species isolated from breast infections referred to the United Kingdom Anaerobe Reference Unit between 1988 and 2014, and cases describing Actinomyces breast infections published in the medical literature since 1994. Actinomyces species are fastidious organisms which can be difficult to identify and are likely to be underascertained as a cause of breast infections. Due to improved diagnostic methods, they are increasingly associated with chronic, recurrent breast infections and may play a more significant role in these infections than has previously been appreciated. PMID:26224846

  10. Reactive Oxygen Species in Cardiovascular Disease

    PubMed Central

    Sugamura, Koichi; Keaney, John F.

    2011-01-01

    Based on the ‘free-radical theory’ of disease, researchers have been trying to elucidate the role of oxidative stress from free radicals in cardiovascular disease. Considerable data indicate that ROS and oxidative stress are important features of cardiovascular diseases including atherosclerosis, hypertension, and congestive heart failure. However, blanket strategies with antioxidants to ameliorate cardiovascular disease have not generally yielded favorable results. However, our understanding or reactive oxygen species has evolved to the point that we now realize these species have important roles in physiology as well as pathophysiology. Thus, it is overly simplistic to assume a general antioxidant strategy will yield specific effects on cardiovascular disease. Indeed, there are several sources of reactive oxygen species that are known to be active in the cardiovascular system. This review will address our understanding of reactive oxygen species sources in cardiovascular disease and both animal and human data defining how reactive oxygen species contribute to physiology and pathology. PMID:21627987

  11. Agar polysaccharides from Gracilaria species (Rhodophyta, Gracilariaceae).

    PubMed

    Marinho-Soriano, E

    2001-07-26

    Yield, physical and chemical properties of agar from three agarophytes species (Gracilaria gracilis, G. dura and G. bursa-pastoris) were determined. The agar yield from the three species varied significantly (P<0.01). The highest yields of agar (34.8%) and the lowest (30%) were obtained from G. bursa-pastoris and G. gracilis, respectively. Highest gel strength (630+/-15 g cm(-2)) was obtained from agar extracted from G. gracilis and lowest from G. bursa-pastoris (26+/-3.6 g cm(-2)). The values of 3,6-anhydrogalactose were similar for G. gracilis and G. dura and there were no significant differences among the species. The sulfate contents varied significantly (P<0.01) and the higher value was obtained from G. bursa-pastoris. Among the three species, G. gracilis showed superior agar quality than the other two species, hence it can be considered a good potential source for industrial use.

  12. 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

  13. Biodiversity hotspots house most undiscovered plant species

    PubMed Central

    Joppa, Lucas N.; Roberts, David L.; Myers, Norman; Pimm, Stuart L.

    2011-01-01

    For most organisms, the number of described species considerably underestimates how many exist. This is itself a problem and causes secondary complications given present high rates of species extinction. Known numbers of flowering plants form the basis of biodiversity “hotspots”—places where high levels of endemism and habitat loss coincide to produce high extinction rates. How different would conservation priorities be if the catalog were complete? Approximately 15% more species of flowering plant are likely still undiscovered. They are almost certainly rare, and depending on where they live, suffer high risks of extinction from habitat loss and global climate disruption. By using a model that incorporates taxonomic effort over time, regions predicted to contain large numbers of undiscovered species are already conservation priorities. Our results leave global conservation priorities more or less intact, but suggest considerably higher levels of species imperilment than previously acknowledged. PMID:21730155

  14. The importance and benefits of species.

    PubMed

    Gascon, Claude; Brooks, Thomas M; Contreras-MacBeath, Topiltzin; Heard, Nicolas; Konstant, William; Lamoreux, John; Launay, Frederic; Maunder, Michael; Mittermeier, Russell A; Molur, Sanjay; Al Mubarak, Razan Khalifa; Parr, Michael J; Rhodin, Anders G J; Rylands, Anthony B; Soorae, Pritpal; Sanderson, James G; Vié, Jean-Christophe

    2015-05-18

    Humans depend on biodiversity in myriad ways, yet species are being rapidly lost due to human activities. The ecosystem services approach to conservation tries to establish the value that society derives from the natural world such that the true cost of proposed development actions becomes apparent to decision makers. Species are an integral component of ecosystems, and the value they provide in terms of services should be a standard part of ecosystem assessments. However, assessing the value of species is difficult and will always remain incomplete. Some of the most difficult species' benefits to assess are those that accrue unexpectedly or are wholly unanticipated. In this review, we consider recent examples from a wide variety of species and a diverse set of ecosystem services that illustrate this point and support the application of the precautionary principle to decisions affecting the natural world. PMID:25989087

  15. 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.

  16. Region effects influence local tree species diversity.

    PubMed

    Ricklefs, Robert E; He, Fangliang

    2016-01-19

    Global patterns of biodiversity reflect both regional and local processes, but the relative importance of local ecological limits to species coexistence, as influenced by the physical environment, in contrast to regional processes including species production, dispersal, and extinction, is poorly understood. Failure to distinguish regional influences from local effects has been due, in part, to sampling limitations at small scales, environmental heterogeneity within local or regional samples, and incomplete geographic sampling of species. Here, we use a global dataset comprising 47 forest plots to demonstrate significant region effects on diversity, beyond the influence of local climate, which together explain more than 92% of the global variation in local forest tree species richness. Significant region effects imply that large-scale processes shaping the regional diversity of forest trees exert influence down to the local scale, where they interact with local processes to determine the number of coexisting species.

  17. 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

  18. 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 ...

  19. 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...

  20. 78 FR 37840 - Endangered Species Recovery Permit Applications

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-24

    ... 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 of 1973, as amended (Act), prohibits activities with endangered and threatened species unless a...

  1. 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...

  2. 76 FR 39888 - Endangered Species Recovery Permit Applications

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-07

    ... 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...

  3. 78 FR 27249 - Endangered Species Recovery Permit Applications

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-09

    ... 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...

  4. 77 FR 71818 - Endangered Species Recovery Permit Applications

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-04

    ... 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...

  5. 76 FR 20705 - Endangered Species Receipt of Applications for Permit

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-13

    ... 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...

  6. 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.

  7. 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...

  8. 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. PMID:25959973

  9. A new species of Brevipalpus Donnadieu (Acari: Tenuipalpidae) and key to the Egyptian species.

    PubMed

    Halawa, Alaa M; Fawzy, Magdy M

    2014-01-20

    A new species, Brevipalpus noranae sp. nov. (Acari: Tenuipalpidae) is described and illustrated from females collected on Malus domestica Borkh and Citrus aurantium L. A key to the species of the genus Brevipalpus present in Egypt is provided.

  10. A new species of Brevipalpus Donnadieu (Acari: Tenuipalpidae) and key to the Egyptian species.

    PubMed

    Halawa, Alaa M; Fawzy, Magdy M

    2014-01-01

    A new species, Brevipalpus noranae sp. nov. (Acari: Tenuipalpidae) is described and illustrated from females collected on Malus domestica Borkh and Citrus aurantium L. A key to the species of the genus Brevipalpus present in Egypt is provided. PMID:24869810

  11. 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. PMID:25705854

  12. Genetic Sorting of Subordinate Species in Grassland Modulated by Intraspecific Variation in Dominant Species

    PubMed Central

    Gustafson, Danny J.; Major, Charles; Jones, Dewitt; Synovec, John; Baer, Sara G.; Gibson, David J.

    2014-01-01

    Genetic variation in a single species can have predictable and heritable effects on associated communities and ecosystem processes, however little is known about how genetic variation of a dominant species affects plant community assembly. We characterized the genetic structure of a dominant grass (Sorghastrum nutans) and two subordinate species (Chamaecrista fasciculata, Silphium integrifolium), during the third growing season in grassland communities established with genetically distinct (cultivated varieties or local ecotypes) seed sources of the dominant grasses. There were genetic differences between subordinate species growing in the cultivar versus local ecotype communities, indicating that intraspecific genetic variation in the dominant grasses affected the genetic composition of subordinate species during community assembly. A positive association between genetic diversity of S. nutans, C. fasciculata, and S. integrifolium and species diversity established the role of an intraspecific biotic filter during community assembly. Our results show that intraspecific variation in dominant species can significantly modulate the genetic composition of subordinate species. PMID:24637462

  13. 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.

  14. Persistent toxic substances in Mediterranean aquatic species.

    PubMed

    Miniero, Roberto; Abate, Vittorio; Brambilla, Gianfranco; Davoli, Enrico; De Felip, Elena; De Filippis, Stefania P; Dellatte, Elena; De Luca, Silvia; Fanelli, Roberto; Fattore, Elena; Ferri, Fabiola; Fochi, Igor; Rita Fulgenzi, Anna; Iacovella, Nicola; Iamiceli, Anna Laura; Lucchetti, Dario; Melotti, Paolo; Moret, Ivo; Piazza, Rossano; Roncarati, Alessandra; Ubaldi, Alessandro; Zambon, Stefano; di Domenico, Alessandro

    2014-10-01

    Fish and fishery products may represent one of the main sources of dietary exposure to persistent toxic substances (PTSs) such as polychlorinated dibenzodioxins, dibenzofurans, and biphenyls; polybromodiphenyl ethers; organochlorine pesticides; perfluorooctanoic acid and perfluorooctane sulfonate; and inorganic mercury and methyl mercury. In this study, PTS contamination of Mediterranean fish and crustaceans caught in Italian coastal waters was investigated in order to increase the representativeness of the occurrence database for wild species. The objectives were to verify the suitability of regulatory limits for PTSs, identify background concentrations values, if any, and examine the possible sources of variability when assessing the chemical body burdens of aquatic species. Twelve wild species of commercial interest and two farmed fish species were chosen. Excluding methyl mercury, chemical concentrations found in wild species fell generally towards the low ends of the concentration ranges found in Europe according to EFSA database and were quite lower than the tolerable maximum levels established in the European Union; farmed fish always showed contamination levels quite lower than those detected in wild species. The data obtained for wild species seemed to confirm the absence of local sources of contamination in the chosen sampling areas; however, species contamination could exceed regulatory levels even in the absence of specific local sources of contamination as a result of the position in the food web and natural variability in species' lifestyle. A species-specific approach to the management of contamination in aquatic organisms is therefore suggested as an alternative to a general approach based only on contaminant body burden. A chemical-specific analysis performed according to organism position in the food chain strengthened the need to develop this approach. PMID:25020099

  15. Persistent toxic substances in Mediterranean aquatic species.

    PubMed

    Miniero, Roberto; Abate, Vittorio; Brambilla, Gianfranco; Davoli, Enrico; De Felip, Elena; De Filippis, Stefania P; Dellatte, Elena; De Luca, Silvia; Fanelli, Roberto; Fattore, Elena; Ferri, Fabiola; Fochi, Igor; Rita Fulgenzi, Anna; Iacovella, Nicola; Iamiceli, Anna Laura; Lucchetti, Dario; Melotti, Paolo; Moret, Ivo; Piazza, Rossano; Roncarati, Alessandra; Ubaldi, Alessandro; Zambon, Stefano; di Domenico, Alessandro

    2014-10-01

    Fish and fishery products may represent one of the main sources of dietary exposure to persistent toxic substances (PTSs) such as polychlorinated dibenzodioxins, dibenzofurans, and biphenyls; polybromodiphenyl ethers; organochlorine pesticides; perfluorooctanoic acid and perfluorooctane sulfonate; and inorganic mercury and methyl mercury. In this study, PTS contamination of Mediterranean fish and crustaceans caught in Italian coastal waters was investigated in order to increase the representativeness of the occurrence database for wild species. The objectives were to verify the suitability of regulatory limits for PTSs, identify background concentrations values, if any, and examine the possible sources of variability when assessing the chemical body burdens of aquatic species. Twelve wild species of commercial interest and two farmed fish species were chosen. Excluding methyl mercury, chemical concentrations found in wild species fell generally towards the low ends of the concentration ranges found in Europe according to EFSA database and were quite lower than the tolerable maximum levels established in the European Union; farmed fish always showed contamination levels quite lower than those detected in wild species. The data obtained for wild species seemed to confirm the absence of local sources of contamination in the chosen sampling areas; however, species contamination could exceed regulatory levels even in the absence of specific local sources of contamination as a result of the position in the food web and natural variability in species' lifestyle. A species-specific approach to the management of contamination in aquatic organisms is therefore suggested as an alternative to a general approach based only on contaminant body burden. A chemical-specific analysis performed according to organism position in the food chain strengthened the need to develop this approach.

  16. 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

  17. 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

  18. Calcifying species sensitivity distributions for ocean acidification.

    PubMed

    Azevedo, Ligia B; De Schryver, An M; Hendriks, A Jan; Huijbregts, Mark A J

    2015-02-01

    Increasing CO2 atmospheric levels lead to increasing ocean acidification, thereby enhancing calcium carbonate dissolution of calcifying species. We gathered peer-reviewed experimental data on the effects of acidified seawater on calcifying species growth, reproduction, and survival. The data were used to derive species-specific median effective concentrations, i.e., pH50, and pH10, via logistic regression. Subsequently, we developed species sensitivity distributions (SSDs) to assess the potentially affected fraction (PAF) of species exposed to pH declines. Effects on species growth were observed at higher pH than those on species reproduction (mean pH10 was 7.73 vs 7.63 and mean pH50 was 7.28 vs 7.11 for the two life processes, respectively) and the variability in the sensitivity of species increased with increasing number of species available for the PAF (pH10 standard deviation was 0.20, 0.21, and 0.33 for survival, reproduction, and growth, respectively). The SSDs were then applied to two climate change scenarios to estimate the increase in PAF (ΔPAF) by future ocean acidification. In a high CO2 emission scenario, ΔPAF was 3 to 10% (for pH50) and 21 to 32% (for pH10). In a low emission scenario, ΔPAF was 1 to 4% (for pH50) and 7 to 12% (for pH10). Our SSDs developed for the effect of decreasing ocean pH on calcifying marine species assemblages can also be used for comparison with other environmental stressors.

  19. 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

  20. A phylogeographic evaluation of the Amolops mantzorum species group: cryptic species and plateau uplift.

    PubMed

    Lu, Bin; Bi, Ke; Fu, Jinzhong

    2014-04-01

    Phylogeographic analysis brings organism phylogeny, regional geological/climatic history, and population demography together, and provides insights into species history and speciation. Using DNA sequence data from a mitochondrial marker (cytochrome b) and a nuclear marker (cmyc intron 2), we examined phylogeography of the Amolops mantzorum species group. We first constructed Bayesian and maximum-likelihood gene trees and medium-joint networks for the recovered haplotypes, and estimated divergence time for each major lineage. Species boundaries were then delineated using the general mixed Yule-coalescent model (GMYC) and a Bayesian species-delimitation method (BP&P). Potential gene flow between putative species was also estimated using the isolation-with-migration model. Furthermore, species-distribution modeling was used to probe linkage between climatic changes and speciation. Lastly, extended Bayesian skyline plotting was employed to reveal historical demography for each putative species. Our analyses clearly delimit nine species in the group, including four well-recognized species and five putative species, of which three are often listed as synonyms of A. mantzorum. The nominal species A. mantzorum may in fact include two cryptic species. Divergence-time estimates align the speciation events with the recent intense uplift of the Tibetan Plateau in the last 3.6 million years. The species-distribution modeling also reveals different habitat preferences among species that are potentially linked to climatic changes associated with the uplift. Furthermore, three species sustained continuous population growth through the last glaciation, while others expanded only after the last glaciation. The eastern escarpment of Tibet is a biodiversity hotspot; its rich species diversity, unique topography, and well-established geological history provide an excellent system for evolutionary studies.

  1. 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.

  2. 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...

  3. 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. PMID:27053754

  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. Which Models Are Appropriate for Six Subtropical Forests: Species-Area and Species-Abundance Models

    PubMed Central

    Wei, Shi Guang; Li, Lin; Chen, Zhen Cheng; Lian, Ju Yu; Lin, Guo Jun; Huang, Zhong Liang; Yin, Zuo Yun

    2014-01-01

    The species-area relationship is one of the most important topic in the study of species diversity, conservation biology and landscape ecology. The species-area relationship curves describe the increase of species number with increasing area, and have been modeled by various equations. In this paper, we used detailed data from six 1-ha subtropical forest communities to fit three species-area relationship models. The coefficient of determination and F ratio of ANOVA showed all the three models fitted well to the species-area relationship data in the subtropical communities, with the logarithm model performing better than the other two models. We also used the three species-abundance distributions, namely the lognormal, logcauchy and logseries model, to fit them to the species-abundance data of six communities. In this case, the logcauchy model had the better fit based on the coefficient of determination. Our research reveals that the rare species always exist in the six communities, corroborating the neutral theory of Hubbell. Furthermore, we explained why all species-abundance figures appeared to be left-side truncated. This was due to subtropical forests have high diversity, and their large species number includes many rare species. PMID:24755956

  6. 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.

  7. 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

  8. 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. PMID:18577084

  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. 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...

  11. Simple Method to Differentiate among Rickettsia Species

    PubMed Central

    Peniche-Lara, Gaspar; Zavala-Velazquez, Jorge; Dzul-Rosado, Karla; Walker, D.H.; Zavala-Castro, Jorge

    2016-01-01

    In this work we present a new option to identify 11 rickettsial species that cause human rickettsioses, with some advantages over the previous methods described. Using rickettsial isolates from 11 Rickettsia species as a sample, we used the polymerase chain reaction to amplify a 990- to 1,000-bp DNA fragment from the ompB gene, common for the 11 Rickettsia species analyzed in this study, which were digested with AluI restriction enzyme to obtain different digestion patterns. This restriction pattern can be visualized using a polyacrylamide gel electrophoresis technique. Using this method we could differentiate between the 11 Rickettsia species analyzed regardless of the group to which the Rickettsia belonged. We developed a simple method to identify 11 Rickettsia species which cause human rickettsioses using polymerase chain reaction and restriction fragment length polymorphism techniques with the advantage that it only needs one amplicon and only one restriction enzyme to obtain the restriction pattern. The identification of the species infecting vectors, reservoirs, and humans is essential to establish the ecological and behavioral ecosystem involved in its maintenance and transmission in nature in the specific region where the pathogen is circulating. This method is very helpful to identify Rickettsia species in a short time. PMID:23595041

  12. 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.

  13. Species coexistence in a changing world.

    PubMed

    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.

  14. Energetic Constraints on Species Coexistence in Birds.

    PubMed

    Pigot, Alexander L; Tobias, Joseph A; Jetz, Walter

    2016-03-01

    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.

  15. 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.

  16. 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.

  17. Concepts in protistology: species definitions and boundaries.

    PubMed

    Boenigk, Jens; Ereshefsky, Marc; Hoef-Emden, Kerstin; Mallet, James; Bass, David

    2012-05-01

    This paper summarises the Symposium 'Concepts in Protistology', during the VI European Congress of Protistology, Berlin, 25-29 July 2011. There is an increasing focus on cataloguing the number of species on earth, species barcoding initiatives, and the increasing need to reconcile molecular with morphological data in protists within a taxonomic framework. We identify several obstructions to defining species in protists, including the high incidence of asexuality, high levels of both morphological conservation and evolutionary convergence, high levels of genetic diversity that cannot so far be correlated with phenotypic characters, conflicting signals between both genetic and phenotypic taxonomic markers, and different requirements and challenges of species definition in different protist groups. We assert that there is no species 'category' for protists, and recommend that a working definition of species is clarified on a case-by-case basis. Thus, a consensus approach may emerge within protist groups, but any one approach is unlikely to encompass a wide phylogenetic range. However, as long as clarity of intent and method is maintained, the utility of the term 'species' in protists will also be maintained as a reproducible and convenient (if artificial) way of referring to particular lineages within a tightly defined context. PMID:22209540

  18. 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.

  19. Culex Species Mosquitoes and Zika Virus.

    PubMed

    Huang, Yan-Jang S; Ayers, Victoria B; Lyons, Amy C; Unlu, Isik; Alto, Barry W; Cohnstaedt, Lee W; Higgs, Stephen; Vanlandingham, Dana L

    2016-10-01

    Recent reports of Zika virus (ZIKV) isolates from Culex species mosquitoes have resulted in concern regarding a lack of knowledge on the number of competent vector species for ZIKV transmission in the new world. Although observations in the field have demonstrated that ZIKV isolation can be made from Culex species mosquitoes, the detection of ZIKV in these mosquitoes is not proof of their involvement in a ZIKV transmission cycle. Detection may be due to recent feeding on a viremic vertebrate, and is not indicative of replication in the mosquito. In this study, susceptibility of recently colonized Culex species mosquitoes was investigated. The results showed a high degree of refractoriness among members of Culex pipiens complex to ZIKV even when exposed to high-titer bloodmeals. Our finding suggests that the likelihood of Culex species mosquitoes serving as secondary vectors for ZIKV is very low, therefore vector control strategies for ZIKV should remain focused on Aedes species mosquitoes. Our demonstration that Culex quinquefasciatus from Vero Beach, FL, is refractory to infection with ZIKV is especially important and timely. Based on our data, we would conclude that the autochthonous cases of Zika in Florida are not due to transmission by C. quinquefasciatus, and so control efforts should focus on other species, logically Aedes aegypti and Aedes albopictus.

  20. 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

  1. 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.

  2. 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

  3. Concepts in protistology: species definitions and boundaries.

    PubMed

    Boenigk, Jens; Ereshefsky, Marc; Hoef-Emden, Kerstin; Mallet, James; Bass, David

    2012-05-01

    This paper summarises the Symposium 'Concepts in Protistology', during the VI European Congress of Protistology, Berlin, 25-29 July 2011. There is an increasing focus on cataloguing the number of species on earth, species barcoding initiatives, and the increasing need to reconcile molecular with morphological data in protists within a taxonomic framework. We identify several obstructions to defining species in protists, including the high incidence of asexuality, high levels of both morphological conservation and evolutionary convergence, high levels of genetic diversity that cannot so far be correlated with phenotypic characters, conflicting signals between both genetic and phenotypic taxonomic markers, and different requirements and challenges of species definition in different protist groups. We assert that there is no species 'category' for protists, and recommend that a working definition of species is clarified on a case-by-case basis. Thus, a consensus approach may emerge within protist groups, but any one approach is unlikely to encompass a wide phylogenetic range. However, as long as clarity of intent and method is maintained, the utility of the term 'species' in protists will also be maintained as a reproducible and convenient (if artificial) way of referring to particular lineages within a tightly defined context.

  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. Genetic variability in three Amazon parrot species.

    PubMed

    Lopes, I F; Del Lama, M A; Del Lama, S N

    2007-12-01

    Parrots of the genus Amazona are among the most threatened species of the Order Pscittaciformes. This work describes allozyme polymorphisms in three Amazon parrot species--the Blue-fronted Amazon (Amazona aestiva), the Orange-winged Amazon (Amazona amazonica), and the Festive Amazon (Amazona festiva) -, and provides useful data for the evaluation of their genetic variability. We electrophoretically analyzed blood samples from 68 wild-caught individuals, maintained in captivity in three Brazilian zoos. Eight of the ten studied enzyme loci exhibited polymorphism. Glucosephosphate isomerase (Gpi) proved to be a diagnostic locus for the identification of these Amazon species. The expected average heterozygosity of the Blue-fronted Amazon (0.060) differed significantly from the expected heterozygosities of the Orange-winged Amazon and the Festive Amazon (0.040 and 0.039, respectively). This result was discussed as a consequence of hybridization between two geographic A. aestiva subspecies, and alternatively as a particular trait of this species. Genetic variability of the Blue-fronted Amazon compared to birds in general is not low on a species-wide level, despite the fact that this parrot is one of the most illegally traded species. Allozyme analysis proved to be an useful tool in monitoring the genetic variation within the genus Amazona and can be applied in the management program of other threatened species of this genus.

  6. Species Distribution Modeling of Deep Pelagic Eels.

    PubMed

    DeVaney, Shannon C

    2016-10-01

    The ocean's midwaters (the mesopelagic and bathypelagic zones) make up the largest living space on the planet, but are undersampled and relatively poorly understood. The true distribution of many midwater species, let alone the abiotic factors most important in determining that distribution, is not well known. Because collecting specimens and data from the deep ocean is expensive and logistically difficult, it would be useful to be able to predict where species of interest are likely to occur so that sampling effort can be concentrated in appropriate areas. The distribution of two representative midwater fishes, the gulper eel Eurypharynx pelecanoides and the bobtail eel Cyema atrum (Teleostei: Saccopharyngiformes), were modeled with MaxEnt software to examine the viability of species distribution modeling (SDM) for globally distributed midwater fishes using currently available environmental data from the ocean surface and bottom. These species were chosen because they are relatively abundant, easily recognized, and unlikely to have been misidentified in database records, and are true midwater fishes, not known to undertake significant vertical diurnal migration. Models for both species show a generally worldwide distribution with some exceptions, including the Southern Ocean and Bering Sea. Variable contributions show that surface and bottom environmental variables correlate with species presence. Both species are more likely to be found in areas with low levels of silicate. SDM is a promising method for better understanding the ecology of midwater organisms.

  7. Metabolite production by different Ulocladium species.

    PubMed

    Andersen, Birgitte; Hollensted, Morten

    2008-08-15

    Ulocladium, which is phylogenetically related to Alternaria, contains species that are food spoilers and plant pathogens, but also species that have potential as enzyme producers and bio-control agents. Ulocladium spp. are often found on dead vegetation, in soil, air and dust, but also on food and feedstuffs and on water-damaged building materials. The aim was to study the morphological and chemical diversity within the genus Ulocladium. Cultures of 52 Ulocladium strains were identified morphologically, and then extracted and analyzed using automated Chemical Image Analysis. Production of individual metabolites was correlated to species identity and source of isolation (substratum). Chemical analyses corroborated the morphological identifications and showed the existence of several species species-specific metabolites, of which most were known compounds. The production of curvularins was specific to Ulocladium atrum, while most species produced infectopyrones and derivatives of altertoxin I. None of the 52 Ulocladium strains produced alternariols, tenuazonic acid, altersolanols or macrosporin, which are common in species of Alternaria.

  8. 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

  9. Culex Species Mosquitoes and Zika Virus.

    PubMed

    Huang, Yan-Jang S; Ayers, Victoria B; Lyons, Amy C; Unlu, Isik; Alto, Barry W; Cohnstaedt, Lee W; Higgs, Stephen; Vanlandingham, Dana L

    2016-10-01

    Recent reports of Zika virus (ZIKV) isolates from Culex species mosquitoes have resulted in concern regarding a lack of knowledge on the number of competent vector species for ZIKV transmission in the new world. Although observations in the field have demonstrated that ZIKV isolation can be made from Culex species mosquitoes, the detection of ZIKV in these mosquitoes is not proof of their involvement in a ZIKV transmission cycle. Detection may be due to recent feeding on a viremic vertebrate, and is not indicative of replication in the mosquito. In this study, susceptibility of recently colonized Culex species mosquitoes was investigated. The results showed a high degree of refractoriness among members of Culex pipiens complex to ZIKV even when exposed to high-titer bloodmeals. Our finding suggests that the likelihood of Culex species mosquitoes serving as secondary vectors for ZIKV is very low, therefore vector control strategies for ZIKV should remain focused on Aedes species mosquitoes. Our demonstration that Culex quinquefasciatus from Vero Beach, FL, is refractory to infection with ZIKV is especially important and timely. Based on our data, we would conclude that the autochthonous cases of Zika in Florida are not due to transmission by C. quinquefasciatus, and so control efforts should focus on other species, logically Aedes aegypti and Aedes albopictus. PMID:27556838

  10. Coalescent Histories for Lodgepole Species Trees.

    PubMed

    Disanto, Filippo; Rosenberg, Noah A

    2015-10-01

    Coalescent histories are combinatorial structures that describe for a given gene tree and species tree the possible lists of branches of the species tree on which the gene tree coalescences take place. Properties of the number of coalescent histories for gene trees and species trees affect a variety of probabilistic calculations in mathematical phylogenetics. Exact and asymptotic evaluations of the number of coalescent histories, however, are known only in a limited number of cases. Here we introduce a particular family of species trees, the lodgepole species trees (λn)n ≥ 0, in which tree λn has m = 2n+1 taxa. We determine the number of coalescent histories for the lodgepole species trees, in the case that the gene tree matches the species tree, showing that this number grows with m!! in the number of taxa m. This computation demonstrates the existence of tree families in which the growth in the number of coalescent histories is faster than exponential. Further, it provides a substantial improvement on the lower bound for the ratio of the largest number of matching coalescent histories to the smallest number of matching coalescent histories for trees with m taxa, increasing a previous bound of [Formula: see text] to [Formula: see text]. We discuss the implications of our enumerative results for phylogenetic computations. PMID:25973633

  11. 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.

  12. 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

  13. 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

  14. Use of RAD sequencing for delimiting species.

    PubMed

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

    2015-05-01

    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.

  15. Automatic identification of species with neural networks.

    PubMed

    Hernández-Serna, Andrés; 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.

  16. A Five-Species Jungle Game

    PubMed Central

    Kang, Yibin; Pan, Qiuhui; Wang, Xueting; He, Mingfeng

    2016-01-01

    In this paper, we investigate the five-species Jungle game in the framework of evolutionary game theory. We address the coexistence and biodiversity of the system using mean-field theory and Monte Carlo simulations. Then, we find that the inhibition from the bottom-level species to the top-level species can be critical factors that affect biodiversity, no matter how it is distributed, whether homogeneously well mixed or structured. We also find that predators’ different preferences for food affect species’ coexistence. PMID:27332995

  17. 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

  18. 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

  19. A virtual species set for robust and reproducible species distribution modelling tests

    PubMed Central

    Garzon-Lopez, Carol X.; Bastin, Lucy; Foody, Giles M.; Rocchini, Duccio

    2016-01-01

    Predicting species potential and future distribution has become a relevant tool in biodiversity monitoring and conservation. In this data article we present the suitability map of a virtual species generated based on two bioclimatic variables, and a dataset containing more than 700,000 random observations at the extent of Europe. The dataset includes spatial attributes such as: distance to roads, protected areas, country codes, and the habitat suitability of two spatially clustered species (grassland and forest species) and a wide-spread species. PMID:27014734

  20. 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.

  1. 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

  2. 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.

  3. Effects of species evenness and dominant species identity on multiple ecosystem functions in model grassland communities.

    PubMed

    Orwin, Kate H; Ostle, Nick; Wilby, Andrew; Bardgett, Richard D

    2014-03-01

    Ecosystems provide multiple services upon which humans depend. Understanding the drivers of the ecosystem functions that support these services is therefore important. Much research has investigated how species richness influences functioning, but we lack knowledge of how other community attributes affect ecosystem functioning. Species evenness, species spatial arrangement, and the identity of dominant species are three attributes that could affect ecosystem functioning, by altering the relative abundance of functional traits and the probability of synergistic species interactions such as facilitation and complementary resource use. We tested the effect of these three community attributes and their interactions on ecosystem functions over a growing season, using model grassland communities consisting of three plant species from three functional groups: a grass (Anthoxanthum odoratum), a forb (Plantago lanceolata), and a N-fixing forb (Lotus corniculatus). We measured multiple ecosystem functions that support ecosystem services, including ecosystem gas exchange, water retention, C and N loss in leachates, and plant biomass production. Species evenness and dominant species identity strongly influenced the ecosystem functions measured, but spatial arrangement had few effects. By the end of the growing season, evenness consistently enhanced ecosystem functioning and this effect occurred regardless of dominant species identity. The identity of the dominant species under which the highest level of functioning was attained varied across the growing season. Spatial arrangement had the weakest effect on functioning, but interacted with dominant species identity to affect some functions. Our results highlight the importance of understanding the role of multiple community attributes in driving ecosystem functioning. PMID:24213721

  4. 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. PMID:23589258

  5. Effects of species evenness and dominant species identity on multiple ecosystem functions in model grassland communities.

    PubMed

    Orwin, Kate H; Ostle, Nick; Wilby, Andrew; Bardgett, Richard D

    2014-03-01

    Ecosystems provide multiple services upon which humans depend. Understanding the drivers of the ecosystem functions that support these services is therefore important. Much research has investigated how species richness influences functioning, but we lack knowledge of how other community attributes affect ecosystem functioning. Species evenness, species spatial arrangement, and the identity of dominant species are three attributes that could affect ecosystem functioning, by altering the relative abundance of functional traits and the probability of synergistic species interactions such as facilitation and complementary resource use. We tested the effect of these three community attributes and their interactions on ecosystem functions over a growing season, using model grassland communities consisting of three plant species from three functional groups: a grass (Anthoxanthum odoratum), a forb (Plantago lanceolata), and a N-fixing forb (Lotus corniculatus). We measured multiple ecosystem functions that support ecosystem services, including ecosystem gas exchange, water retention, C and N loss in leachates, and plant biomass production. Species evenness and dominant species identity strongly influenced the ecosystem functions measured, but spatial arrangement had few effects. By the end of the growing season, evenness consistently enhanced ecosystem functioning and this effect occurred regardless of dominant species identity. The identity of the dominant species under which the highest level of functioning was attained varied across the growing season. Spatial arrangement had the weakest effect on functioning, but interacted with dominant species identity to affect some functions. Our results highlight the importance of understanding the role of multiple community attributes in driving ecosystem functioning.

  6. Species detection and individual assignment in species delimitation: can integrative data increase efficacy?

    PubMed

    Edwards, Danielle L; Knowles, L Lacey

    2014-02-22

    Statistical species delimitation usually relies on singular data, primarily genetic, for detecting putative species and individual assignment to putative species. Given the variety of speciation mechanisms, singular data may not adequately represent the genetic, morphological and ecological diversity relevant to species delimitation. We describe a methodological framework combining multivariate and clustering techniques that uses genetic, morphological and ecological data to detect and assign individuals to putative species. Our approach recovers a similar number of species recognized using traditional, qualitative taxonomic approaches that are not detected when using purely genetic methods. Furthermore, our approach detects groupings that traditional, qualitative taxonomic approaches do not. This empirical test suggests that our approach to detecting and assigning individuals to putative species could be useful in species delimitation despite varying levels of differentiation across genetic, phenotypic and ecological axes. This work highlights a critical, and often overlooked, aspect of the process of statistical species delimitation-species detection and individual assignment. Irrespective of the species delimitation approach used, all downstream processing relies on how individuals are initially assigned, and the practices and statistical issues surrounding individual assignment warrant careful consideration.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. [Caucasian cryptic species of rodents as models for studying the problem of species and speciation].

    PubMed

    Baskevich, M I; Potapov, S G; Mironova, T A

    2015-01-01

    The problem of species and speciation is considered using as a model the cryptic species of rodents inhabiting the Caucasus, the mountain chain with prominent altitude environmental gradient and insular pattern of mountain habitats. These circumstances open additional possibilities for the choice of species conception (biological or phylogenetic), exploration of ancestry pathways (sympatric or allopatric speciation) of model cryptic species groups, and testing the 'refuge' hypothesis. As model species, sibling-species Sicista from the group 'caucasica' (a group of unstriped birch mice) and representatives of the vole subspecies Terricola (Microtus, Arvicolinae) were used. Based on the new data on karyology, nucleotide sequences of mitochondrial gene cytb, multivariate statistical analysis of odontologic traits, and biogeography of sibling-species Sicista from the group 'caucasica' and voles from subspecies Terricola (Microtus, Arvicolinae), their evolutionary history is reconstructed and applicable species concepts are examined. For the present sibling-species Sicista from the group 'caucasica' the allopatric dispersion is typical, which agrees with the hypothesis of speciation in refuges. The sympatry of Terricola sibling-species in the Caucasus is considered as being secondary, and their phenotypic likeness--as an adaptation to similar environmental conditions. Affirmed coexistence of sibling-species Microtus (Terricola) majori and Microtus (Terricola) daghestanicus in the Caucasus (without their hybridization) supports the biological conception of species. The existence of Sicista allospecies from the group of Caucasian unstriped birch mice is best conformed to the phylogenetic conception. However, the high level of chromosomal differences between sibling-species and, in particular, between extreme variants of common evolutionary line (Sicista kazbegica, Sicista kluchorica) does not contradict the biological conception of species. PMID:26353399

  12. 76 FR 68776 - Invasive Species Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-07

    ... is to provide national leadership regarding invasive species issues. Purpose of Meeting: The meeting... will be no ISAC business conducted during the orientation session, which is closed to the public....

  13. 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.

  14. 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.

  15. 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... ecosystem level; or that, (2) holistically address prevention, eradication, control and...

  16. 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.

  17. Ecological and evolutionary insights from species invasions.

    PubMed

    Sax, Dov F; Stachowicz, John J; Brown, James H; Bruno, John F; Dawson, Michael N; Gaines, Steven D; Grosberg, Richard K; Hastings, Alan; Holt, Robert D; Mayfield, Margaret M; O'Connor, Mary I; Rice, William R

    2007-09-01

    Species invasions provide numerous unplanned and frequently, but imperfectly, replicated experiments that can be used to better understand the natural world. Classic studies by Darwin, Grinnell, Elton and others on these species-invasion experiments provided invaluable insights for ecology and evolutionary biology. Recent studies of invasions have resulted in additional insights, six of which we discuss here; these insights highlight the utility of using exotic species as 'model organisms'. We also discuss a nascent hypothesis that might provide a more general, predictive understanding of invasions and community assembly. Finally, we emphasize how the study of invasions can help to inform our understanding of applied problems, such as extinction, ecosystem function and the response of species to climate change.

  18. 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).

  19. 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.

  20. 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.

  1. 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.

  2. 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)

  3. 75 FR 29359 - Invasive Species Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-25

    ... of the Interior, the Secretary of Agriculture, and the Secretary of Commerce. The duty of the Council.../coastal environments in the world, with over 50 invasive species that threaten the Bay's vibrant...

  4. 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. PMID:25312414

  5. New species of Polysphondylium from Madagascar.

    PubMed

    Cavender, James C; Landolt, John C; Romeralo, Maria; Perrigo, Allison; Vadell, Eduardo M; Stephenson, Steven L

    2016-01-01

    Two series of samples collected for isolation of dictyostelid cellular slime molds (dictyostelids) in Madagascar yielded a relatively large number of isolates of Polysphondylium. Most of these turned out to be species new to science that show varying degrees of clustering from unclustered to coremiform as well as an ability to migrate. Migratory ability (phototaxis) is a common feature of species assigned to Group 2 of the Polysphondylia and is common in the new species from Madagascar. Another common feature, clustering, appears to be a strategy for keeping fruiting bodies erect for a longer time in a climate that is relatively dry, whereas migratory ability may function seasonally when there is more rainfall. Thirteen species are described herein. Each of these is characterized by a particular set of distinguishing features, and collectively they expand our concept of the genus Polysphondylium. PMID:26490703

  6. 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

  7. Species Diversity of Hypogeous Ascomycetes in Israel

    PubMed Central

    Wasser, Solomon P.

    2010-01-01

    We conducted a species diversity study of the hypogeous Ascomycetes of Israel. The hypogeous Ascomycetes in Israel include members of the families Pyronemataceae, Pezizaceae, and Tuberaceae, which are represented by seven species: Hydnocystis piligera, Terfezia arenaria, T. claveryi, T. oligosperma, Tirmania africana, Tuber asa, and T. nitidum; only T. asa is new to Israeli mycobiota. Synonymy, locations, collection data, general distribution, distribution in Israel, descriptions, a key to identification, illustrations, and taxonomic remarks are provided. PMID:23956647

  8. 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.

  9. New species of Aspergillus producing sterigmatocystin.

    PubMed Central

    Rabie, C J; Steyn, M; van Schalkwyk, G C

    1977-01-01

    A number of species belonging to the genus Aspergillus were evaluated for their toxicity to ducklings and the ability to produce sterigmatocystin. Three new species capable of producing sterigmatocystin were found, namely, Aspergillus aurantio-brunneus, Aspergillus quadrilineatus, and Aspergillus ustus. All three were toxic to ducklings. The production of sterigmatocystin by Aspergillus rugulosus was confirmed, and the toxicity of Aspergillus stellatus and Aspergillus multicolor is described. PMID:406838

  10. 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. PMID:24372907

  11. 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

  12. Species diversity of hypogeous ascomycetes in Israel.

    PubMed

    Barseghyan, Gayane S; Wasser, Solomon P

    2010-09-01

    We conducted a species diversity study of the hypogeous Ascomycetes of Israel. The hypogeous Ascomycetes in Israel include members of the families Pyronemataceae, Pezizaceae, and Tuberaceae, which are represented by seven species: Hydnocystis piligera, Terfezia arenaria, T. claveryi, T. oligosperma, Tirmania africana, Tuber asa, and T. nitidum; only T. asa is new to Israeli mycobiota. Synonymy, locations, collection data, general distribution, distribution in Israel, descriptions, a key to identification, illustrations, and taxonomic remarks are provided. PMID:23956647

  13. Supercritical fluid extraction of mercury species.

    PubMed

    Foy, G P; Pacey, G E

    2003-12-23

    Supercritical fluid extraction was used to recover organic and inorganic mercury species. Variations in pressure, water, methanol, and chelator create methods that allowed separation of inorganic from organic mercury species. When extracted using a compromised set of extraction conditions, the order of extraction was methyl, phenyl and inorganic mercury. For the individually optimized conditions, quantitative recoveries were observed. Level as low as 20 ppb were extracted and then determined using ICP.

  14. Comparative Chloroplast Genomes of Camellia Species

    PubMed Central

    Li, Hong-Tao; Yang, Jing; Li, De-Zhu

    2013-01-01

    Background Camellia, comprising more than 200 species, is a valuable economic commodity due to its enormously popular commercial products: tea leaves, flowers, and high-quality edible oils. It is the largest and most important genus in the family Theaceae. However, phylogenetic resolution of the species has proven to be difficult. Consequently, the interspecies relationships of the genus Camellia are still hotly debated. Phylogenomics is an attractive avenue that can be used to reconstruct the tree of life, especially at low taxonomic levels. Methodology/Principal Findings Seven complete chloroplast (cp) genomes were sequenced from six species representing different subdivisions of the genus Camellia using Illumina sequencing technology. Four junctions between the single-copy segments and the inverted repeats were confirmed and genome assemblies were validated by PCR-based product sequencing using 123 pairs of primers covering preliminary cp genome assemblies. The length of the Camellia cp genome was found to be about 157kb, which contained 123 unique genes and 23 were duplicated in the IR regions. We determined that the complete Camellia cp genome was relatively well conserved, but contained enough genetic differences to provide useful phylogenetic information. Phylogenetic relationships were analyzed using seven complete cp genomes of six Camellia species. We also identified rapidly evolving regions of the cp genome that have the potential to be used for further species identification and phylogenetic resolution. Conclusions/Significance In this study, we wanted to determine if analyzing completely sequenced cp genomes could help settle these controversies of interspecies relationships in Camellia. The results demonstrate that cp genome data are beneficial in resolving species definition because they indicate that organelle-based “barcodes”, can be established for a species and then used to unmask interspecies phylogenetic relationships. It reveals that

  15. Raman spectroscopy for identification of wood species

    NASA Astrophysics Data System (ADS)

    Gerasimov, V. A.; Gurovich, A. M.; Kostrin, D. K.; Selivanov, L. M.; Simon, V. A.; Stuchenkov, A. B.; Paltcev, A. V.; Uhov, A. A.

    2016-08-01

    This article discusses the application of Raman spectroscopy for identification of wood species. Use of Raman spectroscopy allows increasing the certainty of determining the type of wood compared to the analysis of spectra of diffuse reflectance. Raman spectrums of different wood samples when irradiated by laser radiation are shown. Ways to improve the determination reliability of wood species due to the modernization of the identification technique are discussed. The stages of data processing, allowing carrying out correct further analysis are described.

  16. 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

    2016-07-01

    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.

  17. How selection structures species abundance distributions

    PubMed Central

    Magurran, Anne E.; Henderson, Peter A.

    2012-01-01

    How do species divide resources to produce the characteristic species abundance distributions seen in nature? One way to resolve this problem is to examine how the biomass (or capacity) of the spatial guilds that combine to produce an abundance distribution is allocated among species. Here we argue that selection on body size varies across guilds occupying spatially distinct habitats. Using an exceptionally well-characterized estuarine fish community, we show that biomass is concentrated in large bodied species in guilds where habitat structure provides protection from predators, but not in those guilds associated with open habitats and where safety in numbers is a mechanism for reducing predation risk. We further demonstrate that while there is temporal turnover in the abundances and identities of species that comprise these guilds, guild rank order is conserved across our 30-year time series. These results demonstrate that ecological communities are not randomly assembled but can be decomposed into guilds where capacity is predictably allocated among species. PMID:22787020

  18. 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

    2016-07-01

    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

  19. 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.

  20. 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