Spectroscopy of five V-type asteroids in the middle and outer main belt

NASA Astrophysics Data System (ADS)

Migliorini, Alessandra; De Sanctis, M. C.; Lazzaro, D.; Ammannito, E.

2018-03-01

The origin of basaltic asteroids found in the middle and outer main belt is an open question. These asteroids are not dynamically linked to the Vesta collisional family and can be the remnants of other large differentiated asteroids present in the early phases of the main belt but destroyed long ago. Spectroscopic investigation of some V-type asteroids in the middle-outer belt, classified as such by their SLOAN photometric colours (Ivezić et al.) and WISE albedos (Masiero et al.), has revealed that their spectra are more similar to other taxonomic classes, like -Q, R, S, or A (Jasmim et al. and Oszkiewicz et al.). Here, we report about the observation, in the near-infrared spectral range, of five V-type asteroids located beyond 2.5 au. These observations allowed us to infer their taxonomic classification. Two asteroids, (21238) Panarea (observed in a previous campaign but here included for comparison) and (105041) 2000 KO41, confirm their basaltic nature. For asteroids (10800) 1992 OM8 and (15898) Kharasterteam a taxonomic classification is more uncertain, being either Q- or S-type. Asteroid (14390) 1990 QP10 classification is difficult to ascribe to the known taxonomic classes, maybe due to the low-quality spectrum. Further observations are desirable for this asteroid.

A gilled mushroom, Gerontomyces lepidotus gen. et sp. nov. (Basidiomycota: Agaricales), in Baltic amber.

PubMed

Poinar, George

2016-09-01

A densely scaled small mushroom in Baltic amber is described as Gerontomyces lepidotus gen. et sp. nov. and is characterized by a convex pileus 1.0 mm in diameter, distant to subdistant lamellae with smooth margins and a centrally inserted cylindrical, solid stipe. Its taxonomic placement is uncertain. This is the first mushroom described from Baltic amber. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Genetic diversity, structure, and patterns of differentiation in the genus vitis

USDA-ARS?s Scientific Manuscript database

Vitis (Vitaceae) is a taxonomically complicated genus with ca. 60 taxa divided into two subgenera, Vitis and Muscadinia. We used population genetic approaches to gain insights into the genetic diversity, patterns of evolutionary differentiation and to decipher the taxonomic status of some of the con...

MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences.

PubMed

Horton, Matthew; Bodenhausen, Natacha; Bergelson, Joy

2010-02-15

We have created a suite of Java-based software to better provide taxonomic assignments to DNA sequences. We anticipate that the program will be useful for protistologists, virologists, mycologists and other microbial ecologists. The program relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manipulated at the command-line to specify a BLAST candidate's query-coverage or percent identity requirements; other options include the ability to set minimal consensus requirements (%) for each of the eight major taxonomic ranks (Domain, Kingdom, Phylum, ...) and whether to consider lower scoring candidates when the top-hit lacks taxonomic classification.

[Taxonomic theory for non-classical systematics].

PubMed

Pavlinov, I Ia

2012-01-01

Outlined briefly are basic principles of construing general taxonomic theory for biological systematics considered in the context of non-classical scientific paradigm. The necessity of such kind of theory is substantiated, and some key points of its elaboration are exposed: its interpretation as a framework concept for the partial taxonomic theories in various schools of systematics; elaboration of idea of cognitive situation including three interrelated components, namely subject, object, and epistemic ones; its construing as a content-wisely interpreted quasi-axiomatics, with strong structuring of its conceptual space including demarcation between axioms and inferring rules; its construing as a "conceptual pyramid" of concepts of various levels of generality; inclusion of a basic model into definition of the taxonomic system (classification) regulating its content. Two problems are indicated as fundamental: definition of taxonomic diversity as a subject domain for the systematics as a whole; definition of onto-epistemological status of taxonomic system (classification) in general and of taxa in particular.

Taxonomic status of Parotia berlepschi Kleinschmidt, 1897 based on analysis of external appearance, voice and behavior (Aves: Paradisaeidae).

PubMed

Scholes, Edwin; Beehler, Bruce M; Laman, Timothy G

2017-10-10

Described from trade-skins of unknown origins, Parotia berlepschi Kleinschmidt, 1897 was the subject of a longstanding ornithological mystery that remained unresolved for well over a century. With few specimens and no known wild population, most taxonomic assessments over the last century have treated P. berlepschi as a subspecies of Parotia carolae Meyer, 1894. Following discovery of its geographical home in 2005, most authorities returned to giving P. berlepschi full species status. However, evidence supporting the delineation of P. berlepschi from P. carolae has not yet been fully articulated in the literature. Here, we assess phenotypic differentiation and the taxonomic status of P. berlepschi relative to P. carolae based on specimens and recordings of wild birds. With regard to external appearance and voice, which are important intersexual signals among polygynous birds-of-paradise, our analysis confirms that P. berlepschi is well-differentiated from P. carolae and should be treated as specifically distinct. Evidence for differentiation in courtship behavior is inconclusive and requires further study.

Knowledge Management in Taxonomy and Biostratigraphy using TaxonConcept Software

NASA Astrophysics Data System (ADS)

Klump, J.; Huber, R.; Goetz, S.

2005-12-01

The use of fossils to constrain age models for geological samples is not as straightforward as it might seem. Even though index fossils have been defined as biostratigraphic time markers ambiguity arises from the synonymous use of taxonomic names. Progress in our understanding of the origin of certain species have sometimes lead to substantial changes in the taxonomic classification of these organisms. TaxonConcept was created as part of the Stratigraphy.net initiative as a tool to manage taxonomic information and complex knowledge networks to help resolve taxonomic ambiguities in biostratigraphy. Its workflow is based on the principles of open nomenclature. Open nomenclature allows researchers to comment on the identification of a specimen which cannot exactly be determined and is frequently used in synonymy lists. The use of such synonymy lists in TaxonConcept allows to work with taxonomic classifications that are uncertain, or where several versions exist. Every single taxonomic entity in TaxonConcept is recorded with its relevant citations in the literature. This allows to manage information on taxonomy. The members of working groups using TaxonConcept can record their opinion on the taxonomic classification of each taxon in the framework of open nomenclature and annotate it in free text. This managed and structured collection of taxonomic opinions is an example of knowledge management. Taxonomic opinions are otherwise dispersed throughout the literature, if recorded at all, and are only available to the specialist. Assembled as a collection, they represent our knowledge on the taxonomy of a certain group of organisms. In the terminology of computer science, the semantic relationships between taxonomic terms are an ontology. Open nomenclature offers a formal framework that lends itself very well to describe the nature of the relations between taxonomic terms. The use of such synonymy lists in a taxonomic information system allows interesting search options, ranging from tracking name changes to the investigation of complex taxonomic topologies. In addition to its synonymy and literature management, TaxonConcept allows to store many other information categories such as textual descriptions (e.g. diagnoses and comments), images, bioevents and specimen and collection data. Ecological information is scheduled for a later stage of the project. Already now TaxonConcept is linked to taxon names in paleoenvironmental data of the World Data Center for Marine Environmental Sciences (WDC-MARE), interfaces to other databases are planned. WDC-MARE stores environmental, marine and geological research data and frequently uses taxon names in its parameters. By linking TaxonConcept and WDC-MARE, synonymous names can be included in queries, e.g. when researching for stable isotope data measured on microfossils. TaxonConcept is not a project on authoritative taxonomic information, but is a tool for taxonomic projects to use to find a taxonomic consensus, e.g. to define a taxonomic framework for biostratigraphic studies. Both, the project specific hierarchical classification of selected taxa, as well as a project specific selection of any other information categories is supported by TaxonConcept. The results of such a taxonomic consensus can be used to create Fossilium Catalogus style summaries in various output formats which can later be used to create online or print publications.

AnthWest, occurrence records for wool carder bees of the genus Anthidium (Hymenoptera, Megachilidae, Anthidiini) in the Western Hemisphere.

PubMed

Griswold, Terry; Gonzalez, Victor H; Ikerd, Harold

2014-01-01

This paper describes AnthWest, a large dataset that represents one of the outcomes of a comprehensive, broadly comparative study on the diversity, biology, biogeography, and evolution of Anthidium Fabricius in the Western Hemisphere. In this dataset a total of 22,648 adult occurrence records comprising 9657 unique events are documented for 92 species of Anthidium, including the invasive range of two introduced species from Eurasia, A. oblongatum (Illiger) and A. manicatum (Linnaeus). The geospatial coverage of the dataset extends from northern Canada and Alaska to southern Argentina, and from below sea level in Death Valley, California, USA, to 4700 m a.s.l. in Tucumán, Argentina. The majority of records in the dataset correspond to information recorded from individual specimens examined by the authors during this project and deposited in 60 biodiversity collections located in Africa, Europe, North and South America. A fraction (4.8%) of the occurrence records were taken from the literature, largely California records from a taxonomic treatment with some additional records for the two introduced species. The temporal scale of the dataset represents collection events recorded between 1886 and 2012. The dataset was developed employing SQL server 2008 r2. For each specimen, the following information is generally provided: scientific name including identification qualifier when species status is uncertain (e.g. "Questionable Determination" for 0.4% of the specimens), sex, temporal and geospatial details, coordinates, data collector, host plants, associated organisms, name of identifier, historic identification, historic identifier, taxonomic value (i.e., type specimen, voucher, etc.), and repository. For a small portion of the database records, bees associated with threatened or endangered plants (~ 0.08% of total records) as well as specimens collected as part of unpublished biological inventories (~17%), georeferencing is presented only to nearest degree and the information on floral host, locality, elevation, month, and day has been withheld. This database can potentially be used in species distribution and niche modeling studies, as well as in assessments of pollinator status and pollination services. For native pollinators, this large dataset of occurrence records is the first to be simultaneously developed during a species-level systematic study.

Selection and validation of an AFLP marker core collection for the wild potato Solanum microdontum

USDA-ARS?s Scientific Manuscript database

Solanum microdontum is a diploid potato species with features that make it a good model for research into management and use of germplasm in the genebank. Its taxonomic status is unambiguous and it is in the taxonomic series of wild species closest to cultivated forms. It is represented by about 100...

The gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis contains a group I intron.

PubMed Central

De Wachter, R; Neefs, J M; Goris, A; Van de Peer, Y

1992-01-01

The nucleotide sequence of the gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis was determined. It revealed the presence of a group I intron with a length of 411 nucleotides. This is the third occurrence of such an intron discovered in a small subunit rRNA gene encoded by a eukaryotic nuclear genome. The other two occurrences are in Pneumocystis carinii, a fungus of uncertain taxonomic status, and Ankistrodesmus stipitatus, a green alga. The nucleotides of the conserved core structure of 101 group I intron sequences present in different genes and genome types were aligned and their evolutionary relatedness was examined. This revealed a cluster including all group I introns hitherto found in eukaryotic nuclear genes coding for small and large subunit rRNAs. A secondary structure model was designed for the area of the Ustilago maydis small ribosomal subunit RNA precursor where the intron is situated. It shows that the internal guide sequence pairing with the intron boundaries fits between two helices of the small subunit rRNA, and that minimal rearrangement of base pairs suffices to achieve the definitive secondary structure of the 18S rRNA upon splicing. PMID:1561081

POPULATION GENETICS OF THE MOSQUITO CULEX PIPIENS PALLENS REVEALS SEX-LINKED ASYMMETRIC INTROGRESSION BY CULEX QUINQUEFASCIATUS

PubMed Central

Fonseca, Dina M.; Smith, Julie L.; Kim, Heung-Chol; Mogi, Motoyoshi

2009-01-01

The Culex pipiens complex in Asia includes a temperate subspecies, Culex pipiens pallens, of uncertain taxonomic status. The shape of the male genitalia suggests it is a hybrid between Cx. pipiens and Cx. quinquefasciatus. We studied populations of Cx. p. pallens in Japan, Korea, and China and compared them to local populations of Cx. quinquefasciatus and Cx. p. pipiens. We examined variation in a nuclear intron in the acetylcholinesterase-2 gene [ACE] and eight microsatellite loci. We found a distinct microsatellite signature for Cx. p. pallens indicating restricted gene flow between Eastern and Western populations of Cx. pipiens, supporting the existence of two subspecies. Furthermore, a multilocus genotype analysis revealed current hybridization between Cx. p. pallens and Cx. quinquefasciatus in southern Japan, Republic of Korea, and China but not in Hokkaido, in northern Japan. Surprisingly, however, we found that the sex-linked ACE locus in chromosome I has introgressed asymmetrically through the males such that all male Cx. p. pallens have a copy of the Cx. quinquefasciatus ACE locus. This result highlights some of the potential consequences of hybridization between local and introduced species to disease transmission worldwide. PMID:19584006

Insights into assessing water quality using taxonomic distinctness based on a small species pool of biofilm-dwelling ciliate fauna in coastal waters of the Yellow Sea, northern China.

PubMed

Zhang, Wei; Liu, Yuanyuan; Warren, Alan; Xu, Henglong

2014-12-15

The aim of this study is to determine the feasibility of using a small species pool from a raw dataset of biofilm-dwelling ciliates for bioassessment based on taxonomic diversity. Samples were collected monthly at four stations within a gradient of environmental stress in coastal waters of the Yellow Sea, northern China from August 2011 to July 2012. A 33-species subset was identified from the raw 137-species dataset using a multivariate method. The spatial patterns of this subset were significantly correlated with the changes in the nutrients and chemical oxygen demand. The taxonomic diversity indices were significantly correlated with nutrients. The pair-wise indices of average taxonomic distinctness (Δ(+)) and the taxonomic distinctness (Λ(+)) showed a clear departure from the expected taxonomic pattern. These findings suggest that this small ciliate assemblage might be used as an adequate species pool for discriminating water quality status based on taxonomic distinctness in marine ecosystems. Copyright © 2014 Elsevier Ltd. All rights reserved.

Application of an indicator based on taxonomic relatedness of ciliated protozoan assemblages for marine environmental assessment.

PubMed

Xu, Henglong; Jiang, Yong; Al-Rasheid, Khaled A S; Al-Farraj, Saleh A; Song, Weibo

2011-08-01

Ciliated protozoa play important roles in aquatic ecosystems especially regarding their functions in micro-food web and have many advantages in environmental assessment compared with most other eukaryotic organisms. The aims of this study were focused on analyzing the application of an indicator based on taxonomic relatedness of ciliated protozoan assemblages for marine environmental assessment. The spatial taxonomic patterns and diversity measures in response to physical-chemical variables were studied based on data from samples collected during 1-year cycle in the semi-enclosed Jiaozhou Bay, northern China. The spatial patterns of ciliate communities were significantly correlated with the changes of environmental status. The taxonomic distinctness (Δ*) and the average taxonomic distinctness (Δ+) were significantly negatively correlated with the changes of nutrients (e.g., nitrate nitrogen and soluble active phosphate; P<0.05). Pairwise indices of Δ+ and the variation in taxonomic distinctness (Λ+) showed a decreasing trend of departure from the expected taxonomic breadth in response to the eutrophication stress and anthropogenic impact. The taxonomic relatedness (especially the pairwise Δ+ and Λ+) indices of ciliate communities are robust as an indicator with scientifically operational value in marine environmental assessment.

DNA Barcodes Confirm the Taxonomic and Conservation Status of a Species of Tree on the Brink of Extinction in the Pacific.

PubMed

Costion, Craig M; Kress, W John; Crayn, Darren M

2016-01-01

The taxonomic status of a single island, narrow range endemic plant species from Palau, Micronesia (Timonius salsedoi) was assessed using DNA barcode markers, additional plastid loci, and morphology in order to verify its conservation status. DNA barcode loci distinguished T. salsedoi from all other Timonius species sampled from Palau, and were supported by sequence data from the atpB-rbcL intergenic spacer region. Timonius salsedoi was only known from two mature individual trees in 2012. Due to its extremely narrow range and population size, it had previously been recommended to be listed as Critically Endangered Status under three separate IUCN Criteria. In 2014 a second survey of the population following a typhoon revealed that the only two known trees had died suggesting that this species may now be extinct. Comprehensive follow up surveys of suitable habitat for this species are urgently required.

On the taxonomic status of Gegeneophis nadkarnii Bhatta & Prashanth, 2004 (Amphibia: Gymnophiona: Indotyphlidae).

PubMed

Gower, David J; Giri, Varad; Torsekar, Varun R; Gaikwad, Kshamata

2013-01-29

Examination of type material and new collections from Goa, southern Maharashtra and northern Karnataka, leads to the conclusion that Gegeneophis nadkarnii Bhatta & Prashanth, 2004 is a subjective junior synonym of Gegeneophis danieli Giri, Wilkinson & Gower, 2003. The purported differences between these species are very minor and attributable to nor-mal individual variation, except for some features of the dentition that are peculiar to the exceptionally abnormal paratype of G. nadkarnii. This taxonomic revision extends the known geographic range of G. danieli and suggests it could be trans-ferred from Data Deficient to Least Concern status in the IUCN Red List.

Characterization of Lake Michigan coastal lakes using zooplankton assemblages

USGS Publications Warehouse

Whitman, Richard L.; Nevers, Meredith B.; Goodrich, Maria L.; Murphy, Paul C.; Davis, Bruce M.

2004-01-01

Zooplankton assemblages and water quality were examined bi-weekly from 17 April to 19 October 1998 in 11 northeastern Lake Michigan coastal lakes of similar origin but varied in trophic status and limnological condition. All lakes were within or adjacent to Sleeping Bear Dunes National Lakeshore, Michigan. Zooplankton (principally microcrustaceans and rotifers) from triplicate Wisconsin net (80 I?m) vertical tows taken at each lake's deepest location were analyzed. Oxygen-temperature-pH-specific conductivity profiles and surface water quality were concurrently measured. Bray-Curtis similarity analysis showed small variations among sample replicates but large temporal differences. The potential use of zooplankton communities for environmental lake comparisons was evaluated by means of BIOENV (Primer 5.1) and principal component analyses. Zooplankton analyzed at the lowest identified taxonomic level yielded greatest sensitivity to limnological variation. Taxonomic and ecological aggregations of zooplankton data performed comparably, but less well than the finest taxonomic analysis. Secchi depth, chlorophyll a, and sulfate concentrations combined to give the best correlation with patterns of variation in the zooplankton data set. Principal component analysis of these variables revealed trophic status as the most influential major limnological gradient among the study lakes. Overall, zooplankton abundance was an excellent indicator of variation in trophic status.

Taxonomic status and paleoecology of Rusingoryx atopocranion (Mammalia, Artiodactyla), an extinct Pleistocene bovid from Rusinga Island, Kenya

NASA Astrophysics Data System (ADS)

Faith, J. Tyler; Choiniere, Jonah N.; Tryon, Christian A.; Peppe, Daniel J.; Fox, David L.

2011-05-01

Rusingoryx atopocranion is a poorly known extinct alcelaphine bovid, documented in Pleistocene deposits associated with Middle Stone Age artifacts on Rusinga Island, Kenya. Following its initial description, Rusingoryx was subsumed into Megalotragus, which includes the extinct giant wildebeests, on the basis of its cranial architecture. Renewed investigations of the Pleistocene deposits on Rusinga Island recovered a large sample of Rusingoryx specimens that provide new taxonomic and paleoecological insight. This study (1) reviews the morphological and phylogenetic evidence concerning the taxonomic status of Rusingoryx and (2) evaluates its paleoecology and dietary habits . The morphology and phylogenetic data indicate that Rusingoryx is distinct from Megalotragus; they likely shared a common ancestor in the late Pliocene. Ecomorphology and mesowear analysis point to a specialized grazing adaptation, and its association with arid-adapted ungulates suggests a preference for arid grasslands. The confirmation of Rusingoryx as a valid taxonomic entity, together with the presence of other extinct taxa (including Megalotragus) on Rusinga Island, suggests an increasingly complex pattern of ungulate biogeography and extinctions in the late Quaternary of East Africa. Rusingoryx appears to have been part of an arid-adapted faunal community that potentially persisted in East Africa until the onset of the Holocene.

A distinct species, Dodona formosana, detected in the Dodona eugenes species complex: clarification of the taxonomic status of the Punch butterfly in Taiwan

PubMed Central

Wu, Li-Wei; Lin, Wen-Jie; Hsu, Yu-Feng

2018-01-01

Abstract The Tailed Punch, Dodona eugenes, is widely distributed in East Asia with seven subspecies currently recognized. However, two of them, namely ssp. formosana and ssp. esakii found in Taiwan, are hard to distinguish from each other due to ambiguous diagnostic characters. In this study, their taxonomic status is clarified by comparing genitalia characters and phylogenetic relationships based on mitochondrial sequences, COI and COII (total 2211 bps). Our results show that there is no reliable feature to separate these two subspecies. Surprisingly we found that Dodona in Taiwan is more closely related to the Orange Punch, D. egeon, than to other subspecies of D. eugenes. Therefore, the following nomenclatural changes are proposed: Dodona eugenes formosana is revised to specific status as Dodona formosana Matsumura, 1919, stat. rev, and ssp. esakii is sunk to a junior synonym of Dodona formosana syn. n. PMID:29674868

Synopsis of Dorstenia (Moraceae) in Rio Grande do Sul, Southern Brazil.

PubMed

Boeni, Bruna De Oliveira; Singer, Rodrigo Bustos

2015-01-01

A taxonomic synopsis of Dorstenia (Moraceae) in Rio Grande do Sul (RS), Southern Brazil, is presented. Three species were recorded: D. brasiliensis, D. carautae, a new record for the state of RS, and D. tenuis. All species are described and illustrated through detailed photos of living specimens. A taxonomic key to separate the species, as well as details on distribution, overall phenology, habitat, conservation status and ecology are presented.

Taxonomic status of Ligophorus mugilinus (Hargis, 1955) (Monogenea: Ancyrocephalidae), with a description of a new species of Ligophorus from Mugil cephalus (Teleostei: Mugilidae) in the Mediterranean Basin.

PubMed

Sarabeev, Volodimir Leonidovich; Balbuena, Juan Antonio; Euzet, Louis

2005-12-01

Ligophorus mugilinus was originally described on the flathead mullet Mugil cephalus from the Gulf of Mexico. The species was later recorded in the Mediterranean Sea on the flathead mullet and in the Caribbean Sea on the white mullet Mugil curema. After examination of the type material and additional specimens of Ligophorus from the northwest Atlantic coast, the Caribbean Sea, and the Mediterranean and Black Sea, we observed morphological differences concerning haptoral and male copulatory structures between L. mugilinus from the northwest Atlantic and the forms from the Mediterranean and Black Seas. Accordingly, the latter specimens are described as a new species, Ligophorus mediterraneus n. sp. A redescription of L. mugilinus, including new morphometric data, is also given. The morphometric analysis of the Caribbean specimens suggested that their ascription to L. mugilinus is uncertain, but additional material is needed to clarify their specific identity. The results of this study, together with previous zoogeographical evidence, indicate that flathead mullets from different seas harbor different species complexes of Ligophorus. Given the coastal habits of the host, it is suggested that open oceans could act as geographical barriers favoring speciation within disjointed flathead mullet populations.

Evolutionary lineages of marine snails identified using molecular phylogenetics and geometric morphometric analysis of shells.

PubMed

Vaux, Felix; Trewick, Steven A; Crampton, James S; Marshall, Bruce A; Beu, Alan G; Hills, Simon F K; Morgan-Richards, Mary

2018-06-15

The relationship between morphology and inheritance is of perennial interest in evolutionary biology and palaeontology. Using three marine snail genera Penion, Antarctoneptunea and Kelletia, we investigate whether systematics based on shell morphology accurately reflect evolutionary lineages indicated by molecular phylogenetics. Members of these gastropod genera have been a taxonomic challenge due to substantial variation in shell morphology, conservative radular and soft tissue morphology, few known ecological differences, and geographical overlap between numerous species. Sampling all sixteen putative taxa identified across the three genera, we infer mitochondrial and nuclear ribosomal DNA phylogenetic relationships within the group, and compare this to variation in adult shell shape and size. Results of phylogenetic analysis indicate that each genus is monophyletic, although the status of some phylogenetically derived and likely more recently evolved taxa within Penion is uncertain. The recently described species P. lineatus is supported by genetic evidence. Morphology, captured using geometric morphometric analysis, distinguishes the genera and matches the molecular phylogeny, although using the same dataset, species and phylogenetic subclades are not identified with high accuracy. Overall, despite abundant variation, we find that shell morphology accurately reflects genus-level classification and the corresponding deep phylogenetic splits identified in this group of marine snails. Copyright © 2018 Elsevier Inc. All rights reserved.

Polychaetes of Greece: an updated and annotated checklist

PubMed Central

Simboura, Nomiki; Katsiaras, Nikolaos; Chatzigeorgiou, Giorgos; Arvanitidis, Christos

2017-01-01

Abstract Background The last annotated checklist of marine polychaetes in Greece was published in 2001. Since then, global taxonomic progress, combined with many new species records for Greece, required a thorough review of the taxonomic, nomenclatural and biogeographic status of the national species list. This checklist revises the status of all extant polychaete species reported from the Greek Exclusive Economic Zone since 1832. The work was undertaken as part of the efforts on compiling a national species inventory (Greek Taxon Information System initiative) in the framework of the LifeWatchGreece Research Infrastructure. New information This checklist comprises an updated and annotated inventory of polychaete species in Greek waters, compiled from literature reports, online databases, museum collections and unpublished datasets. The list provides information on 836 species-level taxa from Greece, of which 142 are considered questionable. An additional 84 species reported in the past are currently considered absent from Greece; reasons for the exclusion of each species are given. Fourteen species are reported here for the first time from Greek waters. At least 52 species in the present list constitute in fact a complex of cryptic or pseudo-cryptic species. Forty-seven species are considered non-native to the area. In addition to the species-level taxa reported in this checklist, eleven genera have been recorded from Greece with no representatives identified to species level. One replacement name is introduced. For each species, a comprehensive bibliographic list of occurrence records in Greece and the synonyms used in these publications are provided as supplementary material. Where necessary, the taxonomic, nomenclatural or biogeographic status is discussed. Finally, the findings are discussed in the wider context of Mediterranean polychaete biogeography, taxonomic practice and worldwide research progress. PMID:29362552

Taxonomic status and redescription of the genus Brasicystis Thatcher, 1979 (Digenea: Didymozoidae).

PubMed

Melo, Francisco Tiago de Vasconcelos; Silva, Jefferson Pereira E; Gonçalves, Evonnildo Costa; Furtado, Adriano Penha; Giese, Elane Guerreiro; Santos, Cláudia Portes; Santos, Jeannie Nascimento

2013-04-01

Brasicystis bennetti Thatcher, 1979 was first described from specimens obtained from the subcutaneous tissues of the mouth and operculum of Plagioscyion squamosissimus from the Amazon River in Brazil, however since 2008, Brasicystis has been considered a genus inquirendum. This study reviews some of the diagnostic characters from the original description of B. bennetti from the Amazon Delta, and redescribes the genus and species with a discussion of their taxonomic status. Ultrastructural and molecular approaches complement the data presented on this monotypic genus. The diagnosis of the tribe Didymozoini Monticelli, 1888 is amended to incorporate the genus Brasicystis, which is redescribed and revalidated here, with the proposal of an amended key. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

AnthWest, occurrence records for wool carder bees of the genus Anthidium (Hymenoptera, Megachilidae, Anthidiini) in the Western Hemisphere

PubMed Central

Griswold, Terry; Gonzalez, Victor H.; Ikerd, Harold

2014-01-01

Abstract This paper describes AnthWest, a large dataset that represents one of the outcomes of a comprehensive, broadly comparative study on the diversity, biology, biogeography, and evolution of Anthidium Fabricius in the Western Hemisphere. In this dataset a total of 22,648 adult occurrence records comprising 9657 unique events are documented for 92 species of Anthidium, including the invasive range of two introduced species from Eurasia, A. oblongatum (Illiger) and A. manicatum (Linnaeus). The geospatial coverage of the dataset extends from northern Canada and Alaska to southern Argentina, and from below sea level in Death Valley, California, USA, to 4700 m a.s.l. in Tucumán, Argentina. The majority of records in the dataset correspond to information recorded from individual specimens examined by the authors during this project and deposited in 60 biodiversity collections located in Africa, Europe, North and South America. A fraction (4.8%) of the occurrence records were taken from the literature, largely California records from a taxonomic treatment with some additional records for the two introduced species. The temporal scale of the dataset represents collection events recorded between 1886 and 2012. The dataset was developed employing SQL server 2008 r2. For each specimen, the following information is generally provided: scientific name including identification qualifier when species status is uncertain (e.g. “Questionable Determination” for 0.4% of the specimens), sex, temporal and geospatial details, coordinates, data collector, host plants, associated organisms, name of identifier, historic identification, historic identifier, taxonomic value (i.e., type specimen, voucher, etc.), and repository. For a small portion of the database records, bees associated with threatened or endangered plants (~ 0.08% of total records) as well as specimens collected as part of unpublished biological inventories (~17%), georeferencing is presented only to nearest degree and the information on floral host, locality, elevation, month, and day has been withheld. This database can potentially be used in species distribution and niche modeling studies, as well as in assessments of pollinator status and pollination services. For native pollinators, this large dataset of occurrence records is the first to be simultaneously developed during a species-level systematic study. PMID:24899835

Documenting persistence of most Eastern North American bee species (Hymenoptera: Apoidea: Anthophila) to 1990-2009

USDA-ARS?s Scientific Manuscript database

The status of wild bees, the major group of pollinators in most biomes, has gained recognition as an important ecological and economic issue. Insufficient baseline data and taxonomic expertise for this understudied group has hindered efforts to assess the conservation status of the majority of wild ...

Taxonomic status of Tropiocolotes cf. steudneri with a description of a new species of Tropiocolotes (Reptilia: Squamata: Gekkonidae) in southern Iran.

PubMed

Rajabizadeh, Mahdi; Faizi, Hiva; Anderson, Steven C; Zarrintab, Mohammad; Nazarov, Roman

2018-03-01

We review the status of an Iranian gecko population previously referred to Tropiocolotes cf. steudneri and describe it as a new species, Tropiocolotes hormozganensis sp. nov. We discuss the taxonomic history of this population and compare its characters with those of the other species in the genus. The new species is distinguished from other species of Tropiocolotes by possessing weakly keeled dorsal scales and smooth ventral scales, having imbricate scales on dorsal and ventral tail, possessing clearly tricarinatesubdigital scales, 48-55 dorsal scales, two pairs of postmental shields, of which the second pair is about half of the size of the first, 100-107 scales longitudinally along underside of body, 15-19 scales across head and 16-19 subdigital lamellae.

Sympatry in the Culicoides variipennis complex (Diptera: Ceratopogonidae): a taxonomic reassessment.

PubMed

Holbrook, F R; Tabachnick, W J; Schmidtmann, E T; McKinnon, C N; Bobian, R J; Grogan, W L

2000-01-01

We report sympatry among larval populations of the Culicoides variipennis complex in widespread and diverse aquatic habitats throughout the United States. Six sites in California, Nevada, New Mexico, and Texas were co-inhabited by C. v. occidentalis and C. v. sonorensis, whereas 8 sites in Florida, Georgia, Louisiana, Maryland, and Texas were co-occupied by C. v. sonorensis and C. v. variipennis. No intermediate forms were identified either electrophoretically or morphologically in adults reared from field-collected larvae and pupae. The absence of intergrades in zones of sympatry represents sufficient evidence to confirm species status for Culicoides variipennis (Coquillett) and Culicoides occidentalis Wirth & Jones, and to elevate Culicoides sonorensis to species rank (NEW STATUS). Culicoides v. albertensis Wirth & Jones is a synonym of C. sonorensis (NEW SYNONYMY); C. v. australis Wirth & Jones also is confirmed as a synonym of C. sonorensis. We also demonstrated a correlation between population taxonomic status as determined by electrophoresis and adult morphology.

Chilli anthracnose disease caused by Colletotrichum species.

PubMed

Than, Po Po; Prihastuti, Haryudian; Phoulivong, Sitthisack; Taylor, Paul W J; Hyde, Kevin D

2008-10-01

Anthracnose disease is one of the major economic constraints to chilli production worldwide, especially in tropical and subtropical regions. Accurate taxonomic information is necessary for effective disease control management. In the Colletotrichum patho-system, different Colletotrichum species can be associated with anthracnose of the same host. Little information is known concerning the interactions of the species associated with the chilli anthracnose although several Colletotrichum species have been reported as causal agents of chilli anthracnose disease worldwide. The ambiguous taxonomic status of Colletotrichum species has resulted in inaccurate identification which may cause practical problems in plant breeding and disease management. Although the management and control of anthracnose disease are still being extensively researched, commercial cultivars of Capsicum annuum that are resistant to the pathogens that cause chilli anthracnose have not yet been developed. This paper reviews the causal agents of chilli anthracnose, the disease cycle, conventional methods in identification of the pathogen and molecular approaches that have been used for the identification of Colletotrichum species. Pathogenetic variation and population structure of the causal agents of chilli anthracnose along with the current taxonomic status of Colletotrichum species are discussed. Future developments leading to the disease management strategies are suggested.

Chilli anthracnose disease caused by Colletotrichum species§

PubMed Central

Than, Po Po; Prihastuti, Haryudian; Phoulivong, Sitthisack; Taylor, Paul W.J.; Hyde, Kevin D.

2008-01-01

Anthracnose disease is one of the major economic constraints to chilli production worldwide, especially in tropical and subtropical regions. Accurate taxonomic information is necessary for effective disease control management. In the Colletotrichum patho-system, different Colletotrichum species can be associated with anthracnose of the same host. Little information is known concerning the interactions of the species associated with the chilli anthracnose although several Colletotrichum species have been reported as causal agents of chilli anthracnose disease worldwide. The ambiguous taxonomic status of Colletotrichum species has resulted in inaccurate identification which may cause practical problems in plant breeding and disease management. Although the management and control of anthracnose disease are still being extensively researched, commercial cultivars of Capsicum annuum that are resistant to the pathogens that cause chilli anthracnose have not yet been developed. This paper reviews the causal agents of chilli anthracnose, the disease cycle, conventional methods in identification of the pathogen and molecular approaches that have been used for the identification of Colletotrichum species. Pathogenetic variation and population structure of the causal agents of chilli anthracnose along with the current taxonomic status of Colletotrichum species are discussed. Future developments leading to the disease management strategies are suggested. PMID:18837103

A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites.

PubMed

Côté, Nathalie M L; Daligault, Julien; Pruvost, Mélanie; Bennett, E Andrew; Gorgé, Olivier; Guimaraes, Silvia; Capelli, Nicolas; Le Bailly, Matthieu; Geigl, Eva-Maria; Grange, Thierry

2016-01-01

Human gastrointestinal parasites are good indicators for hygienic conditions and health status of past and present individuals and communities. While microscopic analysis of eggs in sediments of archeological sites often allows their taxonomic identification, this method is rarely effective at the species level, and requires both the survival of intact eggs and their proper identification. Genotyping via PCR-based approaches has the potential to achieve a precise species-level taxonomic determination. However, so far it has mostly been applied to individual eggs isolated from archeological samples. To increase the throughput and taxonomic accuracy, as well as reduce costs of genotyping methods, we adapted a PCR-based approach coupled with next-generation sequencing to perform precise taxonomic identification of parasitic helminths directly from archeological sediments. Our study of twenty-five 100 to 7,200 year-old archeological samples proved this to be a powerful, reliable and efficient approach for species determination even in the absence of preserved eggs, either as a stand-alone method or as a complement to microscopic studies.

Habitat and conservation status of the beaver in the Sierra San Luis Sonora, Mexico

Treesearch

Karla Pelz Serrano; Eduardo Ponce Guevara; Carlos A. Lopez Gonzalez

2005-01-01

The status of beaver (Castor canadensis) in northeastern Sonora, Mexico, is uncertain. We surveyed the Cajon Bonito River to assess the beaver’s status and habitat and found five colonies. Limiting factors appear to be pollution due to animal waste, deforestation of riparian trees, and human exploitation. Beavers did not appear to require habitat...

The Evolution of Classroom Physics Knowledge in Relation to Certainty and Uncertainty

ERIC Educational Resources Information Center

Tiberghien, Andrée; Cross, David; Sensevy, Gérard

2014-01-01

This paper deals with the joint construction of knowledge by the teacher and the students in a physics classroom. It is focused on the status of epistemic certainty/uncertainty of knowledge. The same element of knowledge can be introduced as possible and thus uncertain and then evolve towards a status of epistemic certainty; the status of other…

Application of the Red-List Index at a national level for multiple species groups.

PubMed

Juslén, Aino; Hyvärinen, Esko; Virtanen, Laura K

2013-04-01

The International Union for Conservation of Nature (IUCN) Red List Index (RLI) is recognized as one of the key indicators of trends in the status of species. The red-list assessment done by Finnish authorities of species in Finland is taxonomically one of the most extensive national assessments. We used the Finnish Red Lists from 2000 and 2010 to calculate for the first time the national RLIs for 11 taxonomic groups at different trophic levels and with different life cycles. The red-list index is calculated on the basis of changes in red-list categories and indicates trends in the status of biological diversity of sets of species. The RLI value ranges from 0 to 1. The lower the value the faster the set of species is heading toward extinction. If the value is 1, all species in the set are least concern and if the value is 0, all species are (regionally) extinct. The overall RLI of Finnish species decreased. This means that, in Finland, these taxonomic groups were heading toward extinction faster in 2010 than in 2000. Of the analyzed groups of organisms, RLIs of 5 decreased and RLIs of 6 increased. At the national level, the RLIs and status trends varied markedly between species groups. Thus, we concluded that generalizations on the basis of RLIs of a few taxa only may yield a biased view of ongoing trends in the status of biological diversity at the species level. In addition, one overall RLI that includes many different species groups may also be misleading if variation in RLI among species groups is not considered and if RLI values are not presented separately for each group. © 2013 Society for Conservation Biology.

The hydrobioid freshwater gastropods (Caenogastropoda, Truncatelloidea) of Greece: new records, taxonomic re-assessments using DNA sequence data and an update of the IUCN Red List Categories

PubMed Central

Radea, Canella; Parmakelis, Aristeidis; Papadogiannis, Vassilis; Charou, Despoina; Triantis, Kostas A.

2013-01-01

Abstract Hydrobioid freshwater gastropods were collected from mainland and insular Greece. Several threatened taxa, such as Graecoanatolica vegorriticola, Pseudamnicola negropontina, Pseudamnicola pieperi, Pseudobithynia eubooensis and Pseudoislamia balcanica, were recorded from new localities. Trichonia trichonica, which has been considered extinct from its type locality for the last twenty eight years, was re-discovered, whereas the presence of Daphniola exigua, G. vegorriticola, Marstoniopsis graeca, P. pieperi and Pseudobithynia trichonis in their type localities was verified. The taxonomic status of P. negropontina and the newly discovered populations of G. vegorriticola was elucidated using COI sequence data. The new data recorded during this survey indicate that the IUCN status of some Greek endemic hydrobioids needs to be updated. PMID:24294081

Revision of the freshwater genus Atyaephyra (Crustacea, Decapoda, Atyidae) based on morphological and molecular data

PubMed Central

Christodoulou, Magdalini; Antoniou, Aglaia; Antonios Magoulas;  Athanasios Koukouras

2012-01-01

Abstract Atyaephyra de Brito Capello, 1867 was described from the Mediterranean region almost 200 years ago. Since then, the genus has been recorded from various freshwater habitats in Europe, North Africa and the Middle East. Despite its long history, the taxonomic status of Atyaephyra species remains confusing and uncertain. Consequently numerous specimens from the known range of Atyaephyra were analysed using morphological characters and mitochondrial COI sequences in an attempt to clarify the taxonomy of this genus. The present study recognises seven Atyaephyra species, more than twice as many as previously recorded (three), four of which are considered as new. The new species are described, additional information to the original descriptions are provided for the remaining three taxa, while neotypes of Atyaephyra desmarestii Millet, 1831 and Atyaephyra stankoi Karaman, 1972 are designated to stabilize their taxonomy. Non-overlapping distinguishing morphological characters are used to discriminate the examined material into five species, e.g., Atyaephyra desmarestii, Atyaephyra stankoi, Atyaephyra orientalis Bouvier, 1913, Atyaephyra thyamisensis sp. n., Atyaephyra strymonensis sp. n. In addition, the genetic analysis supports the existence of multiple phylogenetic clades in the broader Mediterranean area and distinguishes two new cryptic species, namely Atyaephyra tuerkayi sp. n. and Atyaephyra acheronensis sp. n. The geographic distribution of these species is confirmed and their phylogenetic relationships are described. PMID:23166474

The systematic position and structure of the genus Leyogonimus Ginetsinskaya, 1948 (Platyhelminthes: Digenea) with comments on the taxonomy of the superfamily Microphalloidea Ward, 1901.

PubMed

Kanarek, Gerard; Zaleśny, Grzegorz; Sitko, Jiljí; Tkach, Vasyl V

2017-09-26

The systematic position, phylogenetic relationships and composition of the genus Leyogonimus Ginetsinskaya, 1948 have always been uncertain. In the present study, we investigate the taxonomic position and phylogenetic relationships between the type-species L. polyoon (Linstow, 1887) and L. postgonoporus (Neiland, 1951) (previously classified as Macyella), based on newly obtained partial sequences of the nuclear large ribosomal subunit DNA. To test some of the previously proposed systematic arrangements, we have also sequenced specimens of Stomylotrema vicarium Braun, 1901 and Phaneropsolus sp. Our results clearly demonstrate that both L. polyoon and L. postgonoporus belong to the family Pleurogenidae Looss, 1899 within the superfamily Microphalloidea. Thus, the Leyogonimidae Dollfus, 1951 should be recognized as a synonym of the Pleurogenidae. Leyogonimus polyoon clearly constitutes a separate, sister branch to the clade consisting of Collyricloides massanae Vaucher, 1969 and L. postgonoporus. Based on these results, we resurrect the genus Macyella Neiland, 1951 with type-species M. postgonoporus. Besides, Collyricloides Vaucher, 1968 is synonymized with Macyella resulting in new combination Macyella massanae (Vaucher, 1968) comb. nov. Molecular phylogenetic analysis has demonstrated the lack of a close phylogenetic relationships between Stomylotema vicarium and Leyogonimus previously placed by several authors into the family Stomylotrematidae Poche, 1925. The status of the Phaneropsolidae Mehra, 1935 as independent family was confirmed with the addition of the newly sequenced Phaneropsolus sp. from China.

A New Fossil of Necrotauliidae (Insecta: Trichoptera) from the Jiulongshan Formation of China and Its Taxonomic Significance

PubMed Central

Liu, Yujia; Zhang, Weiting; Yao, Yunzhi; Ren, Dong

2014-01-01

Background Acisarcuatus variradius gen. et sp. nov., an extinct new species representing a new genus, is described from the Middle Jurassic Jiulongshan Formation in Daohugou Village, Inner Mongolia, China. Methodology/Principal Findings In this paper, we revised the diagnosis of Necrotauliidae Handlirsch, 1906. One new genus and species of Necrotauliidae is described. An analysis based on the fossil morphological characters clarified the taxonomic status of the new taxa. Conclusions/Significance New fossil evidence supports the viewpoint that the family Necrotauliidae belongs to the Integripalpia. PMID:25494387

Beta

USDA-ARS?s Scientific Manuscript database

This chapter covers the use of wild beets in sugar beet improvement, including the basic botany of the species, its distribution; geographical locations of genetic diversity; morphology; cytology and karyotype; genome size; taxonomic position; agricultural status (model plant/weeds/invasive species/...

History of tachinid classification (Diptera, Tachinidae)

PubMed Central

O’Hara, James E.

2013-01-01

Abstract The history of the classification of the Tachinidae (Diptera) is traced from Meigen to the present. The contributions of Robineau-Desvoidy, Townsend, Villeneuve, Mesnil, Herting, Wood and many others are discussed within a chronological, taxonomic, and geographic context. The gradual development of the Tachinidae into its modern concept as a family of the Oestroidea and the emergence of the classificatory scheme of tribes and subfamilies in use today are reviewed. Certain taxa that have in the past been difficult to place, or continue to be of uncertain affinity, are considered and some are given in a table to show their varied historical treatments. The more significant systematic works published on the Tachinidae in recent decades are enumerated chronologically. PMID:23878512

Incorporating evolutionary measures into conservation prioritization.

PubMed

Redding, David W; Mooers, Arne Ø

2006-12-01

Conservation prioritization is dominated by the threat status of candidate species. However, species differ markedly in the shared genetic information they embody, and this information is not taken into account if species are prioritized by threat status alone. We developed a system of prioritization that incorporates both threat status and genetic information and applied it to 9546 species of birds worldwide. We devised a simple measure of a species' genetic value that takes into account the shape of the entire taxonomic tree of birds. This measure approximates the evolutionary history that each species embodies and sums to the phylogenetic diversity of the entire taxonomic tree. We then combined this genetic value with each species' probability of extinction to create a species-specific measure of expected loss of genetic information. The application of our methods to the world's avifauna showed that ranking species by expected loss of genetic information may help preserve bird evolutionary history by upgrading those threatened species with fewer close relatives. We recommend developing a mechanism to incorporate a species' genetic value into the prioritization framework.

Evaluation of the Systematic Status of Geographical Variations in Arcuphantes hibanus (Arachnida: Araneae: Linyphiidae), with Descriptions of Two New Species.

PubMed

Nakano, Takafumi; Ihara, Yoh; Kumasaki, Yusuke; Baba, Yuki G; Tomikawa, Ko

2017-08-01

The systematic status of geographical variants of Arcuphantes hibanus Saito, 1992 belonging to the A. longiscapus species group, indigenous to western Honshu and Shikoku, Japan, was evaluated using morphological and molecular data. Two species, A. enmusubi Ihara, Nakano and Tomikawa, sp. nov. and A. occidentalis Ihara, Nakano and Tomikawa, sp. nov., are described, and A. hibanus is redescribed with redefinition of its taxonomic status. These three species are diagnosed by the characteristics of paracymbium, pseudolamella, and epigynal basal part. Phylogenetic trees obtained with mitochondrial cytochrome c oxidase subunit I and 16S rRNA markers showed that the variants are mutually genetically highly diverged. However, the mtDNA phylogenies failed to recover the monophyly of A. hibanus redefined herein. Contrary to the mtDNA phylogenetic analyses, a neighbor-network analysis of nuclear internal transcribed spacer 1 sequences of A. hibanus, A. enmusubi and A. occidentalis spiders showed that each of them forms a cluster. The results of mitochondrial and nuclear DNA analyses in each of the three species are briefly discussed, along with their taxonomic identities.

Taxonomic status and biology of the Cuban blackhawk, Buteogallus anthracinus gundlachii (AVES: Accipitridae)

USGS Publications Warehouse

Wiley, J.W.; Garrido, O.H.

2005-01-01

We reevaluate the taxonomic status of the Cuban population of the Common Black-Hawk (Buteogallus anthracinus) based on our examination of additional specimens, nests, eggs, and voice data. Buteogallus a. gundlachii is smaller than mainland populations of anthracinus and differs from mainland birds in plumage coloration and pattern. The common (alarm) call of gundlachii is a series of three or four notes, differing from that of mainland anthracinus, whose call consists of 9-24 notes. In the Isla de Pinos, Cuba, we observed gundlachii eating two species of land crabs (71.4%), centipedes (7.1%), lizards (10.7%), mammals (7.1%), and a bird (3.6%). We consider Buteogallus gundlachii Cabanis 1854 (1855), the Cuban Black-Hawk, to be a full species, endemic to Cuba, Isla de Pinos, and many of the cays of the Cuban Archipelago. ?? 2005 The Raptor Research Foundation, Inc.

A taxonomic review of the Neoserica (sensu lato) abnormis group (Coleoptera, Scarabaeidae, Sericini)

PubMed Central

Ahrens, Dirk; Liu, Wan-Gang; Fabrizi, Silvia; Bai, Ming; Yang, Xing-Ke

2014-01-01

Abstract The present paper revises the species belonging to the Neoserica (sensu lato) abnormis group, so far known only with two nominal species. Twenty new species are herein described from Indochina and southern China: N. abnormoides sp. n. (Vietnam, China), N. allolaotica sp. n., N. namthaensis sp. n., N. simplicissima sp. n. (Laos), N. thailandensis sp. n. (Thailand), N. alloputaoana sp. n., N. kanphantensis sp. n., N. natmatoungensis sp. n., N. putaoana sp. n., N. taunggyiana sp. n. (Myanmar), N. lamellosa sp. n., N. tonkinea sp. n. (Vietnam), N. bairailingshanica sp. n., N. euyunnanica sp. n., N. huangi sp. n., N. jiangxiensis sp. n., N. trifida sp. n., N. yaoi sp. n., N. yingjiangensis sp. n. (China), N. cardamomensis sp. n. (Indochina and southern China). One new combination is established: Neoserica ponderosa Arrow, 1946, comb. n. The lectotypes of Neoserica abnormis Moser, 1908 and the taxonomically uncertain N. inclinata Brenske, 1898, which very likely also belongs to this species group, are designated herein. A key to the species and to species groups is given, the genitalia of all species including their habitus are illustrated. Maps of species distribution are included. PMID:25317056

Two new species of the genus Daptonema Cobb, 1920 (Nematoda: Xyalidae) found in an intertidal seagrass bed on the coast of the Andaman Sea, Thailand, with reference to the taxonomic status of the genus Trichotheristus Wieser, 1956.

PubMed

Aryuthaka, Chittima; Kito, Kenji

2018-03-12

Daptonema chonispiculum sp. n. and D. phuketense sp. n. are described from the Ban Pa Khlok seagrass bed, Phuket Province, Thailand. Daptonema chonispiculum sp. n. is characterized by spicules with funnel-shaped proximal ends, and D. phuketense sp. n. is unique in having the third caudal gland filled with fibrous contents. Each new species also differs from most related species in body length, de Man's indices, length of the cephalic setae and somatic/cervical setae, distance of the amphids from the anterior of the body, and length of the spicules. The new species most closely resemble D. hirsutum, D. platonovae, and D. robustum, with similar body lengths, long cervical setae located in the anterior pharyngeal region, small amphids, L-shaped spicules and a gubernaculum with a long dorso-caudal apophysis. Regarding the taxonomic status of Daptonema and Trichotheristus, we agree with the synonymization of Trichotheristus with Daptonema by Tchesunov (1990), based on taxonomic review of Trichotheristus and a comparison of the diagnostic features separating the genera. We propose a new combination, Daptonema galeatum comb. n., and a new name, Daptonema nearticulatum sp. n. for Trichotheristus articulatus Huang Zhang, 2006.

Genomic insights into the taxonomic status of the Bacillus cereus group

PubMed Central

Liu, Yang; Lai, Qiliang; Göker, Markus; Meier-Kolthoff, Jan P.; Wang, Meng; Sun, Yamin; Wang, Lei; Shao, Zongze

2015-01-01

The identification and phylogenetic relationships of bacteria within the Bacillus cereus group are controversial. This study aimed at determining the taxonomic affiliations of these strains using the whole-genome sequence-based Genome BLAST Distance Phylogeny (GBDP) approach. The GBDP analysis clearly separated 224 strains into 30 clusters, representing eleven known, partially merged species and accordingly 19–20 putative novel species. Additionally, 16S rRNA gene analysis, a novel variant of multi-locus sequence analysis (nMLSA) and screening of virulence genes were performed. The 16S rRNA gene sequence was not sufficient to differentiate the bacteria within this group due to its high conservation. The nMLSA results were consistent with GBDP. Moreover, a fast typing method was proposed using the pycA gene, and where necessary, the ccpA gene. The pXO plasmids and cry genes were widely distributed, suggesting little correlation with the phylogenetic positions of the host bacteria. This might explain why classifications based on virulence characteristics proved unsatisfactory in the past. In summary, this is the first large-scale and systematic study of the taxonomic status of the bacteria within the B. cereus group using whole-genome sequences, and is likely to contribute to further insights into their pathogenicity, phylogeny and adaptation to diverse environments. PMID:26373441

Fat-soluble vitamin status in response to non-surgical weight loss in overweight post-menopausal women

USDA-ARS?s Scientific Manuscript database

Obesity is associated with an increased risk of fat soluble vitamin (FSV) deficiencies. The effect of dietary weight loss on FSV status is uncertain. We measured plasma concentrations of carotenoids, alpha-tocopherol, retinol, phylloquinone, and 25-hydroxyvitamin D (25(OH)D) in 112 overweight post-...

Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae)

PubMed Central

Francisco, Jessica Nayara Carvalho; Lohmann, Lúcia G.

2018-01-01

Abstract Pachyptera DC. is a small genus of neotropical lianas included in tribe Bignonieae (Bignoniaceae). The genus has a complicated taxonomic history but currently includes species distributed from Belize to Southern Amazon. Pachyptera is characterised by four main synapomorphies, namely, a papery peeling bark, prophylls of the axillary buds organised in a series of three, patelliform glands arranged in lines in the upper portions of the calyx and corolla tube. Furthermore, members of the genus also have stems with four phloem wedges in cross-section and conspicuous extrafloral nectaries between the interpetiolar region and at the petiole apex, although these characters are also shared with other genera of tribe Bignonieae. Here, we present a taxonomic revision of Pachyptera, which includes a complete list of synonyms, detailed morphological descriptions of species and an identification key, as well as information on the habitat, distribution and phenology, nomenclatural notes, taxonomic comments and illustrations of all the species. In addition, we designate three lectotypes, propose one new combination, raise one variety to species status and describe a new species. After these adjustments, a Pachyptera with five well-defined species is recognised. PMID:29416412

Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae).

PubMed

Francisco, Jessica Nayara Carvalho; Lohmann, Lúcia G

2018-01-01

Pachyptera DC. is a small genus of neotropical lianas included in tribe Bignonieae (Bignoniaceae). The genus has a complicated taxonomic history but currently includes species distributed from Belize to Southern Amazon. Pachyptera is characterised by four main synapomorphies, namely, a papery peeling bark, prophylls of the axillary buds organised in a series of three, patelliform glands arranged in lines in the upper portions of the calyx and corolla tube. Furthermore, members of the genus also have stems with four phloem wedges in cross-section and conspicuous extrafloral nectaries between the interpetiolar region and at the petiole apex, although these characters are also shared with other genera of tribe Bignonieae. Here, we present a taxonomic revision of Pachyptera , which includes a complete list of synonyms, detailed morphological descriptions of species and an identification key, as well as information on the habitat, distribution and phenology, nomenclatural notes, taxonomic comments and illustrations of all the species. In addition, we designate three lectotypes, propose one new combination, raise one variety to species status and describe a new species. After these adjustments, a Pachyptera with five well-defined species is recognised.

The Role of Integrative Taxonomy in the Conservation Management of Cryptic Species: The Taxonomic Status of Endangered Earless Dragons (Agamidae: Tympanocryptis) in the Grasslands of Queensland, Australia

PubMed Central

Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

2014-01-01

Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered ‘species’ of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available. PMID:25076129

The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis) in the grasslands of Queensland, Australia.

PubMed

Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

2014-01-01

Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.

Anaerococcus degenerii sp. nov., isolated from human clinical specimens.

PubMed

Veloo, A C M; Elgersma, P E; van Winkelhoff, A J

2015-06-01

Four clinical isolates of gram-positive strict anaerobic cocci were isolated from four different human mixed anaerobic infections. The taxonomical status of the four strains could not be established using standard identification techniques. The biochemical features of the strains were established and their taxonomic position was determined using 16S rRNA sequencing. The four strains form a homogeneous phenotypical and genotypical cluster. A new Anaerococcus species is proposed for these isolates: Anaerococcus degenerii sp. nov. The type strain is UMCG-104(T) = DSM29674(T) (accession number AM176528). Copyright © 2015 Elsevier Ltd. All rights reserved.

CALYPTOSPORA FUNDULI (APICOMPLEXA): LIFE CYCLE AND TAXONOMY

EPA Science Inventory

The taxonomic status of the extraintestinal piscine coccidium Calyptospora funduli is based in part on its requirement of an intermediate host (the daggerblade grass shrimp, Palaemonetes pugio). Grass shrimp fed livers of Gulf killifish (Fundulus grandis) infected with sporulated...

LIFE CYCLE OF CALYPTOSPORA FUNDULI (APICOMPLEXA: CALYPTOSPORIDAE)

EPA Science Inventory

The taxonomic status of the extraintestinal piscine coccidium Calyptospora funduli is based in part on its requirement of an intermediate host (the daggerblade grass shrimp, Palaemonetes pugio). In this study, grass shrimp fed livers of Gulf killifish (Fundulus grandis) infected ...

Dementia in Adults with Mental Retardation: Assessment at a Single Point in Time

ERIC Educational Resources Information Center

Silverman, Wayne; Schupf, Nicole; Zigman, Warren; Devenny, Darlynne; Miezejeski, Charles; Schubert, Romaine; Ryan, Robert

2004-01-01

Dementia status of 273 adults with mental retardation was rated based upon two extensive evaluations conducted 18 months apart. Overall, 184 individuals did not have dementia, 33 had possible or definite dementia, and 66 had findings suggesting uncertain or questionable status. These ratings were compared to binary classifications (dementia vs. no…

Patterns of Freshwater Species Richness, Endemism, and Vulnerability in California

PubMed Central

Furnish, Joseph; Gardali, Thomas; Grantham, Ted; Katz, Jacob V. E.; Kupferberg, Sarah; McIntyre, Patrick; Moyle, Peter B.; Ode, Peter R.; Peek, Ryan; Quiñones, Rebecca M.; Rehn, Andrew C.; Santos, Nick; Schoenig, Steve; Serpa, Larry; Shedd, Jackson D.; Slusark, Joe; Viers, Joshua H.; Wright, Amber; Morrison, Scott A.

2015-01-01

The ranges and abundances of species that depend on freshwater habitats are declining worldwide. Efforts to counteract those trends are often hampered by a lack of information about species distribution and conservation status and are often strongly biased toward a few well-studied groups. We identified the 3,906 vascular plants, macroinvertebrates, and vertebrates native to California, USA, that depend on fresh water for at least one stage of their life history. We evaluated the conservation status for these taxa using existing government and non-governmental organization assessments (e.g., endangered species act, NatureServe), created a spatial database of locality observations or distribution information from ~400 data sources, and mapped patterns of richness, endemism, and vulnerability. Although nearly half of all taxa with conservation status (n = 1,939) are vulnerable to extinction, only 114 (6%) of those vulnerable taxa have a legal mandate for protection in the form of formal inclusion on a state or federal endangered species list. Endemic taxa are at greater risk than non-endemics, with 90% of the 927 endemic taxa vulnerable to extinction. Records with spatial data were available for a total of 2,276 species (61%). The patterns of species richness differ depending on the taxonomic group analyzed, but are similar across taxonomic level. No particular taxonomic group represents an umbrella for all species, but hotspots of high richness for listed species cover 40% of the hotspots for all other species and 58% of the hotspots for vulnerable freshwater species. By mapping freshwater species hotspots we show locations that represent the top priority for conservation action in the state. This study identifies opportunities to fill gaps in the evaluation of conservation status for freshwater taxa in California, to address the lack of occurrence information for nearly 40% of freshwater taxa and nearly 40% of watersheds in the state, and to implement adequate protections for freshwater taxa where they are currently lacking. PMID:26147215

Taxonomic revision of the genus Carasobarbus Karaman, 1971 (Actinopterygii, Cyprinidae)

PubMed Central

Borkenhagen, Kai; Krupp, Friedhelm

2013-01-01

Abstract Representatives of the fish genus Carasobarbus Karaman, 1971 (Actinopterygii: Cyprinidae) from the Middle East and North Africa were previously placed in 14 different genus-group taxa (Barbellion, Barbus, Barynotus, Capoeta, Carasobarbus, Cyclocheilichthys, Kosswigobarbus, Labeobarbus, Luciobarbus, Pseudotor, Puntius, Systomus, Tor and Varicorhinus). The generic assignment of several species changed frequently, necessitating a re-evaluation of their taxonomic status. In this study, the genus Carasobarbus is revised based on comparative morphological examinations of about 1300 preserved specimens from collections of several museums and freshly collected material. The species Carasobarbus apoensis, Carasobarbus canis, Carasobarbus chantrei, Carasobarbus exulatus, Carasobarbus fritschii, Carasobarbus harterti, Carasobarbus kosswigi, Carasobarbus luteus and Carasobarbus sublimus form a monophyletic group that shares the following combination of characters: medium-sized barbels with a smooth last unbranched dorsal-fin ray, nine or 10 branched dorsal-fin rays and six branched anal fin-rays; scales large, shield-shaped, with many parallel radii; the lateral line containing 25 to 39 scales; the pharyngeal teeth hooked, 2.3.5-5.3.2 or 2.3.4-4.3.2; one or two pairs of barbels. The species are described in detail, their taxonomic status is re-evaluated and an identification key is provided. A lectotype of Systomus luteus Heckel, 1843 is designated. Carasobarbus Karaman, 1971, Kosswigobarbus Karaman, 1971, and Pseudotor Karaman, 1971 are subjective synonyms, and acting as First Reviser we gave precedence to the name Carasobarbus. PMID:24146585

Clinical and Taxonomic Status of Pathogenic Nonpigmented or Late-Pigmenting Rapidly Growing Mycobacteria

PubMed Central

Brown-Elliott, Barbara A.; Wallace, Richard J.

2002-01-01

The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are reviewed. Community-acquired disease and health care-associated disease are highlighted for each species. The latter grouping includes health care-associated outbreaks and pseudo-outbreaks as well as sporadic disease cases. Treatment recommendations for each species and type of disease are also described. Special emphasis is on the Mycobacterium fortuitum group, including M. fortuitum, M. peregrinum, and the unnamed third biovariant complex with its recent taxonomic changes and newly recognized species (including M. septicum, M. mageritense, and proposed species M. houstonense and M. bonickei). The clinical and taxonomic status of M. chelonae, M. abscessus, and M. mucogenicum is also detailed, along with that of the closely related new species, M. immunogenum. Additionally, newly recognized species, M. wolinskyi and M. goodii, as well as M. smegmatis sensu stricto, are included in a discussion of the M. smegmatis group. Laboratory diagnosis of RGM using phenotypic methods such as biochemical testing and high-performance liquid chromatography and molecular methods of diagnosis are also discussed. The latter includes PCR-restriction fragment length polymorphism analysis, hybridization, ribotyping, and sequence analysis. Susceptibility testing and antibiotic susceptibility patterns of the RGM are also annotated, along with the current recommendations from the National Committee for Clinical Laboratory Standards (NCCLS) for mycobacterial susceptibility testing. PMID:12364376

Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria.

PubMed

Brown-Elliott, Barbara A; Wallace, Richard J

2002-10-01

The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are reviewed. Community-acquired disease and health care-associated disease are highlighted for each species. The latter grouping includes health care-associated outbreaks and pseudo-outbreaks as well as sporadic disease cases. Treatment recommendations for each species and type of disease are also described. Special emphasis is on the Mycobacterium fortuitum group, including M. fortuitum, M. peregrinum, and the unnamed third biovariant complex with its recent taxonomic changes and newly recognized species (including M. septicum, M. mageritense, and proposed species M. houstonense and M. bonickei). The clinical and taxonomic status of M. chelonae, M. abscessus, and M. mucogenicum is also detailed, along with that of the closely related new species, M. immunogenum. Additionally, newly recognized species, M. wolinskyi and M. goodii, as well as M. smegmatis sensu stricto, are included in a discussion of the M. smegmatis group. Laboratory diagnosis of RGM using phenotypic methods such as biochemical testing and high-performance liquid chromatography and molecular methods of diagnosis are also discussed. The latter includes PCR-restriction fragment length polymorphism analysis, hybridization, ribotyping, and sequence analysis. Susceptibility testing and antibiotic susceptibility patterns of the RGM are also annotated, along with the current recommendations from the National Committee for Clinical Laboratory Standards (NCCLS) for mycobacterial susceptibility testing.

The taxonomy statistic uncovers novel clinical patterns in a population of ischemic stroke patients.

PubMed

Tukiendorf, Andrzej; Kaźmierski, Radosław; Michalak, Sławomir

2013-01-01

In this paper, we describe a simple taxonomic approach for clinical data mining elaborated by Marczewski and Steinhaus (M-S), whose performance equals the advanced statistical methodology known as the expectation-maximization (E-M) algorithm. We tested these two methods on a cohort of ischemic stroke patients. The comparison of both methods revealed strong agreement. Direct agreement between M-S and E-M classifications reached 83%, while Cohen's coefficient of agreement was κ = 0.766(P < 0.0001). The statistical analysis conducted and the outcomes obtained in this paper revealed novel clinical patterns in ischemic stroke patients. The aim of the study was to evaluate the clinical usefulness of Marczewski-Steinhaus' taxonomic approach as a tool for the detection of novel patterns of data in ischemic stroke patients and the prediction of disease outcome. In terms of the identification of fairly frequent types of stroke patients using their age, National Institutes of Health Stroke Scale (NIHSS), and diabetes mellitus (DM) status, when dealing with rough characteristics of patients, four particular types of patients are recognized, which cannot be identified by means of routine clinical methods. Following the obtained taxonomical outcomes, the strong correlation between the health status at moment of admission to emergency department (ED) and the subsequent recovery of patients is established. Moreover, popularization and simplification of the ideas of advanced mathematicians may provide an unconventional explorative platform for clinical problems.

Fish-based indicators of estuarine condition that do not require reference data

NASA Astrophysics Data System (ADS)

Tweedley, James R.; Warwick, Richard M.; Hallett, Chris S.; Potter, Ian C.

2017-05-01

The species composition of fish communities in 15 microtidal estuaries in south-western Australia, ranging from permanently-open to normally-closed, is shown to be related to the geomorphological and hydrological regimes and not to environmental condition. This study then explored the effectiveness of using qualitative taxonomic distinctness and ABC curves for fish data as indicators of the environmental condition in nearshore, shallow waters of these estuaries and, in the case of taxonomic distinctness, also of their offshore, deeper waters. Neither of these indices require spatial or temporal reference data, which may be either prohibitively expensive and time-consuming to collect or unavailable. Taxonomic distinctness, in both nearshore and offshore waters, varied consistently among estuaries in relation to their recorded environmental status, and is thus a good indicator of overall estuarine condition. ABC analyses, however, did not prove a good measure of the environmental condition of the estuaries, because their results largely reflect differences in accessibility of the estuary to marine estuarine-opportunist species and especially those that grow to a larger size. It is concluded that taxonomic distinctness indices provide a rapid and cost-effective method for assessing the environmental condition of estuaries, particularly those with limited spatial or temporal reference data.

Evolutionary history of Leishmania killicki (synonymous Leishmania tropica) and taxonomic implications.

PubMed

Chaara, Dhekra; Ravel, Christophe; Bañuls, Anne- Laure; Haouas, Najoua; Lami, Patrick; Talignani, Loïc; El Baidouri, Fouad; Jaouadi, Kaouther; Harrat, Zoubir; Dedet, Jean-Pierre; Babba, Hamouda; Pratlong, Francine

2015-04-01

The taxonomic status of Leishmania (L.) killicki, a parasite that causes chronic cutaneous leishmaniasis, is not well defined yet. Indeed, some researchers suggested that this taxon could be included in the L. tropica complex, whereas others considered it as a distinct phylogenetic complex. To try to solve this taxonomic issue we carried out a detailed study on the evolutionary history of L. killicki relative to L. tropica. Thirty-five L. killicki and 25 L. tropica strains isolated from humans and originating from several countries were characterized using the MultiLocus Enzyme Electrophoresis (MLEE) and the MultiLocus Sequence Typing (MLST) approaches. The results of the genetic and phylogenetic analyses strongly support the hypothesis that L. killicki belongs to the L. tropica complex. Our data suggest that L. killicki emerged from a single founder event and that it evolved independently from L. tropica. However, they do not validate the hypothesis that L. killicki is a distinct complex. Therefore, we suggest naming this taxon L. killicki (synonymous L. tropica) until further epidemiological and phylogenetic studies justify the L. killicki denomination. This study provides taxonomic and phylogenetic information on L. killicki and improves our knowledge on the evolutionary history of this taxon.

New pieces of the Trichinella puzzle

USDA-ARS?s Scientific Manuscript database

Contrary to our understanding of just a few decades ago, the genus Trichinella now consists of a complex assemblage of no less than 9 different species and 3 additional genotypes whose taxonomic status remains in flux. New data and methodologies have allowed advancements in detection and differentia...

Whitefly (Bemisia tabaci) management program for ornamental plants

USDA-ARS?s Scientific Manuscript database

Bemisia tabaci (Gennadius) commonly known as silverleaf whitefly, is a polyphagous pest considered to be one of the most notorious invasive arthropods worldwide. The pest status of Bemisia tabaci is complicated because of their well debated taxonomic architecture which was previously identified to c...

The taxonomic status of genetically divergent populations of Lutzomyia longipalpis (Diptera: Psychodidae) based on the distribution of mitochondrial and isozyme variation.

PubMed

Arrivillaga, Jazzmin; Mutebi, John-Paul; Piñango, Hermes; Norris, Douglas; Alexander, Bruce; Feliciangeli, M Dora; Lanzaro, Gregory C

2003-09-01

The sand fly, Lutzomyia longipalpis (Lutz & Neiva) reputedly is a complex of cryptic species; however, there is currently no consensus as to the number of species in the complex or their geographic distributions. We conducted phylogenetic analyses of 31 populations from throughout the species range, using seven isozyme loci and genes in the mitochondrial genome. Analyses of these two independent sets of markers were largely concordant and revealed four distinct clades that support the existence of four species. The four clades have distinct geographic ranges: (1) Brazil (Species A = Lu. longipalpis sensu stricto), (2) Laran (Species B = Lu. pseudolongipalpis), (3) cis-Andean (Species C), and (4) trans-Andean (Species D). The cis-Andean clade may be subdivided further into two groups, one in Colombia and one in northwestern Venezuela, but their taxonomic status remains unresolved. Knowledge that Lu. longipalpis is a complex of species may ultimately shed light on anomalies in the epidemiology of visceral leishmaniasis in the New World.

Refining the Global Spatial Limits of Dengue Virus Transmission by Evidence-Based Consensus

PubMed Central

Brady, Oliver J.; Gething, Peter W.; Bhatt, Samir; Messina, Jane P.; Brownstein, John S.; Hoen, Anne G.; Moyes, Catherine L.; Farlow, Andrew W.; Scott, Thomas W.; Hay, Simon I.

2012-01-01

Background Dengue is a growing problem both in its geographical spread and in its intensity, and yet current global distribution remains highly uncertain. Challenges in diagnosis and diagnostic methods as well as highly variable national health systems mean no single data source can reliably estimate the distribution of this disease. As such, there is a lack of agreement on national dengue status among international health organisations. Here we bring together all available information on dengue occurrence using a novel approach to produce an evidence consensus map of the disease range that highlights nations with an uncertain dengue status. Methods/Principal Findings A baseline methodology was used to assess a range of evidence for each country. In regions where dengue status was uncertain, additional evidence types were included to either clarify dengue status or confirm that it is unknown at this time. An algorithm was developed that assesses evidence quality and consistency, giving each country an evidence consensus score. Using this approach, we were able to generate a contemporary global map of national-level dengue status that assigns a relative measure of certainty and identifies gaps in the available evidence. Conclusion The map produced here provides a list of 128 countries for which there is good evidence of dengue occurrence, including 36 countries that have previously been classified as dengue-free by the World Health Organization and/or the US Centers for Disease Control. It also identifies disease surveillance needs, which we list in full. The disease extents and limits determined here using evidence consensus, marks the beginning of a five-year study to advance the mapping of dengue virus transmission and disease risk. Completion of this first step has allowed us to produce a preliminary estimate of population at risk with an upper bound of 3.97 billion people. This figure will be refined in future work. PMID:22880140

Refining the global spatial limits of dengue virus transmission by evidence-based consensus.

PubMed

Brady, Oliver J; Gething, Peter W; Bhatt, Samir; Messina, Jane P; Brownstein, John S; Hoen, Anne G; Moyes, Catherine L; Farlow, Andrew W; Scott, Thomas W; Hay, Simon I

2012-01-01

Dengue is a growing problem both in its geographical spread and in its intensity, and yet current global distribution remains highly uncertain. Challenges in diagnosis and diagnostic methods as well as highly variable national health systems mean no single data source can reliably estimate the distribution of this disease. As such, there is a lack of agreement on national dengue status among international health organisations. Here we bring together all available information on dengue occurrence using a novel approach to produce an evidence consensus map of the disease range that highlights nations with an uncertain dengue status. A baseline methodology was used to assess a range of evidence for each country. In regions where dengue status was uncertain, additional evidence types were included to either clarify dengue status or confirm that it is unknown at this time. An algorithm was developed that assesses evidence quality and consistency, giving each country an evidence consensus score. Using this approach, we were able to generate a contemporary global map of national-level dengue status that assigns a relative measure of certainty and identifies gaps in the available evidence. The map produced here provides a list of 128 countries for which there is good evidence of dengue occurrence, including 36 countries that have previously been classified as dengue-free by the World Health Organization and/or the US Centers for Disease Control. It also identifies disease surveillance needs, which we list in full. The disease extents and limits determined here using evidence consensus, marks the beginning of a five-year study to advance the mapping of dengue virus transmission and disease risk. Completion of this first step has allowed us to produce a preliminary estimate of population at risk with an upper bound of 3.97 billion people. This figure will be refined in future work.

Systematics and position of Nephrops among the lobsters.

PubMed

Tshudy, Dale

2013-01-01

This chapter presents and explains the position of Nephrops norvegicus in the classification of lobsters. Covered, in order, are systematic classification of Nephrops, taxonomic history of Nephrops, and analysis of Nephrops in nephropid phylogeny. The genus Nephrops was erected by Leach in 1814 and has a long and interesting taxonomic history. Prior to 1972, Nephrops was known by 14 Recent species. All but one of these, N. norvegicus, were removed to a new genus, Metanephrops, by Jenkins (1972). Today, N. norvegicus is still the only known living representative of the genus. Similarly, Nephrops is known by only one fossil species, the Miocene Nephrops kvistgaardae, although several other fossil species have been previously referred to this genus. Nephrops, along with the other familiar and commercially important marine clawed lobsters, is referred to Family Nephropidae, one of 17 marine clawed lobster families arrayed in 3 infraorders, 6 families each in the Astacidea and Glypheidea and 5 in the Polychelida. Infraorder Astacidea includes the Superfamily Nephropoidea, as well as the lesser known 'reef lobsters' of the Superfamily Enoplometopoidea, and the freshwater crayfish, Superfamily Astacoidea. In phylogenetic analyses, the freshwater crayfish form a sister group to the Nephropoidea. It is interpreted that freshwater crayfish evolved from nephropoid lobsters, but from which lobster group is uncertain. The taxonomic placement of N. norvegicus is stable at all levels, from species on up. Despite that, the phylogenetic relationships of Nephrops to other nephropid genera are unsettled due to conflicting results in morphological and molecular analyses. Currently, new morphological characters and new genes are being analysed in the hope of elucidating nephropid phylogeny. Copyright © 2013 Elsevier Ltd. All rights reserved.

A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema.

PubMed

Trojan, Daniela; Schreiber, Lars; Bjerg, Jesper T; Bøggild, Andreas; Yang, Tingting; Kjeldsen, Kasper U; Schramm, Andreas

2016-07-01

Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exact phylogeny is uncertain, as most studies so far have reported only short partial 16S rRNA sequences or have relied on identification by a combination of filament morphology and 16S rRNA-targeted fluorescence in situ hybridization with a Desulfobulbaceae-specific probe. In this study, nearly full-length 16S rRNA gene sequences of 16 individual cable bacteria filaments from freshwater, salt marsh, and marine sites of four geographic locations are presented. These sequences formed a distinct, monophyletic sister clade to the genus Desulfobulbus and could be divided into six coherent, species-level clusters, arranged as two genus-level groups. The same grouping was retrieved by phylogenetic analysis of full or partial dsrAB genes encoding the dissimilatory sulfite reductase. Based on these results, it is proposed to accommodate cable bacteria within two novel candidate genera: the mostly marine "Candidatus Electrothrix", with four candidate species, and the mostly freshwater "Candidatus Electronema", with two candidate species. This taxonomic framework can be used to assign environmental sequences confidently to the cable bacteria clade, even without morphological information. Database searches revealed 185 16S rRNA gene sequences that affiliated within the clade formed by the proposed cable bacteria genera, of which 120 sequences could be assigned to one of the six candidate species, while the remaining 65 sequences indicated the existence of up to five additional species. Copyright © 2016 The Author(s). Published by Elsevier GmbH.. All rights reserved.

Molecular studies on the species complex of Trichosirocalus horridus in the biological control of Carduinae weeds.

USDA-ARS?s Scientific Manuscript database

The genus Trichosirocalus Colonnelli, 1979, (Coleoptera, Curculionidae, Ceutorhynchinae) includes 17 Palaearctic species mainly feeding on Plantaginaceae and Asteraceae. We studied the taxonomic status of the species complex of Trichosirocalus horridus (TH) by means of molecular markers. We used bot...

Brief research report: uncertainty-inducing and reassuring facts about HPV: a descriptive study of French Canadian women.

PubMed

Rosen, Natalie O; Knäuper, Bärbel; Pagé, Gabrielle; Di Dio, Pasqualina; Morrison, Eleshia; Mayrand, Marie-Hélène; Franco, Eduardo L; Rosberger, Zeev

2009-10-01

We sought to describe information that makes women feel (1) uncertain and (2) reassured about their human papillomavirus (HPV) status and the potential health implications of an HPV DNA test result and (3) to examine information seeking after receiving their result. Thirty women (previously tested HPV negative) read factual information on HPV and cervical cancer and were asked which facts were uncertainty inducing and which were reassuring. Twenty-four facts reassured women of their HPV negative status, 11 facts made women feel uncertain, and 10 facts made them feel both. The most common reason for seeking information in the future was receiving a positive test result. The authors outline what specific facts about HPV health providers can emphasize to alleviate anxiety and encourage women to feel reassured of their low cancer risk following a negative test result.

Taxonomic status of Trichosirocalus species (Curculionidae) attacking Carduus, Cirsium and Onopordum species

USDA-ARS?s Scientific Manuscript database

The genus Trichosirocalus Colonnelli includes some host-specific weevil species or biotypes with a relatively narrow host-range limited to some thistles of the subfamily Carduinae. An Italian population of T. horridus (Panzer) was introduced in 1974 into the USA, and a population from Germany was in...

Review of the systematics, biology and ecology of lice from pinnipeds and river otters (Insecta: Phthiraptera: Anoplura: Echinophthiriidae).

PubMed

Soledad Leonardi, Maria; Palma, Ricardo Luis

2013-01-01

We present a literature review of the sucking louse family Echinophthiriidae, its five genera and twelve species parasitic on pinnipeds (fur seals, sea lions, walruses, true seals) and the North American river otter. We give detailed synonymies and published records for all taxonomic hierarchies, as well as hosts, type localities and repositories of type material; we highlight significant references and include comments on the current taxonomic status of the species. We provide a summary of present knowledge of the biology and ecology for eight species. Also, we give a host-louse list, and a bibliography to the family as complete as possible.

Taxonomic status of the coquette hummingbird of Guerrero, Mexico

USGS Publications Warehouse

Banks, Richard C.

1990-01-01

An isolated population of small hummingbirds in the state of Guerrero, Mexico, was originally named as a subspecies (brachylopha) of the much more southerly Lophornis delattrei, the Rufous-crested Coquette (Moore 1949). The form was not reported again until rediscovered by Ornelas (1987) and remains known by only three male and two female specimens. Examination of two of the males indicates that the population deserves specific status as Lophornis brachylopha Moore, for which I propose the English name Shortcrested Coquette.

Lophotrochozoan mitochondrial genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valles, Yvonne; Boore, Jeffrey L.

2005-10-01

Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animalsmore » across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.« less

A new species of Liolaemus related to L. nigroviridis from the Andean highlands of Central Chile (Iguania, Liolaemidae)

PubMed Central

Troncoso-Palacios, Jaime; Elorza, Alvaro A.; Puas, German I.; Alfaro-Pardo, Edmundo

2016-01-01

Abstract The Liolaemus nigroviridis group is a clade of highland lizards endemic to Chile. These species are distributed from northern to central Chile, and currently there are no cases of sympatric distribution. This study describes a new species, Liolaemus uniformis sp. n., from this group, and provides a detailed morphological characterization and mitochondrial phylogeny using cytochrome-b. Liolaemus uniformis was found in sympatry with Liolaemus nigroviridis but noticeably differed in size, scalation, and markedly in the color pattern, without sexual dichromatism. This new species has probably been confused with Liolaemus monticola and Liolaemus bellii, both of which do not belong to the nigroviridis group. The taxonomic issues of this group that remain uncertain are also discussed. PMID:26877688

Gut microbiomes of Indian children of varying nutritional status.

PubMed

Ghosh, Tarini Shankar; Gupta, Sourav Sen; Bhattacharya, Tanudeep; Yadav, Deepak; Barik, Anamitra; Chowdhury, Abhijit; Das, Bhabatosh; Mande, Sharmila S; Nair, G Balakrish

2014-01-01

Malnutrition is a global health problem affecting more than 300 million pre-school children worldwide. It is one of the major health concerns in India since around 50% of children below the age of two suffer from various forms of malnutrition. The gut microbiome plays an important role in nutrient pre-processing, assimilation and energy harvest from food. Consequently, dysbiosis of the gut microbiota has been implicated in malnutrition. Metagenomics approach was adopted to investigate the gut microbiome sampled from 20 rural Indian children with varying nutritional status. The changes in the abundances of various taxonomic and functional groups were investigated across these gut microbiomes. A core set of 23 genera were observed across samples, with some showing differential abundances with varying nutritional status. One of the findings of the current study is the positive/negative associations of specific taxonomic and functional groups with the nutritional status of the children. Notable alterations in the architecture of the inter-microbial co-occurrence networks were also observed with changes in nutritional status. A key example is the clustering of potentially pathogenic groups into a distinct hub in severely malnourished gut. Our data does not demonstrate causality with the microbiome patterns that we observed, rather a description of some interesting patterns, whose underlying mechanism remains to be uncovered. The present study envisioned interrelationships between the pattern of gut microbiome and the nutritional status of children. The cause of this pattern needs to be explored. However, insights obtained from the present study form the basis for further metagenomic investigations on larger population of children. Results of such studies will be useful in identifying the key microbial groups that can be utilized for targeted therapeutic interventions for managing severe acute malnutrition.

Gut Microbiomes of Indian Children of Varying Nutritional Status

PubMed Central

Bhattacharya, Tanudeep; Yadav, Deepak; Barik, Anamitra; Chowdhury, Abhijit; Das, Bhabatosh; Mande, Sharmila S.; Nair, G. Balakrish

2014-01-01

Background Malnutrition is a global health problem affecting more than 300 million pre-school children worldwide. It is one of the major health concerns in India since around 50% of children below the age of two suffer from various forms of malnutrition. The gut microbiome plays an important role in nutrient pre-processing, assimilation and energy harvest from food. Consequently, dysbiosis of the gut microbiota has been implicated in malnutrition. Methodology/Principal Findings Metagenomics approach was adopted to investigate the gut microbiome sampled from 20 rural Indian children with varying nutritional status. The changes in the abundances of various taxonomic and functional groups were investigated across these gut microbiomes. A core set of 23 genera were observed across samples, with some showing differential abundances with varying nutritional status. One of the findings of the current study is the positive/negative associations of specific taxonomic and functional groups with the nutritional status of the children. Notable alterations in the architecture of the inter-microbial co-occurrence networks were also observed with changes in nutritional status. A key example is the clustering of potentially pathogenic groups into a distinct hub in severely malnourished gut. Our data does not demonstrate causality with the microbiome patterns that we observed, rather a description of some interesting patterns, whose underlying mechanism remains to be uncovered. Conclusions The present study envisioned interrelationships between the pattern of gut microbiome and the nutritional status of children. The cause of this pattern needs to be explored. However, insights obtained from the present study form the basis for further metagenomic investigations on larger population of children. Results of such studies will be useful in identifying the key microbial groups that can be utilized for targeted therapeutic interventions for managing severe acute malnutrition. PMID:24763225

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.

PubMed

O'Leary, Nuala A; Wright, Mathew W; Brister, J Rodney; Ciufo, Stacy; Haddad, Diana; McVeigh, Rich; Rajput, Bhanu; Robbertse, Barbara; Smith-White, Brian; Ako-Adjei, Danso; Astashyn, Alexander; Badretdin, Azat; Bao, Yiming; Blinkova, Olga; Brover, Vyacheslav; Chetvernin, Vyacheslav; Choi, Jinna; Cox, Eric; Ermolaeva, Olga; Farrell, Catherine M; Goldfarb, Tamara; Gupta, Tripti; Haft, Daniel; Hatcher, Eneida; Hlavina, Wratko; Joardar, Vinita S; Kodali, Vamsi K; Li, Wenjun; Maglott, Donna; Masterson, Patrick; McGarvey, Kelly M; Murphy, Michael R; O'Neill, Kathleen; Pujar, Shashikant; Rangwala, Sanjida H; Rausch, Daniel; Riddick, Lillian D; Schoch, Conrad; Shkeda, Andrei; Storz, Susan S; Sun, Hanzhen; Thibaud-Nissen, Francoise; Tolstoy, Igor; Tully, Raymond E; Vatsan, Anjana R; Wallin, Craig; Webb, David; Wu, Wendy; Landrum, Melissa J; Kimchi, Avi; Tatusova, Tatiana; DiCuccio, Michael; Kitts, Paul; Murphy, Terence D; Pruitt, Kim D

2016-01-04

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Biochemical evidence that Dendroctonus frontalis consists of two sibling species in Belize and Chiapas, Mexico

Treesearch

Brian T. Sullivan; Alicia Nino; Benjamin Moreno; Cavell Brownie; Jorge Macias-Samano; Stephen R. Clarke; Lawrence R. Kirkendall; Gerardo. and Zuniga

2012-01-01

Dendroctonus frontalis Zimmermann (Coleoptera: Curculionidae: Scolytinae) is a major economic pest of pines in the United States, Mexico, and Central America. We report biochemical investigations relevant to the taxonomic status and semiochemistry of two distinct morphotypes of D. frontalis recently detected in the Central American...

Pinus ponderosa: a taxonomic review with five subspecies in the United States

Treesearch

Robert Z. Callaham

2013-01-01

Various forms of Pinus ponderosa Douglas ex C. Lawson are found from British Columbia southward and eastward through 16 states and, perhaps, into Mexico. The status of many names previously associated with this species, but excluded here, has been clarified. Accumulated evidence based on variation in morphology and xylem monoterpenes,...

"Invented Invaders": An Engaging Activity to Teach Characteristics Control of Invasive Species

ERIC Educational Resources Information Center

Lampert, Evan

2015-01-01

Invasive species, defined as exotic species that reach pest status, are major threats to global biodiversity. Although invasive species can belong to any taxonomic group, general characteristics such as rapid growth and reproduction are shared by many invasive species. "Invented Invaders" is a collaborative activity in which students…

Automatic Encoding of Superordinate and Subordinate Taxonomic Categories in Different Populations.

ERIC Educational Resources Information Center

Nakayama, Susan Y.; Kee, Daniel W.

1980-01-01

Proactive interference (PI) build-up and release from PI were used to study automatic conceptual encoding of superordinate and subordinate category lists in low-socioeconomic status (SES) Black children and middle-SES White children (grades 2 and 4). (Results for each population on the three category lists are described). (GDC)

Streptomyces leeuwenhoekii sp. nov., the producer of chaxalactins and chaxamycins, forms a distinct branch in Streptomyces gene trees

USDA-ARS?s Scientific Manuscript database

A polyphasic study was carried out to establish the taxonomic status of an Atacama Desert isolate, Streptomyces strain C34T, which synthesises novel antibiotics, the chaxalactins and chaxamycins. The organism was shown to have chemotaxonomic, cultural, and morphological properties consistent with it...

Morphology, taxonomic status and distribution of the opisthobranch mollusc Coryphella (s.l.) japonica from the central deep water basin of the Sea of Japan

NASA Astrophysics Data System (ADS)

Martynov, Alexander V.

2013-02-01

The opisthobranch fauna (Gastropoda: Opisthobranchia) of the deep sea basins of the Sea of Japan is reviewed. A detailed description of the most common deep sea nudibranch species Coryphella japonicaVolodchenko, 1941 is given based on materials from various expeditions (including R/V "Vityaz" cruises and SoJaBio project). Distinct morphological features of C. japonica are discussed and its valid taxonomic status is confirmed. The considerable radular variability of C. japonica for the first time is documented using a scanning electron microscope. Unique features of the bathymetric distribution of C. japonica ranging from shelf to the abyssal depths are discussed in connection with the "pseudabyssal area" concept. C. japonica was compared to its assumed synonym C. salmonacea, and to similar C. athadona. Material from all these species, including types of C. japonica, was examined externally, anatomically via dissection, and SEM. C. salmonacea is restricted to North Atlantic and Arctic only, whereas C. japonica inhabits NE Pacific including deep water basins of the Sea of Japan.

Taxonomic history and current status of Stachybotrys chartarum and related species.

PubMed

Li, D-W; Yang, C S

2005-01-01

The fungus Stachybotrys chartarum is the type species of the genus Stachybotrys. It is a cellulolytic saprophyte with a worldwide distribution and is frequently recovered in water-damaged buildings. Three isolates of S. chartarum were studied morphologically from single-spore isolations. Significant differences were found with the sizes, lengths, width, and L/W ratio of conidia and phialides among the isolates. QPCR analysis on S. chartarum, S. yunnanensis, S. chlorohalonata, S. elegans, S. microspora, and S. nephrospora showed that the primers and probe for detecting S. chartarum used by commercial laboratories were not able to differentiate S. chartarum from S. chlorohalonata and S. yunnanensis. Results suggested that S. chartarum may not be well delineated even after S. chlorohalonata was recently segregated from the species complex. Further study on the taxonomic status of the epithet S. chartarum is necessary. Six species of Stachybotrys are present indoors. Differentiation of Stachybotrys chartarum from S. chlorohalonata, and S. yunnanensis can be challenging using either morphological or QPCR methods. Caution should be taken to identify S. chartarum and closely related species and to explain their health effects implication for indoor air quality investigations.

Genetic Diversity of Anopheles triannulatus s.l. (Diptera: Culicidae) from Northwestern and Southeastern Colombia

PubMed Central

Rosero, Doris A.; Jaramillo, Luz M.; Gutiérrez, Lina A.; Conn, Jan E.; Correa, Margarita M.

2012-01-01

Anopheles triannulatus s.l. is a species complex, however in Colombia its taxonomic status is unclear. This study was conducted to understand the level of genetic differentiation or population structure of specimens of An. triannulatus s.l. from northwestern and southeastern Colombia. Cytochrome oxidase subunit I (COI) and internal transcribed spacer (ITS2) sequence analyses suggested high genetic differentiation between the NW and SE populations. A TCS network and Bayesian inference analysis based on 814 bp of COI showed two main groups: group I included samples from the NW and group II samples from the SE. Two main ITS2-polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) patterns were found. Pattern I is present in both the NW and SE, and pattern II is found in the SE specimens. To further elucidate the taxonomic status of An. triannulatus s.l. in Colombia and how these COI lineages are related to the Triannulatus Complex species, the evaluation of immature stages, male genitalia, and additional mitochondrial and nuclear markers will be needed. PMID:22949519

Genetic diversity of Anopheles triannulatus s.l. (Diptera: Culicidae) from northwestern and southeastern Colombia.

PubMed

Rosero, Doris A; Jaramillo, Luz M; Gutiérrez, Lina A; Conn, Jan E; Correa, Margarita M

2012-11-01

Anopheles triannulatus s.l. is a species complex, however in Colombia its taxonomic status is unclear. This study was conducted to understand the level of genetic differentiation or population structure of specimens of An. triannulatus s.l. from northwestern and southeastern Colombia. Cytochrome oxidase subunit I (COI) and internal transcribed spacer (ITS2) sequence analyses suggested high genetic differentiation between the NW and SE populations. A TCS network and Bayesian inference analysis based on 814 bp of COI showed two main groups: group I included samples from the NW and group II samples from the SE. Two main ITS2-polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) patterns were found. Pattern I is present in both the NW and SE, and pattern II is found in the SE specimens. To further elucidate the taxonomic status of An. triannulatus s.l. in Colombia and how these COI lineages are related to the Triannulatus Complex species, the evaluation of immature stages, male genitalia, and additional mitochondrial and nuclear markers will be needed.

Reef sharks: recent advances in ecological understanding to inform conservation.

PubMed

Osgood, G J; Baum, J K

2015-12-01

Sharks are increasingly being recognized as important members of coral-reef communities, but their overall conservation status remains uncertain. Nine of the 29 reef-shark species are designated as data deficient in the IUCN Red List, and three-fourths of reef sharks had unknown population trends at the time of their assessment. Fortunately, reef-shark research is on the rise. This new body of research demonstrates reef sharks' high site restriction, fidelity and residency on coral reefs, their broad trophic roles connecting reef communities and their high population genetic structure, all information that should be useful for their management and conservation. Importantly, recent studies on the abundance and population trends of the three classic carcharhinid reef sharks (grey reef shark Carcharhinus amblyrhynchos, blacktip reef shark Carcharhinus melanopterus and whitetip reef shark Triaenodon obesus) may contribute to reassessments identifying them as more vulnerable than currently realized. Because over half of the research effort has focused on only these three reef sharks and the nurse shark Ginglymostoma cirratum in only a few locales, there remain large taxonomic and geographic gaps in reef-shark knowledge. As such, a large portion of reef-shark biodiversity remains uncharacterized despite needs for targeted research identified in their red list assessments. A research agenda for the future should integrate abundance, life history, trophic ecology, genetics, habitat use and movement studies, and expand the breadth of such research to understudied species and localities, in order to better understand the conservation requirements of these species and to motivate effective conservation solutions. © 2015 The Fisheries Society of the British Isles.

Molecular and morphological discrimination of stipitate hydnoids in the genera Hydnellum and Phellodon.

PubMed

Parfitt, David; Martyn Ainsworth, A; Simpson, Deborah; Rogers, Hilary J; Boddy, Lynne

2007-07-01

Hydnellum and Phellodon species, generally considered ectomycorrhizal partners of a range of woody angiosperms and gymnosperms particularly within Fagaceae and Pinaceae, appear to be declining in continental Europe. They are listed as priority species in the UK Biodiversity Action Plan, but their UK conservation status remains uncertain. Interpretation of species distribution data is hampered by a lack of consensus regarding some key discriminatory morphological characters and difficulties with their interpretation. DNA sequencing of the ITS1 region of the ribosomal gene cluster discriminated between the known British species of Phellodon but revealed more terminal clusters than currently recognised taxa. Although the main focus within Hydnellum was on the very similar species pair H. concrescens and H. scrobiculatum, a few samples of H. caeruleum, H. ferrugineum, H. peckii, and H. spongiosipes were included in the study for reference. DNA sequencing of material identified on spore-based criteria as H. concrescens yielded two main groups, but samples received as H. scrobiculatum were generally more variable. Of these, two were reassigned and the remaining group, with very similar spores (although shorter than in published descriptions of H. scrobiculatum), had highly variable sequence data. The results and conservation importance of these fungi highlight the need for a taxonomic reassessment of P. melaleucus, P. niger, H. concrescens, and H. scrobiculatum collections from Britain and continental Europe using a combined molecular and morphological approach. Specific PCR primers were constructed to discriminate fruit bodies, mycelium, and mycorrhizal roots of P. niger and P. confluens from each other and from other stipitate hydnoids.

Taxonomic status and morphological variation of Hydrodynastes bicinctus (Hermann, 1804) (Serpentes: Dipsadidae).

PubMed

Murta-Fonseca, Roberta A; Franco, Francisco L; Fernandes, Daniel Silva

2016-08-26

Hydrodynastes bicinctus was described with no type material or locality and it has two subspecies currently recognized that are not taxonomically well defined. We tested the validity of the two subspecies through meristic, morphometric, and color pattern characters. Two apparently distinct color patterns of H. bicinctus were noticed, one from the Cerrado open formations and the other from the Amazon rainforest. These aforementioned patterns, however, exhibited a high degree of geographic overlap and many specimens showed a blended pattern. Based on these results we propose synonymizing H. bicinctus schultzi with the nominal taxon. Furthermore, we designate a neotype for the species, present data on geographic distribution, and provide morphological descriptions of the hemipenis, cephalic glands, and skull.

Biology and genetics of human head and body lice.

PubMed

Veracx, Aurélie; Raoult, Didier

2012-12-01

Head lice and body lice have distinct ecologies and differ slightly in morphology and biology, questioning their taxonomic status. Over the past 10 years many genetic studies have been undertaken. Controversial data suggest that not only body lice but also head lice can serve as vectors of Bartonella quintana, and a better understanding of louse epidemiology is crucial. Here, we review taxonomic studies based on biology and genetics, including genomic data on lice, lice endosymbionts, and louse-transmitted bacteria. We recommend that studies of human lice employ morphological and biological characteristics in conjunction with transcriptomic date because lice seem to differ mainly in gene expression (and not in gene content), leading to different phenotypes. Copyright © 2012 Elsevier Ltd. All rights reserved.

Global patterns of extinction risk in marine and non-marine systems.

PubMed

Webb, Thomas J; Mindel, Beth L

2015-02-16

Despite increasing concern over the effects of human activities on marine ecosystems, extinction in the sea remains scarce: 19-24 out of a total of >850 recorded extinctions implies a 9-fold lower marine extinction rate compared to non-marine systems. The extent of threats faced by marine systems, and their resilience to them, receive considerable attention, but the detectability of marine extinctions is less well understood. Before its extinction or threat status is recorded, a species must be both taxonomically described and then formally assessed; lower rates of either process for marine species could thus impact patterns of extinction risk, especially as species missing from taxonomic inventories may often be more vulnerable than described species. We combine data on taxonomic description with conservation assessments from the International Union for Conservation of Nature (IUCN) to test these possibilities across almost all marine and non-marine eukaryotes. We find that the 9-fold lower rate of recorded extinctions and 4-fold lower rate of ongoing extinction risk across marine species can be explained in part by differences in the proportion of species assessed by the IUCN (3% cf. 4% of non-marine species). Furthermore, once taxonomic knowledge and conservation assessments pass a threshold level, differences in extinction risk between marine and non-marine groups largely disappear. Indeed, across the best-studied taxonomic groups, there is no difference between marine and non-marine systems, with on average between 20% and 25% of species being threatened with extinction, regardless of realm. Copyright © 2015 Elsevier Ltd. All rights reserved.

COHO SALMON DEPENDENCE ON INTERMITTENT STREAMS

EPA Science Inventory

In February 2006, the US Supreme Court heard cases that may affect whether intermittent streams are jurisdictional waters under the Clean Water Act. In June 2006, however, the cases were remanded to the circuit court, leaving the status of intermittent streams uncertain once agai...

DNA barcode-based delineation of putative species: efficient start for taxonomic workflows

PubMed Central

Kekkonen, Mari; Hebert, Paul D N

2014-01-01

The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths. OTUs supported by all three approaches were viewed as robust, but 20% of the OTUs were only recognized by one or two of the methods. These OTUs were examined for three criteria to clarify their status. Monophyly and diagnostic nucleotides were both uninformative, but information on ranges was useful as sympatric sister OTUs were viewed as distinct, while allopatric OTUs were merged. This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species. Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies. PMID:24479435

Is Widely Cultivated "Pleurotus sajor-caju", Especially in Asia, Indeed an Independent Species?

PubMed

Zmitrovich, Ivan V; Wasser, Solomon P

2016-01-01

In modern mycology, the name "Pleurotus sajor-caju" has 2 meanings: a strict taxonomical meaning refers to its nomenclatural synonym Lentinus sajor-caju, and a more widely distributed biotechnological meaning refers to a strain determined as "Pleurotus sajor-caju" but that belongs to true Pleurotus. The main purpose of this article is to highlight the taxonomic status and to give the correct name for this problematic member of Pleurotus. Both microscopic analysis and BLAST search results (internal transcribed spacer homology varies between 97% and 100%) provide the position of the fungus in question into the range of infraspecific radiation of P. pulmonarius. It was shown that the fungus represents a tropical ecotype of P. pulmonarius, and a new variety (P. pulmonarius var. stechangii) was described for its taxonomic representation. This variety was named in honor of Professor S.-T. Chang, a great mycologist who introduced this taxon to the mushroom industry. A formal change in the anamorphic name of the fungus in question is provided, too, and a new name is presented: Antromycopsis stechangii.

Molecular characterization and species delimiting of plant-parasitic nematodes of the genus Pratylenchus from the penetrans group (Nematoda: Pratylenchidae).

PubMed

Janssen, Toon; Karssen, Gerrit; Orlando, Valeria; Subbotin, Sergei A; Bert, Wim

2017-12-01

Root-lesion nematodes of the genus Pratylenchus are an important pest parasitizing a wide range of vascular plants including several economically important crops. However, morphological diagnosis of the more than 100 species is problematic due to the low number of diagnostic features, high morphological plasticity and incomplete taxonomic descriptions. In order to employ barcoding based diagnostics, a link between morphology and species specific sequences has to be established. In this study, we reconstructed a multi-gene phylogeny of the Penetrans group using nuclear ribosomal and mitochondrial gene sequences. A combination of this phylogenetic framework with molecular species delineation analysis, population genetics, morphometric information and sequences from type location material allowed us to establish the species boundaries within the Penetrans group and as such clarify long-standing controversies about the taxonomic status of P. penetrans, P. fallax and P. convallariae. Our study also reveals a remarkable amount of cryptic biodiversity within the genus Pratylenchus confirming that identification on morphology alone can be inconclusive in this taxonomically confusing genus. Copyright © 2017 Elsevier Inc. All rights reserved.

Shedding subspecies: The influence of genetics on reptile subspecies taxonomy.

PubMed

Torstrom, Shannon M; Pangle, Kevin L; Swanson, Bradley J

2014-07-01

The subspecies concept influences multiple aspects of biology and management. The 'molecular revolution' altered traditional methods (morphological traits) of subspecies classification by applying genetic analyses resulting in alternative or contradictory classifications. We evaluated recent reptile literature for bias in the recommendations regarding subspecies status when genetic data were included. Reviewing characteristics of the study, genetic variables, genetic distance values and noting the species concepts, we found that subspecies were more likely elevated to species when using genetic analysis. However, there was no predictive relationship between variables used and taxonomic recommendation. There was a significant difference between the median genetic distance values when researchers elevated or collapsed a subspecies. Our review found nine different concepts of species used when recommending taxonomic change, and studies incorporating multiple species concepts were more likely to recommend a taxonomic change. Since using genetic techniques significantly alter reptile taxonomy there is a need to establish a standard method to determine the species-subspecies boundary in order to effectively use the subspecies classification for research and conservation purposes. Copyright © 2014 Elsevier Inc. All rights reserved.

Unveiling Distribution Patterns of Freshwater Phytoplankton by a Next Generation Sequencing Based Approach

PubMed Central

Eiler, Alexander; Drakare, Stina; Bertilsson, Stefan; Pernthaler, Jakob; Peura, Sari; Rofner, Carina; Simek, Karel; Yang, Yang; Znachor, Petr; Lindström, Eva S.

2013-01-01

The recognition and discrimination of phytoplankton species is one of the foundations of freshwater biodiversity research and environmental monitoring. This step is frequently a bottleneck in the analytical chain from sampling to data analysis and subsequent environmental status evaluation. Here we present phytoplankton diversity data from 49 lakes including three seasonal surveys assessed by next generation sequencing (NGS) of 16S ribosomal RNA chloroplast and cyanobacterial gene amplicons and also compare part of these datasets with identification based on morphology. Direct comparison of NGS to microscopic data from three time-series showed that NGS was able to capture the seasonality in phytoplankton succession as observed by microscopy. Still, the PCR-based approach was only semi-quantitative, and detailed NGS and microscopy taxa lists had only low taxonomic correspondence. This is probably due to, both, methodological constraints and current discrepancies in taxonomic frameworks. Discrepancies included Euglenophyta and Heterokonta that were scarce in the NGS but frequently detected by microscopy and Cyanobacteria that were in general more abundant and classified with high resolution by NGS. A deep-branching taxonomically unclassified cluster was frequently detected by NGS but could not be linked to any group identified by microscopy. NGS derived phytoplankton composition differed significantly among lakes with different trophic status, showing that our approach can resolve phytoplankton communities at a level relevant for ecosystem management. The high reproducibility and potential for standardization and parallelization makes our NGS approach an excellent candidate for simultaneous monitoring of prokaryotic and eukaryotic phytoplankton in inland waters. PMID:23349714

Identification of Rays through DNA Barcoding: An Application for Ecologists

PubMed Central

Cerutti-Pereyra, Florencia; Meekan, Mark G.; Wei, Nu-Wei V.; O'Shea, Owen; Bradshaw, Corey J. A.; Austin, Chris M.

2012-01-01

DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera) of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the Neotrygon kuhlii species complex and the Aetobatus species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the ‘uarnak’ complex. Two sets of problems limited the successful application of DNA barcoding: (1) the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2) insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data. PMID:22701556

Conservation genetics of North American freshwater mussels Amblema and Megalonaias

USGS Publications Warehouse

Mulvey, M.; Lydeard, C.; Pyer, D.L.; Hicks, K.M.; Brim-Box, J.; Williams, J.D.; Butler, R.S.

1997-01-01

Freshwater bivalves are among the most endangered groups of organisms in North America. Efforts to protect the declining mussel fauna are confounded by ambiguities associated with recognition of distinct evolutionary entities or species. This, in part, is due to the paucity of reliable morphological characters for differentiating taxa. We have employed allozymes and DNA sequence data to search for diagnosably distinct evolutionary entities within two problematic genera of unionid mussels, Amblema and Megalonaias. Within the genus Amblema three species are recognized based on our DNA sequence data for the mitochondrial 16S rRNA and allozyme data (Amblema neislerii, A. plicata, and A. elliotti). Only one taxonomically distinct entity is recognized within the genus Megalonaias—M. nervosa. Megalonaias boykiniana of the Apalachicolan Region is not diagnosable and does not warrant specific taxonomic status. Interestingly, Megalonaias from west of the Mississippi River, including the Mississippi, exhibited an allozyme and mtDNA haplotype frequency shift suggestive of an east-west dichotomy. The results of this study eliminate one subspecies of Amblema and increase the range of A. plicata. This should not affect the conservation status of “currently stable” assigned to A. plicata by Williams et al. (1993). The conservation status of A. elliotti needs to be reexamined because its distribution appears to be limited to the Coosa River System in Alabama and Georgia.

Genetic and Morphometric Evidence for the Conspecific Status of the Bumble Bees, Bombus melanopygus and Bombus edwardsii

PubMed Central

Owen, Robin E.; Whidden, Troy L.; Plowright, R.C.

2010-01-01

The taxonomic status of closely related bumble bee species is often unclear. The relationship between the two nominate taxa, Bombus melanopygus Nylander (Hymenoptera: Apidae) and Bombus edwardsii Cresson (Hymenoptera: Apidae), was investigated using genetic (enzyme electrophoretic) and morphometric analyses. The taxa differ in the color of the abdominal terga two and three, being ferruginous in B. melanopygus and black in B. edwardsii. B. edwardsii occurs throughout California, while B. melanopygus extends north through Oregon, to Alaska and Canada. They are sympatric only in southern Oregon and northern California. The taxonomic status of these taxa was questioned when Owen and Plowright (1980) reared colonies from queens collected in the area of sympatry, and discovered that pile coloration was due to a single, biallelic Mendelian gene, with the red (R) allele dominant to the black (r). Here it is shown that all the taxa, whether from California, Oregon, or Alberta, have the same electrophoretic profile and cannot be reliably distinguished by wing morphometrics. This strongly supports the conclusion that B. melanopygus and B. edwardsii are conspecific and should be synonymized under the name B. melanopygus. Hence, there is a gene frequency cline running from north to south, where the red allele is completely replaced by the black allele over a distance of about 600 km. PMID:20874396

Correlates of vulnerability in Chiricahua fox squirrels

Treesearch

Bret S. Pasch; John L. Koprowski

2005-01-01

Chiricahua fox squirrels (Sciurus nayaritensis chiricahuae) are endemic to the Chiricahua Mountains of southeastern Arizona. A paucity of natural history information and uncertain conservation status served as impetus for us to initiate a descriptive ecological study of the species. We examined reproductive and population ecology of Chiricahua fox...

Evaluative Research in Corrections: The Uncertain Road.

ERIC Educational Resources Information Center

Adams, Stuart

Martinson's provocative article in Public Interest (Spring, 1974), denying efficacy in prisoner reform, singled out one of the uncertainties in correctional research. In their totality, these uncertainties embrace not only rehabilitative programs but also the method, theory, and organization of correctional research. To comprehend the status and…

[Morphology of some tricostrongilinae (Strongylida) from the National Helminth Collection, Institute of Biology, UNAM, Mexico].

PubMed

Falcón-Ordaz, Jorge; García-Prieto, Luis

2004-06-01

The present study analyses the taxonomic status of eleven species of trichostrongylins that parasitize rodents and lagomorphs deposited in the Colección Nacional de Helmintos, Instituto de Biología. UNAM. Mexico. This analysis is based on the morphology of the synlophe, characteristic that had not been studied for most of these nematode species and at present, it has a very important taxonomic value. As a result of this study, the identity of five species is ratified (Trichostrongylus calcaratus, Obeliscoides cuniculi, Carolinensis huehuetlana. Stilestrongylus peromysci and Nippostrongylus brasiliensis), the transference suggested previously for two more (Vexillata convoluta and Vexillata vexillata) is confirmed, Trichostrongylus chiapensis is synonymized with Boehmiella willsoni, and finally Lamothiella romerolagi is re-determined as Teporingonema cerropeladoensis and Stilestrongylus atlatilpinensis as Stilestrongylus hidalguensis.

New Approaches to Systematics of Trypanosomatidae: Criteria for Taxonomic (Re)description.

PubMed

Votýpka, Jan; d'Avila-Levy, Claudia M; Grellier, Philippe; Maslov, Dmitri A; Lukeš, Julius; Yurchenko, Vyacheslav

2015-10-01

While dixenous trypanosomatids represent one of the most dangerous pathogens for humans and domestic animals, their monoxenous relatives have frequently become model organisms for studies of diversity of parasitic protists and host-parasite associations. Yet, the classification of the family Trypanosomatidae is not finalized and often confusing. Here we attempt to make a blueprint for future studies in this field. We would like to elicit a discussion about an updated procedure, as traditional taxonomy was not primarily designed to be used for protists, nor can molecular phylogenetics solve all the problems alone. The current status, specific cases, and examples of generalized solutions are presented under conditions where practicality is openly favored over rigid taxonomic codes or blind phylogenetic approach. Copyright © 2015 Elsevier Ltd. All rights reserved.

Girls' Groups as a Component of Anti-Sexist Practice--One Primary School's Experience.

ERIC Educational Resources Information Center

Reay, Diane

1990-01-01

In an effort to improve their achievement and confidence, girls at a London elementary school were segregated and taught subjects designed to counter traditional role limitations. Boys, meanwhile, felt their status was being undermined, and teachers were uncertain about the rightness of countering societal norms. (DM)

Kid Categories: A Comparison of the Category Productions of LSES and MSES Elementary School Children

ERIC Educational Resources Information Center

Williams, Rihana S.; Terry, Nicole Patton; Metzger, Isha

2013-01-01

The current study compares the productivity (number of responses) and the typical responses to taxonomic and slot-filler prompts in 39 African American children from low-income backgrounds and a diverse group of 21 children from middle-income backgrounds. The authors tested the hypothesis that socioeconomic status would exert a global influence on…

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Treesearch

L.N. Hudson; T. Newbold; S. Contu

2014-01-01

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that...

Streptomyces aridus sp. nov., isolated from a high altitude Atacama Desert soil and emended description of Streptomyces noboritoensis Isono et al. 1957

USDA-ARS?s Scientific Manuscript database

A polyphasic study was undertaken to determine the taxonomic status of a Streptomyces strain which had been isolated from a high altitude Atacama Desert soil and shown to have bioactive properties. The strain, isolate H9T, was found to have chemotaxonomic, cultural, and morphological properties that...

Streptomyces asenjonii sp. nov., isolated from arid Atacama Desert soils and emended description of Streptomyces viridosporus Pridham et al. 1958

USDA-ARS?s Scientific Manuscript database

A polyphasic study was undertaken to establish the taxonomic status of Streptomyces strains isolated from arid Atacama Desert soils. Analysis of the 16S rRNA gene sequences of the isolates showed that they formed a well-defined lineage that was loosely associated with the type strains of several Str...

Population growth rate of dry bulb mite, Aceria tulipae (Keifer) (Acariformes: Eriophyidae) on agriculturally important plants and implications on taxonomic status

USDA-ARS?s Scientific Manuscript database

Dry bulb mite (DBM), Aceria tulipae, is an economically important mite with a worldwide distribution and a broad host range. As a generalist, it is the most important eriophyoid mite attacking bulbous plants such as garlic, onion, and tulip. To date, DBM has been recorded on host plants belonging to...

Diversity of Ptychadena in Rwanda and taxonomic status of P. chrysogaster Laurent, 1954 (Amphibia, Anura, Ptychadenidae)

PubMed Central

Dehling, J. Maximilian; Sinsch, Ulrich

2013-01-01

Abstract We assess the diversity of Ptychadena species in Rwanda based on re-examination of voucher specimens in museum collections and our own data from recent assessment of the species composition of amphibian communities in Rwanda. We recognize five species which we allocate to the following available names: P. anchietae, P. chrysogaster, P. nilotica, P. porosissima, and P. uzungwensis. We did not find evidence for the presence of P. grandisonae and P. oxyrhynchus which have been listed for the country. The five species can be distinguished by quantitative morphometrics (discriminant analysis, success rate: 100 %) and a number of qualitative characters of external morphology. We provide an identification key to the Rwandan species and describe the morphology of each species in detail. The taxonomic status and the phylogenetic position of Ptychadena chrysogaster are further assessed based on the partial sequence of the mitochondrial 16S rRNA. The species differs genetically from available homologous sequences from congeners by an uncorrected p distance of at least 4.2 % and appears to be most closely related to specimens assigned to P. porosissima, P. mahnerti, “P. aff. uzungwensis” and “P. aff. bibroni”. PMID:24363574

Utility of DNA barcoding for rapid and accurate assessment of bat diversity in Malaysia in the absence of formally described species.

PubMed

Wilson, J-J; Sing, K-W; Halim, M R A; Ramli, R; Hashim, R; Sofian-Azirun, M

2014-02-19

Bats are important flagship species for biodiversity research; however, diversity in Southeast Asia is considerably underestimated in the current checklists and field guides. Incorporation of DNA barcoding into surveys has revealed numerous species-level taxa overlooked by conventional methods. Inclusion of these taxa in inventories provides a more informative record of diversity, but is problematic as these species lack formal description. We investigated how frequently documented, but undescribed, bat taxa are encountered in Peninsular Malaysia. We discuss whether a barcode library provides a means of recognizing and recording these taxa across biodiversity inventories. Tissue was sampled from bats trapped at Pasir Raja, Dungun Terengganu, Peninsular Malaysia. The DNA was extracted and the COI barcode region amplified and sequenced. We identified 9 species-level taxa within our samples, based on analysis of the DNA barcodes. Six specimens matched to four previously documented taxa considered candidate species but currently lacking formal taxonomic status. This study confirms the high diversity of bats within Peninsular Malaysia (9 species in 13 samples) and demonstrates how DNA barcoding allows for inventory and documentation of known taxa lacking formal taxonomic status.

A revision of the genus Muricea Lamouroux, 1821 (Anthozoa, Octocorallia) in the eastern Pacific. Part II

PubMed Central

Breedy, Odalisca; Guzman, Hector M.

2016-01-01

Abstract The species of the genus Muricea were mainly described from 1846 to 1870. After that very few contributions were published. Although the highest richness of Muricea species is in the eastern Pacific shallow waters, a comprehensive systematic study of the genus does not exist. Recently we started a taxonomic review of the genus in order to validate the status of four species previously included in the genus Eumuricea. Herein we present the second part of the Muricea revision dealing with the species-group characterised by shelf-like calyces instead of tubular-like calyces (the Muricea squarrosa-group). Original type material was morphologically analysed and illustrated using optical and scanning electron microscopy. Comparative character tables are provided for the genus. The taxonomic status of the species was analysed and established by designating lectotypes, alternatively by recognising a holotype by monotypy. We conclude that the genus Muricea comprises 20 valid species, including the previous four in the Muricea squarrosa-group. We propose 10 lectotypes, a new combination and three more species groups for the genus based on morphology: the Muricea fruticosa-group, Muricea plantaginea-group and Muricea austera-group. PMID:27199581

Pandora formicae, a specialist ant pathogenic fungus: New insights into biology and taxonomy.

PubMed

Małagocka, Joanna; Jensen, Annette Bruun; Eilenberg, Jørgen

2017-02-01

Among fungi from the order Entomophthorales (Entomophthoromycota), there are many specialized, obligatory insect-killing pathogens. Pandora formicae (Humber & Bałazy) Humber is a rare example of an entomophthoralean fungus adapted to exclusively infect social insects: wood ants from the genus Formica. There is limited information available on P. formicae; many important aspects of this host-pathogen system remain hitherto unknown, and the taxonomical status of the fungus is unclear. Our study fills out some main gaps in the life history of P. formicae, such as seasonal prevalence and overwintering strategy. Field studies of infection prevalence show a disease peak in late summer and early autumn. Typical thick-walled entomophthoralean resting spores of P. formicae are documented and described for the first time. The proportion of cadavers with resting spores increased from late summer throughout autumn, suggesting that these spores are the main overwintering fungal structures. In addition, the phylogenetic status of Pandora formicae is outlined. Finally, we review the available taxonomical literature and conclude that the name P. formicae should be used rather than the name P. myrmecophaga for ant-infecting fungi displaying described morphological features. Copyright © 2016 Elsevier Inc. All rights reserved.

Molecular taxonomy of Dunaliella (Chlorophyceae), with a special focus on D. salina: ITS2 sequences revisited with an extensive geographical sampling

PubMed Central

2012-01-01

We used an ITS2 primary and secondary structure and Compensatory Base Changes (CBCs) analyses on new French and Spanish Dunallela salina strains to investigate their phylogenetic position and taxonomic status within the genus Dunaliella. Our analyses show a great diversity within D. salina (with only some clades not statistically supported) and reveal considerable genetic diversity and structure within Dunaliella, although the CBC analysis did not bolster the existence of different biological groups within this taxon. The ITS2 sequences of the new Spanish and French D. salina strains were very similar except for two of them: ITC5105 "Janubio" from Spain and ITC5119 from France. Although the Spanish one had a unique ITS2 sequence profile and the phylogenetic tree indicates that this strain can represent a new species, this hypothesis was not confirmed by CBCs, and clarification of its taxonomic status requires further investigation with new data. Overall, the use of CBCs to define species boundaries within Dunaliella was not conclusive in some cases, and the ITS2 region does not contain a geographical signal overall. PMID:22520929

Cyathostoma (Cyathostoma) phenisci Baudet, 1937 (Nematoda: Syngamidae), a parasite of respiratory tract of African penguin Spheniscus demersus: morphological and molecular characterisation with some ecological and veterinary notes.

PubMed

Kanarek, Gerard; Horne, Elizabeth C; Zaleśny, Grzegorz

2013-10-01

Here we provide a morphological and molecular analysis of the taxonomic status of Cyathostoma (Cyathostoma) phenisci Baudet, 1937, a rare nematode parasite of African penguin Spheniscus demersus. Taxonomical evaluation is supplemented wi th ecological and epidemiological analysis of the nematode's occurrence in the African penguin's population. Tracheae and air sacs of 13 among the 94 necropsied birds (overall prevalence 13.8%) contained a total of 33 nematode specimens (20 females, 13 males). The highest prevalence was observed in juveniles (6 infected, 25%) and "blues" (6 infected, 14.3%), followed by nestlings (1 infected, 7.7%); no nematodes were found in adults. Our morphological and morphometric analysis shows that C. phenisci is closely related to another species, Cyathostoma (Cyathostoma) verrucosum (Hovorka & Macko, 1959). The doubtful status of the latter species was confirmed by molecular data: comparison of ITS2 sequence of C. phenisci with previously deposited sequences of C. verrucosum showed 96.3% similarity in this region. On this basis, we recognized Cyathostoma (Cyathostoma) verrucosum (Hovorka & Macko, 1959) as a synonym of Cyathostoma (Cyathostoma) phenisci Baudet, 1937. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Contribution to knowledge of the genus Chydaeus in Xizang Autonomous Region [Tibet] and Yunnan Province, China (Coleoptera, Carabidae, Harpalini)

PubMed Central

Kataev, Boris M.; Liang, Hongbin; Kavanaugh, David H.

2012-01-01

Abstract Five new species of the genus Chydaeus Chaudoir, 1854 are described from China: Chydaeus fugongensis sp. n. (Shibali, Fugong County, Yunnan Province), Chydaeus gutangensis sp. n. (Gutang, Medog County, Xizang Autonomous Region [Tibet]), Chydaeus hanmiensis sp. n. (Hanmi, Medog County, Xizang Autonomous Region [Tibet]), Chydaeus asetosus sp. n. (NE of Fugong, Yunnan Province), and Chydaeus baoshanensis sp. n. (N of Baoshan, Yunnan Province). Taxonomic and faunistic notes on eleven other species occurring in Xizang and Yunnan are also provided. Chydaeus shunichii Ito, 2006 is re-described, based on specimens from Lushui County, Yunnan. Chydaeus kumei Ito, 1992 is treated as a subspecies of Chydaeus andrewesi Schauberger, 1932 [NEW STATUS]. The taxonomic status of Chydaeus guangxiensis Ito, 2006 is discussed. The following taxa are recorded from China for the first time: Chydaeus obtusicollis Schauberger, 1932 (Xizang and Yunnan), Chydaeus malaisei Kataev & Schmidt, 2006 (Yunnan), Chydaeus semenowi (Tschitschérine, 1899) (Xizang and Yunnan), Chydaeus andrewesi andrewesi Schauberger, 1932 (Xizang and Yunnan), Chydaeus andrewesi kumei Ito (Yunnan), Chydaeus bedeli interjectus Kataev & Schmidt, 2002 (Xizang), and Chydaeus bedeli vietnamensis Kataev & Schmidt, 2002 (Yunnan). PMID:22423195

Novelties in secretory structures and anatomy of Rhynchosia (Fabaceae).

PubMed

De Vargas, Wanderleia; Sartori, Ângela L B; Dias, Edna S

2015-03-01

A comparative anatomical study was carried out on the secretory structures of leaflets from taxa belonging to the genus Rhynchosia - taxa difficult to delimit because of uncertain interspecific relations - in order to evaluate the potential diagnostic value of these anatomical traits for taxonomic assignment. A further objective was to establish consensual denomination for these secretory structures. The new anatomical features found in these taxa were sufficiently consistent to separate the species evaluated. The presence and localization of glandular-punctate structures bulbous-based trichomes, the number of layers in the palisade parenchyma and the arrangement of vascular units distinguish the taxa investigated and these characteristics can be extended to other species of Papilionoideae. The trichomes analyzed were described and classified into five types. Depicted in diagrams, photomicrographs, and by scanning electron microscopy, and listed for the first time at the genus and species levels. The information obtained served to effectively distinguish the taxa investigated among species of Papilonoideae.

Silurian sponges and some associated fossils from the Heceta Limestone, Prince of Wales Island, southeastern Alaska

USGS Publications Warehouse

Rigby, J.K.; Rohr, D.M.; Blodgett, R.B.; Britt, B.B.

2008-01-01

A small faunule of hypercalcified agelasiid demosponges has been recovered from outcrops of the Silurian Heceta Formation on Prince of Wales Island in southeastern Alaska. Included are abundant Girtyocoeliana epiporata (Rigby and Potter, 1986), of the Girtyocoeliidae Finks and Rigby, 2004; fragments of Alaskaspongiella laminosa n. gen. and sp., Polyplacospongia nodosa n. gen. and sp., and Monolaminospongia gigantia n. gen. and sp., of the Auriculospongiidae Termier and Termier, 1977, and Cladospongia alaskensis n. gen. and sp., Virgulaspongia uniforma n. gen. and sp., and Stipespongia laminata n. gen. and sp. of the Preperonidellidae Finks and Rigby, 2004. Also included are a few fossils of uncertain taxonomic placement, including Turbospongia biperforata n. gen. and sp., along with a small, chambered, tubular fragment and several porous tubular stems that may be additional poriferans. Some isolated octactine-based heteractinid spicules were also recovered from the etched residues. Copyright ?? 2008, The Paleontological Society.

Taxonomy of the bee species Anthrenoides nigrinasis (Vachal, 1909) n. comb.: redescription of the type, description of the female, and new distribution records (Hymenoptera: Apoidea).

PubMed

Ramos, Kelli S

2018-02-07

Protandrenini includes approximately 420 species of short-tongued bees, which are exclusively distributed in the Americas (Michener 2007; Moure et al. 2007; Ascher Pickering 2017). Members of this tribe are mostly found in xeric and temperate areas in South America, and their diversity is still greatly underestimated. In fact, a major challenge to the systematics of Protandrenini is the outstanding number of species unplaced in genera or awaiting formal description (Ruz Chiappa 2004; Ramos Melo 2006; Michener 2007; Moure et al. 2007; Ramos Rozen 2014). In addition to several taxa currently considered of uncertain position within the tribe, many South American genera are in need of taxonomic revision, such as Rhophitulus Ducke, Anthrenoides Ducke, and Psaenythia Gerstaecker (Silveira et al. 2002; Michener 2007; Ramos Melo 2010; Moure et al. 2007).

Insights from ecological niche modeling on the taxonomic distinction and niche differentiation between the black-spotted and red-spotted tokay geckoes (Gekko gecko).

PubMed

Zhang, Yueyun; Chen, Chongtao; Li, Li; Zhao, Chengjian; Chen, Weicai; Huang, Yong

2014-09-01

The black-spotted tokay and the red-spotted tokay are morphologically distinct and have largely allopatric distributions. The black-spotted tokay is characterized by a small body size and dark skin with sundry spots, while the red-spotted tokay has a relatively large body size and red spots. Based on morphological, karyotypic, genetic, and distribution differences, recent studies suggested their species status; however, their classifications remain controversial, and additional data such as ecological niches are necessary to establish firm hypotheses regarding their taxonomic status. We reconstructed their ecological niches models using climatic and geographic data. We then performed niche similarity tests (niche identity and background tests) and point-based analyses to explore whether ecological differentiation has occurred, and whether such differences are sufficient to explain the maintenance of their separate segments of environmental ranges. We found that both niche models of the black- and the red-spotted tokay had a good fit and a robust performance, as indicated by the high area under the curve (AUC) values ("black" = 0.982, SD = ± 0.002, "red" = 0.966 ± 0.02). Significant ecological differentiation across the entire geographic range was found, indicating that the involvement of ecological differentiation is important for species differentiation. Divergence along the environmental axes is highly associated with climatic conditions, with isothermality being important for the "black" form, while temperature seasonality, precipitation of warmest quarter, and annual temperature range together being important for the "red" form. These factors are likely important factors in niche differentiation between the two forms, which result in morphological replacement. Overall, beside morphological and genetic differentiation information, our results contribute to additional insights into taxonomic distinction and niche differentiation between the black- and the red-spotted tokay.

Phylogenetic Molecular Species Delimitations Unravel Potential New Species in the Pest Genus Spodoptera Guenée, 1852 (Lepidoptera, Noctuidae)

PubMed Central

Dumas, Pascaline; Barbut, Jérôme; Le Ru, Bruno; Silvain, Jean-François; Clamens, Anne-Laure; d’Alençon, Emmanuelle; Kergoat, Gael J.

2015-01-01

Nowadays molecular species delimitation methods promote the identification of species boundaries within complex taxonomic groups by adopting innovative species concepts and theories (e.g. branching patterns, coalescence). As some of them can efficiently deal with large single-locus datasets, they could speed up the process of species discovery compared to more time consuming molecular methods, and benefit from the existence of large public datasets; these methods can also particularly favour scientific research and actions dealing with threatened or economically important taxa. In this study we aim to investigate and clarify the status of economically important moths species belonging to the genus Spodoptera (Lepidoptera, Noctuidae), a complex group in which previous phylogenetic analyses and integrative approaches already suggested the possible occurrence of cryptic species and taxonomic ambiguities. In this work, the effectiveness of innovative (and faster) species delimitation approaches to infer putative species boundaries has been successfully tested in Spodoptera, by processing the most comprehensive dataset (in terms of number of species and specimens) ever achieved; results are congruent and reliable, irrespective of the set of parameters and phylogenetic models applied. Our analyses confirm the existence of three potential new species clusters (for S. exigua (Hübner, 1808), S. frugiperda (J.E. Smith, 1797) and S. mauritia (Boisduval, 1833)) and support the synonymy of S. marima (Schaus, 1904) with S. ornithogalli (Guenée, 1852). They also highlight the ambiguity of the status of S. cosmiodes (Walker, 1858) and S. descoinsi Lalanne-Cassou & Silvain, 1994. This case study highlights the interest of molecular species delimitation methods as valuable tools for species discovery and to emphasize taxonomic ambiguities. PMID:25853412

Current and future perspectives on the systematics, taxonomy and nomenclature of testate amoebae.

PubMed

Kosakyan, Anush; Gomaa, Fatma; Lara, Enrique; Lahr, Daniel J G

2016-09-01

Testate amoebae are a polyphyletic assemblage of at least three major, unrelated taxonomic groups of unicellular amoeboid eukaryotes exhibiting a test. The focus on testate amoebae in scientific research has greatly increased in the past 20 years: from an average of about 5 papers a year in the mid-1990s to the current rate of more than 50 papers published yearly. The application range of these organisms is rapidly expanding as well: from the traditional fields of environmental monitoring and paleoecology, to forensic sciences and ecotoxicology studies. These developments are nevertheless strongly dependent on reliable taxonomy and nomenclature. However, scientometric data reveal that despite an ever-increasing necessity for the use of names (the product of taxonomy), the corresponding effort has not been achieved for improving testate amoebae systematics. As a consequence, inaccurate taxonomy yields to misinterpretations in the diversity of the organisms and to potentially incorrect conclusions. These and related problems are discussed in this study, highlighting the outcome of poor taxonomic expertise in accurate classification and phylogeny of testate amoebae, and the consequences derived from it. Additionally, this study is aimed to discuss the current status of testate amoebae classification, and to present all nomenclature and taxonomic changes in higher and lower taxonomic levels of testate amoebae, as a result of recent molecular reconstructions. Finally, we conclude with a list of the needs and suggestions toward a unified and modernized taxonomy of testate amoebae. Copyright © 2016 Elsevier GmbH. All rights reserved.

The frequency of CSF oligoclonal banding in multiple sclerosis increases with latitude.

PubMed

Lechner-Scott, J; Spencer, B; de Malmanche, T; Attia, J; Fitzgerald, M; Trojano, M; Grand'Maison, F; Gomez, J Antonio C; Izquierdo, G; Duquette, P; Girard, M; Grammond, P; Oreja-Guevara, C; Hupperts, R; Bergamaschi, R; Boz, C; Giuliani, G; van Pesch, V; Iuliano, G; Fiol, M; Cristiano, E; Verheul, F; Saladino, M Laura; Slee, M; Barnett, M; Deri, N; Flechter, S; Vella, N; Shaw, C; Herbert, J; Moore, F; Petkovska-Boskova, T; Jokubaitis, V; Butzkueven, H

2012-07-01

With the advent of MRI scanning, the value of lumbar puncture to assess oligoclonal band (OCB) status-for the diagnosis of multiple sclerosis (MS) is increasingly uncertain. One major issue is that the reported frequency of cerebrospinal fluid (CSF)-restricted oligoclonal banding for the diagnosis of MS varies considerably in different studies. In addition, the relationship between OCB positivity and disease outcome remains uncertain, as reported studies are generally too small to assess comparative disability outcomes with sufficient power. In order to further investigate variation of OCB positivity in patients with MS, we utilized MSBase, a longitudinal, Web-based collaborative MS outcomes registry following clinical cohorts in several continents and latitudes. We also assessed whether OCB positivity affects long-term disability outcome. A total of 13,242 patient records were obtained from 37 MS specialist centres in 19 different countries. OCB status was documented in 4481 (34%) patients and 80% of these were OCB positive. The presence of OCB was associated with degree of latitude (p = 0.02). Furthermore, the outcome of patients negative for CSF-specific OCB was significantly better in comparison to the OCB positive patients, as assessed by Expanded Disability Status Scale change (p < 0.001). The results of this study indicate that latitude could explain some of the inconsistencies in OCB status reported in different populations. The study confirms that OCB positivity in MS is associated with a worse long-term prognosis.

Fauna Europaea: Annelida - Terrestrial Oligochaeta (Enchytraeidae and Megadrili), Aphanoneura and Polychaeta

PubMed Central

2015-01-01

Abstract Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. This paper provides updated information on the taxonomic composition and distribution of the Annelida - terrestrial Oligochaeta (Megadrili and Enchytraeidae), Aphanoneura and Polychaeta, recorded in Europe. Data on 18 families, 11 autochthonous and 7 allochthonous, represented in our continent by a total of 800 species, are reviewed, beginning from their distinctness, phylogenetic status, diversity and global distribution, and following with major recent developments in taxonomic and faunistic research in Europe. A rich list of relevant references is appended. The Fauna Europaea Annelida - terrestrial Oligochaeta data-set, as completed in 2004, will be updated accordingly. PMID:26379463

Cryptic diversity in the Azorean beetle genus Tarphius Erichson, 1845 (Coleoptera: Zopheridae): An integrative taxonomic approach with description of four new species.

PubMed

Borges, Paulo A V; Amorim, Isabel R; Terzopoulou, Sofia; Rigal, François; Emerson, Brent C; Serrano, Artur R M

2017-02-23

Recent findings based on molecular data support the occurrence in the Azores of several independently evolving lineages of the beetle genus Tarphius Erichson, 1845 (Coleoptera: Zopheridae Solier, 1834) and higher species richness masked by cryptic diversity, needing formal taxonomic description. All Tarphius from the Azores are revised using an integrative taxonomic approach, using evidence from morphology, morphometrics and molecular data to delimit species. Our results reveal that Azorean Tarphius comprise at least five phyletic lineages, two of which share a similar morphology, despite being divergent at the molecular level. A total of four new species are described grouped into two complexes: i) two new species in the "complex tornvalli" with the new taxa Tarphius relictus sp. nov. (Terceira) and Tarphius furtadoi sp. nov. (São Jorge, Faial and Pico) and; ii) two new species in the "complex azoricus-wollastoni-depressus" with the new taxa Tarphius gabrielae sp. nov. (Pico) and Tarphius floresensis sp. nov. (Flores). Descriptions, photographs of holotypes and morphological details, and remarks on diagnostic features comparing similar species are presented. Additional information on the distribution and conservation status of the 12 described species in the archipelago is also provided.

Microcos magnifica (Sparrmanniaceae) a new species of cloudforest tree from Cameroon

PubMed Central

2017-01-01

Background Although many new species to science have been discovered from thousands of specimens resulting from botanical inventories to support conservation management in Cameroon in recent years, additional species remain to be formally evaluated taxonomically and described. These include species from genera which have been taxonomically neglected for many decades in Africa, such as Microcos. Methods This study is based mainly on herbarium specimens and field observations made in Cameroon during a series of botanical surveys. Herbarium material was examined with a Leica Wild M8 dissecting binocular microscope fitted with an eyepiece graticule. Principal Findings Microcos magnifica Cheek (Malvaceae-Grewioideae or Sparrmanniaceae) is described as an Endangered (EN B2 ab(iii)) new tree species from the submontane forests of Cameroon. It is illustrated and described, and its conservation status and taxonomic affinities are assessed. It is the first new Microcos described from Africa in more than 90 years and is unique on the continent in having sculptured fruits. Discussion A systematic revision, with a molecular phylogenetic study, of Microcos Burm. ex L. in Africa is necessary if the affinities of the species, including M. magnifica, are to be reliably established. PMID:29230369

A novel multilocus phylogenetic estimation reveals unrecognized diversity in Asian horned toads, genus Megophrys sensu lato (Anura: Megophryidae).

PubMed

Chen, Jin-Min; Zhou, Wei-Wei; Poyarkov, Nikolay A; Stuart, Bryan L; Brown, Rafe M; Lathrop, Amy; Wang, Ying-Yong; Yuan, Zhi-Yong; Jiang, Ke; Hou, Mian; Chen, Hong-Man; Suwannapoom, Chatmongkon; Nguyen, Sang Ngoc; Duong, Tang Van; Papenfuss, Theodore J; Murphy, Robert W; Zhang, Ya-Ping; Che, Jing

2017-01-01

The horned toad assemblage, genus Megophrys sensu lato, currently includes three groups previously recognized as the genera Atympanophrys, Xenophrys and Megophrys sensu stricto. The taxonomic status and species composition of the three groups remain controversial due to conflicting phenotypic analyses and insufficient phylogenetic reconstruction; likewise, the position of the monotypic Borneophrys remains uncertain with respect to the horned toads. Further, the diversity of the horned toads remains poorly understood, especially for widespread species. Herein, we evaluate species-level diversity based on 45 of the 57 described species from throughout southern China, Southeast Asia and the Himalayas using Bayesian inference trees and the Generalized Mixed Yule Coalescent (GMYC) approach. We estimate the phylogeny using both mitochondrial and nuclear DNA data. Analyses reveal statistically significant mito-nuclear discordance. All analyses resolve paraphyly for horned toads involving multiple strongly supported clades. These clades correspond with geography. We resurrect the genera Atympanophrys and Xenophrys from the synonymy of Megophrys to eliminate paraphyly of Megophrys s.l. and to account for the morphological, molecular and biogeographic differences among these groups, but we also provide an alternative option. Our study suggests that Borneophrys is junior synonym of Megophrys sensu stricto. We provide an estimation of timeframe for the horned toads. The mitochondrial and nuclear trees indicate the presence of many putative undescribed species. Widespread species, such as Xenophrys major and X. minor, likely have dramatically underestimated diversity. The integration of morphological and molecular evidence can validate this discovery. Montane forest dynamics appear to play a significant role in driving diversification of horned toads. Copyright © 2016 Elsevier Inc. All rights reserved.

Intense genomic reorganization in the genus Oecomys (Rodentia, Sigmodontinae): comparison between DNA barcoding and mapping of repetitive elements in three species of the Brazilian Amazon

PubMed Central

Gomes Júnior, Renan Gabriel; Schneider, Carlos Henrique; de Lira, Thatianna; Carvalho, Natália Dayane Moura; Feldberg, Eliana; da Silva, Maria Nazareth Ferreira; Gross, Maria Claudia

2016-01-01

Abstract Oecomys Thomas, 1906 is one of the most diverse and widely distributed genera within the tribe Oryzomyini. At least sixteen species in this genus have been described to date, but it is believed this genus contains undescribed species. Morphological, molecular and cytogenetic study has revealed an uncertain taxonomic status for several Oecomys species, suggesting the presence of a complex of species. The present work had the goal of contributing to the genetic characterization of the genus Oecomys in the Brazilian Amazon. Thirty specimens were collected from four locations in the Brazilian Amazon and three nominal species recognized: Oecomys auyantepui (Tate, 1939), Oecomys bicolor (Tomes, 1860) and Oecomys rutilus (Anthony, 1921). COI sequence analysis grouped Oecomys auyantepui, Oecomys bicolor and Oecomys rutilus specimens into one, three and two clades, respectively, which is consistent with their geographic distribution. Cytogenetic data for Oecomys auyantepui revealed the sympatric occurrence of two different diploid numbers, 2n=64/NFa=110 and 2n=66/NFa=114, suggesting polymorphism while Oecomys bicolor exhibited 2n=80/NFa=142 and Oecomys rutilus 2n=54/NFa=90. The distribution of constitutive heterochromatin followed a species-specific pattern. Interspecific variation was evident in the chromosomal location and number of 18S rDNA loci. However, not all loci showed signs of activity. All three species displayed a similar pattern for 5S rDNA, with only one pair carrying this locus. Interstitial telomeric sites were found only in Oecomys auyantepui. The data presented in this work reinforce intra- and interspecific variations observed in the diploid number of Oecomys species and indicate that chromosomal rearrangements have led to the appearance of different diploid numbers and karyotypic formulas. PMID:27830049

Hybridization, agency discretion, and implementation of the U.S. Endangered Species Act.

PubMed

Lind-Riehl, Jennifer F; Mayer, Audrey L; Wellstead, Adam M; Gailing, Oliver

2016-12-01

The U.S. Endangered Species Act (ESA) requires that the "best available scientific and commercial data" be used to protect imperiled species from extinction and preserve biodiversity. However, it does not provide specific guidance on how to apply this mandate. Scientific data can be uncertain and controversial, particularly regarding species delineation and hybridization issues. The U.S. Fish and Wildlife Service (FWS) had an evolving hybrid policy to guide protection decisions for individuals of hybrid origin. Currently, this policy is in limbo because it resulted in several controversial conservation decisions in the past. Biologists from FWS must interpret and apply the best available science to their recommendations and likely use considerable discretion in making recommendations for what species to list, how to define those species, and how to recover them. We used semistructured interviews to collect data on FWS biologists' use of discretion to make recommendations for listed species with hybridization issues. These biologists had a large amount of discretion to determine the best available science and how to interpret it but generally deferred to the scientific consensus on the taxonomic status of an organism. Respondents viewed hybridization primarily as a problem in the context of the ESA, although biologists who had experience with hybridization issues were more likely to describe it in more nuanced terms. Many interviewees expressed a desire to continue the current case-by-case approach for handling hybridization issues, but some wanted more guidance on procedures (i.e., a "flexible" hybrid policy). Field-level information can provide critical insight into which policies are working (or not working) and why. The FWS biologists' we interviewed had a high level of discretion, which greatly influenced ESA implementation, particularly in the context of hybridization. © 2016 Society for Conservation Biology.

Intense genomic reorganization in the genus Oecomys (Rodentia, Sigmodontinae): comparison between DNA barcoding and mapping of repetitive elements in three species of the Brazilian Amazon.

PubMed

Gomes Júnior, Renan Gabriel; Schneider, Carlos Henrique; de Lira, Thatianna; Carvalho, Natália Dayane Moura; Feldberg, Eliana; da Silva, Maria Nazareth Ferreira; Gross, Maria Claudia

2016-01-01

Oecomys Thomas, 1906 is one of the most diverse and widely distributed genera within the tribe Oryzomyini. At least sixteen species in this genus have been described to date, but it is believed this genus contains undescribed species. Morphological, molecular and cytogenetic study has revealed an uncertain taxonomic status for several Oecomys species, suggesting the presence of a complex of species. The present work had the goal of contributing to the genetic characterization of the genus Oecomys in the Brazilian Amazon. Thirty specimens were collected from four locations in the Brazilian Amazon and three nominal species recognized: Oecomys auyantepui (Tate, 1939), Oecomys bicolor (Tomes, 1860) and Oecomys rutilus (Anthony, 1921). COI sequence analysis grouped Oecomys auyantepui , Oecomys bicolor and Oecomys rutilus specimens into one, three and two clades, respectively, which is consistent with their geographic distribution. Cytogenetic data for Oecomys auyantepui revealed the sympatric occurrence of two different diploid numbers, 2n=64/NFa=110 and 2n=66/NFa=114, suggesting polymorphism while Oecomys bicolor exhibited 2n=80/NFa=142 and Oecomys rutilus 2n=54/NFa=90. The distribution of constitutive heterochromatin followed a species-specific pattern. Interspecific variation was evident in the chromosomal location and number of 18S rDNA loci. However, not all loci showed signs of activity. All three species displayed a similar pattern for 5S rDNA, with only one pair carrying this locus. Interstitial telomeric sites were found only in Oecomys auyantepui . The data presented in this work reinforce intra- and interspecific variations observed in the diploid number of Oecomys species and indicate that chromosomal rearrangements have led to the appearance of different diploid numbers and karyotypic formulas.

Evolution and Conservation on Top of the World: Phylogeography of the Marbled Water Frog (Telmatobius marmoratus Species Complex; Anura, Telmatobiidae) in Protected Areas of Chile.

PubMed

Victoriano, Pedro F; Muñoz-Mendoza, Carla; Sáez, Paola A; Salinas, Hugo F; Muñoz-Ramírez, Carlos; Sallaberry, Michel; Fibla, Pablo; Méndez, Marco A

2015-01-01

The Andean Altiplano has served as a complex setting throughout its history, driving dynamic processes of diversification in several taxa. We investigated phylogeographic processes in the Telmatobius marmoratus species complex occurring in this region by studying the geographic patterns of genetic variability, genealogies, and historical migration, using the cytochrome b (cyt-b) gene as a marker. DNA sequences from Telmatobius gigas and Telmatobius culeus, Bolivian species with an uncertain taxonomic status, were also included. Additionally, we evaluated the phylogenetic diversity (PD) represented within Chilean protected areas and the complementary contribution from unprotected populations. Phylogenetic reconstructions from 148 cyt-b sequences revealed 4 main clades, one of which corresponded to T. culeus. T. gigas was part of T. marmoratus clade indicating paraphyletic relationships. Haplotypes from Chilean and Bolivian sites were not reciprocally monophyletic. Geographic distribution of lineages, spatial Bayesian analysis, and migration patterns indicated that T. marmoratus displays a weaker geographic structure than expected based on habitat distribution and physiological requirements. Demographic and statistical phylogeography analyses pointed out to a scenario of recent population expansion and high connectivity events of a more recent age than the post Last Glacial Maximum, probably associated to more humid events in Altiplano. PD of T. marmoratus populations within protected areas represents 55.6% of the total estimated PD. The unprotected populations that would contribute the most to PD are Caquena and Quebe (21%). Recent evolutionary processes and paleoclimatic changes, potentially driving shifts in habitat connectivity levels and population sizes, could explain the phylogeographic patterns recovered herein. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Power fosters context-independent, analytic cognition.

PubMed

Miyamoto, Yuri; Ji, Li-Jun

2011-11-01

The present research tested the hypothesis that power, defined as the capacity to influence others, promotes analytic cognitive processing, by examining the use of linguistic categories and the categorization of objects. Supporting the hypothesis, recalling instances of influencing others facilitated the use of adjectives and discouraged the use of verbs to describe others (Study 1). Recalling instances of influencing others also promoted taxonomic, instead of thematic, categorization (Study 2). Furthermore, the authors also examined the effect of power in a real-life context. They examined whether socioeconomic status (SES) differences in cognitive processing can be partly explained by sense of agency, an antecedent of power (Study 3); high SES individuals made more taxonomic categorization than did low SES individuals, and a sense of agency partially mediated the SES differences in categorization. These findings underscore the role of power in shaping cognitive processes.

A historical note on the association between the legal status of expedited partner therapy and physician practice.

PubMed

Cramer, Ryan; Hogben, Matthew; Handsfield, H Hunter

2013-05-01

Potential legal liability for practicing expedited partner therapy is a common concern among providers, although it has been uncertain how these concerns translate into clinical practice. This study suggests that providers are more likely to practice expedited partner therapy in more favorable legal environments.

Cognitive impairment in folate-deficient rats corresponds to depleted brain phosphatidylcholine and is prevented by methionine without lowering homocysteine

USDA-ARS?s Scientific Manuscript database

Poor folate status is associated with cognitive decline and dementia in older adults. Although impaired brain methylation activity and homocysteine toxicity are widely believed to account for this association, how folate deficiency impairs cognition is uncertain. To better define the role of folate ...

New taxonomic and conservation status of Ossiculum (Vandeae, Orchidaceae), a highly threatened and narrow-endemic angraecoid orchid from Central Africa

PubMed Central

Simo-Droissart, Murielle; Stévart, Tariq; Sonké, Bonaventure; Sandrine Mayogo; Kamdem, Narcisse; Droissart, Vincent

2018-01-01

Abstract In the context of producing a revised phylogenetic Linnean taxonomy of angraecoid orchids, the monotypic and narrow-endemic genus Ossiculum is synonymised with Calyptrochilum. Accordingly, a new combination in Calyptrochilum is proposed for Ossiculum aurantiacum. The morphological and DNA-based evidence for this transfer is discussed. Moreover, Calyptrochilum aurantiacum is here firstly reported outside Cameroon, with a record from the Republic of the Congo. The Red List conservation status of this species is reassessed and it is to be downgraded from “Critically Endangered” (CR) to “Endangered” (EN), following the recent discovery of additional subpopulations in Cameroon.

Applying molecular genetic tools to the conservation and action plan for the critically endangered Far Eastern leopard (Panthera pardus orientalis).

PubMed

Uphyrkina, Olga; O'Brien, Stephen J

2003-08-01

A role for molecular genetic approaches in conservation of endangered taxa is now commonly recognized. Because conservation genetic analyses provide essential insights on taxonomic status, recent evolutionary history and current health of endangered taxa, they are considered in nearly all conservation programs. Genetic analyses of the critically endangered Far Eastern, or Amur leopard, Panthera pardus orientalis, have been done recently to address all of these questions and develop strategies for survival of the leopard in the wild. The genetic status and implication for conservation management of the Far Eastern leopard subspecies are discussed.

Reveromycins A and B from Streptomyces sp. 3–10: Antifungal activity against plant pathogenic fungi in vitro and in a strawberry food model system

USDA-ARS?s Scientific Manuscript database

This study was conducted to determine the antifungal activity of the metabolites from Streptomyces sp. 3–10, and to purify and identify the metabolites. Meanwhile, the taxonomic status of strain 3–10 was re-evaluated. The cultural filtrates of strain 3–10 in potato dextrose broth were extract...

A new species of Dicrotendipes (Diptera: Chironomidae) from Florida.

PubMed

Epler, J H

2016-12-14

A new species of Dicrotendipes is described in all life stages from Florida. Adults of this new species are nearly identical to D. modestus (Say); pupae are similar to D. modestus, D. neomodestus (Malloch) and D. tritomus (Kieffer); while the larvae are unique and were keyed by Epler (1992, 1995, 2001) as Dicrotendipes sp. A. The taxonomic status of D. modestus and D. pulsus (Walker) is discussed.

Avian haematozoa 3. Color atlas of leucocytozoon simondi

USGS Publications Warehouse

Herman, C.M.; Desser, S.S.; Bennett, G.F.; Tarshis, I.B.

1977-01-01

The life cycle of Leucocytozoon simondi is Illustrated in a series of color photomicrographs of the various stages of development in the blackfly vector and in the tissues and blood of Anatidae. A brief discussion of the life cycle is presented and taxonomic status of the parasite is reviewed. The bibliography includes references to the stages depicted and other phases of the development, morphology and pathogenesis of .L. simondi.

What's in a name: the taxonomic status of human head and body lice.

PubMed

Light, Jessica E; Toups, Melissa A; Reed, David L

2008-06-01

Human head lice (Anoplura: Pediculidae: Pediculus) are pandemic, parasitizing countless school children worldwide due to the evolution of insecticide resistance, and human body (clothing) lice are responsible for the deaths of millions as a result of vectoring several deadly bacterial pathogens. Despite the obvious impact these lice have had on their human hosts, it is unclear whether head and body lice represent two morphological forms of a single species or two distinct species. To assess the taxonomic status of head and body lice, we provide a synthesis of publicly available molecular data in GenBank, and we compare phylogenetic and population genetic methods using the most diverse geographic and molecular sampling presently available. Our analyses find reticulated networks, gene flow, and a lack of reciprocal monophyly, all of which indicate that head and body lice do not represent genetically distinct evolutionary units. Based on these findings, as well as inconsistencies of morphological, behavioral, and ecological variability between head and body lice, we contend that no known species concept would recognize these louse morphotypes as separate species. We recommend recognizing head and body lice as morphotypes of a single species, Pediculus humanus, until compelling new data and analyses (preferably analyses of fast evolving nuclear markers in a coalescent framework) indicate otherwise.

The "Post-Racial" Politics of Race: Changing Student Assignment Policy in Three School Districts

ERIC Educational Resources Information Center

McDermott, Kathryn A.; Frankenberg, Erica; Diem, Sarah

2015-01-01

Many school districts have recently revised, or tried to revise, their policies for assigning students to schools, because the legal and political status of racial and other kinds of diversity is uncertain, and the districts are facing fiscal austerity. This article presents case studies of politics and student assignment policy in three large…

Phylogeny and taxonomy of the genus Gliocephalotrichum.

PubMed

Lombard, L; Serrato-Diaz, L M; Cheewangkoon, R; French-Monar, R D; Decock, C; Crous, P W

2014-06-01

Species in the genus Gliocephalotrichum (= Leuconectria) (Hypocreales, Nectriaceae) are soilborne fungi, associated with post-harvest fruit spoilage of several important tropical fruit crops. Contemporary taxonomic studies of these fungi have relied on morphology and DNA sequence comparisons of the internal transcribed spacer region of the nuclear rDNA (ITS) and the β-tubulin gene regions. Employing DNA sequence data from four loci (β-tubulin, histone H3, ITS, and translation elongation factor 1-alpha) and morphological comparisons, the taxonomic status of the genus Gliocephalotrichum was re-evaluated. As a result five species are newly described, namely G. humicola (Taiwan, soil), G. mexicanum (rambutan fruit from Mexico), G. nephelii (rambutan fruit from Guatemala), G. queenslandicum (Australia, endophytic isolations) and G. simmonsii (rambutan fruit from Guatemala). Although species of Gliocephalotrichum are generally not regarded as important plant pathogens, their ability to cause post-harvest fruit rot could have an impact on fruit export and storage.

Phylogenetics of the phlebotomine sand fly group Verrucarum (Diptera: Psychodidae: Lutzomyia).

PubMed

Cohnstaedt, Lee W; Beati, Lorenza; Caceres, Abraham G; Ferro, Cristina; Munstermann, Leonard E

2011-06-01

Within the sand fly genus Lutzomyia, the Verrucarum species group contains several of the principal vectors of American cutaneous leishmaniasis and human bartonellosis in the Andean region of South America. The group encompasses 40 species for which the taxonomic status, phylogenetic relationships, and role of each species in disease transmission remain unresolved. Mitochondrial cytochrome c oxidase I (COI) phylogenetic analysis of a 667-bp fragment supported the morphological classification of the Verrucarum group into series. Genetic sequences from seven species were grouped in well-supported monophyletic lineages. Four species, however, clustered in two paraphyletic lineages that indicate conspecificity--the Lutzomyia longiflocosa-Lutzomyia sauroida pair and the Lutzomyia quasitownsendi-Lutzomyia torvida pair. COI sequences were also evaluated as a taxonomic tool based on interspecific genetic variability within the Verrucarum group and the intraspecific variability of one of its members, Lutzomyia verrucarum, across its known distribution.

Phylogenetics of the Phlebotomine Sand Fly Group Verrucarum (Diptera: Psychodidae: Lutzomyia)

PubMed Central

Cohnstaedt, Lee W.; Beati, Lorenza; Caceres, Abraham G.; Ferro, Cristina; Munstermann, Leonard E.

2011-01-01

Within the sand fly genus Lutzomyia, the Verrucarum species group contains several of the principal vectors of American cutaneous leishmaniasis and human bartonellosis in the Andean region of South America. The group encompasses 40 species for which the taxonomic status, phylogenetic relationships, and role of each species in disease transmission remain unresolved. Mitochondrial cytochrome c oxidase I (COI) phylogenetic analysis of a 667-bp fragment supported the morphological classification of the Verrucarum group into series. Genetic sequences from seven species were grouped in well-supported monophyletic lineages. Four species, however, clustered in two paraphyletic lineages that indicate conspecificity—the Lutzomyia longiflocosa–Lutzomyia sauroida pair and the Lutzomyia quasitownsendi–Lutzomyia torvida pair. COI sequences were also evaluated as a taxonomic tool based on interspecific genetic variability within the Verrucarum group and the intraspecific variability of one of its members, Lutzomyia verrucarum, across its known distribution. PMID:21633028

Morphological distinctiveness of Javan Tupaia hypochrysa (Scandentia, Tupaiidae)

USGS Publications Warehouse

Sargis, Eric J.; Woodman, Neal; Morningstar, Natalie C.; Reese, Aspen T.; Olson, Link E.

2013-01-01

The common treeshrew, Tupaia glis, represents a species complex with a complicated taxonomic history. It is distributed mostly south of the Isthmus of Kra on the Malay Peninsula and surrounding islands. In our recent revision of a portion of this species complex, we did not fully assess the population from Java (T. “glis” hypochrysa) because of our limited sample. Herein, we revisit this taxon using multivariate analyses in comparisons with T. glis, T. chrysogaster of the Mentawai Islands, and T. ferruginea from Sumatra. Analyses of both the manus and skull of Javan T. “glis” hypochrysa show it to be most similar to T. chrysogaster and distinct from both T. glis and T. ferruginea. Yet, the Javan population and T. chrysogaster have different mammae counts, supporting recognition of T. hypochrysa as a distinct species. The change in taxonomic status of T. hypochrysa has conservation implications for both T. glis and this Javan endemic.

Biosystematics and Conservation: A Case Study with Two Enigmatic and Uncommon Species of Crassula from New Zealand

PubMed Central

De Lange, P. J.; Heenan, P. B.; Keeling, D. J.; Murray, B. G.; Smissen, R.; Sykes, W. R.

2008-01-01

Background and Aims Crassula hunua and C. ruamahanga have been taxonomically controversial. Here their distinctiveness is assessed so that their taxonomic and conservation status can be clarified. Methods Populations of these two species were analysed using morphological, chromosomal and DNA sequence data. Key Results It proved impossible to differentiate between these two species using 12 key morphological characters. Populations were found to be chromosomally variable with 11 different chromosome numbers ranging from 2n = 42 to 2n = 100. Meiotic behaviour and levels of pollen stainability were both variable. Phylogenetic analyses showed that differences exist in both nuclear and plastid DNA sequences between individual plants, sometimes from the same population. Conclusions The results suggest that these plants are a species complex that has evolved through interspecific hybridization and polyploidy. Their high levels of chromosomal and DNA sequence variation present a problem for their conservation. PMID:18055560

Disease status in chronic inflammatory demyelinating polyneuropathy: inter-centre comparative analysis and correlates.

PubMed

Rajabally, Y A; Cassereau, J; Robbe, A; Nicolas, G

2015-11-01

Chronic inflammatory demyelinating polyneuropathy (CIDP) may have variable evolution profiles, which have not been compared between cohorts. The relationship of disease status with motor strength, function and electrophysiology is uncertain. Disease status was studied with a simplified proposed scale in two patient cohorts totalling 72 subjects from Leicester, U.K., and Angers, France. Clinical and electrophysiological records were analysed. Independent ascertainment of disease status in each cohort revealed similar rates of remission (P = 0.23), stable/improving disease (P = 0.34) and unstable/active disease (P = 1). No correlation was ascertained with strength or function. Median nerve compound muscle action potential was the only independent electrophysiological predictor of disease status ascertained (P = 0.046). Disease status distribution may represent an important comparative indicator for management of CIDP cohorts and could be useful for benchmarking service and treatment provision. Degree of upper limb motor axonal loss may represent a useful electrophysiological marker of disease status in CIDP. © 2015 EAN.

Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level

PubMed Central

Menke, Sebastian; Wasimuddin; Meier, Matthias; Melzheimer, Jörg; Mfune, John K. E.; Heinrich, Sonja; Thalwitzer, Susanne; Wachter, Bettina; Sommer, Simone

2014-01-01

Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from “abnormal” microbial compositions that affect host health requires knowledge of the “normal” microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes. PMID:25352837

Shoot ionome to predict the synergism and antagonism between nutrients as affected by substrate and physiological status.

PubMed

Pii, Youry; Cesco, Stefano; Mimmo, Tanja

2015-09-01

The elemental composition of a tissue or organism is defined as ionome. However, the combined effects on the shoot ionome determined by the taxonomic character, the nutrient status and different substrates have not been investigated. This study tests the hypothesis that phylogenetic variation of monocots and dicots grown in iron deficiency can be distinguished by the shoot ionome. We analyzed 18 elements in barley, cucumber and tomato and in two substrates (hydroponic vs soil) with different nutritional regimes. Multivariate analysis evidenced a clear separation between the species. In hydroponic conditions the main drivers separating the species are non essential-nutrients as Ti, Al, Na and Li, which were positively correlated with macro- (P, K) and micronutrients (Fe, Zn, Mo, B). The separation between species is confirmed when plants are grown on soil, but the distribution is determined especially by macronutrients (S, P, K, Ca, Mg) and micronutrients (B). A number of macro (Mg, Ca, S, P, K) and micronutrients (Fe, Mn, Zn, Cu, Mo, B) contribute to plant growth and several other important physiological and metabolic plant activities. The results reported here confirmed that the synergism and antagonism between them and other non-essential elements (Ti, Al, Si, Na) define the plant taxonomic character. The ionome profile might thus be exploited as a tool for the diagnosis of plants physiological/nutritional status but also in defining biofortification strategies to optimize both mineral enrichment of staple food crops and the nutrient input as fertilizers. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

A new species of Bryoleuca Hampson, 1908 from Afghanistan (Lepidoptera, Noctuidae, Bryophilinae).

PubMed

Pekarsky, Oleg

2015-11-13

A new species of the raptricula species-group, Bryoleuca pljushtchi sp. n. is described. A diagnostic comparison is made with Bryoleuca raptricula ([Denis & Schiffermüller], 1775), Bryoleuca felina (Eversmann, 1852), Bryoleuca orthogramma (Boursin, 1954), Bryoleuca volodia An, Choi & Ronkay, 2013 and Bryoleuca nahnybidai Pekarsky, 2014. Adults and female genitalia of the new species and its closest relatives are illustrated. Modern taxonomic studies of the raptricula-group started by Fibiger et al. (2009) and got progress by the clarification of the taxonomic status of B. felina (Pekarsky & Ronkay 2010). Subsequently, further two newly recognised species were described in the last two years, B. volodia and B. nahnybidai. The first attempt to prepare the checklist of the subfamily was made by Hacker (1990) and, later, European check list was given in the Noctuidae Europaeae, Vol. 11 (Fibiger et al. 2009). As for the fauna of Afghanistan, Koçak and Kemal (2012) listed twelve Bryophilinae species one of which, B. raptricula, belongs to the genus Bryoleuca. The taxonomic situation of the raptricula species-complex is far not completely known yet. Present paper contains the description of a new Bryoleuca species from Afghanistan. The single female of this new species was collected by Ukrainian entomologists Igor Pljushtch and Oleg Pak in Central Afghanistan in 2013.

Insights on the genus Acronymolpus Samuelson with new synonymies and exclusion of Stethotes Baly from the fauna of New Caledonia (Coleoptera, Chrysomelidae, Eumolpinae).

PubMed

Gómez-Zurita, Jesús

2017-01-01

In this work, several taxonomic problems affecting the recently erected genus Acronymolpus Samuelson, 2015, endemic to New Caledonia, are addressed. Two of the three New Caledonian species described in Stethotes Baly are transferred to Acronymolpus and their priority is recognized over the names proposed in the revision of this genus. Moreover, different forms of Acronymolpus always found in sympatry, one reddish and larger, and the other black and smaller, were each given species status in that revision, but they are recognized here as the females and males, respectively, of the same species. The taxonomic summary of these discoveries is: (i) A. bertiae (Jolivet, Verma & Mille, 2007), comb. n. = A. meteorus Samuelson, 2015, syn. n. , and A. turbo Samuelson, 2015, syn. n. ; and (ii) A. jourdani (Jolivet, Verma & Mille, 2013), comb. n. = A. gressitti Samuelson, 2015, syn. n. , and A. joliveti Samuelson, 2015, syn. n. New distribution data and the male genitalia and the spermatheca of the two valid species of Acronymolpus are described for the first time with reference to taxonomically important characters. Finally, the last New Caledonian species described in Stethotes is recognized here as a member of the endemic genus Taophila Heller: T. mandjeliae (Jolivet, Verma & Mille, 2010), comb. n.

Evaluation of the taxonomic status of populations assigned to Phyllomedusa hypochondrialis (Anura, Hylidae, Phyllomedusinae) based on molecular, chromosomal, and morphological approach

PubMed Central

2013-01-01

Background The taxonomic and phylogenetic relationships of the genus Phyllomedusa have been amply discussed. The marked morphological similarities among some species hamper the reliable identification of specimens and may often lead to their incorrect taxonomic classification on the sole basis of morphological traits. Phenotypic variation was observed among populations assigned to either P. azurea or P. hypochondrialis. In order to evaluate whether the variation observed in populations assigned to P. hypochondrialis is related to that in genotypes, a cytogenetic analysis was combined with phylogenetic inferences based on mitochondrial and nuclear sequences. Results The inter- and intra-population variation in the external morphology observed among the specimens analyzed in the present study do not reflect the phylogenetic relationships among populations. A monophyletic clade was recovered, grouping all the specimens identified as P. hypochondrialis and specimens assigned P. azurea from Minas Gerais state. This clade is characterized by conserved chromosomal morphology and a common C-banding pattern. Extensive variation in the nucleolar organizing region (NOR) was observed among populations, with four distinct NOR positions being recognized in the karyotypes. Intra-population polymorphism of the additional rDNA clusters observed in specimens from Barreiras, Bahia state, also highlights the marked genomic instability of the rDNA in the genome of this group. Based on the topology obtained in the phylogenetic analyses, the re-evaluation of the taxonomic status of the specimens from the southernmost population known in Brazil is recommended. Conclusions The results of this study support the need for a thorough revision of the phenotypic features used to discriminate P. azurea and P. hypochondrialis. The phylogenetic data presented here also contribute to an extension of the geographic range of P. hypochondrialis, which is known to occur in the Amazon basin and neighboring areas of the Cerrado savanna, where it may be sympatric with P. azurea, within contact zones. The misidentification of specimens may have led to inconsistencies in the original definition of the geographic range of P. azurea. The variability observed in the NOR of P. hypochondrialis reinforces the conclusion that these sites represent hotspots of rearrangement. Intraspecific variation in the location of these sites is the result of constant rearrangements that are not detected by classical cytogenetic methods or are traits of an ancestral, polymorphic karyotype, which would not be phylogenetically informative for this group. PMID:23937545

Protectiveness of species sensitivity distribution hazard concentrations for acute toxicity used in endangered species risk assessment.

PubMed

Raimondo, Sandy; Vivian, Deborah N; Delos, Charles; Barron, Mace G

2008-12-01

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 species, safety factors, and species sensitivity distributions (SSDs) of chemical toxicity; however, the protectiveness of these approaches can be uncertain. We comprehensively evaluated the protectiveness of SSD first and fifth percentile hazard concentrations (HC1, HC5) relative to the application of safety factors using 68 SSDs generated from 1,482 acute (lethal concentration of 50%, or LC50) toxicity records for 291 species, including 24 endangered species (20 fish, four mussels). The SSD HC5s and HCls were lower than 97 and 99.5% of all endangered species mean acute LC50s, respectively. The HC5s were significantly less than the concentrations derived from applying safety factors of 5 and 10 to rainbow trout (Oncorhynchus mykiss) toxicity data, and the HCls were generally lower than the concentrations derived from a safety factor of 100 applied to rainbow trout toxicity values. Comparison of relative sensitivity (SSD percentiles) of broad taxonomic groups showed that crustaceans were generally the most sensitive taxa and taxa sensitivity was related to chemical mechanism of action. Comparison of relative sensitivity of narrow fish taxonomic groups showed that standard test fish species were generally less sensitive than salmonids and listed fish. We recommend the use of SSDs as a distribution-based risk assessment approach that is generally protective of listed species.

Status, distribution and morphometric/meristic characteristics of Cobitis elongata Heckel et Kner 1858 from Slovenia.

PubMed

Povz, Meta; Sumer, Suzana

2003-01-01

Cobitis elongata Heckel et Kner inhabits the rivers Sava, Kolpa, Krka, Gracnica and Hudinja (the Danube river basin). The species is common in its distribution area. In the Red List of endangered Pisces and Cyclostomata in Slovenia, it is classified as endangered. Status and distribution data of the species from previous reports and recent research were summarized. A total of 31 specimens from the river Kolpa were morphologically studied. Sixteen morphometric and four meristic characteristics were analysed using standard numerical taxonomic techniques. 99.8% of the total variation of standard length was explained by preanal distance, dorsal and ventral fin lengths as well as minimum body height.

Functional redundancy as a tool for bioassessment: A test using riparian vegetation.

PubMed

Bruno, D; Gutiérrez-Cánovas, C; Velasco, J; Sánchez-Fernández, D

2016-10-01

There is an urgent need to track how natural systems are responding to global change in order to better guide management efforts. Traditionally, taxonomically based metrics have been used as indicators of ecosystem integrity and conservation status. However, functional approaches offer promising advantages that can improve bioassessment performance. In this study, we aim to test the applicability of functional redundancy (FR), a functional feature related to the stability, resistance and resilience of ecosystems, as a tool for bioassessment, looking at woody riparian communities in particular. We used linear mixed-effect models to investigate the response of FR and other traditional biomonitoring indices to natural (drought duration) and anthropogenic stress gradients (flow regulation and agriculture) in a Mediterranean basin. Such indices include species richness, a taxonomic index, and the Riparian Quality Index, which is an index of ecological status. Then, we explored the ability of FR and the other indices to discriminate between different intensities of human alteration. FR showed higher explanatory capacity in response to multiple stressors, although we found significant negative relationships between all the biological indices (taxonomic, functional and ecological quality) and stress gradients. In addition, FR was the most accurate index to discriminate among different categories of human alteration in both perennial and intermittent river reaches, which allowed us to set threshold values to identify undisturbed (reference condition), moderately disturbed and highly disturbed reaches in the two types of river. Using these thresholds and the best-fitting model, we generated a map of human impact on the functional redundancy of riparian communities for all the stretches of the river network. Our results demonstrate that FR presents clear advantages over traditional methods, which suggests that it should be part of the biomonitoring toolbox used for environmental management so as to obtain better predictions of ecosystem response to environmental changes. Copyright © 2016 Elsevier B.V. All rights reserved.

On the taxonomic status of the European Scolelepis (Scolelepis) squamata (Polychaeta: Spionidae), with description of a new species from southern Europe On the taxonomic status of the European Scolelepis (Scolelepis) squamata (Polychaeta: Spionidae), with description of a new species from southern Europe

PubMed

Surugiu, Victor

2016-09-05

In order to clarify taxonomic problems relating to the identity of Scolelepis (Scolelepis) specimens from the Black Sea, the identified material was compared with specimens of Scolelepis cirratulus (Delle Chiaje, 1829) from the Mediterranean, of S. squamata (Abildgaard, in O.F. Müller, 1806) from the North Sea and the Atlantic coast of Spain, and with the syntypes of S. mesnili (Bellan & Lagardère, 1971) from the Atlantic coast of France. The examination of a large number of specimens (both juveniles and adults) reveals that the currently accepted morphological differences distinguishing all species show size-related patterns, suggesting that they all belong to one species. Therefore, this study supports the view that Scolelepis cirratulus and Scolelepis mesnili are junior synonyms of Scolelepis (Scolelepis) squamata. As a result of the re-assessment of the species limits of Scolelepis (Scolelepis) squamata, a new species, Scolelepis (Scolelepis) neglecta sp. nov., is distinguished and described from the Cantabrian coast of Spain. It inhabits shallow sublittoral fine sands and was earlier misidentified and reported from the Atlantic coast of Europe and the Mediterranean Sea as Scolelepis squamata, Scolelepis mesnili, Scolelepis cantabra (Rioja, 1918), or Dispio uncinata Hartman, 1951. The new species is characterized by having a trilobate prostomium with an acuminate medial portion, a short peristomium with well-developed dorso-lateral wings, short palps with two longitudinal bands of elevated lobes, neuropodial postchaetal lamellae notched from chaetigers 14-41, and strongly curved bidentate neuropodial hooded hooks with a slight constriction on the shaft starting from chaetigers 19-49. The morphology, diagnostic characters and ecology of both Scolelepis (Scolelepis) squamata and Scolelepis (Scolelepis) neglecta sp. nov. are discussed.

[Some problems of the study and representation of Siberian flora biodiversity in connection with its conservation].

PubMed

Olonova, M V

2007-01-01

The present knowledge of flora of Siberia is quite insufficient, which is a considerable obstacle to the detection of its biodiversity for conserving the gene pool. Planning conservation measures should be focused not only on species, but also on intraspecific taxa and their phylogenetic uniqueness. In the absence of genetic data, available morphological and geographical methods should be used, so that, when it is impossible to establish the actual origin and relationship of taxa, the existing morphological diverstity is at least represented, as far as it is known to be based on genetic diversity. Phenetic maps can be of much use in the study of intraspecific morphological diversity. The estimation of geographic variability and morphological diversity, as well as the evaluation of territories, can be based on such maps. To represent adequately the biodiversity existing within poorly studied, presumably hybrid plant groups, until actual origin and relationship are known, they should probably be forcedly and provisionally considered as a special type of hybrid complexes, representing the unclear present day taxonomic situation. Such complexes could include populations and individuals with morphological characters of two or more different species, until the systematic position of such populations and individuals is further explored. Until the actual taxonomic status and relationship of the components are established, they could be regarded as subspecies permitted by the Code, or as certain recorded morphological deviations from the type, without assigning any taxonomic status to them--depending on the available data on variability and distribution. In the future, the resulting provisional information on morphological diversity would help to concentrate the efforts of biologists, in possession of the newest methods, on the most important objects, and serve as the scientific base for effective measures aimed at the conservation and management of the vast gene pool of the Siberian flora.

Review of the genera of Conoderinae (Coleoptera, Curculionidae) from North America, Central America, and the Caribbean

PubMed Central

Anzaldo, Salvatore S.

2017-01-01

Abstract The thirty-nine extant genera of Conoderinae known to occur in North America, Central America, and the Caribbean are reviewed based on external morphology. An identification key is provided along with diagnoses, distributions, species counts, and natural history information, when known, for each genus. Morphological character systems of importance for weevil classification are surveyed, potential relationships among the tribes and genera are discussed, and groups most in need of taxonomic and phylogenetic attention are identified. The following genera are transferred to new tribes: Acoptus LeConte, 1876 from the Lechriopini to the Othippiini (new placement) and the South American genus Hedycera Pascoe, 1870 from the Lechriopini to the Piazurini (new placement). Philides Champion, 1906 and Philinna Champion, 1906 are transferred from the Lechriopini to Conoderinae incertae sedis (new placement) although their placement as conoderines is uncertain. The species Copturomimus cinereus Heller, 1895 is designated as the type species of the genus Copturomimus Heller, 1895. PMID:28769729

ACCF/ASE/AHA/ASNC/HFSA/HRS/SCAI/SCCM/SCCT/SCMR 2011 Appropriate Use Criteria for Echocardiography. A Report of the American College of Cardiology Foundation Appropriate Use Criteria Task Force, American Society of Echocardiography, American Heart Association, American Society of Nuclear Cardiology, Heart Failure Society of America, Heart Rhythm Society, Society for Cardiovascular Angiography and Interventions, Society of Critical Care Medicine, Society of Cardiovascular Computed Tomography, Society for Cardiovascular Magnetic Resonance American College of Chest Physicians.

PubMed

Douglas, Pamela S; Garcia, Mario J; Haines, David E; Lai, Wyman W; Manning, Warren J; Patel, Ayan R; Picard, Michael H; Polk, Donna M; Ragosta, Michael; Parker Ward, R; Weiner, Rory B

2011-03-01

The American College of Cardiology Foundation (ACCF), in partnership with the American Society of Echocardiography (ASE) and along with key specialty and subspecialty societies, conducted a review of common clinical scenarios where echocardiography is frequently considered. This document combines and updates the original transthoracic and transesophageal echocardiography appropriateness criteria published in 2007 (1) and the original stress echocardiography appropriateness criteria published in 2008 (2). This revision reflects new clinical data, reflects changes in test utilization patterns,and clarifies echocardiography use where omissions or lack of clarity existed in the original criteria.The indications (clinical scenarios)were derived from common applications or anticipated uses, as well as from current clinical practice guidelines and results of studies examining the implementation of the original appropriate use criteria (AUC).The 202 indications in this document were developed by a diverse writing group and scored by a separate independent technical panel on a scale of 1 to 9,to designate appropriate use(median 7 to 9), uncertain use(median 4 to 6), and inappropriate use (median 1 to 3). Ninety-seven indications were rated as appropriate, 34 were rated as uncertain, and 71 were rated as inappropriate. In general,the use of echocardiography for initial diagnosis when there is a change in clinical status or when the results of the echocardiogram are anticipated to change patient management were rated appropriate. Routine testing when there was no change in clinical status or when results of testing were unlikely to modify management were more likely to be inappropriate than appropriate/uncertain.The AUC for echocardiography have the potential to impact physician decision making,healthcare delivery, and reimbursement policy. Furthermore,recognition of uncertain clinical scenarios facilitates identification of areas that would benefit from future research.

Ribosomal RNA gene detection and targeted culture of novel nitrogen-responsive fungal taxa from temperate pine forest soil.

PubMed

Hesse, Cedar N; Torres-Cruz, Terry J; Tobias, Terri Billingsley; Al-Matruk, Maryam; Porras-Alfaro, Andrea; Kuske, Cheryl R

Soil fungal communities are responsible for carbon and nitrogen (N) cycling. The high complexity of the soil fungal community and the high proportion of taxonomically unidentifiable sequences confound ecological interpretations in field studies because physiological information is lacking for many organisms known only by their rRNA sequences. This situation forces experimental comparisons to be made at broader taxonomic racks where functions become difficult to infer. The objective of this study was to determine OTU (operational taxonomic units) level responses of the soil fungal community to N enrichment in a temperate pine forest experiment and to use the sequencing data to guide culture efforts of novel N-responsive fungal taxa. Replicate samples from four soil horizons (up to 10 cm depth) were obtained from ambient, enriched CO 2 and N-fertilization plots. Through a fungal large subunit rRNA gene (LSU) sequencing survey, we identified two novel fungal clades that were abundant in our soil sampling (representing up to 27% of the sequences in some samples) and responsive to changes in soil N. The two N-responsive taxa with no predicted taxonomic association were targeted for isolation and culturing from specific soil samples where their sequences were abundant. Representatives of both OTUs were successfully cultured using a filtration approach. One taxon (OTU6) was most closely related to Saccharomycotina; the second taxon (OTU69) was most closely related to Mucoromycotina. Both taxa likely represent novel species. This study shows how observation of specific OTUs level responses to altered N status in a large rRNA gene field survey provided the impetus to design targeted culture approaches for isolation of novel N-responsive fungal taxa.

Impact of insurance carrier, prior authorization, and socioeconomic status on appropriate use of SPECT myocardial perfusion imaging in private community-based office practice.

PubMed

Doukky, Rami; Hayes, Kathleen; Frogge, Nathan; Nazir, Noreen T; Collado, Fareed M; Williams, Kim A

2015-05-01

The impact of health insurance carrier and socioeconomic status (SES) on the adherence to appropriate use criteria (AUC) for radionuclide myocardial perfusion imaging (MPI) is unknown. Health insurance carrier's prior authorization and patient's SES impact adherence to AUC for MPI in a fee-for-service setting. We conducted a prospective cohort study of 1511 consecutive patients who underwent outpatient MPI in a multi-site, office-based, fee-for-service setting. The patients were stratified according to the 2009 AUC into appropriate/uncertain appropriateness and inappropriate use groups. Insurance status was categorized as Medicare (does not require prior authorization) vs commercial (requires prior authorization). Socioeconomic status was determined by the median household income in the ZIP code of residence. The proportion of patients with Medicare was 33% vs 67% with commercial insurance. The rate of inappropriate use was higher among patients with commercial insurance vs Medicare (55% vs 24%; P < 0.001); this difference was not significant after adjusting for confounders known to impact AUC determination (odds ratio: 1.06, 95% confidence interval: 0.62-1.82, P = 0.82). The mean annual household income in the residential areas of patients with inappropriate use as compared to those with appropriate/uncertain use was $72 000 ± 21 000 vs $68 000 ± 20 000, respectively (P < 0.001). After adjusting for covariates known to impact AUC determination, SES (top vs bottom quartile income area) was not independently predictive of inappropriate MPI use (odds ratio: 0.9, 95% confidence interval: 0.53-1.52, P = 0.69). Insurance carriers prior authorization and SES do not seem to play a significant role in determining physicians adherence to AUC for MPI. © 2015 Wiley Periodicals, Inc.

Additions and corrections to the check list of the Noctuoidea (Insecta, Lepidoptera) of North America north of Mexico

PubMed Central

Lafontaine, J. Donald; Schmidt, B. Christian

2011-01-01

Abstract A total of 115 additions and corrections are listed and discussed for the check list of the Noctuoidea of North America north of Mexico published in 2010. Thirty-two of these are changes in authorship and/or date of publication or spelling. Taxonomic changes are 33 new or revised synonymies, three new combinations, and six revisions in status from synonymy to valid species. PMID:22207802

A new species of Bachia (Squamata: Gymnophthalmidae) with pleisomorphic limb morphology

USGS Publications Warehouse

Kizirian, D.A.; McDiarmid, R.W.

1998-01-01

We describe a new species of Bachia from the upper Rio Negro drainage of southeastern Colombia and southern Venezuela. The new taxon is diagnosed by a complement of phalanges that is unique among gymnophthalmid lizards and intermediate relative to other Bachia and closely related genera. Variation in limb osteology among the species of Bachia and close relatives is reported. We discuss the distribution of B. panoplia and the taxonomic status of B. flavescens.

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

PubMed

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

2015-10-28

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

Synonyms for some species of Mexican anoles (Squamata: Dactyloidae).

PubMed

De Oca, Adrián Nieto Montes; Poe, Steven; Scarpetta, Simon; Gray, Levi; Lieb, Carl S

2013-01-01

We studied type material and freshly collected topotypical specimens to assess the taxonomic status of five names associated with species of Mexican Anolis. We find A. schmidti to be a junior synonym of A. nebulosus, A. breedlovei to be a junior synonym of A. cuprinus, A. polyrhachis to be a junior synonym of A. rubiginosus, A. simmonsi to be a junior synonym of A. nebuloides, and A. adleri to be a junior synonym of A. liogaster.

The taxonomic status of Japanese threadfin bream Nemipterus japonicus (Bloch, 1791) (Perciformes: Nemipteridae) with a redescription of this species from the south china sea based on morphology and DNA barcodes

NASA Astrophysics Data System (ADS)

Ning, Ping; Sha, Zhongli; Hebert, Paul D. N.; Russell, Barry

2015-02-01

Because of its importance as a food source, Nemipterus japonicus (Bloch, 1791) (Nemipteridae) or Japanese threadfin bream is the best studied of these taxa, and numerous investigations have examined its fisheries, its biology and biochemistry. Despite such intensive work, the taxonomic status of N. japonicus has never been seriously questioned and it is regarded as a common species, widely distributed throughout the Indo-Western Pacific Ocean. In fact, Bloch's description of the type specimen of N. japonicus has ambiguous collection data and lacks a designation for the type locality, though it is probably Java. In this paper, DNA barcode results based on COI gene support the existence of two geographically separated lineages of the Japanese threadfin bream, both being an Indian Ocean and western Pacific lineage, with 2.7% sequence divergence, and the results indicate a possible existing of some cryptic species. The two lineages also possess a diagnostic difference in their belly color, with specimens in the South China Sea having a silver belly, while those from the Indian Ocean isolate specimen have a yellow coloration. Based upon new collections from the South China Sea, this species from the western Pacific is morphologically redescribed and its details of DNA barcode diversity are shown for the future investigations.

Taxonomic circumscription of Adenomera martinezi (Bokermann, 1956) (Anura: Leptodactylidae: Leptodactylinae) with the recognition of a new cryptic taxon through a bioacoustic approach.

PubMed

De Carvalho, Thiago Ribeiro; Giaretta, Ariovaldo Antonio

2013-01-01

In this paper, we provide a taxonomic circumscription of Adenomera martinezi from its type locality (Cachimbo, southwestern State of Pará) since its description (57 years ago) based on a newly collected series of eleven adult topotypes, and through a bioacoustic approach, recognize an undescribed cryptic taxon under this nominal species, which is widely distributed in central and northern Brazil. Adenomera martinezi and Adenomera saci sp. nov. can be diagnosed from all congeners by their distinctive 4-6 symmetrically arranged rows of longitudinal dark-colored spots on dorsum. They differ from each other through advertisement call structure, pulsed in Adenomera martinezi (audibly pulsed to the human ear), and non-pulsed in Adenomera saci sp. nov. (a whistle to the human ear). The recognition of Adenomera saci sp. nov. has conservation implications. Based on our assumed distribution of A. martinezi and A denomera saci sp. nov., the IUCN conservation status of A. martinezi requires a reassessment, inasmuch as we herein reconsider this species, as far as we know, as endemic to Cachimbo, southwestern State of Pará, Brazil. The 2004 extinction risk assessment included both A. martinezi and Adenomera saci sp. nov., and the conservation status category of 'Least Concern' might only be applied to Adenomera saci sp. nov., a widely distributed and abundant species in central and northern Brazil.

New species of Rhyacodrilus (Annelida: Clitellata: Rhyacodrilinae) of North America, with re-description of R. sodalis (Eisen, 1879)

USGS Publications Warehouse

Rodriguez, Pilar; Fend, Steven V.

2013-01-01

Six new Nearctic species of the aquatic oligochaete genus Rhyacodrilus (Annelida, Clitellata, Rhyacodrilinae), are de-scribed, five (R. saelonae sp. n., R. quileuticus sp. n., R. clio sp. n., R. alcyoneus sp. n. and R. longichaeta sp. n.) from western and one (R. propiporus sp. n.) from eastern North America. The taxonomy of the most common Rhyacodrilus species reported in the Nearctic region has been based largely on chaetal characters, which has generated certain confu-sion. The new species give a new perspective on the genus Rhyacodrilus in North America, suggesting a much higher diversity than previously expected. The description of R. longichaeta sp. n. questions the taxonomic status of R. montana (Brinkhurst), which is here regarded as species inquirenda. The taxonomic status of R. sodalis (Eisen) is discussed based on characters of the reproductive system, the existing Lake Tahoe neotype series is invalidated, and a neotype is described from Eisen's type locality. Based on the discussion of the characters of the genus Rhyacodrilus, the genus Stochidrilus Martínez-Ansemil et al. is proposed as a junior synonym of that genus. The presence of the widely reported species R. coccineus has not been confirmed in the study collections, although the species requires a sound revision. A key to the species bearing hair chaetae is provided, based mainly on features of the reproductive system.

Morphometric divergence in populations of Anastrepha obliqua (Diptera, Tephritidae) from Colombia and some Neotropical locations

PubMed Central

Castañeda, Maria R.; Selivon, Denise; Hernández-Ortiz, Vicente; Soto, Alberto; Canal, Nelson A.

2015-01-01

Abstract The West Indian fruit fly, Anastrepha obliqua, is one of seven species of quarantine importance of its genus and is one of the most economically important fruit fly pests in Colombia. The taxonomic status of this species is a key issue for further implementation of any pest management program. Several molecular studies have shown enough variability within Anastrepha obliqua to suggest its taxonomic status could be revised; however, there are no morphological studies supporting this hypothesis. The aim of this work was to describe the morphological variability of Colombian populations of Anastrepha obliqua, comparing this variability with that of other samples from the Neotropics. Measurements were performed on individuals from 11 populations collected from different geographic Colombian localities and were compared with populations from Mexico (2), Dominica Island (1), Peru (1) and Brazil (2). Linear morphometric analyses were performed using 23 female morphological traits, including seven variables of the aculeus, three of the thorax, and six of the wing; seven ratios among them were also considered. Discriminant function analyses showed significant morphological differentiation among the Colombian populations, separating them into two groups. Furthermore, in the comparisons between Colombian samples with those from other countries, three clusters were observed. The possibility of finding more than one species within the nominal Anastrepha obliqua population is discussed. PMID:26798254

The genome sequence of 'Mycobacterium massiliense' strain CIP 108297 suggests the independent taxonomic status of the Mycobacterium abscessus complex at the subspecies level.

PubMed

Cho, Yong-Joon; Yi, Hana; Chun, Jongsik; Cho, Sang-Nae; Daley, Charles L; Koh, Won-Jung; Shin, Sung Jae

2013-01-01

Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that are emerging as human pathogens. The M. abscessus complex was previously composed of three species, namely M. abscessus sensu stricto, 'M. massiliense', and 'M. bolletii'. In 2011, 'M. massiliense' and 'M. bolletii' were united and reclassified as a single subspecies within M. abscessus: M. abscessus subsp. bolletii. However, the placement of 'M. massiliense' within the boundary of M. abscessus subsp. bolletii remains highly controversial with regard to clinical aspects. In this study, we revisited the taxonomic status of members of the M. abscessus complex based on comparative analysis of the whole-genome sequences of 53 strains. The genome sequence of the previous type strain of 'Mycobacterium massiliense' (CIP 108297) was determined using next-generation sequencing. The genome tree based on average nucleotide identity (ANI) values supported the differentiation of 'M. bolletii' and 'M. massiliense' at the subspecies level. The genome tree also clearly illustrated that 'M. bolletii' and 'M. massiliense' form a distinct phylogenetic clade within the radiation of the M. abscessus complex. The genomic distances observed in this study suggest that the current M. abscessus subsp. bolletii taxon should be divided into two subspecies, M. abscessus subsp. massiliense subsp. nov. and M. abscessus subsp. bolletii, to correspondingly accommodate the previously known 'M. massiliense' and 'M. bolletii' strains.

Taxonomic status of the Columbia duskysnail (Truncatelloidea, Amnicolidae, Colligyrus).

PubMed

Liu, Hsiu-Ping; Hershler, Robert; Rossel, Christopher S

2015-01-01

Undescribed freshwater snails (Amnicolidae: Colligyrus) from the Mount Hood region (northwestern United States) identified as a new species (commonly known as the Columbia duskysnail) in grey literature have been provided federal protection under the "survey and manage" provisions of the Northwest Forest Plan and have been placed on conservation watch lists. However, there are no published studies of the identity of these snails aside from a molecular phylogenetic analysis which delineated a close relationship between the single sampled population and Colligyrusgreggi, which is distributed more than 750 km to the east of the Mount Hood area. Here we examine the taxonomic status of the Columbia duskysnail based on additional molecular sampling of mitochondrial DNA sequences (COI) and morphological evidence. We found that the Columbia duskysnail is not a monophyletic group and forms a strongly supported clade with Colligyrusgreggi. The COI divergence between these broadly disjunct groups (2.1%) was somewhat larger than that within Colligyrusgreggi (1.0%) but considerably less than that among the three currently recognized species of Colligyrus (8.7-12.1%). Additionally we found that the Columbia duskysnail and Colligyrusgreggi cannot be consistently differentiated by previously reported diagnostic characters (size and shape of shell spire, pigmentation of body and penis) and are closely similar in other aspects of morphology. Based on these results we conclude that the Columbia duskysnail is conspecific with Colligyrusgreggi.

New Directions in U.S. Foreign Assistance and New Roles for Anthropologists. Studies in Third World Societies, Publication Number Forty-Four.

ERIC Educational Resources Information Center

Mason, John P., Ed.; Clark, Mari H., Ed.

Given recent developments throughout the world, the status of U.S. foreign assistance policies is uncertain. This document is a collection of papers whose authors, all anthropologists concerned with developing nations, critically examine new directions in development assistance in the 1990s. The papers include an introduction (M. Clark; J. Mason);…

Phylogeny of Priapulida.

PubMed

Shapeero, W L

1961-03-24

The systematic position of the small invertebrate group, Priapulida, is uncertain. In more recent publications they are classified usually as pseudocoelomates in the division Aschelminthes. A histological investigation of Priapulus caudatus, a widely distributed species, reveals the body cavity to be a coelom, its lining a peritoneum. These features, and others, indicate the priapulids to be. coelomates rather than pseudocoelomates. Unique morphology perhaps qualifies the group for the status of phylum.

Island Evolution and Systematic Revision of Comoran Snakes: Why and When Subspecies Still Make Sense

PubMed Central

Hawlitschek, Oliver; Nagy, Zoltán T.; Glaw, Frank

2012-01-01

Species delimitation and species concepts have been a matter of debate among biodiversity researchers in the last decades, resulting in integrative taxonomy approaches and the use of modern species concepts, such as the phylogenetic, evolutionary or general lineage species concepts. The discussion of subspecies status and concepts has been addressed much less extensively, with some researchers completely refraining from recognizing subspecies. However, allopatric insular populations that are particularly differentiated have traditionally been assigned subspecies status. We studied the molecular phylogeny and morphology of endemic Comoran tree snakes of the genus Lycodryas. Taking an integrative taxonomic approach, we used the concept of independent lines of evidence to discriminate between evidence for specific and subspecific status. Molecular (mtDNA) and morphological data provided sufficient evidence to support four different taxa within Comoran Lycodryas. In a revision of this group, we propose two species, each with two subspecies. We present a discussion of the strong sexual dichromatism unique to Comoran Lycodryas within the genus and related genera that may be explained by sexual selection in combination with the absence of major predators. Then, we discuss the effects of insular evolution and the “island rule” on morphological traits in Comoran Lycodryas and in Liophidium mayottensis, another snake endemic to the Comoros. The absence of larger-bodied snakes may have promoted an increase in body size and the number of dorsal scale rows in these species. Finally, we discuss the subspecies concept, its applications and its significance for integrative taxonomy and for limiting taxonomic inflation. We emphasize that taxon descriptions should be based on an integrative approach using several lines of evidence, preferably in combination with statements on the underlying species concepts or operational criteria, to increase the objectivity and comparability of descriptions. PMID:22937005

Separating astrophysical sources from indirect dark matter signals

PubMed Central

Siegal-Gaskins, Jennifer M.

2015-01-01

Indirect searches for products of dark matter annihilation and decay face the challenge of identifying an uncertain and subdominant signal in the presence of uncertain backgrounds. Two valuable approaches to this problem are (i) using analysis methods which take advantage of different features in the energy spectrum and angular distribution of the signal and backgrounds and (ii) more accurately characterizing backgrounds, which allows for more robust identification of possible signals. These two approaches are complementary and can be significantly strengthened when used together. I review the status of indirect searches with gamma rays using two promising targets, the Inner Galaxy and the isotropic gamma-ray background. For both targets, uncertainties in the properties of backgrounds are a major limitation to the sensitivity of indirect searches. I then highlight approaches which can enhance the sensitivity of indirect searches using these targets. PMID:25304638

Causal uncertainty, claimed and behavioural self-handicapping.

PubMed

Thompson, Ted; Hepburn, Jonathan

2003-06-01

Causal uncertainty beliefs involve doubts about the causes of events, and arise as a consequence of non-contingent evaluative feedback: feedback that leaves the individual uncertain about the causes of his or her achievement outcomes. Individuals high in causal uncertainty are frequently unable to confidently attribute their achievement outcomes, experience anxiety in achievement situations and as a consequence are likely to engage in self-handicapping behaviour. Accordingly, we sought to establish links between trait causal uncertainty, claimed and behavioural self-handicapping. Participants were N=72 undergraduate students divided equally between high and low causally uncertain groups. We used a 2 (causal uncertainty status: high, low) x 3 (performance feedback condition: success, non-contingent success, non-contingent failure) between-subjects factorial design to examine the effects of causal uncertainty on achievement behaviour. Following performance feedback, participants completed 20 single-solution anagrams and 12 remote associate tasks serving as performance measures, and 16 unicursal tasks to assess practice effort. Participants also completed measures of claimed handicaps, state anxiety and attributions. Relative to low causally uncertain participants, high causally uncertain participants claimed more handicaps prior to performance on the anagrams and remote associates, reported higher anxiety, attributed their failure to internal, stable factors, and reduced practice effort on the unicursal tasks, evident in fewer unicursal tasks solved. These findings confirm links between trait causal uncertainty and claimed and behavioural self-handicapping, highlighting the need for educators to facilitate means by which students can achieve surety in the manner in which they attribute the causes of their achievement outcomes.

Hiding deep in the trees: discovery of divergent mitochondrial lineages in Malagasy chameleons of the Calumma nasutum group

PubMed Central

Gehring, Philip-Sebastian; Tolley, Krystal A; Eckhardt, Falk Sebastian; Townsend, Ted M; Ziegler, Thomas; Ratsoavina, Fanomezana; Glaw, Frank; Vences, Miguel

2012-01-01

We conducted a comprehensive molecular phylogenetic study for a group of chameleons from Madagascar (Chamaeleonidae: Calumma nasutum group, comprising seven nominal species) to examine the genetic and species diversity in this widespread genus. Based on DNA sequences of the mitochondrial gene (ND2) from 215 specimens, we reconstructed the phylogeny using a Bayesian approach. Our results show deep divergences among several unnamed mitochondrial lineages that are difficult to identify morphologically. We evaluated lineage diversification using a number of statistical phylogenetic methods (general mixed Yule-coalescent model; SpeciesIdentifier; net p-distances) to objectively delimit lineages that we here consider as operational taxonomic units (OTUs), and for which the taxonomic status remains largely unknown. In addition, we compared molecular and morphological differentiation in detail for one particularly diverse clade (the C. boettgeri complex) from northern Madagascar. To assess the species boundaries within this group we used an integrative taxonomic approach, combining evidence from two independent molecular markers (ND2 and CMOS), together with genital and other external morphological characters, and conclude that some of the newly discovered OTUs are separate species (confirmed candidate species, CCS), while others should best be considered as deep conspecific lineages (DCLs). Our analysis supports a total of 33 OTUs, of which seven correspond to described species, suggesting that the taxonomy of the C. nasutum group is in need of revision. PMID:22957155

The endangered Florida pondweed (Potamogeton floridanus) is a hybrid: Why we need to understand biodiversity thoroughly.

PubMed

Kaplan, Zdeněk; Fehrer, Judith; Bambasová, Veronika; Hellquist, C Barre

2018-01-01

Thorough understanding of biodiversity is a fundamental prerequisite for biological research. A lack of taxonomic knowledge and species misidentifications are particularly critical for conservation. Here we present an example of Potamogeton floridanus, the Florida Pondweed, an endangered taxon endemic to a small area in the Florida panhandle, whose taxonomic status remained controversial for more than a century, and all previous attempts to elucidate its identity have failed. We applied molecular approaches to tackle the origin of the mysterious taxon and supplemented them with morphological and anatomical investigations of both historical herbarium collections and plants recently collected in the type area for a comprehensive taxonomic reassessment. Sequencing of two nuclear ribosomal markers and one chloroplast non-coding spacer resulted in the surprising discovery that P. floridanus is a hybrid of P. pulcher and P. oakesianus, with the former being the maternal parent. The hybrid colony is currently geographically isolated from the distribution range of P. oakesianus. We show that previous molecular analyses have failed to reveal its hybrid identity due to inadequate nuclear DNA sequence editing. This is an example how the uncritical use of automized sequence reads can hamper molecular species identifications and also affect phylogenetic tree construction and interpretation. This unique hybrid taxon, P. ×floridanus, adds another case study to the debate on hybrid protection; consequences for its conservation are discussed.

The endangered Florida pondweed (Potamogeton floridanus) is a hybrid: Why we need to understand biodiversity thoroughly

PubMed Central

Fehrer, Judith; Bambasová, Veronika; Hellquist, C. Barre

2018-01-01

Thorough understanding of biodiversity is a fundamental prerequisite for biological research. A lack of taxonomic knowledge and species misidentifications are particularly critical for conservation. Here we present an example of Potamogeton floridanus, the Florida Pondweed, an endangered taxon endemic to a small area in the Florida panhandle, whose taxonomic status remained controversial for more than a century, and all previous attempts to elucidate its identity have failed. We applied molecular approaches to tackle the origin of the mysterious taxon and supplemented them with morphological and anatomical investigations of both historical herbarium collections and plants recently collected in the type area for a comprehensive taxonomic reassessment. Sequencing of two nuclear ribosomal markers and one chloroplast non-coding spacer resulted in the surprising discovery that P. floridanus is a hybrid of P. pulcher and P. oakesianus, with the former being the maternal parent. The hybrid colony is currently geographically isolated from the distribution range of P. oakesianus. We show that previous molecular analyses have failed to reveal its hybrid identity due to inadequate nuclear DNA sequence editing. This is an example how the uncritical use of automized sequence reads can hamper molecular species identifications and also affect phylogenetic tree construction and interpretation. This unique hybrid taxon, P. ×floridanus, adds another case study to the debate on hybrid protection; consequences for its conservation are discussed. PMID:29608584

Integrative taxonomy and preliminary assessment of species limits in the Liolaemus walkeri complex (Squamata, Liolaemidae) with descriptions of three new species from Peru

PubMed Central

Aguilar, César; Wood Jr, Perry L.; Cusi, Juan C.; Guzmán, Alfredo; Huari, Frank; Lundberg, Mikael; Mortensen, Emma; Ramírez, César; Robles, Daniel; Suárez, Juana; Ticona, Andres; Vargas, Víctor J.; Venegas, Pablo J.; Sites Jr, Jack W.

2013-01-01

Abstract Species delimitation studies based on integrative taxonomic approaches have received considerable attention in the last few years, and have provided the strongest hypotheses of species boundaries. We used three lines of evidence (molecular, morphological, and niche envelopes) to test for species boundaries in Peruvian populations of the Liolaemus walkeri complex. Our results show that different lines of evidence and analyses are congruent in different combinations, for unambiguous delimitation of three lineages that were “hidden” within known species, and now deserve species status. Our phylogenetic analysis shows that L. walkeri, L. tacnae and the three new species are strongly separated from other species assigned to the alticolor-bibronii group. Few conventional morphological characters distinguish the new species from closely related taxa and this highlights the need to integrate other sources of data to erect strong hypothesis of species limits. A taxonomic key for known Peruvian species of the subgenus Lioalemus is provided. PMID:24453545

Reappraisal of the two axiid genera Manaxius Kensley, 2003 and Calaxidium Sakai, 2014, and description of a new species of Calaxius Sakai & de Saint Laurent, 1989 from French Polynesia, Southwest Pacific
(Crustacea: Decapoda: Axiidea).

PubMed

Komai, Tomoyuki

2016-04-07

Discovery of an undescribed species of axiid shrimp from French Polynesia, Southwest Pacific, led the author to assess the taxonomic status of the two nominal genera, Manaxius Kensley, 2003 and Calaxidium Sakai, 2014. As a result, these two genera are synonymized under Calaxius Sakai & de Saint Laurent, 1989, because there are no significant differences in generic characters among the three taxa. An emended generic diagnosis of Calaxius is presented. The new species, Calaxius poupini, is morphologically similar to C. euophthalmus (De Man, 1905), C. izuensis Komai, 2011, C. kensleyi Clark, Galil & Poore, 2007, C. mimasensis (Sakai, 1967), C. pailoloensis (Rathbun, 1906) and C. sibogae (De Man, 1925), but the poorly developed armature on the ventral margin of each cheliped merus distinguishes the new species from the other six allied species. Some points of taxonomic confusion relating to Calaxius are clarified.

Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis.

PubMed

Gomila, Margarita; Busquets, Antonio; Mulet, Magdalena; García-Valdés, Elena; Lalucat, Jorge

2017-01-01

The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae , and P. savastanoi are later synonyms of P. amygdali and that " P. coronafaciens " should be revived as a nomenspecies.

Criterion 1: Conservation of biological diversity - Indicator 7: The status (threatened, rare, vulnerable, endangered, or extinct) of forest dependent species at risk of not maintaining viable breeding populations, as determined by legislation or scientific assessment

Treesearch

Curtis H. Flather; Taylor H. Ricketts; Carolyn Hull Sieg; Michael S. Knowles; John P. Fay; Jason McNees

2003-01-01

As the number of species classified as rare increases, the likelihood of species extinction also increases. This indicator focuses on species that have the greatest chance of being lost from the biotic community and therefore presages potential declines in species richness. The trend in species extinction since the turn of the 20th century varies by taxonomic group....

Reweaving the Tapestry: a Supertree of Birds

PubMed Central

Davis, Katie E; Page, Roderic D. M.

2014-01-01

Our knowledge of the avian tree of life remains uncertain, particularly at deeper levels due to the rapid diversification early in their evolutionary history. They are the most abundant land vertebrate on the planet and have been of great historical interest to systematists. Birds are also economically and ecologically important and as a result are intensively studied, yet despite their importance and interest to humans around 13% of taxa currently on the endangered species list perhaps as a result of human activity. Despite all this no comprehensive phylogeny that includes both extinct and extant species currently exists. Here we present a species-level supertree, constructed using the Matrix Representation with Parsimony method, of Aves containing approximately two thirds of all species from nearly 1000 source phylogenies with a broad taxonomic coverage. The source data for the tree were collected and processed according to a strict protocol to ensure robust and accurate data handling. The resulting tree topology is largely consistent with molecular hypotheses of avian phylogeny. We identify areas that are in broad agreement with current views on avian systematics and also those that require further work. We also highlight the need for leaf-based support measures to enable the identification of rogue taxa in supertrees. This is a first attempt at a supertree of both extinct and extant birds, it is not intended to be utilised in an overhaul of avian systematics or as a basis for taxonomic re-classification but provides a strong basis on which to base further studies on macroevolution, conservation, biodiversity, comparative biology and character evolution, in particular the inclusion of fossils will allow the study of bird evolution and diversification throughout deep time. PMID:24944845

Diversity and population structure of sewage derived microorganisms in wastewater treatment plant influent

PubMed Central

McLellan, S.L.; Huse, S.M.; Mueller-Spitz, S.R.; Andreishcheva, E.N.; Sogin, M.L.

2009-01-01

The release of untreated sewage introduces non-indigenous microbial populations of uncertain composition into surface waters. We used massively parallel 454 sequencing of hypervariable regions in rRNA genes to profile microbial communities from eight untreated sewage influent samples of two wastewater treatment plants (WWTP) in metropolitan Milwaukee. The sewage profiles included a discernable human fecal signature made up of several taxonomic groups including multiple Bifidobacteriaceae, Coriobacteriaceae, Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae genera. The fecal signature made up a small fraction of the taxa present in sewage but the relative abundance of these sequence tags mirrored the population structures of human fecal samples. These genera were much more prevalent in the sewage influent than standard indicators species. High-abundance sequences from taxonomic groups within the Beta- and Gammaproteobacteria dominated the sewage samples but occurred at very low levels in fecal and surface water samples, suggesting that these organisms proliferate within the sewer system. Samples from Jones Island (JI – servicing residential plus a combined sewer system) and South Shore (SS – servicing a residential area) WWTPs had very consistent community profiles, with greater similarity between WWTPs on a given collection day than the same plant collected on different days. Rainfall increased influent flows at SS and JI WWTPs, and this corresponded to greater diversity in the community at both plants. Overall, the sewer system appears to be a defined environment with both infiltration of rainwater and stormwater inputs modulating community composition. Microbial sewage communities represent a combination of inputs from human fecal microbes and enrichment of specific microbes from the environment to form a unique population structure. PMID:19840106

Genomic diversity guides conservation strategies among rare terrestrial orchid species when taxonomy remains uncertain.

PubMed

Ahrens, Collin W; Supple, Megan A; Aitken, Nicola C; Cantrill, David J; Borevitz, Justin O; James, Elizabeth A

2017-06-01

Species are often used as the unit for conservation, but may not be suitable for species complexes where taxa are difficult to distinguish. Under such circumstances, it may be more appropriate to consider species groups or populations as evolutionarily significant units (ESUs). A population genomic approach was employed to investigate the diversity within and among closely related species to create a more robust, lineage-specific conservation strategy for a nationally endangered terrestrial orchid and its relatives from south-eastern Australia. Four putative species were sampled from a total of 16 populations in the Victorian Volcanic Plain (VVP) bioregion and one population of a sub-alpine outgroup in south-eastern Australia. Morphological measurements were taken in situ along with leaf material for genotyping by sequencing (GBS) and microsatellite analyses. Species could not be differentiated using morphological measurements. Microsatellite and GBS markers confirmed the outgroup as distinct, but only GBS markers provided resolution of population genetic structure. The nationally endangered Diuris basaltica was indistinguishable from two related species ( D. chryseopsis and D. behrii ), while the state-protected D. gregaria showed genomic differentiation. Genomic diversity identified among the four Diuris species suggests that conservation of this taxonomically complex group will be best served by considering them as one ESU rather than separately aligned with species as currently recognized. This approach will maximize evolutionary potential among all species during increased isolation and environmental change. The methods used here can be applied generally to conserve evolutionary processes for groups where taxonomic uncertainty hinders the use of species as conservation units. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Patterns of DNA barcode variation in Canadian marine molluscs.

PubMed

Layton, Kara K S; Martel, André L; Hebert, Paul D N

2014-01-01

Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonstrated in other studies, this is the first effort to construct a DNA barcode registry for marine molluscs across such a large geographic area. This study examines patterns of DNA barcode variation in 227 species of Canadian marine molluscs. Intraspecific sequence divergences ranged from 0-26.4% and a barcode gap existed for most taxa. Eleven cases of relatively deep (>2%) intraspecific divergence were detected, suggesting the possible presence of overlooked species. Structural variation was detected in COI with indels found in 37 species, mostly bivalves. Some indels were present in divergent lineages, primarily in the region of the first external loop, suggesting certain areas are hotspots for change. Lastly, mean GC content varied substantially among orders (24.5%-46.5%), and showed a significant positive correlation with nearest neighbour distances. DNA barcoding is an effective tool for the identification of Canadian marine molluscs and for revealing possible cases of overlooked species. Some species with deep intraspecific divergence showed a biogeographic partition between lineages on the Atlantic, Arctic and Pacific coasts, suggesting the role of Pleistocene glaciations in the subdivision of their populations. Indels were prevalent in the barcode region of the COI gene in bivalves and gastropods. This study highlights the efficacy of DNA barcoding for providing insights into sequence variation across a broad taxonomic group on a large geographic scale.

Group members differ in relative prototypicality: Effects on the individual and the group.

PubMed

Hogg, Michael A

2016-01-01

All groups are differentiated into more or less group-prototypical members. Central members readily influence and lead the group, and they define its identity. Peripheral members can feel voiceless and marginalized, as well as uncertain about their membership status - they may engage in extreme behaviors to try to win acceptance. These relative prototypicality dynamics sometimes benefit group performance but sometimes compromise performance.

CO2 enrichment inhibits shoot nitrate assimilation in C3 but not C4 plants and slows growth under nitrate in C3 plants.

PubMed

Bloom, Arnold J; Asensio, Jose Salvador Rubaio; Randall, Lesley; Rachmilevitch, Shimon; Cousins, Asaph B; Carlisle, Eli A

2012-02-01

The CO2 concentration in Earth's atmosphere may double during this century. Plant responses to such an increase depend strongly on their nitrogen status, but the reasons have been uncertain. Here, we assessed shoot nitrate assimilation into amino acids via the shift in shoot CO2 and O2 fluxes when plants received nitrate instead of ammonium as a nitrogen source (deltaAQ). Shoot nitrate assimilation became negligible with increasing CO2 in a taxonomically diverse group of eight C3 plant species, was relatively insensitive to CO2 in three C4 species, and showed an intermediate sensitivity in two C3-C4 intermediate species. We then examined the influence of CO2 level and ammonium vs. nitrate nutrition on growth, assessed in terms of changes in fresh mass, of several C3 species and a Crassulacean acid metabolism (CAM) species. Elevated CO2 (720 micromol CO2/mol of all gases present) stimulated growth or had no effect in the five C3 species tested when they received ammonium as a nitrogen source but inhibited growth or had no effect if they received nitrate. Under nitrate, two C3 species grew faster at sub-ambient (approximately 310 micromol/mol) than elevated CO2. A CAM species grew faster at ambient than elevated or sub-ambient CO2 under either ammonium or nitrate nutrition. This study establishes that CO2 enrichment inhibits shoot nitrate assimilation in a wide variety of C3 plants and that this phenomenon can have a profound effect on their growth. This indicates that shoot nitrate assimilation provides an important contribution to the nitrate assimilation of an entire C3 plant. Thus, rising CO2 and its effects on shoot nitrate assimilation may influence the distribution of C3 plant species.

Genetic characterization of Rhipicephalus sanguineus (sensu lato) ticks from dogs in Portugal.

PubMed

Dantas-Torres, Filipe; Maia, Carla; Latrofa, Maria Stefania; Annoscia, Giada; Cardoso, Luís; Otranto, Domenico

2017-03-13

The taxonomic status of the brown dog tick Rhipicephalus sanguineus (sensu stricto) is a subject of on-going debate; there is a consensus that populations of this tick species should be referred to as R. sanguineus (sensu lato) until its taxonomic status is resolved. Recent genetic studies revealed the existence of more than one lineage of R. sanguineus (s.l.) in temperate countries. In this study, we assessed the genetic identity of ticks collected from rural dogs living in several areas located in all major geographical regions of Portugal. A total of 347 ticks were collected from rural dogs living in different regions of Portugal. These ticks were morphologically identified and partial mitochondrial 16S rRNA gene sequences (~300 bp) were obtained from representative specimens. The ticks were morphologically identified as Ixodes ricinus (seven males and 27 females), Rhipicephalus bursa (one male), Rhipicephalus pusillus (one female) and R. sanguineus (s.l.) (two larvae, 101 nymphs, 108 males and 100 females). Partial mitochondrial 16S rRNA gene sequences were obtained from 58 R. sanguineus (s.l.) specimens, and all of them were genetically identified as belonging to the so-called temperate lineage of R. sanguineus (s.l.) CONCLUSIONS: These results strongly suggest that the temperate species of R. sanguineus (s.l.) is the only representative of this tick group found on dogs in Portugal. It also adds weight to the hypothesis that Rhipicephalus turanicus is not present in this country, although further investigations are necessary to confirm this.

Genetic characterization of Echinostoma revolutum and Echinoparyphium recurvatum (Trematoda: Echinostomatidae) in Thailand and phylogenetic relationships with other isolates inferred by ITS1 sequence.

PubMed

Saijuntha, Weerachai; Tantrawatpan, Chairat; Sithithaworn, Paiboon; Andrews, Ross H; Petney, Trevor N

2011-03-01

Echinostomatidae are common, widely distributed intestinal parasites causing significant disease in both animals and humans worldwide. In spite of their importance, the taxonomy of these echinostomes is still controversial. The taxonomic status of two species, Echinostoma revolutum and Echinoparyphium recurvatum, which commonly infect poultry and other birds, as well as human, is problematical. Previous phylogenetic analyses of Southeast Asian strains indicate that these species cluster as sister taxa. In the present study, the first internal transcribed spacer (ITS1) sequence was used for genetic characterization and to examine the phylogenetic relationships between an isolate from Thailand with other isolates available from GenBank database. Interspecies differences in ITS1 sequence between E. revolutum and E. recurvatum were detected at 6 (3%) of the 203 alignment positions. Of these, nucleotide deletion at positions 25, 26, and 27, pyrimidine transition at 50, 189, and pyrimidine transversion at 118 were observed. Phylogenetic analysis revealed that E. recurvatum from Thailand clustered as a sister taxa with E. revolutum and not with other members of the genus Echinoparyphium. Interestingly, this result confirms a previous report based on allozyme electrophoresis and mitochondrial DNA that E. revolutum and E. recurvatum in Southeast Asia are sister species. Hence, the taxonomic status of E. recurvatum in Thailand, as well as in Southeast Asian countries needs to be confirmed and revised using more comprehensive analyses based on morphology and other molecular techniques.

Streptococcus azizii sp. nov., isolated from naïve weanling mice.

PubMed

Shewmaker, Patricia Lynn; Whitney, Anne M; Gulvik, Christopher A; Lipman, Neil S

2017-12-01

Three isolates of a previously reported novel catalase-negative, Gram-stain-positive, coccoid, alpha-haemolytic, Streptococcus species that were associated with meningoencephalitis in naïve weanling mice were further evaluated to confirm their taxonomic status and to determine additional phenotypic and molecular characteristics. Comparative 16S rRNA gene sequence analysis showed nearly identical intra-species sequence similarity (≥99.9 %), and revealed the closest phylogenetically related species, Streptococcus acidominimus and Streptococcuscuniculi, with 97.0 and 97.5 % sequence similarity, respectively. The rpoB, sodA and recN genes were identical for the three isolates and were 87.6, 85.7 and 82.5 % similar to S. acidominimus and 89.7, 86.2 and 80.7 % similar to S. cuniculi, respectively. In silico DNA-DNA hybridization analyses of mouse isolate 12-5202 T against S. acidominimus CCUG 27296 T and S. cuniculi CCUG 65085 T produced estimated values of 26.4 and 25.7 % relatedness, and the calculated average nucleotide identity values were 81.9 and 81.7, respectively. These data confirm the taxonomic status of 12-5202 T as a distinct Streptococcus species, and we formally propose the type strain, Streptococcusazizii 12-5202 T (=CCUG 69378 T =DSM 103678 T ). The genome of Streptococcus azizii sp. nov. 12-5202 T contains 2062 total genes with a size of 2.34 Mbp, and an average G+C content of 42.76 mol%.

Lectotypifications, synonymy, and a new name in Capsicum (Solanoideae, Solanaceae)

PubMed Central

Barboza, Gloria E.

2011-01-01

Abstract Considerable confusion exists within Capsicum (Solanaceae) regarding the status and typification of several names, in part due to misidentifications. Some types were destroyed in Berlin during the Second World War, some have not been found by modern systematics, while others exhibit uncertain locality data or contain material from more than one species. Fourteen lectotypes, synonyms, and a new name, Capsicum eshbaughii Barboza nom. nov.,are proposed here. PMID:22171173

Teenage Drug Use: Uncertain Linkages with Either Pregnancy or School Dropout. Report to the Chairman, Select Committee on Narcotics Abuse and Control, House of Representatives.

ERIC Educational Resources Information Center

General Accounting Office, Washington, DC.

The study reported in this document is a follow-up to earlier reviews of drugs and other youth problems. It addressed the current status of and the recent trends in teenage drug use, pregnancy, and dropping out of school, and the post-1987 research about the relationship between teenage drug use and either pregnancy or dropping out. Statistics…

PESI - a taxonomic backbone for Europe.

PubMed

de Jong, Yde; Kouwenberg, Juliana; Boumans, Louis; Hussey, Charles; Hyam, Roger; Nicolson, Nicola; Kirk, Paul; Paton, Alan; Michel, Ellinor; Guiry, Michael D; Boegh, Phillip S; Pedersen, Henrik Ærenlund; Enghoff, Henrik; von Raab-Straube, Eckhard; Güntsch, Anton; Geoffroy, Marc; Müller, Andreas; Kohlbecker, Andreas; Berendsohn, Walter; Appeltans, Ward; Arvanitidis, Christos; Vanhoorne, Bart; Declerck, Joram; Vandepitte, Leen; Hernandez, Francisco; Nash, Róisín; Costello, Mark John; Ouvrard, David; Bezard-Falgas, Pascale; Bourgoin, Thierry; Wetzel, Florian Tobias; Glöckler, Falko; Korb, Günther; Ring, Caroline; Hagedorn, Gregor; Häuser, Christoph; Aktaç, Nihat; Asan, Ahmet; Ardelean, Adorian; Borges, Paulo Alexandre Vieira; Dhora, Dhimiter; Khachatryan, Hasmik; Malicky, Michael; Ibrahimov, Shaig; Tuzikov, Alexander; De Wever, Aaike; Moncheva, Snejana; Spassov, Nikolai; Chobot, Karel; Popov, Alexi; Boršić, Igor; Sfenthourakis, Spyros; Kõljalg, Urmas; Uotila, Pertti; Olivier, Gargominy; Dauvin, Jean-Claude; Tarkhnishvili, David; Chaladze, Giorgi; Tuerkay, Michael; Legakis, Anastasios; Peregovits, László; Gudmundsson, Gudmundur; Ólafsson, Erling; Lysaght, Liam; Galil, Bella Sarah; Raimondo, Francesco M; Domina, Gianniantonio; Stoch, Fabio; Minelli, Alessandro; Spungis, Voldermars; Budrys, Eduardas; Olenin, Sergej; Turpel, Armand; Walisch, Tania; Krpach, Vladimir; Gambin, Marie Therese; Ungureanu, Laurentia; Karaman, Gordan; Kleukers, Roy M J C; Stur, Elisabeth; Aagaard, Kaare; Valland, Nils; Moen, Toril Loennechen; Bogdanowicz, Wieslaw; Tykarski, Piotr; Węsławski, Jan Marcin; Kędra, Monika; M de Frias Martins, Antonio; Abreu, António Domingos; Silva, Ricardo; Medvedev, Sergei; Ryss, Alexander; Šimić, Smiljka; Marhold, Karol; Stloukal, Eduard; Tome, Davorin; Ramos, Marian A; Valdés, Benito; Pina, Francisco; Kullander, Sven; Telenius, Anders; Gonseth, Yves; Tschudin, Pascal; Sergeyeva, Oleksandra; Vladymyrov, Volodymyr; Rizun, Volodymyr Bohdanovych; Raper, Chris; Lear, Dan; Stoev, Pavel; Penev, Lyubomir; Rubio, Ana Casino; Backeljau, Thierry; Saarenmaa, Hannu; Ulenberg, Sandrine

2015-01-01

Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.

PESI - a taxonomic backbone for Europe

PubMed Central

Kouwenberg, Juliana; Boumans, Louis; Hussey, Charles; Hyam, Roger; Nicolson, Nicola; Kirk, Paul; Paton, Alan; Michel, Ellinor; Guiry, Michael D.; Boegh, Phillip S.; Pedersen, Henrik Ærenlund; Enghoff, Henrik; von Raab-Straube, Eckhard; Güntsch, Anton; Geoffroy, Marc; Müller, Andreas; Kohlbecker, Andreas; Berendsohn, Walter; Appeltans, Ward; Arvanitidis, Christos; Vanhoorne, Bart; Declerck, Joram; Vandepitte, Leen; Hernandez, Francisco; Nash, Róisín; Costello, Mark John; Ouvrard, David; Bezard-Falgas, Pascale; Bourgoin, Thierry; Wetzel, Florian Tobias; Glöckler, Falko; Korb, Günther; Ring, Caroline; Hagedorn, Gregor; Häuser, Christoph; Aktaç, Nihat; Asan, Ahmet; Ardelean, Adorian; Borges, Paulo Alexandre Vieira; Dhora, Dhimiter; Khachatryan, Hasmik; Malicky, Michael; Ibrahimov, Shaig; Tuzikov, Alexander; De Wever, Aaike; Moncheva, Snejana; Spassov, Nikolai; Chobot, Karel; Popov, Alexi; Boršić, Igor; Sfenthourakis, Spyros; Kõljalg, Urmas; Uotila, Pertti; Olivier, Gargominy; Dauvin, Jean-Claude; Tarkhnishvili, David; Chaladze, Giorgi; Tuerkay, Michael; Legakis, Anastasios; Peregovits, László; Gudmundsson, Gudmundur; Ólafsson, Erling; Lysaght, Liam; Galil, Bella Sarah; Raimondo, Francesco M.; Domina, Gianniantonio; Stoch, Fabio; Minelli, Alessandro; Spungis, Voldermars; Budrys, Eduardas; Olenin, Sergej; Turpel, Armand; Walisch, Tania; Krpach, Vladimir; Gambin, Marie Therese; Ungureanu, Laurentia; Karaman, Gordan; Kleukers, Roy M.J.C.; Stur, Elisabeth; Aagaard, Kaare; Valland, Nils; Moen, Toril Loennechen; Bogdanowicz, Wieslaw; Tykarski, Piotr; Węsławski, Jan Marcin; Kędra, Monika; M. de Frias Martins, Antonio; Abreu, António Domingos; Silva, Ricardo; Medvedev, Sergei; Ryss, Alexander; Šimić, Smiljka; Marhold, Karol; Stloukal, Eduard; Tome, Davorin; Ramos, Marian A.; Valdés, Benito; Pina, Francisco; Kullander, Sven; Telenius, Anders; Gonseth, Yves; Tschudin, Pascal; Sergeyeva, Oleksandra; Vladymyrov, Volodymyr; Rizun, Volodymyr Bohdanovych; Raper, Chris; Lear, Dan; Stoev, Pavel; Penev, Lyubomir; Rubio, Ana Casino; Backeljau, Thierry; Saarenmaa, Hannu; Ulenberg, Sandrine

2015-01-01

Abstract Background Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. New information This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs. PMID:26491393

Conservation Genetics of the Philippine Tarsier: Cryptic Genetic Variation Restructures Conservation Priorities for an Island Archipelago Primate

PubMed Central

Brown, Rafe M.; Weghorst, Jennifer A.; Olson, Karen V.; Duya, Mariano R. M.; Barley, Anthony J.; Duya, Melizar V.; Shekelle, Myron; Neri-Arboleda, Irene; Esselstyn, Jacob A.; Dominy, Nathaniel J.; Ong, Perry S.; Moritz, Gillian L.; Luczon, Adrian; Diesmos, Mae Lowe L.; Diesmos, Arvin C.; Siler, Cameron D.

2014-01-01

Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies, and a lack of vouchered specimens and genetic samples available for study in biodiversity repositories. Consequently, conservation priorities are unclear. In this study we use mitochondrial and nuclear DNA to empirically infer geographic partitioning of genetic variation and to identify evolutionarily distinct lineages for conservation action. The distribution of Philippine tarsier genetic diversity is neither congruent with expectations based on biogeographical patterns documented in other Philippine vertebrates, nor does it agree with the most recent Philippine tarsier taxonomic arrangement. We identify three principal evolutionary lineages that do not correspond to the currently recognized subspecies, highlight the discovery of a novel cryptic and range-restricted subcenter of genetic variation in an unanticipated part of the archipelago, and identify additional geographically structured genetic variation that should be the focus of future studies and conservation action. Conservation of this flagship species necessitates establishment of protected areas and targeted conservation programs within the range of each genetically distinct variant of the Philippine tarsier. PMID:25136854

Range extension for the common dolphin (Delphinus sp.) to the Colombian Caribbean, with taxonomic implications from genetic barcoding and phylogenetic analyses

PubMed Central

Chávez-Carreño, Paula Alejandra; Jiménez-Pinedo, Cristina; Palacios, Daniel M.; Caicedo, Dalila; Trujillo, Fernando; Caballero, Susana

2017-01-01

The nearest known population of common dolphins (Delphinus sp.) to the Colombian Caribbean occurs in a fairly restricted range in eastern Venezuela. These dolphins have not been previously reported in the Colombian Caribbean, likely because of a lack of study of the local cetacean fauna. We collected cetacean observations in waters of the Guajira Department, northern Colombia (~11°N, 73°W) during two separate efforts: (a) a seismic vessel survey (December 2009—March 2010), and (b) three coastal surveys from small boats (May—July 2012, May 2013, and May 2014). Here we document ten sightings of common dolphins collected during these surveys, which extend the known range of the species by ~1000 km into the southwestern Caribbean. We also collected nine skin biopsies in 2013 and 2014. In order to determine the taxonomic identity of the specimens, we conducted genetic barcoding and phylogenetic analyses using two mitochondrial markers, the Control Region (mtDNA) and Cytochrome b (Cytb). Results indicate that these specimens are genetically closer to the short-beaked common dolphin (Delphinus delphis) even though morphologically they resemble a long-beaked form (Delphinus sp.). However, the specific taxonomic status of common dolphins in the Caribbean and in the Western Atlantic remains unresolved. It is also unclear whether the distribution of the species between northern Colombia and eastern Venezuela is continuous or disjoined, or whether they can be considered part of the same stock. PMID:28192446

Snake species of the world: A taxonomic and geographic reference. v. 1

USGS Publications Warehouse

McDiarmid, R.W.; Campbell, J.A.; Toure, T.

1999-01-01

Given the absence of a current source on snake diversity and nomenclature and the expressed global need to understand better the diversity of our biota, we think that a catalogue of the world snake fauna complete with synonymies at the familial, generic, and specific levels is essential. We provide that here beginning with publication of the first volume. This compendium will facilitate comparative studies on the ecology, genetics, and behavior of snakes and, we hope, contribute to their conservation. At the very least, this work, when completed, will provide a readily available reference to the current taxonomic statuses and geographic distributions of snakes on a global scale. No comprehensive, up-to-date catalogue of snake species exists, and it is obvious that a detailed and inclusive treatment is long overdue. Snake Species of the World provides a comprehensive treatment of 31 families, 450 genera, and more than 2500 species of living snakes. The magnitude of the compilation requires publication in several volumes. This volume, the first of three, covers 682 species. A primary goal of this synthesis is to provide interested readers with a means for tracking scientific names that have been applied to a snake and determining the currently accepted name of that species. A secondary goal is to alert those interested in snakes as research subjects that in general many species are poorly known, that some have limited distributions, and that several are characterized by taxonomic problems.

Range extension for the common dolphin (Delphinus sp.) to the Colombian Caribbean, with taxonomic implications from genetic barcoding and phylogenetic analyses.

PubMed

Farías-Curtidor, Nohelia; Barragán-Barrera, Dalia C; Chávez-Carreño, Paula Alejandra; Jiménez-Pinedo, Cristina; Palacios, Daniel M; Caicedo, Dalila; Trujillo, Fernando; Caballero, Susana

2017-01-01

The nearest known population of common dolphins (Delphinus sp.) to the Colombian Caribbean occurs in a fairly restricted range in eastern Venezuela. These dolphins have not been previously reported in the Colombian Caribbean, likely because of a lack of study of the local cetacean fauna. We collected cetacean observations in waters of the Guajira Department, northern Colombia (~11°N, 73°W) during two separate efforts: (a) a seismic vessel survey (December 2009-March 2010), and (b) three coastal surveys from small boats (May-July 2012, May 2013, and May 2014). Here we document ten sightings of common dolphins collected during these surveys, which extend the known range of the species by ~1000 km into the southwestern Caribbean. We also collected nine skin biopsies in 2013 and 2014. In order to determine the taxonomic identity of the specimens, we conducted genetic barcoding and phylogenetic analyses using two mitochondrial markers, the Control Region (mtDNA) and Cytochrome b (Cytb). Results indicate that these specimens are genetically closer to the short-beaked common dolphin (Delphinus delphis) even though morphologically they resemble a long-beaked form (Delphinus sp.). However, the specific taxonomic status of common dolphins in the Caribbean and in the Western Atlantic remains unresolved. It is also unclear whether the distribution of the species between northern Colombia and eastern Venezuela is continuous or disjoined, or whether they can be considered part of the same stock.

Phylogenetic analysis of Haemaphysalis erinacei Pavesi, 1884 (Acari: Ixodidae) from China, Turkey, Italy and Romania.

PubMed

Hornok, Sándor; Wang, Yuanzhi; Otranto, Domenico; Keskin, Adem; Lia, Riccardo Paolo; Kontschán, Jenő; Takács, Nóra; Farkas, Róbert; Sándor, Attila D

2016-12-15

Haemaphysalis erinacei is one of the few ixodid tick species for which valid names of subspecies exist. Despite their disputed taxonomic status in the literature, these subspecies have not yet been compared with molecular methods. The aim of the present study was to investigate the phylogenetic relationships of H. erinacei subspecies, in the context of the first finding of this tick species in Romania. After morphological identification, DNA was extracted from five adults of H. e. taurica (from Romania and Turkey), four adults of H. e. erinacei (from Italy) and 17 adults of H. e. turanica (from China). From these samples fragments of the cytochrome c oxidase subunit 1 (cox1) and 16S rRNA genes were amplified via PCR and sequenced. Results showed that cox1 and 16S rRNA gene sequence divergences between H. e. taurica from Romania and H. e. erinacei from Italy were below 2%. However, the sequence divergences between H. e. taurica from Romania and H. e. turanica from China were high (up to 7.3% difference for the 16S rRNA gene), exceeding the reported level of sequence divergence between closely related tick species. At the same time, two adults of H. e. taurica from Turkey had higher 16S rRNA gene similarity to H. e. turanica from China (up to 97.5%) than to H. e. taurica from Romania (96.3%), but phylogenetically clustered more closely to H. e. taurica than to H. e. turanica. This is the first finding of H. erinacei in Romania, and the first (although preliminary) phylogenetic comparison of H. erinacei subspecies. Phylogenetic analyses did not support that the three H. erinacei subspecies evaluated here are of equal taxonomic rank, because the genetic divergence between H. e. turanica from China and H. e. taurica from Romania exceeded the usual level of sequence divergence between closely related tick species, suggesting that they might represent different species. Therefore, the taxonomic status of the subspecies of H. erinacei needs to be revised based on a larger number of specimens collected throughout its geographical range.

Algal taxonomy: a road to nowhere?

PubMed

De Clerck, Olivier; Guiry, Michael D; Leliaert, Frederik; Samyn, Yves; Verbruggen, Heroen

2013-04-01

The widespread view of taxonomy as an essentially retrogressive and outmoded science unable to cope with the current biodiversity crisis stimulated us to analyze the current status of cataloguing global algal diversity. Contrary to this largely pessimistic belief, species description rates of algae through time and trends in the number of active taxonomists, as revealed by the web resource AlgaeBase, show a much more positive picture. More species than ever before are being described by a large community of algal taxonomists. The lack of any decline in the rate at which new species and genera are described, however, is indicative of the large proportion of undiscovered diversity and bears heavily on any prediction of global algal species diversity and the time needed to catalogue it. The saturation of accumulation curves of higher taxa (family, order, and classes) on the other hand suggest that at these taxonomic levels most diversity has been discovered. This reasonably positive picture does not imply that algal taxonomy does not face serious challenges in the near future. The observed levels of cryptic diversity in algae, combined with the shift in methods used to characterize them, have resulted in a rampant uncertainty about the status of many older species. As a consequence, there is a tendency in phycology to move gradually away from traditional names to a more informal system whereby clade-, specimen- or strain-based identifiers are used to communicate biological information. Whether these informal names for species-level clades represent a temporary situation stimulated by the lag between species discovery and formal description, or an incipient alternative or parallel taxonomy, will be largely determined by how well we manage to integrate historical collections into modern taxonomic research. Additionally, there is a pressing need for a consensus about the organizational framework to manage the information about algal species names. An eventual strategy should preferably come out of an international working group that includes the various databases as well as the various phycological societies. In this strategy, phycologists should link up to major international initiatives that are currently being developed, such as the compulsory registration of taxonomic and nomenclatural acts and the introduction of Life Science Identifiers. © 2012 Phycological Society of America.

A Falsification of the Citation Impediment in the Taxonomic Literature

PubMed Central

Steiner, Florian M.; Pautasso, Marco; Zettel, Herbert; Moder, Karl; Arthofer, Wolfgang; Schlick-Steiner, Birgit C.

2015-01-01

Current science evaluation still relies on citation performance, despite criticisms of purely bibliometric research assessments. Biological taxonomy suffers from a drain of knowledge and manpower, with poor citation performance commonly held as one reason for this impediment. But is there really such a citation impediment in taxonomy? We compared the citation numbers of 306 taxonomic and 2291 non-taxonomic research articles (2009–2012) on mosses, orchids, ciliates, ants, and snakes, using Web of Science (WoS) and correcting for journal visibility. For three of the five taxa, significant differences were absent in citation numbers between taxonomic and non-taxonomic papers. This was also true for all taxa combined, although taxonomic papers received more citations than non-taxonomic ones. Our results show that, contrary to common belief, taxonomic contributions do not generally reduce a journal's citation performance and might even increase it. The scope of many journals rarely featuring taxonomy would allow editors to encourage a larger number of taxonomic submissions. Moreover, between 1993 and 2012, taxonomic publications accumulated faster than those from all biological fields. However, less than half of the taxonomic studies were published in journals in WoS. Thus, editors of highly visible journals inviting taxonomic contributions could benefit from taxonomy's strong momentum. The taxonomic output could increase even more than at its current growth rate if: (i) taxonomists currently publishing on other topics returned to taxonomy and (ii) non-taxonomists identifying the need for taxonomic acts started publishing these, possibly in collaboration with taxonomists. Finally, considering the high number of taxonomic papers attracted by the journal Zootaxa, we expect that the taxonomic community would indeed use increased chances of publishing in WoS indexed journals. We conclude that taxonomy's standing in the present citation-focused scientific landscape could easily improve—if the community becomes aware that there is no citation impediment in taxonomy. PMID:25944475

A Falsification of the Citation Impediment in the Taxonomic Literature.

PubMed

Steiner, Florian M; Pautasso, Marco; Zettel, Herbert; Moder, Karl; Arthofer, Wolfgang; Schlick-Steiner, Birgit C

2015-09-01

Current science evaluation still relies on citation performance, despite criticisms of purely bibliometric research assessments. Biological taxonomy suffers from a drain of knowledge and manpower, with poor citation performance commonly held as one reason for this impediment. But is there really such a citation impediment in taxonomy? We compared the citation numbers of 306 taxonomic and 2291 non-taxonomic research articles (2009-2012) on mosses, orchids, ciliates, ants, and snakes, using Web of Science (WoS) and correcting for journal visibility. For three of the five taxa, significant differences were absent in citation numbers between taxonomic and non-taxonomic papers. This was also true for all taxa combined, although taxonomic papers received more citations than non-taxonomic ones. Our results show that, contrary to common belief, taxonomic contributions do not generally reduce a journal's citation performance and might even increase it. The scope of many journals rarely featuring taxonomy would allow editors to encourage a larger number of taxonomic submissions. Moreover, between 1993 and 2012, taxonomic publications accumulated faster than those from all biological fields. However, less than half of the taxonomic studies were published in journals in WoS. Thus, editors of highly visible journals inviting taxonomic contributions could benefit from taxonomy's strong momentum. The taxonomic output could increase even more than at its current growth rate if: (i) taxonomists currently publishing on other topics returned to taxonomy and (ii) non-taxonomists identifying the need for taxonomic acts started publishing these, possibly in collaboration with taxonomists. Finally, considering the high number of taxonomic papers attracted by the journal Zootaxa, we expect that the taxonomic community would indeed use increased chances of publishing in WoS indexed journals. We conclude that taxonomy's standing in the present citation-focused scientific landscape could easily improve-if the community becomes aware that there is no citation impediment in taxonomy. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Pollen morphology and plant taxonomy of red oaks in eastern North America

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solomon, A.M.

Identification of Quercus (oak) pollen taxa could enhance Quaternary palynological interpretations from eastern North America. A first step is to determine a morphological and taxonomic basis for such identifications. Scanning electron microscopy was utilized to examine exine-surface features of 266 specimens representing 21 red oak (subgen. Erythrobalanus) species from eastern North America, and two intermediate oak (subgen. Protobalanus) species from the desert southwest. Twenty pollen morphological characteristics defined previously were tabulated for each of 324 pollen grains. The data were subjected to cluster analyses. Cluster diagrams were compared with traditional oak systematics. Pollen morphology and plant taxonomy compared poorly withmore » respect to series and species relationships among the red oaks, apparently due as much to high intraspecific and low interspecific variability in pollen-morphological characters as to the uncertain taxonomy of red oaks. Pollen morphology, however, does support the hypothesis of subgeneric oak evolution from intermediate oaks to the series Virentes of white oaks, and from more advanced white oaks to the red oak species. 19 references, 25 figures, 1 table.« less

Autistic Heterogeneity: Linking Uncertainties and Indeterminacies

PubMed Central

Hollin, Gregory

2017-01-01

Abstract Autism is a highly uncertain entity and little is said about it with any degree of certainty. Scientists must, and do, work through these uncertainties in the course of their work. Scientists explain uncertainty in autism research through discussion of epistemological uncertainties which suggest that diverse methods and techniques make results hard to reconcile, ontological uncertainties which suggest doubt over taxonomic coherence, but also through reference to autism’s indeterminacy which suggests that the condition is inherently heterogeneous. Indeed, indeterminacy takes two forms—an inter-personal form which suggests that there are fundamental differences between individuals with autism and an intra-personal form which suggests that no one factor is able to explain all features of autism within a given individual. What is apparent in the case of autism is that scientists put uncertainty and indeterminacy into discussion with one another and, rather than a well-policed epistemic-ontic boundary, there is a movement between, and an entwinement of, the two. Understanding scientists’ dialogue concerning uncertainty and indeterminacy is of importance for understanding autism and autistic heterogeneity but also for understanding uncertainty and ‘uncertainty work’ within science more generally. PMID:28515574

Medical Entomology Studies - VII. The Subgenus Stegomyia of Aedes in Southeast Asia. II - The Edwardsi Group of Species. III - The W-Albus Group of Species. (Diptera: Culicidae). VIII: Notes on the Taxonomic Status of Aedes Vittatus (Deptera: Culicidae) (Contributions of the American Entomological Institute. Volume 14, Number 1)

DTIC Science & Technology

1977-01-01

Netherlands India. Geneesk. Tijdschr. Ned. -1nd. 72 (Bijblad 2): 35-119. BOREL, E. 1928. Les moustiques de la Cochinchine et du Sud-Annam-(II.) Arch. Inst...particular reference to Aedes (Stegomyiu) vittatus (Bigot). Bull. Entomol. Res. 52: 709-25. BOREL, E. 1928. Les moustiques de la Cochin-chine et du Sud

Differential staining of bacteria: gram stain.

PubMed

Moyes, Rita B; Reynolds, Jackie; Breakwell, Donald P

2009-11-01

In 1884, Hans Christian Gram, a Danish doctor, developed a differential staining technique that is still the cornerstone of bacterial identification and taxonomic division. This multistep, sequential staining protocol separates bacteria into four groups based on cell morphology and cell wall structure: Gram-positive cocci, Gram-negative cocci, Gram-positive rods, and Gram-negative rods. The Gram stain is useful for assessing bacterial contamination of tissue culture samples or for examining the Gram stain status and morphological features of bacteria isolated from mixed or isolated bacterial cultures. (c) 2009 by John Wiley & Sons, Inc.

List of recent land mammals from Mexico, 2014

USGS Publications Warehouse

Ramirez-Pulido, Jose; Gonzalez-Ruiz, Noe; Gardner, Alfred L.; Arroyo-Cabrales, Joaquin

2014-01-01

We provide an updated list of the Recent land mammals of Mexico and include information on the taxonomy of certain species, and where appropriate, the endemic and threatened status of all species listed. Several taxonomic and nomenclatural changes have been made since publication of the last list of the Mexican terrestrial mammalian fauna. Within the period from 2005 to present, there have been at least 209 changes concerning the nomenclature of this fauna; these we evaluated in this paper. The land mammals of Mexico comprise 168 genera, 496 species, and 881 subspecies.

Guide to the Correct Use of Filoviral Nomenclature.

PubMed

Kuhn, Jens H

2017-01-01

The International Committee on Taxonomy of Viruses (ICTV) currently recognizes three genera and seven species as part of the mononegaviral family Filoviridae. Eight distinct filoviruses (Bundibugyo virus, Ebola virus, Lloviu virus, Marburg virus, Ravn virus, Reston virus, Sudan virus, and Taï Forest virus) have been assigned to these seven species. This chapter briefly summarizes the status quo of filovirus classification and focuses on the importance of differentiating between filoviral species and filoviruses and the correct use of taxonomic and vernacular filovirus names and abbreviations in written and oral discourse.

Cumulative Trauma Among Mayas Living in Southeast Florida.

PubMed

Millender, Eugenia I; Lowe, John

2017-06-01

Mayas, having experienced genocide, exile, and severe poverty, are at high risk for the consequences of cumulative trauma that continually resurfaces through current fear of an uncertain future. Little is known about the mental health and alcohol use status of this population. This correlational study explored t/he relationship of cumulative trauma as it relates to social determinants of health (years in the United States, education, health insurance status, marital status, and employment), psychological health (depression symptoms), and health behaviors (alcohol use) of 102 Guatemalan Mayas living in Southeast Florida. The results of this study indicated that, as specific social determinants of health and cumulative trauma increased, depression symptoms (particularly among women) and the risk for harmful alcohol use (particularly among men) increased. Identifying risk factors at an early stage before serious disease or problems are manifest provides room for early screening leading to early identification, early treatment, and better outcomes.

Inequalities in Tooth Decay in Australian Children by Neighbourhood Characteristics and Indigenous Status.

PubMed

Lalloo, Ratilal; Jamieson, Lisa M; Ha, Diep; Luzzi, Liana

2016-01-01

Tooth decay is related to poverty, measured at individual and neighbourhood levels. It is however uncertain if living in an advantaged neighbourhood reduces tooth decay similarly in Australian Indigenous and non-Indigenous children. This study describes tooth decay by neighbourhood characteristics and Indigenous status, and examines inequalities by Indigenous status. In deciduous dentition the percentage of children with tooth decay and untreated decay decreased on average 26% and 20% respectively in the non-Indigenous sample from poor to affluent neighbourhoods. In Indigenous children tooth decay and untreated decay decreased on average 6% and 8%, respectively, from poor to affluent neighbourhoods. While all children from affluent areas had less tooth decay, the gap between non-Indigenous and Indigenous children remained significant across neighbourhood characteristics. This suggests that both universal and targeted prevention programs should be considered for all Indigenous children irrespective of where they live.

Inequalities in Tooth Decay in Australian Children by Neighbourhood Characteristics and Indigenous Status.

PubMed

Lalloo, Ratilal; Jamieson, Lisa M; Ha, Diep; Luzzi, Liana

2016-02-01

Tooth decay is related to poverty, measured at individual and neighbourhood levels. It is however uncertain if living in an advantaged neighbourhood reduces tooth decay similarly in Australian Indigenous and non-Indigenous children. This study describes tooth decay by neighbourhood characteristics and Indigenous status, and examines inequalities by Indigenous status. In deciduous dentition the percentage of children with tooth decay and untreated decay decreased on average 26% and 20% respectively in the non-Indigenous sample from poor to affluent neighbourhoods. In Indigenous children tooth decay and untreated decay decreased on average 6% and 8%, respectively, from poor to affluent neighbourhoods. While all children from affluent areas had less tooth decay, the gap between non-Indigenous and Indigenous children remained significant across neighbourhood characteristics. This suggests that both universal and targeted prevention programs should be considered for all Indigenous children irrespective of where they live.

Anxiety and depression in adults in their eighties: do gender differences remain?

PubMed

Pachana, Nancy A; McLaughlin, Deirdre; Leung, Janni; Byrne, Gerard; Dobson, Annette

2012-01-01

Women report higher rates of depression and anxiety than men; however, it is uncertain whether this gender difference continues into advanced old age. 78 men and 111 women aged 82-87 years from the Men, Women and Ageing Project completed measures of anxiety (Geriatric Anxiety Inventory), depression (Patient Health Questionnaire; PHQ9), general psychological well-being (Mental Health subscale of SF-36), general health (general health item of SF-36) and cognitive status (Telephone Interview for Cognitive Status; TICS). Results revealed no significant gender differences on any of the psychological measures, after controlling for cognitive status, general health and education. These results support the proposition that the female predominance in psychological distress diminishes with increasing age. The congruence between men and women may reflect changes in identity associated with age or the effect of decreased emotional valence of some social roles.

A taxonomic study of crested caracaras (Falconidae)

USGS Publications Warehouse

Dove, C.J.; Banks, R.C.

1999-01-01

The taxonomic status of the crested caracaras (Caracara spp., Falconidae) has been unsettled for many years. Current sources such as the AOU Check-list recognize a single species that includes three taxa formerly considered distinct, citing observations by Hellmayr and Conover (1949) on two specimens considered to be intermediate. We studied plumage characters and measurements of over 392 museum specimens and found no evidence of clinal change between the northern and southern continental populations. Sixteen specimens from localities near the Amazon River where these two populations sporadically meet exhibit a mosaic of plumage elements from both forms. Measurements of wing chord, bill length, and bill depth indicate that size is positively correlated with latitude north and south of the equator and that females are larger than males in the northern population. These populations do not meet in western South America. We conclude that three biological species can be identified in the crested caracaras: the insular Guadalupe Caracara (Caracara lutosus); and two continental species, Northern (C. cheriway) and Southern caracara (C. plancus), neither of which shows subspecific variation.

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems.

PubMed

Pawlowski, Jan; Kelly-Quinn, Mary; Altermatt, Florian; Apothéloz-Perret-Gentil, Laure; Beja, Pedro; Boggero, Angela; Borja, Angel; Bouchez, Agnès; Cordier, Tristan; Domaizon, Isabelle; Feio, Maria Joao; Filipe, Ana Filipa; Fornaroli, Riccardo; Graf, Wolfram; Herder, Jelger; van der Hoorn, Berry; Iwan Jones, J; Sagova-Mareckova, Marketa; Moritz, Christian; Barquín, Jose; Piggott, Jeremy J; Pinna, Maurizio; Rimet, Frederic; Rinkevich, Buki; Sousa-Santos, Carla; Specchia, Valeria; Trobajo, Rosa; Vasselon, Valentin; Vitecek, Simon; Zimmerman, Jonas; Weigand, Alexander; Leese, Florian; Kahlert, Maria

2018-05-15

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs. Copyright © 2018 Elsevier B.V. All rights reserved.

Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis

PubMed Central

Gomila, Margarita; Busquets, Antonio; Mulet, Magdalena; García-Valdés, Elena; Lalucat, Jorge

2017-01-01

The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae, and P. savastanoi are later synonyms of P. amygdali and that “P. coronafaciens” should be revived as a nomenspecies. PMID:29270162

National Training Center Fort Irwin expansion area aquatic resources survey

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cushing, C.E.; Mueller, R.P.

1996-02-01

Biologists from Pacific Northwest National Laboratory (PNNL) were requested by personnel from Fort Irwin to conduct a biological reconnaissance of the Avawatz Mountains northeast of Fort Irwin, an area for proposed expansion of the Fort. Surveys of vegetation, small mammals, birds, reptiles, amphibians, and aquatic resources were conducted during 1995 to characterize the populations and habitats present with emphasis on determining the presence of any species of special concern. This report presents a description of the sites sampled, a list of the organisms found and identified, and a discussion of relative abundance. Taxonomic identifications were done to the lowest levelmore » possible commensurate with determining the status of the taxa relative to its possible listing as a threatened, endangered, or candidate species. Consultation with taxonomic experts was undertaken for the Coleoptera ahd Hemiptera. In addition to listing the macroinvertebrates found, the authors also present a discussion related to the possible presence of any threatened or endangered species or species of concern found in Sheep Creek Springs, Tin Cabin Springs, and the Amargosa River.« less

Homogenization patterns of the world’s freshwater fish faunas

PubMed Central

Villéger, Sébastien; Blanchet, Simon; Beauchard, Olivier; Oberdorff, Thierry; Brosse, Sébastien

2011-01-01

The world is currently undergoing an unprecedented decline in biodiversity, which is mainly attributable to human activities. For instance, nonnative species introduction, combined with the extirpation of native species, affects biodiversity patterns, notably by increasing the similarity among species assemblages. This biodiversity change, called taxonomic homogenization, has rarely been assessed at the world scale. Here, we fill this gap by assessing the current homogenization status of one of the most diverse vertebrate groups (i.e., freshwater fishes) at global and regional scales. We demonstrate that current homogenization of the freshwater fish faunas is still low at the world scale (0.5%) but reaches substantial levels (up to 10%) in some highly invaded river basins from the Nearctic and Palearctic realms. In these realms experiencing high changes, nonnative species introductions rather than native species extirpations drive taxonomic homogenization. Our results suggest that the “Homogocene era” is not yet the case for freshwater fish fauna at the worldwide scale. However, the distressingly high level of homogenization noted for some biogeographical realms stresses the need for further understanding of the ecological consequences of homogenization processes. PMID:22025692

Homogenization patterns of the world's freshwater fish faunas.

PubMed

Villéger, Sébastien; Blanchet, Simon; Beauchard, Olivier; Oberdorff, Thierry; Brosse, Sébastien

2011-11-01

The world is currently undergoing an unprecedented decline in biodiversity, which is mainly attributable to human activities. For instance, nonnative species introduction, combined with the extirpation of native species, affects biodiversity patterns, notably by increasing the similarity among species assemblages. This biodiversity change, called taxonomic homogenization, has rarely been assessed at the world scale. Here, we fill this gap by assessing the current homogenization status of one of the most diverse vertebrate groups (i.e., freshwater fishes) at global and regional scales. We demonstrate that current homogenization of the freshwater fish faunas is still low at the world scale (0.5%) but reaches substantial levels (up to 10%) in some highly invaded river basins from the Nearctic and Palearctic realms. In these realms experiencing high changes, nonnative species introductions rather than native species extirpations drive taxonomic homogenization. Our results suggest that the "Homogocene era" is not yet the case for freshwater fish fauna at the worldwide scale. However, the distressingly high level of homogenization noted for some biogeographical realms stresses the need for further understanding of the ecological consequences of homogenization processes.

Karyotype description of Pomacea patula catemacensis (Caenogastropoda, Ampullariidae), with an assessment of the taxonomic status of Pomacea patula.

PubMed

Diupotex-Chong, María Esther; Cazzaniga, Néstor J; Hernández-Santoyo, Alejandra; Betancourt-Rule, José Miguel

2004-12-01

Mitotic chromosomes of the freshwater snail Pomacea patula catemacensis (Baker 1922) were analyzed on gill tissue of specimens from the type locality (Lake Catemaco, Mexico). The diploid number of chromosomes is 2n = 26, including nine metacentric and four submetacentric pairs; therefore, the fundamental number is FN = 52, No sex chromosomes could be identified. The same chromosome number and morphology were already reported for P. flagellata, i.e., the other species of the genus living in Mexico. The basic haploid number for family Ampullariidae was reported to be n = 14 in the literature; so, its reduction to n = 13 is probably an apomorphy of the Mexican Pomacea snails. Lanistes bolteni, from Egypt, also shows n = 13, but its karyotype is much more asymmetrical, and seems to have evolved independently from P. flagellata and P. patula catemacensis. The nominotypical subspecies, P. patula patula (Reeve 1856), is a poorly known taxon, whose original locality is unknown. A taxonomical account is presented here, and a Mexican origin postulated as the most parsimonious hypothesis.

Decision analysis for designing marine protected areas for multiple species with uncertain fishery status.

PubMed

White, J Wilson; Botsford, Louis W; Moffitt, Elizabeth A; Fischer, Douglas T

2010-09-01

Marine protected areas (MPAs) are growing in popularity as a conservation tool, and there are increasing calls for additional MPAs. Meta-analyses indicate that most MPAs successfully meet the minimal goal of increasing biomass inside the MPA, while some do not, leaving open the important question of what makes MPAs successful. An often-overlooked aspect of this problem is that the success of fishery management outside MPA boundaries (i.e., whether a population is overfished) affects how well MPAs meet both conservation goals (e.g., increased biomass) and economic goals (e.g., minimal negative effects on fishery yield). Using a simple example of a system with homogeneous habitat and periodically spaced MPAs, we show that, as area in MPAs increases, (1) conservation value (biomass) may initially be zero, implying no benefit, then at some point increases monotonically; and (2) fishery yield may be zero, then increases monotonically to a maximum beyond which further increase in MPA area causes yield to decline. Importantly, the points at which these changes in slope occur vary among species and depend on management outside MPAs. Decision makers considering the effects of a potential system of MPAs on multiple species are confronted by a number of such cost-benefit curves, and it is usually impossible to maximize benefits and minimize costs for all species. Moreover, the precise shape of each curve is unknown due to uncertainty regarding the fishery status of each species. Here we describe a decision-analytic approach that incorporates existing information on fishery stock status to present decision makers with the range of likely outcomes of MPA implementation. To summarize results from many species whose overfishing status is uncertain, our decision-analysis approach involves weighted averages over both overfishing uncertainty and species. In an example from an MPA decision process in California, USA, an optimistic projection of future fishery management success led to recommendation of fewer and smaller MPAs than that derived from a more pessimistic projection of future management success. This example illustrates how information on fishery status can be used to project potential outcomes of MPA implementation within a decision analysis framework and highlights the need for better population information.

Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials.

PubMed

Savic, Olivera; Savic, Andrej M; Kovic, Vanja

2017-01-01

We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280-460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520-600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation.

Deanol acetamidobenzoate treatment in choreiform movement disorders.

PubMed

Tarsy, D; Bralower, M

1977-12-01

Deanol acetamidobenzoate was administered in double-blind, crossover fashion with placebo to five patients with tardive dyskinesia, three patients with Huntington's chorea, and one patient with posthemiplegic chorea. No significant effect on dyskinesia was observed. Preliminary administration of physostigmine salicylate to patients with tardive dyskinesia had a variable effect, while benztropine mesylate produced no change. Since the status of deanol as an effective precursor of acetylcholine is uncertain, further trials with putative cholinergic agents remain warranted in choreiform syndromes.

Application of 2011 American College of Cardiology Foundation/American Society of Echocardiography appropriateness use criteria in hospitalized patients referred for transthoracic echocardiography in a community setting.

PubMed

Ballo, Piercarlo; Bandini, Fabrizio; Capecchi, Irene; Chiodi, Leandro; Ferro, Giuseppe; Fortini, Alberto; Giuliani, Gabriele; Landini, Giancarlo; Laureano, Raffaele; Milli, Massimo; Nenci, Gabriele; Pizzarelli, Francesco; Santoro, Giovanni Maria; Vannelli, Pasquale; Cappelletti, Carlo; Zuppiroli, Alfredo

2012-06-01

A recent American College of Cardiology Foundation and American Society of Echocardiography document updated previous appropriate use criteria (AUC) for echocardiography. The aim of this study was to explore the application of the new AUC, and the resulting appropriateness rate, in hospitalized patients referred for transthoracic echocardiography (TTE) in a community setting. A total of 931 consecutive inpatients referred for TTE were prospectively recruited in five community hospitals. Patients were categorized as having appropriate, uncertain, or inappropriate indications for TTE according to the AUC. An additional group of 259 inpatients, discharged without having been referred for TTE, was also considered. In the group referred for TTE, the large majority of indications (98.8%) were classifiable according to the AUC with good interobserver reproducibility. Indications were appropriate in 739 patients (80.3%), of uncertain appropriateness in 46 (5.0%), and inappropriate in 135 (14.7%). Compared with patients with appropriate or uncertain indications, those with inappropriate indications were younger and more often referred by noncardiologists. Most common causes of inappropriate indications were related to the lack of changes in clinical status or to the absence of cardiovascular symptoms and signs. Examinations with appropriate or uncertain indications had an impact on clinical decision making more often than those with inappropriate indications (86.7% vs 14.1%, P < .0001). In the group discharged without having been referred for TTE, TTE might have been appropriate in 16.2% of cases. Clinical application of the new AUC was highly feasible in a community setting. Although inpatient referral for TTE was appropriate in most patients, strategies aimed at implementing these criteria in clinical practice are desirable. Copyright © 2012 American Society of Echocardiography. Published by Mosby, Inc. All rights reserved.

Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials

PubMed Central

Savic, Olivera; Savic, Andrej M.; Kovic, Vanja

2017-01-01

We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280–460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520–600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation. PMID:29236767

Application of the Red List Index for conservation assessment of Spanish vascular plants.

PubMed

Saiz, Juan Carlos Moreno; Lozano, Felipe Domínguez; Gómez, Manuel Marrero; Baudet, Ángel Bañares

2015-06-01

The International Union for Conservation of Nature (IUCN) Red List Index (RLI) is used to measure trends in extinction risk of species over time. The development of 2 red lists for Spanish vascular flora during the past decade allowed us to apply the IUCN RLI to vascular plants in an area belonging to a global biodiversity hotspot. We used the Spanish Red Lists from 2000 and 2010 to assess changes in level of threat at a national scale and at the subnational scales of Canary Islands, Balearic Islands, and peninsular Spain. We assigned retrospective IUCN categories of threat to 98 species included in the Spanish Red List of 2010 but absent in the Spanish Red List of 2000. In addition, we tested the effect of different random and taxonomic and spatial Spanish samples on the overall RLI value. From 2000 to 2010, the IUCN categories of 768 species changed (10% of Spanish flora), mainly due to improved knowledge (63%), modifications in IUCN criteria (14%), and changes in threat status (12%). All measured national and subnational RLI values decreased during this period, indicating a general decline in the conservation status of the Spanish vascular flora. The Canarian RLI value (0.84) was the lowest, although the fastest deterioration in conservation status occurred on peninsular Spain (from 0.93 in 2000 to 0.92 in 2010). The RLI values based on subsamples of the Spanish Red List were not representative of RLI values for the entire country, which would discourage the use of small areas or small taxonomic samples to assess general trends in the endangerment of national biotas. The role of the RLI in monitoring of changes in biodiversity at the global and regional scales needs further reassessment because additional areas and taxa are necessary to determine whether the index is sufficiently sensitive for use in assessing temporal changes in species' risk of extinction. © 2015 Society for Conservation Biology.

On the taxonomic status and distribution of African species of Otomops (Chiroptera: Molossidae).

PubMed

Patterson, Bruce D; Webala, Paul W; Bartonjo, Michael; Nziza, Julius; Dick, Carl W; Demos, Terrence C

2018-01-01

Free-tailed bats of the genus Otomops are poorly known, and most species are documented from a handful of widely scattered localities. Recently, two allopatric species of Otomops were recognized in continental Africa: Otomops martiensseni (Matschie, 1897) in southern, central and western Africa, and the new species O. harrisoni Ralph et al., 2015 in the northeast and in Yemen. We collected additional samples of Otomops in Kenya and Rwanda where the ranges of these taxa approach one another to clarify their geographic ranges and taxonomic status. Mitochondrial and nuclear intron sequences served to identify and delimit species; we also documented their echolocation call variation and ectoparasite complements. Otomops martiensseni , the southern African species, was documented in northern Kenya in Marsabit National Park. O. harrisoni , the northeastern African-Arabian species, was documented in southern Kenya and in a cave in Musanze District, Rwanda. Moreover, individuals of both species were found together at the Musanze cave, establishing them in precise spatial and temporal sympatry. Analyses of mitochondrial and nuclear loci identify no evidence of admixture between these forms, although available samples limit the power of this analysis. Echolocation call differences are also apparent among the three localities we analyzed. Three orders of insects and two families of mites are newly reported as ectoparasites of O. harrisoni. Our results corroborate species rank for O. harrisoni and establish a zone of potential geographic overlap with O. martiensseni spanning at least 800 km of latitude. The new records establish the species in sympatry in northern Rwanda and add an additional species to the bat faunas of both Kenya and Rwanda. Future studies are needed to understand Otomops roosting requirements and movements, thereby explaining the paucity of known colonies and yielding better estimates of their conservation status. The discovery of mixed roosting associations in Rwanda invites further investigation.

The Integrated Impact of Diet On Human Immune Response, the Gut Microbiota, and Nutritional Status During Adaptation to a Spaceflight Analog

NASA Technical Reports Server (NTRS)

Douglas, G. L.; Zwart, S. R.; Young, M.; Kloeris, V.; Crucian, B.; Smith, S. M.; Lorenzi, H.

2017-01-01

Spaceflight impacts human physiology, including well documented immune system dysregulation. Diet, immune function, and the microbiome are interlinked, but diet is the only one of these factors that we have the ability to easily, and significantly, alter on Earth or during flight. As we understand dietary impacts on physiology more thoroughly, we may then improve the spaceflight diet to improve crew health and potentially reduce flight-associated physiological alterations. It is expected that increasing the consumption of fruits and vegetables and bioactive compounds (e.g.,omega-3 fatty acids, lycopene, flavonoids) and therefore enhancing overall nutritional intake from the nominal shelf-stable, fully-processed space food system could serve as a countermeasure to improve human immunological profiles, the taxonomic profile of the gut microbiota, and nutritional status, especially where currently dysregulated during spaceflight. This interdisciplinary study will determine the effect of the current shelf-stable spaceflight diet compared to an "enhanced" shelf-stable spaceflight diet (25% more foods rich in omega-3 fatty acids, lycopene, flavonoids, fruits, and vegetables). The NASA Human Exploration Research Analog (HERA) 2017 missions, consisting of closed chamber confinement, realistic mission simulation, in a high-fidelity mock space vehicle, will serve as a platform to replicate mission stressors and the dysregulated physiology observed in astronauts. Biosampling of crew members will occur at selected intervals, with complete dietary tracking. Outcome measures will include immune markers (e.g., peripheral leukocyte distribution, inflammatory cytokine profiles, T cell function), the taxonomic and metatranscriptomic profile of the gut microbiome, and nutritional status biomarkers and metabolites. Data collection will also include complete dietary tracking. Statistical evaluations will determine physiological and biochemical shifts in relation to nutrient in take and study phase. Beneficial improvements will provide evidence of the impact of diet on crew health and adaptation to this spaceflight analog, and will aid in the design and development of more-efficient targeted dietary interventions.

An illustrated checklist of the genus Elymnias Hübner, 1818 (Nymphalidae, Satyrinae)

PubMed Central

Wei, Chia-Hsuan; Lohman, David J.; Peggie, Djunijanti; Yen, Shen-Horn

2017-01-01

Abstract We review the genus Elymnias Hübner, 1818, a morphologically diverse satyrine butterfly clade involved in multifarious Batesian mimicry relationships throughout Asia and Africa. A variety of different model species are mimicked, and many Elymnias species are sexually dimorphic mimics, with males and females resembling different model species. We revise species and subspecies delimitations in light of an integrative taxonomic investigation using external morphology, male and female genital morphology, and a multi-locus molecular phylogeny. There is little interspecific genitalic variation among species in this group, and previous taxonomists therefore relied almost entirely on wing patterns. Our molecular phylogenetic analysis reveals several examples of polymorphism or wing pattern divergence within a single species currently classified as two or more different species. We also found examples of wing pattern convergence among disparate lineages that mimic the same widespread model species. Frequently, two or more phenotypically similar species were classified as a single species. This comprehensive checklist reviews all names associated with Elymnias to align its taxonomy with the evolutionary history of the group. All available information on nomenclature, type localities, repositories of type specimens, and geographical distributions is summarized, and images of adult specimens and genitalia are provided along with distribution maps of all species and selected subspecies. We identify 2 species incertae sedis, establish 15 monophyletic species groups (including 1 species unplaced in any species group), and make 49 taxonomic changes, including 35 new synonyms, 7 new combinations (2 of which have new status), 1 resurrected combination, 1 resurrected subspecies, and 7 status changes. PMID:28769686

Poles apart: the "bipolar" pteropod species Limacina helicina is genetically distinct between the Arctic and Antarctic oceans.

PubMed

Hunt, Brian; Strugnell, Jan; Bednarsek, Nina; Linse, Katrin; Nelson, R John; Pakhomov, Evgeny; Seibel, Brad; Steinke, Dirk; Würzberg, Laura

2010-03-23

The shelled pteropod (sea butterfly) Limacina helicina is currently recognised as a species complex comprising two sub-species and at least five "forma". However, at the species level it is considered to be bipolar, occurring in both the Arctic and Antarctic oceans. Due to its aragonite shell and polar distribution L. helicina is particularly vulnerable to ocean acidification. As a key indicator of the acidification process, and a major component of polar ecosystems, L. helicina has become a focus for acidification research. New observations that taxonomic groups may respond quite differently to acidification prompted us to reassess the taxonomic status of this important species. We found a 33.56% (+/-0.09) difference in cytochrome c oxidase subunit I (COI) gene sequences between L. helicina collected from the Arctic and Antarctic oceans. This degree of separation is sufficient for ordinal level taxonomic separation in other organisms and provides strong evidence for the Arctic and Antarctic populations of L. helicina differing at least at the species level. Recent research has highlighted substantial physiological differences between the poles for another supposedly bipolar pteropod species, Clione limacina. Given the large genetic divergence between Arctic and Antarctic L. helicina populations shown here, similarly large physiological differences may exist between the poles for the L. helicina species group. Therefore, in addition to indicating that L. helicina is in fact not bipolar, our study demonstrates the need for acidification research to take into account the possibility that the L. helicina species group may not respond in the same way to ocean acidification in Arctic and Antarctic ecosystems.

Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act.

PubMed

King, Tim L; Switzer, John F; Morrison, Cheryl L; Eackles, Michael S; Young, Colleen C; Lubinski, Barbara A; Cryan, Paul

2006-12-01

Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius.

Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act

USGS Publications Warehouse

King, Timothy L.; Switzer, John F.; Morrison, Cheryl L.; Eackles, Michael S.; Young, Colleen C.; Lubinski, Barbara A.; Cryan, Paul M.

2006-01-01

Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius. ?? 2006 The Authors.

Molecular Characterization of the Human Stomach Microbiota in Gastric Cancer Patients.

PubMed

Yu, Guoqin; Torres, Javier; Hu, Nan; Medrano-Guzman, Rafael; Herrera-Goepfert, Roberto; Humphrys, Michael S; Wang, Lemin; Wang, Chaoyu; Ding, Ti; Ravel, Jacques; Taylor, Philip R; Abnet, Christian C; Goldstein, Alisa M

2017-01-01

Helicobacter pylori ( Hp ) is the primary cause of gastric cancer but we know little of its relative abundance and other microbes in the stomach, especially at the time of gastric cancer diagnosis. Here we characterized the taxonomic and derived functional profiles of gastric microbiota in two different sets of gastric cancer patients, and compared them with microbial profiles in other body sites. Paired non-malignant and tumor tissues were sampled from 160 gastric cancer patients with 80 from China and 80 from Mexico. The 16S rRNA gene V3-V4 region was sequenced using MiSeq platform for taxonomic profiles. PICRUSt was used to predict functional profiles. Human Microbiome Project was used for comparison. We showed that Hp is the most abundant member of gastric microbiota in both Chinese and Mexican samples (51 and 24%, respectively), followed by oral-associated bacteria. Taxonomic (phylum-level) profiles of stomach microbiota resembled oral microbiota, especially when the Helicobacter reads were removed. The functional profiles of stomach microbiota, however, were distinct from those found in other body sites and had higher inter-subject dissimilarity. Gastric microbiota composition did not differ by Hp colonization status or stomach anatomic sites, but did differ between paired non-malignant and tumor tissues in either Chinese or Mexican samples. Our study showed that Hp is the dominant member of the non-malignant gastric tissue microbiota in many gastric cancer patients. Our results provide insights on the gastric microbiota composition and function in gastric cancer patients, which may have important clinical implications.

Molecular Characterization of the Human Stomach Microbiota in Gastric Cancer Patients

PubMed Central

Yu, Guoqin; Torres, Javier; Hu, Nan; Medrano-Guzman, Rafael; Herrera-Goepfert, Roberto; Humphrys, Michael S.; Wang, Lemin; Wang, Chaoyu; Ding, Ti; Ravel, Jacques; Taylor, Philip R.; Abnet, Christian C.; Goldstein, Alisa M.

2017-01-01

Helicobacter pylori (Hp) is the primary cause of gastric cancer but we know little of its relative abundance and other microbes in the stomach, especially at the time of gastric cancer diagnosis. Here we characterized the taxonomic and derived functional profiles of gastric microbiota in two different sets of gastric cancer patients, and compared them with microbial profiles in other body sites. Paired non-malignant and tumor tissues were sampled from 160 gastric cancer patients with 80 from China and 80 from Mexico. The 16S rRNA gene V3–V4 region was sequenced using MiSeq platform for taxonomic profiles. PICRUSt was used to predict functional profiles. Human Microbiome Project was used for comparison. We showed that Hp is the most abundant member of gastric microbiota in both Chinese and Mexican samples (51 and 24%, respectively), followed by oral-associated bacteria. Taxonomic (phylum-level) profiles of stomach microbiota resembled oral microbiota, especially when the Helicobacter reads were removed. The functional profiles of stomach microbiota, however, were distinct from those found in other body sites and had higher inter-subject dissimilarity. Gastric microbiota composition did not differ by Hp colonization status or stomach anatomic sites, but did differ between paired non-malignant and tumor tissues in either Chinese or Mexican samples. Our study showed that Hp is the dominant member of the non-malignant gastric tissue microbiota in many gastric cancer patients. Our results provide insights on the gastric microbiota composition and function in gastric cancer patients, which may have important clinical implications. PMID:28730144

Risk factors associated with disease progression and mortality in chronic kidney disease of uncertain etiology: a cohort study in Medawachchiya, Sri Lanka.

PubMed

Senevirathna, Lalantha; Abeysekera, Tilak; Nanayakkara, Shanika; Chandrajith, Rohana; Ratnatunga, Neelakanthi; Harada, Kouji H; Hitomi, Toshiaki; Komiya, Toshiyuki; Muso, Eri; Koizumi, Akio

2012-05-01

The alarming rise in the prevalence of chronic kidney disease of uncertain etiology (CKDu) among the low socioeconomic farming community in the North Central Province of Sri Lanka has been recognized as an emerging public health issue in the country. This study sought to determine the possible factors associated with the progression and mortality of CKDu. The study utilized a single-center cohort registered in 2003 and followed up until 2009 in a regional clinic in the endemic region, and used a Cox proportional hazards model. We repeatedly found an association between disease progression and hypertension. Men were at higher risk of CKDu than women. A significant proportion of the patients in this cohort were underweight, which emphasized the need for future studies on the nutritional status of these patients. Compared with findings in western countries and other regions of Asia, we identified hypertension as a major risk factor for progression of CKDu in this cohort.

Status of DORIS stations in Antarctica for precise geodesy

NASA Technical Reports Server (NTRS)

Willis, P.; Amalvict, M.; Shibuya, K.

2005-01-01

In Antarctica, besides the quite numerous GPS stations, four DORIS stations are permanently operating. In addition to the permanent DORIS stations, episodic campaigns took place at DomeC/Conccordia and on Sorsdal and Lambert glaciers. In this paper, we first collect general information concerning the stations and the campaigns (location, start of measurements, etc). We then present the results of observations of the permanent stations keeping in mind that we are primarily interested here in the vertical component, which is the most uncertain component.

Charting taxonomic knowledge through ontologies and ranking algorithms

NASA Astrophysics Data System (ADS)

Huber, Robert; Klump, Jens

2009-04-01

Since the inception of geology as a modern science, paleontologists have described a large number of fossil species. This makes fossilized organisms an important tool in the study of stratigraphy and past environments. Since taxonomic classifications of organisms, and thereby their names, change frequently, the correct application of this tool requires taxonomic expertise in finding correct synonyms for a given species name. Much of this taxonomic information has already been published in journals and books where it is compiled in carefully prepared synonymy lists. Because this information is scattered throughout the paleontological literature, it is difficult to find and sometimes not accessible. Also, taxonomic information in the literature is often difficult to interpret for non-taxonomists looking for taxonomic synonymies as part of their research. The highly formalized structure makes Open Nomenclature synonymy lists ideally suited for computer aided identification of taxonomic synonyms. Because a synonymy list is a list of citations related to a taxon name, its bibliographic nature allows the application of bibliometric techniques to calculate the impact of synonymies and taxonomic concepts. TaxonRank is a ranking algorithm based on bibliometric analysis and Internet page ranking algorithms. TaxonRank uses published synonymy list data stored in TaxonConcept, a taxonomic information system. The basic ranking algorithm has been modified to include a measure of confidence on species identification based on the Open Nomenclature notation used in synonymy list, as well as other synonymy specific criteria. The results of our experiments show that the output of the proposed ranking algorithm gives a good estimate of the impact a published taxonomic concept has on the taxonomic opinions in the geological community. Also, our results show that treating taxonomic synonymies as part of on an ontology is a way to record and manage taxonomic knowledge, and thus contribute to the preservation our scientific heritage.

Taxonomic indexing--extending the role of taxonomy.

PubMed

Patterson, David J; Remsen, David; Marino, William A; Norton, Cathy

2006-06-01

Taxonomic indexing refers to a new array of taxonomically intelligent network services that use nomenclatural principles and elements of expert taxonomic knowledge to manage information about organisms. Taxonomic indexing was introduced to help manage the increasing amounts of digital information about biology. It has been designed to form a near basal layer in a layered cyberinfrastructure that deals with biological information. Taxonomic Indexing accommodates the special problems of using names of organisms to index biological material. It links alternative names for the same entity (reconciliation), and distinguishes between uses of the same name for different entities (disambiguation), and names are placed within an indefinite number of hierarchical schemes. In order to access all information on all organisms, Taxonomic indexing must be able to call on a registry of all names in all forms for all organisms. NameBank has been developed to meet that need. Taxonomic indexing is an area of informatics that overlaps with taxonomy, is dependent on the expert input of taxonomists, and reveals the relevance of the discipline to a wide audience.

Selective extinction drives taxonomic and functional alpha and beta diversities in island bird assemblages.

PubMed

Si, Xingfeng; Baselga, Andrés; Leprieur, Fabien; Song, Xiao; Ding, Ping

2016-03-01

Taxonomic diversity considers all species being equally different from each other and thus disregards species' different ecological functions. Exploring taxonomic and functional aspects of biodiversity simultaneously can better understand the processes of community assembly. We analysed taxonomic and functional alpha and beta diversities of breeding bird assemblages on land-bridge islands in the Thousand Island Lake, China. Given the high dispersal ability of most birds at this spatial scale (several kilometres), we predicted (i) selective extinction driving alpha and beta diversities after the creation of land-bridge islands of varying area and (ii) low taxonomic and functional beta diversities that were not correlated to spatial distance. Breeding birds were surveyed on 37 islands annually from 2007 to 2014. We decomposed beta diversity of breeding birds into spatial turnover and nestedness-resultant components, and related taxonomic and functional diversities to island area and isolation using power regression models (for alpha diversity) and multiple regression models on distance matrices (for beta diversity). We then ran simulations to assess the strength of the correlations between taxonomic and functional diversities. Results revealed that both taxonomic and functional alpha diversities increased with island area. The taxonomic nestedness-resultant and turnover components increased and decreased with difference in area, respectively, but functional counterparts did not. Isolation played a minor role in explaining alpha- and beta-diversity patterns. By partitioning beta diversity, we found low levels of overall taxonomic and functional beta diversities. The functional nestedness-resultant component dominated overall functional beta diversity, whereas taxonomic turnover was the dominant component for taxonomic beta diversity. The simulation showed that functional alpha and beta diversities were significantly correlated with taxonomic diversities, and the observed values of correlations were significantly different from null expectations of random extinction. Our assessment of island bird assemblages validated the predictions of no distance effects and low beta diversity due to pervasive dispersal events among islands and also suggested that selective extinction drives taxonomic and functional alpha and beta diversities. The contrasting turnover and nestedness-resultant components of taxonomic and functional beta diversities demonstrate the importance of considering the multifaceted nature of biodiversity when examining community assembly. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Quality of life concerns and depression among hematopoietic stem cell transplant survivors.

PubMed

Mosher, Catherine E; DuHamel, Katherine N; Rini, Christine; Corner, Geoffrey; Lam, Joanne; Redd, William H

2011-09-01

This study examined quality of life, transplant-related concerns, and depressive symptoms and their demographic and medical correlates at 1 to 3 years following hematopoietic stem cell transplantation (HSCT). HSCT survivors (N=406) completed telephone-administered questionnaires that assessed demographic variables, functional status, quality of life, transplant-related concerns, and depressive symptoms. The most prevalent concerns among HSCT survivors included physical symptoms (e.g., fatigue and pain), maintaining current health status and employment, changes in appearance, and lack of sexual interest and satisfaction. In addition, almost one-third (32%) of survivors age 40 years and younger reported concern about their ability to have children. Unemployed survivors and those with lower incomes and worse functional status were more likely to experience poorer quality of life in multiple domains. Fifteen percent of the sample reported moderate to severe depressive symptoms, and these symptoms were higher among allogeneic transplant recipients and those with lower functional status. Results suggest that interventions are needed to address physical symptoms, coping with an uncertain future, infertility, and sexual issues during the early phase of HSCT survivorship.

Five new species of Syzygium (Myrtaceae) from Sulawesi, Indonesia

PubMed Central

Brambach, Fabian; Byng, James W.; Culmsee, Heike

2017-01-01

Abstract Following ongoing ecological research on the tree diversity of the Indonesian island of Sulawesi, we describe five new species of Syzygium. These are the first descriptions of Syzygium species from the island since Blume (1850, Jambosa celebica and J. cornifolia), highlighting the significant lack of taxonomic research on the genus for the region. The five species proposed as new are Syzygium balgooyi sp. nov., Syzygium contiguum sp. nov., Syzygium devogelii sp. nov., Syzygium eymae sp. nov., and Syzygium galanthum sp. nov. All species are illustrated and information on their distribution, ecology, and conservation status is given. PMID:28785165

Type catalog from the fish collection of the Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul, Brazil.

PubMed

Bertaco, Vinicius A; Azevedo, Marco A

2018-03-07

The catalog of type material deposited at the fish collection of the Museu de Ciências Naturais (MCN), Fundação Zoobotânica do Rio Grande do Sul, includes 315 specimens from 96 lots, representing six holotypes and 309 paratypes of 34 nominal species. Currently, two of them are synonymy and one have a questionable taxonomic status. Corrections and additional information from the original descriptions are included in the remarks for each species or lot. Photos of holotypes and paratypes are presented.

LATE PLEISTOCENE ENVIRONMENTAL CHANGES LEAD TO UNSTABLE DEMOGRAPHY AND POPULATION DIVERGENCE OF ANOPHELES ALBIMANUS IN THE NORTHERN NEOTROPICS

PubMed Central

Loaiza, Jose R.; Scott, Marilyn E.; Bermingham, Eldredge; Sanjur, Oris I.; Wilkerson, Richard; Rovira, Jose; Gutiérrez, Lina A.; Correa, Margarita M.; Grijalva, Mario; Birnberg, Lotty; Bickersmith, Sara; Conn, Jan E.

2011-01-01

We investigated the historical demography of Anopheles albimanus using mosquitoes from five countries and three different DNA regions, the mitochondrial cytochrome oxidase subunit I gene (COI), the single copy nuclear white gene and the ribosomal internal transcribed spacer two (ITS2). All the molecular markers supported the taxonomic status of a single species of An. albimanus. Furthermore, agreement between the COI and the white genes suggested a scenario of Pleistocene geographic fragmentation (i.e., population contraction) and subsequent range expansion across southern Central America. PMID:20888924

Multiple approaches to understanding the taxonomic status of an enigmatic new scorpion species of the genus Tityus (Buthidae) from the biogeographic island of Paraje Tres Cerros (Argentina)

PubMed Central

Adilardi, Renzo S.; Cajade, Rodrigo; Ramírez, Martín J.; Ceccarelli, F. Sara; Mola, Liliana M.

2017-01-01

Tityus curupi n. sp., belonging to the bolivianus complex, is described from the biogeographically distinct area of Paraje Tres Cerros in north-eastern Argentina. We also present a molecular species delimitation analysis between Tityus curupi n. sp. and its sister species Tityus uruguayensis Borelli 1901 to confirm species integrity. Furthermore, a cytogenetic analysis is presented for these two species which contain different multivalent associations in meiosis, as a consequence of chromosome rearrangements, and the highest chromosome numbers in the genus. PMID:28746406

Planaxidae (Mollusca, Gastropoda) from the South China Sea

NASA Astrophysics Data System (ADS)

Chen, Zhiyun; Zhang, Junlong; Lian, Xiping; Tan, Yehui

2018-03-01

Planaxidae is a family of tropical and subtropical marine gastropods that are adapted to an intertidal, rocky environment. The present study deals with three species in the family Planaxidae from the South China Sea: Planaxis sulcatus (von Born, 1778), Angiola longispira (Smith, 1872), and Supplanaxis niger (Quoy and Gaimard, 1833), based on specimens deposited in the Marine Biodiversity Collections of the South China Sea, Chinese Academy of Sciences. The taxonomic status, main morphological characteristics of the shell and radula, distribution, and habitat of these three planaxid species are presented. We also briefly discuss their morphological differences and the biogeographic distribution.

The taxonomic status of the white-tailed kite

USGS Publications Warehouse

Clark, W.S.; Banks, R.C.

1992-01-01

The White-tailed Kite (Elanus leucurus) of the Americas has been merged with the Black-shouldered (or Black-winged) Kite (E. caeruleus) of the Old World and the Australian Black-shouldered Kite (E. axillaris) by North American authorities (but not elsewhere), primarily because of similarity in plumage. However, American kites differ from Old World kites in greater size and weight, in proportions (relatively longer tail and smaller bill and feet), plumage pattern (particularly of juveniles), and in behavior. Here we argue that these characters are sufficiently distinctive to warrant recognition of E. leucurus at the species level.

Three New Species of Cyphellophora (Chaetothyriales) Associated with Sooty Blotch and Flyspeck

PubMed Central

Gao, Liu; Ma, Yongqiang; Zhao, Wanyu; Wei, Zhuoya; Gleason, Mark L.; Chen, Hongcai; Hao, Lu; Sun, Guangyu; Zhang, Rong

2015-01-01

The genus Cyphellophora includes human- and plant-related species from mammal skin and nails, plant materials, and food. On the basis of analysis of ITS, LSU, TUB2 and RPB1 data and morphological characters, three new species, Cyphellophora phyllostachysdis, C. artocarpi and C. musae, associated with sooty blotch and flyspeck disease, were added to this genus. The 2D structure of ITS1 and ITS2 confirmed this taxonomic status. Pathogenicity tests on apple fruit indicated that C. artocarpi could be a sooty blotch and flyspeck pathogen of apple. PMID:26398347

The taxonomic status of "Halobacterium marismortui" from the Dead Sea: a comparison with Halobacterium vallismortis

NASA Technical Reports Server (NTRS)

Oren, A.; Lau, P. P.; Fox, G. E.

1988-01-01

A Halobacterium strain, isolated by Ginzburg et al. from the Dead Sea in the late 1960's, often referred to as "Halobacterium marismortui" or "Halobacterium of the Dead Sea" (deposited in the American Type Culture Collection as ATCC 43049) was compared with Halobacterium (Haloarcula) vallismortis ATCC 29715. The strains appeared to be very closely related, as shown by the near identity of their 5S and 16S ribosomal RNA's, and a large number of other common properties. Distinct differences exist, however, in cell morphology, and in their potency to utilize different sugars and other compounds.

Multiple approaches to understanding the taxonomic status of an enigmatic new scorpion species of the genus Tityus (Buthidae) from the biogeographic island of Paraje Tres Cerros (Argentina).

PubMed

Ojanguren-Affilastro, Andrés A; Adilardi, Renzo S; Cajade, Rodrigo; Ramírez, Martín J; Ceccarelli, F Sara; Mola, Liliana M

2017-01-01

Tityus curupi n. sp., belonging to the bolivianus complex, is described from the biogeographically distinct area of Paraje Tres Cerros in north-eastern Argentina. We also present a molecular species delimitation analysis between Tityus curupi n. sp. and its sister species Tityus uruguayensis Borelli 1901 to confirm species integrity. Furthermore, a cytogenetic analysis is presented for these two species which contain different multivalent associations in meiosis, as a consequence of chromosome rearrangements, and the highest chromosome numbers in the genus.

Description of a new species of Petrolisthes in the Indo-West Pacific with a redefinition of P.hastatus Stimpson, 1858 and resurrection of P.inermis (Heller, 1862) (Crustacea, Anomura, Porcellanidae).

PubMed

Werding, Bernd; Hiller, Alexandra

2015-01-01

The porcellanid crab Petrolistheshastatus Stimpson, 1858, has been traditionally viewed as a highly variable species with a wide distribution in the West Pacific. For more than a century there has been taxonomic confusion of this species with morphologically similar taxa, some of which were synonymized with Stimpson's taxon. We redefine Petrolistheshastatus, resurrect Petrolisthesinermis as a valid species, discuss the status of Petrolisthestenkatei De Man, 1893, and describe a new species as Petrolistheselegantissimus from Indonesia.

Partial Knowledge of Word Meanings: Thematic and Taxonomic Representations

ERIC Educational Resources Information Center

Whitmore, Jeannette M.; Shore, Wendelyn J.; Smith, Peg Hull

2004-01-01

The type of information (taxonomic or thematic) available at different levels of knowledge was investigated. Following extensive norming to identify taxonomic and thematic associates of low-frequency nouns, participants determined if taxonomic or thematic associates were meaningfully related to target words at three levels of knowledge: target…

Is the creation of artificial life morally significant?

PubMed Central

Douglas, Thomas; Powell, Russell; Savulescu, Julian

2013-01-01

In 2010, the Venter lab announced that it had created the first bacterium with an entirely synthetic genome. This was reported to be the first instance of ‘artificial life,’ and in the ethical and policy discussions that followed it was widely assumed that the creation of artificial life is in itself morally significant. We cast doubt on this assumption. First we offer an account of the creation of artificial life that distinguishes this from the derivation of organisms from existing life and clarify what we mean in asking whether the creation of artificial life has moral significance. We then articulate and evaluate three attempts to establish that the creation of artificial life is morally significant. These appeal to (1) the claim that the creation of artificial life involves playing God, as expressed in three distinct formulations; (2) the claim that the creation of artificial life will encourage reductionist attitudes toward the living world that undermine the special moral value accorded to life; and (3) the worry that artificial organisms will have an uncertain functional status and consequently an uncertain moral status. We argue that all three attempts to ground the moral significance of the creation of artificial life fail, because none of them establishes that the creation of artificial life is morally problematic in a way that the derivation of organisms from existing life forms is not. We conclude that the decisive moral consideration is not how life is created but what non-genealogical properties it possesses. PMID:23810562

Is the creation of artificial life morally significant?

PubMed

Douglas, Thomas; Powell, Russell; Savulescu, Julian

2013-12-01

In 2010, the Venter lab announced that it had created the first bacterium with an entirely synthetic genome. This was reported to be the first instance of 'artificial life,' and in the ethical and policy discussions that followed it was widely assumed that the creation of artificial life is in itself morally significant. We cast doubt on this assumption. First we offer an account of the creation of artificial life that distinguishes this from the derivation of organisms from existing life and clarify what we mean in asking whether the creation of artificial life has moral significance. We then articulate and evaluate three attempts to establish that the creation of artificial life is morally significant. These appeal to (1) the claim that the creation of artificial life involves playing God, as expressed in three distinct formulations; (2) the claim that the creation of artificial life will encourage reductionist attitudes toward the living world that undermine the special moral value accorded to life; and (3) the worry that artificial organisms will have an uncertain functional status and consequently an uncertain moral status. We argue that all three attempts to ground the moral significance of the creation of artificial life fail, because none of them establishes that the creation of artificial life is morally problematic in a way that the derivation of organisms from existing life forms is not. We conclude that the decisive moral consideration is not how life is created but what non-genealogical properties it possesses. Copyright © 2013 Elsevier Ltd. All rights reserved.

Taxonomic review of the Ornithocheirus complex (Pterosauria) from the Cretaceous of England

PubMed Central

Rodrigues, Taissa; Kellner, Alexander Wilhelm Armin

2013-01-01

Abstract Over a decade after the last major review of the Cambridge Greensand pterosaurs, their systematics remains one of the most disputed points in pterosaur taxonomy. Ornithocheiridae is still a wastebasket for fragmentary taxa, and some nomenclatural issues are still a problem. Here, the species from the Cretaceous of England that, at some point, were referred in Ornithocheirus, are reviewed. Investigation of the primary literature confirmed that Criorhynchus should be considered an objective junior synonym of Ornithocheirus. Taxonomic review of more than 30 species known from fragmentary remains showed that 16 of them are undiagnosable (nomina dubia): Palaeornis cliftii, Cimoliornis diomedeus, Pterodactylus compressirostris, Pterodactylus fittoni, Pterodactylus woodwardi, Ornithocheirus brachyrhinus, Ornithocheirus carteri, Ornithocheirus crassidens, Ornithocheirus dentatus, Ornithocheirus enchorhynchus, Ornithocheirus eurygnathus, Ornithocheirus oxyrhinus, Ornithocheirus scaphorhynchus, Ornithocheirus tenuirostris, Ornithocheirus xyphorhynchus, and Pterodactylus sagittirostris. Fourteen species are considered valid, and diagnoses are provided to all of them: Ornithocheirus simus, Lonchodraco giganteus comb. n., Lonchodraco machaerorhynchus comb. n., Lonchodraco(?) microdon comb. n., Coloborhynchus clavirostris, ‘Ornithocheirus’ capito, Camposipterus nasutus comb. n., Camposipterus(?) sedgwickii comb. n., Camposipterus(?) colorhinus comb. n., Cimoliopterus cuvieri comb. n., ‘Ornithocheirus’ polyodon, ‘Ornithocheirus’ platystomus, ‘Pterodactylus’ daviesii, and ‘Ornithocheirus’ denticulatus. These species are referred in the genera Ornithocheirus, Lonchodraco gen. n., Coloborhynchus, Cimoliopterus gen. n., and Camposipterus gen. n., but additional genera are probably present, as indicated by the use of single quotation marks throughout the text. A cladistic analysis demonstrates that Anhangueridae lies within a newly recognized clade, here named Anhangueria, which also includes the genera Cearadactylus, Brasileodactylus, Ludodactylus, and Camposipterus. The anhanguerian ‘Cearadactylus’ ligabuei belongs to a different genus than Cearadactylus atrox. Lonchodraconidae fam. n. (more or less equivalent to Lonchodectidae sensu Unwin 2001) is a monophyletic entity, but its exact phylogenetic position remains uncertain, as is the case of Ornithocheirus simus. Therefore, it is proposed that Ornithocheiridae should be constricted to its type species and thus is redundant. Other taxa previously referred as “ornithocheirids” are discussed in light of the revised taxonomy. PMID:23794925

Whence the red panda?

PubMed

Flynn, J J; Nedbal, M A; Dragoo, J W; Honeycutt, R L

2000-11-01

The evolutionary history of the red panda (Ailurus fulgens) plays a pivotal role in the higher-level phylogeny of the "bear-like" arctoid carnivoran mammals. Characters from morphology and molecules have provided inconsistent evidence for placement of the red panda. Whereas it certainly is an arctoid, there has been major controversy about whether it should be placed with the bears (ursids), ursids plus pinnipeds (seals, sea lions, walrus), raccoons (procyonids), musteloids (raccoons plus weasels, skunks, otters, and badgers [mustelids]), or as a monotypic lineage of uncertain phylogenetic affinities. Nucleotide sequence data from three mitochondrial genes and one nuclear intron were analyzed, with more complete taxonomic sampling of relevant taxa (arctoids) than previously available in analyses of primary molecular data, to clarify the phylogenetic relationships of the red panda to other arctoid carnivorans. This study provides detailed phylogenetic analyses (both parsimony and maximum-likelihood) of primary character data for arctoid carnivorans, including bootstrap and decay indices for all arctoid nodes, and three statistical tests of alternative phylogenetic hypotheses for the placement of the red panda. Combined phylogenetic analyses reject the hypotheses that the red panda is most closely related to the bears (ursids) or to the raccoons (procyonids). Rather, evidence from nucleotide sequences strongly support placement of the red panda within a broad Musteloidea (sensu lato) clade, including three major lineages (the red panda, the skunks [mephitids], and a clearly monophyletic clade of procyonids plus mustelids [sensu stricto, excluding skunks]). Within the Musteloidea, interrelationships of the three major lineages are unclear and probably are best considered an unresolved trichotomy. These data provide compelling evidence for the relationships of the red panda and demonstrate that small taxonomic sample sizes can result in misleading or possibly erroneous (based on prior modeling, as well as conflict between the results of our analyses of less and more complete data sets) conclusions about phylogenetic relationships and taxonomy. Copyright 2000 Academic Press.

A Taxonomic Search Engine: Federating taxonomic databases using web services

PubMed Central

Page, Roderic DM

2005-01-01

Background The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. Results The Taxonomic Search Engine (TSE) is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID) authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata) for each name. Conclusion The Taxonomic Search Engine is available at and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names. PMID:15757517

Revision of the genus Bradyporus Charpentier, 1825 (Orthoptera: Tettigoniidae: Bradyporinae).

PubMed

Ünal, Mustafa

2017-05-31

The genus Bradyporus Charpentier is taxonomically revised using information obtained from numerous recently collected specimens. Bradyporus is divided into two subgenera Bradyporus Charpentier s.str. and Callimenus Fischer von Waldheim. Five species groups are distinguished in the latter subgenus. Sixteen species and subspecies are listed. Bradyporus (Callimenus) multituberculatus multituberculatus (Fischer von Waldheim, 1833) and Bradyporus (Callimenus) multituberculatus montandoni (Burr, 1898) are designated subspecies for the first time. Previously synonymized Bradyporus (Callimenus) macrogaster skopjensis Karaman, 1961 is reinstated as a valid species. A new species, Bradyporus (Callimenus) gocmeni Ünal, sp. nov. from Eastern Turkey and the previously unknown female of Bradyporus (Callimenus) skopjensis Karaman, 1961 are described. A Neotype for Bradyporus (Callimenus) macrogaster longicollis (Fieber, 1853) is designated. Nomenclatural and taxonomical problems are discussed under the relevant taxa. Phylogenetic relationships based on morphology of the subgenera, species groups, and the species and subspecies of each species group are proposed. Morphological derived and ancestral characters are discussed. A key to the lower taxa of the genus is provided with 207 original figures including 3 distributional maps. A check-list of the lower taxa of the genus is given. Additionally the IUCN Red List statuses of the species and subspecies are included.

An audit of some processing effects in aggregated occurrence records.

PubMed

Mesibov, Robert

2018-01-01

A total of ca 800,000 occurrence records from the Australian Museum (AM), Museums Victoria (MV) and the New Zealand Arthropod Collection (NZAC) were audited for changes in selected Darwin Core fields after processing by the Atlas of Living Australia (ALA; for AM and MV records) and the Global Biodiversity Information Facility (GBIF; for AM, MV and NZAC records). Formal taxon names in the genus- and species-groups were changed in 13-21% of AM and MV records, depending on dataset and aggregator. There was little agreement between the two aggregators on processed names, with names changed in two to three times as many records by one aggregator alone compared to records with names changed by both aggregators. The type status of specimen records did not change with name changes, resulting in confusion as to the name with which a type was associated. Data losses of up to 100% were found after processing in some fields, apparently due to programming errors. The taxonomic usefulness of occurrence records could be improved if aggregators included both original and the processed taxonomic data items for each record. It is recommended that end-users check original and processed records for data loss and name replacements after processing by aggregators.

Molecular phylogeny of the genus Chondracanthus (Rhodophyta), focusing on the resurrection of C. okamurae and the description of C. cincinnus sp. nov.

NASA Astrophysics Data System (ADS)

Yang, Mi Yeon; Kim, Myung Sook

2016-09-01

Determining the taxonomic status of the red algal genus Chondracanthus based on morphological characters is challenging due to the similarity and high degree of plasticity of the thallus. Since the taxonomic history of several Chondracanthus species remains unclear, we analyzed the plastid rbcL and mitochondrial COI genes of the specimens from Korea and Japan, in combination with morphological observations, to examine their phylogenetic relationships. Our results confirmed the distinction of C. okamurae, which is separated from C. intermedius, and identified a novel species, C. cincinnus sp. nov. Three species ( C. okamurae, C. intermedius and C. cincinnus) formed a monophyletic clade with C. tenellus. C. okamurae is distinguished by linear, narrow, cylindrical to compressed, slightly recurved axes, and a high-intertidal to subtidal distribution. It was collected from Korea and Japan, while C. intermedius was identified from Japan only. A new species, Chondracanthus cincinnus sp. nov., is characterized by linear, compressed, strongly recurved axes, and a low-intertidal to subtidal distiribution. Based on the molecular phylogeny using rbcL and COI data, we herein resurrect C. okamurae as a distinct species and identify C. cincinnus as a new species.

A Framework for Inferring Taxonomic Class of Asteroids.

NASA Technical Reports Server (NTRS)

Dotson, J. L.; Mathias, D. L.

2017-01-01

Introduction: Taxonomic classification of asteroids based on their visible / near-infrared spectra or multi band photometry has proven to be a useful tool to infer other properties about asteroids. Meteorite analogs have been identified for several taxonomic classes, permitting detailed inference about asteroid composition. Trends have been identified between taxonomy and measured asteroid density. Thanks to NEOWise (Near-Earth-Object Wide-field Infrared Survey Explorer) and Spitzer (Spitzer Space Telescope), approximately twice as many asteroids have measured albedos than the number with taxonomic classifications. (If one only considers spectroscopically determined classifications, the ratio is greater than 40.) We present a Bayesian framework that provides probabilistic estimates of the taxonomic class of an asteroid based on its albedo. Although probabilistic estimates of taxonomic classes are not a replacement for spectroscopic or photometric determinations, they can be a useful tool for identifying objects for further study or for asteroid threat assessment models. Inputs and Framework: The framework relies upon two inputs: the expected fraction of each taxonomic class in the population and the albedo distribution of each class. Luckily, numerous authors have addressed both of these questions. For example, the taxonomic distribution by number, surface area and mass of the main belt has been estimated and a diameter limited estimate of fractional abundances of the near earth asteroid population was made. Similarly, the albedo distributions for taxonomic classes have been estimated for the combined main belt and NEA (Near Earth Asteroid) populations in different taxonomic systems and for the NEA population specifically. The framework utilizes a Bayesian inference appropriate for categorical data. The population fractions provide the prior while the albedo distributions allow calculation of the likelihood an albedo measurement is consistent with a given taxonomic class. These inputs allows calculation of the probability an asteroid with a specified albedo belongs to any given taxonomic class.

A phylogeny for the pomatiopsidae (Gastropoda: Rissooidea): a resource for taxonomic, parasitological and biodiversity studies.

PubMed

Liu, Liang; Huo, Guan-Nan; He, Hong-Bin; Zhou, Benjiang; Attwood, Stephen W

2014-02-18

The Pomatiopsidae are reported from northern India into southern China and Southeast Asia, with two sub-families, the Pomatiopsinae (which include freshwater, amphibious, terrestrial and marine species) and the freshwater Triculinae. Both include species acting as intermediate host for species of the blood-fluke Schistosoma which cause a public health problem in East Asia. Also, with around 120 species, triculine biodiversity exceeds that of any other endemic freshwater molluscan fauna. Nevertheless, the origins of the Pomatiopsidae, the factors driving such a diverse radiation and aspects of their co-evolution with Schistosoma are not fully understood. Many taxonomic questions remain; there are problems identifying medically relevant species. The predicted range is mostly unsurveyed and the true biodiversity of the family is underestimated. Consequently, the aim of the study was to collect DNA-sequence data for as many pomatiopsid taxa as possible, as a first step in providing a resource for identification of epidemiologically significant species (by non-malacologists), for use in resolving taxonomic confusion and for testing phylogeographical hypotheses. The evolutionary radiation of the Triculinae was shown to have been rapid and mostly post late Miocene. Molecular dating indicated that the radiation of these snails was driven first by the uplift of the Himalaya and onset of a monsoon system, and then by late-Pliocene global warming. The status of Erhaia as Anmicolidae is supported. The genera Tricula and Neotricula are shown to be non-monophyletic and the tribe Jullieniini may be polyphyletic (based on convergent characters). Triculinae from northern Vietnam could be derived from Gammatricula of Fujian/Yunnan, China. The molecular dates and phylogenetic estimates in this study are consistent with an Australasian origin for the Pomatiopsidae and an East to West radiation via Oligocene Borneo-Philippines island hopping to Japan and then China (Triculinae arising mid-Miocene in Southeast China), and less so with a triculine origin in Tibet. The lack of monophyly in the medically important genera and indications of taxonomic inaccuracies, call for further work to identify epidemiologically significant taxa (e.g., Halewisia may be potential hosts for Schistosoma mekongi) and highlight the need for surveys to determine the true biodiversity of the Triculinae.

Analysing taxonomic structures and local ecological processes in temperate forests in North Eastern China.

PubMed

Fan, Chunyu; Tan, Lingzhao; Zhang, Chunyu; Zhao, Xiuhai; von Gadow, Klaus

2017-10-30

One of the core issues of forest community ecology is the exploration of how ecological processes affect community structure. The relative importance of different processes is still under debate. This study addresses four questions: (1) how is the taxonomic structure of a forest community affected by spatial scale? (2) does the taxonomic structure reveal effects of local processes such as environmental filtering, dispersal limitation or interspecific competition at a local scale? (3) does the effect of local processes on the taxonomic structure vary with the spatial scale? (4) does the analysis based on taxonomic structures provide similar insights when compared with the use of phylogenetic information? Based on the data collected in two large forest observational field studies, the taxonomic structures of the plant communities were analyzed at different sampling scales using taxonomic ratios (number of genera/number of species, number of families/number of species), and the relationship between the number of higher taxa and the number of species. Two random null models were used and the "standardized effect size" (SES) of taxonomic ratios was calculated, to assess possible differences between the observed and simulated taxonomic structures, which may be caused by specific ecological processes. We further applied a phylogeny-based method to compare results with those of the taxonomic approach. As expected, the taxonomic ratios decline with increasing grain size. The quantitative relationship between genera/families and species, described by a linearized power function, showed a good fit. With the exception of the family-species relationship in the Jiaohe study area, the exponents of the genus/family-species relationships did not show any scale dependent effects. The taxonomic ratios of the observed communities had significantly lower values than those of the simulated random community under the test of two null models at almost all scales. Null Model 2 which considered the spatial dispersion of species generated a taxonomic structure which proved to be more consistent with that in the observed community. As sampling sizes increased from 20 m × 20 m to 50 m × 50 m, the magnitudes of SESs of taxonomic ratios increased. Based on the phylogenetic analysis, we found that the Jiaohe plot was phylogenetically clustered at almost all scales. We detected significant phylogenetically overdispersion at the 20 m × 20 m and 30 m × 30 m scales in the Liangshui plot. The results suggest that the effect of abiotic filtering is greater than the effects of interspecific competition in shaping the local community at almost all scales. Local processes influence the taxonomic structures, but their combined effects vary with the spatial scale. The taxonomic approach provides similar insights as the phylogenetic approach, especially when we applied a more conservative null model. Analysing taxonomic structure may be a useful tool for communities where well-resolved phylogenetic data are not available.

What Belongs in Your 15-Bean Soup? Using the Learning Cycle to Address Misconceptions about Construction of Taxonomic Keys

ERIC Educational Resources Information Center

Ross, Ann; Vanderspool, Staria

2004-01-01

Students can use seed characteristics to discriminate between the different kinds of legumes using taxonomic classification processes of sorting and ranking, followed by construction of taxonomic keys. The application of the Learning Cycle process to taxonomic principles, hierarchical classification, and construction of keys presents the…

New Mid-Cretaceous (Latest Albian) Dinosaurs from Winton, Queensland, Australia

PubMed Central

Hocknull, Scott A.; White, Matt A.; Tischler, Travis R.; Cook, Alex G.; Calleja, Naomi D.; Sloan, Trish; Elliott, David A.

2009-01-01

Background Australia's dinosaurian fossil record is exceptionally poor compared to that of other similar-sized continents. Most taxa are known from fragmentary isolated remains with uncertain taxonomic and phylogenetic placement. A better understanding of the Australian dinosaurian record is crucial to understanding the global palaeobiogeography of dinosaurian groups, including groups previously considered to have had Gondwanan origins, such as the titanosaurs and carcharodontosaurids. Methodology/Principal Findings We describe three new dinosaurs from the late Early Cretaceous (latest Albian) Winton Formation of eastern Australia, including; Wintonotitan wattsi gen. et sp. nov., a basal titanosauriform; Diamantinasaurus matildae gen. et sp. nov., a derived lithostrotian titanosaur; and Australovenator wintonensis gen. et sp. nov., an allosauroid. We compare an isolated astragalus from the Early Cretaceous of southern Australia; formerly identified as Allosaurus sp., and conclude that it most-likely represents Australovenator sp. Conclusion/Significance The occurrence of Australovenator from the Aptian to latest Albian confirms the presence in Australia of allosauroids basal to the Carcharodontosauridae. These new taxa, along with the fragmentary remains of other taxa, indicate a diverse Early Cretaceous sauropod and theropod fauna in Australia, including plesiomorphic forms (e.g. Wintonotitan and Australovenator) and more derived forms (e.g. Diamantinasaurus). PMID:19584929

Inductive reasoning.

PubMed

Hayes, Brett K; Heit, Evan; Swendsen, Haruka

2010-03-01

Inductive reasoning entails using existing knowledge or observations to make predictions about novel cases. We review recent findings in research on category-based induction as well as theoretical models of these results, including similarity-based models, connectionist networks, an account based on relevance theory, Bayesian models, and other mathematical models. A number of touchstone empirical phenomena that involve taxonomic similarity are described. We also examine phenomena involving more complex background knowledge about premises and conclusions of inductive arguments and the properties referenced. Earlier models are shown to give a good account of similarity-based phenomena but not knowledge-based phenomena. Recent models that aim to account for both similarity-based and knowledge-based phenomena are reviewed and evaluated. Among the most important new directions in induction research are a focus on induction with uncertain premise categories, the modeling of the relationship between inductive and deductive reasoning, and examination of the neural substrates of induction. A common theme in both the well-established and emerging lines of induction research is the need to develop well-articulated and empirically testable formal models of induction. Copyright © 2010 John Wiley & Sons, Ltd. For further resources related to this article, please visit the WIREs website. Copyright © 2010 John Wiley & Sons, Ltd.

Functional groups of fossil marattialeans: Chemotaxonomic implications for Pennsylvanian tree ferns and pteridophylls

USGS Publications Warehouse

Psenicka, J.; Zodrow, E.L.; Mastalerz, Maria; Bek, J.

2005-01-01

Marattialean-fossil foliage, assigned to Pecopteris Brongniart, was an important and widespread floral component in Late Pennsylvanian mires, with phylogenetic affinity to extant marattialean taxa in tropical regions. Marattialean fossil taxonomy is, however, still uncertain. Specimens from the Pilsen limnic Basin, Westphalian D, Czech Republic, represent fertile marattialean foliage of Pecopteris (Asterotheca) nyranensis and Pecopteris (Asterotheca) miltonii, and sterile foliage of Pecopteris aspidioides and Pecopteris polypodioides. Taxonomic parameters for their assignments included cuticle, stomatal morphologies (studied for the first time), and in situ reproductive organs and spores. Chemotaxonomic interpretations hinge on fidelity of preservation of compounds, or molecular fragments thereof, that were synthesized by the once-living plants. This preservation state was possibly due to the thermal history (maximum temperature of 130 ??C) in the Pilsen Basin, acidic preservation conditions, lithology and facies stability. Although subtle, the four pecopterid species are differentiable from one another by combined FTIR characteristics, supporting taxonomy. The ratio of CH2/CH3 is hypothesized to be a chemotaxonomic parameter for Pennsylvanian pteridophylls, both in seed and true ferns that have previously been studied. It will, however, be supplemented by additional biochemical markers. ?? 2004 Elsevier B.V. All rights reserved.

[Bacterial flora of the conjunctival sac of the horse].

PubMed

Cattabiani, F; Cabassi, E; Allodi, C; Gianelli, F

1976-01-01

The AA. report the results of taxonomic research conducted on the conjunctival sac of 59 horses for identification of the present bacterial flora. In the controlled animals, it was observed, at the level of the considered niche, a community constituted of normal bacterial populations, but not autochtonous in the significance they attributed from DUBOS et al., relative to the characterization of the indigenous microbiota of the intestine. The isolated normal bacterial flora seems to be constituted of: Micrococcus (subgroup 6 of Baird-Parker, M. luteus, Micrococcus spp.) isolated in 49,15% of the samples; Staphylococcus aureus and St. epidermidis (18,64%); Moraxella osloensis, M. phenylpiruvica, M. equi and Moraxella spp. (11,86%); Bacillus cereus (11,86%); Neisseria catarrhalis (8,47%); Streptococcus equi and Str. zooepidemicus (6,77%); Corynebacterium spp. (6,77%) and Acinetobacter lwoffi (5,08%). The AA. have found, besides, a particular group of bacteria of uncertain classification, attributed to the coryneforms and found in 30,50% of the examined horses. So-called transient bacteria taxa have been considered are Streptomyces spp., isolated in the 10,16% of the controlled subjects, Aerococcus viridans and Bacillus spp. found in only one equine.

The fragmentation of Pangaea and Mesozoic terrestrial vertebrate biodiversity

PubMed Central

2016-01-01

During the Mesozoic (242–66 million years ago), terrestrial regions underwent a massive shift in their size, position and connectivity. At the beginning of the era, the land masses were joined into a single supercontinent called Pangaea. However, by the end of the Mesozoic, terrestrial regions had become highly fragmented, both owing to the drifting apart of the continental plates and the extremely high sea levels that flooded and divided many regions. How terrestrial biodiversity was affected by this fragmentation and large-scale flooding of the Earth's landmasses is uncertain. Based on a model using the species–area relationship (SAR), terrestrial vertebrate biodiversity would be expected to nearly double through the Mesozoic owing to continental fragmentation, despite a decrease of 24% in total terrestrial area. Previous studies of Mesozoic vertebrates have generally found increases in terrestrial diversity towards the end of the era, although these increases are often attributed to intrinsic or climatic factors. Instead, continental fragmentation over this time may largely explain any observed increase in terrestrial biodiversity. This study demonstrates the importance that non-intrinsic effects can have on the taxonomic success of a group, and the importance of geography to understanding past biodiversity. PMID:27651536

Mitochondrial DNA phylogeny of camel spiders (Arachnida: Solifugae) from Iran.

PubMed

Maddahi, Hassan; Khazanehdari, Mahsa; Aliabadian, Mansour; Kami, Haji Gholi; Mirshamsi, Amin; Mirshamsi, Omid

2017-11-01

In the present study, the mitochondrial DNA phylogeny of five solifuge families of Iran is presented using phylogenetic analysis of mitochondrial cytochrome c oxidase, subunit 1 (COI) sequence data. Moreover, we included available representatives from seven families from GenBank to examine the genetic distance between Old and New World taxa and test the phylogenetic relationships among more solifuge families. Phylogenetic relationships were reconstructed based on the two most probabilistic methods, Maximum Likelihood (ML) and Bayesian inference (BI) approaches. Resulting topologies demonstrated the monophyly of the families Daesiidae, Eremobatidae, Galeodidae, Karschiidae and Rhagodidae, whereas the monophyly of the families Ammotrechidae and Gylippidae was not supported. Also, within the family Eremobatidae, the subfamilies Eremobatinae and Therobatinae and the genus Hemerotrecha were paraphyletic or polyphyletic. According to the resulted topologies, the taxonomic placements of Trichotoma michaelseni (Gylippidae) and Nothopuga sp. 1 (Ammotrechidae) are still remain under question and their revision might be appropriate. According to the results of this study, within the family Galeodidae, the validity of the genus Galeodopsis is supported, while the validity of the genus Paragaleodes still remains uncertain. Moreover, our results revealed that the species Galeodes bacillatus, and Rhagodes melanochaetus are junior synonyms of G. caspius, and R. eylandti, respectively.

The fragmentation of Pangaea and Mesozoic terrestrial vertebrate biodiversity.

PubMed

Vavrek, Matthew J

2016-09-01

During the Mesozoic (242-66 million years ago), terrestrial regions underwent a massive shift in their size, position and connectivity. At the beginning of the era, the land masses were joined into a single supercontinent called Pangaea. However, by the end of the Mesozoic, terrestrial regions had become highly fragmented, both owing to the drifting apart of the continental plates and the extremely high sea levels that flooded and divided many regions. How terrestrial biodiversity was affected by this fragmentation and large-scale flooding of the Earth's landmasses is uncertain. Based on a model using the species-area relationship (SAR), terrestrial vertebrate biodiversity would be expected to nearly double through the Mesozoic owing to continental fragmentation, despite a decrease of 24% in total terrestrial area. Previous studies of Mesozoic vertebrates have generally found increases in terrestrial diversity towards the end of the era, although these increases are often attributed to intrinsic or climatic factors. Instead, continental fragmentation over this time may largely explain any observed increase in terrestrial biodiversity. This study demonstrates the importance that non-intrinsic effects can have on the taxonomic success of a group, and the importance of geography to understanding past biodiversity. © 2016 The Author(s).

Further consideration of the phylogeny of some "traditional" heterotrichs (Protista, Ciliophora) of uncertain affinities, based on new sequences of the small subunit rRNA gene.

PubMed

Miao, Miao; Song, Weibo; Clamp, John C; Al-Rasheid, Khaled A S; Al-Khedhairy, Abdulaziz A; Al-Arifi, Saud

2009-01-01

The systematic relationships and taxonomic positions of the traditional heterotrich genera Condylostentor, Climacostomum, Fabrea, Folliculina, Peritromus, and Condylostoma, as well as the licnophorid genus Licnophora, were re-examined using new data from sequences of the gene coding for small subunit ribosomal RNA. Trees constructed using distance-matrix, Bayesian inference, and maximum-parsimony methods all showed the following relationships: (1) the "traditional" heterotrichs consist of several paraphyletic groups, including the current classes Heterotrichea, Armophorea and part of the Spirotrichea; (2) the class Heterotrichea was confirmed as a monophyletic assemblage based on our analyses of 31 taxa, and the genus Peritromus was demonstrated to be a peripheral group; (3) the genus Licnophora occupied an isolated branch on one side of the deepest divergence in the subphylum Intramacronucleata and was closely affiliated with spirotrichs, armophoreans, and clevelandellids; (4) Condylostentor, a recently defined genus with several truly unique morphological features, is more closely related to Condylostoma than to Stentor; (5) Folliculina, Eufolliculina, and Maristentor always clustered together with high bootstrap support; and (6) Climacostomum occupied a paraphyletic position distant from Fabrea, showing a close relationship with Condylostomatidae and Chattonidiidae despite of modest support.

Integrative taxonomy helps to reveal the mask of the genus Gynandropaa (Amphibia: Anura: Dicroglossidae).

PubMed

Huang, Yan; Hu, Junhua; Wang, Bin; Song, Zhaobin; Zhou, Caiquan; Jiang, Jianping

2016-03-01

Species of the genus Gynandropaa within the family Dicroglossidae are typical spiny frogs whose taxonomic status has long been in doubt. We used integrative methods, involving morphological and molecular analyses, to elucidate the phylogenetic relationships, and to determine identities and the geographic distribution of each valid species. We obtained DNA sequence data of 5 species of Gynandropaa (complete sequences of the mitochondrial NADH dehydrogenase subunit 2 [ND2] gene, and 890 bp of 12S rRNA and 16S rRNA partial sequences) from 37 localities (including the topotypes of 5 described species) and constructed Bayesian and maximum-likelihood trees to examine the patterns of phylogeography. A total of 28 morphological variables were taken on 624 specimens. Three clades with clear geographic patterns were recognized: clade C (from south-western Sichuan Province and central Yunnan Province), clade E (western Guizhou Province and eastern to central Yunnan Province) and clade W (western to southern Yunnan Province). Integrating morphological characteristics and distribution information, the clades W, E and C represent Gynandropaa yunnanensis, G. phrynoides and G. sichuanensis, respectively. We draw the following conclusions: (i) the taxon G. phrynoides, formerly evaluated as a junior synonym of G. yunnanensis, is revalidated herein at the rank of species; (ii) G. liui is a junior synonym of G. sichuanensis; and (iii) G. yunnanensis is a valid species while G. bourreti is probably a subspecies of G. yunnanensis, with the distribution range from Vietnam to southern Yunnan Province. This study clears up the taxonomic status of Gynandropaa and provides important information for understanding the evolution and conservation of these spiny frogs. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

Changing Names with Changed Address: Integrated Taxonomy and Species Delimitation in the Holarctic Colymbetes paykulli Group (Coleoptera: Dytiscidae)

PubMed Central

Drotz, Marcus K.; Brodin, Tomas; Nilsson, Anders N.

2015-01-01

Species delimitation of geographically isolated forms is a long-standing problem in less studied insect groups. Often taxonomic decisions are based directly on morphologic variation, and lack a discussion regarding sample size and the efficiency of migration barriers or dispersal/migration capacity of the studied species. These problems are here exemplified in a water beetle complex from the Bering Sea region that separates North America from Eurasia. Only a few sampled specimens occur from this particular area and they are mostly found in museum and private collections. Here we utilize the theory of integrated taxonomy to discuss the speciation of the Holarctic Colymbetes paykulli water beetle complex, which historically has included up to five species of which today only two are recognized. Three delimitation methods are used; landmark based morphometry of body shape, variation in reticulation patterns of the pronotum exo-skeleton and sequence variation of the partial mitochondrial gene Cyt b. Our conclusion is that the Palearctic and Nearctic populations of C. paykulli are given the status of separate species, based on the fact that all methods showed significant separation between populations. As a consequence the name of the Palearctic species is C. paykulli Erichson and the Nearctic species should be known as C. longulus LeConte. There is no clear support for delineation between Palearctic and Nearctic populations of C. dahuricus based on mtDNA. However, significant difference in size and reticulation patterns from the two regions is shown. The combined conclusion is that the C. dahuricus complex needs a more thorough investigation to fully disentangle its taxonomic status. Therefore it is here still regarded as a Holarctic species. This study highlights the importance to study several diagnosable characters that has the potential to discriminate evolutionary lineage during speciation. PMID:26619278

Maternal group B Streptococcus and the infant gut microbiota.

PubMed

Cassidy-Bushrow, A E; Sitarik, A; Levin, A M; Lynch, S V; Havstad, S; Ownby, D R; Johnson, C C; Wegienka, G

2016-02-01

Early patterns of gut colonization may predispose children to adult disease. Exposures in utero and during delivery are associated with the infant gut microbiome. Although ~35% of women carry group B strep (GBS; Streptococcus agalactiae) during pregnancy, it is unknown if GBS presence influences the infant gut microbiome. As part of a population-based, general risk birth cohort, stool specimens were collected from infant's diapers at research visits conducted at ~1 and 6 months of age. Using the Illumina MiSeq (San Diego, CA) platform, the V4 region of the bacterial 16S rRNA gene was sequenced. Infant gut bacterial community compositional differences by maternal GBS status were evaluated using permutational multivariate analysis of variance. Individual operational taxonomic units (OTUs) were tested using a zero-inflated negative binomial model. Data on maternal GBS and infant gut microbiota from either 1 (n=112) or 6-month-old stool (n=150) specimens was available on 262 maternal-child pairs. Eighty women (30.5%) were GBS+, of who 58 (72.5%) were given intrapartum antibiotics. After adjusting for maternal race, prenatal antifungal use and intrapartum antibiotics, maternal GBS status was statistically significantly associated with gut bacterial composition in the 6 month visit specimen (Canberra R 2=0.008, P=0.008; Unweighted UniFrac R 2=0.010, P=0.011). Individual OTU tests revealed that infants of GBS+ mothers were significantly enriched for specific members of the Clostridiaceae, Ruminococcoceae, and Enterococcaceae in the 6 month specimens compared with infants of GBS- mothers. Whether these taxonomic differences in infant gut microbiota at 6 months lead to differential predisposition for adult disease requires additional study.

Allocating conservation resources between areas where persistence of a species is uncertain.

PubMed

McDonald-Madden, Eve; Chadès, Iadine; McCarthy, Michael A; Linkie, Matthew; Possingham, Hugh P

2011-04-01

Research on the allocation of resources to manage threatened species typically assumes that the state of the system is completely observable; for example whether a species is present or not. The majority of this research has converged on modeling problems as Markov decision processes (MDP), which give an optimal strategy driven by the current state of the system being managed. However, the presence of threatened species in an area can be uncertain. Typically, resource allocation among multiple conservation areas has been based on the biggest expected benefit (return on investment) but fails to incorporate the risk of imperfect detection. We provide the first decision-making framework for confronting the trade-off between information and return on investment, and we illustrate the approach for populations of the Sumatran tiger (Panthera tigris sumatrae) in Kerinci Seblat National Park. The problem is posed as a partially observable Markov decision process (POMDP), which extends MDP to incorporate incomplete detection and allows decisions based on our confidence in particular states. POMDP has previously been used for making optimal management decisions for a single population of a threatened species. We extend this work by investigating two populations, enabling us to explore the importance of variation in expected return on investment between populations on how we should act. We compare the performance of optimal strategies derived assuming complete (MDP) and incomplete (POMDP) observability. We find that uncertainty about the presence of a species affects how we should act. Further, we show that assuming full knowledge of a species presence will deliver poorer strategic outcomes than if uncertainty about a species status is explicitly considered. MDP solutions perform up to 90% worse than the POMDP for highly cryptic species, and they only converge in performance when we are certain of observing the species during management: an unlikely scenario for many threatened species. This study illustrates an approach to allocating limited resources to threatened species where the conservation status of the species in different areas is uncertain. The results highlight the importance of including partial observability in future models of optimal species management when the species of concern is cryptic in nature.

Molecular evidence confirms the taxonomic separation of Lutzomyia tihuiliensis from Lutzomyia pia (Diptera: Psychodidae) and the usefulness of pleural pigmentation patterns in species identification.

PubMed

Pérez-Doria, Alveiro; Bejarano, Eduar Elías; Sierra, Diana; Vélez, Iván Darío

2008-07-01

The phlebotomine sand flies Lutzomyia pia (Fairchild & Hertig 1961) and Lutzomyia tihuiliensis Le Pont, Torrez-Espejo & Dujardin 1997 (Diptera: Psychodidae) belong to the pia series of the Lu. verrucarum species group, which includes several species that bite humans in Andean foci of leishmaniasis. The females of these two species exhibit isometry and isomorphism in anatomical structures of the head and terminalia commonly used in taxonomic identification of sand flies. They can only be differentiated based on subtle differences in the pigmentation of the pleura. In Lu. tihuiliensis, this is restricted to the basal portions of the katepimeron and katepisternum, whereas in Lu. pia both structures are totally pigmented. Taking into account the subtle morphological differences between these species, the objective of the current study was to evaluate the specific taxonomic status of Lu. tihuiliensis with respect to Lu. pia. A 475-bp portion of the mitochondrial genome was sequenced, composed of the 3' end of the cytochrome b gene, intergenic spacer 1, the transfer RNA gene for serine, intergenic spacer 2, and the 3' end of the gene NAD dehydrogenase 1. Genetic analysis confirms that Lu. tihuiliensis and Lu. pia constitute two distinct species and this is supported by four strong lines of evidence, i.e., the paired genetic distances, size differences and amino acid composition of the cytochrome b protein, presence and absence of intergenic spacer one and divergence observed in the sequence of the transfer RNA gene for serine. It also confirms the validity of the pleural pigmentation pattern as a species diagnostic character and the importance of performing a detailed examination of this character during morphological determination of phlebotomine sand flies in the series pia.

Combined effects of solar ultraviolet radiation and nutrients addition on growth, biomass and taxonomic composition of coastal marine phytoplankton communities of Patagonia.

PubMed

Marcoval, M Alejandra; Villafañe, Virginia E; Helbling, E Walter

2008-05-29

Experiments (6-8 days) were conducted during late summer, late fall and late winter, 2003 with waters collected off Bahía Nueva, Chubut, Argentina (42.7 degrees S, 65 degrees W) to determine the combined effects of solar ultraviolet radiation (UVR, 280-400 nm) and nutrient addition on phytoplankton communities. Samples were put in UVR-transparent containers and incubated under two radiation treatments: (a) Samples exposed to full solar radiation (PAB treatment, 280-400 nm) and (b) Samples exposed only to PAR (PAR treatment, 400-700 nm). At the beginning of the experiments, nutrients (i.e., NaPO(4)H(2) and NaNO(3)) were added to one set of samples from each radiation treatment (N cultures) whereas in the other set, nutrients remained at the concentration of the seawater. Chlorophyll a, biomass, UV-absorbing compounds and taxonomic composition were recorded throughout the experiments. N cultures always had significantly higher growth rates (P<0.05) than that in non-enriched cultures. At the beginning of experiments, phytoplankton communities were generally dominated by monads and flagellates but by the end, diatoms comprised the bulk of biomass, with only one to four taxa dominating, suggesting a selection towards more tolerant/less sensitive species. Over the experimental time frame, the observed taxonomic changes were mostly due to nutrient availability, and to a lesser extent to solar UVR exposure. Overall, the results indicate that environmental conditions (i.e., light history, nutrient concentration) together with the physiological status of the cells play a very important role at the time to assess the combined effect of nutrient addition and solar radiation on coastal phytoplankton assemblages from Patagonia.

Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota.

PubMed

Petitjean, Céline; Deschamps, Philippe; López-García, Purificación; Moreira, David

2014-12-19

The first 16S rRNA-based phylogenies of the Archaea showed a deep division between two groups, the kingdoms Euryarchaeota and Crenarchaeota. This bipartite classification has been challenged by the recent discovery of new deeply branching lineages (e.g., Thaumarchaeota, Aigarchaeota, Nanoarchaeota, Korarchaeota, Parvarchaeota, Aenigmarchaeota, Diapherotrites, and Nanohaloarchaeota) which have also been given the same taxonomic status of kingdoms. However, the phylogenetic position of some of these lineages is controversial. In addition, phylogenetic analyses of the Archaea have often been carried out without outgroup sequences, making it difficult to determine if these taxa actually define lineages at the same level as the Euryarchaeota and Crenarchaeota. We have addressed the question of the position of the root of the Archaea by reconstructing rooted archaeal phylogenetic trees using bacterial sequences as outgroup. These trees were based on commonly used conserved protein markers (32 ribosomal proteins) as well as on 38 new markers identified through phylogenomic analysis. We thus gathered a total of 70 conserved markers that we analyzed as a concatenated data set. In contrast with previous analyses, our trees consistently placed the root of the archaeal tree between the Euryarchaeota (including the Nanoarchaeota and other fast-evolving lineages) and the rest of archaeal species, which we propose to class within the new kingdom Proteoarchaeota. This implies the relegation of several groups previously classified as kingdoms (e.g., Crenarchaeota, Thaumarchaeota, Aigarchaeota, and Korarchaeota) to a lower taxonomic rank. In addition to taxonomic implications, this profound reorganization of the archaeal phylogeny has also consequences on our appraisal of the nature of the last archaeal ancestor, which most likely was a complex organism with a gene-rich genome. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota

PubMed Central

Petitjean, Céline; Deschamps, Philippe; López-García, Purificación; Moreira, David

2015-01-01

The first 16S rRNA-based phylogenies of the Archaea showed a deep division between two groups, the kingdoms Euryarchaeota and Crenarchaeota. This bipartite classification has been challenged by the recent discovery of new deeply branching lineages (e.g., Thaumarchaeota, Aigarchaeota, Nanoarchaeota, Korarchaeota, Parvarchaeota, Aenigmarchaeota, Diapherotrites, and Nanohaloarchaeota) which have also been given the same taxonomic status of kingdoms. However, the phylogenetic position of some of these lineages is controversial. In addition, phylogenetic analyses of the Archaea have often been carried out without outgroup sequences, making it difficult to determine if these taxa actually define lineages at the same level as the Euryarchaeota and Crenarchaeota. We have addressed the question of the position of the root of the Archaea by reconstructing rooted archaeal phylogenetic trees using bacterial sequences as outgroup. These trees were based on commonly used conserved protein markers (32 ribosomal proteins) as well as on 38 new markers identified through phylogenomic analysis. We thus gathered a total of 70 conserved markers that we analyzed as a concatenated data set. In contrast with previous analyses, our trees consistently placed the root of the archaeal tree between the Euryarchaeota (including the Nanoarchaeota and other fast-evolving lineages) and the rest of archaeal species, which we propose to class within the new kingdom Proteoarchaeota. This implies the relegation of several groups previously classified as kingdoms (e.g., Crenarchaeota, Thaumarchaeota, Aigarchaeota, and Korarchaeota) to a lower taxonomic rank. In addition to taxonomic implications, this profound reorganization of the archaeal phylogeny has also consequences on our appraisal of the nature of the last archaeal ancestor, which most likely was a complex organism with a gene-rich genome. PMID:25527841

Genetic evaluation of the evolutionary distinctness of a federally endangered butterfly, Lange's Metalmark.

PubMed

Proshek, Benjamin; Dupuis, Julian R; Engberg, Anna; Davenport, Ken; Opler, Paul A; Powell, Jerry A; Sperling, Felix A H

2015-04-25

The Mormon Metalmark (Apodemia mormo) species complex occurs as isolated and phenotypically variable colonies in dryland areas across western North America. Lange's Metalmark, A. m. langei, one of the 17 subspecies taxonomically recognized in the complex, is federally listed under the U.S. Endangered Species Act of 1973. Metalmark taxa have traditionally been described based on phenotypic and ecological characteristics, and it is unknown how well this nomenclature reflects their genetic and evolutionary distinctiveness. Genetic variation in six microsatellite loci and mitochondrial cytochrome oxidase subunit I sequence was used to assess the population structure of the A. mormo species complex across 69 localities, and to evaluate A. m. langei's qualifications as an Evolutionarily Significant Unit. We discovered substantial genetic divergence within the species complex, especially across the Continental Divide, with population genetic structure corresponding more closely with geographic proximity and local isolation than with taxonomic divisions originally based on wing color and pattern characters. Lange's Metalmark was as genetically divergent as several other locally isolated populations in California, and even the unique phenotype that warranted subspecific and conservation status is reminiscent of the morphological variation found in some other populations. This study is the first genetic treatment of the A. mormo complex across western North America and potentially provides a foundation for reassessing the taxonomy of the group. Furthermore, these results illustrate the utility of molecular markers to aid in demarcation of biological units below the species level. From a conservation point of view, Apodemia mormo langei's diagnostic taxonomic characteristics may, by themselves, not support its evolutionary significance, which has implications for its formal listing as an Endangered Species.

Poles Apart: The “Bipolar” Pteropod Species Limacina helicina Is Genetically Distinct Between the Arctic and Antarctic Oceans

PubMed Central

Bednarsek, Nina; Linse, Katrin; Nelson, R. John; Pakhomov, Evgeny; Seibel, Brad; Steinke, Dirk; Würzberg, Laura

2010-01-01

The shelled pteropod (sea butterfly) Limacina helicina is currently recognised as a species complex comprising two sub-species and at least five “forma”. However, at the species level it is considered to be bipolar, occurring in both the Arctic and Antarctic oceans. Due to its aragonite shell and polar distribution L. helicina is particularly vulnerable to ocean acidification. As a key indicator of the acidification process, and a major component of polar ecosystems, L. helicina has become a focus for acidification research. New observations that taxonomic groups may respond quite differently to acidification prompted us to reassess the taxonomic status of this important species. We found a 33.56% (±0.09) difference in cytochrome c oxidase subunit I (COI) gene sequences between L. helicina collected from the Arctic and Antarctic oceans. This degree of separation is sufficient for ordinal level taxonomic separation in other organisms and provides strong evidence for the Arctic and Antarctic populations of L. helicina differing at least at the species level. Recent research has highlighted substantial physiological differences between the poles for another supposedly bipolar pteropod species, Clione limacina. Given the large genetic divergence between Arctic and Antarctic L. helicina populations shown here, similarly large physiological differences may exist between the poles for the L. helicina species group. Therefore, in addition to indicating that L. helicina is in fact not bipolar, our study demonstrates the need for acidification research to take into account the possibility that the L. helicina species group may not respond in the same way to ocean acidification in Arctic and Antarctic ecosystems. PMID:20360985

Towards stressor-specific macroinvertebrate indices: Which traits and taxonomic groups are associated with vulnerable and tolerant taxa?

PubMed

Berger, Elisabeth; Haase, Peter; Schäfer, Ralf B; Sundermann, Andrea

2018-04-01

Monitoring of macroinvertebrate communities is frequently used to define the ecological health status of rivers. Ideally, biomonitoring should also give an indication on the major stressors acting on the macroinvertebrate communities supporting the selection of appropriate management measures. However, most indices are affected by more than one stressor. Biological traits (e.g. size, generation time, reproduction) could potentially lead to more stressor-specific indices. However, such an approach has rarely been tested. In this study we classify 324 macroinvertebrate taxa as vulnerable (decreasing abundances) or tolerant (increasing abundances) along 21 environmental gradients (i.e. nutrients, major ions, oxygen and micropollutants) from 422 monitoring sites in Germany using Threshold Indicator Taxa Analysis (TITAN). Subsequently, we investigate which biological traits and taxonomic groups are associated with taxa classified as vulnerable or tolerant with regard to specific gradients. The response of most taxa towards different gradients was similar and especially high for correlated gradients. Traits associated with vulnerable taxa across most gradients included: larval aquatic life stages, isolated cemented eggs, reproductive cycle per year <1, scrapers, aerial and aquatic active dispersal and plastron respiration. Traits associated with tolerant taxa included: adult aquatic life stages, polyvoltinism, ovoviviparity or egg clutches in vegetation, food preference for dead animals or living microinvertebrates, substrate preference for macrophytes, microphytes, silt or mud and a body size >2-4cm. Our results question whether stressor-specific indices based on macroinvertebrate assemblages can be achieved using single traits, because we observed that similar taxa responded to different gradients and also similar traits were associated with vulnerable and tolerant taxa across a variety of water quality gradients. Future studies should examine whether combinations of traits focusing on specific taxonomic groups achieve higher stressor specificity. Copyright © 2017 Elsevier B.V. All rights reserved.

Improving taxonomic accuracy for fungi in public sequence databases: applying ‘one name one species’ in well-defined genera with Trichoderma/Hypocrea as a test case

PubMed Central

Strope, Pooja K; Chaverri, Priscila; Gazis, Romina; Ciufo, Stacy; Domrachev, Michael; Schoch, Conrad L

2017-01-01

Abstract The ITS (nuclear ribosomal internal transcribed spacer) RefSeq database at the National Center for Biotechnology Information (NCBI) is dedicated to the clear association between name, specimen and sequence data. This database is focused on sequences obtained from type material stored in public collections. While the initial ITS sequence curation effort together with numerous fungal taxonomy experts attempted to cover as many orders as possible, we extended our latest focus to the family and genus ranks. We focused on Trichoderma for several reasons, mainly because the asexual and sexual synonyms were well documented, and a list of proposed names and type material were recently proposed and published. In this case study the recent taxonomic information was applied to do a complete taxonomic audit for the genus Trichoderma in the NCBI Taxonomy database. A name status report is available here: https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi. As a result, the ITS RefSeq Targeted Loci database at NCBI has been augmented with more sequences from type and verified material from Trichoderma species. Additionally, to aid in the cross referencing of data from single loci and genomes we have collected a list of quality records of the RPB2 gene obtained from type material in GenBank that could help validate future submissions. During the process of curation misidentified genomes were discovered, and sequence records from type material were found hidden under previous classifications. Source metadata curation, although more cumbersome, proved to be useful as confirmation of the type material designation. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353 PMID:29220466

Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major).

PubMed

Kropáčková, Lucie; Pechmanová, Hana; Vinkler, Michal; Svobodová, Jana; Velová, Hana; Těšičký, Martin; Martin, Jean-François; Kreisinger, Jakub

2017-01-01

The gastrointestinal tract of vertebrates is inhabited by diverse bacterial communities that induce marked effects on the host physiology and health status. The composition of the gastrointestinal microbiota is characterized by pronounced taxonomic and functional variability among different regions of the vertebrate gastrointestinal tract. Despite the relatively solid knowledge on the among-region variations of the gastrointestinal microbiota in model mammalian species, there are only a few studies concerning among-region variations of the gastrointestinal microbiota in free-living non-mammalian vertebrate taxa. We used Illumina MiSeq sequencing of bacterial 16S rRNA amplicons to compare the diversity as well as taxonomic composition of bacterial communities in proximal vs. distal parts of the gastrointestinal tract (represented by oral swabs and faecal samples, respectively) in a wild passerine bird, the great tit (Parus major). The diversity of the oral microbiota was significantly higher compared to the faecal microbiota, whereas interindividual variation was higher in faecal than in oral samples. We also observed a pronounced difference in taxonomic content between the oral and faecal microbiota. Bacteria belonging to the phyla Proteobacteria, Firmicutes and Actinobacteria typically dominated in both oral and faecal samples. A high abundance of bacteria belonging to Tenericutes was observed only in faecal samples. Surprisingly, we found only a slight correlation between the faecal and oral microbiota at the within-individual level, suggesting that the microbial composition in these body sites is shaped by independent regulatory processes. Given the independence of these two communities at the individual level, we propose that simultaneous sampling of the faecal and oral microbiota will extend our understanding of host vs. microbiota interactions in wild populations.

Hitting the right target: taxonomic challenges for, and of, plant invasions

PubMed Central

Pyšek, Petr; Hulme, Philip E.; Meyerson, Laura A.; Smith, Gideon F.; Boatwright, James S.; Crouch, Neil R.; Figueiredo, Estrela; Foxcroft, Llewellyn C.; Jarošík, Vojtěch; Richardson, David M.; Suda, Jan; Wilson, John R. U.

2013-01-01

This paper explores how a lack of taxonomic expertise, and by implication a dearth of taxonomic products such as identification tools, has hindered progress in understanding and managing biological invasions. It also explores how the taxonomic endeavour could benefit from studies of invasive species. We review the literature on the current situation in taxonomy with a focus on the challenges of identifying alien plant species and explore how this has affected the study of biological invasions. Biosecurity strategies, legislation dealing with invasive species, quarantine, weed surveillance and monitoring all depend on accurate and rapid identification of non-native taxa. However, such identification can be challenging because the taxonomic skill base in most countries is diffuse and lacks critical mass. Taxonomic resources are essential for the effective management of invasive plants and incorrect identifications can impede ecological studies. On the other hand, biological invasions have provided important tests of basic theories about species concepts. Better integration of classical alpha taxonomy and modern genetic taxonomic approaches will improve the accuracy of species identification and further refine taxonomic classification at the level of populations and genotypes in the field and laboratory. Modern taxonomy therefore needs to integrate both classical and new concepts and approaches. In particular, differing points of view between the proponents of morphological and molecular approaches should be negotiated because a narrow taxonomic perspective is harmful; the rigour of taxonomic decision-making clearly increases if insights from a variety of different complementary disciplines are combined and confronted. Taxonomy plays a critical role in the study of plant invasions and in turn benefits from the insights gained from these studies.

Increasing numbers of bird species result from taxonomic progress, not taxonomic inflation

PubMed Central

Sangster, George

2009-01-01

The impact and significance of modern taxonomy on other fields in biology have been subjects of much debate. It has been proposed that increasing numbers of vertebrate species are largely owing to ‘taxonomic inflation’. According to this hypothesis, newly recognized species result from reinterpretations of species limits based on phylogenetic species concepts (PSCs) rather than from new discoveries. Here, I examine 747 proposals to change the taxonomic rank of birds in the period 1950–2007. The trend to recognize more species of birds started at least two decades before the introduction of PSCs. Most (84.6%) newly recognized species were supported by new taxonomic data. Proposals to recognize more species resulted from application of all six major taxonomic criteria. Many newly recognized species (63.4%) were not based exclusively on PSC-based criteria (diagnosability, monophyly and exclusive coalescence of gene trees). Therefore, this study finds no empirical support for the idea that the increase in species is primarily epistemological rather than data-driven. This study shows that previous claims about the causes and effects of taxonomic inflation lack empirical support. I argue that a more appropriate term for the increase in species is ‘taxonomic progress’. PMID:19520805

The Neural Bases of Taxonomic and Thematic Conceptual Relations: An MEG Study

PubMed Central

Lewis, Gwyneth A.; Poeppel, David; Murphy, Gregory L.

2015-01-01

Converging evidence from behavioral and neuroimaging studies of human concepts indicate distinct neural systems for taxonomic and thematic knowledge. A recent study of naming in aphasia found involvement of the anterior temporal lobe (ATL) during taxonomic (feature-based) processing, and involvement of the temporoparietal junction (TPJ) during thematic (function-based) processing. We conducted an online magnetoencephalography (MEG) study to examine the spatio-temporal nature of taxonomic and thematic relations. We measured participants’ brain responses to words preceded by either a taxonomically or thematically related item (e.g., cottage→castle, king→castle). In a separate experiment we collected relatedness ratings of the word pairs from participants. We examined effects of relatedness and relation type on activation in ATL and TPJ regions of interest (ROIs) using permutation t-tests to identify differences in ROI activation between conditions as well as single-trial correlational analyses to examine the millisecond-by-millisecond influence of the stimulus variables on the ROIs. Taxonomic relations strongly predicted ATL activation, and both kinds of relations influenced the TPJ. Our results further strengthen the view of the ATL's importance to taxonomic knowledge. Moreover, they provide a nuanced view of thematic relations as involving taxonomic knowledge. PMID:25582406

Biomonitoring of intermittent rivers and ephemeral streams in Europe: Current practice and priorities to enhance ecological status assessments.

PubMed

Stubbington, Rachel; Chadd, Richard; Cid, Núria; Csabai, Zoltán; Miliša, Marko; Morais, Manuela; Munné, Antoni; Pařil, Petr; Pešić, Vladimir; Tziortzis, Iakovos; Verdonschot, Ralf C M; Datry, Thibault

2018-03-15

Intermittent rivers and ephemeral streams (IRES) are common across Europe and dominate some Mediterranean river networks. In all climate zones, IRES support high biodiversity and provide ecosystem services. As dynamic ecosystems that transition between flowing, pool, and dry states, IRES are typically poorly represented in biomonitoring programmes implemented to characterize EU Water Framework Directive ecological status. We report the results of a survey completed by representatives from 20 European countries to identify current challenges to IRES status assessment, examples of best practice, and priorities for future research. We identify five major barriers to effective ecological status classification in IRES: 1. the exclusion of IRES from Water Framework Directive biomonitoring based on their small catchment size; 2. the lack of river typologies that distinguish between contrasting IRES; 3. difficulties in defining the 'reference conditions' that represent unimpacted dynamic ecosystems; 4. classification of IRES ecological status based on lotic communities sampled using methods developed for perennial rivers; and 5. a reliance on taxonomic characterization of local communities. Despite these challenges, we recognize examples of innovative practice that can inform modification of current biomonitoring activity to promote effective IRES status classification. Priorities for future research include reconceptualization of the reference condition approach to accommodate spatiotemporal fluctuations in community composition, and modification of indices of ecosystem health to recognize both taxon-specific sensitivities to intermittence and dispersal abilities, within a landscape context. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory; processing, taxonomy, and quality control of benthic macroinvertebrate samples

USGS Publications Warehouse

Moulton, Stephen R.; Carter, James L.; Grotheer, Scott A.; Cuffney, Thomas F.; Short, Terry M.

2000-01-01

Qualitative and quantitative methods to process benthic macroinvertebrate (BMI) samples have been developed and tested by the U.S. Geological Survey?s National Water Quality Laboratory Biological Group. The qualitative processing method is based on visually sorting a sample for up to 2 hours. Sorting focuses on attaining organisms that are likely to result in taxonomic identifications to lower taxonomic levels (for example, Genus or Species). Immature and damaged organisms are also sorted when they are likely to result in unique determinations. The sorted sample remnant is scanned briefly by a second person to determine if obvious taxa were missed. The quantitative processing method is based on a fixed-count approach that targets some minimum count, such as 100 or 300 organisms. Organisms are sorted from randomly selected 5.1- by 5.1-centimeter parts of a gridded subsampling frame. The sorted remnant from each sample is resorted by a second individual for at least 10 percent of the original sort time. A large-rare organism search is performed on the unsorted remnant to sort BMI taxa that were not likely represented in the sorted grids. After either qualitatively or quantitatively sorting the sample, BMIs are identified by using one of three different types of taxonomic assessment. The Standard Taxonomic Assessment is comparable to the U.S. Environmental Protection Agency Rapid Bioassessment Protocol III and typically provides Genus- or Species-level taxonomic resolution. The Rapid Taxonomic Assessment is comparable to the U.S. Environmental Protection Agency Rapid Bioassessment Protocol II and provides Familylevel and higher taxonomic resolution. The Custom Taxonomic Assessment provides Species-level resolution whenever possible for groups identified to higher taxonomic levels by using the Standard Taxonomic Assessment. The consistent use of standardized designations and notes facilitates the interpretation of BMI data within and among water-quality studies. Taxonomic identifications are quality assured by verifying all referenced taxa and randomly reviewing 10 percent of the taxonomic identifications performed weekly by Biological Group taxonomists. Taxonomic errors discovered during this review are corrected. BMI data are reviewed for accuracy and completeness prior to release. BMI data are released phylogenetically in spreadsheet format and unprocessed abundances are corrected for laboratory and field subsampling when necessary.

Doctor, Teacher, and Stethoscope: Neural Representation of Different Types of Semantic Relations.

PubMed

Xu, Yangwen; Wang, Xiaosha; Wang, Xiaoying; Men, Weiwei; Gao, Jia-Hong; Bi, Yanchao

2018-03-28

Concepts can be related in many ways. They can belong to the same taxonomic category (e.g., "doctor" and "teacher," both in the category of people) or be associated with the same event context (e.g., "doctor" and "stethoscope," both associated with medical scenarios). How are these two major types of semantic relations coded in the brain? We constructed stimuli from three taxonomic categories (people, manmade objects, and locations) and three thematic categories (school, medicine, and sports) and investigated the neural representations of these two dimensions using representational similarity analyses in human participants (10 men and nine women). In specific regions of interest, the left anterior temporal lobe (ATL) and the left temporoparietal junction (TPJ), we found that, whereas both areas had significant effects of taxonomic information, the taxonomic relations had stronger effects in the ATL than in the TPJ ("doctor" and "teacher" closer in ATL neural activity), with the reverse being true for thematic relations ("doctor" and "stethoscope" closer in TPJ neural activity). A whole-brain searchlight analysis revealed that widely distributed regions, mainly in the left hemisphere, represented the taxonomic dimension. Interestingly, the significant effects of the thematic relations were only observed after the taxonomic differences were controlled for in the left TPJ, the right superior lateral occipital cortex, and other frontal, temporal, and parietal regions. In summary, taxonomic grouping is a primary organizational dimension across distributed brain regions, with thematic grouping further embedded within such taxonomic structures. SIGNIFICANCE STATEMENT How are concepts organized in the brain? It is well established that concepts belonging to the same taxonomic categories (e.g., "doctor" and "teacher") share neural representations in specific brain regions. How concepts are associated in other manners (e.g., "doctor" and "stethoscope," which are thematically related) remains poorly understood. We used representational similarity analyses to unravel the neural representations of these different types of semantic relations by testing the same set of words that could be differently grouped by taxonomic categories or by thematic categories. We found that widely distributed brain areas primarily represented taxonomic categories, with the thematic categories further embedded within the taxonomic structure. Copyright © 2018 the authors 0270-6474/18/383303-15$15.00/0.

Challenges and New Opportunities for Clinical Nutrition Interventions in the Aged123

PubMed Central

Johnson, Mary Ann; Dwyer, Johanna T.; Jensen, Gordon L.; Miller, Joshua W.; Speakman, John R.; Starke-Reed, Pamela; Volpi, Elena

2011-01-01

Nutritional status plays a critical role in the prevention and management of many chronic health conditions that are common in the elderly and are likely to become more prevalent as the population ages. This paper highlights several aspects of nutrition that require additional basic science and clinical application research to improve the health and well-being of older adults. Topics addressed are selected demographic and health indices, the uncertain benefits of energy restriction in aged humans compared with other species, the impact of food insecurity on health, the relationship between dietary protein and sarcopenia, the prevention and management of obesity while maintaining muscle mass and functional status, and controversy regarding high intakes of folic acid. Research needs regarding the safety, efficacy, and application of clinical interventions related to these topics also are discussed. PMID:21270372

Of Paleo-Genes and Perch: What if an “Alien” Is Actually a Native?

PubMed Central

Stager, J. Curt; Sporn, Lee Ann; Johnson, Melanie; Regalado, Sean

2015-01-01

Documenting whether a biotic taxon is native or alien to an ecosystem has theoretical value for ecological and evolutionary studies, and has practical value because it can potentially identify a taxon as a desirable component of an ecosystem or target it for removal. In some cases, however, such background information is inadequate or unavailable. Here we use paleo-DNA to re-evaluate the historical status of yellow perch in the 6 million acre Adirondack State Park of northern New York. Yellow perch DNA in a 2200-year sediment record reveals a long-term native status for these supposedly alien fish and challenges assumptions that they necessarily exclude native trout from upland lakes. Similar approaches could be applied to other species with uncertain historical distributions and could help to identify unrecognized pockets of biodiversity. PMID:25751263

Rhipicephalus appendiculatus and R. zambeziensis (Acari: Ixodidae) from Zambia: a molecular reassessment of their species status and identification.

PubMed

Mtambo, J; Madder, M; Van Bortel, W; Berkvens, D; Backeljau, T

2007-01-01

The closely related species Rhipicephalus appendiculatus and R. zambeziensis co-occur in a wide area in Zambia. In this area, specimens of both species have been collected on the same individual host at the same time. In addition, specimens that are morphologically intermediate between R. appendiculatus and R. zambeziensis have been found in this area. These observations cast some doubt on the species status of R. appendiculatus and R. zambeziensis. Because the two taxa have varied influences on the epidemiology of East Coast fever (ECF), a cattle disease for which they act as vectors, it is essential that their taxonomic status is clarified and their identification is accurate. Therefore a phylogenetic analysis of nucleotide sequences of the ITS2 and a fragment of the mitochondrial 12S rDNA was performed to reassess the specific status of both taxa. This revealed two well supported clades coinciding with R. appendiculatus and R. zambeziensis as two separate species. In order to facilitate species identification a PCR-RFLP diagnostic assay was developed based on BauI digestion of the ITS2 gene. This assay produced clear diagnostic banding patterns for the two species and is applicable over a wide range of both species' distribution.

A new Cernosvitoviella species (Clitellata: Enchytraeidae) and its comparison with other Cernosvitoviella species from Sphagnum mires in Hungary.

PubMed

Dózsa-Farkas, Klára; Csitári, Bianka; Felföldi, Tamás

2017-04-18

Results of a comparative investigation on five Cernosvitoviella species from Hungarian Sphagnum mires including their distribution and the description of a new species, Cernosvitoviella farkasi sp. n., are presented in this paper. Cernosvitoviella atrata, C. aggtelekiensis, C. crassoductus and C. farkasi sp. n. could be easily distinguished from each other based on both morphological and molecular taxonomic analyses. However, C. minor seems to be a species complex on the basis of these investigations, so it was referred as C. minor sensu lato. The status of the C. minor variants requires further studies.

Unveiling the complete genome sequence of clerodendrum chlorotic spot virus, a putative dichorhavirus infecting ornamental plants.

PubMed

Ramos-González, Pedro Luis; Chabi-Jesus, Camila; Banguela-Castillo, Alexander; Tassi, Aline Daniele; Rodrigues, Mariane da Costa; Kitajima, Elliot Watanabe; Harakava, Ricardo; Freitas-Astúa, Juliana

2018-06-04

The genus Dichorhavirus includes plant-infecting rhabdoviruses with bisegmented genomes that are horizontally transmitted by false spider mites of the genus Brevipalpus. The complete genome sequences of three isolates of the putative dichorhavirus clerodendrum chlorotic spot virus were determined using next-generation sequencing (Illumina) and traditional RT-PCR. Their genome organization, sequence similarity and phylogenetic relationship to other viruses, and transmissibility by Brevipalpus yothersi mites support the assignment of these viruses to a new species of dichorhavirus, as suggested previously. New data are discussed stressing the reliability of the current rules for species demarcation and taxonomic status criteria within the genus Dichorhavirus.

Rediscovery and redescription of Leodice laurillardi (Quatrefages, 1866) comb. nov. (Annelida: Eunicidae)-a rare European polychaete or just an overlooked species?

PubMed

Arias, Andrés; Fernández-Álvarez, Fernando Á; Martins, Roberto; Anadón, Nuria

2015-06-04

The eunicid polychaete, Eunice laurillardi Quatrefages, 1866, originally described from the central Mediterranean, has been discovered on the northern Iberian Peninsula, constituting the first report of the species since its original description. The new specimens are compared with the type collection and the species is redescribed. Furthermore, the species is assigned to the genus Leodice Savigny in Lamarck, 1818, based on information provided by re-examination of type material and the newly collected specimens. A summary of the complex taxonomic history of the species and a discussion of its current status are also provided.

New record and redescription of Calanopia thompsoni A. Scott, 1909 (Copepoda, Calanoida, Pontellidae) from the Red Sea, with notes on the taxonomic status of C. parathompsoni Gaudy, 1969 and a key to species.

PubMed

Al-Aidaroos, Ali M; Salama, Adnan J; El-Sherbiny, Mohsen M

2016-01-01

During a plankton sampling programme around Al-Wajh area, Saudi Arabian coast of the northern Red Sea, a copepod Calanopia thompsoni A. Scott, 1909 (Calanoida: Pontellidae) was reported for the first time in the Red Sea. Both sexes are fully redescribed and compared to previous descriptions as well as the closely related species, Calanopia parathompsoni. The zoogeographical distribution of the species confirms that it is of Indo-Pacific origin. A dichotomous key for the identification of males and females of the species of Calanopia is included.

Morphological features of an endangered Japanese strain of Cyprinus carpio: reconstruction based on seven SNP markers.

PubMed

Atsumi, K; Song, H Y; Senou, H; Inoue, K; Mabuchi, K

2017-03-01

Morphological analyses of 183 specimens of Japanese common carp Cyprinus carpio (171 from Lake Biwa and 12 from nursery ponds) using genetic hybrid indices demonstrated that the typical native Japanese strain of C. carpio has a more elongate body, more branched dorsal-fin rays, fewer and shorter gill rakers, more developed pneumatic bulb, more coiled pneumatic duct, longer posterior swimbladder and shorter intestine than the typical introduced C. carpio. These results provide a basis for a better understanding of the ecological characteristics and taxonomic status of the endangered Japanese strain of C. carpio. © 2016 The Fisheries Society of the British Isles.

[Catch-up vaccination of worldwide newcoming (adopted, refugee or migrant) children in France].

PubMed

de Monléon, J-V; Regnier, F; Ajana, F; Baptiste, C; Callamand, P; Cheymol, J; Gillet, Y; Hau-Rainsard, I; Lorrot, M; Reinert, P; Marchand, S; Okaïs, C; Picherot, G

2014-03-01

In France, international adoption includes around to 90,000 children since 1980 and near 300,000 immigrant children were counted in 2008. This population is heterogeneous, according to age and country of origin, and its large number. It is not easy to completely and surely assess the vaccine status of the child. Due to a great variability of individual situations, it is not possible to have systematic and unchangeable rules. This article aims to give an update of catch-up vaccination of internationally adopted or refugee or migrant children in France. The vaccination status of a child who recently arrived in France is complex and has to be adapted to his country of origin. Some of them were never vaccinated whereas the vaccine status of others is uncertain or unknown. Three parameters have to be considered: the age of the child, the country of origin, and sometimes serology in the case of doubts of his vaccine status. Catch-up vaccination of foreign children has to be adapted to French vaccine recommendations, as a reference, and to vaccines already administered to the child. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Sunlight, vitamin D and food allergy.

PubMed

Rudders, Susan A; Camargo, Carlos A

2015-08-01

The role of vitamin D in the development of food allergy is unclear. We summarize recent data on the epidemiologic link between sunlight (UVB) and food allergy, and evidence for and against a specific role for vitamin D status. Since 2007, most epidemiologic studies have supported low sunlight (as measured by season of birth and latitude) as a risk factor for food allergy. Investigators have also looked directly at vitamin D status (as measured by serum 25OHD level) and its potential role. Although conflicting, the vitamin D studies suggest a more complicated association than a linear dose response in all individuals, with some studies indicating different associations based on host characteristics (e.g. concominant eczema, genetic polymorphisms, country of birth). Most studies have not fully examined the myriad effects of sunlight but have instead focused on a single maternal, neonatal or childhood 25OHD level. Many studies have linked sunlight with the development of food allergy but whether this is directly related to vitamin D status or a myriad of other sunlight-derived, seasonal and/or geographic factors remains uncertain. More studies are needed to investigate the role of sunlight and vitamin D status in food allergy because of their potential for primary prevention and disease modification.

Cybertaxonomy to accomplish big things in aphid systematics.

PubMed

Favret, Colin

2014-06-01

Biodiversity sciences have progressed at such a pace that the taxonomic community has been unable to grow concomitantly to keep up with the influx of biological data. This "taxonomic impediment" has led some to suggest that taxonomy is no longer pertinent and to the development of methodologies that circumvent the taxonomic process. This article does not seek to argue for the importance of taxonomy but rather is a call to the aphid taxonomy community to rise to the challenge by dramatically increasing the volume and comprehensiveness of its output without sacrificing quality. Recent informatics technology allows us to mobilize the 2 most important aphid taxonomy resources: experts and specimens, both distributed globally. "Cyberspecimens," museum specimens digitally rendered at a resolution sufficient for remote identification, and open "cybertaxonomic" tools will allow the international aphid taxonomic community to carry out large, ambitious, projects. The global aphid cybertaxonomy proposed here will serve not only the ends of research aphidologists, but also provide a model for other taxonomic communities to adapt and adopt as we confront both the taxonomic impediment and the taxonomic naysayers. © 2013 Institute of Zoology, Chinese Academy of Sciences.

Predischarge screening for chronic obstructive pulmonary disease in patients with acute coronary syndrome and smoking history.

PubMed

Campo, Gianluca; Pavasini, Rita; Barbetta, Carlo; Maietti, Elisa; Mascetti, Susanna; Biscaglia, Simone; Zaraket, Fatima; Spitaleri, Giosafat; Gallo, Francesco; Tonet, Elisabetta; Papi, Alberto; Ferrari, Roberto; Contoli, Marco

2016-11-01

Several studies suggested that chronic obstructive pulmonary disease (COPD) is largely underdiagnosed in patients with acute coronary syndrome (ACS) contributing to further affect clinical outcome. Our aim was to validate a screening procedure to identify, in ACS patients, those with negligible risk of undiagnosed COPD. From December 2014 to August 2015, 169 ACS patients with smoking history underwent screening procedure. Screening procedure combined peak expiratory flow rate (PEFR, defined as positive if <80% of predicted) and respiratory health status questionnaire (RHSQ, defined as positive if >19.5 points). The screening was considered negative if both tests provided negative results, positive if both were positive, uncertain in presence of discrepancy. Spirometry was planned after 2months to identify or not the presence of irreversible airflow obstruction (undiagnosed COPD). The primary endpoint was the negative predictive value of screening for undiagnosed COPD. Overall, 137 (81%) patients received spirometry (final study population). Screening was negative, uncertain and positive in 58 (42%), 46 (34%) and 33 (24%) patients, respectively. We found undiagnosed COPD in 39 (29%) patients. Only 3 patients with negative screening showed undiagnosed COPD. Negative screening showed the best ability to discriminate patients without COPD (negative predictive value 95%). Two-month health status in patients with undiagnosed COPD was significantly poor. Undiagnosed COPD is relatively frequent in ACS patients with smoking history and a simple screening procedure including PEFR and RHSQ can be administered before hospital discharge to discriminate those at negligible risk of undiagnosed COPD (ClinicalTrials.gov, NCT02324660). Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Correlates of requesting home HIV self-testing kits on online social networks among African-American and Latino men who have sex with men.

PubMed

Chiu, ChingChe J; Young, Sean D

2016-01-01

High levels of HIV stigma are one of the main difficulties in engaging African-American and Latino men who have sex with men (MSM) in HIV testing. The availability of home HIV test and the possibility of self-testing in private may improve uptake and counteract stigma. This paper sought to determine the correlates of requesting home HIV test kits among a sample of MSM social media users. The odds of participants requesting a test kit were significantly associated with using social networks to seek sexual partners (aOR: 2.47, 95% CI: 1.07-6.06) and thinking it is easier to use social networks for seeking sexual partners (1.87, 1.2-3.12), uncertain HIV status (4.29, 1.37-14.4), and having sex under the influence of alcohol (2.46, 1.06-5.77). Participants who had not been tested for more than 6 months were more likely to request a test kit than those who were tested in the past 6 months (2.53, 1.02-6.37). Participants who frequently talked to others about having sex with men online were less likely to request a test kit (0.73, 0.56-0.92). By reaching people over social media and offering them access to test kits, we were able to reach at-risk individuals who were uncertain about their HIV status and had not been regularly tested. The findings of the study will help to inform future HIV testing interventions.

Diagnosis of nosocomial pneumonia in intubated, intensive care unit patients.

PubMed

Salata, R A; Lederman, M M; Shlaes, D M; Jacobs, M R; Eckstein, E; Tweardy, D; Toossi, Z; Chmielewski, R; Marino, J; King, C H

1987-02-01

The clinical distinction between bacterial colonization of the tracheobronchial tree and nosocomial pneumonia is difficult, especially in intubated patients. We studied 51 intubated, intensive care unit patients prospectively by serial examinations of tracheal aspirates for elastin fibers, graded Gram's stains, and quantitative bacterial cultures in conjunction with clinical and radiologic observations in an attempt to develop criteria for the early detection of pulmonary infection. Patients with infection had new or progressive pulmonary infiltrates plus 1 of the following: positive blood culture results, radiographic evidence of cavitation, or histologic evidence of pneumonia, or 2 or more of the following: new fever, new leukocytosis, or grossly purulent tracheal aspirates. Twenty-one patients developed infection, 22 remained colonized, and 8 had an uncertain status. Infiltrates developed in 34 patients (21 infected, 8 colonized, 5 uncertain status). Gram-negative bacilli were most commonly isolated and were more frequent in infected patients (81 versus 47%, p less than 0.05); Pseudomonas aeruginosa and Serratia marcescens were most often associated with infection. No differences were observed between infected and colonized patients in demographic features, smoking history, underlying disease, previous antibiotic therapy, days in hospital before intubation, preexisting pneumonia upon intubation, or highest temperature or leukocyte count during course. By univariate analysis, infected patients had a longer duration of intubation (p less than 0.05), higher Gram's stain grading for neutrophils (p less than 0.05) or bacteria (p less than 0.005), higher bacterial colony counts (p less than 0.05), and more frequent detection of elastin fibers in tracheal aspirates (p less than 0.02).(ABSTRACT TRUNCATED AT 250 WORDS)

Taxonomic minimalism.

PubMed

Beattle, A J; Oliver, I

1994-12-01

Biological surveys are in increasing demand while taxonomic resources continue to decline. How much formal taxonomy is required to get the job done? The answer depends on the kind of job but it is possible that taxonomic minimalism, especially (1) the use of higher taxonomic ranks, (2) the use of morphospecies rather than species (as identified by Latin binomials), and (3) the involvement of taxonomic specialists only for training and verification, may offer advantages for biodiversity assessment, environmental monitoring and ecological research. As such, formal taxonomy remains central to the process of biological inventory and survey but resources may be allocated more efficiently. For example, if formal Identification is not required, resources may be concentrated on replication and increasing sample sizes. Taxonomic minimalism may also facilitate the inclusion in these activities of important but neglected groups, especially among the invertebrates, and perhaps even microorganisms. Copyright © 1994. Published by Elsevier Ltd.

Nutritional Status and Energy Intake as Predictors of Functional Status After Cardiac Rehabilitation in Elderly Inpatients With Heart Failure　- A Retrospective Cohort Study.

PubMed

Katano, Satoshi; Hashimoto, Akiyoshi; Ohori, Katsuhiko; Watanabe, Ayako; Honma, Remi; Yanase, Rimi; Ishigo, Tomoyuki; Fujito, Takefumi; Ohnishi, Hirofumi; Tsuchihashi, Kazufumi; Ishiai, Sumio; Miura, Tetsuji

2018-05-25

Whether the short-term effect of cardiac rehabilitation (CR) in elderly patients with heart failure (HF) is influenced by nutritional status is uncertain, so the present study investigated the effect of nutritional status on functional recovery after CR in elderly HF inpatients.Methods and Results:We enrolled 145 patients admitted for treatment of HF who were aged ≥65 years and had a low functional status defined as a Barthel index (BI) score ≤85 points at the commencement of CR. Nutritional status was assessed by the Mini Nutritional Assessment Short Form (MNA-SF) and total energy intake per day. The primary endpoint was functional status determined by the BI score at discharge. The median CR period was 20 days (interquartile range: 14-34 days), and 87 patients (60%) were functionally dependent (BI score ≤85) at discharge. Multivariate logistic regression analysis showed that MNA-SF score (odds ratio [OR]: 0.76, P=0.02) and total energy intake at the commencement of CR (OR: 0.91, P=0.02) were independent predictors of functional dependence after CR. MNA-SF score ≤7 and total energy intake ≤24.5 kcal/kg/day predicted functional dependence at discharge with moderate sensitivity and specificity. MNA-SF score and total energy intake at the commencement of CR are novel predictors of the extent of functional recovery of elderly HF inpatients after in-hospital CR.

Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis.

PubMed

Luo, Gang; Fotidis, Ioannis A; Angelidaki, Irini

2016-01-01

Biogas production is a very complex process due to the high complexity in diversity and interactions of the microorganisms mediating it, and only limited and diffuse knowledge exists about the variation of taxonomic and functional patterns of microbiomes across different biogas reactors, and their relationships with the metabolic patterns. The present study used metagenomic sequencing and radioisotopic analysis to assess the taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors operated under various conditions treating either sludge or manure. The results from metagenomic analysis showed that the dominant methanogenic pathway revealed by radioisotopic analysis was not always correlated with the taxonomic and functional compositions. It was found by radioisotopic experiments that the aceticlastic methanogenic pathway was dominant, while metagenomics analysis showed higher relative abundance of hydrogenotrophic methanogens. Principal coordinates analysis showed the sludge-based samples were clearly distinct from the manure-based samples for both taxonomic and functional patterns, and canonical correspondence analysis showed that the both temperature and free ammonia were crucial environmental variables shaping the taxonomic and functional patterns. The study further the overall patterns of functional genes were strongly correlated with overall patterns of taxonomic composition across different biogas reactors. The discrepancy between the metabolic patterns determined by metagenomic analysis and metabolic pathways determined by radioisotopic analysis was found. Besides, a clear correlation between taxonomic and functional patterns was demonstrated for biogas reactors, and also the environmental factors that shaping both taxonomic and functional genes patterns were identified.

The rDNA Internal Transcribed Spacer Region as a Taxonomic Marker for Nematodes

PubMed Central

Powers, T. O.; Todd, T. C.; Burnell, A. M.; Murray, P. C. B.; Fleming, C. C.; Szalanski, A. L.; Adams, B. A.; Harris, T. S.

1997-01-01

The ITS region from a wide taxonomic range of nematodes, including secernentean and adenophorean taxa, and free-living, entomopathogenic, and plant-parasitic species, was evaluated as a taxonomic marker. Size of the amplified product aided in the initial determination of group membership, and also suggested groups that may require taxonomic reevaluation. Congeneric species often displayed identically sized ITS regions, but genera such as Pratylenchus and Tylenchorhynchus had species with large differences in size. ITS heterogeneity in individuals and populations was identified in several nematode taxa. PCR-RFLP of ITS1 is advocated as a method of taxonomic analysis in genera such as Helicotylenchus that contain numerous species with few diagnostic morphological characteristics. PMID:19274180

Taxa: An R package implementing data standards and methods for taxonomic data

PubMed Central

Foster, Zachary S.L.; Chamberlain, Scott; Grünwald, Niklaus J.

2018-01-01

The taxa R package provides a set of tools for defining and manipulating taxonomic data. The recent and widespread application of DNA sequencing to community composition studies is making large data sets with taxonomic information commonplace. However, compared to typical tabular data, this information is encoded in many different ways and the hierarchical nature of taxonomic classifications makes it difficult to work with. There are many R packages that use taxonomic data to varying degrees but there is currently no cross-package standard for how this information is encoded and manipulated. We developed the R package taxa to provide a robust and flexible solution to storing and manipulating taxonomic data in R and any application-specific information associated with it. Taxa provides parsers that can read common sources of taxonomic information (taxon IDs, sequence IDs, taxon names, and classifications) from nearly any format while preserving associated data. Once parsed, the taxonomic data and any associated data can be manipulated using a cohesive set of functions modeled after the popular R package dplyr. These functions take into account the hierarchical nature of taxa and can modify the taxonomy or associated data in such a way that both are kept in sync. Taxa is currently being used by the metacoder and taxize packages, which provide broadly useful functionality that we hope will speed adoption by users and developers. PMID:29707201

The Effects of the Previous Outcome on Probabilistic Choice in Rats

PubMed Central

Marshall, Andrew T.; Kirkpatrick, Kimberly

2014-01-01

This study examined the effects of previous outcomes on subsequent choices in a probabilistic-choice task. Twenty-four rats were trained to choose between a certain outcome (1 or 3 pellets) versus an uncertain outcome (3 or 9 pellets), delivered with a probability of .1, .33, .67, and .9 in different phases. Uncertain outcome choices increased with the probability of uncertain food. Additionally, uncertain choices increased with the probability of uncertain food following both certain-choice outcomes and unrewarded uncertain choices. However, following uncertain-choice food outcomes, there was a tendency to choose the uncertain outcome in all cases, indicating that the rats continued to “gamble” after successful uncertain choices, regardless of the overall probability or magnitude of food. A subsequent manipulation, in which the probability of uncertain food varied within each session as a function of the previous uncertain outcome, examined how the previous outcome and probability of uncertain food affected choice in a dynamic environment. Uncertain-choice behavior increased with the probability of uncertain food. The rats exhibited increased sensitivity to probability changes and a greater degree of win–stay/lose–shift behavior than in the static phase. Simulations of two sequential choice models were performed to explore the possible mechanisms of reward value computations. The simulation results supported an exponentially decaying value function that updated as a function of trial (rather than time). These results emphasize the importance of analyzing global and local factors in choice behavior and suggest avenues for the future development of sequential-choice models. PMID:23205915

The amphibians and reptiles of Mindanao Island, southern Philippines, II: the herpetofauna of northeast Mindanao and adjacent islands.

PubMed

Sanguila, Marites B; Cobb, Kerry A; Siler, Cameron D; Diesmos, Arvin C; Alcala, Angel C; Brown, Rafe M

2016-01-01

We summarize all available amphibian and reptile species distribution data from the northeast Mindanao faunal region, including small islands associated with this subcenter of endemic vertebrate biodiversity. Together with all publicly available historical information from biodiversity repositories, we present new data from several major herpetological surveys, including recently conducted inventories on four major mountains of northeast Mindanao, and adjacent islands of Camiguin Sur, Dinagat, and Siargao. We present species accounts for all taxa, comment on unresolved taxonomic problems, and provide revisions to outdated IUCN conservation status assessments in cases where our new data significantly alter earlier classification status summaries. Together, our comprehensive analysis of this fauna suggests that the greater Mindanao faunal region possesses distinct subcenters of amphibian and reptile species diversity, and that until this area is revisited and its fauna and actually studied, with on-the-ground field work including targeted surveys of species distributions coupled to the study their natural history, our understanding of the diversity and conservation status of southern Philippine herpetological fauna will remain incomplete. Nevertheless, the northeast Mindanao geographical area (Caraga Region) appears to have the highest herpetological species diversity (at least 126 species) of any comparably-sized Philippine faunal subregion.

Taxonomic chauvinism revisited: insight from parental care research.

PubMed

Stahlschmidt, Zachary R

2011-01-01

Parental care (any non-genetic contribution by a parent that appears likely to increase the fitness of its offspring) is a widespread trait exhibited by a broad range of animal taxa. In addition to influencing the fitness of parent(s) and offspring, parental care may be inextricably involved in other evolutionary processes, such as sexual selection and the evolution of endothermy. Yet, recent work has demonstrated that bias related to taxonomy is prevalent across many biological disciplines, and research in parental care may be similarly burdened. Thus, I used parental care articles published in six leading journals of fundamental behavioral sciences (Animal Behaviour, Behavioral Ecology, Behavioral Ecology and Sociobiology, Ethology, Hormones and Behavior, and Physiology & Behavior) from 2001-2010 (n = 712) to examine the year-to-year dynamics of two types of bias related to taxonomy across animals: (1) taxonomic bias, which exists when research output is not proportional to the frequency of organisms in nature, and (2) taxonomic citation bias, which is a proxy for the breadth of a given article-specifically, the proportion of articles cited that refer solely to the studied taxon. I demonstrate that research on birds likely represents a disproportionate amount of parental care research and, thus, exhibits taxonomic bias. Parental care research on birds and mammals also refers to a relatively narrow range of taxonomic groups when discussing its context and, thus, exhibits taxonomic citation bias. Further, the levels of taxonomic bias and taxonomic citation bias have not declined over the past decade despite cautionary messages about similar bias in related disciplines--in fact, taxonomic bias may have increased. As in Bonnet et al. (2002), my results should not be interpreted as evidence of an 'ornithological Mafia' conspiring to suppress other taxonomic groups. Rather, I generate several rational hypotheses to determine why bias persists and to guide future work.

Complete DNA barcode reference library for a country's butterfly fauna reveals high performance for temperate Europe

PubMed Central

Dincă, Vlad; Zakharov, Evgeny V.; Hebert, Paul D. N.; Vila, Roger

2011-01-01

DNA barcoding aims to accelerate species identification and discovery, but performance tests have shown marked differences in identification success. As a consequence, there remains a great need for comprehensive studies which objectively test the method in groups with a solid taxonomic framework. This study focuses on the 180 species of butterflies in Romania, accounting for about one third of the European butterfly fauna. This country includes five eco-regions, the highest of any in the European Union, and is a good representative for temperate areas. Morphology and DNA barcodes of more than 1300 specimens were carefully studied and compared. Our results indicate that 90 per cent of the species form barcode clusters allowing their reliable identification. The remaining cases involve nine closely related species pairs, some whose taxonomic status is controversial or that hybridize regularly. Interestingly, DNA barcoding was found to be the most effective identification tool, outperforming external morphology, and being slightly better than male genitalia. Romania is now the first country to have a comprehensive DNA barcode reference database for butterflies. Similar barcoding efforts based on comprehensive sampling of specific geographical regions can act as functional modules that will foster the early application of DNA barcoding while a global system is under development. PMID:20702462

Modelling alpha-diversities of coastal lagoon fish assemblages from the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Riera, R.; Tuset, V. M.; Betancur-R, R.; Lombarte, A.; Marcos, C.; Pérez-Ruzafa, A.

2018-07-01

Coastal lagoons are marine ecosystems spread worldwide with high ecological value; however, they are increasingly becoming deteriorated as a result of anthropogenic activity. Their conservation requires a better understanding of the biodiversity factors that may help identifying priority areas. The present study is focused on 37 Mediterranean coastal lagoons and we use predictive modelling approaches based on Generalized Linear Model (GLM) analysis to investigate variables (geomorphological, environmental, trophic or biogeographic) that may predict variations in alpha-diversity. It included taxonomic diversity, average taxonomic distinctness, and phylogenetic and functional diversity. Two GLM models by index were built depending on available variables for lagoons: in the model 1 all lagoons were used, and in the model 2 only 23. All alpha-diversity indices showed variability between lagoons associated to exogenous factors considered. The biogeographic region strongly conditioned most of models, being the first variable introduced in the models. The salinity and chlorophyll a concentration played a secondary role for the models 1 and 2, respectively. In general, the highest values of alpha-diversities were found in northwestern Mediterranean (Balearic Sea, Alborán Sea and Gulf of Lion), hence they might be considered "hotspots" at the Mediterranean scale and should have a special status for their protection.

A snapshot of gut microbiota of an adult urban population from Western region of India.

PubMed

Tandon, Disha; Haque, Mohammed Monzoorul; R, Saravanan; Shaikh, Shafiq; P, Sriram; Dubey, Ashok Kumar; Mande, Sharmila S

2018-01-01

The human gut microbiome contributes to a broad range of biochemical and metabolic functions that directly or indirectly affect human physiology. Several recent studies have indicated that factors like age, geographical location, genetic makeup, and individual health status significantly influence the diversity, stability, and resilience of the gut microbiome. Of the mentioned factors, geographical location (and related dietary/socio-economic context) appears to explain a significant portion of microbiome variation observed in various previously conducted base-line studies on human gut microbiome. Given this context, we have undertaken a microbiome study with the objective of cataloguing the taxonomic diversity of gut microbiomes sampled from an urban cohort from Ahmedabad city in Western India. Computational analysis of microbiome sequence data corresponding to 160 stool samples (collected from 80 healthy individuals at two time-points, 60 days apart) has indicated a Prevotella-dominated microbial community. Given that the typical diet of participants included carbohydrate and fibre-rich components (predominantly whole grains and legume-based preparations), results appear to validate the proposed correlation between diet/geography and microbiome composition. Comparative analysis of obtained gut microbiome profiles with previously published microbiome profiles from US, China, Finland, and Japan additionally reveals a distinct taxonomic and (inferred) functional niche for the sampled microbiomes.

On Kiefer’s American Eucyclops (Copepoda, Eucyclopinae): redescriptions and comments on the historical records of E. delachauxi, E. prionophorus, E. bondi and E. leptacanthus

PubMed Central

Mercado-Salas, Nancy F.; Suárez-Morales, Eduardo

2014-01-01

Abstract The freshwater copepod genus Eucyclops contains many supposedly cosmopolitan species whose taxonomic status is still under discussion; some of them represent species complexes. The problem is not exclusive to these widespread species; there are several American Eucyclops needing a taxonomic re-evaluation. Based on the examination of Friedrich Kiefer’s collection in Karlsruhe, Germany, the type specimens of four American species of Eucyclops (E. delachauxi (Kiefer, 1926), E. prionophorus Kiefer, 1931, E. bondi Kiefer, 1934, E. leptacanthus Kiefer, 1956) were re-examined and redescribed using upgraded descriptive standards. Kiefer’s translated descriptions and unpublished original drawings of these species are also presented. Characters like the ornamentation of the antennal basis, ornamentation of intercoxal sclerites of the swimming legs 1–4, length of basipodal seta of leg 1, ornamentation of caudal rami, the presence of aesthetascs and modified setae on the antennules in male, and the structure of the male sixth leg are compared herein to aid a more accurate separation of these American species. A revision of the American records of these species confirms that some are likely to refer to undescribed species. Overall, the diversity of the American Eucyclops appears to be underestimated and certainly deserves further study. PMID:24843261

The status of Demodex cornei: description of the species and developmental stages, and data on demodecid mites in the domestic dog Canis lupus familiaris.

PubMed

Izdebska, J N; Rolbiecki, L

2018-03-30

Demodecosis canina is one of the most important dog parasitoses, but its aetiology is still not well known. There are currently two known species of demodecid mite specific to the domestic dog Canis lupus familiaris Linnaeus, 1758 (Carnivora: Canidae). These are Demodex canis Leydig, 1859 (Acariformes: Demodecidae) and Demodex injai Desch & Hillier, 2003. There have also been many reports of the so-called 'short form', considered to be a separate species functioning under the name Demodex cornei nomen nudum, for which, however, no formal valid description has been documented. Taxonomic analysis of short forms of dog demodecid mites, associated with the stratum corneum, was performed, in line with the taxonomic criteria of Demodecidae systematics. This form was found to be a distinct species with features that differ from those of the other known species of this family. The species, including the adult and immature stages, is described. It is likely that different Demodex species parasitizing the domestic dog may be responsible for differentiated symptoms and different courses of demodecosis. However, the basis for clarifying this issue should be the correct, unambiguous identification of the species causing parasitosis. © 2018 The Royal Entomological Society.

Patterns of genetic divergence of three Canarian endemic Lotus (Fabaceae): implications for the conservation of the endangered L. kunkelii.

PubMed

Oliva-Tejera, Felicia; Caujapé-Castells, Juli; Navarro-Déniz, Josefa; Reyes-Betancort, Alfredo; Scholz, Stephan; Baccarani-Rosas, Mario; Cabrera-García, Nereida

2006-08-01

We examined data for 11 allozyme loci in 14 populations that represent the distribution of the endangered Lotus kunkelii, the narrowly distributed L. arinagensis (both endemic to Gran Canaria), and the broad-ranging L. lancerottensis (endemic to the easternmost Canary Islands, Fuerteventura and Lanzarote) to explore and construe patterns of genetic variation and use this data to assess the controversial taxonomic status of L. kunkelii relative to L. lancerottensis. While L. kunkelii maintains low levels of variation, presumably as a consequence of prolonged inbreeding due to very low population size and sharp geographic isolation, the other two taxa have much higher indicators of polymorphism than those reported for other oceanic island endemics. Lotus arinagensis has the highest genetic polymorphism and the lowest interpopulation differentiation, presumably because of its considerable antiquity and habitat stability, despite recent fragmentation. The high interpopulation differentiation in L. lancerottensis is attributed to the Atlantic acting as a barrier, reducing gene flow within islands. Evolutionary analysis of the allozyme evidence indicates that L. kunkelii is genetically closer to L. arinagensis than to L. lancerottensis, thereby dispelling the taxonomic uncertainty and supporting L. kunkelii as a distinct species, warranting legal protection in the forthcoming catalog of threatened Canarian species.

DIVERSITY AND HOST SPECIFICITY OF AZOLLA CYANOBIONTS(1).

PubMed

Papaefthimiou, Dimitra; Van Hove, Charles; Lejeune, André; Rasmussen, Ulla; Wilmotte, Annick

2008-02-01

A unique, hereditary symbiosis exists between the water fern Azolla and cyanobacteria that reside within a cavity in the dorsal leaf-lobe of the plant. This association has been studied extensively, and questions have frequently been raised regarding the number and diversity of cyanobionts (cyanobacterial symbionts) among the different Azolla strains and species. In this work, denaturating gradient gel electrophoresis (DGGE) and a clone library based on the 16S rRNA gene were used to study the genetic diversity and host specificity of the cyanobionts in 35 Azolla strains covering a wide taxonomic and geographic range. DNA was extracted directly from the cyanobacterial packets, isolated after enzymatic digestion of the Azolla leaves. Our results indicated the existence of different cyanobiont strains among Azolla species, and diversity within a single Azolla species, independent of the geographic origin of the host. Furthermore, the cyanobiont exhibited host-species specificity and showed most divergence between the two sections of genus Azolla, Azolla and Rhizosperma. These findings are in agreement with the recent redefinition of the taxon Azolla cristata within the section Azolla. With regard to the taxonomic status of the cyanobiont, the genus Anabaena of the Nostocaceae family was identified as the closest relative by this work. © 2008 Phycological Society of America.

Frullania knightbridgei, a new liverwort (Frullaniaceae, Marchantiophyta) species from the deep south of Aotearoa-New Zealand based on an integrated evidence-based approach

PubMed Central

von Konrat, Matt; de Lange, Peter; Greif, Matt; Strozier, Lynika; Hentschel, Jörn; Heinrichs, Jochen

2012-01-01

Abstract Frullania is a large and taxonomically complex genus. A new liverwort species, Frullania knightbridgei sp. nov. from southern New Zealand, is described and illustrated. The new species, and its placement in Frullania subg. Microfrullania, is based on an integrated evidence-based approach derived from morphology, ecology, experimental growth studies of plasticity, as well as sequence data. Diagnostic characters associated with the leaf and lobule cell-wall anatomy, oil bodies, and spore ultra-structure distinguish it from all other New Zealand species of Frullania. A critical comparison is also made between Frullania knightbridgei and morphologically allied species of botanical regions outside the New Zealand region and an artificial key is provided. The new species is similar to some forms of the widespread Australasian species, Frullania rostrata, but has unique characters associated with the lobule and oil bodies. Frullania knightbridgei is remarkably interesting in comparison with the majority of Frullania species, and indeed liverworts in general, in that it is at least partially halotolerant. Maximum parsimony and maximum likelihood analyses of nuclear ribosomal ITS2 and plastidic trnL-trnF sequences from purported related speciesconfirms its independent taxonomic status and corroborates its placement within Frullania subg. Microfrullania. PMID:22287928

Molecular and morphological differentiation between two Miocene-divergent lineages of Amazonian shrimps, with the description of a new species (Decapoda, Palaemonidae, Palaemon)

PubMed Central

Carvalho, Fabrício Lopes; Magalhães, Célio; Mantelatto, Fernando Luis

2014-01-01

Abstract Palaemon carteri (Gordon, 1935) and Palaemon ivonicus (Holthuis, 1950) are morphologically similar species of South American freshwater shrimps. Past studies have questioned the taxonomic status of both species, which are supposed to have partially sympatric geographic distributions in the Amazon basin. We analyzed a 550 bp fragment of the mitochondrial 16S rRNA gene from these Amazonian Palaemon species as well as from 11 palaemonids as the outgroup. Additionally, we checked diagnostic characters of the genus and family as well as other morphological characters that have been little explored before. Palaemon carteri and Palaemon ivonicus are allocated in two sister lineages, with wide genetic divergence and little morphological differentiation. The divergence time between these lineages was estimated as approximately 10 million years ago. Both molecular and morphological data support the taxonomic validity of both Palaemon carteri and Palaemon ivonicus, refuting the hypothesis of synonymy. In addition, a new species, Palaemon yuna sp. n., closely related to Palaemon ivonicus, is described. Our findings indicate that these species can be differentiated using the projection of the anterolateral margin and anterolateral spine of the first antennular segment, shape of the rostrum, and relative size of the appendix masculina. PMID:25561832

Cut from the same cloth: The convergent evolution of dwarf morphotypes of the Carex flava group (Cyperaceae) in Circum-Mediterranean mountains

PubMed Central

Benítez-Benítez, Carmen; Fernández-Mazuecos, Mario; Martín-Bravo, Santiago

2017-01-01

Plants growing in high-mountain environments may share common morphological features through convergent evolution resulting from an adaptative response to similar ecological conditions. The Carex flava species complex (sect. Ceratocystis, Cyperaceae) includes four dwarf morphotypes from Circum-Mediterranean mountains whose taxonomic status has remained obscure due to their apparent morphological resemblance. In this study we investigate whether these dwarf mountain morphotypes result from convergent evolution or common ancestry, and whether there are ecological differences promoting differentiation between the dwarf morphotypes and their taxonomically related large, well-developed counterparts. We used phylogenetic analyses of nrDNA (ITS) and ptDNA (rps16 and 5’trnK) sequences, ancestral state reconstruction, multivariate analyses of macro- and micromorphological data, and species distribution modeling. Dwarf morphotype populations were found to belong to three different genetic lineages, and several morphotype shifts from well-developed to dwarf were suggested by ancestral state reconstructions. Distribution modeling supported differences in climatic niche at regional scale between the large forms, mainly from lowland, and the dwarf mountain morphotypes. Our results suggest that dwarf mountain morphotypes within this sedge group are small forms of different lineages that have recurrently adapted to mountain habitats through convergent evolution. PMID:29281689

Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato

PubMed Central

Beukes, Chrizelle W.; Palmer, Marike; Manyaka, Puseletso; Chan, Wai Y.; Avontuur, Juanita R.; van Zyl, Elritha; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, T. B. K.; Daum, Chris; Shapiro, Nicole; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Woyke, Tanja; Blom, Jochen; Whitman, William B.; Venter, Stephanus N.; Steenkamp, Emma T.

2017-01-01

Although the taxonomy of Burkholderia has been extensively scrutinized, significant uncertainty remains regarding the generic boundaries and composition of this large and heterogeneous taxon. Here we used the amino acid and nucleotide sequences of 106 conserved proteins from 92 species to infer robust maximum likelihood phylogenies with which to investigate the generic structure of Burkholderia sensu lato. These data unambiguously supported five distinct lineages, of which four correspond to Burkholderia sensu stricto and the newly introduced genera Paraburkholderia, Caballeronia, and Robbsia. The fifth lineage was represented by P. rhizoxinica. Based on these findings, we propose 13 new combinations for those species previously described as members of Burkholderia but that form part of Caballeronia. These findings also suggest revision of the taxonomic status of P. rhizoxinica as it is does not form part of any of the genera currently recognized in Burkholderia sensu lato. From a phylogenetic point of view, Burkholderia sensu stricto has a sister relationship with the Caballeronia+Paraburkholderia clade. Also, the lineages represented by P. rhizoxinica and R. andropogonis, respectively, emerged prior to the radiation of the Burkholderia sensu stricto+Caballeronia+Paraburkholderia clade. Our findings therefore constitute a solid framework, not only for supporting current and future taxonomic decisions, but also for studying the evolution of this assemblage of medically, industrially and agriculturally important species. PMID:28694797

Genus age, provincial area and the taxonomic structure of marine faunas.

PubMed

Harnik, Paul G; Jablonski, David; Krug, Andrew Z; Valentine, James W

2010-11-22

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf-Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area.

Genus age, provincial area and the taxonomic structure of marine faunas

PubMed Central

Harnik, Paul G.; Jablonski, David; Krug, Andrew Z.; Valentine, James W.

2010-01-01

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf–Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area. PMID:20534619

Distinct progression of the deterioration of thematic and taxonomic links in natural and manufactured objects in Alzheimer's disease.

PubMed

Simoes Loureiro, Isabelle; Lefebvre, Laurent

2016-10-01

Taxonomic and thematic relationships are core elements of lexico-semantic networks. However, the weight of both links differs in semantic memory, with distinct support for natural and manufactured objects: natural objects tend to be more taxonomically identified while manufactured objects benefit more from the underlying thematic relationships. Alzheimer's disease (AD) causes early semantic memory impairment characterized by a category-specific deterioration, where natural objects are more sensitive to the disease than manufactured objects. However, relatively few studies have examined the progressive deterioration of specific thematic versus taxonomic relations in both categories of objects in AD. To better understand semantic memory disorganization in AD and analyze the potential interaction effect between the category (natural/manufactured), the condition (thematic/taxonomic) and AD, we will investigate the lexico-semantic network in 82 AD patients (divided into three groups depending on their global cognitive deterioration and their performance in a preliminary semantic knowledge questionnaire (mild (AD1), moderate (AD2) and advanced (AD3) stages of semantic knowledge alteration). The experimental protocol contains two tasks: an implicit semantic priming paradigm and an explicit card-sorting test that uses the same items, equally divided between natural and manufactured objects. Results show a distinct taxonomic and thematic evolution pattern with early taxonomic deterioration. Natural objects are also more vulnerable to the disease. Lastly, there is an interaction effect between the category and the condition in the priming task indicating that natural objects are more taxonomically organized and manufactured objects benefit more from both thematic and taxonomic organizations, reinforcing the idea of the robustness of this category. The theoretical accounts of these observations will be discussed in detail. Copyright © 2016 Elsevier Ltd. All rights reserved.

Trends in Taxonomic and Functional Composition of Soil Microbiome Along a Precipitation Gradient in Israel.

PubMed

Tripathi, Binu M; Moroenyane, Itumeleng; Sherman, Chen; Lee, Yoo Kyung; Adams, Jonathan M; Steinberger, Yosef

2017-07-01

The soil microbiome is important for the functioning of terrestrial ecosystems. However, the impacts of climate on taxonomic and functional diversity of soil microbiome are not well understood. A precipitation gradient along regional scale transects may offer a model setting for understanding the effect of climate on the composition and function of the soil microbiome. Here, we compared taxonomic and functional attributes of soil microorganisms in arid, semiarid, Mediterranean, and humid Mediterranean climatic conditions of Israel using shotgun metagenomic sequencing. We hypothesized that there would be a distinct taxonomic and functional soil community for each precipitation zone, with arid environments having lower taxonomic and functional diversity, greater relative abundance of stress response and sporulation-related genes, and lower relative abundance of genes related to nutrient cycling and degradation of complex organic compounds. As hypothesized, our results showed a distinct taxonomic and functional community in each precipitation zone, revealing differences in soil taxonomic and functional selection in the different climates. Although the taxonomic diversity remained similar across all sites, the functional diversity was-as hypothesized-lower in the arid environments, suggesting that functionality is more constrained in "extreme" environments. Also, with increasing aridity, we found a significant increase in genes related to dormancy/sporulation and a decrease in those related to nutrient cycling (genes related to nitrogen, potassium, and sulfur metabolism), respectively. However, relative abundance of genes related to stress response were lower in arid soils. Overall, these results indicate that climatic conditions play an important role in shaping taxonomic and functional attributes of soil microbiome. These findings have important implications for understanding the impacts of climate change (e.g., precipitation change) on structure and function of the soil microbiome.

Colletotrichum – current status and future directions

PubMed Central

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

2012-01-01

A review is provided of the current state of understanding of Colletotrichum systematics, focusing on species-level data and the major clades. The taxonomic placement of the genus is discussed, and the evolution of our approach to species concepts and anamorph-teleomorph relationships is described. The application of multilocus technologies to phylogenetic analysis of Colletotrichum is reviewed, and selection of potential genes/loci for barcoding purposes is discussed. Host specificity and its relation to speciation and taxonomy is briefly addressed. A short review is presented of the current status of classification of the species clusters that are currently without comprehensive multilocus analyses, emphasising the orbiculare and destructivum aggregates. The future for Colletotrichum biology will be reliant on consensus classification and robust identification tools. In support of these goals, a Subcommission on Colletotrichum has been formed under the auspices of the International Commission on Taxonomy of Fungi, which will administer a carefully curated barcode database for sequence-based identification of species within the BioloMICS web environment. PMID:23136460

Dietary iron intake, iron status, and gestational diabetes.

PubMed

Zhang, Cuilin; Rawal, Shristi

2017-12-01

Pregnant women are particularly vulnerable to iron deficiency and related adverse pregnancy outcomes and, as such, are routinely recommended for iron supplementation. Emerging evidence from both animal and population-based studies, however, has raised potential concerns because significant associations have been observed between greater iron stores and disturbances in glucose metabolism, including increased risk of type 2 diabetes among nonpregnant individuals. Yet, the evidence is uncertain regarding the role of iron in the development of gestational diabetes mellitus (GDM), a common pregnancy complication which has short-term and long-term adverse health ramifications for both women and their children. In this review, we critically and systematically evaluate available data examining the risk of GDM associated with dietary iron, iron supplementation, and iron status as measured by blood concentrations of several indicators. We also discuss major methodologic concerns regarding the available epidemiologic studies on iron and GDM. © 2017 American Society for Nutrition.

Brain MRI findings in two cases with eclampsia.

PubMed

Unal, M; Senakayli, O C; Serçe, K

1996-08-01

Neurological complications in patients with eclampsia are varied and include headache, visual disturbances, focal neurological deficits, altered mental status and coma. Occasionally, a focal neurological deficit includes a variety of visual disturbances. The pathophysiology of CNS abnormalities in patients with eclampsia is uncertain. Our cases, combined with a review of the literature, demonstrate that there is no correlation among severity of hypertension, parity, and location of lesions at initial magnetic resonance (MR) imaging findings or between the severity of hypertension and neurological symptoms. Two typical patterns are seen on MR images of patients with eclampsia. Lesions in the region of the posterior cerebral circulation are most common and are frequently associated with visual disturbances. Although there are lesions in the deep white matter or basal ganglia, a focal neurological deficit or alterations in mental status may not develop. This demonstrates the sensitivity of MR imaging in the detection of abnormalities in patients with eclampsia, even those without neurological deficits.

IMMIGRATION ENFORCEMENT AND MIXED-STATUS FAMILIES: THE EFFECTS OF RISK OF DEPORTATION ON MEDICAID USE

PubMed Central

Vargas, Edward D.

2015-01-01

As Congress priorities the immigration debate on increased border security, the fate of an estimated 11 million undocumented citizens remains uncertain. Stuck in between partisan politics and practical solutions are mixed-status families in which some members of the family are U.S. citizens while other members are in the country without proper authorization. This paper, examines the relationship between risk of deportation and Medicaid use drawing from a nationally sample of mothers from the Fragile Families and Child Wellbeing Survey. These data are then merged with data from the U.S. Citizenship and Immigration Services to create a contextual risk of deportation measure. Findings suggest that an increase in risk of deportation is associated with a decrease in Medicaid use. The implications of this work have tremendous impacts for health service providers and policy makers interested in preventing and reducing health disparities in complex family structures. PMID:26435562

Advance directives in the UK: legal, ethical, and practical considerations for doctors.

PubMed

Kessel, A S; Meran, J

1998-05-01

In the United Kingdom (UK), advance directives have recently received considerable attention from professional and voluntary organizations as well as medical journals and the media. However, despite such exposure, many doctors remain uncertain of the importance or relevance of advance directives with regard to their own clinical practice. This paper addresses these uncertainties by first explaining what advance directives are and then describing the current legal status of such directives in the UK. Examination of the cases underpinning this status reveals several key elements: competence, information, anticipation, applicability, and freedom from duress. Each is discussed. Although this paper focuses on legal issues, it is important that medical law does not dominate medical ethics. Accordingly, the paper also discusses some important philosophical and sociological considerations that have remained largely unexplored in the medical press. Finally, the paper deals with practical matters, including how the general practitioner might be involved.

Verification of the Specific Status of the Endangered Anthony's River Snail, Athearnia anthonyi, Using Allozyme Electrophoresis

USGS Publications Warehouse

Dillon, R.T.; Ahlstedt, S.A.

1997-01-01

Although nominally the single surviving representative of a unique pleurocerid taxon, Athearnia anthonyi (Budd, in Redfield, 1854) is so rarely collected that even its specific status has been uncertain. We used allozyme electrophoresis to compare a population of A. anthonyi to the similar pleurocerid snail, Leptoxis praerosa (Say, 1821), co-occurring with it in the Sequatchie River of Tennessee, and to a second population of L. praerosa collected approximately 500 km distant. Observed levels of heterozygosity offered no evidence of inbreeding or unusually severe population bottlenecking in any of these populations. Strikingly different allele frequencies at five of the eleven enzyme loci examined, together with differences in shell morphology especially apparent in young individuals, confirmed that A. anthonyi and L. praerosa are distinct species. Their similarity at the six loci remaining supports previous suggestions that Athearnia may be a subgenus of Leptoxis.

The Effects of Objective and Subjective Socioeconomic Status on Subjective Well-Being among Rural-to-Urban Migrants in China: The Moderating Role of Subjective Social Mobility

PubMed Central

Huang, Silin; Hou, Jiawei; Sun, Ling; Dou, Donghui; Liu, Xia; Zhang, Hongchuan

2017-01-01

Although previous investigations have agreed that Chinese rural-to-urban migrants’ socioeconomic status (SES) increases with their migration, the association between SES and subjective well-being is uncertain. To address this research gap, the present study proposed that the association between objective SES and subjective well-being is mediated by subjective SES. This model was tested with a sample of 432 Chinese rural-to-urban migrants. The results indicate a significant association between objective SES and subjective well-being and a partial mediating effect of subjective SES. Furthermore, subjective social mobility, which is one’s expectation about the possibility to move upward in the social hierarchy, was found to moderate both the direct path from objective SES to subjective well-being and the indirect path from subjective SES to subjective well-being. These findings suggest that Chinese rural-to-urban migrants gained in subjective well-being not only because of direct financial achievement but also because of their perceptions and beliefs about their relative social status. PMID:28588531

Elementary Students' Scientific Epistemological Beliefs in Relation to Socio-Economic Status and Gender

NASA Astrophysics Data System (ADS)

Ozkal, Kudret; Tekkaya, Ceren; Sungur, Semra; Cakiroglu, Jale; Cakiroglu, Erdinc

2011-03-01

This study investigated students' scientific epistemological beliefs in relation to socio-economic status (SES) and gender. Data were obtained from 1,152 eight grade Turkish elementary school students using Scientific Epistemological Beliefs instrument. Canonical correlation analysis indicated that students with a working mother and educated parents as well as greater number of books at home together with a separate study room are more likely to have tentative views and less likely to have fixed views about science compared to students with unemployed mother, uneducated parents, less books at home, and no separate study room. Generally, results revealed while family SES correlated positively with tentative views, it was negatively associated with fixed views, implying that students from high SES family were more likely to believe that knowledge is uncertain and not handed down by authority compared to students from low SES family. This study, however, failed to indicate any relationship between father work-status, buying daily newspaper and epistemological beliefs. In addition, Multivariate Analysis of Variance indicated that boys more likely to have tentative beliefs compared to girls.

Elementary Students' Scientific Epistemological Beliefs in Relation to Socio-Economic Status and Gender

NASA Astrophysics Data System (ADS)

Ozkal, Kudret; Tekkaya, Ceren; Sungur, Semra; Cakiroglu, Jale; Cakiroglu, Erdinc

2010-11-01

This study investigated students’ scientific epistemological beliefs in relation to socio-economic status (SES) and gender. Data were obtained from 1,152 eight grade Turkish elementary school students using Scientific Epistemological Beliefs instrument. Canonical correlation analysis indicated that students with a working mother and educated parents as well as greater number of books at home together with a separate study room are more likely to have tentative views and less likely to have fixed views about science compared to students with unemployed mother, uneducated parents, less books at home, and no separate study room. Generally, results revealed while family SES correlated positively with tentative views, it was negatively associated with fixed views, implying that students from high SES family were more likely to believe that knowledge is uncertain and not handed down by authority compared to students from low SES family. This study, however, failed to indicate any relationship between father work-status, buying daily newspaper and epistemological beliefs. In addition, Multivariate Analysis of Variance indicated that boys more likely to have tentative beliefs compared to girls.

Structure of the human gastric bacterial community in relation to Helicobacter pylori status.

PubMed

Maldonado-Contreras, Ana; Goldfarb, Kate C; Godoy-Vitorino, Filipa; Karaoz, Ulas; Contreras, Mónica; Blaser, Martin J; Brodie, Eoin L; Dominguez-Bello, Maria G

2011-04-01

The human stomach is naturally colonized by Helicobacter pylori, which, when present, dominates the gastric bacterial community. In this study, we aimed to characterize the structure of the bacterial community in the stomach of patients of differing H. pylori status. We used a high-density 16S rRNA gene microarray (PhyloChip, Affymetrix, Inc.) to hybridize 16S rRNA gene amplicons from gastric biopsy DNA of 10 rural Amerindian patients from Amazonas, Venezuela, and of two immigrants to the United States (from South Asia and Africa, respectively). H. pylori status was determined by PCR amplification of H. pylori glmM from gastric biopsy samples. Of the 12 patients, 8 (6 of the 10 Amerindians and the 2 non-Amerindians) were H. pylori glmM positive. Regardless of H. pylori status, the PhyloChip detected Helicobacteriaceae DNA in all patients, although with lower relative abundance in patients who were glmM negative. The G2-chip taxonomy analysis of PhyloChip data indicated the presence of 44 bacterial phyla (of which 16 are unclassified by the Taxonomic Outline of the Bacteria and Archaea taxonomy) in a highly uneven community dominated by only four phyla: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Positive H. pylori status was associated with increased relative abundance of non-Helicobacter bacteria from the Proteobacteria, Spirochetes and Acidobacteria, and with decreased abundance of Actinobacteria, Bacteroidetes and Firmicutes. The PhyloChip detected richness of low abundance phyla, and showed marked differences in the structure of the gastric bacterial community according to H. pylori status.

Structure of the human gastric bacterial community in relation to Helicobacter pylori status

PubMed Central

Maldonado-Contreras, Ana; Goldfarb, Kate C; Godoy-Vitorino, Filipa; Karaoz, Ulas; Contreras, Mónica; Blaser, Martin J; Brodie, Eoin L; Dominguez-Bello, Maria G

2011-01-01

The human stomach is naturally colonized by Helicobacter pylori, which, when present, dominates the gastric bacterial community. In this study, we aimed to characterize the structure of the bacterial community in the stomach of patients of differing H. pylori status. We used a high-density 16S rRNA gene microarray (PhyloChip, Affymetrix, Inc.) to hybridize 16S rRNA gene amplicons from gastric biopsy DNA of 10 rural Amerindian patients from Amazonas, Venezuela, and of two immigrants to the United States (from South Asia and Africa, respectively). H. pylori status was determined by PCR amplification of H. pylori glmM from gastric biopsy samples. Of the 12 patients, 8 (6 of the 10 Amerindians and the 2 non-Amerindians) were H. pylori glmM positive. Regardless of H. pylori status, the PhyloChip detected Helicobacteriaceae DNA in all patients, although with lower relative abundance in patients who were glmM negative. The G2-chip taxonomy analysis of PhyloChip data indicated the presence of 44 bacterial phyla (of which 16 are unclassified by the Taxonomic Outline of the Bacteria and Archaea taxonomy) in a highly uneven community dominated by only four phyla: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Positive H. pylori status was associated with increased relative abundance of non-Helicobacter bacteria from the Proteobacteria, Spirochetes and Acidobacteria, and with decreased abundance of Actinobacteria, Bacteroidetes and Firmicutes. The PhyloChip detected richness of low abundance phyla, and showed marked differences in the structure of the gastric bacterial community according to H. pylori status. PMID:20927139

Neuroanatomical dissociation for taxonomic and thematic knowledge in the human brain

PubMed Central

Schwartz, Myrna F.; Kimberg, Daniel Y.; Walker, Grant M.; Brecher, Adelyn; Faseyitan, Olufunsho K.; Dell, Gary S.; Mirman, Daniel; Coslett, H. Branch

2011-01-01

It is thought that semantic memory represents taxonomic information differently from thematic information. This study investigated the neural basis for the taxonomic-thematic distinction in a unique way. We gathered picture-naming errors from 86 individuals with poststroke language impairment (aphasia). Error rates were determined separately for taxonomic errors (“pear” in response to apple) and thematic errors (“worm” in response to apple), and their shared variance was regressed out of each measure. With the segmented lesions normalized to a common template, we carried out voxel-based lesion-symptom mapping on each error type separately. We found that taxonomic errors localized to the left anterior temporal lobe and thematic errors localized to the left temporoparietal junction. This is an indication that the contribution of these regions to semantic memory cleaves along taxonomic-thematic lines. Our findings show that a distinction long recognized in the psychological sciences is grounded in the structure and function of the human brain. PMID:21540329

Bovine Teat Microbiome Analysis Revealed Reduced Alpha Diversity and Significant Changes in Taxonomic Profiles in Quarters with a History of Mastitis

PubMed Central

Falentin, Hélène; Rault, Lucie; Nicolas, Aurélie; Bouchard, Damien S.; Lassalas, Jacques; Lamberton, Philippe; Aubry, Jean-Marc; Marnet, Pierre-Guy; Le Loir, Yves; Even, Sergine

2016-01-01

Mastitis is a mammary gland inflammatory disease often due to bacterial infections. Like many other infections, it used to be considered as a host-pathogen interaction driven by host and bacterial determinants. Until now, the involvement of the bovine mammary gland microbiota in the host-pathogen interaction has been poorly investigated, and mainly during the infectious episode. In this study, the bovine teat microbiome was investigated in 31 quarters corresponding to 27 animals, which were all free of inflammation at sampling time but which had different histories regarding mastitis: from no episode of mastitis on all the previous lactations (Healthy quarter, Hq) to one or several clinical mastitis events (Mastitic quarter, Mq). Several quarters whose status was unclear (possible history of subclinical mastitis) were classified as NDq. Total bacterial DNA was extracted from foremilk samples and swab samples of the teat canal. Taxonomic profiles were determined by pyrosequencing on 16s amplicons of the V3-4 region. Hq quarters showed a higher diversity compared to Mq ones (Shannon index: ~8 and 6, respectively). Clustering of the quarters based on their bacterial composition made it possible to separate Mq and Hq quarters into two separate clusters (C1 and C2, respectively). Discriminant analysis of taxonomic profiles between these clusters revealed several differences and allowed the identification of taxonomic markers in relation to mastitis history. C2 quarters were associated with a higher proportion of the Clostridia class (including genera such as Ruminococcus, Oscillospira, Roseburia, Dorea, etc.), the Bacteroidetes phylum (Prevotella, Bacteroides, Paludibacter, etc.), and the Bifidobacteriales order (Bifidobacterium), whereas C1 quarters showed a higher proportion of the Bacilli class (Staphylococcus) and Chlamydiia class. These results indicate that microbiota is altered in udders which have already developed mastitis, even far from the infectious episode. Microbiome alteration may have resulted from the infection itself and or the associated antibiotic treatment. Alternatively, differences in microbiome composition in udders with a history of mastitis may have occurred prior to the infection and even contributed to infection development. Further investigations on the dynamics of mammary gland microbiota will help to elucidate the contribution of this endogenous microbiota to the mammary gland health. PMID:27242672

A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda)

PubMed Central

Mateus, Octávio; Benson, Roger B.J.

2015-01-01

Diplodocidae are among the best known sauropod dinosaurs. Several species were described in the late 1800s or early 1900s from the Morrison Formation of North America. Since then, numerous additional specimens were recovered in the USA, Tanzania, Portugal, and Argentina, as well as possibly Spain, England, Georgia, Zimbabwe, and Asia. To date, the clade includes about 12 to 15 nominal species, some of them with questionable taxonomic status (e.g., ‘Diplodocus’ hayi or Dyslocosaurus polyonychius), and ranging in age from Late Jurassic to Early Cretaceous. However, intrageneric relationships of the iconic, multi-species genera Apatosaurus and Diplodocus are still poorly known. The way to resolve this issue is a specimen-based phylogenetic analysis, which has been previously implemented for Apatosaurus, but is here performed for the first time for the entire clade of Diplodocidae. The analysis includes 81 operational taxonomic units, 49 of which belong to Diplodocidae. The set of OTUs includes all name-bearing type specimens previously proposed to belong to Diplodocidae, alongside a set of relatively complete referred specimens, which increase the amount of anatomically overlapping material. Non-diplodocid outgroups were selected to test the affinities of potential diplodocid specimens that have subsequently been suggested to belong outside the clade. The specimens were scored for 477 morphological characters, representing one of the most extensive phylogenetic analyses of sauropod dinosaurs. Character states were figured and tables given in the case of numerical characters. The resulting cladogram recovers the classical arrangement of diplodocid relationships. Two numerical approaches were used to increase reproducibility in our taxonomic delimitation of species and genera. This resulted in the proposal that some species previously included in well-known genera like Apatosaurus and Diplodocus are generically distinct. Of particular note is that the famous genus Brontosaurus is considered valid by our quantitative approach. Furthermore, “Diplodocus” hayi represents a unique genus, which will herein be called Galeamopus gen. nov. On the other hand, these numerical approaches imply synonymization of “Dinheirosaurus” from the Late Jurassic of Portugal with the Morrison Formation genus Supersaurus. Our use of a specimen-, rather than species-based approach increases knowledge of intraspecific and intrageneric variation in diplodocids, and the study demonstrates how specimen-based phylogenetic analysis is a valuable tool in sauropod taxonomy, and potentially in paleontology and taxonomy as a whole. PMID:25870766

A phylogeny for the pomatiopsidae (Gastropoda: Rissooidea): a resource for taxonomic, parasitological and biodiversity studies

PubMed Central

2014-01-01

Background The Pomatiopsidae are reported from northern India into southern China and Southeast Asia, with two sub-families, the Pomatiopsinae (which include freshwater, amphibious, terrestrial and marine species) and the freshwater Triculinae. Both include species acting as intermediate host for species of the blood-fluke Schistosoma which cause a public health problem in East Asia. Also, with around 120 species, triculine biodiversity exceeds that of any other endemic freshwater molluscan fauna. Nevertheless, the origins of the Pomatiopsidae, the factors driving such a diverse radiation and aspects of their co-evolution with Schistosoma are not fully understood. Many taxonomic questions remain; there are problems identifying medically relevant species. The predicted range is mostly unsurveyed and the true biodiversity of the family is underestimated. Consequently, the aim of the study was to collect DNA-sequence data for as many pomatiopsid taxa as possible, as a first step in providing a resource for identification of epidemiologically significant species (by non-malacologists), for use in resolving taxonomic confusion and for testing phylogeographical hypotheses. Results The evolutionary radiation of the Triculinae was shown to have been rapid and mostly post late Miocene. Molecular dating indicated that the radiation of these snails was driven first by the uplift of the Himalaya and onset of a monsoon system, and then by late-Pliocene global warming. The status of Erhaia as Anmicolidae is supported. The genera Tricula and Neotricula are shown to be non-monophyletic and the tribe Jullieniini may be polyphyletic (based on convergent characters). Triculinae from northern Vietnam could be derived from Gammatricula of Fujian/Yunnan, China. Conclusions The molecular dates and phylogenetic estimates in this study are consistent with an Australasian origin for the Pomatiopsidae and an East to West radiation via Oligocene Borneo-Philippines island hopping to Japan and then China (Triculinae arising mid-Miocene in Southeast China), and less so with a triculine origin in Tibet. The lack of monophyly in the medically important genera and indications of taxonomic inaccuracies, call for further work to identify epidemiologically significant taxa (e.g., Halewisia may be potential hosts for Schistosoma mekongi) and highlight the need for surveys to determine the true biodiversity of the Triculinae. PMID:24548800

Automatic processing of semantic relations in fMRI: neural activation during semantic priming of taxonomic and thematic categories.

PubMed

Sachs, Olga; Weis, Susanne; Zellagui, Nadia; Huber, Walter; Zvyagintsev, Mikhail; Mathiak, Klaus; Kircher, Tilo

2008-07-07

Most current models of knowledge organization are based on hierarchical or taxonomic categories (animals, tools). Another important organizational pattern is thematic categorization, i.e. categories held together by external relations, a unifying scene or event (car and garage). The goal of this study was to compare the neural correlates of these categories under automatic processing conditions that minimize strategic influences. We used fMRI to examine neural correlates of semantic priming for category members with a short stimulus onset asynchrony (SOA) of 200 ms as subjects performed a lexical decision task. Four experimental conditions were compared: thematically related words (car-garage); taxonomically related (car-bus); unrelated (car-spoon); non-word trials (car-derf). We found faster reaction times for related than for unrelated prime-target pairs for both thematic and taxonomic categories. However, the size of the thematic priming effect was greater than that of the taxonomic. The imaging data showed signal changes for the taxonomic priming effects in the right precuneus, postcentral gyrus, middle frontal and superior frontal gyri and thematic priming effects in the right middle frontal gyrus and anterior cingulate. The contrast of neural priming effects showed larger signal changes in the right precuneus associated with the taxonomic but not with thematic priming response. We suggest that the greater involvement of precuneus in the processing of taxonomic relations indicates their reduced salience in the knowledge structure compared to more prominent thematic relations.

Designing Multimedia Games for Young Children's Taxonomic Concept Development

ERIC Educational Resources Information Center

Sung, Yao-Ting; Chang, Kuo-En; Lee, Meng-Da

2008-01-01

This study aimed to design and evaluate multimedia games which were based on the theories of children's development of taxonomic concepts. Factors that might affect children's classification skills, such as use of single physical characteristics of objects, competition between thematic and taxonomic relationships, difficulty in forming…

Preschool Children's Taxonomic Knowledge of Animal Species

ERIC Educational Resources Information Center

Allen, Michael

2015-01-01

Although taxonomic proficiency is a prerequisite for understanding ideas central to biology, previous research has established that learners frequently misclassify animals by not following the tenets of accepted taxonomic rubrics. This has immediate relevance with the recently revised English National Curriculum now requiring concepts of animal…

bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics

PubMed Central

Page, Roderic DM

2009-01-01

Background Linking together the data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) requires services that can mint, resolve, and discover globally unique identifiers (including, but not limited to, DOIs, HTTP URIs, and LSIDs). Results bioGUID implements a range of services, the core ones being an OpenURL resolver for bibliographic resources, and a LSID resolver. The LSID resolver supports Linked Data-friendly resolution using HTTP 303 redirects and content negotiation. Additional services include journal ISSN look-up, author name matching, and a tool to monitor the status of biodiversity data providers. Conclusion bioGUID is available at . Source code is available from . PMID:19900301

The taxonomic status of Petropedetes newtonii (Amphibia, Anura, Petropedetidae).

PubMed

Sánchez-Vialas, Alberto; Calvo-Revuelta, Marta; Castroviejo-Fisher, Santiago; la Riva, Ignacio De

2018-01-01

The taxon Petropedetes newtonii was described in 1895 by Bocage, from Bioko Island (Equatorial Guinea). This taxon, whose holotype is lost, has been misidentified since Boulenger's revision of the genus in 1900 and its relationships with other taxa ( P. vulpiae and P. johnstoni ) is confusing. Currently, P. newtonii is considered a synonym of P. johnstoni . In this work, by revising morphological characters of non-webbed Petropedetes of Bioko, we demonstrate the morphological singularity of these specimens with respect to P. johnstoni and P. vulpiae and their association with the name Petropedetes newtonii . Consequently, we provide the subsequent designation of a neotype of P. newtonii and revalidate this species from its synonym with P. johnstoni .

The Macrobiotus hufelandi group (Tardigrada) revisited.

PubMed

Kaczmarek, Łukasz; Michalczyk, Łukasz

2017-12-08

Species of the Macrobiotus hufelandi group are one of the most often recorded tardigrades throughout the globe. For over a century M. hufelandi has been considered cosmopolitan but in recent decades numerous species of similar morphologies have been described from various continents, which suggests that what was originally defined as a single taxon is, in fact, a complex of species. The definition of the hufelandi group is subject to a long-standing discussion and in this paper we propose a refined set of characters that are hoped to elucidate the taxonomic status of the group. In order to aid interspecific comparisons, we also propose a unified nomenclature for the crucial morphological traits and clar.

Phylogenetic relationships of Sonoran Desert cactus beetles in the tribe Hololeptini (Coleoptera: Histeridae: Histerinae), with comments on the taxonomic status of Iliotona beyeri.

PubMed

Pfeiler, Edward; Vergara-Quintanar, Joel E; Castrezana, Sergio; Caterino, Michael S; Markow, Therese A

2010-07-01

Nucleotide sequences from 16S rRNA and cytochrome c oxidase subunit I (COI) were used to examine phylogenetic relationships and evolution of beetles from the tribe Hololeptini (Coleoptera: Histeridae: Histerinae) that inhabit necrotic tissue of columnar cacti in the Sonoran Desert. Phylogenetic and morphological analyses revealed the presence of seven separate lineages, three representing species in the genus Iliotona, including I. beyeri stat. nov., and four species belonging to the genus Hololepta (sensu lato). The possible roles of historical vicariance and host plant associations on the evolution of the Hololeptini from the Sonoran Desert are discussed. Copyright 2010 Elsevier Inc. All rights reserved.

Taxonomic and floristic novelties for Echeveria (Crassulaceae) in Central Michoacan, Mexico

PubMed Central

García-Ruiz, Ignacio; Valentín-Martínez, Dagoberto; Carrillo-Reyes, Pablo; Costea, Mihai

2016-01-01

Abstract A new species, Echeveria coruana, is described and illustrated from the malpaís near San Andrés Corú, Michoacan, Mexico. The species belongs to series Gibbiflorae and the new taxon was compared with Echeveria purhepecha and Echeveria patriotica, with whom it shares the closest morphological affinities. Additionally, Echeveria yalmanantlaensis an endangered species from Sierra of Manantlán Biosphere Reserve, State of Colima, was also discovered near San Andrés Corú and is reported for the first time from the State of Michoacan. The conservation status of both species was (re)evaluated according to the criteria of the International Union for Conservation of Nature. PMID:28127240

A multilocus phylogeny of Malagasy scincid lizards elucidates the relationships of the fossorial genera Androngo and Cryptoscincus.

PubMed

Crottini, Angelica; Dordel, Janina; Köhler, Jörn; Glaw, Frank; Schmitz, Andreas; Vences, Miguel

2009-10-01

A phylogeny for 29 species of scincine lizards from Madagascar, based on 3693 bp of six mitochondrial and five nuclear genes, revealed multiple parallel evolution of adaptations for a burrowing life, and unexpected relationships of the monotypic genera Androngo and Cryptoscincus. Androngo trivittatus was sister to Pygomeles braconnieri, and Cryptoscincus minimus was deeply nested within the genus Paracontias, all of these being fossorial taxa of elongated bodies and partly or fully reduced limbs. To account for these results, we place Cryptoscincus as a junior synonym of Paracontias, and discuss possible taxonomic consequences that may affect the status of Androngo, once additional data become available.

Taxonomic and floristic novelties for Echeveria (Crassulaceae) in Central Michoacan, Mexico.

PubMed

García-Ruiz, Ignacio; Valentín-Martínez, Dagoberto; Carrillo-Reyes, Pablo; Costea, Mihai

2016-01-01

A new species, Echeveria coruana , is described and illustrated from the malpaís near San Andrés Corú, Michoacan, Mexico. The species belongs to series Gibbiflorae and the new taxon was compared with Echeveria purhepecha and Echeveria patriotica , with whom it shares the closest morphological affinities. Additionally, Echeveria yalmanantlaensis an endangered species from Sierra of Manantlán Biosphere Reserve, State of Colima, was also discovered near San Andrés Corú and is reported for the first time from the State of Michoacan. The conservation status of both species was (re)evaluated according to the criteria of the International Union for Conservation of Nature.

Integrating DNA barcode data and taxonomic practice: determination, discovery, and description.

PubMed

Goldstein, Paul Z; DeSalle, Rob

2011-02-01

DNA barcodes, like traditional sources of taxonomic information, are potentially powerful heuristics in the identification of described species but require mindful analytical interpretation. The role of DNA barcoding in generating hypotheses of new taxa in need of formal taxonomic treatment is discussed, and it is emphasized that the recursive process of character evaluation is both necessary and best served by understanding the empirical mechanics of the discovery process. These undertakings carry enormous ramifications not only for the translation of DNA sequence data into taxonomic information but also for our comprehension of the magnitude of species diversity and its disappearance. This paper examines the potential strengths and pitfalls of integrating DNA sequence data, specifically in the form of DNA barcodes as they are currently generated and analyzed, with taxonomic practice.

A taxonomic wish-list for community ecology.

PubMed Central

Gotelli, Nicholas J

2004-01-01

Community ecology seeks to explain the number and relative abundance of coexisting species. Four research frontiers in community ecology are closely tied to research in systematics and taxonomy: the statistics of species richness estimators, global patterns of biodiversity, the influence of global climate change on community structure, and phylogenetic influences on community structure. The most pressing needs for taxonomic information in community ecology research are usable taxonomic keys, current nomenclature, species occurrence records and resolved phylogenies. These products can best be obtained from Internet-based phylogenetic and taxonomic resources, but the lack of trained professional systematists and taxonomists threatens this effort. Community ecologists will benefit most directly from research in systematics and taxonomy by making better use of resources in museums and herbaria, and by actively seeking training, information and collaborations with taxonomic specialists. PMID:15253346

Identifying taxonomic and functional surrogates for spring biodiversity conservation.

PubMed

Jyväsjärvi, Jussi; Virtanen, Risto; Ilmonen, Jari; Paasivirta, Lauri; Muotka, Timo

2018-02-27

Surrogate approaches are widely used to estimate overall taxonomic diversity for conservation planning. Surrogate taxa are frequently selected based on rarity or charisma, whereas selection through statistical modeling has been applied rarely. We used boosted-regression-tree models (BRT) fitted to biological data from 165 springs to identify bryophyte and invertebrate surrogates for taxonomic and functional diversity of boreal springs. We focused on these 2 groups because they are well known and abundant in most boreal springs. The best indicators of taxonomic versus functional diversity differed. The bryophyte Bryum weigelii and the chironomid larva Paratrichocladius skirwithensis best indicated taxonomic diversity, whereas the isopod Asellus aquaticus and the chironomid Macropelopia spp. were the best surrogates of functional diversity. In a scoring algorithm for priority-site selection, taxonomic surrogates performed only slightly better than random selection for all spring-dwelling taxa, but they were very effective in representing spring specialists, providing a distinct improvement over random solutions. However, the surrogates for taxonomic diversity represented functional diversity poorly and vice versa. When combined with cross-taxon complementarity analyses, surrogate selection based on statistical modeling provides a promising approach for identifying groundwater-dependent ecosystems of special conservation value, a key requirement of the EU Water Framework Directive. © 2018 Society for Conservation Biology.

Biodiversity Analysis of Forest Litter Ant Assemblages in the Wayanad Region of Western Ghats Using Taxonomic and Conventional Diversity Measures

PubMed Central

Anu, Anto; Sabu, Thomas K.

2007-01-01

The diversity of litter ant assemblages in evergreen, deciduous and Shola evergreen (Shola) forest vegetation types of the Wayanad region of the Western Ghats was assessed employing conventional and taxonomic diversity indices. Non-dependence on quantitative data and the ability to relate the phylogenetic structure of assemblages with ecological conditions of the habitat, and to ascertain priorities for conservation of habitats, makes non-parametric taxonomic diversity measures, such as variation in taxonomic distinctness Λ+ and average taxonomic distinctness Δ+, highly useful tools for assessment of litter ant biodiversity. Although Δ+ values saturated leading to closer values for the 3 litter ant assemblages, Λ+ proved to be a more dependable index. Evenness in taxonomic spread was high in ant assemblages in deciduous forests and low in evergreen forests compared to the regional master list. Low Λ+ of ant assemblage in deciduous forests indicates that among the 3 forest vegetation types, deciduous forests provided the most favorable habitat conditions for litter ants. Low evenness, as is indicated by Λ+ in evergreen forests, was attributed to the presence of a group of taxonomically closely related ant assemblage more adapted to prevail in moist and wet ecological conditions. PMID:20334594

A review of insect parasitoids associated with Lobesia botrana (Denis & Schiffermüller, 1775) in Italy. 1. DipteraTachinidae and HymenopteraBraconidae (Lepidoptera, Tortricidae).

PubMed

Scaramozzino, Pier Luigi; Loni, Augusto; Lucchi, Andrea

2017-01-01

This paper is aimed to summarize the information available on the parasitoid complex of the European Grapevine Moth (EGVM), Lobesia botrana (Denis & Schiffermüller, 1775) (Lepidoptera Tortricidae) in Italy. The list is the result of the consultation of a vast bibliography published in Italy for almost two hundred years, from 1828 to date. This allowed the clarification and correction of misunderstandings and mistakes on the taxonomic position of each species listed. In Italy the complex of parasitoids detected on EGVM includes approximately 90 species belonging to ten families of Hymenoptera (Braconidae, Ichneumonidae, Chalcididae, Eulophidae, Eupelmidae, Eurytomidae, Pteromalidae, Torymidae, Trichogrammatidae, and Bethylidae) and one family of Diptera (Tachinidae). This paper deals with EGVM parasitoids of the families Tachinidae (Diptera) and Braconidae (Hymenoptera). Only two species of Tachinidae are associated to EGVM larvae in Italy, Actia pilipennis (Fallen) and Phytomyptera nigrina (Meigen), whereas the record of Eurysthaea scutellaris (Robineau-Desvoidy) is doubtful. Moreover, 21 species of Braconidae are reported to live on EGVM, but, unfortunately, eight of them were identified only at generic level. Bracon mellitor Say has been incorrectly listed among the parasitoids of Lobesia botrana . Records concerning Ascogaster rufidens Wesmael, Meteorus sp., Microgaster rufipes Nees, and Microplitis tuberculifer (Wesmael) are uncertain.

A review of insect parasitoids associated with Lobesia botrana (Denis & Schiffermüller, 1775) in Italy. 1. Diptera Tachinidae and Hymenoptera Braconidae (Lepidoptera, Tortricidae)

PubMed Central

Scaramozzino, Pier Luigi; Loni, Augusto; Lucchi, Andrea

2017-01-01

Abstract This paper is aimed to summarize the information available on the parasitoid complex of the European Grapevine Moth (EGVM), Lobesia botrana (Denis & Schiffermüller, 1775) (Lepidoptera Tortricidae) in Italy. The list is the result of the consultation of a vast bibliography published in Italy for almost two hundred years, from 1828 to date. This allowed the clarification and correction of misunderstandings and mistakes on the taxonomic position of each species listed. In Italy the complex of parasitoids detected on EGVM includes approximately 90 species belonging to ten families of Hymenoptera (Braconidae, Ichneumonidae, Chalcididae, Eulophidae, Eupelmidae, Eurytomidae, Pteromalidae, Torymidae, Trichogrammatidae, and Bethylidae) and one family of Diptera (Tachinidae). This paper deals with EGVM parasitoids of the families Tachinidae (Diptera) and Braconidae (Hymenoptera). Only two species of Tachinidae are associated to EGVM larvae in Italy, Actia pilipennis (Fallen) and Phytomyptera nigrina (Meigen), whereas the record of Eurysthaea scutellaris (Robineau-Desvoidy) is doubtful. Moreover, 21 species of Braconidae are reported to live on EGVM, but, unfortunately, eight of them were identified only at generic level. Bracon mellitor Say has been incorrectly listed among the parasitoids of Lobesia botrana. Records concerning Ascogaster rufidens Wesmael, Meteorus sp., Microgaster rufipes Nees, and Microplitis tuberculifer (Wesmael) are uncertain. PMID:28325964

Effect of smoking status on the efficacy of the SMART regimen in high risk asthma.

PubMed

Pilcher, Janine; Patel, Mitesh; Reddel, Helen K; Pritchard, Alison; Black, Peter; Shaw, Dominick; Holt, Shaun; Weatherall, Mark; Beasley, Richard

2016-07-01

The optimal management of people with asthma with a significant smoking history is uncertain. The aim of this study was to determine whether the efficacy/safety profile of single combination inhaled corticosteroid (ICS)/long acting beta-agonist (LABA) inhaler maintenance and reliever therapy is influenced by smoking status. We undertook secondary analyses from an open-label 24-week randomized study of 303 high risk adult asthma patients randomized to budesonide/formoterol 200/6-µg-metred dose inhaler for maintenance (two actuations twice daily) and either budesonide/formoterol 200/6-µg-metred dose inhaler one actuation ('single ICS/LABA maintenance and reliever therapy (SMART)' regimen) or salbutamol 100 µg 1-2 actuations for symptom relief ('Standard' regimen). Smoking status was classified in to three groups, as 'current', 'ex' or 'never', and a smoking/treatment interaction term tested for each outcome variable. The primary outcome variable was number of participants with at least one severe exacerbation. There were 59 current, 97 ex and 147 never smokers included in the analyses. The smoking status/treatment interaction term was not statistically significant for any of the outcome measures. With adjustment for smoking status, the number of participants with severe exacerbations was lower with the SMART regimen (OR 0.45, 95% CI: 0.26-0.77, P = 0.004; P value for interaction between smoking status and treatment 0.29). We conclude that the favourable safety/efficacy profile of the SMART regimen applies to patients with high risk asthma, irrespective of smoking status. © 2016 Asian Pacific Society of Respirology.

Sarcopenia Is Highly Prevalent in Older Medical Patients With Mobility Limitation.

PubMed

Maeda, Keisuke; Shamoto, Hiroshi; Wakabayashi, Hidetaka; Akagi, Junji

2017-02-01

The association of sarcopenia with disability with ambulatory status is uncertain because most studies have targeted people who could walk independently. This study explored the prevalence of sarcopenia regardless of ambulatory status and the impact of ambulatory status on sarcopenia. In total, 778 consecutive patients, aged ≥65 years and admitted to a hospital, were enrolled. Ambulatory status was divided into 4 grades according to mobility as described in the Barthel index. Sarcopenia was defined as a loss of appendicular muscle mass index (AMI) with bioelectrical impedance and decreased muscle strength with handgrip strength (HGS); cutoff values were adopted from the Asian Working Group for Sarcopenia. The mean patient age was 83.2 ± 8.3 years; 37.8% were male patients. Mobility limitation was associated with higher age, underweight body mass index, malnourishment, and comorbidities (all P < .001). AMI and HGS gradually decreased with declining ambulatory status ( P < .001). The prevalence of sarcopenia in the independent walk, walk with help, wheelchair, and immobile groups was 57.9%, 76.1%, 89.4%, and 91.7%, respectively. AMI prevalence declined and sarcopenia drastically increased in patients who were unable to walk independently compared with those who could walk independently ( P < .001). Multivariate regression analyses showed that mobility limitation was an independent indicator of decreasing AMI and sarcopenia after adjustment for confounders. Patients with dependent ambulatory status experienced a higher prevalence of sarcopenia compared with those with ambulation; in addition, decline in ambulatory status was an independent indicator for the presence of sarcopenia after adjustment for potential confounders.

Individual differences in the strength of taxonomic versus thematic relations

PubMed Central

Mirman, Daniel; Graziano, Kristen M.

2011-01-01

Knowledge about word and object meanings can be organized taxonomically (fruits, mammals, etc.) based on shared features, or thematically (eating breakfast, taking a dog for a walk, etc.) based on participation in events or scenarios. An eye-tracking study showed that both kinds of knowledge are activated during comprehension of a single spoken word, even when the listener is not required to perform any active task. The results further revealed that an individual’s relative activation of taxonomic relations compared to thematic relations predicts that individual’s tendency to favor taxonomic over thematic relations when asked to choose between them in a similarity judgment task. These results argue that individuals differ in the relative strengths of their taxonomic and thematic semantic knowledge and suggest that meaning information is organized in two parallel, complementary semantic systems. PMID:22201413

Parasite biodiversity and its determinants in coastal marine teleost fishes of Brazil.

PubMed

Luque, J L; Mouillot, D; Poulin, R

2004-06-01

Recent studies of the forces behind the diversification of parasite assemblages have shed light on many aspects of parasite biodiversity. By using only parasite species richness as their measure of diversity, however, previous investigations have ignored the relatedness among parasite species and the taxonomic structure of the assemblages, which contain much information about their evolutionary origins. Here, we performed a comparative analysis across 50 species of fish from the coast of Brazil; we evaluated the effects of several host traits (body size, social behaviour, feeding habits, preference for benthic vs. pelagic habitats, depth range, and ability to enter brackish waters) on the diversity of their assemblages of metazoan parasites. As measures of diversity, we used parasite species richness, as well as the average taxonomic distinctness of the assemblage and its variance; the latter measures are based on the average taxonomic distance between any two parasite species in an assemblage. Unlike parasite species richness, taxonomic distinctness was unaffected by the number of host individuals examined per species. Fish body length proved to be the main predictor of parasite species richness, even when controlling for the confounding influences of host phylogeny and sampling effort, although it did not correlate with measures of parasite taxonomic distinctness. Predatory fish also had higher parasite species richness than planktivores, but this trend could not be confirmed using phylogenetically independent contrasts between host taxa. The main host feature associated with the taxonomic diversity of parasites was schooling behaviour, with schooling fish having more taxonomically diverse parasite assemblages than those of their non-schooling relatives. When focusing on endoparasite species only, both predatory feeding habits and a broad depth range were associated with the taxonomic distinctness of parasites. Our results suggest that certain host traits (i.e. body size) determine how many parasite species a host can accumulate over evolutionary time, whereas different host features influence the processes causing the taxonomic diversification of parasite assemblages.

Two Influential Primate Classifications Logically Aligned

PubMed Central

Franz, Nico M.; Pier, Naomi M.; Reeder, Deeann M.; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2016-01-01

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2–317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3–483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments—in the sense of the same name identifying congruent taxonomic meanings. The RCC-5 alignment approach is potentially widely applicable in systematics and can achieve scalable, precise resolution of semantically evolving name usages in synthetic, next-generation biodiversity, and phylogeny data platforms. PMID:27009895

NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean.

PubMed

Pagliosa, Paulo R; Doria, João G; Misturini, Dairana; Otegui, Mariana B P; Oortman, Mariana S; Weis, Wilson A; Faroni-Perez, Larisse; Alves, Alexandre P; Camargo, Maurício G; Amaral, A Cecília Z; Marques, Antonio C; Lana, Paulo C

2014-01-01

Networks can greatly advance data sharing attitudes by providing organized and useful data sets on marine biodiversity in a friendly and shared scientific environment. NONATObase, the interactive database on polychaetes presented herein, will provide new macroecological and taxonomic insights of the Southwestern Atlantic region. The database was developed by the NONATO network, a team of South American researchers, who integrated available information on polychaetes from between 5°N and 80°S in the Atlantic Ocean and near the Antarctic. The guiding principle of the database is to keep free and open access to data based on partnerships. Its architecture consists of a relational database integrated in the MySQL and PHP framework. Its web application allows access to the data from three different directions: species (qualitative data), abundance (quantitative data) and data set (reference data). The database has built-in functionality, such as the filter of data on user-defined taxonomic levels, characteristics of site, sample, sampler, and mesh size used. Considering that there are still many taxonomic issues related to poorly known regional fauna, a scientific committee was created to work out consistent solutions to current misidentifications and equivocal taxonomy status of some species. Expertise from this committee will be incorporated by NONATObase continually. The use of quantitative data was possible by standardization of a sample unit. All data, maps of distribution and references from a data set or a specified query can be visualized and exported to a commonly used data format in statistical analysis or reference manager software. The NONATO network has initialized with NONATObase, a valuable resource for marine ecologists and taxonomists. The database is expected to grow in functionality as it comes in useful, particularly regarding the challenges of dealing with molecular genetic data and tools to assess the effects of global environment change. Database URL: http://nonatobase.ufsc.br/.

Microbial community profiling of fresh basil and pitfalls in taxonomic assignment of enterobacterial pathogenic species based upon 16S rRNA amplicon sequencing.

PubMed

Ceuppens, Siele; De Coninck, Dieter; Bottledoorn, Nadine; Van Nieuwerburgh, Filip; Uyttendaele, Mieke

2017-09-18

Application of 16S rRNA (gene) amplicon sequencing on food samples is increasingly applied for assessing microbial diversity but may as unintended advantage also enable simultaneous detection of any human pathogens without a priori definition. In the present study high-throughput next-generation sequencing (NGS) of the V1-V2-V3 regions of the 16S rRNA gene was applied to identify the bacteria present on fresh basil leaves. However, results were strongly impacted by variations in the bioinformatics analysis pipelines (MEGAN, SILVAngs, QIIME and MG-RAST), including the database choice (Greengenes, RDP and M5RNA) and the annotation algorithm (best hit, representative hit and lowest common ancestor). The use of pipelines with default parameters will lead to discrepancies. The estimate of microbial diversity of fresh basil using 16S rRNA (gene) amplicon sequencing is thus indicative but subject to biases. Salmonella enterica was detected at low frequencies, between 0.1% and 0.4% of bacterial sequences, corresponding with 37 to 166 reads. However, this result was dependent upon the pipeline used: Salmonella was detected by MEGAN, SILVAngs and MG-RAST, but not by QIIME. Confirmation of Salmonella sequences by real-time PCR was unsuccessful. It was shown that taxonomic resolution obtained from the short (500bp) sequence reads of the 16S rRNA gene containing the hypervariable regions V1-V3 cannot allow distinction of Salmonella with closely related enterobacterial species. In conclusion 16S amplicon sequencing, getting the status of standard method in microbial ecology studies of foods, needs expertise on both bioinformatics and microbiology for analysis of results. It is a powerful tool to estimate bacterial diversity but amenable to biases. Limitations concerning taxonomic resolution for some bacterial species or its inability to detect sub-dominant (pathogenic) species should be acknowledged in order to avoid overinterpretation of results. Copyright © 2017 Elsevier B.V. All rights reserved.

Borrelia burgdorferi Sensu Lato Spirochetes in Wild Birds in Northwestern California: Associations with Ecological Factors, Bird Behavior and Tick Infestation

PubMed Central

Newman, Erica A.; Eisen, Lars; Eisen, Rebecca J.; Fedorova, Natalia; Hasty, Jeomhee M.; Vaughn, Charles; Lane, Robert S.

2015-01-01

Although Borrelia burgdorferi sensu lato (s.l.) are found in a great diversity of vertebrates, most studies in North America have focused on the role of mammals as spirochete reservoir hosts. We investigated the roles of birds as hosts for subadult Ixodes pacificus ticks and potential reservoirs of the Lyme disease spirochete B. burgdorferi sensu stricto (s.s.) in northwestern California. Overall, 623 birds representing 53 species yielded 284 I. pacificus larvae and nymphs. We used generalized linear models and zero-inflated negative binomial models to determine associations of bird behaviors, taxonomic relationships and infestation by I. pacificus with borrelial infection in the birds. Infection status in birds was best explained by taxonomic order, number of infesting nymphs, sampling year, and log-transformed average body weight. Presence and counts of larvae and nymphs could be predicted by ground- or bark-foraging behavior and contact with dense oak woodland. Molecular analysis yielded the first reported detection of Borrelia bissettii in birds. Moreover, our data suggest that the Golden-crowned Sparrow (Zonotrichia atricapilla), a non-resident species, could be an important reservoir for B. burgdorferi s.s. Of 12 individual birds (9 species) that carried B. burgdorferi s.l.-infected larvae, no birds carried the same genospecies of B. burgdorferi s.l. in their blood as were present in the infected larvae removed from them. Possible reasons for this discrepancy are discussed. Our study is the first to explicitly incorporate both taxonomic relationships and behaviors as predictor variables to identify putative avian reservoirs of B. burgdorferi s.l. Our findings underscore the importance of bird behavior to explain local tick infestation and Borrelia infection in these animals, and suggest the potential for bird-mediated geographic spread of vector ticks and spirochetes in the far-western United States. PMID:25714376

NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean

PubMed Central

Pagliosa, Paulo R.; Doria, João G.; Misturini, Dairana; Otegui, Mariana B. P.; Oortman, Mariana S.; Weis, Wilson A.; Faroni-Perez, Larisse; Alves, Alexandre P.; Camargo, Maurício G.; Amaral, A. Cecília Z.; Marques, Antonio C.; Lana, Paulo C.

2014-01-01

Networks can greatly advance data sharing attitudes by providing organized and useful data sets on marine biodiversity in a friendly and shared scientific environment. NONATObase, the interactive database on polychaetes presented herein, will provide new macroecological and taxonomic insights of the Southwestern Atlantic region. The database was developed by the NONATO network, a team of South American researchers, who integrated available information on polychaetes from between 5°N and 80°S in the Atlantic Ocean and near the Antarctic. The guiding principle of the database is to keep free and open access to data based on partnerships. Its architecture consists of a relational database integrated in the MySQL and PHP framework. Its web application allows access to the data from three different directions: species (qualitative data), abundance (quantitative data) and data set (reference data). The database has built-in functionality, such as the filter of data on user-defined taxonomic levels, characteristics of site, sample, sampler, and mesh size used. Considering that there are still many taxonomic issues related to poorly known regional fauna, a scientific committee was created to work out consistent solutions to current misidentifications and equivocal taxonomy status of some species. Expertise from this committee will be incorporated by NONATObase continually. The use of quantitative data was possible by standardization of a sample unit. All data, maps of distribution and references from a data set or a specified query can be visualized and exported to a commonly used data format in statistical analysis or reference manager software. The NONATO network has initialized with NONATObase, a valuable resource for marine ecologists and taxonomists. The database is expected to grow in functionality as it comes in useful, particularly regarding the challenges of dealing with molecular genetic data and tools to assess the effects of global environment change. Database URL: http://nonatobase.ufsc.br/ PMID:24573879

[Use of multiple locus variable number tandem repeats analysis for the Brucella systematization].

PubMed

Kulakov, Iu K; Kovalev, D A; Misetova, E N; Golovneva, S I; Liapustina, L V; Zheludkov, M M

2012-01-01

The methods of molecular-genetic differentiation to strain level acquire increasing significance in the current system of struggle with brucellosis. MLVA (multiple locus variable number tandem repeats analysis) was selected for molecular-genetic differentiation to strain level and simultaneous establishment of the genetic relationship of investigated Brucella strains. The goal of this work was MLVA typing of three pathogenic Brucella species strains with the analysis of stability of chosen loci, discrimination power and concordance to conventional phenotypic methods of the Brucella differentiation for use in systematization of brucellosis causing agents. Twenty six Brucella strains representing reference (n = 15), vaccine (n = 2) and field strains of three pathogenic Brucella species were tested: B. melitensis (n = 3), B. abortus (n = 2), B. suis (n = 2), and isolates (n = 2) with unidentified taxonomic position using MLVA with 9 pairs primers on known variable loci of Brucella genome. The analysis of the stability of chosen loci, discrimination power on Hunter-Gaston discrimination index (HGDI) and consistency to phenotypic methods of identification was performed. MLVA was confirmed for the results of phenotypic methods of identification, stability of the chosen loci in majority reference, and vaccine strains with a high index of variability HGDI 0.9969 for all loci. A dendrogram was plotted on the basis of MLVA data on distributed Brucella strains in related clusters according to its taxonomic species and biovar positions and construction of 25 genotypes. B. melitensis strains formed cluster related to the reference strain of B. melitensis 63/9 biovar 2. Australian isolates of Brucella 83-4 and Brucella 83-6 isolated from rodents formed a cluster distant from other strains of Brucella. MLVA is a promising method for differentiation of Brucella strains with known and unresolved taxonomic status for their systematization and creation of MLVA genotype catalogue that will promote qualitative improvement of brucellosis surveillance system in Russia.

Borrelia burgdorferi sensu lato spirochetes in wild birds in northwestern California: associations with ecological factors, bird behavior and tick infestation.

PubMed

Newman, Erica A; Eisen, Lars; Eisen, Rebecca J; Fedorova, Natalia; Hasty, Jeomhee M; Vaughn, Charles; Lane, Robert S

2015-01-01

Although Borrelia burgdorferi sensu lato (s.l.) are found in a great diversity of vertebrates, most studies in North America have focused on the role of mammals as spirochete reservoir hosts. We investigated the roles of birds as hosts for subadult Ixodes pacificus ticks and potential reservoirs of the Lyme disease spirochete B. burgdorferi sensu stricto (s.s.) in northwestern California. Overall, 623 birds representing 53 species yielded 284 I. pacificus larvae and nymphs. We used generalized linear models and zero-inflated negative binomial models to determine associations of bird behaviors, taxonomic relationships and infestation by I. pacificus with borrelial infection in the birds. Infection status in birds was best explained by taxonomic order, number of infesting nymphs, sampling year, and log-transformed average body weight. Presence and counts of larvae and nymphs could be predicted by ground- or bark-foraging behavior and contact with dense oak woodland. Molecular analysis yielded the first reported detection of Borrelia bissettii in birds. Moreover, our data suggest that the Golden-crowned Sparrow (Zonotrichia atricapilla), a non-resident species, could be an important reservoir for B. burgdorferi s.s. Of 12 individual birds (9 species) that carried B. burgdorferi s.l.-infected larvae, no birds carried the same genospecies of B. burgdorferi s.l. in their blood as were present in the infected larvae removed from them. Possible reasons for this discrepancy are discussed. Our study is the first to explicitly incorporate both taxonomic relationships and behaviors as predictor variables to identify putative avian reservoirs of B. burgdorferi s.l. Our findings underscore the importance of bird behavior to explain local tick infestation and Borrelia infection in these animals, and suggest the potential for bird-mediated geographic spread of vector ticks and spirochetes in the far-western United States.

Status of women in India: a comparison by state.

PubMed

Devi, D R

1993-12-01

Reformers in India have worked since the late 19th century to abolish practices such as the patriarchal joint-family system, the structure of property ownership, early marriage, and the self-immolation of widows which have been detrimental to the development of women. As a result, independent India has taken steps to protect the rights and equality of women. In order to analyze the objective status of women, secondary data were used to make 1) interstate comparisons, 2) intrastate comparisons with the status of men, and 3) comparisons in relation to overall development. Data from the early 1980s were analyzed from the 14 states which had a population of 10 million or more. 7 variables describe educational status, 3 are employment indicators, 2 are health indicators, 3 are demographic indicators, and 13 represent various aspects of development. The taxonomic method designed by Polish mathematicians in 1952 was used to rank states on the basis of each of the indicators. This method allows the determination of homogeneous units in an n-dimensional space without using such statistical tools as regression, variance, and correlation. It was found that the status indicators resulted in similar rankings for males and females in many states, but that in some states (Orissa, Madhya Pradesh, Bihar, and Uttar Pradesh) the health, employment, and educational status of women is low. These states also show a low ranking in overall development status, thus highlighting the direct link between the status of women and the level of development. This study leads to the question of whether women's status can be studied at the macro level using macro-level data. If this is possible, then the lack of significant differences found in the present study either indicates that the indicators chosen did not reveal the differences or that, in fact, no differences exist. The observed direct link between ranks of development and status, however, indicates that what was read as status differences are simply differences in levels of development. In depth studies which focus on the self-perceptions of status of men and women as compared with macro-level analyses will be necessary to answer this question.

Conservation Genetics of a Critically Endangered Limpet Genus and Rediscovery of an Extinct Species

PubMed Central

Ó Foighil, Diarmaid; Li, Jingchun; Lee, Taehwan; Johnson, Paul; Evans, Ryan; Burch, John B.

2011-01-01

Background A third of all known freshwater mollusk extinctions worldwide have occurred within a single medium-sized American drainage. The Mobile River Basin (MRB) of Alabama, a global hotspot of temperate freshwater biodiversity, was intensively industrialized during the 20th century, driving 47 of its 139 endemic mollusk species to extinction. These include the ancylinid limpet Rhodacmea filosa, currently classified as extinct (IUCN Red List), a member of a critically endangered southeastern North American genus reduced to a single known extant population (of R. elatior) in the MRB. Methodology/Principal Findings We document here the tripling of known extant populations of this North American limpet genus with the rediscovery of enduring Rhodacmea filosa in a MRB tributary and of R. elatior in its type locality: the Green River, Kentucky, an Ohio River Basin (ORB) tributary. Rhodacmea species are diagnosed using untested conchological traits and we reassessed their systematic and conservation status across both basins using morphometric and genetic characters. Our data corroborated the taxonomic validity of Rhodacmea filosa and we inferred a within-MRB cladogenic origin from a common ancestor bearing the R. elatior shell phenotype. The geographically-isolated MRB and ORB R. elatior populations formed a cryptic species complex: although overlapping morphometrically, they exhibited a pronounced phylogenetic disjunction that greatly exceeded that of within-MRB R. elatior and R. filosa sister species. Conclusions/Significance Rhodacmea filosa, the type species of the genus, is not extinct. It persists in a Coosa River tributary and morphometric and phylogenetic analyses confirm its taxonomic validity. All three surviving populations of the genus Rhodacmea merit specific status. They collectively contain all known survivors of a phylogenetically highly distinctive North American endemic genus and therefore represent a concentrated fraction of continental freshwater gastropod biodiversity. We recommend the establishment of a proactive targeted conservation program that may include their captive propagation and reintroduction. PMID:21655221

Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade

PubMed Central

Lo, Pei-Chun; Liu, Shu-Hui; Nor, Siti Azizah Mohd

2017-01-01

The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene—Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a revision of Nibea and proposed a new genus Pseudolarimichthys. PMID:28453569

Linking benthic biodiversity and environmental conditions at the sea floor combining statistical and mechanistic modeling. Case study on the Black Sea's northwestern shelf.

NASA Astrophysics Data System (ADS)

Drion, Roxanne; Capet, Arthur; Gregoire, Marilaure

2014-05-01

The preservation of the health and biodiversity of benthic ecosystems is a crucial priority in order to achieve the Good Environmental Status (GES) of marine waters. The multiple pressures acting on the ocean, and in particular, on the coastal zone may prevent the maintenance of biodiversity either directly (e.g. trawling, dredging) or indirectly by modifying environmental conditions at the sea floor (e.g. eutrophication, pollution, acidification, warming). The management of the GES of the benthos in a changing environment and the definition of management strategies (e.g. nutrient reduction) that would preserve GES require tools able to predict the modifications of environmental conditions and to link these modifications to the status of the benthic system. Coupled biogeochemical-circulation models provide a large amount of information on physical (e.g. currents, salinity, temperature, shear stress) and biochemical conditions (e.g. oxygen, inorganic nutrients, sinking detritus) but cannot provide an information on species richness. We propose to link these aspects by applying canonical ordination techniques (e.g. Redundancy Analysis, CoInertia Analysis) on a large data set on macrobenthos collected on the Black Sea's north-western shelf with in-situ sediment data (e.g. granulometry, carbon and nitrogen content, C/N ratio, CaCO3 content) and bottom conditions (e.g. shear stress, level of oxygen stress, flux of organic matter to the sediments) provided by a three dimensional model. Beyond taxonomic description, the analysis is performed on the functional composition of the macrobenthos: A trait-based approach is used to assess the functional composition of the macrobenthos by associating the considered species to a list of biological, ecological and behavioral traits. This approach allows to appraise how local conditions determine the functional and taxonomical diversity and provides a mean to evaluate the impact of habitat alteration on the ecological role of benthic assemblages. A particular attention is given to the influence of seasonal hypoxia on benthic biotopes composition.

Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade.

PubMed

Lo, Pei-Chun; Liu, Shu-Hui; Nor, Siti Azizah Mohd; Chen, Wei-Jen

2017-01-01

The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a revision of Nibea and proposed a new genus Pseudolarimichthys.

Panamanian frog species host unique skin bacterial communities

PubMed Central

Belden, Lisa K.; Hughey, Myra C.; Rebollar, Eria A.; Umile, Thomas P.; Loftus, Stephen C.; Burzynski, Elizabeth A.; Minbiole, Kevin P. C.; House, Leanna L.; Jensen, Roderick V.; Becker, Matthew H.; Walke, Jenifer B.; Medina, Daniel; Ibáñez, Roberto; Harris, Reid N.

2015-01-01

Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd), that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species) community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26%) were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in these skin symbiont microbial systems as it is in many macro-systems. PMID:26579083

Conservation genetics of a critically endangered limpet genus and rediscovery of an extinct species.

PubMed

Ó Foighil, Diarmaid; Li, Jingchun; Lee, Taehwan; Johnson, Paul; Evans, Ryan; Burch, John B

2011-01-01

A third of all known freshwater mollusk extinctions worldwide have occurred within a single medium-sized American drainage. The Mobile River Basin (MRB) of Alabama, a global hotspot of temperate freshwater biodiversity, was intensively industrialized during the 20(th) century, driving 47 of its 139 endemic mollusk species to extinction. These include the ancylinid limpet Rhodacmea filosa, currently classified as extinct (IUCN Red List), a member of a critically endangered southeastern North American genus reduced to a single known extant population (of R. elatior) in the MRB. We document here the tripling of known extant populations of this North American limpet genus with the rediscovery of enduring Rhodacmea filosa in a MRB tributary and of R. elatior in its type locality: the Green River, Kentucky, an Ohio River Basin (ORB) tributary. Rhodacmea species are diagnosed using untested conchological traits and we reassessed their systematic and conservation status across both basins using morphometric and genetic characters. Our data corroborated the taxonomic validity of Rhodacmea filosa and we inferred a within-MRB cladogenic origin from a common ancestor bearing the R. elatior shell phenotype. The geographically-isolated MRB and ORB R. elatior populations formed a cryptic species complex: although overlapping morphometrically, they exhibited a pronounced phylogenetic disjunction that greatly exceeded that of within-MRB R. elatior and R. filosa sister species. Rhodacmea filosa, the type species of the genus, is not extinct. It persists in a Coosa River tributary and morphometric and phylogenetic analyses confirm its taxonomic validity. All three surviving populations of the genus Rhodacmea merit specific status. They collectively contain all known survivors of a phylogenetically highly distinctive North American endemic genus and therefore represent a concentrated fraction of continental freshwater gastropod biodiversity. We recommend the establishment of a proactive targeted conservation program that may include their captive propagation and reintroduction.

The Taxonomic Status of Mazama bricenii and the Significance of the Táchira Depression for Mammalian Endemism in the Cordillera de Mérida, Venezuela

PubMed Central

Gutiérrez, Eliécer E.; Maldonado, Jesús E.; Radosavljevic, Aleksandar; Molinari, Jesús; Patterson, Bruce D.; Martínez-C., Juan M.; Rutter, Amy R.; Hawkins, Melissa T. R.; Garcia, Franger J.; Helgen, Kristofer M.

2015-01-01

We studied the taxonomy and biogeography of Mazama bricenii, a brocket deer classified as Vulnerable by the IUCN, drawing on qualitative and quantitative morphology and sequences of the mitochondrial cytochrome-b gene. We used Ecological Niche Modeling (ENM) to evaluate the hypothesis that M. bricenii of the Venezuelan Cordillera de Mérida (CM) might have become isolated from populations of its putative sister species, Mazama rufina, in the Colombian Cordillera Oriental (CO). This hypothesis assumes that warm, dry climatic conditions in the Táchira Depression were unsuitable for the species. Our analyses did not reveal morphological differences between specimens geographically attributable to M. bricenii and M. rufina, and phylogenetic analyses of molecular data recovered M. bricenii nested within the diversity of M. rufina. These results indicate that M. bricenii should be regarded as a junior synonym of M. rufina. ENM analyses revealed the existence of suitable climatic conditions for M. rufina in the Táchira Depression during the last glacial maximum and even at present, suggesting that gene flow between populations in the CO and CM may have occurred until at least the beginning of the current interglacial period and may continue today. Because this pattern might characterize other mammals currently considered endemic to the CM, we examined which of these species match two criteria that we propose herein to estimate if they can be regarded as endemic to the CM with confidence: (1) that morphological or molecular evidence exists indicating that the putative endemic taxon is distinctive from congeneric populations in the CO; and (2) that the putative endemic taxon is restricted to either cloud forest or páramo, or both. Only Aepeomys reigi, Cryptotis meridensis, and Nasuella meridensis matched both criteria; hence, additional research is necessary to assess the true taxonomic status and distribution of the remaining species thought to be CM endemics. PMID:26121688

The Taxonomic Status of Mazama bricenii and the Significance of the Táchira Depression for Mammalian Endemism in the Cordillera de Mérida, Venezuela.

PubMed

Gutiérrez, Eliécer E; Maldonado, Jesús E; Radosavljevic, Aleksandar; Molinari, Jesús; Patterson, Bruce D; Martínez-C, Juan M; Rutter, Amy R; Hawkins, Melissa T R; Garcia, Franger J; Helgen, Kristofer M

2015-01-01

We studied the taxonomy and biogeography of Mazama bricenii, a brocket deer classified as Vulnerable by the IUCN, drawing on qualitative and quantitative morphology and sequences of the mitochondrial cytochrome-b gene. We used Ecological Niche Modeling (ENM) to evaluate the hypothesis that M. bricenii of the Venezuelan Cordillera de Mérida (CM) might have become isolated from populations of its putative sister species, Mazama rufina, in the Colombian Cordillera Oriental (CO). This hypothesis assumes that warm, dry climatic conditions in the Táchira Depression were unsuitable for the species. Our analyses did not reveal morphological differences between specimens geographically attributable to M. bricenii and M. rufina, and phylogenetic analyses of molecular data recovered M. bricenii nested within the diversity of M. rufina. These results indicate that M. bricenii should be regarded as a junior synonym of M. rufina. ENM analyses revealed the existence of suitable climatic conditions for M. rufina in the Táchira Depression during the last glacial maximum and even at present, suggesting that gene flow between populations in the CO and CM may have occurred until at least the beginning of the current interglacial period and may continue today. Because this pattern might characterize other mammals currently considered endemic to the CM, we examined which of these species match two criteria that we propose herein to estimate if they can be regarded as endemic to the CM with confidence: (1) that morphological or molecular evidence exists indicating that the putative endemic taxon is distinctive from congeneric populations in the CO; and (2) that the putative endemic taxon is restricted to either cloud forest or páramo, or both. Only Aepeomys reigi, Cryptotis meridensis, and Nasuella meridensis matched both criteria; hence, additional research is necessary to assess the true taxonomic status and distribution of the remaining species thought to be CM endemics.

Polysemy and the Taxonomic Constraint: Children's Representation of Words That Label Multiple Kinds

ERIC Educational Resources Information Center

Srinivasan, Mahesh; Snedeker, Jesse

2014-01-01

How do children resolve the problem of indeterminacy when learning a new word? By one account, children adopt a "taxonomic assumption" and expect the word to denote only members of a particular taxonomic category. According to one version of this constraint, young children should represent polysemous words that label multiple kinds--for…

Uncertain translation, uncertain benefit and uncertain risk: ethical challenges facing first-in-human trials of induced pluripotent stem (ips) cells.

PubMed

Fung, Ronald K F; Kerridge, Ian H

2013-02-01

The discovery of induced pluripotent stem (iPS) cells in 2006 was heralded as a major breakthrough in stem cell research. Since then, progress in iPS cell technology has paved the way towards clinical application, particularly cell replacement therapy, which has refueled debate on the ethics of stem cell research. However, much of the discourse has focused on questions of moral status and potentiality, overlooking the ethical issues which are introduced by the clinical testing of iPS cell replacement therapy. First-in-human trials, in particular, raise a number of ethical concerns including informed consent, subject recruitment and harm minimisation as well as the inherent uncertainty and risks which are involved in testing medical procedures on humans for the first time. These issues, while a feature of any human research, become more complex in the case of iPS cell therapy, given the seriousness of the potential risks, the unreliability of available animal models, the vulnerability of the target patient group, and the high stakes of such an intensely public area of science. Our paper will present a detailed case study of iPS cell replacement therapy for Parkinson's disease to highlight these broader ethical and epistemological concerns. If we accept that iPS cell technology is fraught with challenges which go far beyond merely refuting the potentiality of the stem cell line, we conclude that iPS cell research should not replace, but proceed alongside embryonic and adult somatic stem cell research to promote cross-fertilisation of knowledge and better clinical outcomes. © 2011 Blackwell Publishing Ltd.

Selection of multiple umbrella species for functional and taxonomic diversity to represent urban biodiversity.

PubMed

Sattler, T; Pezzatti, G B; Nobis, M P; Obrist, M K; Roth, T; Moretti, M

2014-04-01

Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty-one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within- and across-taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity. © 2013 Society for Conservation Biology.

Deaf and hard of hearing adolescents' processing of pictures and written words for taxonomic categories in a priming task of semantic categorization.

PubMed

Li, Degao; Gao, Kejuan; Wu, Xueyun; Chen, Xiaojun; Zhang, Xiaona; Li, Ling; He, Weiwei

2013-01-01

Inspired by research by Li, Yi, and Kim (2011), the authors examined Chinese deaf and hard of hearing adolescents' responses to pictures for taxonomic categories of basic level (exemplar pictures) preceded by exemplar pictures, and to written words for taxonomic categories of basic level (exemplar words) preceded by exemplar words or by written words for those of superordinate level (category names), in a priming task of semantic categorization. Stimulus onset asynchrony (SOA) was manipulated. The adolescents were less aware of taxonomic relations and were more likely to show the advantage of pictures over written words than their hearing counterparts. Their processing of exemplar primes steadily deepened as SOA increased, reaching its deepest level when SOA was 237 ms. Their processing of category names seemed immune to changes in SOA, probably because of their fuzzy representations of taxonomic categories of superordinate level.

Does intolerance of uncertainty predict anticipatory startle responses to uncertain threat?

PubMed

Nelson, Brady D; Shankman, Stewart A

2011-08-01

Intolerance of uncertainty (IU) has been proposed to be an important maintaining factor in several anxiety disorders, including generalized anxiety disorder, obsessive-compulsive disorder, and social phobia. While IU has been shown to predict subjective ratings and decision-making during uncertain/ambiguous situations, few studies have examined whether IU also predicts emotional responding to uncertain threat. The present study examined whether IU predicted aversive responding (startle and subjective ratings) during the anticipation of temporally uncertain shocks. Sixty-nine participants completed three experimental conditions during which they received: no shocks, temporally certain/predictable shocks, and temporally uncertain shocks. Results indicated that IU was negatively associated with startle during the uncertain threat condition in that those with higher IU had a smaller startle response. IU was also only related to startle during the uncertain (and not the certain/predictable) threat condition, suggesting that it was not predictive of general aversive responding, but specific to responses to uncertain aversiveness. Perceived control over anxiety-related events mediated the relation between IU and startle to uncertain threat, such that high IU led to lowered perceived control, which in turn led to a smaller startle response. We discuss several potential explanations for these findings, including the inhibitory qualities of IU. Overall, our results suggest that IU is associated with attenuated aversive responding to uncertain threat. Copyright © 2011 Elsevier B.V. All rights reserved.

Math Attendees Find There's Life After Fermat Proof.

PubMed

Cipra, B

1994-02-04

The uncertain status of the recent proof of Fermat's Last Theorem (Science, 24 December 1993, p. 1967) was the hot topic in the hallways at the joint meetings of the American Mathematical Society and the Mathematical Association of America, held 12-15 January in Cincinnati. But a few other topics did manage to get discussed. Among them: How gambling pays off in computing the volume of high-dimensional shapes; how a mathematical description of water dripping down a window pane might lead to the design of digital pulses that could race through the optical fibers of the future; and how one can be fooled infinitely often by another theorem of Fermat's.

Citizens and scientists: toward a gendered history of scientific practice in post-revolutionary France.

PubMed

Harrison, C E

2001-01-01

Because the French Revolution failed to produce a widely acceptable definition of citizenship, the limits of manhood suffrage in the early nineteenth century were uncertain. Social practices, in particular scientific activity, served as claims to the status of citizen. By engaging in scientific pastimes, bourgeois Frenchmen asserted that they possessed the rationality and autonomy that liberal theorists associated both with manliness and with civic capacity. However, bourgeois science was never a stable signifier of masculinity or of competence. As professional science emerged, the bourgeois amateur increasingly became the feminised object of satire rather than the sober and meritorious citizen-scientist.

How Family Status and Social Security Claiming Options Shape Optimal Life Cycle Portfolios

PubMed Central

Hubener, Andreas; Maurer, Raimond; Mitchell, Olivia S.

2017-01-01

We show how optimal household decisions regarding work, retirement, saving, portfolio allocations, and life insurance are shaped by the complex financial options embedded in U.S. Social Security rules and uncertain family transitions. Our life cycle model predicts sharp consumption drops on retirement, an age-62 peak in claiming rates, and earlier claiming by wives versus husbands and single women. Moreover, life insurance is mainly purchased on men’s lives. Our model, which takes Social Security rules seriously, generates wealth and retirement outcomes that are more consistent with the data, in contrast to earlier and less realistic models. PMID:28659659

Diversified Microbiota of Meconium Is Affected by Maternal Diabetes Status

PubMed Central

Hu, Jianzhong; Nomura, Yoko; Bashir, Ali; Fernandez-Hernandez, Heriberto; Itzkowitz, Steven; Pei, Zhiheng; Stone, Joanne; Loudon, Holly; Peter, Inga

2013-01-01

Objectives This study was aimed to assess the diversity of the meconium microbiome and determine if the bacterial community is affected by maternal diabetes status. Methods The first intestinal discharge (meconium) was collected from 23 newborns stratified by maternal diabetes status: 4 mothers had pre-gestational type 2 diabetes mellitus (DM) including one mother with dizygotic twins, 5 developed gestational diabetes mellitus (GDM) and 13 had no diabetes. The meconium microbiome was profiled using multi-barcode 16S rRNA sequencing followed by taxonomic assignment and diversity analysis. Results All meconium samples were not sterile and contained diversified microbiota. Compared with adult feces, the meconium showed a lower species diversity, higher sample-to-sample variation, and enrichment of Proteobacteria and reduction of Bacteroidetes. Among the meconium samples, the taxonomy analyses suggested that the overall bacterial content significantly differed by maternal diabetes status, with the microbiome of the DM group showing higher alpha-diversity than that of no-diabetes or GDM groups. No global difference was found between babies delivered vaginally versus via Cesarean-section. Regression analysis showed that the most robust predictor for the meconium microbiota composition was the maternal diabetes status that preceded pregnancy. Specifically, Bacteroidetes (phyla) and Parabacteriodes (genus) were enriched in the meconium in the DM group compared to the no-diabetes group. Conclusions Our study provides evidence that meconium contains diversified microbiota and is not affected by the mode of delivery. It also suggests that the meconium microbiome of infants born to mothers with DM is enriched for the same bacterial taxa as those reported in the fecal microbiome of adult DM patients. PMID:24223144

The mammalian faunas endemic to the Cerrado and the Caatinga.

PubMed

Gutiérrez, Eliécer E; Marinho-Filho, Jader

2017-01-01

We undertook a comprehensive, critical review of literature concerning the distribution, conservation status, and taxonomy of species of mammals endemic to the Cerrado and the Caatinga, the two largest biomes of the South American Dry-Diagonal. We present species accounts and lists of species, which we built with criteria that, in our opinion, yielded results with increased scientific rigor relative to previously published lists - e.g., excluding nominal taxa whose statuses as species have been claimed only on the basis of unpublished data, incomplete taxonomic work, or weak evidence. For various taxa, we provided arguments regarding species distributions, conservation and taxonomic statuses previously lacking in the literature. Two major findings are worth highlighting. First, we unveil the existence of a group of species endemic to both the Cerrado and the Caatinga (i.e., present in both biomes and absent in all other biomes). From the biogeographic point of view, this group, herein referred to as Caatinga-Cerrado endemics, deserves attention as a unit - just as in case of the Caatinga-only and the Cerrado-only endemics. We present preliminary hypotheses on the origin of these three endemic faunas (Cerrado-only, Caatinga-only, and Caatinga-Cerrado endemics). Secondly, we discovered that a substantial portion of the endemic mammalian faunas of the Caatinga and the Cerrado faces risks of extinction that are unrecognized in the highly influential Red List of Threatened Species published by the International Union for Conservation of Nature (IUCN). "Data deficient" is a category that misrepresents the real risks of extinction of these species considering that (a) some of these species are known only from a handful of specimens collected in a single or a few localities long ago; (b) the Cerrado and the Caatinga have been sufficiently sampled to guarantee collection of additional specimens of these species if they were abundant; (c) natural habitats of the Cerrado and the Caatinga have been substantially altered or lost in recent decades. Failures either in the design of the IUCN criteria or in their application to assign categories of extinction risks represent an additional important threat to these endemic faunas because their real risks of extinctions become hidden. It is imperative to correct this situation, particularly considering that these species are associated to habitats that are experiencing fast transformation into areas for agriculture, at an unbearable cost for biodiversity.

The mammalian faunas endemic to the Cerrado and the Caatinga

PubMed Central

Gutiérrez, Eliécer E.; Marinho-Filho, Jader

2017-01-01

Abstract We undertook a comprehensive, critical review of literature concerning the distribution, conservation status, and taxonomy of species of mammals endemic to the Cerrado and the Caatinga, the two largest biomes of the South American Dry-Diagonal. We present species accounts and lists of species, which we built with criteria that, in our opinion, yielded results with increased scientific rigor relative to previously published lists – e.g., excluding nominal taxa whose statuses as species have been claimed only on the basis of unpublished data, incomplete taxonomic work, or weak evidence. For various taxa, we provided arguments regarding species distributions, conservation and taxonomic statuses previously lacking in the literature. Two major findings are worth highlighting. First, we unveil the existence of a group of species endemic to both the Cerrado and the Caatinga (i.e., present in both biomes and absent in all other biomes). From the biogeographic point of view, this group, herein referred to as Caatinga-Cerrado endemics, deserves attention as a unit – just as in case of the Caatinga-only and the Cerrado-only endemics. We present preliminary hypotheses on the origin of these three endemic faunas (Cerrado-only, Caatinga-only, and Caatinga-Cerrado endemics). Secondly, we discovered that a substantial portion of the endemic mammalian faunas of the Caatinga and the Cerrado faces risks of extinction that are unrecognized in the highly influential Red List of Threatened Species published by the International Union for Conservation of Nature (IUCN). “Data deficient” is a category that misrepresents the real risks of extinction of these species considering that (a) some of these species are known only from a handful of specimens collected in a single or a few localities long ago; (b) the Cerrado and the Caatinga have been sufficiently sampled to guarantee collection of additional specimens of these species if they were abundant; (c) natural habitats of the Cerrado and the Caatinga have been substantially altered or lost in recent decades. Failures either in the design of the IUCN criteria or in their application to assign categories of extinction risks represent an additional important threat to these endemic faunas because their real risks of extinctions become hidden. It is imperative to correct this situation, particularly considering that these species are associated to habitats that are experiencing fast transformation into areas for agriculture, at an unbearable cost for biodiversity. PMID:28144187

The Integrated Impact of Diet on Human Immune Response, the Gut Microbiota, and Nutritional Status During Adaptation to a Spaceflight Analog

NASA Technical Reports Server (NTRS)

Douglas, G. L.; Zwart, S. R.; Young, M.; Kloeris, V.; Crucian, B.; Smith, S. M.; Lorenzi, H.

2018-01-01

Spaceflight impacts human physiology, including well documented immune system dysregulation. Diet, immune function, and the microbiome are interlinked, but diet is the only one of these factors that we have the ability to easily, and significantly, alter on Earth or during flight. As we understand dietary impacts on physiology more thoroughly, we may then improve the spaceflight diet to improve crew health and potentially reduce spaceflight-associated physiological alterations. It is expected that increasing the consumption of fruits and vegetables and bioactive compounds (e.g., omega-3 fatty acids, lycopene, flavonoids) and therefore enhancing overall nutritional intake from the nominal shelf-stable, fully-processed space food system could serve as a countermeasure to improve human immunological profiles, the taxonomic profile of the gut microbiota, and nutritional status, especially where currently dysregulated during spaceflight. This interdisciplinary study will determine the effect of the current shelf-stable spaceflight diet compared to an "enhanced" shelf-stable spaceflight diet (25% more foods rich in omega-3 fatty acids, lycopene, flavonoids, and more fruits, and vegetables in general). The NASA Human Exploration Research Analog (HERA) 2017 missions, consisting of four 45-day missions with closed chamber confinement and realistic mission simulation in a high-fidelity mock space vehicle, will serve as a platform to replicate mission stressors and the effects on crew biochemistry, immunology, and the gut microbiome. Bio sampling of crewmembers is scheduled for selected intervals pre- and in-mission. Data collection also includes dietary intake recording. Outcome measures will include immune markers (e.g., peripheral leukocyte distribution, inflammatory cytokine profiles, T cell function), the taxonomic and metatranscriptomic profile of the gut microbiome, and nutritional status biomarkers and metabolites. Statistical evaluations will determine physiological and biochemical shifts in relation to nutrient intake and study phase. To date, sample collection has been completed for 2 crewmembers from the first mission, aka Campaign 4 Mission 1. Mission 2 was terminated after 22 days due to effects of Hurricane Harvey, and sample collection was not completed. Sample collection will continue for Campaign 4 Mission 3 and 4 prior to comprehensive sample analysis. Beneficial improvements will provide evidence of the impact of diet on crew health and adaptation to this spaceflight analog, and will aid in the design and development of more-efficient targeted dietary interventions for exploration missions.

Piglet nasal microbiota at weaning may influence the development of Glässer's disease during the rearing period.

PubMed

Correa-Fiz, Florencia; Fraile, Lorenzo; Aragon, Virginia

2016-05-26

The microbiota, the ensemble of microorganisms on a particular body site, has been extensively studied during the last few years, and demonstrated to influence the development of many diseases. However, these studies focused mainly on the human digestive system, while the populations in the respiratory tract have been poorly assessed, especially in pigs. The nasal mucosa of piglets is colonized by an array of bacteria, many of which are unknown. Among the early colonizers, Haemophilus parasuis also has clinical importance, since it is also the etiological agent of Glässer's disease. This disease produces economical losses in all the countries with pig production, and the factors influencing its development are not totally understood. Hence, the purpose of this work was to characterize the nasal microbiota composition of piglets, and its possible role in Glässer's disease development. Seven farms from Spain (4 with Glässer's disease and 3 control farms without any respiratory disease) and three farms from UK (all control farms) were studied. Ten piglets from each farm were sampled at 3-4 weeks of age before weaning. The total DNA extracted from nasal swabs was used to amplify the 16S RNA gene for sequencing in Illumina MiSeq. Sequencing data was quality filtered and analyzed using QIIME software. The diversity of the nasal microbiota was low in comparison with other body sites, showing a maximum number of operational taxonomic units (OTUs) per pig of 1,603, clustered in five phyla. Significant differences were found at various taxonomical levels, when the microbiota was compared regarding the farm health status. Healthy status was associated to higher species richness and diversity, and UK farms demonstrated the highest diversity. The composition of the nasal microbiota of healthy piglets was uncovered and different phylotypes were shown to be significantly altered in animals depending on the clinical status of the farm of origin. Several OTUs at genus level were identified over-represented in piglets from control farms, indicating their potential as probiotics. Although we provide relevant data, fully metagenomic approaches could give light on the genes and metabolic pathways involved in the roles of the nasal microbiota to prevent respiratory diseases.

Lineage-specific responses of microbial communities to environmental change.

PubMed

Youngblut, Nicholas D; Shade, Ashley; Read, Jordan S; McMahon, Katherine D; Whitaker, Rachel J

2013-01-01

A great challenge facing microbial ecology is how to define ecologically relevant taxonomic units. To address this challenge, we investigated how changing the definition of operational taxonomic units (OTUs) influences the perception of ecological patterns in microbial communities as they respond to a dramatic environmental change. We used pyrosequenced tags of the bacterial V2 16S rRNA region, as well as clone libraries constructed from the cytochrome oxidase C gene ccoN, to provide additional taxonomic resolution for the common freshwater genus Polynucleobacter. At the most highly resolved taxonomic scale, we show that distinct genotypes associated with the abundant Polynucleobacter lineages exhibit divergent spatial patterns and dramatic changes over time, while the also abundant Actinobacteria OTUs are highly coherent. This clearly demonstrates that different bacterial lineages demand different taxonomic definitions to capture ecological patterns. Based on the temporal distribution of highly resolved taxa in the hypolimnion, we demonstrate that change in the population structure of a single genotype can provide additional insight into the mechanisms of community-level responses. These results highlight the importance and feasibility of examining ecological change in microbial communities across taxonomic scales while also providing valuable insight into the ecological characteristics of ecologically coherent groups in this system.

Low Functional β-Diversity Despite High Taxonomic β-Diversity among Tropical Estuarine Fish Communities

PubMed Central

Villéger, Sébastien; Miranda, Julia Ramos; Hernandez, Domingo Flores; Mouillot, David

2012-01-01

The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic and functional β-diversity among tropical estuarine fish communities, through space and time. We found extremely low functional β-diversity values among fish communities (<1.5%) despite high dissimilarity in species composition and species dominance. Additionally, in contrast to the high α and γ taxonomic diversities, α and γ functional diversities were very close to the minimal value. These patterns were caused by two dominant functional groups which maintained a similar functional structure over space and time, despite the strong dissimilarity in taxonomic structure along environmental gradients. Our findings suggest that taxonomic and functional β-diversity deserve to be quantified simultaneously since these two facets can show contrasting patterns and the differences can in turn shed light on community assembly rules. PMID:22792395

Taxonomic bias in biodiversity data and societal preferences.

PubMed

Troudet, Julien; Grandcolas, Philippe; Blin, Amandine; Vignes-Lebbe, Régine; Legendre, Frédéric

2017-08-22

Studying and protecting each and every living species on Earth is a major challenge of the 21 st century. Yet, most species remain unknown or unstudied, while others attract most of the public, scientific and government attention. Although known to be detrimental, this taxonomic bias continues to be pervasive in the scientific literature, but is still poorly studied and understood. Here, we used 626 million occurrences from the Global Biodiversity Information Facility (GBIF), the biggest biodiversity data portal, to characterize the taxonomic bias in biodiversity data. We also investigated how societal preferences and taxonomic research relate to biodiversity data gathering. For each species belonging to 24 taxonomic classes, we used the number of publications from Web of Science and the number of web pages from Bing searches to approximate research activity and societal preferences. Our results show that societal preferences, rather than research activity, strongly correlate with taxonomic bias, which lead us to assert that scientists should advertise less charismatic species and develop societal initiatives (e.g. citizen science) that specifically target neglected organisms. Ensuring that biodiversity is representatively sampled while this is still possible is an urgent prerequisite for achieving efficient conservation plans and a global understanding of our surrounding environment.

Zooplankton taxonomic and size diversity in Mediterranean coastal lagoons (NE Iberian Peninsula): Influence of hydrology, nutrient composition, food resource availability and predation

NASA Astrophysics Data System (ADS)

Badosa, Anna; Boix, Dani; Brucet, Sandra; López-Flores, Rocío; Gascón, Stéphanie; Quintana, Xavier D.

2007-01-01

The influence of hydrology, nutrient composition, food resource availability and predation on zooplankton taxonomic and size diversity was analyzed in several shallow lagoons of a Mediterranean salt marsh (Baix Ter Wetlands, NE Iberian Peninsula). Taxonomic diversity correlated better with variables related to the trophic state, such as nutrient concentrations, whereas size diversity was more sensitive to fish predation. However, the fish predation influence on the size diversity was only significant when fishes reached high densities. Under low fish densities no predation effects were observed and the food resource availability (FR a) appeared to be more important in structuring the zooplankton community. Nevertheless, the two diversity indexes showed opposite responses to this factor. With increasing FR a the taxonomic diversity increased and the size diversity decreased. Neither taxonomic nor size diversity of the zooplankton community correlated with other physical or biotic factors such as hydrological variability or macroinvertebrate predation. The relationships found suggest that the size diversity is mainly related to biotic interactions, such as fish predation or inter/intraspecific competition, while the taxonomic diversity appears to be more sensitive to abiotic factors such as the nutrient composition.

Cerulean Warbler Occurrence Atlas for Military Installations

DTIC Science & Technology

2010-04-01

Army Ammuniton Plant (Closed) IN NO 2009 Army IOWA ARMY AMMUNITION PLANT IA UNCERTAIN 2009 USACE J. Percy Priest Lake TN UNCERTAIN 2009 USACE J...Stonewall Jackson Lake WV UNCERTAIN 2009 USACE Summersville Lake WV no POC Army Sunflower Army Ammunition Plant KS no POC USACE Sutton Lake WV UNCERTAIN

The molecular systematics of blowflies and screwworm flies (Diptera: Calliphoridae) using 28S rRNA, COX1 and EF-1α: insights into the evolution of dipteran parasitism.

PubMed

McDonagh, Laura M; Stevens, Jamie R

2011-11-01

The Calliphoridae include some of the most economically significant myiasis-causing flies in the world - blowflies and screwworm flies - with many being notorious for their parasitism of livestock. However, despite more than 50 years of research, key taxonomic relationships within the family remain unresolved. This study utilizes nucleotide sequence data from the protein-coding genes COX1 (mitochondrial) and EF1α (nuclear), and the 28S rRNA (nuclear) gene, from 57 blowfly taxa to improve resolution of key evolutionary relationships within the family Calliphoridae. Bayesian phylogenetic inference was carried out for each single-gene data set, demonstrating significant topological difference between the three gene trees. Nevertheless, all gene trees supported a Calliphorinae-Luciliinae subfamily sister-lineage, with respect to Chrysomyinae. In addition, this study also elucidates the taxonomic and evolutionary status of several less well-studied groups, including the genus Bengalia (either within Calliphoridae or as a separate sister-family), genus Onesia (as a sister-genera to, or sub-genera within, Calliphora), genus Dyscritomyia and Lucilia bufonivora, a specialised parasite of frogs and toads. The occurrence of cross-species hybridisation within Calliphoridae is also further explored, focusing on the two economically significant species Lucilia cuprina and Lucilia sericata. In summary, this study represents the most comprehensive molecular phylogenetic analysis of family Calliphoridae undertaken to date.

Morphological and molecular taxonomic analysis of Pseudopoda Jäger, 2000 (Araneae: Sparassidae: Heteropodinae) in Sichuan Province, China.

PubMed

Jäger, Peter; Li, Shuqiang; Krehenwinkel, Henrik

2015-08-11

The genus Pseudopoda Jäger, 2000 is revised from material collected in Sichuan province. A molecular analysis shows the utility of DNA markers to support taxonomic hypotheses in Sparassidae. Two new species are described: Pseudopoda coenobium spec. nov. from Emeishan (male, female) and Pseudopoda wu spec. nov. from Lugu Lake at the border to Yunnan (male, female). The latter species exhibits a unique reduction of the conductor and a strongly developed embolus. The female of Pseudopoda virgata (Fox, 1936) is described for the first time, the male is redescribed, the known range of the geographical distribution is considerably extended to the East (Baoxing and Tienqiang County), the vertical distribution range is extended from 300 m to slightly more than 2000 m. The male of Pseudopoda signata Jäger, 2001 is described for the first time, the female is redescribed, the known distribution range of this species is extended from Muge Cuo Lake over Kangding town to the valleys of Paomashan, Gonggashan and Yanzi. It shows a strong morphological variation, which may be interpreted as developing subspecies status in different valleys. However, according to results from a molecular analysis it is clearly considered intraspecific variability. Three further species are recorded from Sichuan: Pseudopoda emei Zhang et al., 2013, Pseudopoda sp. cf. yunnanensis (Yang & Hu, 2001) and Pseudopoda rivicola Jäger and Vedel, 2007.

Morphology and taxonomic status of two little-known nematode species parasitizing North American fishes.

PubMed

Moravec, František; Levron, Céline; de Buron, Isaure

2011-04-01

Examination of some freshwater and brackishwater (estuarine) fishes in South Carolina in October 2009 yielded, in addition to other parasites, 2 little-known nematode species identified as Dichelyne fastigatus Chandler, 1935 (Cucullanidae), from the red drum, Sciaenops ocellatus (Linnaeus), from an estuary, and Rhabdochona ovifilamenta Weller, 1938 (Rhabdochonidae), from the shorthead redhorse, Moxostoma macrolepidotum (Lesueur), from Lake Moultrie. Light and scanning electron microscopy (the latter used for the first time for these species) made it possible to describe several important, but previously unreported, taxonomic features in D. fastigatus, such as the location of the excretory pore and deirids, the shape of deirids and a gubernaculum, the shape and size of eggs, the presence of precloacal ventral oblique muscle bands, and 11 pairs of caudal papillae and a pair of phasmids. It distinctly differs from the most similar Dichelyne cotylophora (Ward and Magath, 1917), a parasite of North American freshwater percids, in the number and arrangement of postanal papillae and by a markedly elevated cloacal region. Records of Dichelyne lintoni Barreto, 1922, from S. ocellatus probably concern D. fastigatus. Examination of R. ovifilamenta revealed a high degree of morphologic and biometric variability in this species. Based on our analysis, Rhabdochona laurentiana Lyster, 1940 , Rhabdochona milleri Choquette, 1951, and Rhabdochona catostomi Kayton, Kritsky, and Tobias, 1979, are synonymized with R. ovifilamenta Weller, 1938, typically a parasite of North American catostomids.

Re-examination of the taxonomic status of Enterobacter helveticus, Enterobacter pulveris and Enterobacter turicensis as members of the genus Cronobacter and their reclassification in the genera Franconibacter gen. nov. and Siccibacter gen. nov. as Franconibacter helveticus comb. nov., Franconibacter pulveris comb. nov. and Siccibacter turicensis comb. nov., respectively.

PubMed

Stephan, Roger; Grim, Christopher J; Gopinath, Gopal R; Mammel, Mark K; Sathyamoorthy, Venugopal; Trach, Larisa H; Chase, Hannah R; Fanning, Séamus; Tall, Ben D

2014-10-01

Recently, a taxonomical re-evaluation of the genus Enterobacter, based on multi-locus sequence typing (MLST) analysis, has led to the proposal that the species Enterobacter pulveris, Enterobacter helveticus and Enterobacter turicensis should be reclassified as novel species of the genus Cronobacter. In the present work, new genome-scale analyses, including average nucleotide identity, genome-scale phylogeny and k-mer analysis, coupled with previously reported DNA-DNA hybridization values and biochemical characterization strongly indicate that these three species of the genus Enterobacter are not members of the genus Cronobacter, nor do they belong to the re-evaluated genus Enterobacter. Furthermore, data from this polyphasic study indicated that all three species constitute two new genera. We propose reclassifying Enterobacter pulveris and Enterobacter helveticus in the genus Franconibacter gen. nov. as Franconibacter pulveris comb. nov. (type strain 601/05(T) = LMG 24057(T) = DSM 19144(T)) and Franconibacter helveticus comb. nov. (type strain 513/05(T) = LMG 23732(T) = DSM 18396(T)), respectively, and Enterobacter turicensis in the genus Siccibacter gen. nov. as Siccibacter turicensis comb. nov. (type strain 508/05(T) = LMG 23730(T) = DSM 18397(T)).

Revising the recent evolutionary history of equids using ancient DNA.

PubMed

Orlando, Ludovic; Metcalf, Jessica L; Alberdi, Maria T; Telles-Antunes, Miguel; Bonjean, Dominique; Otte, Marcel; Martin, Fabiana; Eisenmann, Véra; Mashkour, Marjan; Morello, Flavia; Prado, Jose L; Salas-Gismondi, Rodolfo; Shockey, Bruce J; Wrinn, Patrick J; Vasil'ev, Sergei K; Ovodov, Nikolai D; Cherry, Michael I; Hopwood, Blair; Male, Dean; Austin, Jeremy J; Hänni, Catherine; Cooper, Alan

2009-12-22

The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.

The Diversity-Weighted Living Planet Index: Controlling for Taxonomic Bias in a Global Biodiversity Indicator.

PubMed

McRae, Louise; Deinet, Stefanie; Freeman, Robin

2017-01-01

As threats to species continue to increase, precise and unbiased measures of the impact these pressures are having on global biodiversity are urgently needed. Some existing indicators of the status and trends of biodiversity largely rely on publicly available data from the scientific and grey literature, and are therefore prone to biases introduced through over-representation of well-studied groups and regions in monitoring schemes. This can give misleading estimates of biodiversity trends. Here, we report on an approach to tackle taxonomic and geographic bias in one such indicator (Living Planet Index) by accounting for the estimated number of species within biogeographical realms, and the relative diversity of species within them. Based on a proportionally weighted index, we estimate a global population decline in vertebrate species between 1970 and 2012 of 58% rather than 20% from an index with no proportional weighting. From this data set, comprising 14,152 populations of 3,706 species from 3,095 data sources, we also find that freshwater populations have declined by 81%, marine populations by 36%, and terrestrial populations by 38% when using proportional weighting (compared to trends of -46%, +12% and +15% respectively). These results not only show starker declines than previously estimated, but suggests that those species for which there is poorer data coverage may be declining more rapidly.

The Diversity-Weighted Living Planet Index: Controlling for Taxonomic Bias in a Global Biodiversity Indicator

PubMed Central

Deinet, Stefanie; Freeman, Robin

2017-01-01

As threats to species continue to increase, precise and unbiased measures of the impact these pressures are having on global biodiversity are urgently needed. Some existing indicators of the status and trends of biodiversity largely rely on publicly available data from the scientific and grey literature, and are therefore prone to biases introduced through over-representation of well-studied groups and regions in monitoring schemes. This can give misleading estimates of biodiversity trends. Here, we report on an approach to tackle taxonomic and geographic bias in one such indicator (Living Planet Index) by accounting for the estimated number of species within biogeographical realms, and the relative diversity of species within them. Based on a proportionally weighted index, we estimate a global population decline in vertebrate species between 1970 and 2012 of 58% rather than 20% from an index with no proportional weighting. From this data set, comprising 14,152 populations of 3,706 species from 3,095 data sources, we also find that freshwater populations have declined by 81%, marine populations by 36%, and terrestrial populations by 38% when using proportional weighting (compared to trends of -46%, +12% and +15% respectively). These results not only show starker declines than previously estimated, but suggests that those species for which there is poorer data coverage may be declining more rapidly. PMID:28045977

Snake venomics of the pit vipers Porthidium nasutum, Porthidium ophryomegas, and Cerrophidion godmani from Costa Rica: toxicological and taxonomical insights.

PubMed

Lomonte, Bruno; Rey-Suárez, Paola; Tsai, Wan-Chih; Angulo, Yamileth; Sasa, Mahmood; Gutiérrez, José María; Calvete, Juan J

2012-02-16

Within the Neotropical pit vipers, a lineage of primarily Middle American snake species referred to as the "Porthidium group" includes the genera Atropoides, Cerrophidion, and Porthidium. In this study, the venom proteomes of Porthidium nasutum, P. ophryomegas, and Cerrophidion godmani from Costa Rica were analyzed, and correlated to their toxic and enzymatic activities. Their HPLC profiles revealed a higher similarity between the two Porthidium species than between these and C. godmani. Proteins belonging to nine (P. nasutum), eight (P. ophryomegas), and nine (C. godmani) families were identified by mass spectrometry or N-terminal sequencing. Final cataloging of proteins and their relative abundances confirmed the close relationship between venoms of P. nasutum and P. ophryomegas, departing from that of C. godmani. Since the latter species had been taxonomically classified as Porthidium godmani previously, our venomic analyses agree with its current generic status. Venoms of P. nasutum and P. ophryomegas, despite containing abundant metalloproteinases and serine proteinases, lack procoagulant activity on human plasma, in contrast to venom of C. godmani. The latter induced strong myotoxicity in mice, which correlates with its high proportion of phospholipases A(2), whereas venoms from the two Porthidium species, containing lower amounts of these enzymes, induced only mild muscle damage. Copyright © 2011 Elsevier B.V. All rights reserved.

Lactobacillus curtus sp. nov., isolated from beer in Finland.

PubMed

Asakawa, Yuki; Takesue, Nobuchika; Asano, Shizuka; Shimotsu, Satoshi; Iijima, Kazumaru; Suzuki, Koji; Motoyama, Yasuo; Aizawa, Masayuki

2017-10-01

A Gram-stain-positive, catalase-negative and short-rod-shaped organism, designated VTT E-94560, was isolated from beer in Finland and deposited in the VTT culture collection as a strain of Lactobacillus rossiae. However, the results of 16S rRNA gene sequence analysis showed that VTT E-94560 was only related to Lactobacillus rossiae JCM 16176 T with 97.0 % sequence similarity, lower than the 98.7 % regarded as the boundary for the species differentiation. Additional phylogenetic studies on the pheS gene, rpoA gene and 16S-23S rRNA internally transcribed spacer region further reinforced the taxonomically independent status of VTT E-94560 and its related Lactobacillus species including L. rossiae and Lactobacillus siliginis. Strain VTT E-94560 also exhibited several differences in its carbohydrate fermentation profiles from those related Lactobacillus species. In addition, DNA-DNA relatedness between VTT E-94560 and these two type strains was 4 % (L. rossiae JCM 16176 T ) and 12 % (L. siliginins JCM 16155 T ), respectively, which were lower than the 70 % cut-off for general species delineation, indicating that these three strains are not taxonomically identical at the species level. These studies revealed that VTT E-94560 represents a novel species, for which the name Lactobacillus curtus sp. nov. is proposed. The type strain is VTT E-94560 T (=JCM 31185 T ).

Re-examination of the taxonomic status of Enterobacter helveticus, Enterobacter pulveris and Enterobacter turicensis as members of the genus Cronobacter and their reclassification in the genera Franconibacter gen. nov. and Siccibacter gen. nov. as Franconibacter helveticus comb. nov., Franconibacter pulveris comb. nov. and Siccibacter turicensis comb. nov., respectively

PubMed Central

Grim, Christopher J.; Gopinath, Gopal R.; Mammel, Mark K.; Sathyamoorthy, Venugopal; Trach, Larisa H.; Chase, Hannah R.; Fanning, Séamus; Tall, Ben D.

2014-01-01

Recently, a taxonomical re-evaluation of the genus Enterobacter, based on multi-locus sequence typing (MLST) analysis, has led to the proposal that the species Enterobacter pulveris, Enterobacter helveticus and Enterobacter turicensis should be reclassified as novel species of the genus Cronobacter. In the present work, new genome-scale analyses, including average nucleotide identity, genome-scale phylogeny and k-mer analysis, coupled with previously reported DNA–DNA hybridization values and biochemical characterization strongly indicate that these three species of the genus Enterobacter are not members of the genus Cronobacter, nor do they belong to the re-evaluated genus Enterobacter. Furthermore, data from this polyphasic study indicated that all three species constitute two new genera. We propose reclassifying Enterobacter pulveris and Enterobacter helveticus in the genus Franconibacter gen. nov. as Franconibacter pulveris comb. nov. (type strain 601/05T = LMG 24057T = DSM 19144T) and Franconibacter helveticus comb. nov. (type strain 513/05T = LMG 23732T = DSM 18396T), respectively, and Enterobacter turicensis in the genus Siccibacter gen. nov. as Siccibacter turicensis comb. nov. (type strain 508/05T = LMG 23730T = DSM 18397T). PMID:25028159

Pelagodinium gen. nov. and P. béii comb. nov., a dinoflagellate symbiont of planktonic foraminifera.

PubMed

Siano, Raffaele; Montresor, Marina; Probert, Ian; Not, Fabrice; de Vargas, Colomban

2010-07-01

The taxonomic status of the free-living stage of the dinoflagellate Gymnodinium béii, symbiont of the foraminifer Orbulina universa, was reassessed on the basis of detailed morpho-genetic analyses. Electron microscopy observations revealed previously undescribed morphological features of the cell that are important for species recognition. The presence of a single elongated apical vesicle (EAV) ornamented with a row of small knobs, absent in species of the genus Gymnodinium, calls into question the current taxonomic position of the symbiont. The presence of a type E extraplastidial eyespot, the arrangement of the amphiesmal vesicles in series and the absence of trichocysts confirm the affiliation with other symbiotic dinoflagellates and certain genetically related non-symbiotic genera, all belonging to the order Suessiales. The arrangement of the series of vesicles of the analyzed strain is unique within the Suessiales, and the ultrastructure of the pyrenoid is different from other symbiotic dinoflagellates. A large subunit (LSU) rDNA phylogenetic analysis confirmed that the analyzed pelagic symbiont clusters in an independent, well-supported clade within the Suessiales with other sequences of symbiotic dinoflagellates extracted from planktonic foraminifera. Hence a novel genus, Pelagodinium gen. nov., is erected for this pelagic, symbiotic dinoflagellate, and Gymnodinium béii is reclassified as Pelagodinium béii. 2010 Elsevier GmbH. All rights reserved.

DNA barcoding of Iberian Peninsula and North Africa Tawny Owls Strix aluco suggests the Strait of Gibraltar as an important barrier for phylogeography.

PubMed

Doña, Jorge; Ruiz-Ruano, Francisco J; Jovani, Roger

2016-11-01

Eight subspecies have been proposed within the Tawny Owl (Strix aluco) species. However, recent molecular data have challenged this view, encouraging further work in this species complex. Here we reevaluated the taxonomic status between the North-Western African Tawny Owl, S. a. mauritanica, and its closest Iberian Tawny Owl population (from the S. a. sylvatica to S. a. aluco clade) separated by the Strait of Gibraltar. The Tawny Owl is a non-migratory and territorial species, and juvenile dispersal is restricted to a few kilometers around the natal site. This limited dispersal and the barrier imposed by the Strait of Gibraltar predicted a strong differentiation between the two populations. We tested this using DNA barcoding, Bayesian phylogenetic and species delimitation analysis. We found that an 81.1% of variation is due to the intergroups variation. In addition, the inter-intraspecific distances distribution revealed a barcoding gap among the two subspecies. Also, posterior probabilities and the P AB value allowed to reject the hypothesis that observed degree of distinctiveness is due to random coalescence processes. These findings clearly support the Strait of Gibraltar as an isolating barrier for this species. The subspecific status is confirmed and species status is even suggested for S. a. mauritanica.

The amphibians and reptiles of Mindanao Island, southern Philippines, II: the herpetofauna of northeast Mindanao and adjacent islands

PubMed Central

Sanguila, Marites B.; Cobb, Kerry A.; Siler, Cameron D.; Diesmos, Arvin C.; Alcala, Angel C.; Brown, Rafe M.

2016-01-01

Abstract We summarize all available amphibian and reptile species distribution data from the northeast Mindanao faunal region, including small islands associated with this subcenter of endemic vertebrate biodiversity. Together with all publicly available historical information from biodiversity repositories, we present new data from several major herpetological surveys, including recently conducted inventories on four major mountains of northeast Mindanao, and adjacent islands of Camiguin Sur, Dinagat, and Siargao. We present species accounts for all taxa, comment on unresolved taxonomic problems, and provide revisions to outdated IUCN conservation status assessments in cases where our new data significantly alter earlier classification status summaries. Together, our comprehensive analysis of this fauna suggests that the greater Mindanao faunal region possesses distinct subcenters of amphibian and reptile species diversity, and that until this area is revisited and its fauna and actually studied, with on-the-ground field work including targeted surveys of species distributions coupled to the study their natural history, our understanding of the diversity and conservation status of southern Philippine herpetological fauna will remain incomplete. Nevertheless, the northeast Mindanao geographical area (Caraga Region) appears to have the highest herpetological species diversity (at least 126 species) of any comparably-sized Philippine faunal subregion. PMID:27833422

Educating parents about the vaccination status of their children: A user-centered mobile application.

PubMed

Seeber, Lea; Conrad, Tim; Hoppe, Christian; Obermeier, Patrick; Chen, Xi; Karsch, Katharina; Muehlhans, Susann; Tief, Franziska; Boettcher, Sindy; Diedrich, Sabine; Schweiger, Brunhilde; Rath, Barbara

2017-03-01

Parents are often uncertain about the vaccination status of their children. In times of vaccine hesitancy, vaccination programs could benefit from active patient participation. The Vaccination App ( VAccApp ) was developed by the Vienna Vaccine Safety Initiative, enabling parents to learn about the vaccination status of their children, including 25 different routine, special indication and travel vaccines listed in the WHO Immunization Certificate of Vaccination (WHO-ICV). Between 2012 and 2014, the VAccApp was validated in a hospital-based quality management program in Berlin, Germany, in collaboration with the Robert Koch Institute. Parents of 178 children were asked to transfer the immunization data of their children from the WHO-ICV into the VAccApp . The respective WHO-ICV was photocopied for independent, professional data entry (gold standard). Demonstrating the status quo in vaccine information reporting, a Recall Group of 278 parents underwent structured interviews for verbal immunization histories, without the respective WHO-ICV. Only 9% of the Recall Group were able to provide a complete vaccination status; on average 39% of the questions were answered correctly. Using the WHO-ICV with the help of the VAccApp resulted in 62% of parents providing a complete vaccination status; on average 95% of the questions were answered correctly. After using the VAccApp , parents were more likely to remember key aspects of the vaccination history. User-friendly mobile applications empower parents to take a closer look at the vaccination record, thereby taking an active role in providing accurate vaccination histories. Parents may become motivated to ask informed questions and to keep vaccinations up-to-date.

Molecular evidence that zucchini yellow fleck virus is a distinct and variable potyvirus related to papaya ringspot virus and Moroccan watermelon mosaic virus.

PubMed

Desbiez, C; Justafre, I; Lecoq, H

2007-02-01

Zucchini yellow fleck virus (ZYFV, genus Potyvirus) infects cultivated or wild cucurbits in the Mediterranean basin and occasionally causes severe damage in crops. Biological and serological data tend to indicate that ZYFV is related to other cucurbit-infecting potyviruses, mainly papaya ringspot virus (PRSV) and Moroccan watermelon mosaic virus (MWMV). In order to establish unambiguously the taxonomic status of ZYFV, the sequence of the 3' part of the genome - encompassing the CP coding region - of two ZYFV strains originating from Italy and France was obtained and compared with other potyviruses. The results obtained indicate that ZYFV belongs to a distinct potyvirus species, related to but different from PRSV and MWMV.

Comparative cytogenetics of Auchenorrhyncha (Hemiptera, Homoptera): a review

PubMed Central

Kuznetsova, Valentina; Aguin-Pombo, Dora

2015-01-01

Abstract A comprehensive review of cytogenetic features is provided for the large hemipteran suborder Auchenorrhyncha, which currently contains approximately 42,000 valid species. This review is based on the analysis of 819 species, 483 genera, and 31 families representing all presently recognized Auchenorrhyncha superfamilies, e.i. Cicadoidea (cicadas), Cercopoidea (spittle bugs), Membracoidea (leafhoppers and treehoppers), Myerslopioidea (ground-dwelling leafhoppers), and Fulgoroidea (planthoppers). History and present status of chromosome studies are described, as well as the structure of chromosomes, chromosome counts, trends and mechanisms of evolution of karyotypes and sex determining systems, their variation at different taxonomic levels and most characteristic (modal) states, occurrence of parthenogenesis, polyploidy, B-chromosomes and chromosome rearrangements, and methods used for cytogenetic analysis of Auchenorrhyncha. PMID:26807037

The complete mitochondrial genome sequence of the Datong yak (Bos grunniens).

PubMed

Wu, Xiaoyun; Chu, Min; Liang, Chunnian; Ding, Xuezhi; Guo, Xian; Bao, Pengjia; Yan, Ping

2016-01-01

Datong yak is a famous artificially cultivated breed in China. In the present work, we report the complete mitochondrial genome sequence of Datong yak for the first time. The total length of the mitogenome is 16,323 bp long, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one non-coding region (D-loop region). The gene order of Datong yak mitogenome is identical to that observed in most other vertebrates. The overall base composition is 33.71% A, 25.8.0% C, 13.21% G and 27.27% T, with an A + T content of 60.98%. The complete mitogenome sequence information of Datong yak can provide useful data for further studies on molecular breeding and taxonomic status.

Morphological and anatomical evidence support a new wild cassava: Manihot fallax (Crotonoideae, Euphorbiaceae), from Mato Grosso, Brazil.

PubMed

da Silva, Marcos José; Inocencio, Laís de Souza; Sodré, Rodolfo Carneiro; Alonso, Alexandre Antonio

2017-01-01

During the preparation of the taxonomic treatment of Manihot in the Midwest Region of Brazil, a new species was found. Manihot fallax M.J. Silva & L.S. Inocencio is described, illustrated and morphologically compared with similar simple-leaved species. The conservation status, geographic distribution (including map), ecology, phenology and notes about leaf anatomy of the new species are given. The synonymisation of M. robusta M. Mend. & T. B. Cavalc. under M. attenuata Müll. Arg. and lectotypes for M. attenuata and M. brachystachys Pax & K. Hoffm are also proposed. An emended description of M. attenuata is proposed as the original description is incomplete as it lacks information on the pistillate flowers, fruits and seeds.

New records with examples of potential host colonization events for hypopi (Acari: Hypoderatidae) from birds

USGS Publications Warehouse

Pence, Danny B.; Spalding, M.G.; Bergan, J.F.; Cole, Rebecca A.

1997-01-01

New host, geographic records, or both are established for 14 species of hypoderatid deutonymphs from 14 species of birds in North America. Ten of these records are regarded as examples of a potential host colonization event where these hypopi have become established in hosts other than those with which they are normally associated. Herein, potential host colonization events by hypoderatid deutonymphs are regarded as more of an ecologically determined than physiologically specific phenomenon, often specifically related to sharing of nesting sites in the same rookeries by different host taxa. Neottialges ibisicola Young & Pence is placed as a junior synonym of Neottialges plegadicola Fain. The taxonomic status of Hypodectes propus from columbid versus ardeid hosts needs further study.

Morphological and anatomical evidence support a new wild cassava: Manihot fallax (Crotonoideae, Euphorbiaceae), from Mato Grosso, Brazil

PubMed Central

da Silva, Marcos José; Inocencio, Laís de Souza; Sodré, Rodolfo Carneiro; Alonso, Alexandre Antonio

2017-01-01

Abstract During the preparation of the taxonomic treatment of Manihot in the Midwest Region of Brazil, a new species was found. Manihot fallax M.J. Silva & L.S. Inocencio is described, illustrated and morphologically compared with similar simple-leaved species. The conservation status, geographic distribution (including map), ecology, phenology and notes about leaf anatomy of the new species are given. The synonymisation of M. robusta M. Mend. & T. B. Cavalc. under M. attenuata Müll. Arg. and lectotypes for M. attenuata and M. brachystachys Pax & K. Hoffm are also proposed. An emended description of M. attenuata is proposed as the original description is incomplete as it lacks information on the pistillate flowers, fruits and seeds. PMID:29362549

Uniting Tricholoma sulphureum and T. bufonium.

PubMed

Comandini, Ornella; Haug, Ingeborg; Rinaldi, Andrea C; Kuyper, Thomas W

2004-10-01

The taxonomic status and relationship of Tricholoma sulphureum and the similar T. bufonium were investigated using different sets of characters. These included morphological data on fruit bodies, ecological and chorological data, and analysis of the sequence data obtained for the ITS of basidiomes of different ecological and geographic origin. Moreover, the ectomycorrhizas formed by T. bufonium on Abies alba and Quercus sp. were characterised, and anatomical features compared with those of T. sulphureum mycorrhizas on coniferous and broad-leaved host trees. Our results revealed extensive ITS variation in members of the T. sulphureum group, but this variation was not correlated with morphology, ecology, or geographical distribution. We conclude that T. bufonium cannot be maintained as an autonomous taxon and should be treated as an infraspecific variant of T. sulphureum.

Pigment Fluorescence Signatures as an Index to the Taxonomic Structure of Phytoplankton Communities

DTIC Science & Technology

2001-09-30

1 Pigment Fluorescence Signatures as an Index to the Taxonomic Structure of Phytoplankton Communities Dr. Gary Hitchcock Marine Biology and... Fisheries Rosenstiel School of Marine and Atmospheric Science 4600 Rickenbacker Cswy. Miami, FL 3149 phone: (305) 361-4926 fax: (305) 361-4765...ghitchcock.html LONG-TERM GOALS The spatial distribution and taxonomic composition of phytoplankton communities are important determinants of the

Deaf and Hard of Hearing Adolescents' Processing of Pictures and Written Words for Taxonomic Categories in a Priming Task of Semantic Categorization

ERIC Educational Resources Information Center

Li, Degao; Gao, Kejuan; Wu, Xueyun; Chen, Xiaojun; Zhang, Xiaona; Li, Ling; He, Weiwei

2013-01-01

Inspired by research by Li, Yi, and Kim (2011), the authors examined Chinese deaf and hard of hearing adolescents' responses to pictures for taxonomic categories of basic level (exemplar pictures) preceded by exemplar pictures, and to written words for taxonomic categories of basic level (exemplar words) preceded by exemplar words or by written…

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

PubMed Central

Diaz, Naryttza N; Krause, Lutz; Goesmann, Alexander; Niehaus, Karsten; Nattkemper, Tim W

2009-01-01

Background Metagenomics, or the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment, promises direct access to the "unculturable majority". This emerging field offers the potential to lay solid basis on our understanding of the entire living world. However, the taxonomic classification is an essential task in the analysis of metagenomics data sets that it is still far from being solved. We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning. Results Our novel strategy was extensively evaluated using the leave-one-out cross validation strategy on fragments of variable length (800 bp – 50 Kbp) from 373 completely sequenced genomes. TACOA is able to classify genomic fragments of length 800 bp and 1 Kbp with high accuracy until rank class. For longer fragments ≥ 3 Kbp accurate predictions are made at even deeper taxonomic ranks (order and genus). Remarkably, TACOA also produces reliable results when the taxonomic origin of a fragment is not represented in the reference set, thus classifying such fragments to its known broader taxonomic class or simply as "unknown". We compared the classification accuracy of TACOA with the latest intrinsic classifier PhyloPythia using 63 recently published complete genomes. For fragments of length 800 bp and 1 Kbp the overall accuracy of TACOA is higher than that obtained by PhyloPythia at all taxonomic ranks. For all fragment lengths, both methods achieved comparable high specificity results up to rank class and low false negative rates are also obtained. Conclusion An accurate multi-class taxonomic classifier was developed for environmental genomic fragments. TACOA can predict with high reliability the taxonomic origin of genomic fragments as short as 800 bp. The proposed method is transparent, fast, accurate and the reference set can be easily updated as newly sequenced genomes become available. Moreover, the method demonstrated to be competitive when compared to the most current classifier PhyloPythia and has the advantage that it can be locally installed and the reference set can be kept up-to-date. PMID:19210774

Two Influential Primate Classifications Logically Aligned.

PubMed

Franz, Nico M; Pier, Naomi M; Reeder, Deeann M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2016-07-01

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2-317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3-483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments-in the sense of the same name identifying congruent taxonomic meanings. The RCC-5 alignment approach is potentially widely applicable in systematics and can achieve scalable, precise resolution of semantically evolving name usages in synthetic, next-generation biodiversity, and phylogeny data platforms. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

The role of nailfold capillary dropout on mortality in systemic sclerosis.

PubMed

Tieu, Joanna; Hakendorf, Paul; Woodman, Richard J; Patterson, Karen; Walker, Jenny; Roberts-Thomson, Peter

2018-05-01

Semi-quantitative wide-field nailfold capillaroscopy (NFC) is a simple technique with proven utility in the early diagnosis of systemic sclerosis (SSc). Its role in prognosis, however, remains uncertain. To investigate the possible utility of NFC in predicting survival. Patients with SSc listed on the South Australian Scleroderma Register (SASR) with prior NFC performed at Flinders Medical Centre from 1991 to 2015 were included in this study. Baseline demographic data, diagnosis, scleroderma antibody status and mortality status were also collected for each patient. The cohort consisted of 99 patients with limited cutaneous SSc, 30 patients with diffuse cutaneous SSc and 23 with an overlap scleroderma syndrome. Fifty-six patients died during the period of study (censured end June 2015). Patients with diffuse scleroderma had significantly greater capillary dropout compared with limited and overlap scleroderma (P < 0.001). In univariate analysis, both capillary dropout scores (log-rank χ 2 = 8.75, P = 0.003) and antibody status (log-rank χ 2 = 13.94, P = 0.003) were associated with mortality. ANOVA showed a significant association between antibody status and capillary dropout (P < 0.001). In Cox regression, adjustment for capillary dropout attenuated the impact of autoantibody group on survival. Nailfold capillary dropout was significantly associated with mortality and the severity of dropout attenuates survival dictated by antibody status. Together these observations support the hypothesis that capillary dropout is on the causal pathway between induction of scleroderma associated autoantibodies and mortality. © 2018 Royal Australasian College of Physicians.

The influence of patients' nutritional status on the prevalence, course and treatment outcomes of lower limb ischemia: an overview of current evidence.

PubMed

Spychalska-Zwolińska, Marta; Zwoliński, Tomasz; Anaszewicz, Marzena; Budzyński, Jacek

2018-04-01

The association of lower limb ischemia (LLI) with disturbances in nutritional status, in respect to over- or undernutrition, is still uncertain. The aim of this study was to present the current state of knowledge on this issue. Systematic review of papers published between 2006 and 2018. The literature shows inconclusive evidence regarding the impact of nutritional status on the risk, course, prognosis and outcomes of conservative and invasive treatment of LLI. The majority of publications available demonstrate greater LLI prevalence in overweight and obese patients, a worse prognosis both in malnourished and severely obese patients, poorer outcomes of invasive treatment in underweight patients, and better results for endovascular and surgical treatment in patients with overweight and class I obesity, although without such a relationship for conservative therapy. Possible explanations linking nutritional status and LLI seem to be: the endocrine, paracrine, and autocrine activity of adipose tissue, a decrease in physical activity, and the effect of diet-dependent comorbidities, e.g. diabetes mellitus, hypertension and dyslipidemia. There is a growing body of evidence concerning an association between LLI and patients' nutritional status. A so-called "obesity paradox" or "BMI paradox" seems to exist among patients with LLI and mainly concerns outcomes of endovascular and surgical treatment. However, further studies are needed to evaluate the clinical importance of body composition, the distribution and endocrine activity of adipose tissue, and the effect of weight reduction and/or nutritional support in the LLI patient group.

Digitising legacy zoological taxonomic literature: Processes, products and using the output

PubMed Central

Lyal, Christopher H. C.

2016-01-01

Abstract By digitising legacy taxonomic literature using XML mark-up the contents become accessible to other taxonomic and nomenclatural information systems. Appropriate schemas need to be interoperable with other sectorial schemas, atomise to appropriate content elements and carry appropriate metadata to, for example, enable algorithmic assessment of availability of a name under the Code. Legacy (and new) literature delivered in this fashion will become part of a global taxonomic resource from which users can extract tailored content to meet their particular needs, be they nomenclatural, taxonomic, faunistic or other. To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original – the output of the many efforts has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, the means by which many scientific papers are indexed and located is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising taxonomic names is still relatively poor, people’s ability to use search engines effectively is mixed, and many papers cannot be searched directly. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original papers and extract target content manually. This opens the door to dynamic linking of new content with extant systems: automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its children instantly accessible with a single search, comparison of classifications used in different publications, and so on. A means to do this is through marking up content into XML, and the more atomised the mark-up the greater the possibilities for data retrieval and integration. Mark-up requires XML that accommodates the required content elements and is interoperable with other XML schemas, and there are now several written to do this, particularly TaxPub, taxonX and taXMLit, the last of these being the most atomised. We now need to automate this process as far as possible. Manual and automatic data and information retrieval is demonstrated by projects such as INOTAXA and Plazi. As we move to creating and using taxonomic products through the power of the internet, we need to ensure the output, while satisfying in its production the requirements of the Code, is fit for purpose in the future. PMID:26877659

Early Homo and the role of the genus in paleoanthropology.

PubMed

Villmoare, Brian

2018-01-01

The history of the discovery of early fossils attributed to the genus Homo has been contentious, with scholars disagreeing over the generic assignment of fossils proposed as members of our genus. In this manuscript I review the history of discovery and debate over early Homo and evaluate the various taxonomic hypotheses for the genus. To get a sense of how hominin taxonomy compares to taxonomic practice outside paleoanthropology, I compare the diversity of Homo to genera in other vertebrate clades. Finally, I propose a taxonomic model that hews closely to current models for hominin phylogeny and is consistent with taxonomic practice across evolutionary biology. © 2018 American Association of Physical Anthropologists.

Taxonomic revision of deep-sea Ostracoda from the Arctic Ocean

USGS Publications Warehouse

Yasuhara, Moriaki; Stepanova, Anna; Okahashi, Hisayo; Cronin, Thomas M.; Brouwers, Elisabeth M.

2015-01-01

Taxonomic revision of deep-sea Ostracoda from the Arctic Ocean was conducted to reduce taxonomic uncertainty that will improve our understanding of species ecology, biogeography and relationship to faunas from other deep-sea regions. Fifteen genera and 40 species were examined and (re-)illustrated with high-resolution scanning electron microscopy images, covering most of known deep-sea species in the central Arctic Ocean. Seven new species are described: Bythoceratina lomonosovensis n. sp., Cytheropteron parahamatum n. sp., Cytheropteron lanceae n. sp.,Cytheropteron irizukii n. sp., Pedicythere arctica n. sp., Cluthiawhatleyi n. sp., Krithe hunti n. sp. This study provides a robust taxonomic baseline for application to paleoceanographical reconstruction and biodiversity analyses in this climatically sensitive region.

Reptiles of Chubut province, Argentina: richness, diversity, conservation status and geographic distribution maps.

PubMed

Minoli, Ignacio; Morando, Mariana; Avila, Luciano Javier

2015-01-01

An accurate estimation of species and population geographic ranges is essential for species-focused studies and conservation and management plans. Knowledge of the geographic distributions of reptiles from Patagonian Argentina is in general limited and dispersed over manuscripts from a wide variety of topics. We completed an extensive review of reptile species of central Patagonia (Argentina) based on information from a wide variety of sources. We compiled and checked geographic distribution records from published literature and museum records, including extensive new data from the LJAMM-CNP (CENPAT-CONICET) herpetological collection. Our results show that there are 52 taxa recorded for this region and the highest species richness was seen in the families Liolaemidae and Dipsadidae with 31 and 10 species, respectively. The Patagónica was the phytogeographic province most diverse in species and Phymaturus was the genus of conservation concern most strongly associated with it. We present a detailed species list with geographical information, richness species, diversity analyses with comparisons across phytogeographical provinces, conservation status, taxonomic comments and distribution maps for all of these taxa.

Reptiles of Chubut province, Argentina: richness, diversity, conservation status and geographic distribution maps

PubMed Central

Minoli, Ignacio; Morando, Mariana; Avila, Luciano Javier

2015-01-01

Abstract An accurate estimation of species and population geographic ranges is essential for species-focused studies and conservation and management plans. Knowledge of the geographic distributions of reptiles from Patagonian Argentina is in general limited and dispersed over manuscripts from a wide variety of topics. We completed an extensive review of reptile species of central Patagonia (Argentina) based on information from a wide variety of sources. We compiled and checked geographic distribution records from published literature and museum records, including extensive new data from the LJAMM-CNP (CENPAT-CONICET) herpetological collection. Our results show that there are 52 taxa recorded for this region and the highest species richness was seen in the families Liolaemidae and Dipsadidae with 31 and 10 species, respectively. The Patagónica was the phytogeographic province most diverse in species and Phymaturus was the genus of conservation concern most strongly associated with it. We present a detailed species list with geographical information, richness species, diversity analyses with comparisons across phytogeographical provinces, conservation status, taxonomic comments and distribution maps for all of these taxa. PMID:25931966

What Azure blues occur in Canada? A re-assessment of Celastrina Tutt species (Lepidoptera, Lycaenidae)

PubMed Central

Schmidt, B. Christian; Layberry, Ross A.

2016-01-01

Abstract The identity of Celastrina species in eastern Canada is reviewed based on larval host plants, phenology, adult phenotypes, mtDNA barcodes and re-assessment of published data. The status of the Cherry Gall Azure (Celastrina serotina Pavulaan & Wright) as a distinct species in Canada is not supported by any dataset, and is removed from the Canadian fauna. Previous records of this taxon are re-identified as Celastrina lucia (Kirby) and Celastrina neglecta (Edwards). Evidence is presented that both Celastrina lucia and Celastrina neglecta have a second, summer-flying generation in parts of Canada. The summer generation of Celastrina lucia has previously been misidentified as Celastrina neglecta, which differs in phenology, adult phenotype and larval hosts from summer Celastrina lucia. DNA barcodes are highly conserved among at least three North American Celastrina species, and provide no taxonomic information. Celastrina neglecta has a Canadian distribution restricted to southern Ontario, Manitoba, Saskatchewan and easternmost Alberta. The discovery of museum specimens of Celastrina ladon (Cramer) from southernmost Ontario represents a new species for the Canadian butterfly fauna, which is in need of conservation status assessment. PMID:27199600

Fasting, but Not Aging, Dramatically Alters the Redox Status of Cysteine Residues on Proteins in Drosophila melanogaster

PubMed Central

Menger, Katja E.; James, Andrew M.; Cochemé, Helena M.; Harbour, Michael E.; Chouchani, Edward T.; Ding, Shujing; Fearnley, Ian M.; Partridge, Linda; Murphy, Michael P.

2015-01-01

Summary Altering the redox state of cysteine residues on protein surfaces is an important response to environmental challenges. Although aging and fasting alter many redox processes, the role of cysteine residues is uncertain. To address this, we used a redox proteomic technique, oxidative isotope-coded affinity tags (OxICAT), to assess cysteine-residue redox changes in Drosophila melanogaster during aging and fasting. This approach enabled us to simultaneously identify and quantify the redox state of several hundred cysteine residues in vivo. Cysteine residues within young flies had a bimodal distribution with peaks at ∼10% and ∼85% reversibly oxidized. Surprisingly, these cysteine residues did not become more oxidized with age. In contrast, 24 hr of fasting dramatically oxidized cysteine residues that were reduced under fed conditions while also reducing cysteine residues that were initially oxidized. We conclude that fasting, but not aging, dramatically alters cysteine-residue redox status in D. melanogaster. PMID:26095360

Parallel changes of taxonomic interaction networks in lacustrine bacterial communities induced by a polymetallic perturbation

PubMed Central

Laplante, Karine; Sébastien, Boutin; Derome, Nicolas

2013-01-01

Heavy metals released by anthropogenic activities such as mining trigger profound changes to bacterial communities. In this study we used 16S SSU rRNA gene high-throughput sequencing to characterize the impact of a polymetallic perturbation and other environmental parameters on taxonomic networks within five lacustrine bacterial communities from sites located near Rouyn-Noranda, Quebec, Canada. The results showed that community equilibrium was disturbed in terms of both diversity and structure. Moreover, heavy metals, especially cadmium combined with water acidity, induced parallel changes among sites via the selection of resistant OTUs (Operational Taxonomic Unit) and taxonomic dominance perturbations favoring the Alphaproteobacteria. Furthermore, under a similar selective pressure, covariation trends between phyla revealed conservation and parallelism within interphylum interactions. Our study sheds light on the importance of analyzing communities not only from a phylogenetic perspective but also including a quantitative approach to provide significant insights into the evolutionary forces that shape the dynamic of the taxonomic interaction networks in bacterial communities. PMID:23789031

Global hotspots and correlates of alien species richness across taxonomic groups

USGS Publications Warehouse

Dawson, Wayne; Moser, Dietmar; van Kleunen, Mark; Kreft, Holger; Pergl, Jan; Pysek, Petr; Weigelt, Patrick; Winter, Marten; Lenzner, Bernd; Blackburn, Tim M.; Dyer, Ellie; Cassey, Phillip; Scrivens, Sally-Louise; Economo, Evan P.; Guenard, Benoit; Capinha, Cesar; Seebens, Hanno; Garcia-Diaz, Pablo; Nentwig, Wolfgang; Garcia-Berthou, Emili; Casal, Christine; Mandrak, Nicholas E.; Fuller, Pam; Meyer, Carsten; Essl, Franz

2017-01-01

Human-mediated transport beyond biogeographic barriers has led to the introduction and establishment of alien species in new regions worldwide. However, we lack a global picture of established alien species richness for multiple taxonomic groups. Here, we assess global patterns and potential drivers of established alien species richness across eight taxonomic groups (amphibians, ants, birds, freshwater fishes, mammals, vascular plants, reptiles and spiders) for 186 islands and 423 mainland regions. Hotspots of established alien species richness are predominantly island and coastal mainland regions. Regions with greater gross domestic product per capita, human population density, and area have higher established alien richness, with strongest effects emerging for islands. Ants and reptiles, birds and mammals, and vascular plants and spiders form pairs of taxonomic groups with the highest spatial congruence in established alien richness, but drivers explaining richness differ between the taxa in each pair. Across all taxonomic groups, our results highlight the need to prioritize prevention of further alien species introductions to island and coastal mainland regions globally.

Wigeongrass (Ruppia maritima): a literature review

USGS Publications Warehouse

Kantrud, Harold A.

1991-01-01

Wigeongrass (Ruppia maritima L.) is a submersed macrophyte of nearly cosmopolitan distribution and worldwide importance as a waterfowl food. Unfortunately, the plant no longer inhabits vast areas disturbed by human activities. Taxonomic status of the plant is uncertain, especially in North America. In mild climates, in habitats subject to environmental extremes, the plant behaves as an annual (vegetation perishes), or as a perennial in deeper, more stable habitats (some vegetative parts grow year round). Drupelets (seeds) provide a mechanism for wigeongrass to survive periods of drought and excessive water salinity. These sexual propagules can be washed ashore or carried by birds or fish for long distances.Wigeongrass mostly occurs in temporarily to permanently flooded mesohaline-hyperhaline estuarine wetlands, but it also occurs inland in fresh to hypersaline palustrine and lacustrine wetlands. Most populations inhabit warm, relatively unpolluted, and well lit waters 2S conditions. Turbidity frequently limits wigeongrass growth in waters overlying easily suspendible bottom substrates.Wigeongrass often occurs in monotypic stands, yet grows with many other submersed and emergent macrophytes. Dominance in certain wetlands sometimes alternates with dominance by other submersed macrophytes as salinities, seasonal temperature cycles, or other environmental factors change. The shading effect of metaphytic, planktonic, or epiphytic algae often reduces production.Wigeongrass and its detritus provide food and cover for a large invertebrate biota, although direct consumption of the living plants is minimal. Wigeongrass beds in coastal wetlands are heavily used by fish. The plant is recognized worldwide as an important food of migrant and wintering waterfowl, wading birds, and shorebirds. In subtropical climates, wintering waterfowl can quickly consume entire stands.Propagation and management of wigeongrass has occurred for nearly 60 years in the southern and eastern United States. During the seventies and eighties, sophisticated water level and salinity management techniques have been developed to encourage growth of the plant.Future research should concentrate on determining the means to reduce light-limiting turbidity in many wetland types; understanding the ways in which human activities on and near wetlands affect wigeongrass production; and developing reliable and predictable techniques to stimulate wigeongrass production by water level manipulations and other means in different environmental settings. Trophic interactions and the effects of biomanipulation of fish populations in managed wigeongrass habitat--now little understood--also require more study.

Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

PubMed Central

Lu, Hsiao-Pei; Yeh, Yi-Chun; Sastri, Akash R; Shiah, Fuh-Kwo; Gong, Gwo-Ching; Hsieh, Chih-hao

2016-01-01

We propose a method for detecting evolutionary forces underlying community assembly by quantifying the strength of community–environment relationships hierarchically along taxonomic ranks. This approach explores the potential role of phylogenetic conservatism on habitat preferences: wherein, phylogenetically related taxa are expected to exhibit similar environmental responses. Thus, when niches are conserved, broader taxonomic classification should not diminish the strength of community–environment relationships and may even yield stronger associations by summarizing occurrences and abundances of ecologically equivalent finely resolved taxa. In contrast, broader taxonomic classification should weaken community–environment relationships when niches are under great divergence (that is, by combining finer taxa with distinct environmental responses). Here, we quantified the strength of community–environment relationships using distance-based redundancy analysis, focusing on soil and seawater prokaryotic communities. We considered eight case studies (covering a variety of sampling scales and sequencing strategies) and found that the variation in community composition explained by environmental factors either increased or remained constant with broadening taxonomic resolution from species to order or even phylum level. These results support the niche conservatism hypothesis and indicate that broadening taxonomic resolution may strengthen niche-related signals by removing uncertainty in quantifying spatiotemporal distributions of finely resolved taxa, reinforcing the current notion of ecological coherence in deep prokaryotic branches. PMID:27177191

Damage to temporo-parietal cortex decreases incidental activation of thematic relations during spoken word comprehension

PubMed Central

Mirman, Daniel; Graziano, Kristen M.

2012-01-01

Both taxonomic and thematic semantic relations have been studied extensively in behavioral studies and there is an emerging consensus that the anterior temporal lobe plays a particularly important role in the representation and processing of taxonomic relations, but the neural basis of thematic semantics is less clear. We used eye tracking to examine incidental activation of taxonomic and thematic relations during spoken word comprehension in participants with aphasia. Three groups of participants were tested: neurologically intact control participants (N=14), individuals with aphasia resulting from lesions in left hemisphere BA 39 and surrounding temporo-parietal cortex regions (N=7), and individuals with the same degree of aphasia severity and semantic impairment and anterior left hemisphere lesions (primarily inferior frontal gyrus and anterior temporal lobe) that spared BA 39 (N=6). The posterior lesion group showed reduced and delayed activation of thematic relations, but not taxonomic relations. In contrast, the anterior lesion group exhibited longer-lasting activation of taxonomic relations and did not differ from control participants in terms of activation of thematic relations. These results suggest that taxonomic and thematic semantic knowledge are functionally and neuroanatomically distinct, with the temporo-parietal cortex playing a particularly important role in thematic semantics. PMID:22571932

Guidelines for quality assurance and quality control of fish taxonomic data collected as part of the National Water-Quality Assessment Program

USGS Publications Warehouse

Walsh, Stephen Joseph; Meador, Michael R.

1998-01-01

Fish community structure is characterized by the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program as part of a perennial, multidisciplinary approach to evaluating the physical, chemical, and biological conditions of the Nation's water resources. The objective of quality assurance and quality control of fish taxonomic data that are collected as part of the NAWQA Program is to establish uniform guidelines and protocols for the identification, processing, and archiving of fish specimens to ensure that accurate and reliable data are collected. Study unit biologists, collaborating with regional biologists and fish taxonomic specialists, prepare a pre-sampling study plan that includes a preliminary faunal list and identification of an ichthyological curation center for receiving preserved fish specimens. Problematic taxonomic issues and protected taxa also are identified in the study plan, and collecting permits are obtained in advance of sampling activities. Taxonomic specialists are selected to identify fish specimens in the field and to assist in determining what fish specimens should be sacrificed, fixed, and preserved for laboratory identification, independent taxonomic verification, and long-term storage in reference or voucher collections. Quantitative and qualitative sampling of fishes follows standard methods previously established for the NAWQA Program. Common ichthyological techniques are used to process samples in the field and prepare fish specimens to be returned to the laboratory or sent to an institutional repository. Taxonomic identifications are reported by using a standardized list of scientific names that provides nomenclatural consistency and uniformity across study units.

Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome

PubMed Central

Li, Kelvin; Bihan, Monika; Methé, Barbara A.

2013-01-01

Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa (“core”), versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by quantifying the variation among people, across body habitats and over time. The National Institutes of Health (NIH) sponsored Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic core within and across body habitats and individuals through pyrosequencing-based profiling of 16S rRNA gene sequences from oral, skin, distal gut (stool), and vaginal body habitats from over 200 healthy individuals. A two-parameter model is introduced to quantitatively identify the core taxonomic members of each body habitat’s microbiota across the healthy cohort. Using only cutoffs for taxonomic ubiquity and abundance, core taxonomic members were identified for each of the 18 body habitats and also for the 4 higher-level body regions. Although many microbes were shared at low abundance, they exhibited a relatively continuous spread in both their abundance and ubiquity, as opposed to a more discretized separation. The numbers of core taxa members in the body regions are comparatively small and stable, reflecting the relatively high, but conserved, interpersonal variability within the cohort. Core sizes increased across the body regions in the order of: vagina, skin, stool, and oral cavity. A number of “minor” oral taxonomic core were also identified by their majority presence across the cohort, but with relatively low and stable abundances. A method for quantifying the difference between two cohorts was introduced and applied to samples collected on a second visit, revealing that over time, the oral, skin, and stool body regions tended to be more transient in their taxonomic structure than the vaginal body region. PMID:23671663

Learning accurate very fast decision trees from uncertain data streams

NASA Astrophysics Data System (ADS)

Liang, Chunquan; Zhang, Yang; Shi, Peng; Hu, Zhengguo

2015-12-01

Most existing works on data stream classification assume the streaming data is precise and definite. Such assumption, however, does not always hold in practice, since data uncertainty is ubiquitous in data stream applications due to imprecise measurement, missing values, privacy protection, etc. The goal of this paper is to learn accurate decision tree models from uncertain data streams for classification analysis. On the basis of very fast decision tree (VFDT) algorithms, we proposed an algorithm for constructing an uncertain VFDT tree with classifiers at tree leaves (uVFDTc). The uVFDTc algorithm can exploit uncertain information effectively and efficiently in both the learning and the classification phases. In the learning phase, it uses Hoeffding bound theory to learn from uncertain data streams and yield fast and reasonable decision trees. In the classification phase, at tree leaves it uses uncertain naive Bayes (UNB) classifiers to improve the classification performance. Experimental results on both synthetic and real-life datasets demonstrate the strong ability of uVFDTc to classify uncertain data streams. The use of UNB at tree leaves has improved the performance of uVFDTc, especially the any-time property, the benefit of exploiting uncertain information, and the robustness against uncertainty.

Cluster synchronization transmission of different external signals in discrete uncertain network

NASA Astrophysics Data System (ADS)

Li, Chengren; Lü, Ling; Chen, Liansong; Hong, Yixuan; Zhou, Shuang; Yang, Yiming

2018-07-01

We research cluster synchronization transmissions of different external signals in discrete uncertain network. Based on the Lyapunov theorem, the network controller and the identification law of uncertain adjustment parameter are designed, and they are efficiently used to achieve the cluster synchronization and the identification of uncertain adjustment parameter. In our technical scheme, the network nodes in each cluster and the transmitted external signal can be different, and they allow the presence of uncertain parameters in the network. Especially, we are free to choose the clustering topologies, the cluster number and the node number in each cluster.

Homoplasious colony morphology and mito-nuclear phylogenetic discordance among Eastern Pacific octocorals.

PubMed

Ament-Velásquez, Sandra L; Breedy, Odalisca; Cortés, Jorge; Guzman, Hector M; Wörheide, Gert; Vargas, Sergio

2016-05-01

Octocorals are a diverse and ecologically important group of cnidarians. However, the phylogenetic relationships of many octocoral groups are not well understood and are based mostly on mitochondrial sequence data. In addition, the discovery and description of new gorgonian species displaying unusual or intermediate morphologies and uncertain phylogenetic affinities further complicates the study of octocoral systematics and raises questions about the role played by processes such as plasticity, crypsis, and convergence in the evolution of this group of organisms. Here, we use nuclear (i.e. 28S rDNA) and mitochondrial (mtMutS) markers and a sample of Eastern Pacific gorgonians thought to be remarkable from a morphological point of view to shed light on the morphological diversification among these organisms. Our study reveals the loss of the anastomosed colony morphology in two unrelated lineages of the seafan genus Pacifigorgia and offers strong evidence for the independent evolution of a whip-like morphology in two lineages of Eastern Pacific Leptogorgia. Additionally, our data revealed one instance of mito-nuclear discordance in the genera Leptogorgia and Eugorgia, which may be the results of incomplete lineage sorting or ancient hybridization-introgression events. Our study stresses the importance of comprehensive taxonomic sampling and the use of independent sources of evidence to address the phylogenetic relationships and clarifying the evolution of octocorals. Copyright © 2016 Elsevier Inc. All rights reserved.

Parascolymia (Scleractinia: Lobophylliidae) in the Central Paratethys Sea (Vienna Basin, Austria) and its possible biogeographic implications

PubMed Central

Reuter, Markus; Wiedl, Thomas; Piller, Werner E.

2015-01-01

Palaeobiogeographical and palaeodiversity patterns of scleractinian reef corals are generally biased due to uncertain taxonomy and a loss of taxonomic characters through dissolution and recrystallization of the skeletal aragonite in shallow marine limestones. Herein, we describe a fossil lobophylliid coral in mouldic preservation from the early middle Miocene Leitha Limestone of the Central Paratethys Sea (Vienna Basin, Austria). By using grey-scale image inversion and silicone rubber casts for the visualization of the original skeletal anatomy and the detection of distinct micromorphological characters (i.e. shape of septal teeth, granulation of septocostae) Parascolymia bracherti has been identified as a new species in spite of the dissolved skeleton. In the recent era, Parascolymia like all Lobophylliidae is restricted to the Indo-Pacific region, where it is represented by a single species. The new species proves the genus also in the Miocene Mediterranean reef coral province. A review of the spatio-temporal relationships of fossil corals related to Parascolymia indicates that the genus was probably rooted in the Eastern Atlantic‒Western Tethys region during the Paleocene to Eocene and reached the Indo-Pacific region not before the Oligocene. The revealed palaeobiogeographical pattern shows an obvious congruence with that of Acropora and tridacnine bivalves reflecting a gradual equatorwards retreat of the marine biodiversity center parallel to the Cenozoic climate deterioration. PMID:26201071

Ectomycorrhizal fungi contribute to soil organic matter cycling in sub-boreal forests.

PubMed

Phillips, Lori A; Ward, Valerie; Jones, Melanie D

2014-03-01

Soils of northern temperate and boreal forests represent a large terrestrial carbon (C) sink. The fate of this C under elevated atmospheric CO2 and climate change is still uncertain. A fundamental knowledge gap is the extent to which ectomycorrhizal fungi (EMF) and saprotrophic fungi contribute to C cycling in the systems by soil organic matter (SOM) decomposition. In this study, we used a novel approach to generate and compare enzymatically active EMF hyphae-dominated and saprotrophic hyphae-enriched communities under field conditions. Fermentation-humus (FH)-filled mesh bags, surrounded by a sand barrier, effectively trapped EMF hyphae with a community structure comparable to that found in the surrounding FH layer, at both trophic and taxonomic levels. In contrast, over half the sequences from mesh bags with no sand barrier were identified as belonging to saprotrophic fungi. The EMF hyphae-dominated systems exhibited levels of hydrolytic and oxidative enzyme activities that were comparable to or higher than saprotroph-enriched systems. The enzymes assayed included those associated with both labile and recalcitrant SOM degradation. Our study shows that EMF hyphae are likely important contributors to current SOM turnover in sub-boreal systems. Our results also suggest that any increased EMF biomass that might result from higher below-ground C allocation by trees would not suppress C fluxes from sub-boreal soils.

Distinct classical and molecular cytogenetics of Astyanax marionae and A. fasciatus (Characiformes: Characidae): a comparative study of the organization of heterochromatin and repetitive genes.

PubMed

Piscor, Diovani; Centofante, Liano; Parise-Maltempi, Patricia Pasquali

2017-09-01

Genus Astyanax is well distributed in Neotropical freshwater environments and its taxonomic position is uncertain, as is the case with other Characidae genera allocated in the group incertae sedis. This study aimed to analyse the karyotype of different populations of Astyanax fasciatus (Corumbataí River basin) using Giemsa staining, C-band technique, and fluorescence in situ hybridization for the H3 histone and 5S rRNA genes, in addition we describe for the first time the chromosomal organization of H3 histone and 5S rRNAgenes in A. marionae (ParaguayRiver basin). Chromosomes of three A. fasciatus populations were analysed (two with 2n = 50 and one with 2n = 48) and the heterochromatin was organized in two forms (blocks with blurred boundaries and distinct blocks). H3 histone and 5S rRNA genes were observed in all the three populations of A. fasciatus on two chromosome pairs (one metacentric chromosome showing H3 histone and 5S rRNA gene clusters). In A. marionae (2n = 48), H3 histone and 5S rRNA genes were observed in one acrocentric chromosome pair (different pairs). Further, differences between karyotypes and heterochromatin, as well as the chromosomal organization of H3 histone and 5S rRNA genes in Astyanax species, focussing on chromosome evolution in the group are discussed.

Ectomycorrhizal fungi contribute to soil organic matter cycling in sub-boreal forests

PubMed Central

Phillips, Lori A; Ward, Valerie; Jones, Melanie D

2014-01-01

Soils of northern temperate and boreal forests represent a large terrestrial carbon (C) sink. The fate of this C under elevated atmospheric CO2 and climate change is still uncertain. A fundamental knowledge gap is the extent to which ectomycorrhizal fungi (EMF) and saprotrophic fungi contribute to C cycling in the systems by soil organic matter (SOM) decomposition. In this study, we used a novel approach to generate and compare enzymatically active EMF hyphae-dominated and saprotrophic hyphae-enriched communities under field conditions. Fermentation-humus (FH)-filled mesh bags, surrounded by a sand barrier, effectively trapped EMF hyphae with a community structure comparable to that found in the surrounding FH layer, at both trophic and taxonomic levels. In contrast, over half the sequences from mesh bags with no sand barrier were identified as belonging to saprotrophic fungi. The EMF hyphae-dominated systems exhibited levels of hydrolytic and oxidative enzyme activities that were comparable to or higher than saprotroph-enriched systems. The enzymes assayed included those associated with both labile and recalcitrant SOM degradation. Our study shows that EMF hyphae are likely important contributors to current SOM turnover in sub-boreal systems. Our results also suggest that any increased EMF biomass that might result from higher below-ground C allocation by trees would not suppress C fluxes from sub-boreal soils. PMID:24173458

Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi

NASA Astrophysics Data System (ADS)

Shih, Patrick M.; Ward, Lewis M.; Fischer, Woodward W.

2017-10-01

Various lines of evidence from both comparative biology and the geologic record make it clear that the biochemical machinery for anoxygenic photosynthesis was present on early Earth and provided the evolutionary stock from which oxygenic photosynthesis evolved ca. 2.3 billion years ago. However, the taxonomic identity of these early anoxygenic phototrophs is uncertain, including whether or not they remain extant. Several phototrophic bacterial clades are thought to have evolved before oxygenic photosynthesis emerged, including the Chloroflexi, a phylum common across a wide range of modern environments. Although Chloroflexi have traditionally been thought to be an ancient phototrophic lineage, genomics has revealed a much greater metabolic diversity than previously appreciated. Here, using a combination of comparative genomics and molecular clock analyses, we show that phototrophic members of the Chloroflexi phylum are not particularly ancient, having evolved well after the rise of oxygen (ca. 867 million years ago), and thus cannot be progenitors of oxygenic photosynthesis. Similarly, results show that the carbon fixation pathway that defines this clade—the 3-hydroxypropionate bicycle—evolved late in Earth history as a result of a series of horizontal gene transfer events, explaining the lack of geological evidence for this pathway based on the carbon isotope record. These results demonstrate the role of horizontal gene transfer in the recent metabolic innovations expressed within this phylum, including its importance in the development of a novel carbon fixation pathway.

Phylogenomic analysis of Emiliania huxleyi provides evidence for haptophyte-stramenopile association and a chimeric haptophyte nuclear genome.

PubMed

Miller, John J; Delwiche, Charles F

2015-06-01

Emiliania huxleyi is a haptophyte alga of uncertain phylogenetic affinity containing a secondarily derived, chlorophyll c containing plastid. We sought to characterize its relationships with other taxa by quantifying the bipartitions in which it was included from a group of single protein phylogenetic trees in a way that allowed for variation in taxonomic content and accounted for paralogous sequences. The largest number of sequences supported a phylogenetic relationship of E. huxleyi with the stramenopiles, in particular Aureococcus anophagefferens. Far fewer nuclear sequences gave strong support to the placement of this coccolithophorid with the cryptophyte, Guillardia theta. The majority of the sequences that did support this relationship did not have plastid related functions. These results suggest that the haptophytes may be more closely allied with the heterokonts than with the cryptophytes. Another small set of genes associated E. huxleyi with the Viridiplantae with high support. While these genes could have been acquired with a plastid, the lack of plastid related functions among the proteins for which they code and the lack of other organisms with chlorophyll c containing plastids within these bipartitions suggests other explanations may be possible. This study also identified several genes that may have been transferred from the haptophyte lineage to the dinoflagellates Karenia brevis and Karlodinium veneficum as a result of their haptophyte derived plastid, including some with non-photosynthetic functions. Published by Elsevier B.V.

Computers for symbolic processing

NASA Technical Reports Server (NTRS)

Wah, Benjamin W.; Lowrie, Matthew B.; Li, Guo-Jie

1989-01-01

A detailed survey on the motivations, design, applications, current status, and limitations of computers designed for symbolic processing is provided. Symbolic processing computations are performed at the word, relation, or meaning levels, and the knowledge used in symbolic applications may be fuzzy, uncertain, indeterminate, and ill represented. Various techniques for knowledge representation and processing are discussed from both the designers' and users' points of view. The design and choice of a suitable language for symbolic processing and the mapping of applications into a software architecture are then considered. The process of refining the application requirements into hardware and software architectures is treated, and state-of-the-art sequential and parallel computers designed for symbolic processing are discussed.

Dynamic Control of Plans with Temporal Uncertainty

NASA Technical Reports Server (NTRS)

Morris, Paul; Muscettola, Nicola; Vidal, Thierry

2001-01-01

Certain planning systems that deal with quantitative time constraints have used an underlying Simple Temporal Problem solver to ensure temporal consistency of plans. However, many applications involve processes of uncertain duration whose timing cannot be controlled by the execution agent. These cases require more complex notions of temporal feasibility. In previous work, various "controllability" properties such as Weak, Strong, and Dynamic Controllability have been defined. The most interesting and useful Controllability property, the Dynamic one, has ironically proved to be the most difficult to analyze. In this paper, we resolve the complexity issue for Dynamic Controllability. Unexpectedly, the problem turns out to be tractable. We also show how to efficiently execute networks whose status has been verified.

Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

PubMed Central

Porter, Teresita M; Gibson, Joel F; Shokralla, Shadi; Baird, Donald J; Golding, G Brian; Hajibabaei, Mehrdad

2014-01-01

Current methods to identify unknown insect (class Insecta) cytochrome c oxidase (COI barcode) sequences often rely on thresholds of distances that can be difficult to define, sequence similarity cut-offs, or monophyly. Some of the most commonly used metagenomic classification methods do not provide a measure of confidence for the taxonomic assignments they provide. The aim of this study was to use a naïve Bayesian classifier (Wang et al. Applied and Environmental Microbiology, 2007; 73: 5261) to automate taxonomic assignments for large batches of insect COI sequences such as data obtained from high-throughput environmental sequencing. This method provides rank-flexible taxonomic assignments with an associated bootstrap support value, and it is faster than the blast-based methods commonly used in environmental sequence surveys. We have developed and rigorously tested the performance of three different training sets using leave-one-out cross-validation, two field data sets, and targeted testing of Lepidoptera, Diptera and Mantodea sequences obtained from the Barcode of Life Data system. We found that type I error rates, incorrect taxonomic assignments with a high bootstrap support, were already relatively low but could be lowered further by ensuring that all query taxa are actually present in the reference database. Choosing bootstrap support cut-offs according to query length and summarizing taxonomic assignments to more inclusive ranks can also help to reduce error while retaining the maximum number of assignments. Additionally, we highlight gaps in the taxonomic and geographic representation of insects in public sequence databases that will require further work by taxonomists to improve the quality of assignments generated using any method.

Concordance and discordance between taxonomic and functional homogenization: responses of soil mite assemblages to forest conversion.

PubMed

Mori, Akira S; Ota, Aino T; Fujii, Saori; Seino, Tatsuyuki; Kabeya, Daisuke; Okamoto, Toru; Ito, Masamichi T; Kaneko, Nobuhiro; Hasegawa, Motohiro

2015-10-01

The compositional characteristics of ecological assemblages are often simplified; this process is termed "biotic homogenization." This process of biological reorganization occurs not only taxonomically but also functionally. Testing both aspects of homogenization is essential if ecosystem functioning supported by a diverse mosaic of functional traits in the landscape is concerned. Here, we aimed to infer the underlying processes of taxonomic/functional homogenization at the local scale, which is a scale that is meaningful for this research question. We recorded species of litter-dwelling oribatid mites along a gradient of forest conversion from a natural forest to a monoculture larch plantation in Japan (in total 11 stands), and collected data on the functional traits of the recorded species to quantify functional diversity. We calculated the taxonomic and functional β-diversity, an index of biotic homogenization. We found that both the taxonomic and functional β-diversity decreased with larch dominance (stand homogenization). After further deconstructing β-diversity into the components of turnover and nestedness, which reflect different processes of community organization, a significant decrease in the response to larch dominance was observed only for the functional turnover. As a result, there was a steeper decline in the functional β-diversity than the taxonomic β-diversity. This discordance between the taxonomic and functional response suggests that species replacement occurs between species that are functionally redundant under environmental homogenization, ultimately leading to the stronger homogenization of functional diversity. The insights gained from community organization of oribatid mites suggest that the functional characteristics of local assemblages, which support the functionality of ecosystems, are of more concern in human-dominated forest landscapes.

Functional and Taxonomic Differentiation of Macrophyte Assemblages Across the Yangtze River Floodplain Under Human Impacts

PubMed Central

Zhang, Min; García Molinos, Jorge; Zhang, Xiaolin; Xu, Jun

2018-01-01

Human activities and the consequent extirpations of species have been changing the composition of species assemblages worldwide. These anthropogenic impacts alter not only the richness of assemblages but also the biological dissimilarity among them. One of the main gaps in the assessment of biodiversity change in freshwater ecosystems is our limited understanding regarding how taxonomic and functional facets of macrophyte assemblages respond to human impacts on regional scales. Here, we assess the temporal (before 1970s against after 2000s) changes in taxonomic and functional richness and compositional dissimilarities, partitioned into its turnover and nestedness components, of freshwater macrophyte assemblages across the floodplain lakes of the Yangtze River in China. We found that functional and taxonomic assemblage differentiation occurred simultaneously under increasing human impact, concomitant to a general decrease in functional and taxonomic richness. However, this effect weakened when the historical level of taxonomic dissimilarity among assemblages was high. Macrophyte species with large dispersal range and submersed life form were significantly more susceptible to extirpation. The impact of human activities on differentiation was complex but habitat loss and fishery intensity were consistently the main drivers of assemblage change in these lakes, whereas water quality (i.e., light pollution and nutrient enrichment) had weaker effects. Further, macrophyte taxonomic and functional differentiation was mainly driven by the nestedness component of dissimilarity, accounting for changes in assemblage composition related to changes in species richness independent of species replacement. This result, markedly different from previous studies on freshwater fish assemblages conducted in these lakes, represents a novel contribution toward achieving a more holistic understanding of how human impacts contribute to shape community assemblages in natural ecosystems. PMID:29636763

TaxaGloss - A Glossary and Translation Tool for Biodiversity Studies.

PubMed

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

2016-01-01

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

Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act.

PubMed

Haig, Susan M; Beever, Erik A; Chambers, Steven M; Draheim, Hope M; Dugger, Bruce D; Dunham, Susie; Elliott-Smith, Elise; Fontaine, Joseph B; Kesler, Dylan C; Knaus, Brian J; Lopes, Iara F; Loschl, Pete; Mullins, Thomas D; Sheffield, Lisa M

2006-12-01

The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act

USGS Publications Warehouse

Beever, E.A.; Haig, S.M.; Chambers, Steven M.; Draheim, Hope M.; Dugger, Bruce D.; Dunham, Susie; Elliott-Smith, Elise; Fontaine, Joseph B.; Kesler, Dylan C.; Knaus, Brian J.; Lopes, Iara F.; Loschl, Peter J.; Mullins, Thomas D.; Sheffield, Lisa M.

2006-01-01

The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

Characterizing traffic under uncertain disruptions : an experimental approach.

DOT National Transportation Integrated Search

2013-03-01

The objective of the research is to study long-term traffic patterns under uncertain disruptions using : data collected from human subjects who simultaneously make route choices in controlled PC-based : laboratory experiments. Uncertain disruptions t...

Vitamin D and Cardiovascular Disease: Can Novel Measures of Vitamin D Status Improve Risk Prediction and Address the Vitamin D Racial Paradox?

PubMed

Kim, Samuel M; Lutsey, Pamela L; Michos, Erin D

2017-01-01

To provide a state-of-the-art update on some emerging measures of vitamin D status and discuss how assessment of these key vitamin D metabolites might improve prognostication of risk for cardiovascular disease (CVD) outcomes. Vitamin D deficiency is a highly prevalent condition and relatively easy to treat with supplementation and/or modest sunlight exposure. A substantial body of experimental and epidemiological evidence suggest that vitamin D deficiency is a risk factor for CVD. Most epidemiologic studies to date have focused on total 25-hydroxyvitamin D [25(OH)D] concentrations, which is the established marker of vitamin D stores. However, there is emerging evidence that other novel markers of vitamin D metabolism may better characterize 'true' vitamin D status. Some key novel measures include bioavailable 25(OH)D, free 25(OH)D, 1-25 dihydroxyvitamin D, 24,25-dihydroxyvitamin D3 [24,25(OH) 2 D3], and ratio of 24,25(OH) 2 D3 to 25(OH)D [the vitamin D metabolic ratio]. Utilization of these biomarkers may enhance understanding of the association between vitamin D and CVD risk, and may provide explanation for the observation that 25(OH)D is a stronger CVD risk factor in whites than blacks. Novel measures of vitamin D status could potentially change clinical practice regarding how patients are currently screened for vitamin D status and defined as vitamin D deficient or not. However, whether measuring any of these alternate markers of vitamin D status can provide further insight regarding CVD risk beyond the traditionally measured 25(OH)D concentrations is uncertain at this time. This is an area where further research is strongly needed.

Association Between Markers of Inflammation and Total Stroke by Hypertensive Status Among Women

PubMed Central

Rexrode, Kathryn M.; Kotler, Gregory; Everett, Brendan M.; Glynn, Robert J.; Lee, I-Min; Buring, Julie E.; Ridker, Paul M.; Sesso, Howard D.

2016-01-01

BACKGROUND Markers of systemic inflammation (high-sensitivity C-reactive protein [hsCRP], soluble intercellular adhesion molecule 1 [sICAM-1], and fibrinogen) have been associated with a greater risk of total and ischemic stroke, in addition to elevated blood pressure. However, the role of these inflammatory markers on stroke pathophysiology by hypertension status is uncertain. METHODS Blood samples were collected and assayed for hsCRP, sICAM-1, and fibrinogen among 27,330 initially healthy women from the Women’s Health Study, and women were followed up from 1992 to 2013. Prior to randomization, the baseline questionnaire collected self-reported hypertension status, cardiovascular risk factors, and lifestyle factors. New cases of total, ischemic, and hemorrhagic stroke were updated annually through questionnaires and confirmed by medical records according to the National Survey of Stroke criteria. Multivariable Cox models estimated overall associations between each inflammatory marker and stroke and separately stratified by hypertension status. RESULTS We observed 629 incident total strokes over 477,278 person-years. In adjusted analyses, extreme quartiles of hsCRP and sICAM-1 were each associated with a significantly greater risk of total stroke (hsCRP: hazard ratios [HR] = 1.77, 95% confidence interval [CI]: 1.39–2.26; sICAM-1: HR = 1.28, 95% CI: 1.00–1.63). Fibrinogen was not associated with a significantly greater stroke risk. In analyses stratified by hypertension status, elevated hsCRP was associated with a nonstatistically significant greater risk of total stroke among prehypertensive and hypertensive women. CONCLUSIONS These data indicate that hsCRP and sICAM-1 are associated with hypertension status and stroke risk among women. Further work should examine the role of inflammatory markers on ischemic stroke subtypes and clarify mechanisms. PMID:27235695

Vitamin D and Cardiovascular Disease: Can Novel Measures of Vitamin D Status Improve Risk Prediction and Address the Vitamin D Racial Paradox?

PubMed Central

Kim, Samuel M.; Lutsey, Pamela L.; Michos, Erin D.

2017-01-01

Purpose of review To provide a state-of-the-art update on some emerging measures of vitamin D status and discuss how assessment of these key vitamin D metabolites might improve prognostication of risk for cardiovascular disease (CVD) outcomes. Recent findings Vitamin D deficiency is a highly prevalent condition and relatively easy to treat with supplementation and/or modest sunlight exposure. A substantial body of experimental and epidemiological evidence suggest that vitamin D deficiency is a risk factor for CVD. Most epidemiologic studies to date have focused on total 25-hydroxyvitamin D [25(OH)D] concentrations, which is the established marker of vitamin D stores. However, there is emerging evidence that other novel markers of vitamin D metabolism may better characterize ‘true’ vitamin D status. Some key novel measures include bioavailable 25(OH)D, free 25(OH)D, 1–25 dihydroxyvitamin D, 24,25-dihydroxyvitamin D3 [24,25(OH)2D3], and ratio of 24,25(OH)2D3 to 25(OH)D [the vitamin D metabolic ratio]. Utilization of these biomarkers may enhance understanding of the association between vitamin D and CVD risk, and may provide explanation for the observation that 25(OH)D is a stronger CVD risk factor in whites than blacks Summary Novel measures of vitamin D status could potentially change clinical practice regarding how patients are currently screened for vitamin D status and defined as vitamin D deficient or not. However, whether measuring any of these alternate markers of vitamin D status can provide further insight regarding CVD risk beyond the traditionally measured 25(OH)D concentrations is uncertain at this time. This is an area where further research is strongly needed. PMID:28261371

Chinese deaf adolescents' free recall of taxonomic, slot-filler, and thematic categories.

PubMed

Li, Degao; Zhang, Jijia

2009-08-01

Four experiments were conducted to show that deaf adolescents tended to process information in different ways from hearing adolescents. Memorizing items sequentially shown on computer screens under the control of their articulators' movements, deaf adolescents tended to treat items that cohered as taxonomic, thematic, or slot-filler categories as isolated pieces of information. Having to perceive information by means of sign language, however, their achievements were not worse than those of hearing adolescents anymore, no matter whether the stimuli were presented as words or pictures. They could not only utilize categories relations to help memorize categories exemplars but were relatively better aware of slot-filler or thematic than taxonomic relations as well, suggesting that they had a relatively delayed development of taxonomic category representations in comparison with hearing adolescents.

More than just orphans: are taxonomically-restricted genes important in evolution?

PubMed

Khalturin, Konstantin; Hemmrich, Georg; Fraune, Sebastian; Augustin, René; Bosch, Thomas C G

2009-09-01

Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species. Do such 'orphan' or 'taxonomically-restricted' genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes. Here we focus on evidence from Hydra suggesting that taxonomically-restricted genes play a role in the creation of phylum-specific novelties such as cnidocytes, in the generation of morphological diversity, and in the innate defence system. We propose that taxon-specific genes drive morphological specification, enabling organisms to adapt to changing conditions.

A synopsis of the Euphaeidae (Odonata: Zygoptera) of Vietnam, with descriptions of two new species of Euphaea.

PubMed

Phan, Quoc Toan; Kompier, Tom; Karube, Haruki; Hayashi, Fumio

2018-01-24

23 species of Euphaeidae (Odonata: Zygoptera) are reported from Vietnam including two new species of Euphaea, E. saola Phan Hayashi, sp. nov. and E. sanguinea Kompier Hayashi, sp. nov., and four species not recorded previously, Bayadera continentalis Asahina, 1973, B. hyalina Selys, 1879, B. nephelopennis Davies Yang, 1996 and Euphaea pahyapi Hämäläinen, 1985. The females of Anisopleura bipugio Hämäläinen Karube, 2013, Bayadera serrata Davies Yang, 1996 and Euphaea hirta Hämäläinen Karube, 2001 are described for the first time. The mutual taxonomic status of Bayadera hyalina and B. strigata Davies Yang, 1996 is discussed. Distribution maps of all known Vietnamese species, with detailed distribution records, are provided.

Annotated checklist of millipedes (Myriapoda: Diplopoda) of Sri Lanka.

PubMed

Zoysa, H K S De; Nguyen, Anh D; Wickramasinghe, S

2016-01-11

This review lists the currently known species of millepedes in Sri Lanka and discusses their current taxonomic status and distribution based on previous studies from 1865 to date. A total of 104 millipede species belonging to 44 genera, 18 families and nine orders have been recorded in Sri Lanka. Of these, 82 are known only from Sri Lanka; additionally, nine genera and one family are known only from Sri Lanka. Most of the millipede species have been recorded from two localities, namely Pundaluoya and Kandy in the central highlands of Sri Lanka. Current knowledge on the taxonomy, evolutionary relationships, distribution and conservation of the millipedes of Sri Lanka is still limited and scattered. Thus we suggest more intensive surveys to acquire comprehensive data on the millipedes of Sri Lanka.

Designation of a neotype for brook trout, Salvelinus fontinalis

USGS Publications Warehouse

Stauffer, Jay R; King, Timothy L.

2015-01-01

The taxonomic status of Salvelinus fontinalis (Mitchill) is problematic. Difficulties in comparison of populations are exacerbated by the lack of type material. Here we designate a neotype from Connetquot River, Long Island, New York. We provide genetic and morphological data for the neotype, conspecifics, and other populations (Swan Creek, Nissequogue Creek) from Long Island, New York. We demonstrate, using molecular markers, that the population from Connetquot River most likely has not been influenced by the major broodstock strains utilized in the Northeast for supplemental and restorative stocking programs. We distinguish the above populations morphologically from lower interior basin populations, represented by fishes from the Pigeon-French Broad drainage, North Carolina and Tennessee. Finally, we position populations from Long Island, New York, within six distinct lineages of S. fontinalis.

An update on the spider genus Loxosceles (Araneae: Sicariidae) in the Afrotropical region, with description of seven new species.

PubMed

Lotz, L N

2017-11-01

In this paper the present state of knowledge of the genus Loxosceles Heineken & Lowe, 1832 from the Afrotropical region is discussed. The distribution of nine of the 16 described Afrotropical species of Loxosceles is updated and the status of the types of L. bergeri Strand, 1906b and L. pilosa Purcell, 1908 are discussed. A further four new species from South Africa: L. cederbergensis sp. nov.; L. dejagerae sp. nov.; L. haddadi sp. nov.; L. makapanensis sp. nov.; and three from Namibia: L. griffinae sp. nov.; L. irishi sp. nov.; and L. maraisi sp. nov., are described. The female of L. smithi Simon, 1897 is described for the first time. A new taxonomic key to all the Afrotropical species is given.

A novel medical information management and decision model for uncertain demand optimization.

PubMed

Bi, Ya

2015-01-01

Accurately planning the procurement volume is an effective measure for controlling the medicine inventory cost. Due to uncertain demand it is difficult to make accurate decision on procurement volume. As to the biomedicine sensitive to time and season demand, the uncertain demand fitted by the fuzzy mathematics method is obviously better than general random distribution functions. To establish a novel medical information management and decision model for uncertain demand optimization. A novel optimal management and decision model under uncertain demand has been presented based on fuzzy mathematics and a new comprehensive improved particle swarm algorithm. The optimal management and decision model can effectively reduce the medicine inventory cost. The proposed improved particle swarm optimization is a simple and effective algorithm to improve the Fuzzy interference and hence effectively reduce the calculation complexity of the optimal management and decision model. Therefore the new model can be used for accurate decision on procurement volume under uncertain demand.

Revising the recent evolutionary history of equids using ancient DNA

PubMed Central

Orlando, Ludovic; Metcalf, Jessica L.; Alberdi, Maria T.; Telles-Antunes, Miguel; Bonjean, Dominique; Otte, Marcel; Martin, Fabiana; Eisenmann, Véra; Mashkour, Marjan; Morello, Flavia; Prado, Jose L.; Salas-Gismondi, Rodolfo; Shockey, Bruce J.; Wrinn, Patrick J.; Vasil'ev, Sergei K.; Ovodov, Nikolai D.; Cherry, Michael I.; Hopwood, Blair; Male, Dean; Austin, Jeremy J.; Hänni, Catherine; Cooper, Alan

2009-01-01

The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87–688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses. PMID:20007379

Taxonomic and Geographic Bias in Conservation Biology Research: A Systematic Review of Wildfowl Demography Studies.

PubMed

Roberts, Beth E I; Harris, W Edwin; Hilton, Geoff M; Marsden, Stuart J

2016-01-01

Demographic data are important to wildlife managers to gauge population health, to allow populations to be utilised sustainably, and to inform conservation efforts. We analysed published demographic data on the world's wildfowl to examine taxonomic and geographic biases in study, and to identify gaps in knowledge. Wildfowl (order: Anseriformes) are a comparatively well studied bird group which includes 169 species of duck, goose and swan. In all, 1,586 wildfowl research papers published between 1911 and 2010 were found using Web of Knowledge (WoK) and Google Scholar. Over half of the research output involved just 15 species from seven genera. Research output was strongly biased towards 'high income' countries, common wildfowl species, and measures of productivity, rather than survival and movement patterns. There were significantly fewer demographic data for the world's 31 threatened wildfowl species than for non-threatened species. Since 1994, the volume of demographic work on threatened species has increased more than for non-threatened species, but still makes up only 2.7% of total research output. As an aid to research prioritisation, a metric was created to reflect demographic knowledge gaps for each species related to research output for the species, its threat status, and availability of potentially useful surrogate data from congeneric species. According to the metric, the 25 highest priority species include thirteen threatened taxa and nine species each from Asia and South America, and six from Africa.

Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming

PubMed Central

Kroeker, Kristy J; Kordas, Rebecca L; Crim, Ryan; Hendriks, Iris E; Ramajo, Laura; Singh, Gerald S; Duarte, Carlos M; Gattuso, Jean-Pierre

2013-01-01

Ocean acidification represents a threat to marine species worldwide, and forecasting the ecological impacts of acidification is a high priority for science, management, and policy. As research on the topic expands at an exponential rate, a comprehensive understanding of the variability in organisms' responses and corresponding levels of certainty is necessary to forecast the ecological effects. Here, we perform the most comprehensive meta-analysis to date by synthesizing the results of 228 studies examining biological responses to ocean acidification. The results reveal decreased survival, calcification, growth, development and abundance in response to acidification when the broad range of marine organisms is pooled together. However, the magnitude of these responses varies among taxonomic groups, suggesting there is some predictable trait-based variation in sensitivity, despite the investigation of approximately 100 new species in recent research. The results also reveal an enhanced sensitivity of mollusk larvae, but suggest that an enhanced sensitivity of early life history stages is not universal across all taxonomic groups. In addition, the variability in species' responses is enhanced when they are exposed to acidification in multi-species assemblages, suggesting that it is important to consider indirect effects and exercise caution when forecasting abundance patterns from single-species laboratory experiments. Furthermore, the results suggest that other factors, such as nutritional status or source population, could cause substantial variation in organisms' responses. Last, the results highlight a trend towards enhanced sensitivity to acidification when taxa are concurrently exposed to elevated seawater temperature. PMID:23505245

Taxonomy of the Streptomyces strain ZG0656 that produces acarviostatin alpha-amylase inhibitors and analysis of their effects on blood glucose levels in mammalian systems.

PubMed

Geng, P; Bai, G; Shi, Q; Zhang, L; Gao, Z; Zhang, Q

2009-02-01

To clarify the taxonomic status of strain ZG0656 and analyse the effects of its acarviostatin products on blood glucose levels in mammalian systems. Our program to screen for new alpha-amylase inhibitors led to the isolation of strain ZG0656. The polyphasic taxonomic study revealed that strain ZG0656 represents a novel variation of Streptomyces coelicoflavus, for which we propose the name S. coelicoflavus var. nankaiensis. Four chemically distinct alpha-amylase inhibitors, acarviostatins I03, II03, III03 and IV03, were isolated from strain ZG0656. Acarviostatins III03 and IV03 are both novel oligomers. All four acarviostatins are mixed noncompetitive porcine pancreas alpha-amylase inhibitors. Acarviostatin III03 is the most potent alpha-amylase inhibitor known to date. Moreover, in the in vitro and in vivo experiments, acarviostatins III03 showed significant inhibition of starch hydrolysis and glucose transfer to blood. Strain ZG0656 is a novel variation of S. coelicoflavus, whose products are novel effective alpha-amylase inhibitors. Among the products, acarviostatins III03 could significantly depress blood glucose levels in mammalian systems and be developed towards a possible therapeutic agent for diabetes. Acarviostatin III03 is the most potent alpha-amylase inhibitor known to date. The oligomer will benefit the research on the relationship between alpha-amylase and various inhibitors and will offer more choices in diabetes treatments.

Seahorses of the Hippocampus coronatus complex: taxonomic revision, and description of Hippocampus haema, a new species from Korea and Japan (Teleostei, Syngnathidae).

PubMed

Han, Sang-Yun; Kim, Jin-Koo; Kai, Yoshiaki; Senou, Hiroshi

2017-01-01

Morphological and molecular analyses were conducted on 182 specimens belonging to the Hippocampus coronatus complex ( H. coronatus sensu lato), collected in Korea and Japan 1933-2015, in order to clarify the taxonomic status of the species within this complex. Three species are recognized based on the shape of the coronet, the number of trunk rings (TrR) and tail rings (TaR), and presence or absence of a wing-tip spine (WS) at the dorsal fin base. Hippocampus coronatus Temminck & Schlegel, 1850 ( H. coronatus sensu stricto), is diagnosed by 10 TrR, 37-40 TaR, an extremely high coronet (55.7-79.0 % head length) with four tips on the corona flat (CoT), and one WS. Hippocampus sindonis Jordan & Snyder, 1901 is diagnosed by 10 TrR, 35-38 TaR, a moderately high coronet (36.3-55.4 % HL) with five CoT, and no WS. A new species, H. haema is described on the basis of 140 specimens, characterized by 10 TrR, 35-38 TaR, a moderately high coronet (34.1-54.9 % head length) with four CoT, and two WS. Hippocampus haema is only known from the Korea Strait, western Kyushu, and East/Japan Sea. Recognition of the three species is supported by differences in mitochondrial DNA fragments (cytochrome b , 16S rRNA, and 12S rRNA).

Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming.

PubMed

Kroeker, Kristy J; Kordas, Rebecca L; Crim, Ryan; Hendriks, Iris E; Ramajo, Laura; Singh, Gerald S; Duarte, Carlos M; Gattuso, Jean-Pierre

2013-06-01

Ocean acidification represents a threat to marine species worldwide, and forecasting the ecological impacts of acidification is a high priority for science, management, and policy. As research on the topic expands at an exponential rate, a comprehensive understanding of the variability in organisms' responses and corresponding levels of certainty is necessary to forecast the ecological effects. Here, we perform the most comprehensive meta-analysis to date by synthesizing the results of 228 studies examining biological responses to ocean acidification. The results reveal decreased survival, calcification, growth, development and abundance in response to acidification when the broad range of marine organisms is pooled together. However, the magnitude of these responses varies among taxonomic groups, suggesting there is some predictable trait-based variation in sensitivity, despite the investigation of approximately 100 new species in recent research. The results also reveal an enhanced sensitivity of mollusk larvae, but suggest that an enhanced sensitivity of early life history stages is not universal across all taxonomic groups. In addition, the variability in species' responses is enhanced when they are exposed to acidification in multi-species assemblages, suggesting that it is important to consider indirect effects and exercise caution when forecasting abundance patterns from single-species laboratory experiments. Furthermore, the results suggest that other factors, such as nutritional status or source population, could cause substantial variation in organisms' responses. Last, the results highlight a trend towards enhanced sensitivity to acidification when taxa are concurrently exposed to elevated seawater temperature. © 2013 Blackwell Publishing Ltd.

Taxonomic Identification of Mediterranean Pines and Their Hybrids Based on the High Resolution Melting (HRM) and trnL Approaches: From Cytoplasmic Inheritance to Timber Tracing

PubMed Central

Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

2013-01-01

Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples. PMID:23577179

Epizoic communities of prokaryotes on healthy and diseased scleractinian corals in Lingayen Gulf, Philippines.

PubMed

Arboleda, Mark; Reichardt, Wolfgang

2009-01-01

In search for microbiological indicators of coral health and coral diseases, community profiles of coral-associated epizoic prokaryotes were investigated because of their dual potential as a source of coral pathogens and their antagonists. In pairwise samples of visually healthy and diseased coral specimens from Bolinao Bay (Pangasinan, Philippines), mixed biofilm communities of ectoderm- and mucus-colonizing epizoic prokaryotes were compared using fluorescent in situ hybridization (FISH). Oligonucleotide probes targeted 13 phylotypes representing the main taxonomic groups of marine prokaryotes. Coral taxa tended to show specific community profiles. An attempt to separate the profiles of healthy and diseased specimens by applying principal component analysis (PCA) to a (nonselective) collection of corals (affected by various diseases) proved unsuccessful. On the other hand, separate PCA clusters were obtained from healthy and diseased corals belonging to a single species (Pocillopora damicornis) only. This cluster formation was dominated by principal component 1 with the genus Vibrio accounting for 18%. At the same time, reef-site-specific clusters were formed as well. At a reef site exposed to pollution from intensive fish cage (Chanos chanos) farming, healthy P. damicornis were mainly (93%) colonized by unicellular cyanobacteria. The formal calculation of diversity parameters suggested that evenness in particular was driven by both health status and reef site location. Despite the low resolution of taxonomic levels achieved with FISH probes targeting only large phylotype groups, significant differences between healthy and diseased corals and also between polluted and nonpolluted reef sites were observed.

Phenotypic and mtDNA variation in Philippine Kappaphycus cottonii (Gigartinales, Rhodophyta).

PubMed

Dumilag, Richard V; Gallardo, William George M; Garcia, Christian Philip C; You, YeaEun; Chaves, Alyssa Keren G; Agahan, Lance

2017-11-09

Members of the carrageenan-producing seaweeds of the genus Kappapphycus have a complicated taxonomic history particularly with regard to species identification. Many taxonomic challenges in this group have been currently addressed with the use of mtDNA sequences. The phylogenetic status and genetic diversity of one of the lesser known species, Kappaphycus cottonii, have repeatedly come into question. This study explored the genetic variation in Philippine K. cottonii using the mtDNA COI-5P gene and cox2-3 spacer sequences. The six phenotypic forms in K. cottonii did not correspond to the observed genetic variability; hinting at the greater involvement of environmental factors in determining changes to the morphology of this alga. Our results revealed that the Philippine K. cottonii has the richest number of haplotypes that have been detected, so far, for any Kappaphycus species. Our inferred phylogenetic trees suggested two lineages: a lineage, which exclusively includes K. cottonii and another lineage comprising the four known Kappaphycus species: K. alvarezii, K. inermis, K. malesianus, and K. striatus. The dichotomy supports the apparent synamorphy for each of these lineages (the strictly terete thalli, lack of protuberances, and the presence of a hyphal central core in the latter group, while the opposite of these morphologies in K. cottonii). These findings shed new light on understanding the evolutionary history of the genus. Assessing the breadth of the phenotypic and genetic variation in K. cottonii has implications for the conservation and management of the overall Kappaphycus genetic resources, especially in the Philippines.

Designing and conducting in silico analysis for identifying of Echinococcus spp. with discrimination of novel haplotypes: an approach to better understanding of parasite taxonomic.

PubMed

Spotin, Adel; Gholami, Shirzad; Nasab, Abbas Najafi; Fallah, Esmaeil; Oskouei, Mahmoud Mahami; Semnani, Vahid; Shariatzadeh, Seyyed Ali; Shahbazi, Abbas

2015-04-01

The definitive identification of Echinococcus species is currently carried out by sequencing and phylogenetic strategies. However, the application of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) patterns is not broadly used as a result of heterogeneity traits of Echinococcus genome in different regions of the world. Therefore, designing and conducting a standardized pattern should indigenously be considered in under-studied areas. In this investigation, an in silico mapping was designed and developed for eight Echinococcus spp. on the basis of regional sequences in Iran and the world. The numbers of 60 Echinococcus isolates were collected from the liver and lungs of 15 human, 15 sheep, 15 cattle, and 15 camel cases in Semnan province, Central Iran. DNA samples were extracted and examined by polymerase chain reaction of ribosomal DNA (rDNA) internal transcribed spacer 1 (ITS1) and PCR-RFLP via Rsa1 endonuclease enzyme. Moreover, 15 amplicons of cytochrome oxidase 1 (Cox1) were directly sequenced in order to identify the strains/haplotypes. PCR-RFLP and phylogenetic analyses revealed firmly the presence of the G1 and G6 genotypes with heterogeneity (three novel haplotypes) of Cox1 gene although no other expected genotypes were found in the region. Finding shows that the identification of novel haplotypes along with discrimination of Echinococcus spp. through regional patterns can unambiguously illustrate the real taxonomic status of parasite in Central Iran.

Taxonomic identification of mediterranean pines and their hybrids based on the high resolution melting (HRM) and trnL approaches: from cytoplasmic inheritance to timber tracing.

PubMed

Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

2013-01-01

Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples.

Taxonomic review of the Oriental flower beetle Coilodera penicillata species complex (Coleoptera: Scarabaeidae: Cetoniinae).

PubMed

Qiu, Jian-Yue; Xu, Hao; Chen, L I

2017-11-20

The taxonomy of the Coilodera penicillata Hope, 1831 (Coleoptera: Scarabaeidae: Cetoniinae) species complex, which is recognized by the black body and elytra with larger tomentose maculae, is revised. Six Indochinese species assigned to this complex, including C. grandimaculata new species from Tibet, China. Coilodera nigroscutellaris Moser, 1902 revised status and C. formosana Moser, 1910 revised status formerly treated as two subspecies of C. penicillata Hope, 1831 are elevated to species rank. The distribution of C. penicillata in China is confirmed based on examination of specimens from Yunnan and Tibet, and almost all previous Chinese literature records should be referred to C. nigroscutellaris. Coilodera dives (Gory & Percheron, 1833) revised status previously synonymized with C. penicillata is herein considered as a valid species based on the examination of types and additional specimens, and C. miksici Antoine, 1986 new synonymy is regarded as a junior synonym of C. dives. A lectotype is designated for Coilodera dives (Gory & Percheron, 1833). The record of C. mearesii (Westwood, 1842) in southeastern China is attributed to a misidentification of C. nigroscutellaris, and it is here newly recoreded from Tibet near the Nepal-China border. Diagnosis characters and intraspecific variations are illustrated for all six species, new distribution records and a key to species are also presented. Ecological information is provided for all species.