New insights into the classification and nomenclature of cortical GABAergic interneurons.

PubMed

DeFelipe, Javier; López-Cruz, Pedro L; Benavides-Piccione, Ruth; Bielza, Concha; Larrañaga, Pedro; Anderson, Stewart; Burkhalter, Andreas; Cauli, Bruno; Fairén, Alfonso; Feldmeyer, Dirk; Fishell, Gord; Fitzpatrick, David; Freund, Tamás F; González-Burgos, Guillermo; Hestrin, Shaul; Hill, Sean; Hof, Patrick R; Huang, Josh; Jones, Edward G; Kawaguchi, Yasuo; Kisvárday, Zoltán; Kubota, Yoshiyuki; Lewis, David A; Marín, Oscar; Markram, Henry; McBain, Chris J; Meyer, Hanno S; Monyer, Hannah; Nelson, Sacha B; Rockland, Kathleen; Rossier, Jean; Rubenstein, John L R; Rudy, Bernardo; Scanziani, Massimo; Shepherd, Gordon M; Sherwood, Chet C; Staiger, Jochen F; Tamás, Gábor; Thomson, Alex; Wang, Yun; Yuste, Rafael; Ascoli, Giorgio A

2013-03-01

A systematic classification and accepted nomenclature of neuron types is much needed but is currently lacking. This article describes a possible taxonomical solution for classifying GABAergic interneurons of the cerebral cortex based on a novel, web-based interactive system that allows experts to classify neurons with pre-determined criteria. Using Bayesian analysis and clustering algorithms on the resulting data, we investigated the suitability of several anatomical terms and neuron names for cortical GABAergic interneurons. Moreover, we show that supervised classification models could automatically categorize interneurons in agreement with experts' assignments. These results demonstrate a practical and objective approach to the naming, characterization and classification of neurons based on community consensus.

New insights into the classification and nomenclature of cortical GABAergic interneurons

PubMed Central

DeFelipe, Javier; López-Cruz, Pedro L.; Benavides-Piccione, Ruth; Bielza, Concha; Larrañaga, Pedro; Anderson, Stewart; Burkhalter, Andreas; Cauli, Bruno; Fairén, Alfonso; Feldmeyer, Dirk; Fishell, Gord; Fitzpatrick, David; Freund, Tamás F.; González-Burgos, Guillermo; Hestrin, Shaul; Hill, Sean; Hof, Patrick R.; Huang, Josh; Jones, Edward G.; Kawaguchi, Yasuo; Kisvárday, Zoltán; Kubota, Yoshiyuki; Lewis, David A.; Marín, Oscar; Markram, Henry; McBain, Chris J.; Meyer, Hanno S.; Monyer, Hannah; Nelson, Sacha B.; Rockland, Kathleen; Rossier, Jean; Rubenstein, John L. R.; Rudy, Bernardo; Scanziani, Massimo; Shepherd, Gordon M.; Sherwood, Chet C.; Staiger, Jochen F.; Tamás, Gábor; Thomson, Alex; Wang, Yun; Yuste, Rafael; Ascoli, Giorgio A.

2013-01-01

A systematic classification and accepted nomenclature of neuron types is much needed but is currently lacking. This article describes a possible taxonomical solution for classifying GABAergic interneurons of the cerebral cortex based on a novel, web-based interactive system that allows experts to classify neurons with pre-determined criteria. Using Bayesian analysis and clustering algorithms on the resulting data, we investigated the suitability of several anatomical terms and neuron names for cortical GABAergic interneurons. Moreover, we show that supervised classification models could automatically categorize interneurons in agreement with experts’ assignments. These results demonstrate a practical and objective approach to the naming, characterization and classification of neurons based on community consensus. PMID:23385869

Development of archetypes for non-ranking classification and comparison of European National Health Technology Assessment systems.

PubMed

Allen, Nicola; Pichler, Franz; Wang, Tina; Patel, Sundip; Salek, Sam

2013-12-01

European countries are increasingly utilising health technology assessment (HTA) to inform reimbursement decision-making. However, the current European HTA environment is very diverse, and projects are already underway to initiate a more efficient and aligned HTA practice within Europe. This study aims to identify a non-ranking method for classifying the diversity of European HTA agencies process and the organisational architecture of the national regulatory review to reimbursement systems. Using a previously developed mapping methodology, this research created process maps to describe national processes for regulatory review to reimbursement for 33 European jurisdictions. These process maps enabled the creation of 2 HTA taxonomic sets. The confluence of the two taxonomic sets was subsequently cross-referenced to identify 10 HTA archetype groups. HTA is a young, rapidly evolving field and it can be argued that optimal practices for performing HTA are yet to emerge. Therefore, a non-ranking classification approach could objectively characterise and compare the diversity observed in the current European HTA environment. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Integrative analysis of environmental sequences using MEGAN4.

PubMed

Huson, Daniel H; Mitra, Suparna; Ruscheweyh, Hans-Joachim; Weber, Nico; Schuster, Stephan C

2011-09-01

A major challenge in the analysis of environmental sequences is data integration. The question is how to analyze different types of data in a unified approach, addressing both the taxonomic and functional aspects. To facilitate such analyses, we have substantially extended MEGAN, a widely used taxonomic analysis program. The new program, MEGAN4, provides an integrated approach to the taxonomic and functional analysis of metagenomic, metatranscriptomic, metaproteomic, and rRNA data. While taxonomic analysis is performed based on the NCBI taxonomy, functional analysis is performed using the SEED classification of subsystems and functional roles or the KEGG classification of pathways and enzymes. A number of examples illustrate how such analyses can be performed, and show that one can also import and compare classification results obtained using others' tools. MEGAN4 is freely available for academic purposes, and installers for all three major operating systems can be downloaded from www-ab.informatik.uni-tuebingen.de/software/megan.

Unbiased Taxonomic Annotation of Metagenomic Samples

PubMed Central

Fosso, Bruno; Pesole, Graziano; Rosselló, Francesc

2018-01-01

Abstract The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under the receiver operating characteristic (ROC) curve and F-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample. PMID:29028181

[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.

Classifying short genomic fragments from novel lineages using composition and homology

PubMed Central

2011-01-01

Background The assignment of taxonomic attributions to DNA fragments recovered directly from the environment is a vital step in metagenomic data analysis. Assignments can be made using rank-specific classifiers, which assign reads to taxonomic labels from a predetermined level such as named species or strain, or rank-flexible classifiers, which choose an appropriate taxonomic rank for each sequence in a data set. The choice of rank typically depends on the optimal model for a given sequence and on the breadth of taxonomic groups seen in a set of close-to-optimal models. Homology-based (e.g., LCA) and composition-based (e.g., PhyloPythia, TACOA) rank-flexible classifiers have been proposed, but there is at present no hybrid approach that utilizes both homology and composition. Results We first develop a hybrid, rank-specific classifier based on BLAST and Naïve Bayes (NB) that has comparable accuracy and a faster running time than the current best approach, PhymmBL. By substituting LCA for BLAST or allowing the inclusion of suboptimal NB models, we obtain a rank-flexible classifier. This hybrid classifier outperforms established rank-flexible approaches on simulated metagenomic fragments of length 200 bp to 1000 bp and is able to assign taxonomic attributions to a subset of sequences with few misclassifications. We then demonstrate the performance of different classifiers on an enhanced biological phosphorous removal metagenome, illustrating the advantages of rank-flexible classifiers when representative genomes are absent from the set of reference genomes. Application to a glacier ice metagenome demonstrates that similar taxonomic profiles are obtained across a set of classifiers which are increasingly conservative in their classification. Conclusions Our NB-based classification scheme is faster than the current best composition-based algorithm, Phymm, while providing equally accurate predictions. The rank-flexible variant of NB, which we term ε-NB, is complementary to LCA and can be combined with it to yield conservative prediction sets of very high confidence. The simple parameterization of LCA and ε-NB allows for tuning of the balance between more predictions and increased precision, allowing the user to account for the sensitivity of downstream analyses to misclassified or unclassified sequences. PMID:21827705

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 compendium of fossil marine animal families, 2nd edition

NASA Technical Reports Server (NTRS)

Sepkoski, J. J. Jr; Sepkoski JJ, J. r. (Principal Investigator)

1992-01-01

A comprehensive listing of 4075 taxonomic families of marine animals known from the fossil record is presented. This listing covers invertebrates, vertebrates, and animal-like protists, gives time intervals of apparent origination and extinction, and provides literature sources for these data. The time intervals are mostly 81 internationally recognized stratigraphic stages; more than half of the data are resolved to one of 145 substage divisions, providing more highly resolved data for studies of taxic macroevolution. Families are classified by order, class, and phylum, reflecting current classifications in the published literature. This compendium is a new edition of the 1982 publication, correcting errors and presenting greater stratigraphic resolution and more current ideas about acceptable families and their classification.

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.

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…

Classifying the bacterial gut microbiota of termites and cockroaches: A curated phylogenetic reference database (DictDb).

PubMed

Mikaelyan, Aram; Köhler, Tim; Lampert, Niclas; Rohland, Jeffrey; Boga, Hamadi; Meuser, Katja; Brune, Andreas

2015-10-01

Recent developments in sequencing technology have given rise to a large number of studies that assess bacterial diversity and community structure in termite and cockroach guts based on large amplicon libraries of 16S rRNA genes. Although these studies have revealed important ecological and evolutionary patterns in the gut microbiota, classification of the short sequence reads is limited by the taxonomic depth and resolution of the reference databases used in the respective studies. Here, we present a curated reference database for accurate taxonomic analysis of the bacterial gut microbiota of dictyopteran insects. The Dictyopteran gut microbiota reference Database (DictDb) is based on the Silva database but was significantly expanded by the addition of clones from 11 mostly unexplored termite and cockroach groups, which increased the inventory of bacterial sequences from dictyopteran guts by 26%. The taxonomic depth and resolution of DictDb was significantly improved by a general revision of the taxonomic guide tree for all important lineages, including a detailed phylogenetic analysis of the Treponema and Alistipes complexes, the Fibrobacteres, and the TG3 phylum. The performance of this first documented version of DictDb (v. 3.0) using the revised taxonomic guide tree in the classification of short-read libraries obtained from termites and cockroaches was highly superior to that of the current Silva and RDP databases. DictDb uses an informative nomenclature that is consistent with the literature also for clades of uncultured bacteria and provides an invaluable tool for anyone exploring the gut community structure of termites and cockroaches. Copyright © 2015 Elsevier GmbH. All rights reserved.

Fast and sensitive taxonomic classification for metagenomics with Kaiju

PubMed Central

Menzel, Peter; Ng, Kim Lee; Krogh, Anders

2016-01-01

Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows–Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk. PMID:27071849

Fast and sensitive taxonomic classification for metagenomics with Kaiju.

PubMed

Menzel, Peter; Ng, Kim Lee; Krogh, Anders

2016-04-13

Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows-Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk.

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.

Consensus proposals for classification of the family Hepeviridae.

PubMed

Smith, Donald B; Simmonds, Peter; Jameel, Shahid; Emerson, Suzanne U; Harrison, Tim J; Meng, Xiang-Jin; Okamoto, Hiroaki; Van der Poel, Wim H M; Purdy, Michael A

2014-10-01

The family Hepeviridae consists of positive-stranded RNA viruses that infect a wide range of mammalian species, as well as chickens and trout. A subset of these viruses infects humans and can cause a self-limiting acute hepatitis that may become chronic in immunosuppressed individuals. Current published descriptions of the taxonomical divisions within the family Hepeviridae are contradictory in relation to the assignment of species and genotypes. Through analysis of existing sequence information, we propose a taxonomic scheme in which the family is divided into the genera Orthohepevirus (all mammalian and avian hepatitis E virus (HEV) isolates) and Piscihepevirus (cutthroat trout virus). Species within the genus Orthohepevirus are designated Orthohepevirus A (isolates from human, pig, wild boar, deer, mongoose, rabbit and camel), Orthohepevirus B (isolates from chicken), Orthohepevirus C (isolates from rat, greater bandicoot, Asian musk shrew, ferret and mink) and Orthohepevirus D (isolates from bat). Proposals are also made for the designation of genotypes within the human and rat HEVs. This hierarchical system is congruent with hepevirus phylogeny, and the three classification levels (genus, species and genotype) are consistent with, and reflect discontinuities in the ranges of pairwise distances between amino acid sequences. Adoption of this system would include the avoidance of host names in taxonomic identifiers and provide a logical framework for the assignment of novel variants.

Problems of classification in the family Paramyxoviridae.

PubMed

Rima, Bert; Collins, Peter; Easton, Andrew; Fouchier, Ron; Kurath, Gael; Lamb, Robert A; Lee, Benhur; Maisner, Andrea; Rota, Paul; Wang, Lin-Fa

2018-05-01

A number of unassigned viruses in the family Paramyxoviridae need to be classified either as a new genus or placed into one of the seven genera currently recognized in this family. Furthermore, numerous new paramyxoviruses continue to be discovered. However, attempts at classification have highlighted the difficulties that arise by applying historic criteria or criteria based on sequence alone to the classification of the viruses in this family. While the recent taxonomic change that elevated the previous subfamily Pneumovirinae into a separate family Pneumoviridae is readily justified on the basis of RNA dependent -RNA polymerase (RdRp or L protein) sequence motifs, using RdRp sequence comparisons for assignment to lower level taxa raises problems that would require an overhaul of the current criteria for assignment into genera in the family Paramyxoviridae. Arbitrary cut off points to delineate genera and species would have to be set if classification was based on the amino acid sequence of the RdRp alone or on pairwise analysis of sequence complementarity (PASC) of all open reading frames (ORFs). While these cut-offs cannot be made consistent with the current classification in this family, resorting to genus-level demarcation criteria with additional input from the biological context may afford a way forward. Such criteria would reflect the increasingly dynamic nature of virus taxonomy even if it would require a complete revision of the current classification.

A Taxonomy of Introductory Physics Concepts.

NASA Astrophysics Data System (ADS)

Mokaya, Fridah; Savkar, Amit; Valente, Diego

We have designed and implemented a hierarchical taxonomic classification of physics concepts for our introductory physics for engineers course sequence taught at the University of Connecticut. This classification can be used to provide a mechanism to measure student progress in learning at the level of individual concepts or clusters of concepts, and also as part of a tool to measure effectiveness of teaching pedagogy. We examine our pre- and post-test FCI results broken down by topics using Hestenes et al.'s taxonomy classification for the FCI, and compare these results with those found using our own taxonomy classification. In addition, we expand this taxonomic classification to measure performance in our other course exams, investigating possible correlations in results achieved across different assessments at the individual topic level. UCONN CLAS(College of Liberal Arts and Science).

The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

Treesearch

C.L. Schoch; G.-H. Sung; F. Lopez-Giraldez

2009-01-01

We present a six-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the fungi are resolved for...

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.

PubMed

Foster, Zachary S L; Sharpton, Thomas J; Grünwald, Niklaus J

2017-02-01

Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual.

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

PubMed Central

Foster, Zachary S. L.; Sharpton, Thomas J.

2017-01-01

Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual. PMID:28222096

Default taxonomy: Ernst Mayr's view of the microbial world

NASA Technical Reports Server (NTRS)

Woese, C. R.

1998-01-01

This perspective is a response to a taxonomic proposal by E. Mayr ["Two empires or three?" (1998) Proc. Natl. Acad. Sci. USA 95, 9720-9723]. Mayr has suggested that the now accepted classification of life into three primary domains, Archaea, Bacteria, and Eucarya-originally proposed by myself and others--be abandoned in favor of the earlier Prokaryote-Eukaryote classification. Although the matter appears a taxonomic quibble, it is not that simple. At issue here are differing views as to the nature of biological classification, which are underlain by differing views as to what biology is and will be--matters of concern to all biologists.

An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery

PubMed Central

Parker, Michael T.

2016-01-01

Recent advances in sequencing technologies have opened the door for the classification of the human virome. While taxonomic classification can be applied to the viruses identified in such studies, this gives no information as to the type of interaction the virus has with the host. As follow-up studies are performed to address these questions, the description of these virus-host interactions would be greatly enriched by applying a standard set of definitions that typify them. This paper describes a framework with which all members of the human virome can be classified based on principles of ecology. The scaffold not only enables categorization of the human virome, but can also inform research aimed at identifying novel virus-host interactions. PMID:27698618

Hyperspectral Biofilm Classification Analysis for Carrying Capacity of Migratory Birds in the South Bay Salt Ponds

NASA Technical Reports Server (NTRS)

Hsu, Wei-Chen; Kuss, Amber Jean; Ketron, Tyler; Nguyen, Andrew; Remar, Alex Covello; Newcomer, Michelle; Fleming, Erich; Debout, Leslie; Debout, Brad; Detweiler, Angela;

Nursing Classification Systems

PubMed Central

Henry, Suzanne Bakken; Mead, Charles N.

1997-01-01

Abstract Our premise is that from the perspective of maximum flexibility of data usage by computer-based record (CPR) systems, existing nursing classification systems are necessary, but not sufficient, for representing important aspects of “what nurses do.” In particular, we have focused our attention on those classification systems that represent nurses' clinical activities through the abstraction of activities into categories of nursing interventions. In this theoretical paper, we argue that taxonomic, combinatorial vocabularies capable of coding atomic-level nursing activities are required to effectively capture in a reproducible and reversible manner the clinical decisions and actions of nurses, and that, without such vocabularies and associated grammars, potentially important clinical process data is lost during the encoding process. Existing nursing intervention classification systems do not fulfill these criteria. As background to our argument, we first present an overview of the content, methods, and evaluation criteria used in previous studies whose focus has been to evaluate the effectiveness of existing coding and classification systems. Next, using the Ingenerf typology of taxonomic vocabularies, we categorize the formal type and structure of three existing nursing intervention classification systems—Nursing Interventions Classification, Omaha System, and Home Health Care Classification. Third, we use records from home care patients to show examples of lossy data transformation, the loss of potentially significant atomic data, resulting from encoding using each of the three systems. Last, we provide an example of the application of a formal representation methodology (conceptual graphs) which we believe could be used as a model to build the required combinatorial, taxonomic vocabulary for representing nursing interventions. PMID:9147341

Taxonomy of asteroids. [according to polarimetric, spectrophotometric, radiometric, and UBV photometric data

NASA Technical Reports Server (NTRS)

Bowell, E.; Chapman, C. R.; Gradie, J. C.; Zellner, B.; Morrison, D.

1978-01-01

A taxonomic system for asteroids is discussed which is based on seven directly observable parameters from polarimetry, spectrophotometry, radiometry, and UBV photometry. The classification scheme is entirely empirical and independent of specific mineralogical interpretations. Five broad classes (designated C, S, M, E, and R), as well as an 'unclassifiable' designation, are defined on the basis of observational data for 523 asteroids. Computer-generated type classifications and derived diameters are given for the 523 asteroids, and the application of the classification procedure is illustrated. Of the 523 asteroids classified, 190 are identified as C objects, 141 as S type, 13 as type M, three as type E, three as type R, 55 as unclassifiable, and 118 as ambiguous. The present taxonomic system is compared with several other asteroid classification systems.

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

PubMed Central

Liu, Jiemeng; Wang, Haifeng; Yang, Hongxing; Zhang, Yizhe; Wang, Jinfeng; Zhao, Fangqing; Qi, Ji

2013-01-01

Compared with traditional algorithms for long metagenomic sequence classification, characterizing microorganisms’ taxonomic and functional abundance based on tens of millions of very short reads are much more challenging. We describe an efficient composition and phylogeny-based algorithm [Metagenome Composition Vector (MetaCV)] to classify very short metagenomic reads (75–100 bp) into specific taxonomic and functional groups. We applied MetaCV to the Meta-HIT data (371-Gb 75-bp reads of 109 human gut metagenomes), and this single-read-based, instead of assembly-based, classification has a high resolution to characterize the composition and structure of human gut microbiota, especially for low abundance species. Most strikingly, it only took MetaCV 10 days to do all the computation work on a server with five 24-core nodes. To our knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time. PMID:22941634

Concept relationship editor: a visual interface to support the assertion of synonymy relationships between taxonomic classifications

NASA Astrophysics Data System (ADS)

Craig, Paul; Kennedy, Jessie

2008-01-01

An increasingly common approach being taken by taxonomists to define the relationships between taxa in alternative hierarchical classifications is to use a set-based notation which states relationship between two taxa from alternative classifications. Textual recording of these relationships is cumbersome and difficult for taxonomists to manage. While text based GUI tools are beginning to appear which ease the process, these have several limitations. Interactive visual tools offer greater potential to allow taxonomists to explore the taxa in these hierarchies and specify such relationships. This paper describes the Concept Relationship Editor, an interactive visualisation tool designed to support the assertion of relationships between taxonomic classifications. The tool operates using an interactive space-filling adjacency layout which allows users to expand multiple lists of taxa with common parents so they can explore and assert relationships between two classifications.

Cross-Classification and Category Representation in Children's Concepts

ERIC Educational Resources Information Center

Nguyen, Simone P.

2007-01-01

Items commonly belong to many categories. Cross-classification is the classification of a single item into more than one category. This research explored 2- to 6-year-old children's use of 2 different category systems for cross-classification: script (e.g., school-time items, birthday party items) and taxonomic (e.g., animals, clothes). The…

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.

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

A Higher Level Classification of All Living Organisms

PubMed Central

Ruggiero, Michael A.; Gordon, Dennis P.; Orrell, Thomas M.; Bailly, Nicolas; Bourgoin, Thierry; Brusca, Richard C.; Cavalier-Smith, Thomas; Guiry, Michael D.; Kirk, Paul M.

2015-01-01

We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists’ expert opinions in a unified and coherent, hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collaborative effort is to provide a hierarchical classification serving not only the needs of the CoL’s database providers but also the diverse public-domain user community, most of whom are familiar with the Linnaean conceptual system of ordering taxon relationships. This classification is neither phylogenetic nor evolutionary but instead represents a consensus view that accommodates taxonomic choices and practical compromises among diverse expert opinions, public usages, and conflicting evidence about the boundaries between taxa and the ranks of major taxa, including kingdoms. Certain key issues, some not fully resolved, are addressed in particular. Beyond its immediate use as a management tool for the CoL and ITIS (Integrated Taxonomic Information System), it is immediately valuable as a reference for taxonomic and biodiversity research, as a tool for societal communication, and as a classificatory “backbone” for biodiversity databases, museum collections, libraries, and textbooks. Such a modern comprehensive hierarchy has not previously existed at this level of specificity. PMID:25923521

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

Mainzer, A.; Masiero, J.; Bauer, J.

We have combined the NEOWISE and Sloan Digital Sky Survey data to study the albedos of 24,353 asteroids with candidate taxonomic classifications derived using Sloan photometry. We find a wide range of moderate to high albedos for candidate S-type asteroids that are analogous to the S complex defined by previous spectrophotometrically based taxonomic systems. The candidate C-type asteroids, while generally very dark, have a tail of higher albedos that overlaps the S types. The albedo distribution for asteroids with a photometrically derived Q classification is extremely similar to those of the S types. Asteroids with similar colors to (4) Vestamore » have higher albedos than the S types, and most have orbital elements similar to known Vesta family members. Finally, we show that the relative reflectance at 3.4 and 4.6 {mu}m is higher for D-type asteroids and suggest that their red visible and near-infrared spectral slope extends out to these wavelengths. Understanding the relationship between size, albedo, and taxonomic classification is complicated by the fact that the objects with classifications were selected from the visible/near-infrared Sloan Moving Object Catalog, which is biased against fainter asteroids, including those with lower albedos.« less

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.

Classification of Instructional Programs: 2000 Edition.

ERIC Educational Resources Information Center

Morgan, Robert L.; Hunt, E. Stephen

This third revision of the Classification of Instructional Programs (CIP) updates and modifies education program classifications, providing a taxonomic scheme that supports the accurate tracking, assessment, and reporting of field of study and program completions activity. This edition has also been adopted as the standard field of study taxonomy…

A New Tool for Classifying Small Solar System Objects

NASA Astrophysics Data System (ADS)

Desfosses, Ryan; Arel, D.; Walker, M. E.; Ziffer, J.; Harvell, T.; Campins, H.; Fernandez, Y. R.

2011-05-01

An artificial intelligence program, AutoClass, which was developed by NASA's Artificial Intelligence Branch, uses Bayesian classification theory to automatically choose the most probable classification distribution to describe a dataset. To investigate its usefulness to the Planetary Science community, we tested its ability to reproduce the taxonomic classes as defined by Tholen and Barucci (1989). Of the 406 asteroids from the Eight Color Asteroid Survey (ECAS) we chose for our test, 346 were firmly classified and all but 3 (<1%) were classified by Autoclass as they had been in the previous classification system (Walker et al., 2011). We are now applying it to larger datasets to improve the taxonomy of currently unclassified objects. Having demonstrated AutoClass's ability to recreate existing classification effectively, we extended this work to investigations of albedo-based classification systems. To determine how predictive albedo can be, we used data from the Infrared Astronomical Satellite (IRAS) database in conjunction with the large Sloan Digital Sky Survey (SDSS), which contains color and position data for over 200,000 classified and unclassified asteroids (Ivesic et al., 2001). To judge our success we compared our results with a similar approach to classifying objects using IRAS albedo and asteroid color by Tedesco et al. (1989). Understanding the distribution of the taxonomic classes is important to understanding the history and evolution of our Solar System. AutoClass's success in categorizing ECAS, IRAS and SDSS asteroidal data highlights its potential to scan large domains for natural classes in small solar system objects. Based upon our AutoClass results, we intend to make testable predictions about asteroids observed with the Wide-field Infrared Survey Explorer (WISE).

A System to Automatically Classify and Name Any Individual Genome-Sequenced Organism Independently of Current Biological Classification and Nomenclature

PubMed Central

Song, Yuhyun; Leman, Scotland; Monteil, Caroline L.; Heath, Lenwood S.; Vinatzer, Boris A.

2014-01-01

A broadly accepted and stable biological classification system is a prerequisite for biological sciences. It provides the means to describe and communicate about life without ambiguity. Current biological classification and nomenclature use the species as the basic unit and require lengthy and laborious species descriptions before newly discovered organisms can be assigned to a species and be named. The current system is thus inadequate to classify and name the immense genetic diversity within species that is now being revealed by genome sequencing on a daily basis. To address this lack of a general intra-species classification and naming system adequate for today’s speed of discovery of new diversity, we propose a classification and naming system that is exclusively based on genome similarity and that is suitable for automatic assignment of codes to any genome-sequenced organism without requiring any phenotypic or phylogenetic analysis. We provide examples demonstrating that genome similarity-based codes largely align with current taxonomic groups at many different levels in bacteria, animals, humans, plants, and viruses. Importantly, the proposed approach is only slightly affected by the order of code assignment and can thus provide codes that reflect similarity between organisms and that do not need to be revised upon discovery of new diversity. We envision genome similarity-based codes to complement current biological nomenclature and to provide a universal means to communicate unambiguously about any genome-sequenced organism in fields as diverse as biodiversity research, infectious disease control, human and microbial forensics, animal breed and plant cultivar certification, and human ancestry research. PMID:24586551

40 CFR 725.12 - Identification of microorganisms for Inventory and other listing purposes.

Code of Federal Regulations, 2010 CFR

2010-07-01

... for the purpose of taxonomic classification. Upon EPA's request to the submitter, data supporting the taxonomic designation must be provided to EPA. The genetic history of the recipient microorganism should be... distinguishing genotypic characteristics of a microorganism, such as the identity of the introduced genetic...

Drinking Water Microbiome as a Screening Tool for ...

EPA Pesticide Factsheets

Many water utilities in the US using chloramine as disinfectant treatment in their distribution systems have experienced nitrification episodes, which detrimentally impact the water quality. A chloraminated drinking water distribution system (DWDS) simulator was operated through four successive operational schemes, including two stable events (SS) and an episode of nitrification (SF), followed by a ‘chlorine burn’ (SR) by switching disinfectant from chloramine to free chlorine. The current research investigated the viability of biological signatures as potential indicators of operational failure and predictors of nitrification in DWDS. For this purpose, we examined the bulk water (BW) bacterial microbiome of a chloraminated DWDS simulator operated through successive operational schemes, including an episode of nitrification. BW data was chosen because sampling of BW in a DWDS by water utility operators is relatively simpler and easier than collecting biofilm samples from underground pipes. The methodology applied a supervised classification machine learning approach (naïve Bayes algorithm) for developing predictive models for nitrification. Classification models were trained with biological datasets (Operational Taxonomic Unit [OTU] and genus-level taxonomic groups) generated using next generation high-throughput technology, and divided into two groups (i.e. binary) of positives and negatives (Failure and Stable, respectively). We also invest

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.

The normative structure of mathematization in systematic biology.

PubMed

Sterner, Beckett; Lidgard, Scott

2014-06-01

We argue that the mathematization of science should be understood as a normative activity of advocating for a particular methodology with its own criteria for evaluating good research. As a case study, we examine the mathematization of taxonomic classification in systematic biology. We show how mathematization is a normative activity by contrasting its distinctive features in numerical taxonomy in the 1960s with an earlier reform advocated by Ernst Mayr starting in the 1940s. Both Mayr and the numerical taxonomists sought to formalize the work of classification, but Mayr introduced a qualitative formalism based on human judgment for determining the taxonomic rank of populations, while the numerical taxonomists introduced a quantitative formalism based on automated procedures for computing classifications. The key contrast between Mayr and the numerical taxonomists is how they conceptualized the temporal structure of the workflow of classification, specifically where they allowed meta-level discourse about difficulties in producing the classification. Copyright © 2014. Published by Elsevier Ltd.

Accurate phylogenetic classification of DNA fragments based onsequence composition

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

McHardy, Alice C.; Garcia Martin, Hector; Tsirigos, Aristotelis

2006-05-01

Metagenome studies have retrieved vast amounts of sequenceout of a variety of environments, leading to novel discoveries and greatinsights into the uncultured microbial world. Except for very simplecommunities, diversity makes sequence assembly and analysis a verychallenging problem. To understand the structure a 5 nd function ofmicrobial communities, a taxonomic characterization of the obtainedsequence fragments is highly desirable, yet currently limited mostly tothose sequences that contain phylogenetic marker genes. We show that forclades at the rank of domain down to genus, sequence composition allowsthe very accurate phylogenetic 10 characterization of genomic sequence.We developed a composition-based classifier, PhyloPythia, for de novophylogenetic sequencemore » characterization and have trained it on adata setof 340 genomes. By extensive evaluation experiments we show that themethodis accurate across all taxonomic ranks considered, even forsequences that originate fromnovel organisms and are as short as 1kb.Application to two metagenome datasets 15 obtained from samples ofphosphorus-removing sludge showed that the method allows the accurateclassification at genus level of most sequence fragments from thedominant populations, while at the same time correctly characterizingeven larger parts of the samples at higher taxonomic levels.« less

From learning taxonomies to phylogenetic learning: integration of 16S rRNA gene data into FAME-based bacterial classification.

PubMed

Slabbinck, Bram; Waegeman, Willem; Dawyndt, Peter; De Vos, Paul; De Baets, Bernard

2010-01-30

Machine learning techniques have shown to improve bacterial species classification based on fatty acid methyl ester (FAME) data. Nonetheless, FAME analysis has a limited resolution for discrimination of bacteria at the species level. In this paper, we approach the species classification problem from a taxonomic point of view. Such a taxonomy or tree is typically obtained by applying clustering algorithms on FAME data or on 16S rRNA gene data. The knowledge gained from the tree can then be used to evaluate FAME-based classifiers, resulting in a novel framework for bacterial species classification. In view of learning in a taxonomic framework, we consider two types of trees. First, a FAME tree is constructed with a supervised divisive clustering algorithm. Subsequently, based on 16S rRNA gene sequence analysis, phylogenetic trees are inferred by the NJ and UPGMA methods. In this second approach, the species classification problem is based on the combination of two different types of data. Herein, 16S rRNA gene sequence data is used for phylogenetic tree inference and the corresponding binary tree splits are learned based on FAME data. We call this learning approach 'phylogenetic learning'. Supervised Random Forest models are developed to train the classification tasks in a stratified cross-validation setting. In this way, better classification results are obtained for species that are typically hard to distinguish by a single or flat multi-class classification model. FAME-based bacterial species classification is successfully evaluated in a taxonomic framework. Although the proposed approach does not improve the overall accuracy compared to flat multi-class classification, it has some distinct advantages. First, it has better capabilities for distinguishing species on which flat multi-class classification fails. Secondly, the hierarchical classification structure allows to easily evaluate and visualize the resolution of FAME data for the discrimination of bacterial species. Summarized, by phylogenetic learning we are able to situate and evaluate FAME-based bacterial species classification in a more informative context.

From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification

PubMed Central

2010-01-01

Background Machine learning techniques have shown to improve bacterial species classification based on fatty acid methyl ester (FAME) data. Nonetheless, FAME analysis has a limited resolution for discrimination of bacteria at the species level. In this paper, we approach the species classification problem from a taxonomic point of view. Such a taxonomy or tree is typically obtained by applying clustering algorithms on FAME data or on 16S rRNA gene data. The knowledge gained from the tree can then be used to evaluate FAME-based classifiers, resulting in a novel framework for bacterial species classification. Results In view of learning in a taxonomic framework, we consider two types of trees. First, a FAME tree is constructed with a supervised divisive clustering algorithm. Subsequently, based on 16S rRNA gene sequence analysis, phylogenetic trees are inferred by the NJ and UPGMA methods. In this second approach, the species classification problem is based on the combination of two different types of data. Herein, 16S rRNA gene sequence data is used for phylogenetic tree inference and the corresponding binary tree splits are learned based on FAME data. We call this learning approach 'phylogenetic learning'. Supervised Random Forest models are developed to train the classification tasks in a stratified cross-validation setting. In this way, better classification results are obtained for species that are typically hard to distinguish by a single or flat multi-class classification model. Conclusions FAME-based bacterial species classification is successfully evaluated in a taxonomic framework. Although the proposed approach does not improve the overall accuracy compared to flat multi-class classification, it has some distinct advantages. First, it has better capabilities for distinguishing species on which flat multi-class classification fails. Secondly, the hierarchical classification structure allows to easily evaluate and visualize the resolution of FAME data for the discrimination of bacterial species. Summarized, by phylogenetic learning we are able to situate and evaluate FAME-based bacterial species classification in a more informative context. PMID:20113515

EAU standardised medical terminology for urologic imaging: a taxonomic approach.

PubMed

Loch, Tillmann; Carey, Brendan; Walz, Jochen; Fulgham, Pat Fox

2015-05-01

The terminology and abbreviations used in urologic imaging have generally been adopted on an ad hoc basis by different speciality groups; however, there is a need for shared nomenclature to facilitate clinical communication and collaborative research. This work reviews the current nomenclature for urologic imaging used in clinical practice and proposes a taxonomy and terminology for urologic imaging studies. A list of terms used in urologic imaging were compiled from guidelines published by the European Association of Urology and the American Urological Association and from the American College of Radiology Appropriateness Criteria. Terms searched were grouped into broad categories based on technology, and imaging terms were further stratified based on the anatomic extent, contrast or phases, technique or modifiers, and combinations or fusions. Terms that had a high degree of utilisation were classified as accepted. We propose a new taxonomy to define a more useful and acceptable nomenclature model acceptable to all health professionals involved in urology. The major advantage of a taxonomic approach to the classification of urologic imaging studies is that it provides a flexible framework for classifying the modifications of current imaging modalities and allows the incorporation of new imaging modalities. The adoption of this hierarchical classification model ranging from the most general to the most detailed descriptions should facilitate hierarchical searches of the medical literature using both general and specific terms. This work is limited in its scope, as it is not currently all-inclusive. This will hopefully be addressed by future modification as others embrace the concept and work towards uniformity in nomenclature. This paper provides a noncomprehensive list of the most widely used terms across different specialties. This list can be used as the basis for further discussion, development, and enhancement. In this paper we describe a classification system for urologic imaging terms with the aim of aiding health professionals and ensuring that the terms used are more consistent. Copyright © 2014 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Scalable metagenomic taxonomy classification using a reference genome database

PubMed Central

Ames, Sasha K.; Hysom, David A.; Gardner, Shea N.; Lloyd, G. Scott; Gokhale, Maya B.; Allen, Jonathan E.

2013-01-01

Motivation: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. Results: A method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take <20 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample. Availability: Software was implemented in C++ and is freely available at http://sourceforge.net/projects/lmat Contact: allen99@llnl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23828782

Fish Ontology framework for taxonomy-based fish recognition

PubMed Central

Ali, Najib M.; Khan, Haris A.; Then, Amy Y-Hui; Ving Ching, Chong; Gaur, Manas

2017-01-01

Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval. Automated classification for unknown specimens is a unique feature that currently does not appear to exist in other known ontologies. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1,830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users. PMID:28929028

Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018).

PubMed

King, Andrew M Q; Lefkowitz, Elliot J; Mushegian, Arcady R; Adams, Michael J; Dutilh, Bas E; Gorbalenya, Alexander E; Harrach, Balázs; Harrison, Robert L; Junglen, Sandra; Knowles, Nick J; Kropinski, Andrew M; Krupovic, Mart; Kuhn, Jens H; Nibert, Max L; Rubino, Luisa; Sabanadzovic, Sead; Sanfaçon, Hélène; Siddell, Stuart G; Simmonds, Peter; Varsani, Arvind; Zerbini, Francisco Murilo; Davison, Andrew J

2018-05-12

This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses in February 2018. A total of 451 species, 69 genera, 11 subfamilies, 9 families and one new order were added to the taxonomy. The current totals at each taxonomic level now stand at 9 orders, 131 families, 46 subfamilies, 803 genera and 4853 species. A change was made to the International Code of Virus Classification and Nomenclature to allow the use of the names of people in taxon names under appropriate circumstances. An updated Master Species List incorporating the approved changes was released in March 2018 ( https://talk.ictvonline.org/taxonomy/ ).

Incidental Learning and Recall in Children.

ERIC Educational Resources Information Center

Fox, Robert A.; And Others

Incidental learning research with mentally retarded children has produced findings inconsistent with those reported for the intellectually normal population. This study was designed to further investigate the efficacy of incidental semantic classification instructions relative to taxonomic classification instructions or superficial color…

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

USDA-ARS?s Scientific Manuscript database

Community composition data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alt...

Generic Language Facilitates Children's Cross-Classification

ERIC Educational Resources Information Center

Nguyen, Simone P.; Gelman, A.

2012-01-01

Four studies examined the role of generic language in facilitating 4- and 5-year-old children's ability to cross-classify. Participants were asked to classify an item into a familiar (taxonomic or script) category, then cross-classify it into a novel (script or taxonomic) category with the help of a clue expressed in either generic or specific…

Taxonomic triage and the poverty of phylogeny.

PubMed Central

Wheeler, Quentin D

2004-01-01

Revisionary taxonomy is frequently dismissed as merely descriptive, which belies its strong intellectual content and hypothesis-driven nature. Funding for taxonomy is inadequate and largely diverted to studies of phylogeny that neither improve classifications nor nomenclature. Phylogenetic classifications are optimal for storing and predicting information, but phylogeny divorced from taxonomy is ephemeral and erodes the accuracy and information content of the language of biology. Taxonomic revisions and monographs are efficient, high-throughput species hypothesis-testing devices that are ideal for the World Wide Web. Taxonomic knowledge remains essential to credible biological research and is made urgent by the biodiversity crisis. Theoretical and technological advances and threats of mass species extinctions indicate that this is the time for a renaissance in taxonomy. Clarity of vision and courage of purpose are needed from individual taxonomists and natural history museums to bring about this evolution of taxonomy into the information age. PMID:15253345

Photometric survey and taxonomic identifications of 92 near-Earth asteroids

NASA Astrophysics Data System (ADS)

Lin, Chien-Hsien; Ip, Wing-Huen; Lin, Zhong-Yi; Cheng, Yu-Chi; Lin, Hsing-Wen; Chang, Chan-Kao

2018-03-01

A photometric survey of near-Earth asteroids (NEAs) was conducted from 2012 through 2014 at Lulin Observatory, Taiwan. The measurements of the color indices, B-V, V-R, and V-I allow the classification of 92 NEAs into seven taxonomic types. Of these samples, 39 of them are new classifications. The fractional abundances of these taxonomic complexes are: A ∼3%, C∼6.5%, D∼8%, Q∼26%, S∼37%, V∼6.5%, and X∼13%. This result is similar to that of Thomas et al. (2011) even though the populations of the D- and X-complex with low albedos are under-represented. The ratio of the C-cluster to the total population of S + C clusters are 0.22 ± 0.06 for H ≤ 17.0 and 0.31 ± 0.06 for H > 17.0, indicating a slightly higher fraction of dark-object population with sizes smaller than 1 km.

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.

Classification of Pinus patula, P. tecunumanii, P. oocarpa, P. caribaea var. hondurensis, and Related Taxonomic Entities

Treesearch

A.E. Squillace; Jesse P. Perry

1992-01-01

Stem xylem terpenes of 75 pine populations were studied to determine relationships among taxonomic entities. Typical Pinus patula populations occurring in areas north and west of Oaxaca, Mexico, had very high proportions of 3-phellandrene and low proportions of other constituents. Terpene compositions of populations of variety longipeduncalatain...

Genome-Based Taxonomic Classification of Bacteroidetes

DOE PAGES

Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina; ...

2016-12-20

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogeneticmore » analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.« less

Genome-Based Taxonomic Classification of Bacteroidetes

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

Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogeneticmore » analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.« less

Genome-Based Taxonomic Classification of Bacteroidetes

PubMed Central

Hahnke, Richard L.; Meier-Kolthoff, Jan P.; García-López, Marina; Mukherjee, Supratim; Huntemann, Marcel; Ivanova, Natalia N.; Woyke, Tanja; Kyrpides, Nikos C.; Klenk, Hans-Peter; Göker, Markus

2016-01-01

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved. PMID:28066339

Anaplasma marginale major surface protein 1a: a marker of strain diversity with implications for control of bovine anaplasmosis.

PubMed

Cabezas-Cruz, Alejandro; de la Fuente, José

2015-04-01

Classification of bacteria is challenging due to the lack of a theory-based framework. In addition, the adaptation of bacteria to ecological niches often results in selection of strains with diverse virulence, pathogenicity and transmission characteristics. Bacterial strain diversity presents challenges for taxonomic classification, which in turn impacts the ability to develop accurate diagnostics and effective vaccines. Over the past decade, the worldwide diversity of Anaplasma marginale, an economically important tick-borne pathogen of cattle, has become apparent. The extent of A. marginale strain diversity, formerly underappreciated, has contributed to the challenges of classification which, in turn, likely impacts the design and development of improved vaccines. Notably, the A. marginale surface protein 1a (MSP1a) is a model molecule for these studies because it serves as a marker for strain identity, is both an adhesin necessary for infection of cells and an immuno-reactive protein and is also an indicator of the evolution of strain diversity. Herein, we discuss a molecular taxonomic approach for classification of A. marginale strain diversity. Taxonomic analysis of this important molecule provides the opportunity to understand A. marginale strain diversity as it relates geographic and ecological factors and to the development of effective vaccines for control of bovine anaplasmosis worldwide. Copyright © 2015 Elsevier GmbH. All rights reserved.

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

PubMed Central

Werner, Jeffrey J; Koren, Omry; Hugenholtz, Philip; DeSantis, Todd Z; Walters, William A; Caporaso, J Gregory; Angenent, Largus T; Knight, Rob; Ley, Ruth E

2012-01-01

Taxonomic classification of the thousands–millions of 16S rRNA gene sequences generated in microbiome studies is often achieved using a naïve Bayesian classifier (for example, the Ribosomal Database Project II (RDP) classifier), due to favorable trade-offs among automation, speed and accuracy. The resulting classification depends on the reference sequences and taxonomic hierarchy used to train the model; although the influence of primer sets and classification algorithms have been explored in detail, the influence of training set has not been characterized. We compared classification results obtained using three different publicly available databases as training sets, applied to five different bacterial 16S rRNA gene pyrosequencing data sets generated (from human body, mouse gut, python gut, soil and anaerobic digester samples). We observed numerous advantages to using the largest, most diverse training set available, that we constructed from the Greengenes (GG) bacterial/archaeal 16S rRNA gene sequence database and the latest GG taxonomy. Phylogenetic clusters of previously unclassified experimental sequences were identified with notable improvements (for example, 50% reduction in reads unclassified at the phylum level in mouse gut, soil and anaerobic digester samples), especially for phylotypes belonging to specific phyla (Tenericutes, Chloroflexi, Synergistetes and Candidate phyla TM6, TM7). Trimming the reference sequences to the primer region resulted in systematic improvements in classification depth, and greatest gains at higher confidence thresholds. Phylotypes unclassified at the genus level represented a greater proportion of the total community variation than classified operational taxonomic units in mouse gut and anaerobic digester samples, underscoring the need for greater diversity in existing reference databases. PMID:21716311

Mycofier: a new machine learning-based classifier for fungal ITS sequences.

PubMed

Delgado-Serrano, Luisa; Restrepo, Silvia; Bustos, Jose Ricardo; Zambrano, Maria Mercedes; Anzola, Juan Manuel

2016-08-11

The taxonomic and phylogenetic classification based on sequence analysis of the ITS1 genomic region has become a crucial component of fungal ecology and diversity studies. Nowadays, there is no accurate alignment-free classification tool for fungal ITS1 sequences for large environmental surveys. This study describes the development of a machine learning-based classifier for the taxonomical assignment of fungal ITS1 sequences at the genus level. A fungal ITS1 sequence database was built using curated data. Training and test sets were generated from it. A Naïve Bayesian classifier was built using features from the primary sequence with an accuracy of 87 % in the classification at the genus level. The final model was based on a Naïve Bayes algorithm using ITS1 sequences from 510 fungal genera. This classifier, denoted as Mycofier, provides similar classification accuracy compared to BLASTN, but the database used for the classification contains curated data and the tool, independent of alignment, is more efficient and contributes to the field, given the lack of an accurate classification tool for large data from fungal ITS1 sequences. The software and source code for Mycofier are freely available at https://github.com/ldelgado-serrano/mycofier.git .

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.

Solar-phase-angle effects on the taxonomic classification of asteroids

NASA Astrophysics Data System (ADS)

Carvano, J.; Davallos, J.

2014-07-01

Asteroid taxonomy is the effort of grouping asteroids into classes based on similarities of a number of their observational properties. The most used properties include measurements of their spectral reflectance (by means of low-resolution spectra, spectro-photometry, or colors), and geometric albedo. The usefulness of asteroid taxonomic classes derived in this way relies on the assumption that the classes bear some correspondence to the mineralogy of the asteroids, and on the fact that such classification can be made using types of observations that presently are available to a large number of asteroids. Therefore, asteroid taxonomy can be used to infer trends in the distribution of compositions in the main belt and other populations, as an additional parameter in defining asteroid families, and as a selection tool to identify candidates for more detailed observations. However, the fact that the correspondence between taxonomic class and composition is far from perfect is still sometimes overlooked in the literature. Indeed, although a taxonomic classification narrows down the possible mineralogies of a given asteroid, it will seldom point univocally to one particular mineralogy. This happens for a number of reasons, some linked to the intrinsic difficulty involved in the remote characterization of the mineralogy of an asteroid, since it depends on the presence of absorption bands in its reflectance spectrum which may be absent or not completely sampled by the observations used to derive taxonomy. Other problem here is the exposure of the material on the surface of the asteroid to space-weathering effects, such as solar wind implantation and micro-meteorite bombardment, which can change the optical properties of the material. Finally, the overall shape of the reflectance spectrum of an asteroid is also affected by the geometry of the observation, as well as by its shape. In this work, we analyze how the classification of asteroids observed by the Sloan Digital Sky Survey is affected by the solar phase angle of the observation. It is found that the number of observations assigned to several taxonomic classes has a clear dependency on the solar phase angle of the asteroid at the moment of the observation. In order to understand how variations of phase angles affect the reflectance spectra of the individual asteroids listed in the SDSS with multiple observations, we use the reflectance spectra derived from the SDSS colors to define two parameters, which measure the spectral slope in the visible and the depth of the 1-micron band, if present. It is found that most asteroids in the sample tend to be redder at higher phase angles, and that, for the classes showing a 1-μ m band, most show increasing band depth with increasing phase angle. This predominance of positive correlations for both band depth and spectral slope might suffice to explain the offsets in the distribution of classes. However, for both parameters there is a significant fraction in each sample for which there seem to be no correlation at all, and a comparable number seem to display anti-correlation between the parameters and the phase angle. Therefore, although phase-reddening effects, as currently understood in the literature, can account for the offsets in the distribution of taxonomic classes with phase angle, it cannot explain all variability seen in the SDSS data. There is also a dependency on composition and also shape effects involved, which can be reproduced using Hapke reflectance models.

The iPhyClassifier, an interactive online tool for phytoplasma classification and taxonomic assignment

USDA-ARS?s Scientific Manuscript database

The iPhyClassifier is an Internet-based research tool for quick identification and classification of diverse phytoplasmas. The iPhyClassifier simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis and generates virtual restriction fragment length polymorphism (RFLP) p...

Molecular Phylogeny of the Widely Distributed Marine Protists, Phaeodaria (Rhizaria, Cercozoa).

PubMed

Nakamura, Yasuhide; Imai, Ichiro; Yamaguchi, Atsushi; Tuji, Akihiro; Not, Fabrice; Suzuki, Noritoshi

2015-07-01

Phaeodarians are a group of widely distributed marine cercozoans. These plankton organisms can exhibit a large biomass in the environment and are supposed to play an important role in marine ecosystems and in material cycles in the ocean. Accurate knowledge of phaeodarian classification is thus necessary to better understand marine biology, however, phylogenetic information on Phaeodaria is limited. The present study analyzed 18S rDNA sequences encompassing all existing phaeodarian orders, to clarify their phylogenetic relationships and improve their taxonomic classification. The monophyly of Phaeodaria was confirmed and strongly supported by phylogenetic analysis with a larger data set than in previous studies. The phaeodarian clade contained 11 subclades which generally did not correspond to the families and orders of the current classification system. Two families (Challengeriidae and Aulosphaeridae) and two orders (Phaeogromida and Phaeocalpida) are possibly polyphyletic or paraphyletic, and consequently the classification needs to be revised at both the family and order levels by integrative taxonomy approaches. Two morphological criteria, 1) the scleracoma type and 2) its surface structure, could be useful markers at the family level. Copyright © 2015 Elsevier GmbH. All rights reserved.

A vegetation classification system applied to southern California

Treesearch

Timothy E. Paysen; Jeanine A. Derby; Hugh Black; Vernon C. Bleich; John W. Mincks

1980-01-01

A classification system for use in describing vegetation has been developed and is being applied to southern California. It is based upon a hierarchical stratification of vegetation, using physiognomic and taxonomic criteria. The system categories are Formation, Subformation. Series, Association, and Phase. Formations, Subformations, and Series have been specified for...

A revised family-level classification of the Polyporales (Basidiomycota)

Treesearch

Alfredo Justo; Otto Miettinen; Dimitrios Floudas; Beatriz Ortiz-Santana; Elisabet Sjökvist; Daniel Lindner; Karen Nakasone; Tuomo Niemelä; Karl-Henrik Larsson; Leif Ryvarden; David S. Hibbett

2017-01-01

Polyporales is strongly supported as a clade of Agaricomycetes, but the lack of a consensus higher-level classification within the group is a barrier to further taxonomic revision. We amplified nrLSU, nrITS, and rpb1 genes across the Polyporales, with a special focus on the latter. We...

A vegetation classification system for use in California: its conceptual basis

Treesearch

Timothy E. Paysen; Jeanine A. Derby; C. Eugene Conrad

1982-01-01

A taxonomic Vegetation Classification System proposed for use in California is designed to simplify interdisciplinary communication about vegetation. The system structure is an aggregative plant community hierarchy at four levels of precision--the Association, Series, Subformation, and Formation. A flexible Phase category links specific resource management concerns to...

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.

Classifying black and white spruce pollen using layered machine learning.

PubMed

Punyasena, Surangi W; Tcheng, David K; Wesseln, Cassandra; Mueller, Pietra G

2012-11-01

Pollen is among the most ubiquitous of terrestrial fossils, preserving an extended record of vegetation change. However, this temporal continuity comes with a taxonomic tradeoff. Analytical methods that improve the taxonomic precision of pollen identifications would expand the research questions that could be addressed by pollen, in fields such as paleoecology, paleoclimatology, biostratigraphy, melissopalynology, and forensics. We developed a supervised, layered, instance-based machine-learning classification system that uses leave-one-out bias optimization and discriminates among small variations in pollen shape, size, and texture. We tested our system on black and white spruce, two paleoclimatically significant taxa in the North American Quaternary. We achieved > 93% grain-to-grain classification accuracies in a series of experiments with both fossil and reference material. More significantly, when applied to Quaternary samples, the learning system was able to replicate the count proportions of a human expert (R(2) = 0.78, P = 0.007), with one key difference - the machine achieved these ratios by including larger numbers of grains with low-confidence identifications. Our results demonstrate the capability of machine-learning systems to solve the most challenging palynological classification problem, the discrimination of congeneric species, extending the capabilities of the pollen analyst and improving the taxonomic resolution of the palynological record. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.

PubMed

Bokulich, Nicholas A; Kaehler, Benjamin D; Rideout, Jai Ram; Dillon, Matthew; Bolyen, Evan; Knight, Rob; Huttley, Gavin A; Gregory Caporaso, J

2018-05-17

Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. We present q2-feature-classifier ( https://github.com/qiime2/q2-feature-classifier ), a QIIME 2 plugin containing several novel machine-learning and alignment-based methods for taxonomy classification. We evaluated and optimized several commonly used classification methods implemented in QIIME 1 (RDP, BLAST, UCLUST, and SortMeRNA) and several new methods implemented in QIIME 2 (a scikit-learn naive Bayes machine-learning classifier, and alignment-based taxonomy consensus methods based on VSEARCH, and BLAST+) for classification of bacterial 16S rRNA and fungal ITS marker-gene amplicon sequence data. The naive-Bayes, BLAST+-based, and VSEARCH-based classifiers implemented in QIIME 2 meet or exceed the species-level accuracy of other commonly used methods designed for classification of marker gene sequences that were evaluated in this work. These evaluations, based on 19 mock communities and error-free sequence simulations, including classification of simulated "novel" marker-gene sequences, are available in our extensible benchmarking framework, tax-credit ( https://github.com/caporaso-lab/tax-credit-data ). Our results illustrate the importance of parameter tuning for optimizing classifier performance, and we make recommendations regarding parameter choices for these classifiers under a range of standard operating conditions. q2-feature-classifier and tax-credit are both free, open-source, BSD-licensed packages available on GitHub.

A new taxonomic classification for species in Gomphus sensu lato

Treesearch

Admir J. Giachini; Michael A. Castellano

2011-01-01

Taxonomy of the Gomphales has been revisited by combining morphology and molecular data (DNA sequences) to provide a natural classification for the species of Gomphus sensu lato. Results indicate Gomphus s.l. to be non-monophyletic, leading to new combinations and the placement of its species into four genera: Gomphus...

A system of vegetation classification applied to Hawaii

Treesearch

Michael G. Buck; Timothy E. Paysen

1984-01-01

A classification system for use in describing vegetation has been developed for Hawaii. Physiognomic and taxonomic criteria are used for a hierarchical stratification of vegetation in which the system categories are Formation, Subformation, Series, Association, and Phase. The System applies to local resource management activities and serves as a framework for resource...

Forest habitat types of central Idaho

Treesearch

Robert Steele; Robert D. Pfister; Russell A. Ryker; Jay A. Kittams

1981-01-01

A land-classification system based upon potential natural vegetation is presented for the forests of central Idaho. It is based on reconnaissance sampling of about 800 stands. A hierarchical taxonomic classification of forest sites was developed using the habitat type concept. A total of eight climax series, 64 habitat types, and 55 additional phases of habitat types...

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria.

PubMed

Bolduc, Benjamin; Jang, Ho Bin; Doulcier, Guilhem; You, Zhi-Qiang; Roux, Simon; Sullivan, Matthew B

2017-01-01

Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome 'sequence space' that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

PubMed Central

Doulcier, Guilhem; You, Zhi-Qiang; Roux, Simon

2017-01-01

Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome ‘sequence space’ that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure. PMID:28480138

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

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

Bolduc, Benjamin; Jang, Ho Bin; Doulcier, Guilhem

Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined andmore » found to represent areas of viral genome ‘sequence space’ that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.« less

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

DOE PAGES

Bolduc, Benjamin; Jang, Ho Bin; Doulcier, Guilhem; ...

2017-05-03

Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined andmore » found to represent areas of viral genome ‘sequence space’ that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.« less

Complete genomic sequence and taxonomic position of eel virus European X (EVEX), a rhabdovirus of European eel.

PubMed

Galinier, Richard; van Beurden, Steven; Amilhat, Elsa; Castric, Jeannette; Schoehn, Guy; Verneau, Olivier; Fazio, Géraldine; Allienne, Jean-François; Engelsma, Marc; Sasal, Pierre; Faliex, Elisabeth

2012-06-01

Eel virus European X (EVEX) was first isolated from diseased European eel Anguilla anguilla in Japan at the end of seventies. The virus was tentatively classified into the Rhabdoviridae family on the basis of morphology and serological cross reactivity. This family of viruses is organized into six genera and currently comprises approximately 200 members, many of which are still unassigned because of the lack of molecular data. This work presents the morphological, biochemical and genetic characterizations of EVEX, and proposes a taxonomic classification for this virus. We provide its complete genome sequence, plus a comprehensive sequence comparison between isolates from different geographical origins. The genome encodes the five classical structural proteins plus an overlapping open reading frame in the phosphoprotein gene, coding for a putative C protein. Phylogenic relationship with other rhabdoviruses indicates that EVEX is most closely related to the Vesiculovirus genus and shares the highest identity with trout rhabdovirus 903/87. Copyright © 2012 Elsevier B.V. All rights reserved.

A Spectroscopic and Mineralogical Study of Multiple Asteroid Systems

NASA Astrophysics Data System (ADS)

Lindsay, Sean S.; Emery, J. P.; Marchis, F.; Enriquez, J.; Assafin, M.

2013-10-01

There are currently ~200 identified multiple asteroid systems (MASs). These systems display a large diversity in heliocentric distance, size/mass ratio, system angular momentum, mutual orbital parameters, and taxonomic class. These characteristics are simplified under the nomenclature of Descamps and Marchis (2008), which divides MASs into four types: Type-1 - large asteroids with small satellites; Type-2 - similar size double asteroids; Type-3 - small asynchronous systems; and Type-4 - contact-binary asteroids. The large MAS diversity suggests multiple formation mechanisms are required to understand their origins. There are currently three broad formation scenarios: 1) ejecta from impacts; 2) catastrophic disruption followed by rotational fission; and 3) tidal disruption. The taxonomic class and mineralogy of the MASs coupled with the average density and system angular momentum provide a potential means to discriminate between proposed formation mechanisms. We present visible and near-infrared (NIR) spectra spanning 0.45 - 2.45 μm for 23 Main Belt MASs. The data were primarily obtained using the Southern Astrophysical Research Telescope (SOAR) Goodman High Throughput Spectrograph (August 2011 - July 2012) for the visible data and the InfraRed Telescope Facility (IRTF) SpeX Spectrograph (August 2008 - May 2013) for the IR data. Our data were supplemented using previously published data when necessary. The asteroids' Bus-DeMeo taxonomic classes are determined using the MIT SMASS online classification routines. Our sample includes 3 C-types, 1 X-type, 1 K-type, 1 L-type, 4 V-types, 10 S-types, 2 Sq- or Q-types, and 1 ambiguous classification. We calculate the 1- and 2-μm band centers, depths, and areas to determine the pyroxene mineralogy (molar Fs and Wo) of the surfaces using empirically derived equations. The NIR band analysis allows us to determine the S-type subclasses, S(I) - S(VII), which roughly tracks olivine-pyroxene chemistry. A comparison of the orbital parameters, physical parameters (size, density, and angular momentum), collisional family membership, and taxonomy is presented in an effort to find correlations, which may give insights to how these MASs formation mechanisms.

Molecular Phylogeny of the Cliff Ferns (Woodsiaceae: Polypodiales) with a Proposed Infrageneric Classification

PubMed Central

Zhang, Xianchun; Xiang, Qiaoping

2015-01-01

The cliff fern family Woodsiaceae has experienced frequent taxonomic changes at the familial and generic ranks since its establishment. The bulk of its species were placed in Woodsia, while Cheilanthopsis, Hymenocystis, Physematium, and Protowoodsia are segregates recognized by some authors. Phylogenetic relationships among the genera of Woodsiaceae remain unclear because of the extreme morphological diversity and inadequate taxon sampling in phylogenetic studies to date. In this study, we carry out comprehensive phylogenetic analyses of Woodsiaceae using molecular evidence from four chloroplast DNA markers (atpA, matK, rbcL and trnL–F) and covering over half the currently recognized species. Our results show three main clades in Woodsiaceae corresponding to Physematium (clade I), Cheilanthopsis–Protowoodsia (clade II) and Woodsia s.s. (clade III). In the interest of preserving monophyly and taxonomic stability, a broadly defined Woodsia including the other segregates is proposed, which is characterized by the distinctive indument and inferior indusia. Therefore, we present a new subgeneric classification of the redefined Woodsia based on phylogenetic and ancestral state reconstructions to better reflect the morphological variation, geographic distribution pattern, and evolutionary history of the genus. Our analyses of the cytological character evolution support multiple aneuploidy events that have resulted in the reduction of chromosome base number from 41 to 33, 37, 38, 39 and 40 during the evolutionary history of the cliff ferns. PMID:26348852

Chapter II. Taxonomy and Phylogeny

USDA-ARS?s Scientific Manuscript database

The book chapter presents a review of the taxonomic distribution of ornamental geophytic plants (bulbs, tubers, corms, rhizomes) and the modern classification of the families within which they belong....

Forest habitat types of eastern Idaho-western Wyoming

Treesearch

Robert Steele; Stephen V. Cooper; David M. Ondov; David W. Roberts; Robert D. Pfister

1983-01-01

A land-classification system based upon potential natural vegetation is presented for the forests of central Idaho. It is based on reconnaissance sampling of about 980 stands. A hierarchical taxonomic classification of forest sites was developed using the habitat type concept. A total of six climax series, 58 habitat types, and 24 additional phases of habitat types are...

Coniferous forest habitat types of central and southern Utah

Treesearch

Andrew P. Youngblood; Ronald L. Mauk

1985-01-01

A land-classification system based upon potential natural vegetation is presented for the coniferous forests of central and southern Utah. It is based on reconnaissance sampling of about 720 stands. A hierarchical taxonomic classification of forest sites was developed using the habitat type concept. Seven climax series, 37 habitat types, and six additional phases of...

Can Sex Offender Classification Inform Typologies of Male Batterers? A Response to Holtzworth-Munroe and Meehan

ERIC Educational Resources Information Center

Prentky, Robert A.

2004-01-01

Etiologic and taxonomic research on rapists during the past decade suggests three dimensions that may be potentially useful for classification research on male batterers: (a) distinction between those whose anger is exclusively misogynistic and those whose anger is pervasive or undifferentiated with respect to target, (b) attitudes characterized…

(GTG)5-PCR reference framework for acetic acid bacteria.

PubMed

Papalexandratou, Zoi; Cleenwerck, Ilse; De Vos, Paul; De Vuyst, Luc

2009-11-01

One hundred and fifty-eight strains of acetic acid bacteria (AAB) were subjected to (GTG)(5)-PCR fingerprinting to construct a reference framework for their rapid classification and identification. Most of them clustered according to their respective taxonomic designation; others had to be reclassified based on polyphasic data. This study shows the usefulness of the method to determine the taxonomic and phylogenetic relationships among AAB and to study the AAB diversity of complex ecosystems.

Automatic Picking of Foraminifera: Design of the Foraminifera Image Recognition and Sorting Tool (FIRST) Prototype and Results of the Image Classification Scheme

NASA Astrophysics Data System (ADS)

de Garidel-Thoron, T.; Marchant, R.; Soto, E.; Gally, Y.; Beaufort, L.; Bolton, C. T.; Bouslama, M.; Licari, L.; Mazur, J. C.; Brutti, J. M.; Norsa, F.

2017-12-01

Foraminifera tests are the main proxy carriers for paleoceanographic reconstructions. Both geochemical and taxonomical studies require large numbers of tests to achieve statistical relevance. To date, the extraction of foraminifera from the sediment coarse fraction is still done by hand and thus time-consuming. Moreover, the recognition of morphotypes, ecologically relevant, requires some taxonomical skills not easily taught. The automatic recognition and extraction of foraminifera would largely help paleoceanographers to overcome these issues. Recent advances in automatic image classification using machine learning opens the way to automatic extraction of foraminifera. Here we detail progress on the design of an automatic picking machine as part of the FIRST project. The machine handles 30 pre-sieved samples (100-1000µm), separating them into individual particles (including foraminifera) and imaging each in pseudo-3D. The particles are classified and specimens of interest are sorted either for Individual Foraminifera Analyses (44 per slide) and/or for classical multiple analyses (8 morphological classes per slide, up to 1000 individuals per hole). The classification is based on machine learning using Convolutional Neural Networks (CNNs), similar to the approach used in the coccolithophorid imaging system SYRACO. To prove its feasibility, we built two training image datasets of modern planktonic foraminifera containing approximately 2000 and 5000 images each, corresponding to 15 & 25 morphological classes. Using a CNN with a residual topology (ResNet) we achieve over 95% correct classification for each dataset. We tested the network on 160,000 images from 45 depths of a sediment core from the Pacific ocean, for which we have human counts. The current algorithm is able to reproduce the downcore variability in both Globigerinoides ruber and the fragmentation index (r2 = 0.58 and 0.88 respectively). The FIRST prototype yields some promising results for high-resolution paleoceanographic studies and evolutionary studies.

Categorical and dimensional approaches in the evaluation of the relationship between attachment and personality disorders: an empirical study.

PubMed

Chiesa, Marco; Cirasola, Antonella; Williams, Riccardo; Nassisi, Valentina; Fonagy, Peter

2017-04-01

Although several studies have highlighted the relationship between attachment states of mind and personality disorders, their findings have not been consistent, possibly due to the application of the traditional taxonomic classification model of attachment. A more recently developed dimensional classification of attachment representations, including more specific aspects of trauma-related representations, may have advantages. In this study, we compare specific associations and predictive power of the categorical attachment and dimensional models applied to 230 Adult Attachment Interview transcripts obtained from personality disordered and nonpsychiatric subjects. We also investigate the role that current levels of psychiatric distress may have in the prediction of PD. The results showed that both models predict the presence of PD, with the dimensional approach doing better in discriminating overall diagnosis of PD. However, both models are less helpful in discriminating specific PD diagnostic subtypes. Current psychiatric distress was found to be the most consistent predictor of PD capturing a large share of the variance and obscuring the role played by attachment variables. The results suggest that attachment parameters correlate with the presence of PD alone and have no specific associations with particular PD subtypes when current psychiatric distress is taken into account.

Does the Chemical Diversity of the Order Haplosclerida (Phylum Porifera: Class Demospongia) Fit with Current Taxonomic Classification?

PubMed

Tribalat, Marie-Aude; Marra, Maria V; McCormack, Grace P; Thomas, Olivier P

2016-06-01

Sponges and their associated microbiota are well known to produce a large diversity of natural products, also called specialized metabolites. In addition to their potential use in the pharmaceutical industry, these rather species-specific compounds may help in the classification of some particular sponge groups. We review herein compounds isolated from haplosclerid sponges (Class Demospongia, Order Haplosclerida) in order to help in the revision of this large group of marine invertebrates. We focus only on 3-alkylpyridine derivatives and polyacetylenic compounds, as these two groups of natural products are characteristic of haplosclerid species and are highly diverse. A close collaboration between chemists and biologists is required in order to fully apply chemotaxonomical approaches, and whenever possible biological data should include morphological and molecular data and some insight into their microbial abundance. Georg Thieme Verlag KG Stuttgart · New York.

Stratification of co-evolving genomic groups using ranked phylogenetic profiles

PubMed Central

Freilich, Shiri; Goldovsky, Leon; Gottlieb, Assaf; Blanc, Eric; Tsoka, Sophia; Ouzounis, Christos A

2009-01-01

Background Previous methods of detecting the taxonomic origins of arbitrary sequence collections, with a significant impact to genome analysis and in particular metagenomics, have primarily focused on compositional features of genomes. The evolutionary patterns of phylogenetic distribution of genes or proteins, represented by phylogenetic profiles, provide an alternative approach for the detection of taxonomic origins, but typically suffer from low accuracy. Herein, we present rank-BLAST, a novel approach for the assignment of protein sequences into genomic groups of the same taxonomic origin, based on the ranking order of phylogenetic profiles of target genes or proteins across the reference database. Results The rank-BLAST approach is validated by computing the phylogenetic profiles of all sequences for five distinct microbial species of varying degrees of phylogenetic proximity, against a reference database of 243 fully sequenced genomes. The approach - a combination of sequence searches, statistical estimation and clustering - analyses the degree of sequence divergence between sets of protein sequences and allows the classification of protein sequences according to the species of origin with high accuracy, allowing taxonomic classification of 64% of the proteins studied. In most cases, a main cluster is detected, representing the corresponding species. Secondary, functionally distinct and species-specific clusters exhibit different patterns of phylogenetic distribution, thus flagging gene groups of interest. Detailed analyses of such cases are provided as examples. Conclusion Our results indicate that the rank-BLAST approach can capture the taxonomic origins of sequence collections in an accurate and efficient manner. The approach can be useful both for the analysis of genome evolution and the detection of species groups in metagenomics samples. PMID:19860884

Conflicting patterns of DNA barcoding and taxonomy in the cicada genus Tettigettalna from Southern Europe (Hemiptera: Cicadidae).

PubMed

Nunes, Vera L; Mendes, Raquel; Marabuto, Eduardo; Novais, Bruno M; Hertach, Thomas; Quartau, José A; Seabra, Sofia G; Paulo, Octávio S; Simões, Paula C

2014-01-01

DNA barcodes have great potential to assist in species identification, especially when high taxonomical expertise is required. We investigated the utility of the 5' mitochondrial cytochrome c oxidase I (COI) region to discriminate between 13 European cicada species. These included all nine species currently recognized under the genus Tettigettalna, from which seven are endemic to the southern Iberian Peninsula. These cicadas have species-specific male calling songs but are morphologically very similar. Mean COI divergence between congeners ranged from 0.4% to 10.6%, but this gene was proven insufficient to determine species limits within genus Tettigettalna because a barcoding gap was absent for several of its species, that is, the highest intraspecific distance exceeded the lowest interspecific distance. The genetic data conflicted with current taxonomic classification for T. argentata and T. mariae. Neighbour-joining and Bayesian analyses revealed that T. argentata is geographically structured (clades North and South) and might constitute a species complex together with T. aneabi and T. mariae. The latter diverges very little from the southern clade of T. argentata and shares with it its most common haplotype. T. mariae is often in sympatry with T. argentata but it remains unclear whether introgression or incomplete lineage sorting may be responsible for the sharing of haplotypes. T. helianthemi and T. defauti also show high intraspecific variation that might signal hidden cryptic diversity. These taxonomic conflicts must be re-evaluated with further studies using additional genes and extensive morphological and acoustic analyses. © 2013 John Wiley & Sons Ltd.

The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification.

PubMed

Aiewsakun, Pakorn; Simmonds, Peter

2018-02-20

The International Committee on Taxonomy of Viruses (ICTV) classifies viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus descriptions. Virus taxonomic assignments have traditionally been based upon virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of viruses detected in environmental (metagenomic) studies that lack any phenotypic data. The current study sought to determine whether the existing virus taxonomy could be reproduced by examination of genetic relationships through the extraction of protein-coding gene signatures and genome organisational features. We found large-scale consistency between genetic relationships and taxonomic assignments for viruses of all genome configurations and genome sizes. The analysis pipeline that we have called 'Genome Relationships Applied to Virus Taxonomy' (GRAViTy) was highly effective at reproducing the current assignments of viruses at family level as well as inter-family groupings into orders. Its ability to correctly differentiate assigned viruses from unassigned viruses, and classify them into the correct taxonomic group, was evaluated by threefold cross-validation technique. This predicted family membership of eukaryotic viruses with close to 100% accuracy and specificity potentially enabling the algorithm to predict assignments for the vast corpus of metagenomic sequences consistently with ICTV taxonomy rules. In an evaluation run of GRAViTy, over one half (460/921) of (near)-complete genome sequences from several large published metagenomic eukaryotic virus datasets were assigned to 127 novel family-level groupings. If corroborated by other analysis methods, these would potentially more than double the number of eukaryotic virus families in the ICTV taxonomy. A rapid and objective means to explore metagenomic viral diversity and make informed recommendations for their assignments at each taxonomic layer is essential. GRAViTy provides one means to make rule-based assignments at family and order levels in a manner that preserves the integrity and underlying organisational principles of the current ICTV taxonomy framework. Such methods are increasingly required as the vast virosphere is explored.

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.

Metabolomic analysis applied to chemosystematics and evolution of megadiverse Brazilian Vernonieae (Asteraceae).

PubMed

Gallon, Marília Elias; Monge, Marcelo; Casoti, Rosana; Da Costa, Fernando Batista; Semir, João; Gobbo-Neto, Leonardo

2018-06-01

Vernonia sensu lato is the largest and most complex genus of the tribe Vernonieae (Asteraceae). The tribe is chemically characterized by the presence of sesquiterpene lactones and flavonoids. Over the years, several taxonomic classifications have been proposed for Vernonia s.l. and for the tribe; however, there has been no consensus among the researches. According to traditional classification, Vernonia s.l. comprises more than 1000 species divided into sections, subsections and series (sensu Bentham). In a more recent classification, these species have been segregated into other genera and some subtribes were proposed, while the genus Vernonia sensu stricto was restricted to 22 species distributed mainly in North America (sensu Robinson). In this study, species from the subtribes Vernoniinae, Lepidaploinae and Rolandrinae were analyzed by UHPLC-UV-HRMS followed by multivariate statistical analysis. Data mining was performed using unsupervised (HCA and PCA) and supervised methods (OPLS-DA). The HCA showed the segregation of the species into four main groups. Comparing the HCA with taxonomical classifications of Vernonieae, we observed that the groups of the dendogram, based on metabolic profiling, were in accordance with the generic classification proposed by Robinson and with previous phylogenetic studies. The species of the genera Stenocephalum, Stilpnopappus, Strophopappus and Rolandra (Group 1) were revealed to be more related to the species of the genus Vernonanthura (Group 2), while the genera Cyrtocymura, Chrysolaena and Echinocoryne (Group 3) were chemically more similar to the genera Lessingianthus and Lepidaploa (Group 4). These findings indicated that the subtribes Vernoniinae and Lepidaploinae are non-chemically homogeneous groups and highlighted the application of untargeted metabolomic tools for taxonomy and as indicators of species evolution. Discriminant compounds for the groups obtained by OPLS-DA were determined. Groups 1 and 2 were characterized by the presence of 3',4'-dimethoxyluteolin, glaucolide A and 8-tigloyloxyglaucolide A. The species of Groups 3 and 4 were characterized by the presence of putative acacetin 7-O-rutinoside and glaucolide B. Therefore, untargeted metabolomic approach combined with multivariate statistical analysis, as proposed herein, allowed the identification of potential chemotaxonomic markers, helping in the taxonomic classifications. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

Phylogenetic Inferences Reveal a Large Extent of Novel Biodiversity in Chemically Rich Tropical Marine Cyanobacteria

PubMed Central

Gunasekera, Sarath P.; Gerwick, William H.

2013-01-01

Benthic marine cyanobacteria are known for their prolific biosynthetic capacities to produce structurally diverse secondary metabolites with biomedical application and their ability to form cyanobacterial harmful algal blooms. In an effort to provide taxonomic clarity to better guide future natural product drug discovery investigations and harmful algal bloom monitoring, this study investigated the taxonomy of tropical and subtropical natural product-producing marine cyanobacteria on the basis of their evolutionary relatedness. Our phylogenetic inferences of marine cyanobacterial strains responsible for over 100 bioactive secondary metabolites revealed an uneven taxonomic distribution, with a few groups being responsible for the vast majority of these molecules. Our data also suggest a high degree of novel biodiversity among natural product-producing strains that was previously overlooked by traditional morphology-based taxonomic approaches. This unrecognized biodiversity is primarily due to a lack of proper classification systems since the taxonomy of tropical and subtropical, benthic marine cyanobacteria has only recently been analyzed by phylogenetic methods. This evolutionary study provides a framework for a more robust classification system to better understand the taxonomy of tropical and subtropical marine cyanobacteria and the distribution of natural products in marine cyanobacteria. PMID:23315747

Biodiversity in targeted metabolomics analysis of filamentous fungal pathogens by 1H NMR-based studies.

PubMed

Ząbek, Adam; Klimek-Ochab, Magdalena; Jawień, Ewa; Młynarz, Piotr

2017-07-01

The taxonomical classification among fungi kingdom in the last decades was evolved. In this work the targeted metabolomics study based on 1 H NMR spectroscopy combined with chemometrics tools was reported to be useful for differentiation of three model of fungal strains, which represent various genus of Ascomycota (Aspergillus pallidofulvus, Fusarium oxysporum, Geotrichum candidum) were selected in order to perform metabolomics studies. Each tested species, revealed specific metabolic profile of primary endo-metabolites. The species of A. pallidofulvus is represented by the highest concentration of glycerol, glucitol and Unk5. While, F. oxysporum species is characterised by increased level of propylene glycol, ethanol, 4-aminobutyrate, succinate, xylose, Unk1 and Unk4. In G. candidum, 3-methyl-2-oxovalerate, glutamate, pyruvate, glutamine and citrate were elevated. Additionally, a detailed analysis of metabolic changes among A. pallidofulvus, F. oxysporum and G. candidum showed that A. pallidofulvus seems to be the most pathogenic fungi. The obtained results demonstrated that targeted metabolomics analysis could be utilized in the future as a supporting taxonomical tool for currently methods.

A three-parameter asteroid taxonomy

NASA Technical Reports Server (NTRS)

Tedesco, Edward F.; Williams, James G.; Matson, Dennis L.; Veeder, Glenn J.; Gradie, Jonathan C.

1989-01-01

Broadband U, V, and x photometry together with IRAS asteroid albedos have been used to construct an asteroid classification system. The system is based on three parameters (U-V and v-x color indices and visual geometric albedo), and it is able to place 96 percent of the present sample of 357 asteroids into 11 taxonomic classes. It is noted that all but one of these classes are analogous to those previously found using other classification schemes. The algorithm is shown to account for the observational uncertainties in each of the classification parameters.

Classification of grass pollen through the quantitative analysis of surface ornamentation and texture.

PubMed

Mander, Luke; Li, Mao; Mio, Washington; Fowlkes, Charless C; Punyasena, Surangi W

2013-11-07

Taxonomic identification of pollen and spores uses inherently qualitative descriptions of morphology. Consequently, identifications are restricted to categories that can be reliably classified by multiple analysts, resulting in the coarse taxonomic resolution of the pollen and spore record. Grass pollen represents an archetypal example; it is not routinely identified below family level. To address this issue, we developed quantitative morphometric methods to characterize surface ornamentation and classify grass pollen grains. This produces a means of quantifying morphological features that are traditionally described qualitatively. We used scanning electron microscopy to image 240 specimens of pollen from 12 species within the grass family (Poaceae). We classified these species by developing algorithmic features that quantify the size and density of sculptural elements on the pollen surface, and measure the complexity of the ornamentation they form. These features yielded a classification accuracy of 77.5%. In comparison, a texture descriptor based on modelling the statistical distribution of brightness values in image patches yielded a classification accuracy of 85.8%, and seven human subjects achieved accuracies between 68.33 and 81.67%. The algorithmic features we developed directly relate to biologically meaningful features of grass pollen morphology, and could facilitate direct interpretation of unsupervised classification results from fossil material.

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.

The use of bile - esculin agar for the taxonomic classification of the family Enterobacteriaceae.

PubMed

Edberg, S C; Pittman, S; Singer, J M

1977-01-01

Bile-esculin medium has been used for many years for the presumptive identification of group D Streptococcus. The test is based on the ability of a bacterium to grow in the presence of 40% bile and produce esculinase. 2935 strains of Enterobacteriaceae were inoculated onto bile-esculin agar slants and incubated at 35 C. Esculin hydrolysis was determined after 24 and 48 hours. At 24 hours of incubation esculin hydrolysis was limited to the genera Klebsiella, Enterobacter, Serratia, and the species P. vulgaris, P. rettgeri, and C. diversus. Not all strains of these species were positive, however. All other members of the family were negative. At 48 hours of incubation 37% of E. coli gave a positive reaction; all other Enterobacteriaceae which were negative at 24 hours remained negative. Esculin hydrolysis is a valuable test for the taxonomic classification of the family Enterobacteriaceae.

DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts.

PubMed

Lara, Ariagna; Ponce de León, José Luis; Rodríguez, Rodet; Casane, Didier; Côté, Guillaume; Bernatchez, Louis; García-Machado, Erik

2010-05-01

Despite ongoing efforts to protect species and ecosystems in Cuba, habitat degradation, overuse and introduction of alien species have posed serious challenges to native freshwater fish species. In spite of the accumulated knowledge on the systematics of this freshwater ichthyofauna, recent results suggested that we are far from having a complete picture of the Cuban freshwater fish diversity. It is estimated that 40% of freshwater Cuban fish are endemic; however, this number may be even higher. Partial sequences (652 bp) of the mitochondrial gene COI (cytochrome c oxidase subunit I) were used to barcode 126 individuals, representing 27 taxonomically recognized species in 17 genera and 10 families. Analysis was based on Kimura 2-parameter genetic distances, and for four genera a character-based analysis (population aggregation analysis) was also used. The mean conspecific, congeneric and confamiliar genetic distances were 0.6%, 9.1% and 20.2% respectively. Molecular species identification was in concordance with current taxonomical classification in 96.4% of cases, and based on the neighbour-joining trees, in all but one instance, members of a given genera clustered within the same clade. Within the genus Gambusia, genetic divergence analysis suggests that there may be at least four cryptic species. In contrast, low genetic divergence and a lack of diagnostic sites suggest that Rivulus insulaepinorum may be conspecific with Rivulus cylindraceus. Distance and character-based analysis were completely concordant, suggesting that they complement species identification. Overall, the results evidenced the usefulness of the DNA barcodes for cataloguing Cuban freshwater fish species and for identifying those groups that deserve further taxonomic attention. © 2009 Blackwell Publishing Ltd.

From genus to phylum: large-subunit and internal transcribed spacer rRNA operon regions show similar classification accuracies influenced by database composition.

PubMed

Porras-Alfaro, Andrea; Liu, Kuan-Liang; Kuske, Cheryl R; Xie, Gary

2014-02-01

We compared the classification accuracy of two sections of the fungal internal transcribed spacer (ITS) region, individually and combined, and the 5' section (about 600 bp) of the large-subunit rRNA (LSU), using a naive Bayesian classifier and BLASTN. A hand-curated ITS-LSU training set of 1,091 sequences and a larger training set of 8,967 ITS region sequences were used. Of the factors evaluated, database composition and quality had the largest effect on classification accuracy, followed by fragment size and use of a bootstrap cutoff to improve classification confidence. The naive Bayesian classifier and BLASTN gave similar results at higher taxonomic levels, but the classifier was faster and more accurate at the genus level when a bootstrap cutoff was used. All of the ITS and LSU sections performed well (>97.7% accuracy) at higher taxonomic ranks from kingdom to family, and differences between them were small at the genus level (within 0.66 to 1.23%). When full-length sequence sections were used, the LSU outperformed the ITS1 and ITS2 fragments at the genus level, but the ITS1 and ITS2 showed higher accuracy when smaller fragment sizes of the same length and a 50% bootstrap cutoff were used. In a comparison using the larger ITS training set, ITS1 and ITS2 had very similar accuracy classification for fragments between 100 and 200 bp. Collectively, the results show that any of the ITS or LSU sections we tested provided comparable classification accuracy to the genus level and underscore the need for larger and more diverse classification training sets.

From Genus to Phylum: Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition

PubMed Central

Liu, Kuan-Liang; Kuske, Cheryl R.

2014-01-01

We compared the classification accuracy of two sections of the fungal internal transcribed spacer (ITS) region, individually and combined, and the 5′ section (about 600 bp) of the large-subunit rRNA (LSU), using a naive Bayesian classifier and BLASTN. A hand-curated ITS-LSU training set of 1,091 sequences and a larger training set of 8,967 ITS region sequences were used. Of the factors evaluated, database composition and quality had the largest effect on classification accuracy, followed by fragment size and use of a bootstrap cutoff to improve classification confidence. The naive Bayesian classifier and BLASTN gave similar results at higher taxonomic levels, but the classifier was faster and more accurate at the genus level when a bootstrap cutoff was used. All of the ITS and LSU sections performed well (>97.7% accuracy) at higher taxonomic ranks from kingdom to family, and differences between them were small at the genus level (within 0.66 to 1.23%). When full-length sequence sections were used, the LSU outperformed the ITS1 and ITS2 fragments at the genus level, but the ITS1 and ITS2 showed higher accuracy when smaller fragment sizes of the same length and a 50% bootstrap cutoff were used. In a comparison using the larger ITS training set, ITS1 and ITS2 had very similar accuracy classification for fragments between 100 and 200 bp. Collectively, the results show that any of the ITS or LSU sections we tested provided comparable classification accuracy to the genus level and underscore the need for larger and more diverse classification training sets. PMID:24242255

On the nature of global classification

NASA Technical Reports Server (NTRS)

Wheelis, M. L.; Kandler, O.; Woese, C. R.

1992-01-01

Molecular sequencing technology has brought biology into the era of global (universal) classification. Methodologically and philosophically, global classification differs significantly from traditional, local classification. The need for uniformity requires that higher level taxa be defined on the molecular level in terms of universally homologous functions. A global classification should reflect both principal dimensions of the evolutionary process: genealogical relationship and quality and extent of divergence within a group. The ultimate purpose of a global classification is not simply information storage and retrieval; such a system should also function as an heuristic representation of the evolutionary paradigm that exerts a directing influence on the course of biology. The global system envisioned allows paraphyletic taxa. To retain maximal phylogenetic information in these cases, minor notational amendments in existing taxonomic conventions should be adopted.

Divorcing Strain Classification from Species Names.

PubMed

Baltrus, David A

2016-06-01

Confusion about strain classification and nomenclature permeates modern microbiology. Although taxonomists have traditionally acted as gatekeepers of order, the numbers of, and speed at which, new strains are identified has outpaced the opportunity for professional classification for many lineages. Furthermore, the growth of bioinformatics and database-fueled investigations have placed metadata curation in the hands of researchers with little taxonomic experience. Here I describe practical challenges facing modern microbial taxonomy, provide an overview of complexities of classification for environmentally ubiquitous taxa like Pseudomonas syringae, and emphasize that classification can be independent of nomenclature. A move toward implementation of relational classification schemes based on inherent properties of whole genomes could provide sorely needed continuity in how strains are referenced across manuscripts and data sets. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular classification based on apomorphic amino acids (Arthropoda, Hexapoda): Integrative taxonomy in the era of phylogenomics.

PubMed

Wu, Hao-Yang; Wang, Yan-Hui; Xie, Qiang; Ke, Yun-Ling; Bu, Wen-Jun

2016-06-17

With the great development of sequencing technologies and systematic methods, our understanding of evolutionary relationships at deeper levels within the tree of life has greatly improved over the last decade. However, the current taxonomic methodology is insufficient to describe the growing levels of diversity in both a standardised and general way due to the limitations of using only morphological traits to describe clades. Herein, we propose the idea of a molecular classification based on hierarchical and discrete amino acid characters. Clades are classified based on the results of phylogenetic analyses and described using amino acids with group specificity in phylograms. Practices based on the recently published phylogenomic datasets of insects together with 15 de novo sequenced transcriptomes in this study demonstrate that such a methodology can accommodate various higher ranks of taxonomy. Such an approach has the advantage of describing organisms in a standard and discrete way within a phylogenetic framework, thereby facilitating the recognition of clades from the view of the whole lineage, as indicated by PhyloCode. By combining identification keys and phylogenies, the molecular classification based on hierarchical and discrete characters may greatly boost the progress of integrative taxonomy.

Molecular classification based on apomorphic amino acids (Arthropoda, Hexapoda): Integrative taxonomy in the era of phylogenomics

PubMed Central

Wu, Hao-Yang; Wang, Yan-Hui; Xie, Qiang; Ke, Yun-Ling; Bu, Wen-Jun

2016-01-01

With the great development of sequencing technologies and systematic methods, our understanding of evolutionary relationships at deeper levels within the tree of life has greatly improved over the last decade. However, the current taxonomic methodology is insufficient to describe the growing levels of diversity in both a standardised and general way due to the limitations of using only morphological traits to describe clades. Herein, we propose the idea of a molecular classification based on hierarchical and discrete amino acid characters. Clades are classified based on the results of phylogenetic analyses and described using amino acids with group specificity in phylograms. Practices based on the recently published phylogenomic datasets of insects together with 15 de novo sequenced transcriptomes in this study demonstrate that such a methodology can accommodate various higher ranks of taxonomy. Such an approach has the advantage of describing organisms in a standard and discrete way within a phylogenetic framework, thereby facilitating the recognition of clades from the view of the whole lineage, as indicated by PhyloCode. By combining identification keys and phylogenies, the molecular classification based on hierarchical and discrete characters may greatly boost the progress of integrative taxonomy. PMID:27312960

A Monograph of Conostegia (Melastomataceae, Miconieae).

PubMed

Kriebel, Ricardo

2016-01-01

A recent molecular phylogenetic analysis identified a clade containing all species of Conostegia, but that also included species of Clidemia and Miconia nested inside. A taxonomic revision of a more broadly circumscribed Conostegia is presented here. In total, 77 species of Conostegia are recognized. One species from Ecuador, Conostegia ortizae is described as new. Twenty-nine new combinations are proposed for the species of Clidemia and Miconia that fall inside Conostegia. Two new names are proposed for the two species for which the epithet was previously occupied in Conostegia. An infrageneric classification of Conostegia is proposed recognizing three sections based on the results of the molecular phylogeny. This taxonomic revision includes ample documentation of the anatomy and morphology of most species in the genus, taxonomic descriptions, a dichotomous key, and distribution maps for all species.

How many species are there on Earth and in the ocean?

PubMed

Mora, Camilo; Tittensor, Derek P; Adl, Sina; Simpson, Alastair G B; Worm, Boris

2011-08-01

The diversity of life is one of the most striking aspects of our planet; hence knowing how many species inhabit Earth is among the most fundamental questions in science. Yet the answer to this question remains enigmatic, as efforts to sample the world's biodiversity to date have been limited and thus have precluded direct quantification of global species richness, and because indirect estimates rely on assumptions that have proven highly controversial. Here we show that the higher taxonomic classification of species (i.e., the assignment of species to phylum, class, order, family, and genus) follows a consistent and predictable pattern from which the total number of species in a taxonomic group can be estimated. This approach was validated against well-known taxa, and when applied to all domains of life, it predicts ~8.7 million (± 1.3 million SE) eukaryotic species globally, of which ~2.2 million (± 0.18 million SE) are marine. In spite of 250 years of taxonomic classification and over 1.2 million species already catalogued in a central database, our results suggest that some 86% of existing species on Earth and 91% of species in the ocean still await description. Renewed interest in further exploration and taxonomy is required if this significant gap in our knowledge of life on Earth is to be closed.

Why do different oceanic archipelagos harbour contrasting levels of species diversity? The macaronesian endemic genus Pericallis (Asteraceae) provides insight into explaining the 'Azores diversity Enigma'.

PubMed

Jones, K E; Pérez-Espona, S; Reyes-Betancort, J A; Pattinson, D; Caujapé-Castells, J; Hiscock, S J; Carine, M A

2016-10-08

Oceanic archipelagos typically harbour extensive radiations of flowering plants and a high proportion of endemics, many of which are restricted to a single island (Single Island Endemics; SIEs). The Azores represents an anomaly as overall levels of endemism are low; there are few SIEs and few documented cases of intra-archipelago radiations. The distinctiveness of the flora was first recognized by Darwin and has been referred to as the 'Azores Diversity Enigma' (ADE). Diversity patterns in the Macaronesian endemic genus Pericallis (Asteraceae) exemplify the ADE. In this study we used morphometric, Amplified Length Polymorphisms, and bioclimatic data for herbaceous Pericallis lineages endemic to the Azores and the Canaries, to test two key hypotheses proposed to explain the ADE: i) that it is a taxonomic artefact or Linnean shortfall, ie. the under description of taxa in the Azores or the over-splitting of taxa in the Canaries and (ii) that it reflects the greater ecological homogeneity of the Azores, which results in limited opportunity for ecological diversification compared to the Canaries. In both the Azores and the Canaries, morphological patterns were generally consistent with current taxonomic classifications. However, the AFLP data showed no genetic differentiation between the two currently recognized Azorean subspecies that are ecologically differentiated. Instead, genetic diversity in the Azores was structured geographically across the archipelago. In contrast, in the Canaries genetic differentiation was mostly consistent with morphology and current taxonomic treatments. Both Azorean and Canarian lineages exhibited ecological differentiation between currently recognized taxa. Neither a Linnean shortfall nor the perceived ecological homogeneity of the Azores fully explained the ADE-like pattern observed in Pericallis. Whilst variation in genetic data and morphological data in the Canaries were largely congruent, this was not the case in the Azores, where genetic patterns reflected inter-island geographical isolation, and morphology reflected intra-island bioclimatic variation. The combined effects of differences in (i) the extent of geographical isolation, (ii) population sizes and (iii) geographical occupancy of bioclimatic niche space, coupled with the morphological plasticity of Pericallis, may all have contributed to generating the contrasting patterns observed in the archipelagos.

Top 10 Lines of Evidence for Human Evolution.

ERIC Educational Resources Information Center

Nickels, Martin

2001-01-01

Provides 10 lines of evidence that support the theory of human evolution. The evidence relates to hierarchical taxonomic classification, comparative anatomy, comparative embryology and development, comparative biochemistry, adaptive compromises, vestigial structures, biogeography, the fossil sequence, ecological coherence of fossil assemblages,…

Guidance for Determining the Acceptability of Environmental Fate Studies Conducted with Foreign Soils

EPA Pesticide Factsheets

International and U.S. soil taxonomical classification systems, distribution of soil orders in the United States, specific criteria to help scientists determine when foreign soils are representative of U.S. soils at intended pesticide use sites.

[Concepts of rational taxonomy].

PubMed

Pavlinov, I Ia

2011-01-01

The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the standpoint of inductive and hypothetico-deductive argumentation schemes and such fundamental criteria of classifications naturalness as their prognostic capabilities; foundation of a theory of "general taxonomy" as a "general logic", including elements of the axiomatic method. The latter concept constitutes a core of the program of general classiology; it is inconsistent due to absence of anything like "general logic". It is asserted that elaboration of a theory of taxonomy as a biological discipline based on the formal principles of epistemological rationality is not feasible. Instead, it is to be elaborated as ontologically rational one based on biologically sound metatheories about biological diversity causes.

The diversity of ice algal communities on the Greenland Ice Sheet as revealed by oligotyping

PubMed Central

Lutz, Stefanie; McCutcheon, Jenine; McQuaid, James B.; Benning, Liane G.

2018-01-01

The Arctic is being disproportionally affected by climate change compared with other geographic locations, and is currently experiencing unprecedented melt rates. The Greenland Ice Sheet (GrIS) can be regarded as the largest supraglacial ecosystem on Earth, and ice algae are the dominant primary producers on bare ice surfaces throughout the course of a melt season. Ice-algal-derived pigments cause a darkening of the ice surface, which in turn decreases albedo and increases melt rates. The important role of ice algae in changing melt rates has only recently been recognized, and we currently know little about their community compositions and functions. Here, we present the first analysis of ice algal communities across a 100 km transect on the GrIS by high-throughput sequencing and subsequent oligotyping of the most abundant taxa. Our data reveal an extremely low algal diversity with Ancylonema nordenskiöldii and a Mesotaenium species being by far the dominant taxa at all sites. We employed an oligotyping approach and revealed a hidden diversity not detectable by conventional clustering of operational taxonomic units and taxonomic classification. Oligotypes of the dominant taxa exhibit a site-specific distribution, which may be linked to differences in temperatures and subsequently the extent of the melting. Our results help to better understand the distribution patterns of ice algal communities that play a crucial role in the GrIS ecosystem. PMID:29547098

Scientific names of organisms: attribution, rights, and licensing

PubMed Central

2014-01-01

Background As biological disciplines extend into the ‘big data’ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world. Findings The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts. Conclusions A ‘blue list’ identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed. PMID:24495358

Random whole metagenomic sequencing for forensic discrimination of soils.

PubMed

Khodakova, Anastasia S; Smith, Renee J; Burgoyne, Leigh; Abarno, Damien; Linacre, Adrian

2014-01-01

Here we assess the ability of random whole metagenomic sequencing approaches to discriminate between similar soils from two geographically distinct urban sites for application in forensic science. Repeat samples from two parklands in residential areas separated by approximately 3 km were collected and the DNA was extracted. Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles. Full and subsampled metagenomic datasets were then annotated against M5NR/M5RNA (taxonomic classification) and SEED Subsystems (metabolic classification) databases. Further comparative analyses were performed using a number of statistical tools including: hierarchical agglomerative clustering (CLUSTER); similarity profile analysis (SIMPROF); non-metric multidimensional scaling (NMDS); and canonical analysis of principal coordinates (CAP) at all major levels of taxonomic and metabolic classification. Our data showed that shotgun and WGA-based approaches generated highly similar metagenomic profiles for the soil samples such that the soil samples could not be distinguished accurately. An AP-PCR based approach was shown to be successful at obtaining reproducible site-specific metagenomic DNA profiles, which in turn were employed for successful discrimination of visually similar soil samples collected from two different locations.

From 2000years of Ganoderma lucidum to recent developments in nutraceuticals.

PubMed

Bishop, Karen S; Kao, Chi H J; Xu, Yuanye; Glucina, Marcus P; Paterson, R Russell M; Ferguson, Lynnette R

2015-06-01

Medicinal mushrooms have been used for centuries as nutraceuticals to improve health and to treat numerous chronic and infectious diseases. One such mushroom is Ganoderma lucidum, commonly known as Lingzhi, a species revered as a medicinal mushroom for treating assorted diseases and prolonging life. The fungus is found in diverse locations, and this may have contributed to confusion regarding the correct taxonomic classification of the genus Ganoderma. G. lucidum was first used to name a specimen found in England and thereafter was naively applied to a different Ganoderma species found in Asia, commonly known as Chinese Lingzhi. Despite the taxonomic confusion, which has largely been uncorrected, the popularity of Lingzhi has escalated across the globe. The current taxonomic situation is now discussed accurately in this Special Issue on Ganoderma. Today it is a multi-billion dollar industry wherein Lingzhi is cultivated or collected from the wild and consumed as a tea, in alcoholic beverages, and as a nutraceutical to confer numerous health benefits. Consumption of nutraceuticals has grown in popularity, and it is becoming increasingly important that active ingredients be identified and that suppliers make substantiated health claims about their products. The objective of this article is to present a review of G. lucidum over the past 2000 years from prized ancient "herbal" remedy to its use in nutraceuticals and to the establishment of a 2.5 billion $ (US) industry. Copyright © 2015 Elsevier Ltd. All rights reserved.

An improved taxonomic sampling is a necessary but not sufficient condition for resolving inter-families relationships in Caridean decapods.

PubMed

Aznar-Cormano, L; Brisset, J; Chan, T-Y; Corbari, L; Puillandre, N; Utge, J; Zbinden, M; Zuccon, D; Samadi, S

2015-04-01

During the past decade, a large number of multi-gene analyses aimed at resolving the phylogenetic relationships within Decapoda. However relationships among families, and even among sub-families, remain poorly defined. Most analyses used an incomplete and opportunistic sampling of species, but also an incomplete and opportunistic gene selection among those available for Decapoda. Here we test in the Caridea if improving the taxonomic coverage following the hierarchical scheme of the classification, as it is currently accepted, provides a better phylogenetic resolution for the inter-families relationships. The rich collections of the Muséum National d'Histoire Naturelle de Paris are used for sampling as far as possible at least two species of two different genera for each family or subfamily. All potential markers are tested over this sampling. For some coding genes the amplification success varies greatly among taxa and the phylogenetic signal is highly saturated. This result probably explains the taxon-heterogeneity among previously published studies. The analysis is thus restricted to the genes homogeneously amplified over the whole sampling. Thanks to the taxonomic sampling scheme the monophyly of most families is confirmed. However the genes commonly used in Decapoda appear non-adapted for clarifying inter-families relationships, which remain poorly resolved. Genome-wide analyses, like transcriptome-based exon capture facilitated by the new generation sequencing methods might provide a sounder approach to resolve deep and rapid radiations like the Caridea.

Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2015.

PubMed

Janda, J Michael

2016-10-01

A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate and rapid reporting and communication regarding infectious agents of clinical significance. Microbial taxonomy in the age of molecular diagnostics and phylogenetics creates changes in taxonomy at a rapid rate further complicating this process. This update focuses on the description of new species and classification changes proposed in 2015. Copyright © 2016 Elsevier Inc. All rights reserved.

Functional Basis of Microorganism Classification.

PubMed

Zhu, Chengsheng; Delmont, Tom O; Vogel, Timothy M; Bromberg, Yana

2015-08-01

Correctly identifying nearest "neighbors" of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment. Microbial classification based on similarity of physiological and genetic organism traits (polyphasic similarity) is experimentally difficult and, arguably, subjective. Evolutionary relatedness, inferred from phylogenetic markers, facilitates classification but does not guarantee functional identity between members of the same taxon or lack of similarity between different taxa. Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based microorganism classification scheme, functional-repertoire similarity-based organism network (FuSiON; flattened to fusion). Our scheme is phenetic, based on a network of quantitatively defined organism relationships across the known prokaryotic space. It correlates significantly with the current taxonomy, but the observed discrepancies reveal both (1) the inconsistency of functional diversity levels among different taxa and (2) an (unsurprising) bias towards prioritizing, for classification purposes, relatively minor traits of particular interest to humans. Our dynamic network-based organism classification is independent of the arbitrary pairwise organism similarity cut-offs traditionally applied to establish taxonomic identity. Instead, it reveals natural, functionally defined organism groupings and is thus robust in handling organism diversity. Additionally, fusion can use organism meta-data to highlight the specific environmental factors that drive microbial diversification. Our approach provides a complementary view to cladistic assignments and holds important clues for further exploration of microbial lifestyles. Fusion is a more practical fit for biomedical, industrial, and ecological applications, as many of these rely on understanding the functional capabilities of the microbes in their environment and are less concerned with phylogenetic descent.

Functional Basis of Microorganism Classification

PubMed Central

Zhu, Chengsheng; Delmont, Tom O.; Vogel, Timothy M.; Bromberg, Yana

2015-01-01

Correctly identifying nearest “neighbors” of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment. Microbial classification based on similarity of physiological and genetic organism traits (polyphasic similarity) is experimentally difficult and, arguably, subjective. Evolutionary relatedness, inferred from phylogenetic markers, facilitates classification but does not guarantee functional identity between members of the same taxon or lack of similarity between different taxa. Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based microorganism classification scheme, functional-repertoire similarity-based organism network (FuSiON; flattened to fusion). Our scheme is phenetic, based on a network of quantitatively defined organism relationships across the known prokaryotic space. It correlates significantly with the current taxonomy, but the observed discrepancies reveal both (1) the inconsistency of functional diversity levels among different taxa and (2) an (unsurprising) bias towards prioritizing, for classification purposes, relatively minor traits of particular interest to humans. Our dynamic network-based organism classification is independent of the arbitrary pairwise organism similarity cut-offs traditionally applied to establish taxonomic identity. Instead, it reveals natural, functionally defined organism groupings and is thus robust in handling organism diversity. Additionally, fusion can use organism meta-data to highlight the specific environmental factors that drive microbial diversification. Our approach provides a complementary view to cladistic assignments and holds important clues for further exploration of microbial lifestyles. Fusion is a more practical fit for biomedical, industrial, and ecological applications, as many of these rely on understanding the functional capabilities of the microbes in their environment and are less concerned with phylogenetic descent. PMID:26317871

Large-scale assessment of benthic communities across multiple marine protected areas using an autonomous underwater vehicle.

PubMed

Ferrari, Renata; Marzinelli, Ezequiel M; Ayroza, Camila Rezende; Jordan, Alan; Figueira, Will F; Byrne, Maria; Malcolm, Hamish A; Williams, Stefan B; Steinberg, Peter D

2018-01-01

Marine protected areas (MPAs) are designed to reduce threats to biodiversity and ecosystem functioning from anthropogenic activities. Assessment of MPAs effectiveness requires synchronous sampling of protected and non-protected areas at multiple spatial and temporal scales. We used an autonomous underwater vehicle to map benthic communities in replicate 'no-take' and 'general-use' (fishing allowed) zones within three MPAs along 7o of latitude. We recorded 92 taxa and 38 morpho-groups across three large MPAs. We found that important habitat-forming biota (e.g. massive sponges) were more prevalent and abundant in no-take zones, while short ephemeral algae were more abundant in general-use zones, suggesting potential short-term effects of zoning (5-10 years). Yet, short-term effects of zoning were not detected at the community level (community structure or composition), while community structure varied significantly among MPAs. We conclude that by allowing rapid, simultaneous assessments at multiple spatial scales, autonomous underwater vehicles are useful to document changes in marine communities and identify adequate scales to manage them. This study advanced knowledge of marine benthic communities and their conservation in three ways. First, we quantified benthic biodiversity and abundance, generating the first baseline of these benthic communities against which the effectiveness of three large MPAs can be assessed. Second, we identified the taxonomic resolution necessary to assess both short and long-term effects of MPAs, concluding that coarse taxonomic resolution is sufficient given that analyses of community structure at different taxonomic levels were generally consistent. Yet, observed differences were taxa-specific and may have not been evident using our broader taxonomic classifications, a classification of mid to high taxonomic resolution may be necessary to determine zoning effects on key taxa. Third, we provide an example of statistical analyses and sampling design that once temporal sampling is incorporated will be useful to detect changes of marine benthic communities across multiple spatial and temporal scales.

Large-scale assessment of benthic communities across multiple marine protected areas using an autonomous underwater vehicle

PubMed Central

Ayroza, Camila Rezende; Jordan, Alan; Figueira, Will F.; Byrne, Maria; Malcolm, Hamish A.; Williams, Stefan B.; Steinberg, Peter D.

2018-01-01

Marine protected areas (MPAs) are designed to reduce threats to biodiversity and ecosystem functioning from anthropogenic activities. Assessment of MPAs effectiveness requires synchronous sampling of protected and non-protected areas at multiple spatial and temporal scales. We used an autonomous underwater vehicle to map benthic communities in replicate ‘no-take’ and ‘general-use’ (fishing allowed) zones within three MPAs along 7o of latitude. We recorded 92 taxa and 38 morpho-groups across three large MPAs. We found that important habitat-forming biota (e.g. massive sponges) were more prevalent and abundant in no-take zones, while short ephemeral algae were more abundant in general-use zones, suggesting potential short-term effects of zoning (5–10 years). Yet, short-term effects of zoning were not detected at the community level (community structure or composition), while community structure varied significantly among MPAs. We conclude that by allowing rapid, simultaneous assessments at multiple spatial scales, autonomous underwater vehicles are useful to document changes in marine communities and identify adequate scales to manage them. This study advanced knowledge of marine benthic communities and their conservation in three ways. First, we quantified benthic biodiversity and abundance, generating the first baseline of these benthic communities against which the effectiveness of three large MPAs can be assessed. Second, we identified the taxonomic resolution necessary to assess both short and long-term effects of MPAs, concluding that coarse taxonomic resolution is sufficient given that analyses of community structure at different taxonomic levels were generally consistent. Yet, observed differences were taxa-specific and may have not been evident using our broader taxonomic classifications, a classification of mid to high taxonomic resolution may be necessary to determine zoning effects on key taxa. Third, we provide an example of statistical analyses and sampling design that once temporal sampling is incorporated will be useful to detect changes of marine benthic communities across multiple spatial and temporal scales. PMID:29547656

National Plant Diagnostic Network, Taxonomic training videos: Introduction to Aphids - Part 1

USDA-ARS?s Scientific Manuscript database

Training is a critical part of aphid (Hemiptera: Aphididae) identification. This video provides visual instruction on important subject areas for aphid examination and identification. Aphid topics such as classification, morphology, plant disease transmission, and references are discussed. This dis...

Sensitivity and accuracy of high-throughput metabarcoding methods for early detection of invasive fish species

EPA Science Inventory

For early detection biomonitoring of aquatic invasive species, sensitivity to rare individuals and accurate, high-resolution taxonomic classification are critical to minimize detection errors. Given the great expense and effort associated with morphological identification of many...

A k-mer-based barcode DNA classification methodology based on spectral representation and a neural gas network.

PubMed

Fiannaca, Antonino; La Rosa, Massimo; Rizzo, Riccardo; Urso, Alfonso

2015-07-01

In this paper, an alignment-free method for DNA barcode classification that is based on both a spectral representation and a neural gas network for unsupervised clustering is proposed. In the proposed methodology, distinctive words are identified from a spectral representation of DNA sequences. A taxonomic classification of the DNA sequence is then performed using the sequence signature, i.e., the smallest set of k-mers that can assign a DNA sequence to its proper taxonomic category. Experiments were then performed to compare our method with other supervised machine learning classification algorithms, such as support vector machine, random forest, ripper, naïve Bayes, ridor, and classification tree, which also consider short DNA sequence fragments of 200 and 300 base pairs (bp). The experimental tests were conducted over 10 real barcode datasets belonging to different animal species, which were provided by the on-line resource "Barcode of Life Database". The experimental results showed that our k-mer-based approach is directly comparable, in terms of accuracy, recall and precision metrics, with the other classifiers when considering full-length sequences. In addition, we demonstrate the robustness of our method when a classification is performed task with a set of short DNA sequences that were randomly extracted from the original data. For example, the proposed method can reach the accuracy of 64.8% at the species level with 200-bp fragments. Under the same conditions, the best other classifier (random forest) reaches the accuracy of 20.9%. Our results indicate that we obtained a clear improvement over the other classifiers for the study of short DNA barcode sequence fragments. Copyright © 2015 Elsevier B.V. All rights reserved.

A Monograph of Conostegia (Melastomataceae, Miconieae)

PubMed Central

Kriebel, Ricardo

2016-01-01

Abstract A recent molecular phylogenetic analysis identified a clade containing all species of Conostegia, but that also included species of Clidemia and Miconia nested inside. A taxonomic revision of a more broadly circumscribed Conostegia is presented here. In total, 77 species of Conostegia are recognized. One species from Ecuador, Conostegia ortizae is described as new. Twenty-nine new combinations are proposed for the species of Clidemia and Miconia that fall inside Conostegia. Two new names are proposed for the two species for which the epithet was previously occupied in Conostegia. An infrageneric classification of Conostegia is proposed recognizing three sections based on the results of the molecular phylogeny. This taxonomic revision includes ample documentation of the anatomy and morphology of most species in the genus, taxonomic descriptions, a dichotomous key, and distribution maps for all species. PMID:27536193

REORGANIZATION AND EXPANSION OF THE NIDOVIRAL FAMILY ARTERIVIRIDAE

PubMed Central

Kuhn, Jens H.; Lauck, Michael; Bailey, Adam L.; Shchetinin, Alexey M.; Vishnevskaya, Tatyana V.; Bào, Yīmíng; Ng, Terry Fei Fan; LeBreton, Matthew; Schneider, Bradley S.; Gillis, Amethyst; Tamoufe, Ubald; Diffo, Joseph Ledoux; Takuo, Jean Michel; Kondov, Nikola O.; Coffey, Lark L.; Wolfe, Nathan D.; Delwart, Eric; Clawson, Anna N.; Postnikova, Elena; Bollinger, Laura; Lackemeyer, Matthew G.; Radoshitzky, Sheli R.; Palacios, Gustavo; Wada, Jiro; Shevtsova, Zinaida V.; Jahrling, Peter B.; Lapin, Boris A.; Deriabin, Petr G.; Dunowska, Magdalena; Alkhovsky, Sergey V.; Rogers, Jeffrey; Friedrich, Thomas C.; O’Connor, David H.; Goldberg, Tony L.

2017-01-01

The family Arteriviridae presently includes a single genus Arterivirus. This genus includes four species as the taxonomic homes for equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), porcine respiratory and reproductive syndrome virus (PRRSV), and simian hemorrhagic fever virus (SHFV), respectively. A revision of this classification is urgently needed to accommodate the recent description of eleven highly divergent simian arteriviruses in diverse African nonhuman primates, one novel arterivirus in an African forest giant pouched rat, and a novel arterivirus in common brushtails in New Zealand. In addition, the current arterivirus nomenclature is not in accordance with the most recent version of the International Code of Virus Classification and Nomenclature. Here we outline an updated, amended, and improved arterivirus taxonomy based on current data. Taxon-specific sequence cut-offs are established relying on a newly established open reading frame 1b phylogeny and pairwise sequence comparison (PASC) of coding-complete arterivirus genomes. As a result, the current genus Arterivirus is replaced by five genera: Equartevirus (for EAV), Rodartevirus (LDV + PRRSV), Simartevirus (SHFV + simian arteriviruses), Nesartevirus (for the arterivirus from forest giant pouched rats), and Dipartevirus (common brushtail arterivirus). The current species Porcine reproductive and respiratory syndrome virus is divided into two species to accommodate the clear divergence of the European and American “types” of PRRSV, both of which now receive virus status. The current species Simian hemorrhagic fever virus is divided into nine species to accommodate the twelve known simian arteriviruses. Non-Latinized binomial species names are introduced to replace all current species names to clearly differentiate them from virus names, which remain largely unchanged. PMID:26608064

A Comparison of Methods to Analyze Aquatic Heterotrophic Flagellates of Different Taxonomic Groups.

PubMed

Jeuck, Alexandra; Nitsche, Frank; Wylezich, Claudia; Wirth, Olaf; Bergfeld, Tanja; Brutscher, Fabienne; Hennemann, Melanie; Monir, Shahla; Scherwaß, Anja; Troll, Nicole; Arndt, Hartmut

2017-08-01

Heterotrophic flagellates contribute significantly to the matter flux in aquatic and terrestrial ecosystems. Still today their quantification and taxonomic classification bear several problems in field studies, though these methodological problems seem to be increasingly ignored in current ecological studies. Here we describe and test different methods, the live-counting technique, different fixation techniques, cultivation methods like the liquid aliquot method (LAM), and a molecular single cell survey called aliquot PCR (aPCR). All these methods have been tested either using aquatic field samples or cultures of freshwater and marine taxa. Each of the described methods has its advantages and disadvantages, which have to be considered in every single case. With the live-counting technique a detection of living cells up to morphospecies level is possible. Fixation of cells and staining methods are advantageous due to the possible long-term storage and observation of samples. Cultivation methods (LAM) offer the possibility of subsequent molecular analyses, and aPCR tools might complete the deficiency of LAM in terms of the missing detection of non-cultivable flagellates. In summary, we propose a combination of several investigation techniques reducing the gap between the different methodological problems. Copyright © 2017 Elsevier GmbH. All rights reserved.

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

PubMed Central

Hinchliff, Cody E.; Smith, Stephen A.; Allman, James F.; Burleigh, J. Gordon; Chaudhary, Ruchi; Coghill, Lyndon M.; Crandall, Keith A.; Deng, Jiabin; Drew, Bryan T.; Gazis, Romina; Gude, Karl; Hibbett, David S.; Katz, Laura A.; Laughinghouse, H. Dail; McTavish, Emily Jane; Midford, Peter E.; Owen, Christopher L.; Ree, Richard H.; Rees, Jonathan A.; Soltis, Douglas E.; Williams, Tiffani; Cranston, Karen A.

2015-01-01

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics. PMID:26385966

Synthesis of phylogeny and taxonomy into a comprehensive tree of life.

PubMed

Hinchliff, Cody E; Smith, Stephen A; Allman, James F; Burleigh, J Gordon; Chaudhary, Ruchi; Coghill, Lyndon M; Crandall, Keith A; Deng, Jiabin; Drew, Bryan T; Gazis, Romina; Gude, Karl; Hibbett, David S; Katz, Laura A; Laughinghouse, H Dail; McTavish, Emily Jane; Midford, Peter E; Owen, Christopher L; Ree, Richard H; Rees, Jonathan A; Soltis, Douglas E; Williams, Tiffani; Cranston, Karen A

2015-10-13

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips-the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

PubMed Central

Lipinski, Leszek; Dziembowski, Andrzej

2018-01-01

Abstract Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples. PlasFlow can recover plasmid sequences from assembled metagenomes without any prior knowledge of the taxonomical or functional composition of samples with an accuracy up to 96%. It can also recover sequences of both circular and linear plasmids and can perform initial taxonomical classification of sequences. Compared to other currently available tools, PlasFlow demonstrated significantly better performance on test datasets. Analysis of two samples from heavy metal-contaminated microbial mats revealed that plasmids may constitute an important fraction of their metagenomes and carry genes involved in heavy-metal homeostasis, proving the pivotal role of plasmids in microorganism adaptation to environmental conditions. PMID:29346586

Taxonomy-aware feature engineering for microbiome classification.

PubMed

Oudah, Mai; Henschel, Andreas

2018-06-15

What is a healthy microbiome? The pursuit of this and many related questions, especially in light of the recently recognized microbial component in a wide range of diseases has sparked a surge in metagenomic studies. They are often not simply attributable to a single pathogen but rather are the result of complex ecological processes. Relatedly, the increasing DNA sequencing depth and number of samples in metagenomic case-control studies enabled the applicability of powerful statistical methods, e.g. Machine Learning approaches. For the latter, the feature space is typically shaped by the relative abundances of operational taxonomic units, as determined by cost-effective phylogenetic marker gene profiles. While a substantial body of microbiome/microbiota research involves unsupervised and supervised Machine Learning, very little attention has been put on feature selection and engineering. We here propose the first algorithm to exploit phylogenetic hierarchy (i.e. an all-encompassing taxonomy) in feature engineering for microbiota classification. The rationale is to exploit the often mono- or oligophyletic distribution of relevant (but hidden) traits by virtue of taxonomic abstraction. The algorithm is embedded in a comprehensive microbiota classification pipeline, which we applied to a diverse range of datasets, distinguishing healthy from diseased microbiota samples. We demonstrate substantial improvements over the state-of-the-art microbiota classification tools in terms of classification accuracy, regardless of the actual Machine Learning technique while using drastically reduced feature spaces. Moreover, generalized features bear great explanatory value: they provide a concise description of conditions and thus help to provide pathophysiological insights. Indeed, the automatically and reproducibly derived features are consistent with previously published domain expert analyses.

Natural Products from the Lithistida: A Review of the Literature since 2000

PubMed Central

Winder, Priscilla L.; Pomponi, Shirley A.; Wright, Amy E.

2011-01-01

Lithistid sponges are known to produce a diverse array of compounds ranging from polyketides, cyclic and linear peptides, alkaloids, pigments, lipids, and sterols. A majority of these structurally complex compounds have very potent and interesting biological activities. It has been a decade since a thorough review has been published that summarizes the literature on the natural products reported from this amazing sponge order. This review provides an update on the current taxonomic classification of the Lithistida, describes structures and biological activities of 131 new natural products, and discusses highlights from the total syntheses of 16 compounds from marine sponges of the Order Lithistida providing a compilation of the literature since the last review published in 2002. PMID:22363244

Phylogenetic relationship among East Asian species of the Stegana genus group (Diptera, Drosophilidae).

PubMed

Li, Tong; Gao, Jian-jun; Lu, Jin-ming; Ji, Xing-lai; Chen, Hong-wei

2013-01-01

The phylogenetic relationship among 27 East Asian species of the Stegana genus group was reconstructed using DNA sequences of mitochondrial (COI and ND2) and nuclear (28S) genes. The results lent support to the current generic/subgeneric taxonomic classification in the genus group with the exceptions of the paraphyly of the genus Parastegana and the subgenus Oxyphortica in the genus Stegana. The ancestral areas and divergence times in the genus group were reconstructed/estimated, and accordingly, the biogeographical history of this important clade was discussed. It was proposed that, the evolution of the plant family Fagaceae, especially Quercus, may have played a certain role in facilitating the diversification of the Stegana genus group. Copyright © 2012 Elsevier Inc. All rights reserved.

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.

Medical Parasitology Taxonomy Update: January 2012 to December 2015.

PubMed

Simner, P J

2017-01-01

Parasites of medical importance have long been classified taxonomically by morphological characteristics. However, molecular-based techniques have been increasingly used and relied on to determine evolutionary distances for the basis of rational hierarchal classifications. This has resulted in several different classification schemes for parasites and changes in parasite taxonomy. The purpose of this Minireview is to provide a single reference for diagnostic laboratories that summarizes new and revised clinically relevant parasite taxonomy from January 2012 through December 2015. Copyright © 2016 American Society for Microbiology.

Rename the family Ophioviridae and its constituent species

USDA-ARS?s Scientific Manuscript database

A transparent and functional system for virus classification is essential to allow scientists to correctly identify and report on viruses detected in different hosts or locations without ambiguity. This is a taxonomic proposal from the Ophioviridae Study Group of the International Committee on Viral...

Client Resistance in Counseling: Its Theoretical Rationale and Taxonomic Classification.

ERIC Educational Resources Information Center

Otani, Akira

1989-01-01

Reviews 3 theoretical models of client resistance in counseling: anxiety control, noncompliance, and negative social influence. Describes 22 commonly observed client resistance behaviors in 4 separate categories: response quantity resistance, response content resistance, response style resistance, and logistic management resistance. (Author/ABL)

Changing techniques in crop plant classification: molecularization at the National Institute of Agricultural Botany during the 1980s.

PubMed

Holmes, Matthew

2017-04-01

Modern methods of analysing biological materials, including protein and DNA sequencing, are increasingly the objects of historical study. Yet twentieth-century taxonomic techniques have been overlooked in one of their most important contexts: agricultural botany. This paper addresses this omission by harnessing unexamined archival material from the National Institute of Agricultural Botany (NIAB), a British plant science organization. During the 1980s the NIAB carried out three overlapping research programmes in crop identification and analysis: electrophoresis, near infrared spectroscopy (NIRS) and machine vision systems. For each of these three programmes, contemporary economic, statutory and scientific factors behind their uptake by the NIAB are discussed. This approach reveals significant links between taxonomic practice at the NIAB and historical questions around agricultural research, intellectual property and scientific values. Such links are of further importance given that the techniques developed by researchers at the NIAB during the 1980s remain part of crop classification guidelines issued by international bodies today.

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.

PubMed

Zuo, Guanghong; Hao, Bailin

2015-10-01

A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

How Many Species Are There on Earth and in the Ocean?

PubMed Central

Mora, Camilo; Tittensor, Derek P.; Adl, Sina; Simpson, Alastair G. B.; Worm, Boris

2011-01-01

The diversity of life is one of the most striking aspects of our planet; hence knowing how many species inhabit Earth is among the most fundamental questions in science. Yet the answer to this question remains enigmatic, as efforts to sample the world's biodiversity to date have been limited and thus have precluded direct quantification of global species richness, and because indirect estimates rely on assumptions that have proven highly controversial. Here we show that the higher taxonomic classification of species (i.e., the assignment of species to phylum, class, order, family, and genus) follows a consistent and predictable pattern from which the total number of species in a taxonomic group can be estimated. This approach was validated against well-known taxa, and when applied to all domains of life, it predicts ∼8.7 million (±1.3 million SE) eukaryotic species globally, of which ∼2.2 million (±0.18 million SE) are marine. In spite of 250 years of taxonomic classification and over 1.2 million species already catalogued in a central database, our results suggest that some 86% of existing species on Earth and 91% of species in the ocean still await description. Renewed interest in further exploration and taxonomy is required if this significant gap in our knowledge of life on Earth is to be closed. PMID:21886479

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

PubMed Central

Zuo, Guanghong; Hao, Bailin

2015-01-01

A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements. PMID:26563468

A taxonomic review of the Selenophori group (Coleoptera, Carabidae, Harpalini) in the West Indies, with descriptions of new species and notes about classification and biogeography

PubMed Central

Shpeley, Danny; Hunting, Wesley; Ball, George E.

2017-01-01

Abstract Primarily a taxonomic review of the West Indian elements of the selenophorine Harpalini, this paper includes a classification, a key, descriptions and illustrations of taxa, re-rankings, and new synonymies. In total, 45 species and subspecies are treated, six of which are described as new. A new genus and new species are as follows, with type localities in parentheses: Paraulacoryssus gen. n., (type species Selenophorus puertoricensis Mutchler, 1934); Neodiachipteryx davidsoni sp. n., (Zamba, Dominican Republic); Selenophorus spinosus sp. n., seriatoporus species group (Benjamin Constant, state of Amazonas, Brazil); Selenophorus obtusoides sp. n., parumpunctatus species group (near Soroa, Pinar del Rio Province, Cuba); Selenophorus iviei sp. n., nonseriatus species group (Big River, Montserrat, 16°45.719N', 62°11.335W'); Selenophorus irec sp. n., nonseriatus species group (Vernou, Guadeloupe, Lesser Antilles); and Selenophorus fabricii sp. n., opalinus species group (Cabo Rojo, Pedernales Province, Dominican Republic). This last species was misidentified as Selenophorus integer (Fabricius). In turn, that species was misidentified as Selenophorus chalybeus Dejean. Selenophorus chalybeus Dejean is a junior synonym of Selenophorus integer Fabricius, syn. n.; and Isopleurus macleayi Kirby is a junior synonym of Selenophorus pyritosus Dejean, syn. n. Biogeographically, log of land area plotted against log of number of species shows that the equilibrium theory of biogeography applies to the West Indian selenophorine fauna. Taxonomically, the selenophorine taxa of the West Indies are arranged in eight genera. The 30 species/subspecies of Selenophorus (sensu stricto) are arranged in 10 species groups. Geographically, the major sources of the selenophorines are the Bahamas, the Greater Antilles and Lesser Antilles. The West Indian islands probably have been invaded by 26 taxa. Of the currently extant taxa, 11 are classified as immigrant, meaning that they are represented both in the islands and on the mainland (South America or Middle America and southern Florida). Thirty three taxa are classified as precinctive, meaning that they originated where they are now living, the implication being that they have descended from immigrants, thus older in the islands than the current-day immigrants. It is postulated that the West Indian taxa represent three age groups: oldest, ancestors having reached the proto-Antilles by a landspan known as GAARlandia; a middle-age group (Neogene period), their ancestors having reached the islands by dispersal over water, between islands; and a young group of extant taxa, no older than the Pleistocene, also having reached the islands over water. PMID:29118595

A taxonomic review of the Selenophori group (Coleoptera, Carabidae, Harpalini) in the West Indies, with descriptions of new species and notes about classification and biogeography.

PubMed

Shpeley, Danny; Hunting, Wesley; Ball, George E

2017-01-01

Primarily a taxonomic review of the West Indian elements of the selenophorine Harpalini, this paper includes a classification, a key, descriptions and illustrations of taxa, re-rankings, and new synonymies. In total, 45 species and subspecies are treated, six of which are described as new. A new genus and new species are as follows, with type localities in parentheses: Paraulacoryssus gen. n. , (type species Selenophorus puertoricensis Mutchler, 1934); Neodiachipteryx davidsoni sp. n. , (Zamba, Dominican Republic); Selenophorus spinosus sp. n. , seriatoporus species group (Benjamin Constant, state of Amazonas, Brazil); Selenophorus obtusoides sp. n. , parumpunctatus species group (near Soroa, Pinar del Rio Province, Cuba); Selenophorus iviei sp. n. , nonseriatus species group (Big River, Montserrat, 16°45.719N', 62°11.335W'); Selenophorus irec sp. n. , nonseriatus species group (Vernou, Guadeloupe, Lesser Antilles); and Selenophorus fabricii sp. n. , opalinus species group (Cabo Rojo, Pedernales Province, Dominican Republic). This last species was misidentified as Selenophorus integer (Fabricius). In turn, that species was misidentified as Selenophorus chalybeus Dejean. Selenophorus chalybeus Dejean is a junior synonym of Selenophorus integer Fabricius, syn. n. ; and Isopleurus macleayi Kirby is a junior synonym of Selenophorus pyritosus Dejean, syn. n. Biogeographically, log of land area plotted against log of number of species shows that the equilibrium theory of biogeography applies to the West Indian selenophorine fauna. Taxonomically, the selenophorine taxa of the West Indies are arranged in eight genera. The 30 species/subspecies of Selenophorus ( sensu stricto ) are arranged in 10 species groups. Geographically, the major sources of the selenophorines are the Bahamas, the Greater Antilles and Lesser Antilles. The West Indian islands probably have been invaded by 26 taxa. Of the currently extant taxa, 11 are classified as immigrant , meaning that they are represented both in the islands and on the mainland (South America or Middle America and southern Florida). Thirty three taxa are classified as precinctive , meaning that they originated where they are now living, the implication being that they have descended from immigrants, thus older in the islands than the current-day immigrants. It is postulated that the West Indian taxa represent three age groups: oldest, ancestors having reached the proto-Antilles by a landspan known as GAARlandia; a middle-age group (Neogene period), their ancestors having reached the islands by dispersal over water, between islands; and a young group of extant taxa, no older than the Pleistocene, also having reached the islands over water.

Making Mosquito Taxonomy Useful: A Stable Classification of Tribe Aedini that Balances Utility with Current Knowledge of Evolutionary Relationships.

PubMed

Wilkerson, Richard C; Linton, Yvonne-Marie; Fonseca, Dina M; Schultz, Ted R; Price, Dana C; Strickman, Daniel A

2015-01-01

The tribe Aedini (Family Culicidae) contains approximately one-quarter of the known species of mosquitoes, including vectors of deadly or debilitating disease agents. This tribe contains the genus Aedes, which is one of the three most familiar genera of mosquitoes. During the past decade, Aedini has been the focus of a series of extensive morphology-based phylogenetic studies published by Reinert, Harbach, and Kitching (RH&K). Those authors created 74 new, elevated or resurrected genera from what had been the single genus Aedes, almost tripling the number of genera in the entire family Culicidae. The proposed classification is based on subjective assessments of the "number and nature of the characters that support the branches" subtending particular monophyletic groups in the results of cladistic analyses of a large set of morphological characters of representative species. To gauge the stability of RH&K's generic groupings we reanalyzed their data with unweighted parsimony jackknife and maximum-parsimony analyses, with and without ordering 14 of the characters as in RH&K. We found that their phylogeny was largely weakly supported and their taxonomic rankings failed priority and other useful taxon-naming criteria. Consequently, we propose simplified aedine generic designations that 1) restore a classification system that is useful for the operational community; 2) enhance the ability of taxonomists to accurately place new species into genera; 3) maintain the progress toward a natural classification based on monophyletic groups of species; and 4) correct the current classification system that is subject to instability as new species are described and existing species more thoroughly defined. We do not challenge the phylogenetic hypotheses generated by the above-mentioned series of morphological studies. However, we reduce the ranks of the genera and subgenera of RH&K to subgenera or informal species groups, respectively, to preserve stability as new data become available.

Making Mosquito Taxonomy Useful: A Stable Classification of Tribe Aedini that Balances Utility with Current Knowledge of Evolutionary Relationships

PubMed Central

Wilkerson, Richard C.; Linton, Yvonne-Marie; Fonseca, Dina M.; Schultz, Ted R.; Price, Dana C.; Strickman, Daniel A.

2015-01-01

The tribe Aedini (Family Culicidae) contains approximately one-quarter of the known species of mosquitoes, including vectors of deadly or debilitating disease agents. This tribe contains the genus Aedes, which is one of the three most familiar genera of mosquitoes. During the past decade, Aedini has been the focus of a series of extensive morphology-based phylogenetic studies published by Reinert, Harbach, and Kitching (RH&K). Those authors created 74 new, elevated or resurrected genera from what had been the single genus Aedes, almost tripling the number of genera in the entire family Culicidae. The proposed classification is based on subjective assessments of the “number and nature of the characters that support the branches” subtending particular monophyletic groups in the results of cladistic analyses of a large set of morphological characters of representative species. To gauge the stability of RH&K’s generic groupings we reanalyzed their data with unweighted parsimony jackknife and maximum-parsimony analyses, with and without ordering 14 of the characters as in RH&K. We found that their phylogeny was largely weakly supported and their taxonomic rankings failed priority and other useful taxon-naming criteria. Consequently, we propose simplified aedine generic designations that 1) restore a classification system that is useful for the operational community; 2) enhance the ability of taxonomists to accurately place new species into genera; 3) maintain the progress toward a natural classification based on monophyletic groups of species; and 4) correct the current classification system that is subject to instability as new species are described and existing species more thoroughly defined. We do not challenge the phylogenetic hypotheses generated by the above-mentioned series of morphological studies. However, we reduce the ranks of the genera and subgenera of RH&K to subgenera or informal species groups, respectively, to preserve stability as new data become available. PMID:26226613

Nocardiopsis potens sp. nov., isolated from household waste.

PubMed

Yassin, A F; Spröer, C; Hupfer, H; Siering, C; Klenk, H-P

2009-11-01

The taxonomic position of an actinomycete, designated strain IMMIB L-21(T), was determined using a polyphasic taxonomic approach. The organism, which had phenotypic properties consistent with its classification in the genus Nocardiopsis, formed a distinct clade in the 16S rRNA gene sequence tree together with the type strain of Nocardiopsis composta, but was readily distinguished from this species using DNA-DNA relatedness and phenotypic data. The genotypic and phenotypic data show that the organism represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis potens sp. nov. is proposed. The type strain is IMMIB L-21(T) (=DSM 45234(T)=CCUG 56587(T)).

Characterization and Reclassification of Yeasts Used for Biological Control of Postharvest Diseases of Fruits and Vegetables

PubMed Central

McLaughlin, R. J.; Wilson, C. L.; Chalutz, E.; Kurtzman, C. P.; Fett, W. F.; Osman, S. F.

1990-01-01

In previous studies workers have shown that three yeast strains (strains US-7, 82, and 101) have biological control activity against various postharvest fungal pathogens of fruits and vegetables, including Penicillium rots of apples and citrus and Botrytis rot of apples. In these reports the researchers have described these strains as Debaryomyces hansenii (anamorph, Candida famata) or Candida sp. strains. In this study we performed additional physiological, DNA reassociation, and mannan characterization tests that clearly established a new taxonomic classification for these strains, Candida guilliermondii. We also propose amendment of the physiological test profile in the taxonomic description of C. guilliermondii. PMID:16348361

Sensitivity and accuracy of high-throughput metabarcoding methods used to describe aquatic communities for early detection of invasve fish species

EPA Science Inventory

For early detection biomonitoring of aquatic invasive species, sensitivity to rare individuals and accurate, high-resolution taxonomic classification are critical to minimize Type I and II detection errors. Given the great expense and effort associated with morphological identifi...

Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

USDA-ARS?s Scientific Manuscript database

Premise of study: Premise of study: The taxonomic classification of the subspecies of Daucus carota is unresolved. Intercrosses among traditionally recognized subspecies has been well-documented, as have intercrosses with other Daucus species containing 2n = 18 chromosomes (D. sahariensis and D. syr...

Morphological variation, taxonomic distribution, and phylogenetic significance of cornuti in Tortricinae (Lepidoptera: Tortricidae)

USDA-ARS?s Scientific Manuscript database

Based on the examination of 4,218 slide-mounted preparations of male and female genitalia of tortricine moths, representing all major clades of the subfamily worldwide, we propose a classification system for cornuti based on four criteria: (1) presence/absence; (2) deciduous/non-deciduous; (3) type ...

Taxonomic complexity of powdery mildew pathogens found on lentil and pea in the US Pacific Northwest

USDA-ARS?s Scientific Manuscript database

Classification of powdery mildews found on lentil and pea in greenhouse and field production conditions in the US Pacific Northwest was investigated using morphological and molecular characters. Isolates collected from lentil plants grown in the greenhouse or field displayed morphologies in substant...

Taxonomic Proposal: Create sixteen new species in existing genera of the families Alphaflexiviridae and Betaflexiviridae

USDA-ARS?s Scientific Manuscript database

A transparent and functional system for virus classification is essential to allow scientists to correctly identify and report on viruses detected in different hosts or locations without ambiguity. New research into relationships between previously characterized and newly-emerging viruses may requir...

Probabilistic topic modeling for the analysis and classification of genomic sequences

PubMed Central

2015-01-01

Background Studies on genomic sequences for classification and taxonomic identification have a leading role in the biomedical field and in the analysis of biodiversity. These studies are focusing on the so-called barcode genes, representing a well defined region of the whole genome. Recently, alignment-free techniques are gaining more importance because they are able to overcome the drawbacks of sequence alignment techniques. In this paper a new alignment-free method for DNA sequences clustering and classification is proposed. The method is based on k-mers representation and text mining techniques. Methods The presented method is based on Probabilistic Topic Modeling, a statistical technique originally proposed for text documents. Probabilistic topic models are able to find in a document corpus the topics (recurrent themes) characterizing classes of documents. This technique, applied on DNA sequences representing the documents, exploits the frequency of fixed-length k-mers and builds a generative model for a training group of sequences. This generative model, obtained through the Latent Dirichlet Allocation (LDA) algorithm, is then used to classify a large set of genomic sequences. Results and conclusions We performed classification of over 7000 16S DNA barcode sequences taken from Ribosomal Database Project (RDP) repository, training probabilistic topic models. The proposed method is compared to the RDP tool and Support Vector Machine (SVM) classification algorithm in a extensive set of trials using both complete sequences and short sequence snippets (from 400 bp to 25 bp). Our method reaches very similar results to RDP classifier and SVM for complete sequences. The most interesting results are obtained when short sequence snippets are considered. In these conditions the proposed method outperforms RDP and SVM with ultra short sequences and it exhibits a smooth decrease of performance, at every taxonomic level, when the sequence length is decreased. PMID:25916734

Classification of asteroid spectra using a neural network

NASA Technical Reports Server (NTRS)

Howell, E. S.; Merenyi, E.; Lebofsky, L. A.

1994-01-01

The 52-color asteroid survey (Bell et al., 1988) together with the 8-color asteroid survey (Zellner et al., 1985) provide a data set of asteroid spectra spanning 0.3-2.5 micrometers. An artificial neural network clusters these asteroid spectra based on their similarity to each other. We have also trained the neural network with a categorization learning output layer in a supervised mode to associate the established clusters with taxonomic classes. Results of our classification agree with Tholen's classification based on the 8-color data alone. When extending the spectral range using the 52-color survey data, we find that some modification of the Tholen classes is indicated to produce a cleaner, self-consistent set of taxonomic classes. After supervised training using our modified classes, the network correctly classifies both the training examples, and additional spectra into the correct class with an average of 90% accuracy. Our classification supports the separation of the K class from the S class, as suggested by Bell et al. (1987), based on the near-infrared spectrum. We define two end-member subclasses which seem to have compositional significance within the S class: the So class, which is olivine-rich and red, and the Sp class, which is pyroxene-rich and less red. The remaining S-class asteroids have intermediate compositions of both olivine and pyroxene and moderately red continua. The network clustering suggests some additional structure within the E-, M-, and P-class asteroids, even in the absence of albedo information, which is the only discriminant between these in the Tholen classification. New relationships are seen between the C class and related G, B, and F classes. However, in both cases, the number of spectra is too small to interpret or determine the significance of these separations.

Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

PubMed

Franz, Nico M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2015-01-01

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.

Molecular phylogeny of tribe Rhipsalideae (Cactaceae) and taxonomic implications for Schlumbergera and Hatiora.

PubMed

Calvente, Alice; Zappi, Daniela C; Forest, Félix; Lohmann, Lúcia G

2011-03-01

Tribe Rhipsalideae is composed of unusual epiphytic or lithophytic cacti that inhabit humid tropical and subtropical forests. Members of this tribe present a reduced vegetative body, a specialized adventitious root system, usually spineless areoles and flowers and fruits reduced in size. Despite the debate surrounding the classification of Rhipsalideae, no studies have ever attempted to reconstruct phylogenetic relationships among its members or to test the monophyly of its genera using DNA sequence data; all classifications formerly proposed for this tribe have only employed morphological data. In this study, we reconstruct the phylogeny of Rhipsalideae using plastid (trnQ-rps16, rpl32-trnL, psbA-trnH) and nuclear (ITS) markers to evaluate the classifications previously proposed for the group. We also examine morphological features traditionally used to delimit genera within Rhipsalideae in light of the resulting phylogenetic trees. In total new sequences for 35 species of Rhipsalideae were produced (out of 55; 63%). The molecular phylogeny obtained comprises four main clades supporting the recognition of genera Lepismium, Rhipsalis, Hatiora and Schlumbergera. The evidence gathered indicate that a broader genus Schlumbergera, including Hatiora subg. Rhipsalidopsis, should be recognized. Consistent morphological characters rather than homoplastic features are used in order to establish a more coherent and practical classification for the group. Nomenclatural changes and a key for the identification of the genera currently included in Rhipsalideae are provided. Copyright © 2011 Elsevier Inc. All rights reserved.

Ultraviolet reflectance properties of asteroids

NASA Astrophysics Data System (ADS)

Butterworth, P. S.; Meadows, A. J.

1985-05-01

An analysis of the UV spectra of 28 asteroids obtained with the Internal Ultraviolet Explorer (IUE) satellite is presented. The spectra lie within the range 2100-3200 A. The results are examined in terms of both asteroid classification and of current ideas concerning the surface mineralogy of asteroids. For all the asteroids examined, UV reflectivity declines approximately linearly toward shorter wavelengths. In general, the same taxonomic groups are seen in the UV as in the visible and IR, although there is some evidence for asteroids with anomalous UV properties and for UV subclasses within the S class. No mineral absorption features are reported of strength similar to the strongest features in the visible and IR regions, but a number of shallow absorptions do occur and may provide valuable information on the surface composition of many asteroids.

Bunyavirus Taxonomy: Limitations and Misconceptions Associated with the Current ICTV Criteria Used for Species Demarcation.

PubMed

Blitvich, Bradley J; Beaty, Barry J; Blair, Carol D; Brault, Aaron C; Dobler, Gerhard; Drebot, Michael A; Haddow, Andrew D; Kramer, Laura D; LaBeaud, Angelle Desiree; Monath, Thomas P; Mossel, Eric C; Plante, Kenneth; Powers, Ann M; Tesh, Robert B; Turell, Michael J; Vasilakis, Nikos; Weaver, Scott C

2018-04-23

The International Committee on Taxonomy of Viruses (ICTV) has implemented numerous changes to the taxonomic classification of bunyaviruses over the years. Whereas most changes have been justified and necessary because of the need to accommodate newly discovered and unclassified viruses, other changes are a cause of concern, especially the decision to demote scores of formerly recognized species to essentially strains of newly designated species. This practice was first described in the seventh taxonomy report of the ICTV and has continued in all subsequent reports. In some instances, viruses that share less than 75% nucleotide sequence identity across their genomes produce vastly different clinical presentations, possess distinct vector and host associations, have different biosafety recommendations, and occur in nonoverlapping geographic regions are classified as strains of the same species. Complicating the matter is the fact that virus strains have been completely eliminated from ICTV reports; thus, critically important information on virus identities and their associated biological and epidemiological features cannot be readily related to the ICTV classification. Here, we summarize the current status of bunyavirus taxonomy and discuss the adverse consequences associated with the reclassification and resulting omission of numerous viruses of public health importance from ICTV reports. As members of the American Committee on Arthropod-borne Viruses, we encourage the ICTV Bunyavirus Study Group to reconsider their stance on bunyavirus taxonomy, to revise the criteria currently used for species demarcation, and to list additional strains of public and veterinary importance.

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

Taxonomic and functional composition of arthropod assemblages across contrasting Amazonian forests.

PubMed

Lamarre, Greg P A; Hérault, Bruno; Fine, Paul V A; Vedel, Vincent; Lupoli, Roland; Mesones, Italo; Baraloto, Christopher

2016-01-01

Arthropods represent most of global biodiversity, with the highest diversity found in tropical rain forests. Nevertheless, we have a very incomplete understanding of how tropical arthropod communities are assembled. We conducted a comprehensive mass sampling of arthropod communities within three major habitat types of lowland Amazonian rain forest, including terra firme clay, white-sand and seasonally flooded forests in Peru and French Guiana. We examined how taxonomic and functional composition (at the family level) differed across these habitat types in the two regions. The overall arthropod community composition exhibited strong turnover among habitats and between regions. In particular, seasonally flooded forest habitats of both regions comprised unique assemblages. Overall, 17·7% (26 of 147) of arthropod families showed significant preferences for a particular habitat type. We present a first reproducible arthropod functional classification among the 147 taxa based on similarity among 21 functional traits describing feeding source, major mouthparts and microhabitats inhabited by each taxon. We identified seven distinct functional groups whose relative abundance contrasted strongly across the three habitats, with sap and leaf feeders showing higher abundances in terra firme clay forest. Our novel arthropod functional classification provides an important complement to link these contrasting patterns of composition to differences in forest functioning across geographical and environmental gradients. This study underlines that both environment and biogeographical processes are responsible for driving arthropod taxonomic composition while environmental filtering is the main driver of the variance in functional composition. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Association of Cognitive, Affective, Psychomotor and Intuitive Domains in Education, Sönmez Model

ERIC Educational Resources Information Center

Sönmez, Veysel

2017-01-01

Problem statement: Educational goals are classified taxonomically as cognitive, affective, psycho-motor and intuitive. Can these classifications be associated? Sönmez's model represents an attempt for this. Purpose of Study: Is the model regarding the association of four domains developed by Sönmez supported significantly by empirical data? What…

Candidatus Phytoplasma malaysianum, a novel taxon associated with virescence and phyllody of Madagascar periwinkle (Catharanthus roseus)

USDA-ARS?s Scientific Manuscript database

This study addressed the taxonomic position and group classification of a phytoplasma responsible for virescence and phyllody symptoms in naturally diseased Madagascar periwinkle plants in western Malaysia. Unique regions in the 16S rRNA gene from the Malaysian periwinkle virescence (MaPV) phytopla...

Discrimination of grassland species and their classification in botanical families by laboratory scale hyperspectral imaging NIR: preliminary results

USDA-ARS?s Scientific Manuscript database

The objective of this study was to discriminate by on-line hyperspectral imaging, taxonomic plant families comprised of different grassland species. Plants were collected from semi-natural meadows of the National Apuseni Park, Apuseni Mountains, Gârda area (Romania) according to botanical families. ...

Species rarity: definition, causes, and classification

Treesearch

Curtis H. Flather; Carolyn Hull Sieg

2007-01-01

In virtually all ecological communities around the world, most species are represented by few individuals, and most individuals come from only a few of the most common species. Why this distribution of species abundances is so regularly observed among different taxonomic sets in geographically diverse systems is a question that has received considerable theoretical and...

Evolution of a Benthic Imaging System From a Towed Camera to an Automated Habitat Characterization System

DTIC Science & Technology

2008-09-01

automated processing of images for color correction, segmentation of foreground targets from sediment and classification of targets to taxonomic category...element in the development of HabCam as a tool for habitat characterization is the automated processing of images for color correction, segmentation of

Innovation Policies from the European Union: Methods for Classification

ERIC Educational Resources Information Center

Rodriguez, Victor; Montalvo, Carlos

2007-01-01

This study focuses on taxonomic and typological methods of innovation policies in the European institutional context. Although many types of policies affect innovation, no universally accepted criteria exist to classify them. As innovation policy in a myriad of thematic areas--systemic model--has become pluralized, this article offers a method for…

The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents

PubMed Central

Ecker, David J; Sampath, Rangarajan; Willett, Paul; Wyatt, Jacqueline R; Samant, Vivek; Massire, Christian; Hall, Thomas A; Hari, Kumar; McNeil, John A; Büchen-Osmond, Cornelia; Budowle, Bruce

2005-01-01

Background Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks. Results We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. Conclusion The Microbial Rosetta Stone is available at . The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases. PMID:15850481

The Aeronautical Data Link: Taxonomy, Architectural Analysis, and Optimization

NASA Technical Reports Server (NTRS)

Morris, A. Terry; Goode, Plesent W.

2002-01-01

The future Communication, Navigation, and Surveillance/Air Traffic Management (CNS/ATM) System will rely on global satellite navigation, and ground-based and satellite based communications via Multi-Protocol Networks (e.g. combined Aeronautical Telecommunications Network (ATN)/Internet Protocol (IP)) to bring about needed improvements in efficiency and safety of operations to meet increasing levels of air traffic. This paper will discuss the development of an approach that completely describes optimal data link architecture configuration and behavior to meet the multiple conflicting objectives of concurrent and different operations functions. The practical application of the approach enables the design and assessment of configurations relative to airspace operations phases. The approach includes a formal taxonomic classification, an architectural analysis methodology, and optimization techniques. The formal taxonomic classification provides a multidimensional correlation of data link performance with data link service, information protocol, spectrum, and technology mode; and to flight operations phase and environment. The architectural analysis methodology assesses the impact of a specific architecture configuration and behavior on the local ATM system performance. Deterministic and stochastic optimization techniques maximize architectural design effectiveness while addressing operational, technology, and policy constraints.

Towards a phylogenetic classification of Leptothecata (Cnidaria, Hydrozoa)

PubMed Central

Maronna, Maximiliano M.; Miranda, Thaís P.; Peña Cantero, Álvaro L.; Barbeitos, Marcos S.; Marques, Antonio C.

2016-01-01

Leptothecata are hydrozoans whose hydranths are covered by perisarc and gonophores and whose medusae bear gonads on their radial canals. They develop complex polypoid colonies and exhibit considerable morphological variation among species with respect to growth, defensive structures and mode of development. For instance, several lineages within this order have lost the medusa stage. Depending on the author, traditional taxonomy in hydrozoans may be either polyp- or medusa-oriented. Therefore, the absence of the latter stage in some lineages may lead to very different classification schemes. Molecular data have proved useful in elucidating this taxonomic challenge. We analyzed a super matrix of new and published rRNA gene sequences (16S, 18S and 28S), employing newly proposed methods to measure branch support and improve phylogenetic signal. Our analysis recovered new clades not recognized by traditional taxonomy and corroborated some recently proposed taxa. We offer a thorough taxonomic revision of the Leptothecata, erecting new orders, suborders, infraorders and families. We also discuss the origination and diversification dynamics of the group from a macroevolutionary perspective. PMID:26821567

Preliminary Classification of Novel Hemorrhagic Fever-Causing Viruses Using Sequence-Based PAirwise Sequence Comparison (PASC) Analysis.

PubMed

Bào, Yīmíng; Kuhn, Jens H

2018-01-01

During the last decade, genome sequence-based classification of viruses has become increasingly prominent. Viruses can be even classified based on coding-complete genome sequence data alone. Nevertheless, classification remains arduous as experts are required to establish phylogenetic trees to depict the evolutionary relationships of such sequences for preliminary taxonomic placement. Pairwise sequence comparison (PASC) of genomes is one of several novel methods for establishing relationships among viruses. This method, provided by the US National Center for Biotechnology Information as an open-access tool, circumvents phylogenetics, and yet PASC results are often in agreement with those of phylogenetic analyses. Computationally inexpensive, PASC can be easily performed by non-taxonomists. Here we describe how to use the PASC tool for the preliminary classification of novel viral hemorrhagic fever-causing viruses.

Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case

PubMed Central

Franz, Nico M.; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2015-01-01

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations. PMID:25700173

Keys to soil taxonomy by soil survey staff (sixth edition)

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

NONE

1994-12-31

This publication, Keys to Soil Taxonomy, serves two purposes. It provides the taxonomic keys necessary for the classification of soils according to Soil Taxonomy in a form that can be used easily in the field, and it also acquaints users of Soil Taxonomy with recent changes in the classification system. This volume includes all revisions of the keys that have so far been approved, replacing the original keys in Soil Taxonomy: A Basic System of Soil Classification for Making and Interpreting Soil Surveys (1975), the work on which this abridged version, first published in 1983, is based. This publication incorporatesmore » all amendments approved to date and published in National Soil Taxonomy Handbook (NSTH) Issues 1-17.« less

Classification of malignant and benign lung nodules using taxonomic diversity index and phylogenetic distance.

PubMed

de Sousa Costa, Robherson Wector; da Silva, Giovanni Lucca França; de Carvalho Filho, Antonio Oseas; Silva, Aristófanes Corrêa; de Paiva, Anselmo Cardoso; Gattass, Marcelo

2018-05-23

Lung cancer presents the highest cause of death among patients around the world, in addition of being one of the smallest survival rates after diagnosis. Therefore, this study proposes a methodology for diagnosis of lung nodules in benign and malignant tumors based on image processing and pattern recognition techniques. Mean phylogenetic distance (MPD) and taxonomic diversity index (Δ) were used as texture descriptors. Finally, the genetic algorithm in conjunction with the support vector machine were applied to select the best training model. The proposed methodology was tested on computed tomography (CT) images from the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), with the best sensitivity of 93.42%, specificity of 91.21%, accuracy of 91.81%, and area under the ROC curve of 0.94. The results demonstrate the promising performance of texture extraction techniques using mean phylogenetic distance and taxonomic diversity index combined with phylogenetic trees. Graphical Abstract Stages of the proposed methodology.

Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment

PubMed Central

Anwar, Nadia; Hunt, Ela

2009-01-01

Background TreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory. Results We report on a new wrapper supporting taxon queries on TreeBASE by utilising a Taxonomy and Classification Database (TCl-Db) we created. TCl-Db holds merged and consolidated taxonomic names from multiple data sources and can be used to translate hierarchical, vernacular and synonym queries into specific query terms in TreeBASE. The query expansion supported by TCl-Db shows very significant information retrieval quality improvement. The wrapper can be accessed at the URL The methodology we developed is scalable and can be applied to new data, as those become available in the future. Conclusion Significantly improved data retrieval quality is shown for all queries, and additional flexibility is achieved via user-driven taxonomy selection. PMID:19426482

Ancestral State Reconstruction Reveals Rampant Homoplasy of Diagnostic Morphological Characters in Urticaceae, Conflicting with Current Classification Schemes

PubMed Central

Wu, Zeng-Yuan; Milne, Richard I.; Chen, Chia-Jui; Liu, Jie; Wang, Hong; Li, De-Zhu

2015-01-01

Urticaceae is a family with more than 2000 species, which contains remarkable morphological diversity. It has undergone many taxonomic reorganizations, and is currently the subject of further systematic studies. To gain more resolution in systematic studies and to better understand the general patterns of character evolution in Urticaceae, based on our previous phylogeny including 169 accessions comprising 122 species across 47 Urticaceae genera, we examined 19 diagnostic characters, and analysed these employing both maximum-parsimony and maximum-likelihood approaches. Our results revealed that 16 characters exhibited multiple state changes within the family, with ten exhibiting >eight changes and three exhibiting between 28 and 40. Morphological synapomorphies were identified for many clades, but the diagnostic value of these was often limited due to reversals within the clade and/or homoplasies elsewhere. Recognition of the four clades comprising the family at subfamily level can be supported by a small number carefully chosen defining traits for each. Several non-monophyletic genera appear to be defined only by characters that are plesiomorphic within their clades, and more detailed work would be valuable to find defining traits for monophyletic clades within these. Some character evolution may be attributed to adaptive evolution in Urticaceae due to shifts in habitat or vegetation type. This study demonstrated the value of using phylogeny to trace character evolution, and determine the relative importance of morphological traits for classification. PMID:26529598

Plant taxonomy: a historical perspective, current challenges, and perspectives.

PubMed

Rouhan, Germinal; Gaudeul, Myriam

2014-01-01

Taxonomy is the science that explores, describes, names, and classifies all organisms. In this introductory chapter, we highlight the major historical steps in the elaboration of this science that provides baseline data for all fields of biology and plays a vital role for society but is also an independent, complex, and sound hypothesis-driven scientific discipline.In a first part, we underline that plant taxonomy is one of the earliest scientific disciplines that emerged thousands of years ago, even before the important contributions of Greeks and Romans (e.g., Theophrastus, Pliny the Elder, and Dioscorides). In the fifteenth to sixteenth centuries, plant taxonomy benefited from the Great Navigations, the invention of the printing press, the creation of botanic gardens, and the use of the drying technique to preserve plant specimens. In parallel with the growing body of morpho-anatomical data, subsequent major steps in the history of plant taxonomy include the emergence of the concept of natural classification, the adoption of the binomial naming system (with the major role of Linnaeus) and other universal rules for the naming of plants, the formulation of the principle of subordination of characters, and the advent of the evolutionary thought. More recently, the cladistic theory (initiated by Hennig) and the rapid advances in DNA technologies allowed to infer phylogenies and to propose true natural, genealogy-based classifications.In a second part, we put the emphasis on the challenges that plant taxonomy faces nowadays. The still very incomplete taxonomic knowledge of the worldwide flora (the so-called taxonomic impediment) is seriously hampering conservation efforts that are especially crucial as biodiversity enters its sixth extinction crisis. It appears mainly due to insufficient funding, lack of taxonomic expertise, and lack of communication and coordination. We then review recent initiatives to overcome these limitations and to anticipate how taxonomy should and could evolve. In particular, the use of molecular data has been era-splitting for taxonomy and may allow an accelerated pace of species discovery. We examine both strengths and limitations of such techniques in comparison to morphology-based investigations, we give broad recommendations on the use of molecular tools for plant taxonomy, and we highlight the need for an integrative taxonomy based on evidence from multiple sources.

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

USDA-ARS?s Scientific Manuscript database

Multigene phylogenies have been instrumental in revising the classification of ascosporic (teleomorph) yeasts in a natural system based on lines of decent. Although many taxonomic changes have already been implemented for teleomorph taxa, this is not yet the case for the large genus Candida and smal...

Emerging insights into the molecular and cellular basis of glioblastoma

PubMed Central

Dunn, Gavin P.; Rinne, Mikael L.; Wykosky, Jill; Genovese, Giannicola; Quayle, Steven N.; Dunn, Ian F.; Agarwalla, Pankaj K.; Chheda, Milan G.; Campos, Benito; Wang, Alan; Brennan, Cameron; Ligon, Keith L.; Furnari, Frank; Cavenee, Webster K.; Depinho, Ronald A.; Chin, Lynda; Hahn, William C.

2012-01-01

Glioblastoma is both the most common and lethal primary malignant brain tumor. Extensive multiplatform genomic characterization has provided a higher-resolution picture of the molecular alterations underlying this disease. These studies provide the emerging view that “glioblastoma” represents several histologically similar yet molecularly heterogeneous diseases, which influences taxonomic classification systems, prognosis, and therapeutic decisions. PMID:22508724

Complex within complex: integrative taxonomy reveals hidden diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and unexpected relationships with a song divergent relative

USDA-ARS?s Scientific Manuscript database

Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premati...

77 FR 47587 - Endangered and Threatened Wildlife and Plants; Listing 38 Species on Molokai, Lanai, and Maui as...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-09

.... In addition, we propose name changes or corrections for 11 endangered plants and 2 endangered birds... revise taxonomic classifications with name changes or family changes for 11 plant species and 2 bird... Fish and Wildlife Office (see FOR FURTHER INFORMATION CONTACT). Authors The primary authors of this...

Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us.

PubMed

El Baidouri, Fouad; Diancourt, Laure; Berry, Vincent; Chevenet, François; Pratlong, Francine; Marty, Pierre; Ravel, Christophe

2013-01-01

Leishmaniasis is a complex parasitic disease from a taxonomic, clinical and epidemiological point of view. The role of genetic exchanges has been questioned for over twenty years and their recent experimental demonstration along with the identification of interspecific hybrids in natura has revived this debate. After arguing that genetic exchanges were exceptional and did not contribute to Leishmania evolution, it is currently proposed that interspecific exchanges could be a major driving force for rapid adaptation to new reservoirs and vectors, expansion into new parasitic cycles and adaptation to new life conditions. To assess the existence of gene flows between species during evolution we used MLSA-based (MultiLocus Sequence Analysis) approach to analyze 222 Leishmania strains from Africa and Eurasia to accurately represent the genetic diversity of this genus. We observed a remarkable congruence of the phylogenetic signal and identified seven genetic clusters that include mainly independent lineages which are accumulating divergences without any sign of recent interspecific recombination. From a taxonomic point of view, the strong genetic structuration of the different species does not question the current classification, except for species that cause visceral forms of leishmaniasis (L. donovani, L. infantum and L. archibaldi). Although these taxa cause specific clinical forms of the disease and are maintained through different parasitic cycles, they are not clearly distinct and form a continuum, in line with the concept of species complex already suggested for this group thirty years ago. These results should have practical consequences concerning the molecular identification of parasites and the subsequent therapeutic management of the disease.

Identification of Candida lusitaniae as an opportunistic yeast in humans.

PubMed

Holzschu, D L; Presley, H L; Miranda, M; Phaff, H J

1979-08-01

Four yeast strains, causally associated with infection in a patient with acute myelogenous leukemia, were identified by standard methods currently used in yeast taxonomy as representatives of Candida lusitania van Uden et do Carmo-Sousa. Because this species has not been recognized previously as an opportunistic yeast in humans, molecular taxonomic methods were applied to confirm its identity. The nuclear deoxyribonucleic acid (DNA) base composition of two clinical isolates was shown to be 45.1 mol% guanine plus cytosine as compared to 44.7 mol% guanine plus cytosine for the type strain of this species. DNA/DNA reassociation experiments revealed more than 95% complementarity between the DNAs from the clinical isolates and that of the type strain of C. lusitaniae, thus confirming their classification by conventional taxonomy. A key is provided to differentiate C. lusitaniae from two phenotypically similar Candida species.

New infrared spectral data for 27 asteroids: An investigation of meteorite- asteroid relationships by using the modified Gaussian model

NASA Astrophysics Data System (ADS)

Gietzen, Katherine M.

2009-09-01

Asteroids provide unique insights into the origin and early history of the solar system. Since asteroids are considered to be fairly pristine, studying them provides opportunities to learn more about the primordial solar system, its materials, processes and history. Since the discovery in 1801 of the first asteroid, Ceres, during the era when everyone was searching for the "missing planet", astronomers have been trying to understand what they are, where they came from, why they exist and what they can tell us about how our solar system formed and evolved. Within the asteroid population are a number of sub-populations, the primary division is due to the locations of the asteroids. There are the Main Belt Asteroid (MBA) population that resides between the orbits of Mars and Jupiter (1.8 - 3.5 AU) and the Near-Earth Asteroid (NEA) population whose orbits have an aphelion <= 1.3 AU. Within both the MBA and NEA populations are further subdivisions (taxonomic classes) based on physical properties of the asteroids such as albedo, spectral curve and probable composition. There have been a number of taxonomic classification schemes, the most current iteration splits the asteroids into three complexes (C, S, and X) that combined are comprised of twenty-six distinct taxonomic classes. Since the lifetimes of the NEAs are short (10 6 - 10 7 yrs), it is thought that the NEA population is and continues to be populated by the MBA population through various mechanisms like resonances and thermal forces. We have conducted a statistical comparison of the two populations as a whole, by complexes and individual taxonomic classes and found significant differences as well as similarities. On the surface, it appears that the NEA population is not representative of the MBA population. There are voids and relatively small numbers in taxonomic classes that exist in the NEA when compared to the MBA population and there are some important similarities. There are, however, biases that this analysis does not address that may explain our findings. The asteroid taxonomy classification schemas are based on visible wavelength spectra. There are ~2500 classified asteroids of which only a very small percentage have spectra in the infrared wavelength ranges. Here we demonstrate, using asteroid 1989 ML, the need for more asteroid spectra in the near-infrared wavelength range which contains much compositional information. We show that in the visible wavelengths spectra of several meteorites of very different types match the spectrum of 1989 ML. Finally, we examine twenty-seven S and possible S Complex asteroid spectra. We find that most contain pyroxenes in the monoclinic form (clinopyroxene). Clinopyroxenes can contain calcium; however, there are some that do not. The cases of Ca-free clinopyroxenes are rare on Earth, but are readily found in the type 3 unequilibrated ordinary chondrites. Analyses of the asteroids and ordinary chondrites were conducted using the Modified Gaussian Model (MGM) and the Band Area Ratio. We also examined two terrestrial Ca-free clinopyroxenes using the MGM. From our results we conclude that the surfaces of S Complex asteroids are consistent with the type 3 unequilibrated ordinary chondrites.

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification.

PubMed

Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

2015-05-01

Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. ivan.borozan@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

PubMed Central

Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

2015-01-01

Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. Contact: ivan.borozan@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25573913

Toward extending terrestrial laser scanning applications in forestry: a case study of broad- and needle-leaf tree classification

NASA Astrophysics Data System (ADS)

Lin, Yi; Jiang, Miao

2017-01-01

Tree species information is essential for forest research and management purposes, which in turn require approaches for accurate and precise classification of tree species. One such remote sensing technology, terrestrial laser scanning (TLS), has proved to be capable of characterizing detailed tree structures, such as tree stem geometry. Can TLS further differentiate between broad- and needle-leaves? If the answer is positive, TLS data can be used for classification of taxonomic tree groups by directly examining their differences in leaf morphology. An analysis was proposed to assess TLS-represented broad- and needle-leaf structures, followed by a Bayes classifier to perform the classification. Tests indicated that the proposed method can basically implement the task, with an overall accuracy of 77.78%. This study indicates a way of implementing the classification of the two major broad- and needle-leaf taxonomies measured by TLS in accordance to their literal definitions, and manifests the potential of extending TLS applications in forestry.

Polyphasic taxonomy, a consensus approach to bacterial systematics.

PubMed Central

Vandamme, P; Pot, B; Gillis, M; de Vos, P; Kersters, K; Swings, J

1996-01-01

Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question. PMID:8801440

Rapid evolution in lekking grouse: Implications for taxonomic definitions

USGS Publications Warehouse

Oyler-McCance, Sara J.; St. John, Judy; Quinn, Thomas W.

2010-01-01

Species and subspecies delineations were traditionally defined by morphological and behavioral traits, as well as by plumage characteristics. Molecular genetic data have more recently been used to assess these classifications and, in many cases, to redefine them. The recent practice of utilizing molecular genetic data to examine taxonomic questions has led some to suggest that molecular genetic methods are more appropriate than traditional methods for addressing taxonomic uncertainty and management units. We compared the North American Tetraoninae—which have been defined using plumage, morphology, and behavior—and considered the effects of redefinition using only neutral molecular genetic data (mitochondrial control region and cytochrome oxidase subunit 1). Using the criterion of reciprocal monophyly, we failed to recognize the five species whose mating system is highly polygynous, with males displaying on leks. In lek-breeding species, sexual selection can act to influence morphological and behavioral traits at a rate much faster than can be tracked genetically. Thus, we suggest that at least for lek-breeding species, it is important to recognize the possibility that morphological and behavioral changes may occur at an accelerated rate compared with the processes that led to reciprocal monophyly of putatively neutral genetic markers. Therefore, it is particularly important to consider the possible disconnect between such lines of evidence when making taxonomic revisions and definitions of management units.

Coastal habitats as surrogates for taxonomic, functional and trophic structures of benthic faunal communities.

PubMed

Törnroos, Anna; Nordström, Marie C; Bonsdorff, Erik

2013-01-01

Due to human impact, there is extensive degradation and loss of marine habitats, which calls for measures that incorporate taxonomic as well as functional and trophic aspects of biodiversity. Since such data is less easily quantifiable in nature, the use of habitats as surrogates or proxies for biodiversity is on the rise in marine conservation and management. However, there is a critical gap in knowledge of whether pre-defined habitat units adequately represent the functional and trophic structure of communities. We also lack comparisons of different measures of community structure in terms of both between- (β) and within-habitat (α) variability when accounting for species densities. Thus, we evaluated a priori defined coastal habitats as surrogates for traditional taxonomic, functional and trophic zoobenthic community structure. We focused on four habitats (bare sand, canopy-forming algae, seagrass above- and belowground), all easily delineated in nature and defined through classification systems. We analyzed uni- and multivariate data on species and trait diversity as well as stable isotope ratios of benthic macrofauna. A good fit between habitat types and taxonomic and functional structure was found, although habitats were more similar functionally. This was attributed to within-habitat heterogeneity so when habitat divisions matched the taxonomic structure, only bare sand was functionally distinct. The pre-defined habitats did not meet the variability of trophic structure, which also proved to differentiate on a smaller spatial scale. The quantification of trophic structure using species density only identified an epi- and an infaunal unit. To summarize the results we present a conceptual model illustrating the match between pre-defined habitat types and the taxonomic, functional and trophic community structure. Our results show the importance of including functional and trophic aspects more comprehensively in marine management and spatial planning.

Taxonaut: an application software for comparative display of multiple taxonomies with a use case of GBIF Species API.

PubMed

Ytow, Nozomi

2016-01-01

The Species API of the Global Biodiversity Information Facility (GBIF) provides public access to taxonomic data aggregated from multiple data sources. Each data source follows its own classification which can be inconsistent with classifications from other sources. Even with a reference classification e.g. the GBIF Backbone taxonomy, a comprehensive method to compare classifications in the data aggregation is essential, especially for non-expert users. A Java application was developed to compare multiple taxonomies graphically using classification data acquired from GBIF's ChecklistBank via the GBIF Species API. It uses a table to display taxonomies where each column represents a taxonomy under comparison, with an aligner column to organise taxa by name. Each cell contains the name of a taxon if the classification in that column contains the name. Each column also has a cell showing the hierarchy of the taxonomy by a folder metaphor where taxa are aligned and synchronised in the aligner column. A set of those comparative tables shows taxa categorised by relationship between taxonomies. The result set is also available as tables in an Excel format file.

The genus Agaricus in the Caribbean. Nine new taxa mostly based on collections from the Dominican Republic

Treesearch

Luis A. ​Parra; Claudio Angelini; Beatriz Ortiz-Santana; Gerardo Mata; Christophe Billette; Carlos Rojo; Jie Chen; Philippe Callac

2018-01-01

Field collections of Agaricus were collected in the Dominican Republic from 2009–2016 with the intent to evaluate the diversity in this genus, which was quasi-unknown in this country. In the same period, studies on tropical Agaricus revealed tropical clades that remained unclassified. A new taxonomic system of classification...

‘Candidatus Phytoplasma palmicola’, a novel taxon associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique

USDA-ARS?s Scientific Manuscript database

In this study, the taxonomic position and group classification of the phytoplasma associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique were addressed. Pairwise sequence similarity values based on alignment of near full-length 16SrRNA genes (1530 bp) reve...

Relating practitioner needs to research activities

NASA Technical Reports Server (NTRS)

Feather, M. S.; Menzies, T.; Connelly, J. R.

2003-01-01

We present an approach to matching needs (practioner requirements) to solutions (researcher activities). A taxonomical classification scheme acts as intermediary between needs and activities. Expert practitioners exprss their needs in terms of this taxonomy. Researchers express their activities in the same terms. A decision support tool is used to assist in the combination and study of their expressions of needs and activities.

Classification and Taxonomy of Vegetable Macergens

PubMed Central

Aremu, Bukola R.; Babalola, Olubukola O.

2015-01-01

Macergens are bacteria capable of releasing pectic enzymes (pectolytic bacteria). These enzymatic actions result in the separation of plant tissues leading to total plant destruction. This can be attributed to soft rot diseases in vegetables. These macergens primarily belong to the genus Erwinia and to a range of opportunistic pathogens namely: the Xanthomonas spp., Pseudomonas spp., Clostridium spp., Cytophaga spp., and Bacillus spp. They consist of taxa that displayed considerable heterogeneity and intermingled with members of other genera belonging to the Enterobacteriaceae. They have been classified based on phenotypic, chemotaxonomic and genotypic which obviously not necessary in the taxonomy of all bacterial genera for defining bacterial species and describing new ones These taxonomic markers have been used traditionally as a simple technique for identification of bacterial isolates. The most important fields of taxonomy are supposed to be based on clear, reliable and worldwide applicable criteria. Hence, this review clarifies the taxonomy of the macergens to the species level and revealed that their taxonomy is beyond complete. For discovery of additional species, further research with the use modern molecular methods like phylogenomics need to be done. This can precisely define classification of macergens resulting in occasional, but significant changes in previous taxonomic schemes of these macergens. PMID:26640465

Classification and Taxonomy of Vegetable Macergens.

PubMed

Aremu, Bukola R; Babalola, Olubukola O

2015-01-01

Macergens are bacteria capable of releasing pectic enzymes (pectolytic bacteria). These enzymatic actions result in the separation of plant tissues leading to total plant destruction. This can be attributed to soft rot diseases in vegetables. These macergens primarily belong to the genus Erwinia and to a range of opportunistic pathogens namely: the Xanthomonas spp., Pseudomonas spp., Clostridium spp., Cytophaga spp., and Bacillus spp. They consist of taxa that displayed considerable heterogeneity and intermingled with members of other genera belonging to the Enterobacteriaceae. They have been classified based on phenotypic, chemotaxonomic and genotypic which obviously not necessary in the taxonomy of all bacterial genera for defining bacterial species and describing new ones These taxonomic markers have been used traditionally as a simple technique for identification of bacterial isolates. The most important fields of taxonomy are supposed to be based on clear, reliable and worldwide applicable criteria. Hence, this review clarifies the taxonomy of the macergens to the species level and revealed that their taxonomy is beyond complete. For discovery of additional species, further research with the use modern molecular methods like phylogenomics need to be done. This can precisely define classification of macergens resulting in occasional, but significant changes in previous taxonomic schemes of these macergens.

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

NASA Astrophysics Data System (ADS)

Sangal, Vartul; Goodfellow, Michael; Jones, Amanda L.; Schwalbe, Edward C.; Blom, Jochen; Hoskisson, Paul A.; Sutcliffe, Iain C.

2016-12-01

Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance.

A global organism detection and monitoring system for non-native species

USGS Publications Warehouse

Graham, J.; Newman, G.; Jarnevich, C.; Shory, R.; Stohlgren, T.J.

2007-01-01

Harmful invasive non-native species are a significant threat to native species and ecosystems, and the costs associated with non-native species in the United States is estimated at over $120 Billion/year. While some local or regional databases exist for some taxonomic groups, there are no effective geographic databases designed to detect and monitor all species of non-native plants, animals, and pathogens. We developed a web-based solution called the Global Organism Detection and Monitoring (GODM) system to provide real-time data from a broad spectrum of users on the distribution and abundance of non-native species, including attributes of their habitats for predictive spatial modeling of current and potential distributions. The four major subsystems of GODM provide dynamic links between the organism data, web pages, spatial data, and modeling capabilities. The core survey database tables for recording invasive species survey data are organized into three categories: "Where, Who & When, and What." Organisms are identified with Taxonomic Serial Numbers from the Integrated Taxonomic Information System. To allow users to immediately see a map of their data combined with other user's data, a custom geographic information system (GIS) Internet solution was required. The GIS solution provides an unprecedented level of flexibility in database access, allowing users to display maps of invasive species distributions or abundances based on various criteria including taxonomic classification (i.e., phylum or division, order, class, family, genus, species, subspecies, and variety), a specific project, a range of dates, and a range of attributes (percent cover, age, height, sex, weight). This is a significant paradigm shift from "map servers" to true Internet-based GIS solutions. The remainder of the system was created with a mix of commercial products, open source software, and custom software. Custom GIS libraries were created where required for processing large datasets, accessing the operating system, and to use existing libraries in C++, R, and other languages to develop the tools to track harmful species in space and time. The GODM database and system are crucial for early detection and rapid containment of invasive species. ?? 2007 Elsevier B.V. All rights reserved.

A new fungal large subunit ribosomal RNA primer for high throughput sequencing surveys

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

Mueller, Rebecca C.; Gallegos-Graves, La Verne; Kuske, Cheryl R.

The inclusion of phylogenetic metrics in community ecology has provided insights into important ecological processes, particularly when combined with high-throughput sequencing methods; however, these approaches have not been widely used in studies of fungal communities relative to other microbial groups. Two obstacles have been considered: (1) the internal transcribed spacer (ITS) region has limited utility for constructing phylogenies and (2) most PCR primers that target the large subunit (LSU) ribosomal unit generate amplicons that exceed current limits of high-throughput sequencing platforms. We designed and tested a PCR primer (LR22R) to target approximately 300–400 bp region of the D2 hypervariable regionmore » of the fungal LSU for use with the Illumina MiSeq platform. Both in silico and empirical analyses showed that the LR22R–LR3 pair captured a broad range of fungal taxonomic groups with a small fraction of non-fungal groups. Phylogenetic placement of publically available LSU D2 sequences showed broad agreement with taxonomic classification. Comparisons of the LSU D2 and the ITS2 ribosomal regions from environmental samples and known communities showed similar discriminatory abilities of the two primer sets. Altogether, these findings show that the LR22R–LR3 primer pair has utility for phylogenetic analyses of fungal communities using high-throughput sequencing methods.« less

A new fungal large subunit ribosomal RNA primer for high throughput sequencing surveys

DOE PAGES

Mueller, Rebecca C.; Gallegos-Graves, La Verne; Kuske, Cheryl R.

2015-12-09

The inclusion of phylogenetic metrics in community ecology has provided insights into important ecological processes, particularly when combined with high-throughput sequencing methods; however, these approaches have not been widely used in studies of fungal communities relative to other microbial groups. Two obstacles have been considered: (1) the internal transcribed spacer (ITS) region has limited utility for constructing phylogenies and (2) most PCR primers that target the large subunit (LSU) ribosomal unit generate amplicons that exceed current limits of high-throughput sequencing platforms. We designed and tested a PCR primer (LR22R) to target approximately 300–400 bp region of the D2 hypervariable regionmore » of the fungal LSU for use with the Illumina MiSeq platform. Both in silico and empirical analyses showed that the LR22R–LR3 pair captured a broad range of fungal taxonomic groups with a small fraction of non-fungal groups. Phylogenetic placement of publically available LSU D2 sequences showed broad agreement with taxonomic classification. Comparisons of the LSU D2 and the ITS2 ribosomal regions from environmental samples and known communities showed similar discriminatory abilities of the two primer sets. Altogether, these findings show that the LR22R–LR3 primer pair has utility for phylogenetic analyses of fungal communities using high-throughput sequencing methods.« less

[Which definition and taxonomy of incident to use for a French reporting system in primary care settings?].

PubMed

Keriel-Gascou, M; Brami, J; Chanelière, M; Haeringer-Cholet, A; Larrieu, C; Villebrun, F; Robert, T; Michel, P

2014-02-01

There is no widely accepted definition of incident for primary care doctors in France and no taxonomic classification system for epidemiological use. In preparation for a future epidemiological study on primary care incidents in France (the ESPRIT study), this work was designed to identify the definitions and taxonomic classifications used internationally along with the usual methods and results in terms of frequency in the literature. The goal was to determine a French definition and taxonomy. Systematic review of the literature and consensus methods. An exhaustive search of epidemiological surveys was performed. A structured grid was used. After having identified the definitions used in the literature, a definition was chosen using the focus groups method. Taxonomies identified in the literature were classified by relationship, architecture, code number, and number of studies published. Subsequently, a consensus among experts, who independently tested these taxonomies on six incidents, was reached for choosing the most appropriate for epidemiological data collection (little information on a large number of cases). Twenty-four papers reporting 17 studies were selected among 139 articles. Five definitions and eight taxonomies were found. The chosen definition of incident was based on the WHO definition "A patient safety incident is an event or circumstance that could have resulted, or did result, in harm to a patient, and whose wish it is not repeated again". The test of incidents resulted in the choice of the TAPS version of the International Taxonomy of Medical Error in Primary Care for a reproducible and internationally recognized codification and the tempos method for its current use in French general practice. The definitions, taxonomies, data collection characteristics and frequency of incidents results in the international literature on incidents in primary care are key components for the preparation of an epidemiological survey on incidents in primary care. Copyright © 2014. Published by Elsevier Masson SAS.

Metaproteomics analyses as diagnostic tool for differentiation of Escherichia coli strains in outbreaks

NASA Astrophysics Data System (ADS)

Jabbour, Rabih E.; Wright, James D.; Deshpande, Samir V.; Wade, Mary; McCubbin, Patrick; Bevilacqua, Vicky

2013-05-01

The secreted proteins of the enterohemorrhagic and enteropathogenic E. coli (EHEC and EPEC) are the most common cause of hemorrhagic colitis, a bloody diarrhea with EHEC infection, which often can lead to life threatening hemolytic-uremic syndrome (HUS).We are employing a metaproteomic approach as an effective and complimentary technique to the current genomic based approaches. This metaproteomic approach will evaluate the secreted proteins associated with pathogenicity and utilize their signatures as differentiation biomarkers between EHEC and EPEC strains. The result showed that the identified tryptic peptides of the secreted proteins extracted from different EHEC and EPEC growths have difference in their amino acids sequences and could potentially utilized as biomarkers for the studied E. coli strains. Analysis of extract from EHEC O104:H4 resulted in identification of a multidrug efflux protein, which belongs to the family of fusion proteins that are responsible of cell transportation. Experimental peptides identified lies in the region of the HlyD haemolysin secretion protein-D that is responsible for transporting the haemolysin A toxin. Moreover, the taxonomic classification of EHEC O104:H4 showed closest match with E. coli E55989, which is in agreement with genomic sequencing studies that were done extensively on the mentioned strain. The taxonomic results showed strain level classification for the studied strains and distinctive separation among the strains. Comparative proteomic calculations showed separation between EHEC O157:H7 and O104:H4 in replicate samples using cluster analysis. There are no reported studies addressing the characterization of secreted proteins in various enhanced growth media and utilizing them as biomarkers for strain differentiation. The results of FY-2012 are promising to pursue further experimentation to statistically validate the results and to further explore the impact of environmental conditions on the nature of the secreted biomarkers in various E. coli strains that are of public health concerns in various sectors.

Kraken: ultrafast metagenomic sequence classification using exact alignments

PubMed Central

2014-01-01

Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/. PMID:24580807

Microbial community analysis using MEGAN.

PubMed

Huson, Daniel H; Weber, Nico

2013-01-01

Metagenomics, the study of microbes in the environment using DNA sequencing, depends upon dedicated software tools for processing and analyzing very large sequencing datasets. One such tool is MEGAN (MEtaGenome ANalyzer), which can be used to interactively analyze and compare metagenomic and metatranscriptomic data, both taxonomically and functionally. To perform a taxonomic analysis, the program places the reads onto the NCBI taxonomy, while functional analysis is performed by mapping reads to the SEED, COG, and KEGG classifications. Samples can be compared taxonomically and functionally, using a wide range of different charting and visualization techniques. PCoA analysis and clustering methods allow high-level comparison of large numbers of samples. Different attributes of the samples can be captured and used within analysis. The program supports various input formats for loading data and can export analysis results in different text-based and graphical formats. The program is designed to work with very large samples containing many millions of reads. It is written in Java and installers for the three major computer operating systems are available from http://www-ab.informatik.uni-tuebingen.de. © 2013 Elsevier Inc. All rights reserved.

A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies.

PubMed

Yu, J; Blom, J; Glaeser, S P; Jaenicke, S; Juhre, T; Rupp, O; Schwengers, O; Spänig, S; Goesmann, A

2017-11-10

The rapid development of next generation sequencing technology has greatly increased the amount of available microbial genomes. As a result of this development, there is a rising demand for fast and automated approaches in analyzing these genomes in a comparative way. Whole genome sequencing also bears a huge potential for obtaining a higher resolution in phylogenetic and taxonomic classification. During the last decade, several software tools and platforms have been developed in the field of comparative genomics. In this manuscript, we review the most commonly used platforms and approaches for ortholog group analyses with a focus on their potential for phylogenetic and taxonomic research. Furthermore, we describe the latest improvements of the EDGAR platform for comparative genome analyses and present recent examples of its application for the phylogenomic analysis of different taxa. Finally, we illustrate the role of the EDGAR platform as part of the BiGi Center for Microbial Bioinformatics within the German network on Bioinformatics Infrastructure (de.NBI). Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation

PubMed Central

Zhang, Y.; Schoch, C.L.; Fournier, J.; Crous, P.W.; de Gruyter, J.; Woudenberg, J.H.C.; Hirayama, K.; Tanaka, K.; Pointing, S.B.; Spatafora, J.W.; Hyde, K.D.

2009-01-01

Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceae s. str., Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic. PMID:20169024

Identification of Candida lusitaniae as an opportunistic yeast in humans.

PubMed Central

Holzschu, D L; Presley, H L; Miranda, M; Phaff, H J

1979-01-01

Four yeast strains, causally associated with infection in a patient with acute myelogenous leukemia, were identified by standard methods currently used in yeast taxonomy as representatives of Candida lusitania van Uden et do Carmo-Sousa. Because this species has not been recognized previously as an opportunistic yeast in humans, molecular taxonomic methods were applied to confirm its identity. The nuclear deoxyribonucleic acid (DNA) base composition of two clinical isolates was shown to be 45.1 mol% guanine plus cytosine as compared to 44.7 mol% guanine plus cytosine for the type strain of this species. DNA/DNA reassociation experiments revealed more than 95% complementarity between the DNAs from the clinical isolates and that of the type strain of C. lusitaniae, thus confirming their classification by conventional taxonomy. A key is provided to differentiate C. lusitaniae from two phenotypically similar Candida species. PMID:292646

A soil map of a large watershed in China: applying digital soil mapping in a data sparse region

NASA Astrophysics Data System (ADS)

Barthold, F.; Blank, B.; Wiesmeier, M.; Breuer, L.; Frede, H.-G.

2009-04-01

Prediction of soil classes in data sparse regions is a major research challenge. With the advent of machine learning the possibilities to spatially predict soil classes have increased tremendously and given birth to new possibilities in soil mapping. Digital soil mapping is a research field that has been established during the last decades and has been accepted widely. We now need to develop tools to reduce the uncertainty in soil predictions. This is especially challenging in data sparse regions. One approach to do this is to implement soil taxonomic distance as a classification error criterion in classification and regression trees (CART) as suggested by Minasny et al. (Geoderma 142 (2007) 285-293). This approach assumes that the classification error should be larger between soils that are more dissimilar, i.e. differ in a larger number of soil properties, and smaller between more similar soils. Our study area is the Xilin River Basin, which is located in central Inner Mongolia in China. It is characterized by semi arid climate conditions and is representative for the natural occurring steppe ecosystem. The study area comprises 3600 km2. We applied a random, stratified sampling design after McKenzie and Ryan (Geoderma 89 (1999) 67-94) with landuse and topography as stratifying variables. We defined 10 sampling classes, from each class 14 replicates were randomly drawn and sampled. The dataset was split into 100 soil profiles for training and 40 soil profiles for validation. We then applied classification and regression trees (CART) to quantify the relationships between soil classes and environmental covariates. The classification tree explained 75.5% of the variance with land use and geology as most important predictor variables. Among the 8 soil classes that we predicted, the Kastanozems cover most of the area. They are predominantly found in steppe areas. However, even some of the soils at sand dune sites, which were thought to show only little soil formation, can be classified as Kastanozems. Besides the Kastanozems, Regosols are most common at the sand dune sites as well as at sites that are defined as bare soil which are characterized by little or no vegetation. Gleysols are mostly found at sites in the vicinity of the Xilin river, which are connected to the groundwater. They can also be found in small valleys or depressions where sub-surface waters from neighboring areas collect. The richest soils are found in mountain meadow areas. Pedogenetic conditions here are most favorable and lead to the formation of Chernozems with deep humic Ah horizons. Other soil types that occur in the study area are Arenosols, Calcisols, Cambisol and Phaeozems. In addition, soil taxonomic distance is implemented into the decision tree procedure as a measure of classification error. The results of incorporating taxonomic distance as a loss function in the decision tree will be compared with the standard application of the decision tree.

Systematics and biogeography of Orconectes, subgenus Trisellescens, in the southeastern United States, a test of morphology-based classification

Treesearch

Christopher A. Taylor; Susan B. Adams; Guenter A. Schuster

2014-01-01

Diagnosable taxonomic units are fundamental to conservation biology and management of resources and the need for sound science in both fields is more pressing for aquatic ecosystems. Within freshwater crayfishes, the North American genus Orconectes is one of the most diverse in the World. Accurate assessments of species level relationships and species boundaries within...

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

Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome.

PubMed

Montaña, José Salvador; Jiménez, Diego Javier; Hernández, Mónica; Angel, Tatiana; Baena, Sandra

2012-02-01

Total metagenomic DNA was isolated from high Andean forest soil and subjected to taxonomical and functional composition analyses by means of clone library generation and sequencing. The obtained yield of 1.7 μg of DNA/g of soil was used to construct a metagenomic library of approximately 20,000 clones (in the plasmid p-Bluescript II SK+) with an average insert size of 4 Kb, covering 80 Mb of the total metagenomic DNA. Metagenomic sequences near the plasmid cloning site were sequenced and them trimmed and assembled, obtaining 299 reads and 31 contigs (0.3 Mb). Taxonomic assignment of total sequences was performed by BLASTX, resulting in 68.8, 44.8 and 24.5% classification into taxonomic groups using the metagenomic RAST server v2.0, WebCARMA v1.0 online system and MetaGenome Analyzer v3.8 software, respectively. Most clone sequences were classified as Bacteria belonging to phlya Actinobacteria, Proteobacteria and Acidobacteria. Among the most represented orders were Actinomycetales (34% average), Rhizobiales, Burkholderiales and Myxococcales and with a greater number of sequences in the genus Mycobacterium (7% average), Frankia, Streptomyces and Bradyrhizobium. The vast majority of sequences were associated with the metabolism of carbohydrates, proteins, lipids and catalytic functions, such as phosphatases, glycosyltransferases, dehydrogenases, methyltransferases, dehydratases and epoxide hydrolases. In this study we compared different methods of taxonomic and functional assignment of metagenomic clone sequences to evaluate microbial diversity in an unexplored soil ecosystem, searching for putative enzymes of biotechnological interest and generating important information for further functional screening of clone libraries.

Chloroplast variation is incongruent with classification of the Australian bloodwood eucalypts (genus Corymbia, family Myrtaceae)

PubMed Central

Schuster, Tanja M.; Setaro, Sabrina D.; Tibbits, Josquin F. G.; Batty, Erin L.; Fowler, Rachael M.; McLay, Todd G. B.; Wilcox, Stephen; Ades, Peter K.

2018-01-01

Previous molecular phylogenetic analyses have resolved the Australian bloodwood eucalypt genus Corymbia (~100 species) as either monophyletic or paraphyletic with respect to Angophora (9–10 species). Here we assess relationships of Corymbia and Angophora using a large dataset of chloroplast DNA sequences (121,016 base pairs; from 90 accessions representing 55 Corymbia and 8 Angophora species, plus 33 accessions of related genera), skimmed from high throughput sequencing of genomic DNA, and compare results with new analyses of nuclear ITS sequences (119 accessions) from previous studies. Maximum likelihood and maximum parsimony analyses of cpDNA resolve well supported trees with most nodes having >95% bootstrap support. These trees strongly reject monophyly of Corymbia, its two subgenera (Corymbia and Blakella), most taxonomic sections (Abbreviatae, Maculatae, Naviculares, Septentrionales), and several species. ITS trees weakly indicate paraphyly of Corymbia (bootstrap support <50% for maximum likelihood, and 71% for parsimony), but are highly incongruent with the cpDNA analyses, in that they support monophyly of both subgenera and some taxonomic sections of Corymbia. The striking incongruence between cpDNA trees and both morphological taxonomy and ITS trees is attributed largely to chloroplast introgression between taxa, because of geographic sharing of chloroplast clades across taxonomic groups. Such introgression has been widely inferred in studies of the related genus Eucalyptus. This is the first report of its likely prevalence in Corymbia and Angophora, but this is consistent with previous morphological inferences of hybridisation between species. Our findings (based on continent-wide sampling) highlight a need for more focussed studies to assess the extent of hybridisation and introgression in the evolutionary history of these genera, and that critical testing of the classification of Corymbia and Angophora requires additional sequence data from nuclear genomes. PMID:29668710

Comparing genome versus proteome-based identification of clinical bacterial isolates.

PubMed

Galata, Valentina; Backes, Christina; Laczny, Cédric Christian; Hemmrich-Stanisak, Georg; Li, Howard; Smoot, Laura; Posch, Andreas Emanuel; Schmolke, Susanne; Bischoff, Markus; von Müller, Lutz; Plum, Achim; Franke, Andre; Keller, Andreas

2018-05-01

Whole-genome sequencing (WGS) is gaining importance in the analysis of bacterial cultures derived from patients with infectious diseases. Existing computational tools for WGS-based identification have, however, been evaluated on previously defined data relying thereby unwarily on the available taxonomic information.Here, we newly sequenced 846 clinical gram-negative bacterial isolates representing multiple distinct genera and compared the performance of five tools (CLARK, Kaiju, Kraken, DIAMOND/MEGAN and TUIT). To establish a faithful 'gold standard', the expert-driven taxonomy was compared with identifications based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) analysis. Additionally, the tools were also evaluated using a data set of 200 Staphylococcus aureus isolates.CLARK and Kraken (with k =31) performed best with 626 (100%) and 193 (99.5%) correct species classifications for the gram-negative and S. aureus isolates, respectively. Moreover, CLARK and Kraken demonstrated highest mean F-measure values (85.5/87.9% and 94.4/94.7% for the two data sets, respectively) in comparison with DIAMOND/MEGAN (71 and 85.3%), Kaiju (41.8 and 18.9%) and TUIT (34.5 and 86.5%). Finally, CLARK, Kaiju and Kraken outperformed the other tools by a factor of 30 to 170 fold in terms of runtime.We conclude that the application of nucleotide-based tools using k-mers-e.g. CLARK or Kraken-allows for accurate and fast taxonomic characterization of bacterial isolates from WGS data. Hence, our results suggest WGS-based genotyping to be a promising alternative to the MS-based biotyping in clinical settings. Moreover, we suggest that complementary information should be used for the evaluation of taxonomic classification tools, as public databases may suffer from suboptimal annotations.

Taxonomic hierarchy of the phylum Firmicutes and novel Firmicutes species originated from various environments in Korea.

PubMed

Seong, Chi Nam; Kang, Joo Won; Lee, Ji Hee; Seo, So Yeon; Woo, Jung Jae; Park, Chul; Bae, Kyung Sook; Kim, Mi Sun

2018-01-01

This study assessed the taxonomic hierarchy of the phylum Firmicutes as well as elucidated the isolation and classification states of novel Firmicutes species isolated from Korean territory. The hierarchical classification system of the phylum Firmicutes has been developed since 1872 when the genus Bacillus was first reported and has been generally adopted since 2001. However, this taxonomic hierarchy is still being modified. Until Feb. 2017, the phylum Firmicutes consisted of seven classes (Bacilli, Clostridia, Erysipelotrichia, Limnochordia, Negativicutes, Thermolithobacteria, and Tissierellia), 13 orders, 45 families, and 421 genera. Firmicutes species isolated from various environments in Korea have been reported from 2000, and 187 species have been approved as of Feb. 2017. All Firmicutes species were affiliated with three classes (Bacilli, Clostridia, and Erysipelotrichia), four orders (Bacillales, Lactobacillales, Clostridiales, and Erysipelotrichales), 17 families, and 54 genera. A total of 173 species belong to the class Bacilli, of which 151 species were affiliated with the order Bacillales and the remaining 22 species with the order Lactobacillales. Twelve species belonging to the class Clostridia were affiliated within only one order, Clostridiales. The most abundant family was Bacillaceae (67 species), followed by the family Paenibacillaceae (56 species). Thirteen novel genera were created using isolates from the Korean environment. A number of Firmicutes species were isolated from natural environments in Korean territory. In addition, a considerable number of species were isolated from artificial resources such as fermented foods. Most Firmicutes species, belonging to the families Bacillaceae, Planococcaceae, and Staphylococcaceae, isolated from Korean fermented foods and solar salterns were halophilic or halotolerant. Firmicutes species were isolated from the whole territory of Korea, especially large numbers from Provinces Gyeonggi, Chungnam, and Daejeon.

Benthic impacts of intertidal oyster culture, with consideration of taxonomic sufficiency.

PubMed

Forrest, Barrie M; Creese, Robert G

2006-01-01

An investigation of the impacts from elevated intertidal Pacific oyster culture in a New Zealand estuary showed enhanced sedimentation beneath culture racks compared with other sites. Seabed elevation beneath racks was generally lower than between them, suggesting that topographic patterns more likely result from a local effect of rack structures on hydrodynamic processes than from enhanced deposition. Compared with control sites, seabed sediments within the farm had a greater silt/clay and organic content, and a lower redox potential and shear strength. While a marked trend in macrofaunal species richness was not evident, species composition and dominance patterns were consistent with a disturbance gradient, with farm effects not evident 35 m from the perimeter of the racks. Of the environmental variables measured, sediment shear strength was most closely associated with the distribution and density of macrofauna, suggesting that human-induced disturbance from farming operations may have contributed to the biological patterns. To evaluate the taxonomic sufficiency needed to document impacts, aggregation to the family level based on Linnean classification was compared with an aggregation scheme based on ;general groups' identifiable with limited taxonomic expertise. Compared with species-level analyses, spatial patterns of impact were equally discernible at both aggregation levels used, provided density rather than presence/absence data were used. Once baseline conditions are established and the efficacy of taxonomic aggregation demonstrated, a ;general group' scheme provides an appropriate and increasingly relevant tool for routine monitoring.

Taxonaut: an application software for comparative display of multiple taxonomies with a use case of GBIF Species API

PubMed Central

2016-01-01

Abstract Background The Species API of the Global Biodiversity Information Facility (GBIF) provides public access to taxonomic data aggregated from multiple data sources. Each data source follows its own classification which can be inconsistent with classifications from other sources. Even with a reference classification e.g. the GBIF Backbone taxonomy, a comprehensive method to compare classifications in the data aggregation is essential, especially for non-expert users. New information A Java application was developed to compare multiple taxonomies graphically using classification data acquired from GBIF’s ChecklistBank via the GBIF Species API. It uses a table to display taxonomies where each column represents a taxonomy under comparison, with an aligner column to organise taxa by name. Each cell contains the name of a taxon if the classification in that column contains the name. Each column also has a cell showing the hierarchy of the taxonomy by a folder metaphor where taxa are aligned and synchronised in the aligner column. A set of those comparative tables shows taxa categorised by relationship between taxonomies. The result set is also available as tables in an Excel format file. PMID:27932916

Spider Neurotoxins, Short Linear Cationic Peptides and Venom Protein Classification Improved by an Automated Competition between Exhaustive Profile HMM Classifiers

PubMed Central

Koua, Dominique; Kuhn-Nentwig, Lucia

2017-01-01

Spider venoms are rich cocktails of bioactive peptides, proteins, and enzymes that are being intensively investigated over the years. In order to provide a better comprehension of that richness, we propose a three-level family classification system for spider venom components. This classification is supported by an exhaustive set of 219 new profile hidden Markov models (HMMs) able to attribute a given peptide to its precise peptide type, family, and group. The proposed classification has the advantages of being totally independent from variable spider taxonomic names and can easily evolve. In addition to the new classifiers, we introduce and demonstrate the efficiency of hmmcompete, a new standalone tool that monitors HMM-based family classification and, after post-processing the result, reports the best classifier when multiple models produce significant scores towards given peptide queries. The combined used of hmmcompete and the new spider venom component-specific classifiers demonstrated 96% sensitivity to properly classify all known spider toxins from the UniProtKB database. These tools are timely regarding the important classification needs caused by the increasing number of peptides and proteins generated by transcriptomic projects. PMID:28786958

Part-whole reasoning in medical ontologies revisited--introducing SEP triplets into classification-based description logics.

PubMed

Schulz, S; Romacker, M; Hahn, U

1998-01-01

The development of powerful and comprehensive medical ontologies that support formal reasoning on a large scale is one of the key requirements for clinical computing in the next millennium. Taxonomic medical knowledge, a major portion of these ontologies, is mainly characterized by generalization and part-whole relations between concepts. While reasoning in generalization hierarchies is quite well understood, no fully conclusive mechanism as yet exists for part-whole reasoning. The approach we take emulates part-whole reasoning via classification-based reasoning using SEP triplets, a special data structure for encoding part-whole relations that is fully embedded in the formal framework of standard description logics.

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

Part-whole reasoning in medical ontologies revisited--introducing SEP triplets into classification-based description logics.

PubMed Central

Schulz, S.; Romacker, M.; Hahn, U.

1998-01-01

The development of powerful and comprehensive medical ontologies that support formal reasoning on a large scale is one of the key requirements for clinical computing in the next millennium. Taxonomic medical knowledge, a major portion of these ontologies, is mainly characterized by generalization and part-whole relations between concepts. While reasoning in generalization hierarchies is quite well understood, no fully conclusive mechanism as yet exists for part-whole reasoning. The approach we take emulates part-whole reasoning via classification-based reasoning using SEP triplets, a special data structure for encoding part-whole relations that is fully embedded in the formal framework of standard description logics. Images Figure 3 PMID:9929335

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.

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

Taxonomic Approaches to Enlisted Occupational Classification. Volume II,

DTIC Science & Technology

1979-12-01

various media and about the social implications of the more pervasive of these, there is little of communication theory that is useful to those who...Folley’s theory is a system of interrelated definitions, constructs, and hypotheses relating task attributes to training requirements. D. C. Berliner...requirement approach, the task characteristics approach, and a third approach based on information theory . During the third project year, two of the

Taxonomic significance of leaf micromorphology in some selected taxa of Acanthaceae (Peninsular Malaysia)

NASA Astrophysics Data System (ADS)

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

2014-09-01

Comparative leaf micromorphology study was conducted in eight taxa of Acanthaceae from Peninsular Malaysia. Eight chosen taxa were Acanthus ebracteatus Vahl, A. ilicifolius L., A. volubilis Wall, A. montanus T. Anderson, Andrographis paniculata (Burm.f.) Wall. ex Nees, Asystasia gangetica subsp. micrantha (Nees) Ensermu, Chroesthes longifolia (Wight) B. Hansen and Peristrophe roxburghiana (Schult.) Bremek. The objective of this study was to identify the leaf micromorphological characteristics that can be used in species identification and also as supportive data in classification. The procedures involved such as dehydration, critical point drying, gold coated and examination under scanning electron microscope. Findings in this study have demonstrated the similarities and variations in leaf micromorphological characteristics such as in type of epicuticular waxes, cuticular ornamentations, stomata characteristics and in the presence of trichomes. Six types of epicuticular waxes and five types of trichomes were observed. Variations in cuticular ornamentations and stomata structure can be used to differentiate species. One diagnostic character was found and proven to be very useful to identify Acanthus via the presence of simple trichomes (short-conicle like). In conclusion, the results of this study have shown that leaf micromorphological characteristics have taxonomic significance that can be useful in classifications and identification especially at species level.

A singular value decomposition approach for improved taxonomic classification of biological sequences

PubMed Central

2011-01-01

Background Singular value decomposition (SVD) is a powerful technique for information retrieval; it helps uncover relationships between elements that are not prima facie related. SVD was initially developed to reduce the time needed for information retrieval and analysis of very large data sets in the complex internet environment. Since information retrieval from large-scale genome and proteome data sets has a similar level of complexity, SVD-based methods could also facilitate data analysis in this research area. Results We found that SVD applied to amino acid sequences demonstrates relationships and provides a basis for producing clusters and cladograms, demonstrating evolutionary relatedness of species that correlates well with Linnaean taxonomy. The choice of a reasonable number of singular values is crucial for SVD-based studies. We found that fewer singular values are needed to produce biologically significant clusters when SVD is employed. Subsequently, we developed a method to determine the lowest number of singular values and fewest clusters needed to guarantee biological significance; this system was developed and validated by comparison with Linnaean taxonomic classification. Conclusions By using SVD, we can reduce uncertainty concerning the appropriate rank value necessary to perform accurate information retrieval analyses. In tests, clusters that we developed with SVD perfectly matched what was expected based on Linnaean taxonomy. PMID:22369633

Latitudinal variation in nematode diversity and ecological roles along the Chinese coast.

PubMed

Wu, Jihua; Chen, Huili; Zhang, Youzheng

2016-11-01

To test changes in the phylogenetic relatedness, niche breadth, and life-history strategies of nematodes along a latitudinal gradient. Sixteen wetland locations along the Pacific coast of China, from 20°N to 40°N. Linear regression was used to relate nematode phylogenetic relatedness (average taxonomic distinctness (AvTD) and average phylogenetic diversity [AvPD]), life-history group (based on " c - p " colonizer-persister group classification), and dietary specificity (based on guild classification of feeding selectivity) to latitude. Wetland nematode taxonomic diversity (richness and Shannon diversity indices) decreased with increasing latitude along the Chinese coast. Phylogenetic diversity indices (AvTD and AvPD) significantly increased with increasing latitude. This indicates that at lower latitudes, species within the nematode community were more closely related. With increasing latitude, the nematode relative richness and abundance decreased for selective deposit feeders but increased for nonselective deposit feeders. The proportion of general opportunists decreased with increasing latitude, but persisters showed the opposite trend. The annual temperature range and the pH of sediments were more important than vegetation type in structuring nematode communities. Nematode niche breadth was narrower at lower latitudes with respect to dietary specificity. Higher latitudes with a more variable climate favor r over K life-history strategists. Nematode communities at lower latitudes contained more closely related species.

HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts

PubMed Central

Laffy, Patrick W.; Wood-Charlson, Elisha M.; Turaev, Dmitrij; Weynberg, Karen D.; Botté, Emmanuelle S.; van Oppen, Madeleine J. H.; Webster, Nicole S.; Rattei, Thomas

2016-01-01

Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments. PMID:27375564

Walking and talking the tree of life: Why and how to teach about biodiversity.

PubMed

Ballen, Cissy J; Greene, Harry W

2017-03-01

Taxonomic details of diversity are an essential scaffolding for biology education, yet outdated methods for teaching the tree of life (TOL), as implied by textbook content and usage, are still commonly employed. Here, we show that the traditional approach only vaguely represents evolutionary relationships, fails to denote major events in the history of life, and relies heavily on memorizing near-meaningless taxonomic ranks. Conversely, a clade-based strategy-focused on common ancestry, monophyletic groups, and derived functional traits-is explicitly based on Darwin's "descent with modification," provides students with a rational system for organizing the details of biodiversity, and readily lends itself to active learning techniques. We advocate for a phylogenetic classification that mirrors the TOL, a pedagogical format of increasingly complex but always hierarchical presentations, and the adoption of active learning technologies and tactics.

Production of structured triacylglycerols from microalgae.

PubMed

Řezanka, Tomáš; Lukavský, Jaromír; Nedbalová, Linda; Sigler, Karel

2014-08-01

Structured triacylglycerols (TAGs) were isolated from nine cultivated strains of microalgae belonging to different taxonomic groups, i.e. Audouinella eugena, Balbiania investiens, Myrmecia bisecta, Nannochloropsis limnetica, Palmodictyon varium, Phaeodactylum tricornutum, Pseudochantransia sp., Thorea ramosissima, and Trachydiscus minutus. They were separated and isolated by means of NARP-LC/MS-APCI and chiral LC and the positional isomers and enantiomers of TAGs with two polyunsaturated, i.e. arachidonic (A) and eicosapentaenoic (E) acids and one saturated, i.e. palmitic acid (P) were identified. Algae that produce eicosapentaenoic acid were found to biosynthesize more asymmetrical TAGs, i.e. PPE or PEE, whereas algae which produced arachidonic acid give rise to symmetrical TAGs, i.e. PAP or APA, irrespective of their taxonomical classification. Nitrogen and phosphorus starvation consistently reversed the ratio of asymmetrical and symmetrical TAGs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Marine Biodiversity in the Caribbean: Regional Estimates and Distribution Patterns

PubMed Central

Miloslavich, Patricia; Díaz, Juan Manuel; Klein, Eduardo; Alvarado, Juan José; Díaz, Cristina; Gobin, Judith; Escobar-Briones, Elva; Cruz-Motta, Juan José; Weil, Ernesto; Cortés, Jorge; Bastidas, Ana Carolina; Robertson, Ross; Zapata, Fernando; Martín, Alberto; Castillo, Julio; Kazandjian, Aniuska; Ortiz, Manuel

2010-01-01

This paper provides an analysis of the distribution patterns of marine biodiversity and summarizes the major activities of the Census of Marine Life program in the Caribbean region. The coastal Caribbean region is a large marine ecosystem (LME) characterized by coral reefs, mangroves, and seagrasses, but including other environments, such as sandy beaches and rocky shores. These tropical ecosystems incorporate a high diversity of associated flora and fauna, and the nations that border the Caribbean collectively encompass a major global marine biodiversity hot spot. We analyze the state of knowledge of marine biodiversity based on the geographic distribution of georeferenced species records and regional taxonomic lists. A total of 12,046 marine species are reported in this paper for the Caribbean region. These include representatives from 31 animal phyla, two plant phyla, one group of Chromista, and three groups of Protoctista. Sampling effort has been greatest in shallow, nearshore waters, where there is relatively good coverage of species records; offshore and deep environments have been less studied. Additionally, we found that the currently accepted classification of marine ecoregions of the Caribbean did not apply for the benthic distributions of five relatively well known taxonomic groups. Coastal species richness tends to concentrate along the Antillean arc (Cuba to the southernmost Antilles) and the northern coast of South America (Venezuela – Colombia), while no pattern can be observed in the deep sea with the available data. Several factors make it impossible to determine the extent to which these distribution patterns accurately reflect the true situation for marine biodiversity in general: (1) highly localized concentrations of collecting effort and a lack of collecting in many areas and ecosystems, (2) high variability among collecting methods, (3) limited taxonomic expertise for many groups, and (4) differing levels of activity in the study of different taxa. PMID:20689856

Emerging Issues in Virus Taxonomy

PubMed Central

Mahy, Brian W.J.

2004-01-01

Viruses occupy a unique position in biology. Although they possess some of the properties of living systems such as having a genome, they are actually nonliving infectious entities and should not be considered microorganisms. A clear distinction should be drawn between the terms virus, virion, and virus species. Species is the most fundamental taxonomic category used in all biological classification. In 1991, the International Committee on Taxonomy of Viruses (ICTV) decided that the category of virus species should be used in virus classification together with the categories of genus and family. More than 50 ICTV study groups were given the task of demarcating the 1,550 viral species that were recognized in the 7th ICTV report, which was published in 2000. We briefly describe the changes in virus classification that were introduced in that report. We also discuss recent proposals to introduce a nonlatinized binomial nomenclature for virus species. PMID:15078590

Revision of the taxonomic status of Aphis floridanae Tissot (Hemiptera:Aphididae) using morphological and molecular insight

USDA-ARS?s Scientific Manuscript database

Three Aphis species are involved in this study. Aphis floridanae Tissot, 1933 and A. nasturtii Kaltenbach, 1843 are currently treated as synonym, and A. impatientis Thomas, 1878 has a valid taxonomic status. Morphological and cytochrome oxidase 1 (Cox1) data show that Aphis floridanae is not synonym...

Rates of species accumulation and taxonomic diversification during phototrophic biofilm development are controlled by both nutrient supply and current velocity.

PubMed

Larson, Chad A; Passy, Sophia I

2013-03-01

The accumulation of new and taxonomically diverse species is a marked feature of community development, but the role of the environment in this process is not well understood. To address this problem, we subjected periphyton in laboratory streams to low (10-cm · s(-1)), high (30-cm · s(-1)), and variable (9- to 32-cm · s(-1)) current velocity and low- versus high-nutrient inputs. We examined how current velocity and resource supply constrained (i) the rates of species accumulation, a measure of temporal beta-diversity, and (ii) the rates of diversification of higher taxonomic categories, defined here as the rate of higher taxon richness increase with the increase of species richness. Temporal biofilm dynamics were controlled by a strong nutrient-current interaction. Nutrients accelerated the rates of accumulation of new species, when flow velocity was not too stressful. Species were more taxonomically diverse under variable than under low-flow conditions, indicating that flow heterogeneity increased the niche diversity in the high-nutrient treatments. Conversely, the lower diversification rates under high- than under low-nutrient conditions at low velocity are explained with finer resource partitioning among species, belonging to a limited number of related genera. The overall low rates of diversification in high-current treatments suggest that the ability to withstand current stress was conserved within closely related species. Temporal heterogeneity of disturbance has been shown to promote species richness, but here we further demonstrate that it also affects two other components of biodiversity, i.e., temporal beta-diversity and diversification rate. Therefore, management efforts for preserving the inherent temporal heterogeneity of natural ecosystems will have detectable positive effects on biodiversity.

Rates of Species Accumulation and Taxonomic Diversification during Phototrophic Biofilm Development Are Controlled by both Nutrient Supply and Current Velocity

PubMed Central

2013-01-01

The accumulation of new and taxonomically diverse species is a marked feature of community development, but the role of the environment in this process is not well understood. To address this problem, we subjected periphyton in laboratory streams to low (10-cm · s−1), high (30-cm · s−1), and variable (9- to 32-cm · s−1) current velocity and low- versus high-nutrient inputs. We examined how current velocity and resource supply constrained (i) the rates of species accumulation, a measure of temporal beta-diversity, and (ii) the rates of diversification of higher taxonomic categories, defined here as the rate of higher taxon richness increase with the increase of species richness. Temporal biofilm dynamics were controlled by a strong nutrient-current interaction. Nutrients accelerated the rates of accumulation of new species, when flow velocity was not too stressful. Species were more taxonomically diverse under variable than under low-flow conditions, indicating that flow heterogeneity increased the niche diversity in the high-nutrient treatments. Conversely, the lower diversification rates under high- than under low-nutrient conditions at low velocity are explained with finer resource partitioning among species, belonging to a limited number of related genera. The overall low rates of diversification in high-current treatments suggest that the ability to withstand current stress was conserved within closely related species. Temporal heterogeneity of disturbance has been shown to promote species richness, but here we further demonstrate that it also affects two other components of biodiversity, i.e., temporal beta-diversity and diversification rate. Therefore, management efforts for preserving the inherent temporal heterogeneity of natural ecosystems will have detectable positive effects on biodiversity. PMID:23335757

A topographic feature taxonomy for a U.S. national topographic mapping ontology

USGS Publications Warehouse

Varanka, Dalia E.

2013-01-01

Using legacy feature lists from the U.S. National Topographic Mapping Program of the twentieth century, a taxonomy of features is presented for purposes of developing a national topographic feature ontology for geographic mapping and analysis. After reviewing published taxonomic classifications, six basic classes are suggested; terrain, surface water, ecological regimes, built-up areas, divisions, and events. Aspects of ontology development are suggested as the taxonomy is described.

Molecular Phylogeny of the Astrophorida (Porifera, Demospongiae p) Reveals an Unexpected High Level of Spicule Homoplasy

PubMed Central

Cárdenas, Paco; Xavier, Joana R.; Reveillaud, Julie; Schander, Christoffer; Rapp, Hans Tore

2011-01-01

Background The Astrophorida (Porifera, Demospongiae p) is geographically and bathymetrically widely distributed. Systema Porifera currently includes five families in this order: Ancorinidae, Calthropellidae, Geodiidae, Pachastrellidae and Thrombidae. To date, molecular phylogenetic studies including Astrophorida species are scarce and offer limited sampling. Phylogenetic relationships within this order are therefore for the most part unknown and hypotheses based on morphology largely untested. Astrophorida taxa have very diverse spicule sets that make them a model of choice to investigate spicule evolution. Methodology/Principal Findings With a sampling of 153 specimens (9 families, 29 genera, 89 species) covering the deep- and shallow-waters worldwide, this work presents the first comprehensive molecular phylogeny of the Astrophorida, using a cytochrome c oxidase subunit I (COI) gene partial sequence and the 5′ end terminal part of the 28S rDNA gene (C1-D2 domains). The resulting tree suggested that i) the Astrophorida included some lithistid families and some Alectonidae species, ii) the sub-orders Euastrophorida and Streptosclerophorida were both polyphyletic, iii) the Geodiidae, the Ancorinidae and the Pachastrellidae were not monophyletic, iv) the Calthropellidae was part of the Geodiidae clade (Calthropella at least), and finally that v) many genera were polyphyletic (Ecionemia, Erylus, Poecillastra, Penares, Rhabdastrella, Stelletta and Vulcanella). Conclusion The Astrophorida is a larger order than previously considered, comprising ca. 820 species. Based on these results, we propose new classifications for the Astrophorida using both the classical rank-based nomenclature (i.e., Linnaean classification) and the phylogenetic nomenclature following the PhyloCode, independent of taxonomic rank. A key to the Astrophorida families, sub-families and genera incertae sedis is also included. Incongruences between our molecular tree and the current classification can be explained by the banality of convergent evolution and secondary loss in spicule evolution. These processes have taken place many times, in all the major clades, for megascleres and microscleres. PMID:21494664

Spectral Classification of NEOWISE Observed Near-Earth Asteroids

NASA Astrophysics Data System (ADS)

Desira, Christopher

2017-01-01

Near-Earth asteroids (NEAs) allow us to determine the properties of the smallest solar system bodies in the sub-kilometer size range. Large (>few km) NEAs have albedos which span a wide range from ~0.05 to ~0.3 and are known to correlate with asteroid composition, determined by analysing the shape of their optical reflectance spectra. It is, however, still unknown how this relationship extends into the sub-kilometer population.NEOWISE has performed a thermal infrared survey that provides the largest inventory to date of well-determined sizes and albedos for NEAs, including many in the sub-km population. This provides an opportunity to test the albedo-surface composition correlation in a new size regime. If it is found to hold, then a simple optical spectrum can give a well-constrained albedo and size estimate without the need for thermal IR measurements.The sizes and composition of many more sub-km sized NEAs are needed to aid in the understanding of the formation/evolution of the inner solar system and the characterisation of potentially hazardous objects, possible mission targets and even commercial mining operations.We obtained optical spectra of sub-kilometer NEOWISE-observed NEAs using the 1.5m Tillinghast telescope and the FAST spectrograph at the Whipple Observatory on Mt Hopkins, Arizona. We performed a taxonomic classification to identify their likely composition and combined this with NEOWISE data to look for known correlations between main belt asteroid spectral types and their optical albedos. Additionally, we tested the robustness of current data reduction methods in order to increase our confidence in the spectral classifications of NEAs.

Animal-derived natural products of Sowa Rigpa medicine: Their pharmacopoeial description, current utilization and zoological identification.

PubMed

Yeshi, Karma; Morisco, Paolo; Wangchuk, Phurpa

2017-07-31

The Bhutanese Sowa Rigpa medicine (BSM) uses animal parts in the preparation of numerous polyingredient traditional remedies. Our study reports the taxonomical identification of medicinal animals and the description of traditional uses in English medical terminologies. To taxonomically identify the medicinal animals and their derived natural products used as a zootherapeutic agents in BSM. First, the traditional textbooks were reviewed to generate a list of animal products described as ingredients. Second, animal parts that are currently used in Bhutan were identified. Third, the ethnopharmacological uses of each animal ingredients were translated into English medical terminologies by consulting Traditional Physicians, clinical assistants, pharmacognosists, and pharmacists in Bhutan. Fourth, the animal parts were taxonomically identified and their Latin names were confirmed by crosschecking them with online animal databases and relevant scientific literature. The study found 73 natural products belonging to 29 categories derived from 45 medicinal animals (36 vertebrates and 9 invertebrates), comprising of 9 taxonomic categories and 30 zoological families. Out of 116 formulations currently produced, 87 of them contain one or more extracts and products obtained from 13 medicinal animals to treat more than 124 traditionally classified illnesses. Only five animal ingredients were found available in Bhutan and rest of the animal parts are being imported from India. Out of 73 natural products described in the traditional textbooks, only 13 of them (some omitted and few substituted by plants) are currently included in 87 formulations of BSM. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

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.

Walking and talking the tree of life: Why and how to teach about biodiversity

PubMed Central

Ballen, Cissy J.; Greene, Harry W.

2017-01-01

Taxonomic details of diversity are an essential scaffolding for biology education, yet outdated methods for teaching the tree of life (TOL), as implied by textbook content and usage, are still commonly employed. Here, we show that the traditional approach only vaguely represents evolutionary relationships, fails to denote major events in the history of life, and relies heavily on memorizing near-meaningless taxonomic ranks. Conversely, a clade-based strategy—focused on common ancestry, monophyletic groups, and derived functional traits—is explicitly based on Darwin’s “descent with modification,” provides students with a rational system for organizing the details of biodiversity, and readily lends itself to active learning techniques. We advocate for a phylogenetic classification that mirrors the TOL, a pedagogical format of increasingly complex but always hierarchical presentations, and the adoption of active learning technologies and tactics. PMID:28319149

Molecular phylogeny of edge hill virus supports its position in the yellow Fever virus group and identifies a new genetic variant.

PubMed

Macdonald, Joanne; Poidinger, Michael; Mackenzie, John S; Russell, Richard C; Doggett, Stephen; Broom, Annette K; Phillips, Debra; Potamski, Joseph; Gard, Geoff; Whelan, Peter; Weir, Richard; Young, Paul R; Gendle, Debra; Maher, Sheryl; Barnard, Ross T; Hall, Roy A

2010-06-15

Edge Hill virus (EHV) is a mosquito-borne flavivirus isolated throughout Australia during mosquito surveillance programs. While not posing an immediate threat to the human population, EHV is a taxonomically interesting flavivirus since it remains the only member of the yellow fever virus (YFV) sub-group to be detected within Australia. Here we present both an antigenic and genetic investigation of collected isolates, and confirm taxonomic classification of the virus within the YFV-group. Isolates were not clustered based on geographical origin or time of isolation, suggesting that minimal genetic evolution of EHV has occurred over geographic distance or time within the EHV cluster. However, two isolates showed significant differences in antigenic reactivity patterns, and had a much larger divergence from the EHV prototype (19% nucleotide and 6% amino acid divergence), indicating a distinct subtype or variant within the EHV subgroup.

The scarab beetle tribe Pentodontini (Coleoptera: Scarabaeidae: Dynastinae) of Colombia: taxonomy, natural history, and distribution.

PubMed

López-García, Margarita M; Gasca-Álvarez, Héctor J; Amat-García, Germán

2015-11-27

Pentodontini is the most diverse tribe of Dynastinae (Coleoptera: Scarabaeidae), and most of the genera are restricted to a single biogeographic region. In this work, the taxonomic composition of the Pentodontini in Colombia was determined, and genera and species were diagnosed based on external morphology and male genitalia. Records of 1,580 specimens from 31 departments and 398 localities in Colombia were obtained from 24 species in the genera Bothynus Hope, Denhezia Dechambre, Euetheola Bates, Hylobothynus Ohaus, Oxyligyrus Arrow, Parapucaya Prell, Pucaya Ohaus, and Tomarus Erichson. Oxyligyrus cayennensis Endrödi, Tomarus cicatricosus (Prell), and T. pullus (Prell) are reported for the first time from Colombia. Pucaya punctata Endrödi is reduced to synonymy with Pucaya pulchra Arrow. Possible changes in the classification of Denhezia Dechambre are discussed. Dichotomous keys are provided for Colombian genera and species. Taxonomic descriptions and distribution maps are included for all species.

Nuclear DNA Content Variation and Species Relationships in the Genus Lupinus (Fabaceae)

PubMed Central

NAGANOWSKA, BARBARA; WOLKO, BOGDAN; ŚLIWIŃSKA, ELWIRA; KACZMAREK, ZYGMUNT

2003-01-01

The 2C nuclear DNA content has been estimated by flow cytometry in 18 species and botanical forms of the genus Lupinus (family Fabaceae), using propidium iodide as a fluorescent dye. They represented distinct infrageneric taxonomic groups and differed in somatic chromosome numbers. Estimated 2C DNA values ranged from 0·97 pg in L. princei to 2·44 pg in L. luteus, which gives a more than 2·5-fold variation. Statistical analysis of the data obtained resulted in a grouping that supports the generally accepted taxonomic classification of the Old World lupins. The rough-seeded L. princei turned out to be an interesting exception, getting closer to smooth-seeded species. Results of DNA content analyses are discussed with regards to the phylogenetic relationships among the Old World lupins and some aspects of the evolution of the genus. PMID:12853281

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

Taxonomic discrimination of higher plants by pyrolysis mass spectrometry.

PubMed

Kim, S W; Ban, S H; Chung, H J; Choi, D W; Choi, P S; Yoo, O J; Liu, J R

2004-02-01

Pyrolysis mass spectrometry (PyMS) is a rapid, simple, high-resolution analytical method based on thermal degradation of complex material in a vacuum and has been widely applied to the discrimination of closely related microbial strains. Leaf samples of six species and one variety of higher plants (Rosa multiflora, R. multiflora var. platyphylla, Sedum kamtschaticum, S. takesimense, S. sarmentosum, Hepatica insularis, and H. asiatica) were subjected to PyMS for spectral fingerprinting. Principal component analysis of PyMS data was not able to discriminate these plants in discrete clusters. However, canonical variate analysis of PyMS data separated these plants from one another. A hierarchical dendrogram based on canonical variate analysis was in agreement with the known taxonomy of the plants at the variety level. These results indicate that PyMS is able to discriminate higher plants based on taxonomic classification at the family, genus, species, and variety level.

Molecular phylogeny and systematics of the Echinostomatoidea Looss, 1899 (Platyhelminthes: Digenea).

PubMed

Tkach, Vasyl V; Kudlai, Olena; Kostadinova, Aneta

2016-03-01

The Echinostomatoidea is a large, cosmopolitan group of digeneans currently including nine families and 105 genera, the vast majority parasitic, as adults, in birds with relatively few taxa parasitising mammals, reptiles and, exceptionally, fish. Despite the complex structure, diverse content and substantial species richness of the group, almost no attempt has been made to elucidate its phylogenetic relationships at the suprageneric level based on molecules due to the lack of data. Herein, we evaluate the consistency of the present morphology-based classification system of the Echinostomatoidea with the phylogenetic relationships of its members based on partial sequences of the nuclear lsrRNA gene for a broad diversity of taxa (80 species, representing eight families and 40 genera), including representatives of five subfamilies of the Echinostomatidae, which currently exhibits the most complex taxonomic structure within the superfamily. This first comprehensive phylogeny for the Echinostomatoidea challenged the current systematic framework based on comparative morphology. A morphology-based evaluation of this new molecular framework resulted in a number of systematic and nomenclatural changes consistent with the phylogenetic estimates of the generic and suprageneric boundaries and a new phylogeny-based classification of the Echinostomatoidea. In the current systematic treatment: (i) the rank of two family level lineages, the former Himasthlinae and Echinochasminae, is elevated to full family status; (ii) Caballerotrema is distinguished at the family level; (iii) the content and diagnosis of the Echinostomatidae (sensu stricto) (s. str.) are revised to reflect its phylogeny, resulting in the abolition of the Nephrostominae and Chaunocephalinae as synonyms of the Echinostomatidae (s. str.); (iv) Artyfechinostomum, Cathaemasia, Rhopalias and Ribeiroia are re-allocated within the Echinostomatidae (s. str.), resulting in the abolition of the Cathaemasiidae, Rhopaliidae and Ribeiroiinae, which become synonyms of the Echinostomatidae (s. str.); and (v) refinements of the generic boundaries within the Echinostomatidae (s. str.), Psilostomidae and Fasciolidae are made. Copyright © 2015 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Insights from Zootaxa on potential trends in zoological taxonomic activity

PubMed Central

2011-01-01

Background An opinion currently shared by taxonomists and non taxonomists alike is that the work of inventorying biodiversity is unbalanced: firstly, in favour of countries in which taxonomy has been studied for a long time, and, secondly, in favour of vertebrates. In the current context of threats of species extinction, access for taxonomists to biological material and information becomes crucial if the scientific community really aims at a better knowledge of biological diversity before it is severely and irreversibly impoverished. We performed an analysis of 748 papers published in Zootaxa in 2006 and 2007, as well as 434 questionnaires sent to their authors to test these opinions. A generalization of these results to zoological taxonomy as a whole is discussed. Discussion We found that the disequilibrium is not exactly what it usually considered to be. The USA, China and Brazil are currently the three leading countries in zoological taxonomy. Each of them presents, however, a different pattern. Taxonomists from Asia and South America are younger and mainly work in universities, not museums. A bias in favour of vertebrates still exists if we refer to the effort invested in each group to produce taxonomic data, but not to the number of papers. Finally, we insist on the idea that "describing a species" is very different from "knowing a species". Summary The taxonomic involvement of a country, in terms of manpower and funding, appears to be a key factor in the development of fruitful taxonomic research. This message seems to have been understood by the countries that recently decided to increase considerably their taxonomic involvement. It still has to be received by those who did not. PMID:21418568

Genomics dataset on unclassified published organism (patent US 7547531).

PubMed

Khan Shawan, Mohammad Mahfuz Ali; Hasan, Md Ashraful; Hossain, Md Mozammel; Hasan, Md Mahmudul; Parvin, Afroza; Akter, Salina; Uddin, Kazi Rasel; Banik, Subrata; Morshed, Mahbubul; Rahman, Md Nazibur; Rahman, S M Badier

2016-12-01

Nucleotide (DNA) sequence analysis provides important clues regarding the characteristics and taxonomic position of an organism. With the intention that, DNA sequence analysis is very crucial to learn about hierarchical classification of that particular organism. This dataset (patent US 7547531) is chosen to simplify all the complex raw data buried in undisclosed DNA sequences which help to open doors for new collaborations. In this data, a total of 48 unidentified DNA sequences from patent US 7547531 were selected and their complete sequences were retrieved from NCBI BioSample database. Quick response (QR) code of those DNA sequences was constructed by DNA BarID tool. QR code is useful for the identification and comparison of isolates with other organisms. AT/GC content of the DNA sequences was determined using ENDMEMO GC Content Calculator, which indicates their stability at different temperature. The highest GC content was observed in GP445188 (62.5%) which was followed by GP445198 (61.8%) and GP445189 (59.44%), while lowest was in GP445178 (24.39%). In addition, New England BioLabs (NEB) database was used to identify cleavage code indicating the 5, 3 and blunt end and enzyme code indicating the methylation site of the DNA sequences was also shown. These data will be helpful for the construction of the organisms' hierarchical classification, determination of their phylogenetic and taxonomic position and revelation of their molecular characteristics.

MetaStorm: A Public Resource for Customizable Metagenomics Annotation

PubMed Central

Arango-Argoty, Gustavo; Singh, Gargi; Heath, Lenwood S.; Pruden, Amy; Xiao, Weidong; Zhang, Liqing

2016-01-01

Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/), which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution. PMID:27632579

MetaStorm: A Public Resource for Customizable Metagenomics Annotation.

PubMed

Arango-Argoty, Gustavo; Singh, Gargi; Heath, Lenwood S; Pruden, Amy; Xiao, Weidong; Zhang, Liqing

2016-01-01

Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/), which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution.

Potentials of macroalgae as feedstocks for biorefinery.

PubMed

Jung, Kyung A; Lim, Seong-Rin; Kim, Yoori; Park, Jong Moon

2013-05-01

Macroalgae, so-called seaweeds, have recently attracted attention as a possible feedstock for biorefinery. Since macroalgae contain various carbohydrates (which are distinctively different from those of terrestrial biomasses), thorough assessments of macroalgae-based refinery are essential to determine whether applying terrestrial-based technologies to macroalgae or developing completely new technologies is feasible. This comprehensive review was performed to show the potentials of macroalgae as biorefinery feedstocks. Their basic background information was introduced: taxonomical classification, habitat environment, and carbon reserve capacity. Their global production status showed that macroalgae can be mass-cultivated with currently available farming technology. Their various carbohydrate compositions implied that new microorganisms are needed to effectively saccharify macroalgal biomass. Up-to-date macroalgae conversion technologies for biochemicals and biofuels showed that molecular bioengineering would contribute to the success of macroalgae-based biorefinery. It was concluded that more research is required for the utilization of macroalgae as a new promising biomass for low-carbon economy. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities.

PubMed

Mhuantong, Wuttichai; Charoensawan, Varodom; Kanokratana, Pattanop; Tangphatsornruang, Sithichoke; Champreda, Verawat

2015-01-01

As one of the most abundant agricultural wastes, sugarcane bagasse is largely under-exploited, but it possesses a great potential for the biofuel, fermentation, and cellulosic biorefinery industries. It also provides a unique ecological niche, as the microbes in this lignocellulose-rich environment thrive in relatively high temperatures (50°C) with varying microenvironments of aerobic surface to anoxic interior. The microbial community in bagasse thus presents a good resource for the discovery and characterization of new biomass-degrading enzymes; however, it remains largely unexplored. We have constructed a fosmid library of sugarcane bagasse and obtained the largest bagasse metagenome to date. A taxonomic classification of the bagasse metagenome reviews the predominance of Proteobacteria, which are also found in high abundance in other aerobic environments. Based on the functional characterization of biomass-degrading enzymes, we have demonstrated that the bagasse microbial community benefits from a large repertoire of lignocellulolytic enzymes, which allows them to digest different components of lignocelluoses into single molecule sugars. Comparative genomic analyses with other lignocellulolytic and non-lignocellulolytic metagenomes show that microbial communities are taxonomically separable by their aerobic "open" or anoxic "closed" environments. Importantly, a functional analysis of lignocellulose-active genes (based on the CAZy classifications) reveals core enzymes highly conserved within the lignocellulolytic group, regardless of their taxonomic compositions. Cellulases, in particular, are markedly more pronounced compared to the non-lignocellulolytic group. In addition to the core enzymes, the bagasse fosmid library also contains some uniquely enriched glycoside hydrolases, as well as a large repertoire of the newly defined auxiliary activity proteins. Our study demonstrates a conservation and diversification of carbohydrate-active genes among diverse microbial species in different biomass-degrading niches, and signifies the importance of taking a global approach to functionally investigate a microbial community as a whole, as compared to focusing on individual organisms.

Bamboo tea: reduction of taxonomic complexity and application of DNA diagnostics based on rbcL and matK sequence data

PubMed Central

Häser, Annette

2016-01-01

Background Names used in ingredient lists of food products are trivial and in their nature rarely precise. The most recent scientific interpretation of the term bamboo (Bambusoideae, Poaceae) comprises over 1,600 distinct species. In the European Union only few of these exotic species are well known sources for food ingredients (i.e., bamboo sprouts) and are thus not considered novel foods, which would require safety assessments before marketing of corresponding products. In contrast, the use of bamboo leaves and their taxonomic origin is mostly unclear. However, products containing bamboo leaves are currently marketed. Methods We analysed bamboo species and tea products containing bamboo leaves using anatomical leaf characters and DNA sequence data. To reduce taxonomic complexity associated with the term bamboo, we used a phylogenetic framework to trace the origin of DNA from commercially available bamboo leaves within the bambusoid subfamily. For authentication purposes, we introduced a simple PCR based test distinguishing genuine bamboo from other leaf components and assessed the diagnostic potential of rbcL and matK to resolve taxonomic entities within the bamboo subfamily and tribes. Results Based on anatomical and DNA data we were able to trace the taxonomic origin of bamboo leaves used in products to the genera Phyllostachys and Pseudosasa from the temperate “woody” bamboo tribe (Arundinarieae). Currently available rbcL and matK sequence data allow the character based diagnosis of 80% of represented bamboo genera. We detected adulteration by carnation in four of eight tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant to Dianthus chinensis (Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women. PMID:27957401

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.

Epicuticular chemistry reinforces the new taxonomic classification of the Bactrocera dorsalis species complex (Diptera: Tephritidae, Dacinae).

PubMed

Vaníčková, Lucie; Nagy, Radka; Pompeiano, Antonio; Kalinová, Blanka

2017-01-01

Bactrocera invadens Drew, Tsuruta & White, Bactrocera papayae Drew & Hancock, and Bactrocera philippinensis Drew & Hancock, key pest species within the Bactrocera dorsalis species complex, have been recently synonymized under the name Bactrocera dorsalis (Hendel). The closely related Bactrocera carambolae Drew & Hancock remains as a discrete taxonomic entity. Although the synonymizations have been accepted by most researchers, debate about the species limits remains. Because of the economic importance of this group of taxa, any new information available to support or deny the synonymizations is valuable. We investigated the chemical epicuticle composition of males and females of B. dorsalis, B. invadens, B. papayae, B. philippinensis, and B. carambolae by means of one- and two-dimensional gas chromatography-mass spectrometry, followed by multiple factor analyses and principal component analysis. Clear segregation of complex cuticule profiles of both B. carambolae sexes from B. dorsalis (Hendel) was observed. In addition to cuticular hydrocarbons, abundant complex mixtures of sex-specific oxygenated lipids (three fatty acids and 22 fatty acid esters) with so far unknown function were identified in epicuticle extracts from females of all species. The data obtained supports both taxonomic synonymization of B. invadens, B. papayae, and B. philippinensis with B. dorsalis, as well as the exclusion of B. carambolae from B. dorsalis.

Epicuticular chemistry reinforces the new taxonomic classification of the Bactrocera dorsalis species complex (Diptera: Tephritidae, Dacinae)

PubMed Central

Vaníčková, Lucie; Nagy, Radka; Pompeiano, Antonio

2017-01-01

Bactrocera invadens Drew, Tsuruta & White, Bactrocera papayae Drew & Hancock, and Bactrocera philippinensis Drew & Hancock, key pest species within the Bactrocera dorsalis species complex, have been recently synonymized under the name Bactrocera dorsalis (Hendel). The closely related Bactrocera carambolae Drew & Hancock remains as a discrete taxonomic entity. Although the synonymizations have been accepted by most researchers, debate about the species limits remains. Because of the economic importance of this group of taxa, any new information available to support or deny the synonymizations is valuable. We investigated the chemical epicuticle composition of males and females of B. dorsalis, B. invadens, B. papayae, B. philippinensis, and B. carambolae by means of one- and two-dimensional gas chromatography–mass spectrometry, followed by multiple factor analyses and principal component analysis. Clear segregation of complex cuticule profiles of both B. carambolae sexes from B. dorsalis (Hendel) was observed. In addition to cuticular hydrocarbons, abundant complex mixtures of sex-specific oxygenated lipids (three fatty acids and 22 fatty acid esters) with so far unknown function were identified in epicuticle extracts from females of all species. The data obtained supports both taxonomic synonymization of B. invadens, B. papayae, and B. philippinensis with B. dorsalis, as well as the exclusion of B. carambolae from B. dorsalis. PMID:28873446

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

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets.

PubMed

Scheuch, Matthias; Höper, Dirk; Beer, Martin

2015-03-03

Fuelled by the advent and subsequent development of next generation sequencing technologies, metagenomics became a powerful tool for the analysis of microbial communities both scientifically and diagnostically. The biggest challenge is the extraction of relevant information from the huge sequence datasets generated for metagenomics studies. Although a plethora of tools are available, data analysis is still a bottleneck. To overcome the bottleneck of data analysis, we developed an automated computational workflow called RIEMS - Reliable Information Extraction from Metagenomic Sequence datasets. RIEMS assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications. After completion of the analyses, the results are summarised in a clearly structured result protocol organised taxonomically. The high accuracy and performance of RIEMS analyses were proven in comparison with other tools for metagenomics data analysis using simulated sequencing read datasets. RIEMS has the potential to fill the gap that still exists with regard to data analysis for metagenomics studies. The usefulness and power of RIEMS for the analysis of genuine sequencing datasets was demonstrated with an early version of RIEMS in 2011 when it was used to detect the orthobunyavirus sequences leading to the discovery of Schmallenberg virus.

Networks of plants: how to measure similarity in vegetable species.

PubMed

Vivaldo, Gianna; Masi, Elisa; Pandolfi, Camilla; Mancuso, Stefano; Caldarelli, Guido

2016-06-07

Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome similar problems and to exploit possibilities from environment. In this paper we introduce various quantitative measures based on recent advancements in complex network theory that allow to measure the effective similarities of various species. By using this approach on the similarity in fruit-typology ecological traits we obtain a clear plant classification in a way similar to traditional taxonomic classification. This result is not trivial, since a similar analysis done on the basis of diaspore morphological properties do not provide any clear parameter to classify plants species. Complex network theory can then be used in order to determine which feature amongst many can be used to distinguish scope and possibly evolution of plants. Future uses of this approach range from functional classification to quantitative determination of plant communities in nature.

Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda.

PubMed

Wu, Shu; Xiong, Jie; Yu, Yuhe

2015-01-01

Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.

Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda

PubMed Central

Wu, Shu; Xiong, Jie; Yu, Yuhe

2015-01-01

Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1–9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy. PMID:26107258

Chemodiversity of the Essential Oil from Leaves of Abies nebrodensis (Lojac.) Mattei.

PubMed

Schicchi, Rosario; Geraci, Anna; Rosselli, Sergio; Maggio, Antonella; Bruno, Maurizio

2017-02-01

Abies nebrodensis (Lojac.) Mattei (Pinaceae) is a species occurring in a very small population only in a restricted area of Sicily. Its taxonomic classification as different species has been object of discussion. In this work the chemical composition of the essential oil from the leaves is presented for the first time and compared to the essential oils from other euroasiatic species reported in literature. Peculiar characteristics of the essential oil of A. nebrodensis are highlighted. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Permanent draft genome of the malachite-green-tolerant bacterium Rhizobium sp. MGL06.

PubMed

Liu, Yang; Wang, Runping; Zeng, Runying

2014-12-01

Rhizobium sp. MGL06, the first Rhizobium isolate from a marine environment, is a malachite-green-tolerant bacterium with a broader salinity tolerance (range: 0.5% to 9%) than other rhizobia. This study sequences and annotates the draft genome sequence of this strain. Genome sequence information provides a basis for analyzing the malachite green tolerance, broad salinity adaptation, nitrogen fixation properties, and taxonomic classification of the isolate. Copyright © 2014 Elsevier B.V. All rights reserved.

Zur Biosynthese von Phenylalanin und Tyrosin

NASA Astrophysics Data System (ADS)

Lingens, F.; Keller, E.

1983-03-01

With the discovery of arogenic acid two new pathways for the biosynthesis of phenylalanine and tyrosine have been revealed. The occurrence of two, three, or four pathways for the biosynthesis of phenylalanine and tyrosine in microorganisms and plants may be a useful tool for taxonomic classifications. Investigations on enterobacteriaceae, pseudomonads, flavobacteria, streptomycetes, archaebacteria, and on Sphaerotilus, Trichococcus and Leptothrix species from bulking sludge are described. The possible role of arogenate in the evolution of the pathways for tyrosine and phenylalanine biosynthesis is discussed.

Genus-level taxonomic changes implied by the mitochondrial phylogeny of grey mullets (Teleostei: Mugilidae).

PubMed

Durand, Jean-Dominique; Chen, Wei-Jen; Shen, Kang-Ning; Fu, Cuizhang; Borsa, Philippe

2012-01-01

A comprehensive mitochondrial phylogeny of the family Mugilidae (Durand et al., Mol. Phylogenet. Evol. 64 (2012) 73-92) demonstrated the polyphyly or paraphyly of a proportion of the 20 genera in the family. Based on these results, here we propose a revised classification with 25 genera, including 15 genera currently recognized as valid (Agonostomus, Aldrichetta, Cestraeus, Chaenomugil, Chelon, Crenimugil, Ellochelon, Joturus, Mugil, Myxus, Neomyxus, Oedalechilus, Rhinomugil, Sicamugil and Trachystoma), 7 resurrected genera [Dajaus (for Agonostomus monticola), Gracilimugil (for Liza argentea), Minimugil (for Sicamugil cascasia), Osteomugil (for several species currently under Moolgarda and Valamugil, including M. cunnesius, M. engeli, M. perusii, and V. robustus), Planiliza (for Indo-Pacific Chelon spp., Indo-Pacific Liza spp., and Paramugil parmatus), Plicomugil (for Oedalechilus labiosus), and Squalomugil (for Rhinomugil nasutus)] and 3 new genera: Neochelon gen. nov. (for Liza falcipinnis), Parachelon gen. nov. (for L. grandisquamis) and Pseudomyxus gen. nov. (for Myxus capensis). Genus Chelon was shown to include exclusively Chelon spp. and Liza spp. from the Atlantic and the Mediterranean, and Liza spp. species endemic to eastern southern Africa. Genus Crenimugil should now include C. crenilabis, Moolgarda seheli and V. buchanani. Genus names Liza, Moolgarda, Paramugil, Valamugil and Xenomugil should be abandoned because they are no longer valid. Further genetic evidence is required to confirm or infirm the validity of the genus Paracrenimugil Senou 1988. The mitochondrial phylogeny of the 25 genera from the present revision is the following: [(Sicamugil, (Minimugil, Rhinomugil)); Trachystoma; ((Myxus, Neomyxus), (Cestraeus, Chaenomugil, (Agonostomus, Dajaus, Joturus), Mugil)); (Aldrichetta, Gracilimugil); Neochelon gen. nov.; (Pseudomyxus gen. nov., (Chelon, Oedalechilus, Planiliza, Parachelon gen. nov.)); ((Squalomugil, (Ellochelon, Plicomugil)), (Crenimugil, Osteomugil))]. Agonostomus monticola and several species with large distribution ranges (including Moolgarda seheli, Mugil cephalus and M. curema) consist of separate lineages whose geographic distribution suggests they are cryptic species, thus warranting further taxonomic work in the Mugilidae at the infra-generic level. Copyright © 2012 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Prediction and Confirmation of V-type Asteroids Beyond 2.5 AU Based on SDSS Colors

NASA Astrophysics Data System (ADS)

Binzel, Richard P.; Masi, G.; Foglia, S.

2006-09-01

We apply a taxonomic classification system developed by Masi et al. (2006, submitted to Icarus) to identify C-, S-, and V-type asteroids present within the 3rd Release of the Sloan Digital Sky Survey Moving Object Catalog (SDSS MOC3). The classifications deduced by Masi et al. for 43,000 asteroids using SDSS colors are based on the taxonomy of Bus (1999; MIT Ph.D. thesis). To link SDSS colors to the Bus taxonomy, Masi et al. (2006) use 149 objects measured in common by both SDSS and the Small Main-Belt Asteroid Spectroscopic Survey (SMASS) (Bus and Binzel 2002, Icarus 158, 106). We report results of direct testing of SDSS V-type classification predictions for six objects, where the tests were performed by visible wavelength spectroscopy (Lazzaro et al. 2004, Icarus 172, 179) and target of opportunity near-infrared spectroscopy obtained using the NASA Infrared Telescope Facility (IRTF). Vesta-like spectra and a V-type taxonomy are confirmed for five of the six predicted V-type objects sampled. Most interestingly, the SDSS taxonomy correctly predicted the V-type spectral characteristics for asteroid (21238) 1995 WV7, a 6 km asteroid located far from Vesta across the 3:1 mean motion resonance at 2.54 AU. (Proper elements a,e,i: 2.54 AU, 0.14, and 10.8 deg.) Given the 2 km/sec ejection velocity required from Vesta to reach the current orbit, and the difficulty of migrating across the 3:1 resonance (at 2.5 AU) by a process such as Yarkovsky drift or via secular resonances (Carruba et al. 2005, Astron. Astrophys. 441, 819), asteroid 21238 may be a new candidate for a basaltic asteroid having no relationship to Vesta.

Sponge systematics facing new challenges.

PubMed

Cárdenas, P; Pérez, T; Boury-Esnault, N

2012-01-01

Systematics is nowadays facing new challenges with the introduction of new concepts and new techniques. Compared to most other phyla, phylogenetic relationships among sponges are still largely unresolved. In the past 10 years, the classical taxonomy has been completely overturned and a review of the state of the art appears necessary. The field of taxonomy remains a prominent discipline of sponge research and studies related to sponge systematics were in greater number in the Eighth World Sponge Conference (Girona, Spain, September 2010) than in any previous world sponge conferences. To understand the state of this rapidly growing field, this chapter proposes to review studies, mainly from the past decade, in sponge taxonomy, nomenclature and phylogeny. In a first part, we analyse the reasons of the current success of this field. In a second part, we establish the current sponge systematics theoretical framework, with the use of (1) cladistics, (2) different codes of nomenclature (PhyloCode vs. Linnaean system) and (3) integrative taxonomy. Sponges are infamous for their lack of characters. However, by listing and discussing in a third part all characters available to taxonomists, we show how diverse characters are and that new ones are being used and tested, while old ones should be revisited. We then review the systematics of the four main classes of sponges (Hexactinellida, Calcispongiae, Homoscleromorpha and Demospongiae), each time focusing on current issues and case studies. We present a review of the taxonomic changes since the publication of the Systema Porifera (2002), and point to problems a sponge taxonomist is still faced with nowadays. To conclude, we make a series of proposals for the future of sponge systematics. In the light of recent studies, we establish a series of taxonomic changes that the sponge community may be ready to accept. We also propose a series of sponge new names and definitions following the PhyloCode. The issue of phantom species (potential new species revealed by molecular studies) is raised, and we show how they could be dealt with. Finally, we present a general strategy to help us succeed in building a Porifera tree along with the corresponding revised Porifera classification. Copyright © 2012 Elsevier Ltd. All rights reserved.

Making species checklists understandable to machines - a shift from relational databases to ontologies.

PubMed

Laurenne, Nina; Tuominen, Jouni; Saarenmaa, Hannu; Hyvönen, Eero

2014-01-01

The scientific names of plants and animals play a major role in Life Sciences as information is indexed, integrated, and searched using scientific names. The main problem with names is their ambiguous nature, because more than one name may point to the same taxon and multiple taxa may share the same name. In addition, scientific names change over time, which makes them open to various interpretations. Applying machine-understandable semantics to these names enables efficient processing of biological content in information systems. The first step is to use unique persistent identifiers instead of name strings when referring to taxa. The most commonly used identifiers are Life Science Identifiers (LSID), which are traditionally used in relational databases, and more recently HTTP URIs, which are applied on the Semantic Web by Linked Data applications. We introduce two models for expressing taxonomic information in the form of species checklists. First, we show how species checklists are presented in a relational database system using LSIDs. Then, in order to gain a more detailed representation of taxonomic information, we introduce meta-ontology TaxMeOn to model the same content as Semantic Web ontologies where taxa are identified using HTTP URIs. We also explore how changes in scientific names can be managed over time. The use of HTTP URIs is preferable for presenting the taxonomic information of species checklists. An HTTP URI identifies a taxon and operates as a web address from which additional information about the taxon can be located, unlike LSID. This enables the integration of biological data from different sources on the web using Linked Data principles and prevents the formation of information silos. The Linked Data approach allows a user to assemble information and evaluate the complexity of taxonomical data based on conflicting views of taxonomic classifications. Using HTTP URIs and Semantic Web technologies also facilitate the representation of the semantics of biological data, and in this way, the creation of more "intelligent" biological applications and services.

Classification of Pelteobagrus fish in Poyang Lake based on mitochondrial COI gene sequence.

PubMed

Zhong, Bin; Chen, Ting-Ting; Gong, Rui-Yue; Zhao, Zhe-Xia; Wang, Binhua; Fang, Chunlin; Mao, Hui-Ling

2016-11-01

We use DNA molecular marker technology to correct the deficiency of traditional morphological taxonomy. Totality 770 Pelteobagrus fish from Poyang Lake were collected. After preliminary morphological classification, random selected eight samples in each species for DNA extraction. Mitochondrial COI gene sequence was cloned with universal primers and sequenced. The results showed that there are four species of Pelteobagrus living in Poyang Lake. The average of intraspecific genetic distance value was 0.003, while the average interspecific genetic distance was 0.128. The interspecific genetic distance is far more than intraspecific genetic distance. Besides, phylogenetic tree analysis revealed that molecular systematics was in accord with morphological classification. It indicated that COI gene is an effective DNA molecular marker in Pelteobagrus classification. Surprisingly, the intraspecific difference of some individuals (P. e6, P. n6, P. e5, and P. v4) from their original named exceeded species threshold (2%), which should be renewedly classified into Pelteobagrus fulvidraco. However, another individual P. v3 was very different, because its genetic distance was over 8.4% difference from original named Pelteobagrus vachelli. Its taxonomic status remained to be further studied.

Expanding the World of Marine Bacterial and Archaeal Clades

PubMed Central

Yilmaz, Pelin; Yarza, Pablo; Rapp, Josephine Z.; Glöckner, Frank O.

2016-01-01

Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies. PMID:26779174

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

Ruvindy, Rendy; White III, Richard Allen; Neilan, Brett Anthony

Modern microbial mats are potential analogues of some of Earth’s earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic nextgeneration sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marinemore » mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.« less

Taxonomic and phytogeographic implications from ITS phylogeny in Berberis (Berberidaceae).

PubMed

Kim, Young-Dong; Kim, Sung-Hee; Landrum, Leslie R

2004-06-01

A phylogeny based on the internal transcribed spacer (ITS) sequences from 79 taxa representing much of the diversity of Berberis L. (four major groups and 22 sections) was constructed for the first time. The phylogeny was basically congruent with the previous classification schemes at higher taxonomic levels, such as groups and subgroups. A notable exception is the non-monophyly of the group Occidentales of compound-leaved Berberis (previously separated as Mahonia). At lower levels, however, most of previous sections and subsections were not evident especially in simple-leaved Berberis. Possible relationship between section Horridae (group Occidentales) and the simple-leaved Berberis clade implies paraphyly of the compound-leaved Berberis. A well-known South America-Old World (mainly Asia) disjunctive distribution pattern of the simple-leaved Berberis is explained by a vicariance event occurring in the Cretaceous period. The ITS phylogeny also suggests that a possible connection between the Asian and South American groups through the North American species ( Berberis canadensis or B. fendleri) is highly unlikely.

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.

Revised taxonomy and nomenclature of rodent Pasteurellaceae: Implications for monitoring.

PubMed

Boot, R; Nicklas, W; Christensen, H

2018-01-01

Pasteurellosis is a well-recognized disease with similar pathology in all laboratory rodent species. Pasteurella pneumotropica is the most frequently mentioned member of the Pasteurellaceae isolated from mice and rats. Numerous other Pasteurellaceae taxa have been obtained from mice, rats, and other rodent species. Recently, rodent Pasteurellaceae have been submitted to comprehensive genetic and phenotypic (polyphasic) taxonomic studies. As a result they are now classed within six validly published new genera, namely Cricetibacter, Mesocricetibacter, Mannheimia, Muribacter, Necropsobacter, and Rodentibacter. All previously used names such as P. pneumotropica have become obsolete. The new classification forms a firm basis for the correct phenotypic identification of Pasteurellaceae from laboratory animals and for the selection of strains for pathogenicity studies. Consequences of taxonomic changes notably involve molecular methods used for the detection of Pasteurellaceae infection in laboratory animal colonies. Testing may be done using primer sets that detect all Pasteurellaceae taxa or sets developed to detect host-specific members of the family.

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.

PubMed

Fosso, Bruno; Santamaria, Monica; Marzano, Marinella; Alonso-Alemany, Daniel; Valiente, Gabriel; Donvito, Giacinto; Monaco, Alfonso; Notarangelo, Pasquale; Pesole, Graziano

2015-07-01

Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects. BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data). BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent the currently known bacterial and fungal world, showed that BioMaS outperforms QIIME and MOTHUR in terms of extent and accuracy of deep taxonomic sequence assignments.

A multi-gene phylogeny of Chlorophyllum (Agaricaceae, Basidiomycota): new species, new combination and infrageneric classification

PubMed Central

Ge, Zai-Wei; Jacobs, Adriaana; Vellinga, Else C.; Sysouphanthong, Phongeun; van der Walt, Retha; Lavorato, Carmine; An, Yi-Feng; Yang, Zhu L.

2018-01-01

Abstract Taxonomic and phylogenetic studies of Chlorophyllum were carried out on the basis of morphological differences and molecular phylogenetic analyses. Based on the phylogeny inferred from the internal transcribed spacer (ITS), the partial large subunit nuclear ribosomal DNA (nrLSU), the second largest subunit of RNA polymerase II (rpb2) and translation elongation factor 1-α (tef1) sequences, six well-supported clades and 17 phylogenetic species are recognised. Within this phylogenetic framework and considering the diagnostic morphological characters, two new species, C. africanum and C. palaeotropicum, are described. In addition, a new infrageneric classification of Chlorophyllum is proposed, in which the genus is divided into six sections. One new combination is also made. This study provides a robust basis for a more detailed investigation of diversity and biogeography of Chlorophyllum. PMID:29681738

Taxonomic uncertainty and the loss of biodiversity on Christmas Island, Indian Ocean.

PubMed

Eldridge, Mark D B; Meek, Paul D; Johnson, Rebecca N

2014-04-01

The taxonomic uniqueness of island populations is often uncertain which hinders effective prioritization for conservation. The Christmas Island shrew (Crocidura attenuata trichura) is the only member of the highly speciose eutherian family Soricidae recorded from Australia. It is currently classified as a subspecies of the Asian gray or long-tailed shrew (C. attenuata), although it was originally described as a subspecies of the southeast Asian white-toothed shrew (C. fuliginosa). The Christmas Island shrew is currently listed as endangered and has not been recorded in the wild since 1984-1985, when 2 specimens were collected after an 80-year absence. We aimed to obtain DNA sequence data for cytochrome b (cytb) from Christmas Island shrew museum specimens to determine their taxonomic affinities and to confirm the identity of the 1980s specimens. The Cytb sequences from 5, 1898 specimens and a 1985 specimen were identical. In addition, the Christmas Island shrew cytb sequence was divergent at the species level from all available Crocidura cytb sequences. Rather than a population of a widespread species, current evidence suggests the Christmas Island shrew is a critically endangered endemic species, C. trichura, and a high priority for conservation. As the decisions typically required to save declining species can be delayed or deferred if the taxonomic status of the population in question is uncertain, it is hoped that the history of the Christmas Island shrew will encourage the clarification of taxonomy to be seen as an important first step in initiating informed and effective conservation action. © 2013 Society for Conservation Biology.

Forty-first supplement to the American Ornithologists' Union Check-list of North American birds

USGS Publications Warehouse

Banks, R.C.; Fitzpatrick, J.W.; Howell, T.R.; Johnson, N.K.; Monroe, B.L.; Ouellet, H.; Remsen, J.V.; Storer, R.W.

1997-01-01

This seventh supplement after the publication of the 6th edition (1983) of the AOU Check-list of North American Birds includes taxonomic and nomenclatural changes adopted by the Committee on Classification and Nomenclature between 15 March 1995 and 15 March 1997. Because this will be the last supplement before the publication of the 7th edition of the Check-list, it also summarizes other decisions made by the Committee since 1983 that were not intended to affect the 6th edition but rather were to lay the foundation for its successor. Most of those decisions relate to sequence or rank of certain taxonomic categories. The Committee believes that compendia such as the Check-list are not appropriate places for the first appearance of novel taxonomic treatments or rearrangements. Therefore, we take the opportunity of this supplement to inform you of the ways in which the 7th edition will differ from the 6th. The style of this supplement differs from that of the previous six because they were designed to provide detailed changes to the text in the 6th edition; this one also is to provide information on how the 7th edition will differ from the 6th. Many details on reasons for the change will be discussed in the Preface or text of the new volume.

Palyno-morphological characteristics of gymnosperm flora of pakistan and its taxonomic implications with LM and SEM methods.

PubMed

Khan, Raees; Ul Abidin, Sheikh Zain; Ahmad, Mushtaq; Zafar, Muhammad; Liu, Jie; Amina, Hafiza

2018-01-01

The present study is intended to assess gymnosperms pollen flora of Pakistan using Light Microscope (LM) and Scanning Electron Microscopy (SEM) for its taxonomic significance in identification of gymnosperms. Pollens of 35 gymnosperm species (12 genera and five families) were collected from its various distributional sites of gymnosperms in Pakistan. LM and SEM were used to investigate different palyno-morphological characteristics. Five pollen types (i.e., Inaperturate, Monolete, Monoporate, Vesiculate-bisaccate and Polyplicate) were observed. Six In equatorial view seven types of pollens were observed, in which ten species were sub-angular, nine species were Traingular, six species were Perprolate, three species were Rhomboidal, three species were semi-angular, two species were rectangular and two species were prolate. While five types of pollen were observed in polar view, in which ten species were Spheroidal, nine species were Angular, eight were Interlobate, six species were Circular, two species were Elliptic. Eighteen species has rugulate and 17 species has faveolate ornamentation. Eighteen species has verrucate and 17 have gemmate type sculpturing. The data was analysed through cluster analysis. The study showed that these palyno-morphological features have significance value in classification and identification of gymnosperms. Based on these different palyno-morphological features, a taxonomic key was proposed for the accurate and fast identifications of gymnosperms from Pakistan. © 2017 Wiley Periodicals, Inc.

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.

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.

PubMed

Rodriguez-R, Luis M; Gunturu, Santosh; Harvey, William T; Rosselló-Mora, Ramon; Tiedje, James M; Cole, James R; Konstantinidis, Konstantinos T

2018-06-14

The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts. MiGA integrates best practices in sequence quality trimming and assembly and allows input to be raw reads or assemblies from isolate genomes, single-cell sequences, and metagenome-assembled genomes (MAGs). Further, MiGA can take as input hundreds of closely related genomes of the same or closely related species (a so-called 'Clade Project') to assess their gene content diversity and evolutionary relationships, and calculate important clade properties such as the pangenome and core gene sets. Therefore, MiGA is expected to facilitate a range of genome-based taxonomic and diversity studies, and quality assessment across environmental and clinical settings. MiGA is available at http://microbial-genomes.org/.

A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data

PubMed Central

Spring, Stefan; Scheuner, Carmen; Göker, Markus; Klenk, Hans-Peter

2015-01-01

In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov. PMID:25914684

What Is Peromyscus? Evidence from nuclear and mitochondrial DNA sequences suggests the need for a new classification

PubMed Central

Platt, Roy N.; Amman, Brian R.; Keith, Megan S.; Thompson, Cody W.; Bradley, Robert D.

2015-01-01

The evolutionary relationships between Peromyscus, Habromys, Isthmomys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are poorly understood. In order to further explore the evolutionary boundaries of Peromyscus and compare potential taxonomic solutions for this diverse group and its relatives, we conducted phylogenetic analyses of DNA sequence data from alcohol dehydrogenase (Adh1-I2), beta fibrinogen (Fgb-I7), interphotoreceptor retinoid-binding protein (Rbp3), and cytochrome-b (Cytb). Phylogenetic analyses of mitochondrial and nuclear genes produced similar topologies although levels of nodal support varied. The best-supported topology was obtained by combining nuclear and mitochondrial sequences. No monophyletic Peromyscus clade was supported. Instead, support was found for a clade containing Habromys, Megadontomys, Neotomodon, Osgoodomys, Podomys, and Peromyscus suggesting paraphyly of Peromyscus and confirming previous observations. Our analyses indicated an early divergence of Isthmomys from Peromyscus (approximately 8 million years ago), whereas most other peromyscine taxa emerged within the last 6 million years. To recover a monophyletic taxonomy from Peromyscus and affiliated lineages, we detail 3 taxonomic options in which Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are retained as genera, subsumed as subgenera, or subsumed as species groups within Peromyscus. Each option presents distinct taxonomic challenges, and the appropriate taxonomy must reflect the substantial levels of morphological divergence that characterize this group while maintaining the monophyletic relationships obtained from genetic data. PMID:26937047

What Is Peromyscus? Evidence from nuclear and mitochondrial DNA sequences suggests the need for a new classification.

PubMed

Platt, Roy N; Amman, Brian R; Keith, Megan S; Thompson, Cody W; Bradley, Robert D

2015-08-03

The evolutionary relationships between Peromyscus , Habromys , Isthmomys , Megadontomys , Neotomodon , Osgoodomys , and Podomys are poorly understood. In order to further explore the evolutionary boundaries of Peromyscus and compare potential taxonomic solutions for this diverse group and its relatives, we conducted phylogenetic analyses of DNA sequence data from alcohol dehydrogenase ( Adh 1-I2), beta fibrinogen ( Fgb -I7), interphotoreceptor retinoid-binding protein ( Rbp 3), and cytochrome- b ( Cytb ). Phylogenetic analyses of mitochondrial and nuclear genes produced similar topologies although levels of nodal support varied. The best-supported topology was obtained by combining nuclear and mitochondrial sequences. No monophyletic Peromyscus clade was supported. Instead, support was found for a clade containing Habromys , Megadontomys , Neotomodon , Osgoodomys , Podomys , and Peromyscus suggesting paraphyly of Peromyscus and confirming previous observations. Our analyses indicated an early divergence of Isthmomys from Peromyscus (approximately 8 million years ago), whereas most other peromyscine taxa emerged within the last 6 million years. To recover a monophyletic taxonomy from Peromyscus and affiliated lineages, we detail 3 taxonomic options in which Habromys , Megadontomys , Neotomodon , Osgoodomys , and Podomys are retained as genera, subsumed as subgenera, or subsumed as species groups within Peromyscus . Each option presents distinct taxonomic challenges, and the appropriate taxonomy must reflect the substantial levels of morphological divergence that characterize this group while maintaining the monophyletic relationships obtained from genetic data.

Automated classifications of topography from DEMs by an unsupervised nested-means algorithm and a three-part geometric signature

NASA Astrophysics Data System (ADS)

Iwahashi, Junko; Pike, Richard J.

2007-05-01

An iterative procedure that implements the classification of continuous topography as a problem in digital image-processing automatically divides an area into categories of surface form; three taxonomic criteria-slope gradient, local convexity, and surface texture-are calculated from a square-grid digital elevation model (DEM). The sequence of programmed operations combines twofold-partitioned maps of the three variables converted to greyscale images, using the mean of each variable as the dividing threshold. To subdivide increasingly subtle topography, grid cells sloping at less than mean gradient of the input DEM are classified by designating mean values of successively lower-sloping subsets of the study area (nested means) as taxonomic thresholds, thereby increasing the number of output categories from the minimum 8 to 12 or 16. Program output is exemplified by 16 topographic types for the world at 1-km spatial resolution (SRTM30 data), the Japanese Islands at 270 m, and part of Hokkaido at 55 m. Because the procedure is unsupervised and reflects frequency distributions of the input variables rather than pre-set criteria, the resulting classes are undefined and must be calibrated empirically by subsequent analysis. Maps of the example classifications reflect physiographic regions, geological structure, and landform as well as slope materials and processes; fine-textured terrain categories tend to correlate with erosional topography or older surfaces, coarse-textured classes with areas of little dissection. In Japan the resulting classes approximate landform types mapped from airphoto analysis, while in the Americas they create map patterns resembling Hammond's terrain types or surface-form classes; SRTM30 output for the United States compares favorably with Fenneman's physical divisions. Experiments are suggested for further developing the method; the Arc/Info AML and the map of terrain classes for the world are available as online downloads.

Automated classifications of topography from DEMs by an unsupervised nested-means algorithm and a three-part geometric signature

USGS Publications Warehouse

Iwahashi, J.; Pike, R.J.

2007-01-01

An iterative procedure that implements the classification of continuous topography as a problem in digital image-processing automatically divides an area into categories of surface form; three taxonomic criteria-slope gradient, local convexity, and surface texture-are calculated from a square-grid digital elevation model (DEM). The sequence of programmed operations combines twofold-partitioned maps of the three variables converted to greyscale images, using the mean of each variable as the dividing threshold. To subdivide increasingly subtle topography, grid cells sloping at less than mean gradient of the input DEM are classified by designating mean values of successively lower-sloping subsets of the study area (nested means) as taxonomic thresholds, thereby increasing the number of output categories from the minimum 8 to 12 or 16. Program output is exemplified by 16 topographic types for the world at 1-km spatial resolution (SRTM30 data), the Japanese Islands at 270??m, and part of Hokkaido at 55??m. Because the procedure is unsupervised and reflects frequency distributions of the input variables rather than pre-set criteria, the resulting classes are undefined and must be calibrated empirically by subsequent analysis. Maps of the example classifications reflect physiographic regions, geological structure, and landform as well as slope materials and processes; fine-textured terrain categories tend to correlate with erosional topography or older surfaces, coarse-textured classes with areas of little dissection. In Japan the resulting classes approximate landform types mapped from airphoto analysis, while in the Americas they create map patterns resembling Hammond's terrain types or surface-form classes; SRTM30 output for the United States compares favorably with Fenneman's physical divisions. Experiments are suggested for further developing the method; the Arc/Info AML and the map of terrain classes for the world are available as online downloads. ?? 2006 Elsevier B.V. All rights reserved.

Metagenomics of an Alkaline Hot Spring in Galicia (Spain): Microbial Diversity Analysis and Screening for Novel Lipolytic Enzymes.

PubMed

López-López, Olalla; Knapik, Kamila; Cerdán, Maria-Esperanza; González-Siso, María-Isabel

2015-01-01

A fosmid library was constructed with the metagenomic DNA from the water of the Lobios hot spring (76°C, pH = 8.2) located in Ourense (Spain). Metagenomic sequencing of the fosmid library allowed the assembly of 9722 contigs ranging in size from 500 to 56,677 bp and spanning ~18 Mbp. 23,207 ORFs (Open Reading Frames) were predicted from the assembly. Biodiversity was explored by taxonomic classification and it revealed that bacteria were predominant, while the archaea were less abundant. The six most abundant bacterial phyla were Deinococcus-Thermus, Proteobacteria, Firmicutes, Acidobacteria, Aquificae, and Chloroflexi. Within the archaeal superkingdom, the phylum Thaumarchaeota was predominant with the dominant species "Candidatus Caldiarchaeum subterraneum." Functional classification revealed the genes associated to one-carbon metabolism as the most abundant. Both taxonomic and functional classifications showed a mixture of different microbial metabolic patterns: aerobic and anaerobic, chemoorganotrophic and chemolithotrophic, autotrophic and heterotrophic. Remarkably, the presence of genes encoding enzymes with potential biotechnological interest, such as xylanases, galactosidases, proteases, and lipases, was also revealed in the metagenomic library. Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. Six genes conferring lipolytic activity were identified and one was cloned and characterized. This gene was named LOB4Est and it was expressed in a yeast mesophilic host. LOB4Est codes for a novel esterase of family VIII, with sequence similarity to β-lactamases, but with unusual wide substrate specificity. When the enzyme was purified from the mesophilic host it showed half-life of 1 h and 43 min at 50°C, and maximal activity at 40°C and pH 7.5 with p-nitrophenyl-laurate as substrate. Interestingly, the enzyme retained more than 80% of maximal activity in a broad range of pH from 6.5 to 8.

A machine learning approach for viral genome classification.

PubMed

Remita, Mohamed Amine; Halioui, Ahmed; Malick Diouara, Abou Abdallah; Daigle, Bruno; Kiani, Golrokh; Diallo, Abdoulaye Baniré

2017-04-11

Advances in cloning and sequencing technology are yielding a massive number of viral genomes. The classification and annotation of these genomes constitute important assets in the discovery of genomic variability, taxonomic characteristics and disease mechanisms. Existing classification methods are often designed for specific well-studied family of viruses. Thus, the viral comparative genomic studies could benefit from more generic, fast and accurate tools for classifying and typing newly sequenced strains of diverse virus families. Here, we introduce a virus classification platform, CASTOR, based on machine learning methods. CASTOR is inspired by a well-known technique in molecular biology: restriction fragment length polymorphism (RFLP). It simulates, in silico, the restriction digestion of genomic material by different enzymes into fragments. It uses two metrics to construct feature vectors for machine learning algorithms in the classification step. We benchmark CASTOR for the classification of distinct datasets of human papillomaviruses (HPV), hepatitis B viruses (HBV) and human immunodeficiency viruses type 1 (HIV-1). Results reveal true positive rates of 99%, 99% and 98% for HPV Alpha species, HBV genotyping and HIV-1 M subtyping, respectively. Furthermore, CASTOR shows a competitive performance compared to well-known HIV-1 specific classifiers (REGA and COMET) on whole genomes and pol fragments. The performance of CASTOR, its genericity and robustness could permit to perform novel and accurate large scale virus studies. The CASTOR web platform provides an open access, collaborative and reproducible machine learning classifiers. CASTOR can be accessed at http://castor.bioinfo.uqam.ca .

Uberon, an integrative multi-species anatomy ontology

PubMed Central

2012-01-01

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org PMID:22293552

Effects of classification context on categorization in natural categories.

PubMed

Hampton, James A; Dubois, Danièle; Yeh, Wenchi

2006-10-01

The patterns of classification of borderline instances of eight common taxonomic categories were examined under three different instructional conditions to test two predictions: first, that lack of a specified context contributes to vagueness in categorization, and second, that altering the purpose of classification can lead to greater or lesser dependence on similarity in classification. The instructional conditions contrasted purely pragmatic with more technical/quasi-legal contexts as purposes for classification, and these were compared with a no-context control. The measures of category vagueness were between-subjects disagreement and within-subjects consistency, and the measures of similarity-based categorization were category breadth and the correlation of instance categorization probability with mean rated typicality, independently measured in a neutral context. Contrary to predictions, none of the measures of vagueness, reliability, category breadth, or correlation with typicality were generally affected by the instructional setting as a function of pragmatic versus technical purposes. Only one subcondition, in which a situational context was implied in addition to a purposive context, produced a significant change in categorization. Further experiments demonstrated that the effect of context was not increased when participants talked their way through the task, and that a technical context did not elicit more all-or-none categorization than did a pragmatic context. These findings place an important boundary condition on the effects of instructional context on conceptual categorization.

Reconsidering the classification of tick-borne encephalitis virus within the Siberian subtype gives new insights into its evolutionary history.

PubMed

Kovalev, S Y; Mukhacheva, T A

2017-11-01

Tick-borne encephalitis is widespread in Eurasia and transmitted by Ixodes ticks. Classification of its causative agent, tick-borne encephalitis virus (TBEV), includes three subtypes, namely Far-Eastern, European, and Siberian (TBEV-Sib), as well as a group of 886-84-like strains with uncertain taxonomic status. TBEV-Sib is subdivided into three phylogenetic lineages: Baltic, Asian, and South-Siberian. A reason to reconsider TBEV-Sib classification was the analysis of 186 nucleotide sequences of an E gene fragment submitted to GenBank during the last two years. Within the South-Siberian lineage, we have identified a distinct group with prototype strains Aina and Vasilchenko as an individual lineage named East-Siberian. The analysis of reclassified lineages has promoted a new model of the evolutionary history of TBEV-Sib lineages and TBEV-Sib as a whole. Moreover, we present arguments supporting separation of 886-84-like strains into an individual TBEV subtype, which we propose to name Baikalian (TBEV-Bkl). Copyright © 2017 Elsevier B.V. All rights reserved.

Structural Analysis of Biodiversity

PubMed Central

Sirovich, Lawrence; Stoeckle, Mark Y.; Zhang, Yu

2010-01-01

Large, recently-available genomic databases cover a wide range of life forms, suggesting opportunity for insights into genetic structure of biodiversity. In this study we refine our recently-described technique using indicator vectors to analyze and visualize nucleotide sequences. The indicator vector approach generates correlation matrices, dubbed Klee diagrams, which represent a novel way of assembling and viewing large genomic datasets. To explore its potential utility, here we apply the improved algorithm to a collection of almost 17000 DNA barcode sequences covering 12 widely-separated animal taxa, demonstrating that indicator vectors for classification gave correct assignment in all 11000 test cases. Indicator vector analysis revealed discontinuities corresponding to species- and higher-level taxonomic divisions, suggesting an efficient approach to classification of organisms from poorly-studied groups. As compared to standard distance metrics, indicator vectors preserve diagnostic character probabilities, enable automated classification of test sequences, and generate high-information density single-page displays. These results support application of indicator vectors for comparative analysis of large nucleotide data sets and raise prospect of gaining insight into broad-scale patterns in the genetic structure of biodiversity. PMID:20195371

The application of species criteria in avian taxonomy and its implications for the debate over species concepts.

PubMed

Sangster, George

2014-02-01

The debate over species concepts has produced a huge body of literature on how species can, may or should be delimited. By contrast, very few studies have documented how species taxa are delimited in practice. The aims of the present study were to (i) quantify the use of species criteria in taxonomy, (ii) discuss its implications for the debate over species concepts and (iii) assess recent claims about the impact of different species concepts on taxonomic stability and the 'nature' of species. The application of six species criteria was examined in taxonomic studies of birds published between 1950 and 2009. Three types of taxonomic studies were included: descriptions of new species (N = 329), proposals to change the taxonomic rank of species and subspecies (N = 808) and the taxonomic recommendations of the American Ornithologists' Union Committee on Classification and Nomenclature (N = 176). In all three datasets, diagnosability was the most frequently applied criterion, followed by reproductive isolation and degree of difference. This result is inconsistent with the popular notion that the Biological Species Concept is the dominant species concept in avian taxonomy. Since the 1950s, avian species-level taxonomy has become increasingly pluralistic and eclectic. This suggests that taxonomists consider different criteria as complementary rather than as rival approaches to species delimitation. Application of diagnosability more frequently led to the elevation of subspecies to species rank than application of reproductive isolation, although the difference was small. Hypotheses based on diagnosability and reproductive isolation were equally likely to be accepted in a mainstream checklist. These findings contradict recent claims that application of the Phylogenetic Species Concept causes instability and that broader application of the Biological Species Concept can stabilise taxonomy. The criteria diagnosability and monophyly, which are commonly associated with Phylogenetic Species Concepts, were used throughout the study period. Finally, no support was found for the idea that Phylogenetic Species Concepts have caused a change in the 'nature' of species taxa. This study demonstrates that there is a discrepancy between widely held perceptions of how species are delimited and the way species are actually delimited by taxonomists. Theoretically oriented debates over species concepts thus may benefit from empirical data on taxonomic practice. © 2013 The Author. Biological Reviews © 2013 Cambridge Philosophical Society.

Whole Genome Sequence Typing to Investigate the Apophysomyces Outbreak following a Tornado in Joplin, Missouri, 2011

PubMed Central

Etienne, Kizee A.; Gillece, John; Hilsabeck, Remy; Schupp, Jim M.; Colman, Rebecca; Lockhart, Shawn R.; Gade, Lalitha; Thompson, Elizabeth H.; Sutton, Deanna A.; Neblett-Fanfair, Robyn; Park, Benjamin J.; Turabelidze, George; Keim, Paul; Brandt, Mary E.; Deak, Eszter; Engelthaler, David M.

2012-01-01

Case reports of Apophysomyces spp. in immunocompetent hosts have been a result of traumatic deep implantation of Apophysomyces spp. spore-contaminated soil or debris. On May 22, 2011 a tornado occurred in Joplin, MO, leaving 13 tornado victims with Apophysomyces trapeziformis infections as a result of lacerations from airborne material. We used whole genome sequence typing (WGST) for high-resolution phylogenetic SNP analysis of 17 outbreak Apophysomyces isolates and five additional temporally and spatially diverse Apophysomyces control isolates (three A. trapeziformis and two A. variabilis isolates). Whole genome SNP phylogenetic analysis revealed three clusters of genotypically related or identical A. trapeziformis isolates and multiple distinct isolates among the Joplin group; this indicated multiple genotypes from a single or multiple sources. Though no linkage between genotype and location of exposure was observed, WGST analysis determined that the Joplin isolates were more closely related to each other than to the control isolates, suggesting local population structure. Additionally, species delineation based on WGST demonstrated the need to reassess currently accepted taxonomic classifications of phylogenetic species within the genus Apophysomyces. PMID:23209631

Whole genome sequence typing to investigate the Apophysomyces outbreak following a tornado in Joplin, Missouri, 2011.

PubMed

Etienne, Kizee A; Gillece, John; Hilsabeck, Remy; Schupp, Jim M; Colman, Rebecca; Lockhart, Shawn R; Gade, Lalitha; Thompson, Elizabeth H; Sutton, Deanna A; Neblett-Fanfair, Robyn; Park, Benjamin J; Turabelidze, George; Keim, Paul; Brandt, Mary E; Deak, Eszter; Engelthaler, David M

2012-01-01

Case reports of Apophysomyces spp. in immunocompetent hosts have been a result of traumatic deep implantation of Apophysomyces spp. spore-contaminated soil or debris. On May 22, 2011 a tornado occurred in Joplin, MO, leaving 13 tornado victims with Apophysomyces trapeziformis infections as a result of lacerations from airborne material. We used whole genome sequence typing (WGST) for high-resolution phylogenetic SNP analysis of 17 outbreak Apophysomyces isolates and five additional temporally and spatially diverse Apophysomyces control isolates (three A. trapeziformis and two A. variabilis isolates). Whole genome SNP phylogenetic analysis revealed three clusters of genotypically related or identical A. trapeziformis isolates and multiple distinct isolates among the Joplin group; this indicated multiple genotypes from a single or multiple sources. Though no linkage between genotype and location of exposure was observed, WGST analysis determined that the Joplin isolates were more closely related to each other than to the control isolates, suggesting local population structure. Additionally, species delineation based on WGST demonstrated the need to reassess currently accepted taxonomic classifications of phylogenetic species within the genus Apophysomyces.

Network analysis: A new way of understanding psychopathology?

PubMed

Fonseca-Pedrero, Eduardo

Current taxonomic systems are based on a descriptive and categorical approach where psychopathological symptoms and signs are caused by a hypothetical underlying mental disorder. In order to circumvent the limitations of classification systems, it is necessary to incorporate new conceptual and psychometric models that allow to understand, analyze and intervene in psychopathological phenomena from another perspective. The main goal was to present a new approach called network analysis for its application in the field of psychopathology. First of all, a brief introduction where psychopathological disorders are conceived as complex dynamic systems was carried out. Key concepts, as well as the different types of networks and the procedures for their estimation, are discussed. Following this, centrality measures, important for the understanding of the network as well as to examine the relevance of the variables within the network were addressed. These factors were then exemplified by estimating a network of self-reported psychopathological symptoms in a representative sample of adolescents. Finally, a brief recapitulation is made and future lines of research are discussed. Copyright © 2017 SEP y SEPB. Publicado por Elsevier España, S.L.U. All rights reserved.

Phylogeny and systematics of deep-sea precious corals (Anthozoa: Octocorallia: Coralliidae).

PubMed

Tu, Tzu-Hsuan; Dai, Chang-Feng; Jeng, Ming-Shiou

2015-03-01

The phylogeny of Coralliidae is being increasingly studied to elucidate their evolutionary history and species delimitation due to global concerns about their conservation. Previous studies on phylogenetic relationships within Coralliidae have pointed out that the two currently recognized genera are not monophyletic and the Coralliidae should be divided into three genera. In order to provide a comprehensive revision of the taxonomy of Coralliidae, we documented 110 specimens using eight mitochondrial and one nuclear loci to reconstruct their phylogeny. The morphological features of 27 type specimens were also examined. Phylogenetic relationships based on both mitochondrial and nuclear markers revealed two reciprocally monophyletic clades of Coralliidae. One of the clades was further split into two subclades with respect to sequence variation and observable morphological features. Based on the results of genealogical analyses and distinctive morphological features, the three genera classification of Coralliidae proposed by Gray (1867) was redefined. In this revised taxonomic system, Corallium, Hemicorallium, and Pleurocorallium consist of 7, 16 and 14 species, respectively. Our results also showed that the cosmopolitan Hemicorallium laauense is a species complex containing a cryptic species. Copyright © 2015 Elsevier Inc. All rights reserved.

Database on pharmacophore analysis of active principles, from medicinal plants

PubMed Central

Pitchai, Daisy; Manikkam, Rajalakshmi; Rajendran, Sasikala R; Pitchai, Gnanamani

2010-01-01

Plants continue to be a major source of medicines, as they have been throughout human history. In the present days, drug discovery from plants involves a multidisciplinary approach combining ethnobotanical, phytochemical and biological techniques to provide us new chemical compounds (lead molecules) for the development of drugs against various pharmacological targets, including cancer, diabetes and its secondary complications. In view of this need in current drug discovery from medicinal plants, here we describe another web database containing the information of pharmacophore analysis of active principles possessing antidiabetic, antimicrobial, anticancerous and antioxidant properties from medicinal plants. The database provides the botanical, taxonomic classification, biochemical as well as pharmacological properties of medicinal plants. Data on antidiabetic, antimicrobial, anti oxidative, anti tumor and anti inflammatory compounds, and their physicochemical properties, SMILES Notation, Lipinski's properties are included in our database. One of the proposed features in the database is the predicted ADMET values and the interaction of bioactive compounds to the target protein. The database alphabetically lists the compound name and also provides tabs separating for anti microbial, antitumor, antidiabetic, and antioxidative compounds. Availability http://www.hccbif.info / PMID:21346859

Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions

PubMed Central

Conte-Grand, Cecilia; Britz, Ralf; Dahanukar, Neelesh; Raghavan, Rajeev; Pethiyagoda, Rohan; Tan, Heok Hui; Hadiaty, Renny K.; Yaakob, Norsham S.

2017-01-01

Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group. PMID:28931084

The kingdom Protista and its 45 phyla.

PubMed

Corliss, J O

1984-01-01

Because most recent treatments of the protists ('lower' eukaryotes comprising the kingdom PROTISTA Haeckel, 1866) have been preoccupied with either a 'phylogenetic-tree' approach or a discussion of the impact of possible endosymbiotic origins of major intracellular organelles, the overall systematics of the group, from taxonomic and nomenclatural points of view, has been almost totally neglected. As a result, confusion over contained phyla, their places in a classification scheme, and even their names (and authorships) is growing; the situation could become chaotic. The principal objective of the present paper is to recognize the taxonomic interrelationships among all protist groups; and it includes the specific proposal that some 45 phyla, defined and characterized, be assigned to 18 supraphyletic assemblages within the kingdom PROTISTA (itself redefined and contrasted with the other eukaryotic kingdoms recognized here: ANIMALIA, PLANTAE and FUNGI). Vernacular terms are employed for identification of the 18 assemblages, but defensible formal names are proposed at the level of phylum. None is presented as new: authorship-and-date credits are given to preceding workers on the taxonomy of the many groups involved. By presenting taxonomic characterizations as well as relevant nomenclatural data for each taxon described, a comprehensive scheme of overall higher-level classification within the kingdom emerges that may be considered to serve as a solid base or 'taking-off point' for future discussions. The 18 supraphyletic groups and their phyla (in parentheses and including authorships and dates of their formal names) are as follows: I. The rhizopods (phyla Karyoblastea Margulis, 1974; Amoebozoa Lühe, 1913; Acrasia Van Tieghem, 1880; Eumycetozoa Zopf, 1885; Plasmodiophorea Zopf, 1885; Granuloreticulosa De Saedeleer, 1934; incertae sedis Xenophyophora Schulze, 1904). II. The mastigomycetes (Hypochytridiomycota Sparrow, 1959; Oomycota Winter, 1897; incert. sed. Chytridiomycota Sparrow, 1959). III. The chlorobionts (Chlorophyta Pascher, 1914; Prasinophyta Christensen, 1962; Conjugatophyta Engler, 1892; Charophyta Rabenhorst, 1863; incert. sed. Glaucophyta Bohlin, 1901). IV. The euglenozoa (Euglenophyta Pascher, 1931; Kinetoplastidea Honigberg, 1963; incert. sed. Pseudociliata Corliss & Lipscomb, 1982). V. The rhodophytes (Rhodophyta Rabenhorst, 1863). VI. The cryptomonads (Cryptophyta Pascher, 1914). VII. The choanoflagellates (Choanoflagellata Kent, 1880).(ABSTRACT TRUNCATED AT 400 WORDS)

Unresolved Galaxy Classifier for ESA/Gaia mission: Support Vector Machines approach

NASA Astrophysics Data System (ADS)

Bellas-Velidis, Ioannis; Kontizas, Mary; Dapergolas, Anastasios; Livanou, Evdokia; Kontizas, Evangelos; Karampelas, Antonios

A software package Unresolved Galaxy Classifier (UGC) is being developed for the ground-based pipeline of ESA's Gaia mission. It aims to provide an automated taxonomic classification and specific parameters estimation analyzing Gaia BP/RP instrument low-dispersion spectra of unresolved galaxies. The UGC algorithm is based on a supervised learning technique, the Support Vector Machines (SVM). The software is implemented in Java as two separate modules. An offline learning module provides functions for SVM-models training. Once trained, the set of models can be repeatedly applied to unknown galaxy spectra by the pipeline's application module. A library of galaxy models synthetic spectra, simulated for the BP/RP instrument, is used to train and test the modules. Science tests show a very good classification performance of UGC and relatively good regression performance, except for some of the parameters. Possible approaches to improve the performance are discussed.

Brucella taxonomy and evolution

PubMed Central

Ficht, Thomas

2010-01-01

Taxonomy and nomenclature represent man-made systems designed to enhance understanding of the relationship between organisms by comparison of discrete sets of properties. Initial efforts at bacterial taxonomy were flawed as a result of the previous use of nonsystematic approaches including common names resulting in confusing and inaccurate nomenclature. A decision was made to start afresh with bacterial nomenclature and to avoid the hazards experienced in the taxonomic classification of higher organisms. This was achieved by developing new rules designed to simplify classification and avoid unnecessary and confusing changes. This article reviews the work of a number of scientists attempting to reconcile new molecular data describing the phylogenetic relationship between Brucella organisms and a broader family of organisms with widely variant phenotypes that include human virulence and host range against a backdrop of strict regulatory requirements that fail to recognize significant differences between organisms with similar nomenclature. PMID:20521932

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

PubMed Central

Ruvindy, Rendy; White III, Richard Allen; Neilan, Brett Anthony; Burns, Brendan Paul

2016-01-01

Modern microbial mats are potential analogues of some of Earth's earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic next-generation sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats. PMID:26023869

Taxonomic review of the katydid genus Alloteratura (Orthoptera: Tettigoniidae; Meconematinae) with the description of one new species from Thailand.

PubMed

Tan, Ming Kai; Artchawakom, Taksin

2017-01-25

Alloteratura Hebard, 1922 is a genus of katydid from the speciose Meconematinae, most easily characterised by maxillary palpi with extremely short apical segment. Currently, two subgenera exists: subgenus Alloteratura Hebard, 1922 (33 species) and Meconemopsis Karny, 1922 (11 species). In this taxonomic review, one new species of the subgenus Meconemopsis from Thailand is described: A. (M.) dawwruengi sp. nov. Illustrated keys to species for both subgenera are also presented here.

How many species of flowering plants are there?

PubMed Central

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

2011-01-01

We estimate the probable number of flowering plants. First, we apply a model that explicitly incorporates taxonomic effort over time to estimate the number of as-yet-unknown species. Second, we ask taxonomic experts their opinions on how many species are likely to be missing, on a family-by-family basis. The results are broadly comparable. We show that the current number of species should grow by between 10 and 20 per cent. There are, however, interesting discrepancies between expert and model estimates for some families, suggesting that our model does not always completely capture patterns of taxonomic activity. The as-yet-unknown species are probably similar to those taxonomists have described recently—overwhelmingly rare and local, and disproportionately in biodiversity hotspots, where there are high levels of habitat destruction. PMID:20610425

New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones.

PubMed

Moorhouse-Gann, Rosemary J; Dunn, Jenny C; de Vere, Natasha; Goder, Martine; Cole, Nik; Hipperson, Helen; Symondson, William O C

2018-06-04

DNA metabarcoding is a rapidly growing technique for obtaining detailed dietary information. Current metabarcoding methods for herbivory, using a single locus, can lack taxonomic resolution for some applications. We present novel primers for the second internal transcribed spacer of nuclear ribosomal DNA (ITS2) designed for dietary studies in Mauritius and the UK, which have the potential to give unrivalled taxonomic coverage and resolution from a short-amplicon barcode. In silico testing used three databases of plant ITS2 sequences from UK and Mauritian floras (native and introduced) totalling 6561 sequences from 1790 species across 174 families. Our primers were well-matched in silico to 88% of species, providing taxonomic resolution of 86.1%, 99.4% and 99.9% at the species, genus and family levels, respectively. In vitro, the primers amplified 99% of Mauritian (n = 169) and 100% of UK (n = 33) species, and co-amplified multiple plant species from degraded faecal DNA from reptiles and birds in two case studies. For the ITS2 region, we advocate taxonomic assignment based on best sequence match instead of a clustering approach. With short amplicons of 187-387 bp, these primers are suitable for metabarcoding plant DNA from faecal samples, across a broad geographic range, whilst delivering unparalleled taxonomic resolution.

Fangorn Forest (F2): a machine learning approach to classify genes and genera in the family Geminiviridae.

PubMed

Silva, José Cleydson F; Carvalho, Thales F M; Fontes, Elizabeth P B; Cerqueira, Fabio R

2017-09-30

Geminiviruses infect a broad range of cultivated and non-cultivated plants, causing significant economic losses worldwide. The studies of the diversity of species, taxonomy, mechanisms of evolution, geographic distribution, and mechanisms of interaction of these pathogens with the host have greatly increased in recent years. Furthermore, the use of rolling circle amplification (RCA) and advanced metagenomics approaches have enabled the elucidation of viromes and the identification of many viral agents in a large number of plant species. As a result, determining the nomenclature and taxonomically classifying geminiviruses turned into complex tasks. In addition, the gene responsible for viral replication (particularly, the viruses belonging to the genus Mastrevirus) may be spliced due to the use of the transcriptional/splicing machinery in the host cells. However, the current tools have limitations concerning the identification of introns. This study proposes a new method, designated Fangorn Forest (F2), based on machine learning approaches to classify genera using an ab initio approach, i.e., using only the genomic sequence, as well as to predict and classify genes in the family Geminiviridae. In this investigation, nine genera of the family Geminiviridae and their related satellite DNAs were selected. We obtained two training sets, one for genus classification, containing attributes extracted from the complete genome of geminiviruses, while the other was made up to classify geminivirus genes, containing attributes extracted from ORFs taken from the complete genomes cited above. Three ML algorithms were applied on those datasets to build the predictive models: support vector machines, using the sequential minimal optimization training approach, random forest (RF), and multilayer perceptron. RF demonstrated a very high predictive power, achieving 0.966, 0.964, and 0.995 of precision, recall, and area under the curve (AUC), respectively, for genus classification. For gene classification, RF could reach 0.983, 0.983, and 0.998 of precision, recall, and AUC, respectively. Therefore, Fangorn Forest is proven to be an efficient method for classifying genera of the family Geminiviridae with high precision and effective gene prediction and classification. The method is freely accessible at www.geminivirus.org:8080/geminivirusdw/discoveryGeminivirus.jsp .

Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error

PubMed Central

Porter, Teresita M.; Golding, G. Brian

2012-01-01

Nuclear large subunit ribosomal DNA is widely used in fungal phylogenetics and to an increasing extent also amplicon-based environmental sequencing. The relatively short reads produced by next-generation sequencing, however, makes primer choice and sequence error important variables for obtaining accurate taxonomic classifications. In this simulation study we tested the performance of three classification methods: 1) a similarity-based method (BLAST + Metagenomic Analyzer, MEGAN); 2) a composition-based method (Ribosomal Database Project naïve Bayesian classifier, NBC); and, 3) a phylogeny-based method (Statistical Assignment Package, SAP). We also tested the effects of sequence length, primer choice, and sequence error on classification accuracy and perceived community composition. Using a leave-one-out cross validation approach, results for classifications to the genus rank were as follows: BLAST + MEGAN had the lowest error rate and was particularly robust to sequence error; SAP accuracy was highest when long LSU query sequences were classified; and, NBC runs significantly faster than the other tested methods. All methods performed poorly with the shortest 50–100 bp sequences. Increasing simulated sequence error reduced classification accuracy. Community shifts were detected due to sequence error and primer selection even though there was no change in the underlying community composition. Short read datasets from individual primers, as well as pooled datasets, appear to only approximate the true community composition. We hope this work informs investigators of some of the factors that affect the quality and interpretation of their environmental gene surveys. PMID:22558215

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.

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

Imagining Sisyphus happy: DNA barcoding and the unnamed majority.

PubMed

Blaxter, Mark

2016-09-05

The vast majority of life on the Earth is physically small, and is classifiable as micro- or meiobiota. These organisms are numerically dominant and it is likely that they are also abundantly speciose. By contrast, the vast majority of taxonomic effort has been expended on 'charismatic megabionts': larger organisms where a wealth of morphology has facilitated Linnaean species definition. The hugely successful Linnaean project is unlikely to be extensible to the totality of approximately 10 million species in a reasonable time frame and thus alternative toolkits and methodologies need to be developed. One such toolkit is DNA barcoding, particularly in its metabarcoding or metagenetics mode, where organisms are identified purely by the presence of a diagnostic DNA sequence in samples that are not processed for morphological identification. Building on secure Linnaean foundations, classification of unknown (and unseen) organisms to molecular operational taxonomic units (MOTUs) and deployment of these MOTUs in biodiversity science promises a rewarding resolution to the Sisyphean task of naming all the world's species.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

PubMed Central

Freitas, Tracey Allen K.; Li, Po-E; Scholz, Matthew B.; Chain, Patrick S. G.

2015-01-01

A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines Genomic Origins Through Taxonomic CHAllenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools. PMID:25765641

Cuticular hydrocarbons as a tool for the identification of insect species: Puparial cases from Sarcophagidae

PubMed Central

Braga, Marina Vianna; Pinto, Zeneida Teixeira; de Carvalho Queiroz, Margareth Maria; Matsumoto, Nana; Blomquist, Gary James

2013-01-01

The external surface of all insects is covered by a species-specific complex mixture of highly stable, very long chain cuticular hydrocarbons (CHCs). Gas chromatography coupled to mass spectrometry was used to identify CHCs from four species of Sarcophagidae, Peckia (Peckia) chrysostoma, Peckia (Pattonella) intermutans, Sarcophaga (Liopygia) ruficornis and Sarcodexia lambens. The identified CHCs were mostly a mixture of n-alkanes, monomethylalkanes and dimethylalkanes with linear chain lengths varying from 23 to 33 carbons. Only two alkenes were found in all four species. S. lambens had a composition of CHCs with linear chain lengths varying from C23 to C33, while the other three species linear chain lengths from 24 to 31 carbons. n-Heptacosane, n-nonacosane and 3-methylnonacosane, n-triacontane and n-hentriacontane occurred in all four species. The results show that these hydrocarbon profiles may be used for the taxonomic differentiation of insect species and are a useful additional tool for taxonomic classification, especially when only parts of the insect specimen are available. PMID:23932943

Population Abundance of Potentially Pathogenic Organisms in Intestinal Microbiome of Jungle Crow (Corvus macrorhynchos) Shown with 16S rRNA Gene-Based Microbial Community Analysis

PubMed Central

Maeda, Isamu; Siddiki, Mohammad Shohel Rana; Nozawa-Takeda, Tsutomu; Tsukahara, Naoki; Tani, Yuri; Naito, Taki; Sugita, Shoei

2013-01-01

Jungle Crows (Corvus macrorhynchos) prefer human habitats because of their versatility in feeding accompanied with human food consumption. Therefore, it is important from a public health viewpoint to characterize their intestinal microbiota. However, no studies have been involved in molecular characterization of the microbiota based on huge and reliable number of data acquisition. In this study, 16S rRNA gene-based microbial community analysis coupled with the next-generation DNA sequencing techniques was applied to the taxonomic classification of intestinal microbiome for three jungle crows. Clustering of the reads into 130 operational taxonomic units showed that at least 70% of analyzed sequences for each crow were highly homologous to Eimeria sp., which belongs to the protozoan phylum Apicomplexa. The microbiotas of three crows also contained potentially pathogenic bacteria with significant percentages, such as the genera Campylobacter and Brachyspira. Thus, the profiling of a large number of 16S rRNA gene sequences in crow intestinal microbiomes revealed the high-frequency existence or vestige of potentially pathogenic microorganisms. PMID:24058905

Population abundance of potentially pathogenic organisms in intestinal microbiome of jungle crow (Corvus macrorhynchos) shown with 16S rRNA gene-based microbial community analysis.

PubMed

Maeda, Isamu; Siddiki, Mohammad Shohel Rana; Nozawa-Takeda, Tsutomu; Tsukahara, Naoki; Tani, Yuri; Naito, Taki; Sugita, Shoei

2013-01-01

Jungle Crows (Corvus macrorhynchos) prefer human habitats because of their versatility in feeding accompanied with human food consumption. Therefore, it is important from a public health viewpoint to characterize their intestinal microbiota. However, no studies have been involved in molecular characterization of the microbiota based on huge and reliable number of data acquisition. In this study, 16S rRNA gene-based microbial community analysis coupled with the next-generation DNA sequencing techniques was applied to the taxonomic classification of intestinal microbiome for three jungle crows. Clustering of the reads into 130 operational taxonomic units showed that at least 70% of analyzed sequences for each crow were highly homologous to Eimeria sp., which belongs to the protozoan phylum Apicomplexa. The microbiotas of three crows also contained potentially pathogenic bacteria with significant percentages, such as the genera Campylobacter and Brachyspira. Thus, the profiling of a large number of 16S rRNA gene sequences in crow intestinal microbiomes revealed the high-frequency existence or vestige of potentially pathogenic microorganisms.

FIRST RESULTS FROM THE RAPID-RESPONSE SPECTROPHOTOMETRIC CHARACTERIZATION OF NEAR-EARTH OBJECTS USING UKIRT

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

Mommert, M.; Trilling, D. E.; Petersen, E.

2016-04-15

Using the Wide Field Camera for the United Kingdom Infrared Telescope (UKIRT), we measure the near-infrared colors of near-Earth objects (NEOs) in order to put constraints on their taxonomic classifications. The rapid-response character of our observations allows us to observe NEOs when they are close to the Earth and bright. Here we present near-infrared color measurements of 86 NEOs, most of which were observed within a few days of their discovery, allowing us to characterize NEOs with diameters of only a few meters. Using machine-learning methods, we compare our measurements to existing asteroid spectral data and provide probabilistic taxonomic classificationsmore » for our targets. Our observations allow us to distinguish between S-complex, C/X-complex, D-type, and V-type asteroids. Our results suggest that the fraction of S-complex asteroids in the whole NEO population is lower than the fraction of ordinary chondrites in the meteorite fall statistics. Future data obtained with UKIRT will be used to investigate the significance of this discrepancy.« less

Marine biology

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

Thurman, H.V.; Webber, H.H.

1984-01-01

This book discusses both taxonomic and ecological topics on marine biology. Full coverage of marine organisms of all five kingdoms is provided, along with interesting and thorough discussion of all major marine habitats. Organization into six major parts allows flexibility. It also provides insight into important topics such as disposal of nuclear waste at sea, the idea that life began on the ocean floor, and how whales, krill, and people interact. A full-color photo chapter reviews questions, and exercises. The contents are: an overview marine biology: fundamental concepts/investigating life in the ocean; the physical ocean, the ocean floor, the naturemore » of water, the nature and motion of ocean water; general ecology, conditions for life in the sea, biological productivity and energy transfer; marine organisms; monera, protista, mycota and metaphyta; the smaller marine animals, the large animals marine habitats, the intertidal zone/benthos of the continental shelf, the photic zone, the deep ocean, the ocean under stress, marine pollution, appendix a: the metric system and conversion factors/ appendix b: prefixes and suffixes/ appendix c: taxonomic classification of common marine organisms, and glossary, and index.« less

Marine Actinobacteria as a source of compounds for phytopathogen control: An integrative metabolic-profiling / bioactivity and taxonomical approach

PubMed Central

Betancur, Luz A.; Naranjo-Gaybor, Sandra J.; Vinchira-Villarraga, Diana M.; Moreno-Sarmiento, Nubia C.; Maldonado, Luis A.; Suarez-Moreno, Zulma R.; Acosta-González, Alejandro; Padilla-Gonzalez, Gillermo F.; Puyana, Mónica; Castellanos, Leonardo; Ramos, Freddy A.

2017-01-01

Marine bacteria are considered as promising sources for the discovery of novel biologically active compounds. In this study, samples of sediment, invertebrate and algae were collected from the Providencia and Santa Catalina coral reef (Colombian Caribbean Sea) with the aim of isolating Actinobateria-like strain able to produce antimicrobial and quorum quenching compounds against pathogens. Several approaches were used to select actinobacterial isolates, obtaining 203 strains from all samples. According to their 16S rRNA gene sequencing, a total of 24 strains was classified within Actinobacteria represented by three genera: Streptomyces, Micromonospora, and Gordonia. In order to assess their metabolic profiles, the actinobacterial strains were grown in liquid cultures, and LC-MS-based analyses from ethyl acetate fractions were performed. Based on taxonomical classification, screening information of activity against phytopathogenic strains and quorum quenching activity, as well as metabolic profiling, six out of the 24 isolates were selected for follow-up with chemical isolation and structure identification analyses of putative metabolites involved in antimicrobial activities. PMID:28225766

Leaf micro-morphology of Lepisanthes Blume (Sapindaceae) in Peninsular Malaysia

NASA Astrophysics Data System (ADS)

Ghazalli, Mohd Norfaizal; Talib, Noraini; Mohammad, Abdul Latiff

2018-04-01

A detail comparative study on leaf micro-morphology was conducted on the genus Lepisanthes from Peninsular Malaysia, five chosen species namely as L. amoena (Hassk.) Leenh., L. fruticosa (Roxb.) Leenh., L. rubiginosa (Roxb.) Leenh., L. senegalensis (Juss. ex Poir.) Leenh. and L. tetraphylla (Vahl.) Radlk. The objective of this study is to identify the leaf micro-morphological characteristics that can give significance impact for species identification and classification. Lepisanthes is an important tropical rare fruit genus in Malaysia and it is important to characterize and documenting additional taxonomic evidences that can be useful in Sapindaceae taxonomy information which is still lacked. The methods involved dehydration process, critical point drying, gold coated and observation under scanning electron microscope. Leaf micro-morphology showed significance taxonomic value in the genus Lepisanthes and can be used as additional data for species identification. Diagnostic character was found in L. fruticosa via the presence of four different types of trichomes on the abaxial and adaxial epidermal surfaces. As a conclusion, variation in cuticular striation, stomata structure, type of waxes and trichome morphology can be used in Lepisanthes species identification.

A cybertaxonomic revision of the micro-landsnail genus Plectostoma Adam (Mollusca, Caenogastropoda, Diplommatinidae), from Peninsular Malaysia, Sumatra and Indochina

PubMed Central

Liew, Thor-Seng; Vermeulen, Jaap Jan; Marzuki, Mohammad Effendi bin; Schilthuizen, Menno

2014-01-01

Abstract Plectostoma is a micro land snail restricted to limestone outcrops in Southeast Asia. Plectostoma was previously classified as a subgenus of Opisthostoma because of the deviation from regular coiling in many species in both taxa. This paper is the first of a two-part revision of the genus Plectostoma, and includes all non-Borneo species. In the present paper, we examined 214 collection samples of 31 species, and obtained 62 references, 290 pictures, and 155 3D-models of 29 Plectostoma species and 51 COI sequences of 19 species. To work with such a variety of taxonomic data, and then to represent it in an integrated, scaleable and accessible manner, we adopted up-to-date cybertaxonomic tools. All the taxonomic information, such as references, classification, species descriptions, specimen images, genetic data, and distribution data, were tagged and linked with cyber tools and web servers (e.g. Lifedesks, Google Earth, and Barcoding of Life Database). We elevated Plectostoma from subgenus to genus level based on morphological, ecological and genetic evidence. We revised the existing 21 Plectostoma species and described 10 new species, namely, P. dindingensis sp. n., P. mengaburensis sp. n., P. whitteni sp. n., P. kayiani sp. n., P. davisoni sp. n., P. relauensis sp. n., P. kubuensis sp. n., P. tohchinyawi sp. n., P. tenggekensis sp. n., and P. ikanensis sp. n. All the synthesised, semantic-tagged, and linked taxonomic information is made freely and publicly available online. PMID:24715783

Hidden species diversity in Sylvirana nigrovittata (Amphibia: Ranidae) highlights the importance of taxonomic revisions in biodiversity conservation

PubMed Central

Stuart, Bryan L.

2018-01-01

Accurately delimiting species and their geographic ranges is imperative for conservation, especially in areas experiencing rapid habitat loss. Southeast Asia currently has one of the highest rates of deforestation in the world, is home to multiple biodiversity hotspots, and the majority of its countries have developing economies with limited resources for biodiversity conservation. Thus, accurately delimiting species and their ranges is particularly important in this region. We examined genetic and morphological variation in the widespread frog species Sylvirana nigrovittata (and its long-treated junior synonym S. mortenseni) with the goal of clarifying its taxonomic content and geographic range boundaries for conservation. We present evidence that the current concept of S. nigrovittata contains at least eight species, two of which are each known from only two localities, but that S. mortenseni is more geographically widespread than currently realized. Five of these species are described as new to science. PMID:29538432

Comparing K-mer based methods for improved classification of 16S sequences.

PubMed

Vinje, Hilde; Liland, Kristian Hovde; Almøy, Trygve; Snipen, Lars

2015-07-01

The need for precise and stable taxonomic classification is highly relevant in modern microbiology. Parallel to the explosion in the amount of sequence data accessible, there has also been a shift in focus for classification methods. Previously, alignment-based methods were the most applicable tools. Now, methods based on counting K-mers by sliding windows are the most interesting classification approach with respect to both speed and accuracy. Here, we present a systematic comparison on five different K-mer based classification methods for the 16S rRNA gene. The methods differ from each other both in data usage and modelling strategies. We have based our study on the commonly known and well-used naïve Bayes classifier from the RDP project, and four other methods were implemented and tested on two different data sets, on full-length sequences as well as fragments of typical read-length. The difference in classification error obtained by the methods seemed to be small, but they were stable and for both data sets tested. The Preprocessed nearest-neighbour (PLSNN) method performed best for full-length 16S rRNA sequences, significantly better than the naïve Bayes RDP method. On fragmented sequences the naïve Bayes Multinomial method performed best, significantly better than all other methods. For both data sets explored, and on both full-length and fragmented sequences, all the five methods reached an error-plateau. We conclude that no K-mer based method is universally best for classifying both full-length sequences and fragments (reads). All methods approach an error plateau indicating improved training data is needed to improve classification from here. Classification errors occur most frequent for genera with few sequences present. For improving the taxonomy and testing new classification methods, the need for a better and more universal and robust training data set is crucial.

The NEOShield-2 EU Project - The first year of the Italian contribution

NASA Astrophysics Data System (ADS)

Ieva, Simone; Dotto, Elisabetta; Mazzotta Epifani, Elena; Di Paola, Andrea; Speziali, Roberto; Lazzarin, Monica; Bertini, Ivano; Barucci, Maria Antonieta; Perna, Davide; Lazzaro, Daniela; Silva, Sergio; Monteiro, Filipe; Perozzi, Ettore; Micheli, Marco; Cortese, Matteo

2016-10-01

The population of Near Earth Asteroids (NEAs) is responsible for a continuous flux of impactors with our planet. To date, more than 14500 NEAs are known, with a current discovery rate of ˜1500 objects/year.The NEA population show a great diversity in terms of composition and physical properties: (different shapes, rotational states, rotational periods...). NEA diversity is also emphasized by the different taxonomic types found within the population that give some hints about the NEA surface composition.The study of their physical nature is compelling in view of the potential hazard posed to our planet, since it has been acknowledged that whatever the mitigation scenario, it strongly depends upon the composition of the impactor. Unfortunately, only less than 15% of them have been physically characterized, and at the current discovery rate the situation is becoming progressively worse.Within the framework of the Horizon 2020 program, the European Commission promoted the study of NEAs by approving and financing the NEOShield-2 project (2015-2017). One of the main aims of the NEOShield-2 project is to undertake an extensive observational campaign to provide physical and compositional characterization of a large number of NEAs in the 50-300 m size range.INAF-OAR and Padova University, the Italian contributors to the NEOShield-2 project, are responsible for the Task 10.2.1 'Colours and Phase function', with the aim to acquire photometric measurements for a wide sample of NEOs. An operational interface is maintained together with the ESA SSA-NEO Coordination Centre (NEOCC) in order to optimize observations devoted to physical characterization.We will present the results of the first year of the Italian contribution to the project on i) phase function analysis, ii) surface colors and iii) preliminary taxonomical classification and the statistical analysis of the data obtained from several telescopes around the world.This research has been funded with support from the European Commission (grant agreement no: 640351 H2020- PROTEC-2014 - Access technologies and characterisation for Near Earth Objects (NEOs).

Paraphyly and (yeast) classification.

PubMed

Lachance, Marc-André

2016-12-01

Yeast systematics has wholeheartedly embraced the phylogenetic approach. Central to this has been the unspoken convention that taxa at all ranks be strictly monophyletic. This can result in a proliferation of small genera and instances of nomenclatural instability, counter to the expected benefit of phylogenetic systematics. But the literature abounds with examples, at all taxonomic levels, where paraphyly is a reality that can no longer be ignored. The very concepts of Bacteria or Archaea, under the constraint of monophyly, are in peril. It is therefore desirable to effect a shift in practices that will recognize the existence of paraphyletic taxa.

Planetary radar targets 1999 AP10, 2000 TO64, 2000 UJ1, and 2000 XK44: Four S-complex near-Earth asteroids.

NASA Astrophysics Data System (ADS)

Hicks, M.; Lawrence, K.

2009-12-01

We report taxonomic classifications of four near-Earth asteroids (1999 AP10, 2000 TO64, 2000 UJ1, and 2000 XK44) scheduled for radar observation by the JPL radar group at the Arecibo facility in Oct-Nov 2009, using long-slit CCD spectroscopy acquired at the Palomar 5-m telescope on 2009 Nov 09 UT. Table 1 lists the observation circumstances. Normalized reflectance spectra are shown in Figures 1-4 [1]Diversity of small, single-stranded DNA viruses of invertebrates and their chaotic evolutionary past.

PubMed

Tijssen, Peter; Pénzes, Judit J; Yu, Qian; Pham, Hanh T; Bergoin, Max

2016-10-01

A wide spectrum of invertebrates is susceptible to various single-stranded DNA viruses. Their relative simplicity of replication and dependence on actively dividing cells makes them highly pathogenic for many invertebrates (Hexapoda, Decapoda, etc.). We present their taxonomical classification and describe the evolutionary relationships between various groups of invertebrate-infecting viruses, their high degree of recombination, and their relationship to viruses infecting mammals or other vertebrates. They share characteristics of the viruses within the various families, including structure of the virus particle, genome properties, and gene expression strategy. Copyright © 2016. Published by Elsevier Inc.

ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements.

PubMed

Hua Tan, Mun; Ming Gan, Han; Peng Lee, Yin; Linton, Stuart; Grandjean, Frederic; Ladvocat Bartholomei-Santos, Marlise; Miller, Adam D; Austin, Christopher M

2018-05-22

The infraorder Anomura consists of a morphologically and ecologically heterogeneous group of decapod crustaceans, and has attracted interest from taxonomists for decades attempting to find some order out of the seemingly chaotic diversity within the group. Species-level diversity within the Anomura runs the gamut from the "hairy" spindly-legged yeti crab found in deep-sea hydrothermal vent environments to the largest known terrestrial invertebrate, the robust coconut or robber crab. Owing to a well-developed capacity for parallel evolution, as evidenced by the occurrence of multiple independent carcinization events, Anomura has long tested the patience and skill of both taxonomists attempting to find order, and phylogeneticists trying to establish stable hypotheses of evolutionary inter-relationships. In this study, we performed genome skimming to recover the mitogenome sequences of 12 anomuran species including the world's largest extant invertebrate, the robber crab (Birgus latro), thereby over doubling these resources for this group, together with 8 new brachyuran mitogenomes. Maximum-likelihood (ML) and Bayesian-inferred (BI) phylogenetic reconstructions based on amino acid sequences from mitogenome protein-coding genes provided strong support for the monophyly of the Anomura and Brachyura and their sister relationship, consistent with previous studies. The majority of relationships within families were supported and were largely consistent with current taxonomic classifications, whereas many relationships at higher taxonomic levels were unresolved. Nevertheless, we have strong support for a polyphyletic Paguroidea and recovered a well-supported clade of a subset of paguroids (Diogenidae + Coenobitidae) basal to all other anomurans, though this requires further testing with greater taxonomic sampling. We also introduce a new feature to the MitoPhAST bioinformatics pipeline (https://github.com/mht85/MitoPhAST) that enables the extraction of mitochondrial gene order (MGO) information directly from GenBank files and clusters groups based on common MGOs. Using this tool, we compared MGOs across the Anomura and Brachyura, identifying Anomura as a taxonomic "hot spot" with high variability in MGOs among congeneric species from multiple families while noting the broad association of highly-rearranged MGOs with several anomuran lineages inhabiting extreme niches. We also demonstrate the value of MGOs as a source of novel synapomorphies for independently reinforcing tree-based relationships and for shedding light on relationships among challenging groups such as the Aegloidea and Lomisoidea that were unresolved in phylogenetic reconstructions. Overall, this study contributes a substantial amount of new genetic material for Anomura and attempts to further resolve anomuran evolutionary relationships where possible based on a combination of sequence and MGO information. The new feature in MitoPhAST adds to the relatively limited number of bioinformatics tools available for MGO analyses, which can be utilized widely across animal groups. Copyright © 2018. Published by Elsevier Inc.

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.

Resolving cryptic species complexes of major tephritid pests

PubMed Central

Hendrichs, Jorge; Vera, M. Teresa; De Meyer, Marc; Clarke, Anthony R.

2015-01-01

Abstract An FAO/IAEA Co-ordinated Research Project (CRP) on “Resolution of Cryptic Species Complexes of Tephritid Pests to Overcome Constraints to SIT Application and International Trade” was conducted from 2010 to 2015. As captured in the CRP title, the objective was to undertake targeted research into the systematics and diagnostics of taxonomically challenging fruit fly groups of economic importance. The scientific output was the accurate alignment of biological species with taxonomic names; which led to the applied outcome of assisting FAO and IAEA Member States in overcoming technical constraints to the application of the Sterile Insect Technique (SIT) against pest fruit flies and the facilitation of international agricultural trade. Close to 50 researchers from over 20 countries participated in the CRP, using coordinated, multidisciplinary research to address, within an integrative taxonomic framework, cryptic species complexes of major tephritid pests. The following progress was made for the four complexes selected and studied: Anastrepha fraterculus complex – Eight morphotypes and their geographic and ecological distributions in Latin America were defined. The morphotypes can be considered as distinct biological species on the basis of differences in karyotype, sexual incompatibility, post-mating isolation, cuticular hydrocarbon, pheromone, and molecular analyses. Discriminative taxonomic tools using linear and geometric morphometrics of both adult and larval morphology were developed for this complex. Bactrocera dorsalis complex – Based on genetic, cytogenetic, pheromonal, morphometric, and behavioural data, which showed no or only minor variation between the Asian/African pest fruit flies Bactrocera dorsalis, Bactrocera papayae, Bactrocera philippinensis and Bactrocera invadens, the latter three species were synonymized with Bactrocera dorsalis. Of the five target pest taxa studied, only Bactrocera dorsalis and Bactrocera carambolae remain as scientifically valid names. Molecular and pheromone markers are now available to distinguish Bactrocera dorsalis from Bactrocera carambolae. Ceratitis FAR Complex (Ceratitis fasciventris, Ceratitis anonae, Ceratitis rosa) – Morphology, morphometry, genetic, genomic, pheromone, cuticular hydrocarbon, ecology, behaviour, and developmental physiology data provide evidence for the existence of five different entities within this fruit fly complex from the African region. These are currently recognised as Ceratitis anonae, Ceratitis fasciventris (F1 and F2), Ceratitis rosa and a new species related to Ceratitis rosa (R2). The biological limits within Ceratitis fasciventris (i.e. F1 and F2) are not fully resolved. Microsatellites markers and morphological identification tools for the adult males of the five different FAR entities were developed based on male leg structures. Zeugodacus cucurbitae (formerly Bactrocera (Zeugodacus) cucurbitae) – Genetic variability was studied among melon fly populations throughout its geographic range in Africa and the Asia/Pacific region and found to be limited. Cross-mating studies indicated no incompatibility or sexual isolation. Host preference and genetic studies showed no evidence for the existence of host races. It was concluded that the melon fly does not represent a cryptic species complex, neither with regard to geographic distribution nor to host range. Nevertheless, the higher taxonomic classification under which this species had been placed, by the time the CRP was started, was found to be paraphyletic; as a result the subgenus Zeugodacus was elevated to genus level. PMID:26798252

A Proposal for a Genome Similarity-Based Taxonomy for Plant-Pathogenic Bacteria that Is Sufficiently Precise to Reflect Phylogeny, Host Range, and Outbreak Affiliation Applied to Pseudomonas syringae sensu lato as a Proof of Concept.

PubMed

Vinatzer, Boris A; Weisberg, Alexandra J; Monteil, Caroline L; Elmarakeby, Haitham A; Sheppard, Samuel K; Heath, Lenwood S

2017-01-01

Taxonomy of plant pathogenic bacteria is challenging because pathogens of different crops often belong to the same named species but current taxonomy does not provide names for bacteria below the subspecies level. The introduction of the host range-based pathovar system in the 1980s provided a temporary solution to this problem but has many limitations. The affordability of genome sequencing now provides the opportunity for developing a new genome-based taxonomic framework. We already proposed to name individual bacterial isolates based on pairwise genome similarity. Here, we expand on this idea and propose to use genome similarity-based codes, which we now call life identification numbers (LINs), to describe and name bacterial taxa. Using 93 genomes of Pseudomonas syringae sensu lato, LINs were compared with a P. syringae genome tree whereby the assigned LINs were found to be informative of a majority of phylogenetic relationships. LINs also reflected host range and outbreak association for strains of P. syringae pathovar actinidiae, a pathovar for which many genome sequences are available. We conclude that LINs could provide the basis for a new taxonomic framework to address the shortcomings of the current pathovar system and to complement the current taxonomic system of bacteria in general.

Classification of the European Union member states according to the relative level of sustainable development.

PubMed

Anna, Bluszcz

Nowadays methods of measurement and assessment of the level of sustained development at the international, national and regional level are a current research problem, which requires multi-dimensional analysis. The relative assessment of the sustainability level of the European Union member states and the comparative analysis of the position of Poland relative to other countries was the aim of the conducted studies in the article. EU member states were treated as objects in the multi-dimensional space. Dimensions of space were specified by ten diagnostic variables describing the sustainability level of UE countries in three dimensions, i.e., social, economic and environmental. Because the compiled statistical data were expressed in different units of measure, taxonomic methods were used for building an aggregated measure to assess the level of sustainable development of EU member states, which through normalisation of variables enabled the comparative analysis between countries. Methodology of studies consisted of eight stages, which included, among others: defining data matrices, calculating the variability coefficient for all variables, which variability coefficient was under 10 %, division of variables into stimulants and destimulants, selection of the method of variable normalisation, developing matrices of normalised data, selection of the formula and calculating the aggregated indicator of the relative level of sustainable development of the EU countries, calculating partial development indicators for three studies dimensions: social, economic and environmental and the classification of the EU countries according to the relative level of sustainable development. Statistical date were collected based on the Polish Central Statistical Office publication.

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.

PubMed

McDonald, Daniel; Price, Morgan N; Goodrich, Julia; Nawrocki, Eric P; DeSantis, Todd Z; Probst, Alexander; Andersen, Gary L; Knight, Rob; Hugenholtz, Philip

2012-03-01

Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a 'taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408,315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

PubMed Central

McDonald, Daniel; Price, Morgan N; Goodrich, Julia; Nawrocki, Eric P; DeSantis, Todd Z; Probst, Alexander; Andersen, Gary L; Knight, Rob; Hugenholtz, Philip

2012-01-01

Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a ‘taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/. PMID:22134646

Effectiveness of protected areas for vertebrates based on taxonomic and phylogenetic diversity.

PubMed

Quan, Qing; Che, Xianli; Wu, Yongjie; Wu, Yuchun; Zhang, Qiang; Zhang, Min; Zou, Fasheng

2018-04-01

Establishing protected areas is the primary goal and tool for preventing irreversible biodiversity loss. However, the effectiveness of protected areas that target specific species has been questioned for some time because targeting key species for conservation may impair the integral regional pool of species diversity and phylogenetic and functional diversity are seldom considered. We assessed the efficacy of protected areas in China for the conservation of phylogenetic diversity based on the ranges and phylogenies of 2279 terrestrial vertebrates. Phylogenetic and taxonomic diversity were strongly and positively correlated, and only 12.1-43.8% of priority conservation areas are currently protected. However, the patterns and coverage of phylogenetic diversity were affected when weighted by species richness. These results indicated that in China, protected areas targeting high species richness protected phylogenetic diversity well overall but failed to do so in some regions with more unique or threatened communities (e.g., coastal areas of eastern China, where severely threatened avian communities were less protected). Our results suggest that the current distribution of protected areas could be improved, although most protected areas protect both taxonomic and phylogenetic diversity. © 2017 Society for Conservation Biology.

What Images Reveal: a Comparative Study of Science Images between Australian and Taiwanese Junior High School Textbooks

NASA Astrophysics Data System (ADS)

Ge, Yun-Ping; Unsworth, Len; Wang, Kuo-Hua; Chang, Huey-Por

2017-07-01

From a social semiotic perspective, image designs in science textbooks are inevitably influenced by the sociocultural context in which the books are produced. The learning environments of Australia and Taiwan vary greatly. Drawing on social semiotics and cognitive science, this study compares classificational images in Australian and Taiwanese junior high school science textbooks. Classificational images are important kinds of images, which can represent taxonomic relations among objects as reported by Kress and van Leeuwen (Reading images: the grammar of visual design, 2006). An analysis of the images from sample chapters in Australian and Taiwanese high school science textbooks showed that the majority of the Taiwanese images are covert taxonomies, which represent hierarchical relations implicitly. In contrast, Australian classificational images included diversified designs, but particularly types with a tree structure which depicted overt taxonomies, explicitly representing hierarchical super-ordinate and subordinate relations. Many of the Taiwanese images are reminiscent of the specimen images in eighteenth century science texts representing "what truly is", while more Australian images emphasize structural objectivity. Moreover, Australian images support cognitive functions which facilitate reading comprehension. The relationships between image designs and learning environments are discussed and implications for textbook research and design are addressed.

A Bioinformatics Classifier and Database for Heme-Copper Oxygen Reductases

PubMed Central

Sousa, Filipa L.; Alves, Renato J.; Pereira-Leal, José B.; Teixeira, Miguel; Pereira, Manuela M.

2011-01-01

Background Heme-copper oxygen reductases (HCOs) are the last enzymatic complexes of most aerobic respiratory chains, reducing dioxygen to water and translocating up to four protons across the inner mitochondrial membrane (eukaryotes) or cytoplasmatic membrane (prokaryotes). The number of completely sequenced genomes is expanding exponentially, and concomitantly, the number and taxonomic distribution of HCO sequences. These enzymes were initially classified into three different types being this classification recently challenged. Methodology We reanalyzed the classification scheme and developed a new bioinformatics classifier for the HCO and Nitric oxide reductases (NOR), which we benchmark against a manually derived gold standard sequence set. It is able to classify any given sequence of subunit I from HCO and NOR with a global recall and precision both of 99.8%. We use this tool to classify this protein family in 552 completely sequenced genomes. Conclusions We concluded that the new and broader data set supports three functional and evolutionary groups of HCOs. Homology between NORs and HCOs is shown and NORs closest relationship with C Type HCOs demonstrated. We established and made available a classification web tool and an integrated Heme-Copper Oxygen reductase and NOR protein database (www.evocell.org/hco). PMID:21559461

The influence of rickettsiologists on post-modern microbiology.

PubMed

Georgiades, Kalliopi; Merhej, Vicky; Raoult, Didier

2011-01-01

Many of the definitions in microbiology are currently false. We have reviewed the great denominations of microbiology and attempted to free microorganisms from the theories of the twentieth century. The presence of compartmentation and a nucleoid in Planctomycetes clearly calls into question the accuracy of the definitions of eukaryotes and prokaryotes. Archaea are viewed as prokaryotes resembling bacteria. However, the name archaea, suggesting an archaic origin of lifestyle, is inconsistent with the lifestyle of this family. Viruses are defined as small, filterable infectious agents, but giant viruses challenge the size criteria used for the definition of a virus. Pathogenicity does not require the acquisition of virulence factors (except for toxins), and in many cases, gene loss is significantly inked to the emergence of virulence. Species classification based on 16S rRNA is useless for taxonomic purposes of human pathogens, as a 2% divergence would classify all Rickettsiae within the same species and would not identify bacteria specialized for mammal infection. The use of metagenomics helps us to understand evolution and physiology by elucidating the structure, function, and interactions of the major microbial communities, but it neglects the minority populations. Finally, Darwin's descent with modification theory, as represented by the tree of life, no longer matches our current genomic knowledge because genomics has revealed the occurrence of de novo-created genes and the mosaic structure of genomes, the Rhizome of life is therefore more appropriate.

Naming and outline of Dothideomycetes-2014 including proposals for the protection or suppression of generic names.

PubMed

Wijayawardene, Nalin N; Crous, Pedro W; Kirk, Paul M; Hawksworth, David L; Boonmee, Saranyaphat; Braun, Uwe; Dai, Dong-Qin; D'souza, Melvina J; Diederich, Paul; Dissanayake, Asha; Doilom, Mingkhuan; Hongsanan, Singang; Jones, E B Gareth; Groenewald, Johannes Z; Jayawardena, Ruvishika; Lawrey, James D; Liu, Jian-Kui; Lücking, Robert; Madrid, Hugo; Manamgoda, Dimuthu S; Muggia, Lucia; Nelsen, Matthew P; Phookamsak, Rungtiwa; Suetrong, Satinee; Tanaka, Kazuaki; Thambugala, Kasun M; Wanasinghe, Dhanushka N; Wikee, Saowanee; Zhang, Ying; Aptroot, André; Ariyawansa, H A; Bahkali, Ali H; Bhat, D Jayarama; Gueidan, Cécile; Chomnunti, Putarak; De Hoog, G Sybren; Knudsen, Kerry; Li, Wen-Jing; McKenzie, Eric H C; Miller, Andrew N; Phillips, Alan J L; Piątek, Marcin; Raja, Huzefa A; Shivas, Roger S; Slippers, Bernad; Taylor, Joanne E; Tian, Qing; Wang, Yong; Woudenberg, Joyce H C; Cai, Lei; Jaklitsch, Walter M; Hyde, Kevin D

2014-11-01

Article 59.1, of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN; Melbourne Code), which addresses the nomenclature of pleomorphic fungi, became effective from 30 July 2011. Since that date, each fungal species can have one nomenclaturally correct name in a particular classification. All other previously used names for this species will be considered as synonyms. The older generic epithet takes priority over the younger name. Any widely used younger names proposed for use, must comply with Art. 57.2 and their usage should be approved by the Nomenclature Committee for Fungi (NCF). In this paper, we list all genera currently accepted by us in Dothideomycetes (belonging to 23 orders and 110 families), including pleomorphic and nonpleomorphic genera. In the case of pleomorphic genera, we follow the rulings of the current ICN and propose single generic names for future usage. The taxonomic placements of 1261 genera are listed as an outline. Protected names and suppressed names for 34 pleomorphic genera are listed separately. Notes and justifications are provided for possible proposed names after the list of genera. Notes are also provided on recent advances in our understanding of asexual and sexual morph linkages in Dothideomycetes . A phylogenetic tree based on four gene analyses supported 23 orders and 75 families, while 35 families still lack molecular data.

Phylogenetic studies in Psathyrella focusing on sections Pennatae and Spadiceae--new evidence for the paraphyly of the genus.

PubMed

Vasutová, Martina; Antonín, Vladimír; Urban, Alexander

2008-10-01

The sections Pennatae and Spadiceae were chosen to test the agreement of current infrageneric classifications of Psathyrella (Psathyrellaceae, Agaricales) with molecular phylogenetic data and to evaluate the systematic significance of relevant morphological characters. The ITS and partial LSU regions of nu-rDNA from 53 specimens representing 34 species of Psathyrella were sequenced and analysed with parsimony-based and model-based phylogenetic methods. According to our analyses, the sections Pennatae and Spadiceae are polyphyletic and distributed across the family Psathyrellaceae, which is divided into at least five major groups. The first one comprises most of the included Psathyrella species and, probably, the whole genus Coprinellus. The second group is made up of Psathyrella gossypina and P. delineata. The third clade consists of the genus Coprinopsis and includes Psathyrella aff. huronensis and P. marcescibilis. The fourth clade is composed of two sister groups, the subgenus Homophron and the genus Lacrymaria, and the fifth group represents the genus Parasola including Psathyrella conopilus. These results are in agreement with neither the current circumscription of the two subgenera, Psathyra and Psathyrella, nor with the pre-sent disposition of the Psathyrellaceae. Taxonomically important morphological characters in the genus Psathyrella show a high degree of homoplasy. Although these characters are useful for species delimitation, and in some cases for the circumscription of sections, they appear insufficient for a phylogenetically correct generic concept.

Naming and outline of Dothideomycetes–2014 including proposals for the protection or suppression of generic names

PubMed Central

Wijayawardene, Nalin N.; Crous, Pedro W.; Kirk, Paul M.; Hawksworth, David L.; Boonmee, Saranyaphat; Braun, Uwe; Dai, Dong-Qin; D’souza, Melvina J.; Diederich, Paul; Dissanayake, Asha; Doilom, Mingkhuan; Hongsanan, Singang; Jones, E. B.Gareth; Groenewald, Johannes Z.; Jayawardena, Ruvishika; Lawrey, James D.; Liu, Jian-Kui; Lücking, Robert; Madrid, Hugo; Manamgoda, Dimuthu S.; Muggia, Lucia; Nelsen, Matthew P.; Phookamsak, Rungtiwa; Suetrong, Satinee; Tanaka, Kazuaki; Thambugala, Kasun M.; Wanasinghe, Dhanushka N.; Wikee, Saowanee; Zhang, Ying; Aptroot, André; Ariyawansa, H. A.; Bahkali, Ali H.; Bhat, D. Jayarama; Gueidan, Cécile; Chomnunti, Putarak; De Hoog, G. Sybren; Knudsen, Kerry; Li, Wen-Jing; McKenzie, Eric H. C.; Miller, Andrew N.; Phillips, Alan J. L.; Piątek, Marcin; Raja, Huzefa A.; Shivas, Roger S.; Slippers, Bernad; Taylor, Joanne E.; Tian, Qing; Wang, Yong; Woudenberg, Joyce H. C.; Cai, Lei; Jaklitsch, Walter M.

2016-01-01

Article 59.1, of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN; Melbourne Code), which addresses the nomenclature of pleomorphic fungi, became effective from 30 July 2011. Since that date, each fungal species can have one nomenclaturally correct name in a particular classification. All other previously used names for this species will be considered as synonyms. The older generic epithet takes priority over the younger name. Any widely used younger names proposed for use, must comply with Art. 57.2 and their usage should be approved by the Nomenclature Committee for Fungi (NCF). In this paper, we list all genera currently accepted by us in Dothideomycetes (belonging to 23 orders and 110 families), including pleomorphic and nonpleomorphic genera. In the case of pleomorphic genera, we follow the rulings of the current ICN and propose single generic names for future usage. The taxonomic placements of 1261 genera are listed as an outline. Protected names and suppressed names for 34 pleomorphic genera are listed separately. Notes and justifications are provided for possible proposed names after the list of genera. Notes are also provided on recent advances in our understanding of asexual and sexual morph linkages in Dothideomycetes. A phylogenetic tree based on four gene analyses supported 23 orders and 75 families, while 35 families still lack molecular data. PMID:27284275

Molecular phylogenetics of subfamily Ornithogaloideae (Hyacinthaceae) based on nuclear and plastid DNA regions, including a new taxonomic arrangement

PubMed Central

Martínez-Azorín, Mario; Crespo, Manuel B.; Juan, Ana; Fay, Michael F.

2011-01-01

Background and Aims The taxonomic arrangement within subfamily Ornithogaloideae (Hyacinthaceae) has been a matter of controversy in recent decades: several new taxonomic treatments have been proposed, based exclusively on plastid DNA sequences, and these have resulted in classifications which are to a great extent contradictory. Some authors have recognized only a single genus Ornithogalum for the whole subfamily, including 250–300 species of variable morphology, whereas others have recognized many genera. In the latter case, the genera are inevitably much smaller and they are better defined morphologically. However, some are not monophyletic as circumscribed. Methods Phylogenetic analyses of Ornithogaloideae were based on nucleotide sequences of four plastid regions (trnL intron, trnL-F spacer, rbcL and matK) and a nuclear region (ITS). Eighty species covering all relevant taxonomic groups previously recognized in the subfamily were sampled. Parsimony and Bayesian analyses were performed. The molecular data were compared with a matrix of 34 morphological characters. Key Results Combinations of plastid and nuclear data yielded phylogenetic trees which are better resolved than those obtained with any plastid region alone or plastid regions in combination. Three main clades are found, corresponding to the previously recognized tribes Albuceae, Dipcadieae and Ornithogaleae. In these, up to 19 clades are described which are definable by morphology and biogeography. These mostly correspond to previously described taxa, though some need recircumscription. Morphological characters are assessed for their diagnostic value for taxonomy in the subfamily. Conclusions On the basis of the phylogenetic analyses, 19 monophyletic genera are accepted within Ornithogaloideae: Albuca, Avonsera, Battandiera, Cathissa, Coilonox, Dipcadi, Eliokarmos, Elsiea, Ethesia, Galtonia, Honorius, Loncomelos, Melomphis, Neopatersonia, Nicipe, Ornithogalum, Pseudogaltonia, Stellarioides and Trimelopter. Each of these has a particular syndrome of morphological characters. As a result, 105 new combinations are made and two new names are proposed to accommodate the taxa studied in the new arrangement. A short morphological diagnosis, synonymy, details of distribution and an identification key are presented. PMID:21163815

Integrating a Numerical Taxonomic Method and Molecular Phylogeny for Species Delimitation of Melampsora Species (Melampsoraceae, Pucciniales) on Willows in China

PubMed Central

Zhao, Peng; Wang, Qing-Hong; Tian, Cheng-Ming; Kakishima, Makoto

2015-01-01

The species in genus Melampsora are the causal agents of leaf rust diseases on willows in natural habitats and plantations. However, the classification and recognition of species diversity are challenging because morphological characteristics are scant and morphological variation in Melampsora on willows has not been thoroughly evaluated. Thus, the taxonomy of Melampsora species on willows remains confused, especially in China where 31 species were reported based on either European or Japanese taxonomic systems. To clarify the species boundaries of Melampsora species on willows in China, we tested two approaches for species delimitation inferred from morphological and molecular variations. Morphological species boundaries were determined based on numerical taxonomic analyses of morphological characteristics in the uredinial and telial stages by cluster analysis and one-way analysis of variance. Phylogenetic species boundaries were delineated based on the generalized mixed Yule-coalescent (GMYC) model analysis of the sequences of the internal transcribed spacer (ITS1 and ITS2) regions including the 5.8S and D1/D2 regions of the large nuclear subunit of the ribosomal RNA gene. Numerical taxonomic analyses of 14 morphological characteristics recognized in the uredinial-telial stages revealed 22 morphological species, whereas the GMYC results recovered 29 phylogenetic species. In total, 17 morphological species were in concordance with the phylogenetic species and 5 morphological species were in concordance with 12 phylogenetic species. Both the morphological and molecular data supported 14 morphological characteristics, including 5 newly recognized characteristics and 9 traditionally emphasized characteristics, as effective for the differentiation of Melampsora species on willows in China. Based on the concordance and discordance of the two species delimitation approaches, we concluded that integrative taxonomy by using both morphological and molecular variations was an effective approach for delimitating Melampsora species on willows in China. PMID:26680416

Segal's Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project.

PubMed

Pettengill, James B; Rand, Hugh

2017-01-01

Obtaining human population level estimates of the prevalence of foodborne pathogens is critical for understanding outbreaks and ameliorating such threats to public health. Estimates are difficult to obtain due to logistic and financial constraints, but citizen science initiatives like that of the American Gut Project (AGP) represent a potential source of information concerning enteric pathogens. With an emphasis on genera Listeria and Salmonella , we sought to document the prevalence of those two taxa within the AGP samples. The results provided by AGP suggest a surprising 14% and 2% of samples contained Salmonella and Listeria , respectively. However, a reanalysis of those AGP sequences described here indicated that results depend greatly on the algorithm for assigning taxonomy and differences persisted across both a range of parameter settings and different reference databases (i.e., Greengenes and HITdb). These results are perhaps to be expected given that AGP sequenced the V4 region of 16S rRNA gene, which may not provide good resolution at the lower taxonomic levels (e.g., species), but it was surprising how often methods differ in classifying reads-even at higher taxonomic ranks (e.g., family). This highlights the misleading conclusions that can be reached when relying on a single method that is not a gold standard; this is the essence of Segal's Law: an individual with one watch knows what time it is but an individual with two is never sure. Our results point to the need for an appropriate molecular marker for the taxonomic resolution of interest, and calls for the development of more conservative classification methods that are fit for purpose. Thus, with 16S rRNA gene datasets, one must be cautious regarding the detection of taxonomic groups of public health interest (e.g., culture independent identification of foodborne pathogens or taxa associated with a given phenotype).

Mapping the Space of Genomic Signatures

PubMed Central

Kari, Lila; Hill, Kathleen A.; Sayem, Abu S.; Karamichalis, Rallis; Bryans, Nathaniel; Davis, Katelyn; Dattani, Nikesh S.

2015-01-01

We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to k (herein k = 9) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence alignment and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information. This method also correctly finds the mtDNA sequences most closely related to that of the anatomically modern human (the Neanderthal, the Denisovan, and the chimp), and that the sequence most different from it in this dataset belongs to a cucumber. PMID:26000734

Climate change. Accelerating extinction risk from climate change.

PubMed

Urban, Mark C

2015-05-01

Current predictions of extinction risks from climate change vary widely depending on the specific assumptions and geographic and taxonomic focus of each study. I synthesized published studies in order to estimate a global mean extinction rate and determine which factors contribute the greatest uncertainty to climate change-induced extinction risks. Results suggest that extinction risks will accelerate with future global temperatures, threatening up to one in six species under current policies. Extinction risks were highest in South America, Australia, and New Zealand, and risks did not vary by taxonomic group. Realistic assumptions about extinction debt and dispersal capacity substantially increased extinction risks. We urgently need to adopt strategies that limit further climate change if we are to avoid an acceleration of global extinctions. Copyright © 2015, American Association for the Advancement of Science.

A classification scheme for alternative oxidases reveals the taxonomic distribution and evolutionary history of the enzyme in angiosperms.

PubMed

Costa, José Hélio; McDonald, Allison E; Arnholdt-Schmitt, Birgit; Fernandes de Melo, Dirce

2014-11-01

A classification scheme based on protein phylogenies and sequence harmony method was used to clarify the taxonomic distribution and evolutionary history of the alternative oxidase (AOX) in angiosperms. A large data set analyses showed that AOX1 and AOX2 subfamilies were distributed into 4 phylogenetic clades: AOX1a-c/1e, AOX1d, AOX2a-c and AOX2d. High diversity in AOX family compositions was found. While the AOX2 subfamily was not detected in monocots, the AOX1 subfamily has expanded (AOX1a-e) in the large majority of these plants. In addition, Poales AOX1b and 1d were orthologous to eudicots AOX1d and then renamed as AOX1d1 and 1d2. AOX1 or AOX2 losses were detected in some eudicot plants. Several AOX2 duplications (AOX2a-c) were identified in eudicot species, mainly in the asterids. The AOX2b originally identified in eudicots in the Fabales order (soybean, cowpea) was divergent from AOX2a-c showing some specific amino acids with AOX1d and then it was renamed as AOX2d. AOX1d and AOX2d seem to be stress-responsive, facultative and mutually exclusive among species suggesting a complementary role with an AOX1(a) in stress conditions. Based on the data collected, we present a model for the evolutionary history of AOX in angiosperms and highlight specific areas where further research would be most beneficial. Copyright © 2014 Elsevier B.V. All rights reserved.

Chironomus group classification according to the mapping of polytene chromosomes

NASA Astrophysics Data System (ADS)

Salleh, Syafinaz; Kutty, Ahmad Abas

2013-11-01

Chironomus is one of the important genera in Chironomidae family since they are widely diverse and abundance in aquatic ecosystem. Since Chironomus is very diverse, taxonomic work on this genus is very difficult and incomplete. Objective of this study is to form group classification of Chironomus according to the polytene chromosome mapping. The specific characteristics of polytene chromosomes in the salivary gland appeared to be particularly promising for taxonomic diagnosis of chironomid species. Chironomid larvae were collected from pristine sites at Sg. Langat and cultured in laboratory to reach fourth instar stage. The salivary glands were removed from larvae and chromosomes were stained with aceto orcein. Results showed that polytene chromosomes of Chironomus comprise of three long metacentric or submetacentric arms (BF, CD and AE arms) and one short acrocentric (G arm). In regards to nucleolar organizing region (NOR), Balbiani ring (BR), puffings and chromosome rearrangement, a number of four groups of different banding patterns were found. Two groups called as G group A and B have common NOR on arm BF and BR on arm G. However, group A has rearrangement pattern on arm CD and not in group B. This makes group B separated from group A. Another two groups called as groups C and D do not have common NOR on arm BF and also BR on arm G. Groups C and D were separated using arms G and arm AE. At arm G, only group C rearrangement pattern at unit 23c whereas group D was found to have large NOR at arm G and as well as arm AE, only group D has rearrangement pattern at unit 12c. This study indicates that chromosome arrangement could aid in revealing Chironomus diversity.

Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases

PubMed Central

Müller, Albert Leopold; Kjeldsen, Kasper Urup; Rattei, Thomas; Pester, Michael; Loy, Alexander

2015-01-01

The energy metabolism of essential microbial guilds in the biogeochemical sulfur cycle is based on a DsrAB-type dissimilatory (bi)sulfite reductase that either catalyzes the reduction of sulfite to sulfide during anaerobic respiration of sulfate, sulfite and organosulfonates, or acts in reverse during sulfur oxidation. Common use of dsrAB as a functional marker showed that dsrAB richness in many environments is dominated by novel sequence variants and collectively represents an extensive, largely uncharted sequence assemblage. Here, we established a comprehensive, manually curated dsrAB/DsrAB database and used it to categorize the known dsrAB diversity, reanalyze the evolutionary history of dsrAB and evaluate the coverage of published dsrAB-targeted primers. Based on a DsrAB consensus phylogeny, we introduce an operational classification system for environmental dsrAB sequences that integrates established taxonomic groups with operational taxonomic units (OTUs) at multiple phylogenetic levels, ranging from DsrAB enzyme families that reflect reductive or oxidative DsrAB types of bacterial or archaeal origin, superclusters, uncultured family-level lineages to species-level OTUs. Environmental dsrAB sequences constituted at least 13 stable family-level lineages without any cultivated representatives, suggesting that major taxa of sulfite/sulfate-reducing microorganisms have not yet been identified. Three of these uncultured lineages occur mainly in marine environments, while specific habitat preferences are not evident for members of the other 10 uncultured lineages. In summary, our publically available dsrAB/DsrAB database, the phylogenetic framework, the multilevel classification system and a set of recommended primers provide a necessary foundation for large-scale dsrAB ecology studies with next-generation sequencing methods. PMID:25343514

Is geography an accurate predictor of evolutionary history in the millipede family Xystodesmidae?

PubMed Central

Marek, Paul E.

2017-01-01

For the past several centuries, millipede taxonomists have used the morphology of male copulatory structures (modified legs called gonopods), which are strongly variable and suggestive of species-level differences, as a source to understand taxon relationships. Millipedes in the family Xystodesmidae are blind, dispersal-limited and have narrow habitat requirements. Therefore, geographical proximity may instead be a better predictor of evolutionary relationship than morphology, especially since gonopodal anatomy is extremely divergent and similarities may be masked by evolutionary convergence. Here we provide a phylogenetics-based test of the power of morphological versus geographical character sets for resolving phylogenetic relationships in xystodesmid millipedes. Molecular data from 90 species-group taxa in the family were included in a six-gene phylogenetic analysis to provide the basis for comparing trees generated from these alternative character sets. The molecular phylogeny was compared to topologies representing three hypotheses: (1) a prior classification formulated using morphological and geographical data, (2) hierarchical groupings derived from Euclidean geographical distance, and (3) one based solely on morphological data. Euclidean geographical distance was not found to be a better predictor of evolutionary relationship than the prior classification, the latter of which was the most similar to the molecular topology. However, all three of the alternative topologies were highly divergent (Bayes factor >10) from the molecular topology, with the tree inferred exclusively from morphology being the most divergent. The results of this analysis show that a high degree of morphological convergence from substantial gonopod shape divergence generated spurious phylogenetic relationships. These results indicate the impact that a high degree of morphological homoplasy may have had on prior treatments of the family. Using the results of our phylogenetic analysis, we make several changes to the classification of the family, including transferring the rare state-threatened species Sigmoria whiteheadi Shelley, 1986 to the genus Apheloria Chamberlin, 1921—a relationship not readily apparent based on morphology alone. We show that while gonopod differences are a premier source of taxonomic characters to diagnose species pairwise, the traits should be viewed critically as taxonomic features uniting higher levels. PMID:29038750

Towards a collaborative, global infrastructure for biodiversity assessment

PubMed Central

Guralnick, Robert P; Hill, Andrew W; Lane, Meredith

2007-01-01

Biodiversity data are rapidly becoming available over the Internet in common formats that promote sharing and exchange. Currently, these data are somewhat problematic, primarily with regard to geographic and taxonomic accuracy, for use in ecological research, natural resources management and conservation decision-making. However, web-based georeferencing tools that utilize best practices and gazetteer databases can be employed to improve geographic data. Taxonomic data quality can be improved through web-enabled valid taxon names databases and services, as well as more efficient mechanisms to return systematic research results and taxonomic misidentification rates back to the biodiversity community. Both of these are under construction. A separate but related challenge will be developing web-based visualization and analysis tools for tracking biodiversity change. Our aim was to discuss how such tools, combined with data of enhanced quality, will help transform today's portals to raw biodiversity data into nexuses of collaborative creation and sharing of biodiversity knowledge. PMID:17594421

On the identity and taxonomic status of the enigmatic mantid Thespoides bolivari Chopard, 1916 (Mantodea: Mantidae, Angelinae).

PubMed

Rivera, Julio

2014-05-21

Chopard (1916) published a brief paper in which he cited and described a number of praying mantis species from the neotropics. The specimens he studied belonged to the prominent Spanish Entomologist Ignacio Bolívar y Urrutia (1850-1944), whose collection is now housed at the Museo Nacional de Ciencias Naturales in Madrid (MNCN), Spain (Izquierdo et al. 1997). In this publication Chopard described Thespoides bolivari Chopard, 1916 as a new genus and species, based on a single male obtained by French coleopterist René Oberthür in Cauca, Colombia. According to Chopard (1916) the specimen was remarkable for having, among other features, an abdomen that is markedly shorter than the rest of its body-certainly an unusual morphological trait among the Mantodea. Chopard assigned Thespoides to the Miopteryginae (Thespidae), but it was later reassigned (together with Angela Serville, 1839 as the "Angelae group") to the subfamily Schizocephalinae (Mantidae) by Giglio-Tos (1927). Current classifications consider the Angelinae to comprise a distinct subfamily of the Mantidae, with Thespoides and Angela as the only representatives of this subfamily with a Neotropical distribution (e.g. Ehrmann 2002).

Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae).

PubMed

Yang, Chien-Hui; Bracken-Grissom, Heather; Kim, Dohyup; Crandall, Keith A; Chan, Tin-Yam

2012-01-01

The slipper lobsters belong to the family Scyllaridae which contains a total of 20 genera and 89 species distributed across four subfamilies (Arctidinae, Ibacinae, Scyllarinae, and Theninae). We have collected nucleotide sequence data from regions of five different genes (16S, 18S, COI, 28S, H3) to estimate phylogenetic relationships among 54 species from the Scyllaridae with a focus on the species rich subfamily Scyllarinae. We have included in our analyses at least one representative from all 20 genera in the Scyllaridae and 35 of the 52 species within the Scyllarinae. Our resulting phylogenetic estimate shows the subfamilies are monophyletic, except for Ibacinae, which has paraphyletic relationships among genera. Many of the genera within the Scyllarinae form non-monophyletic groups, while the genera from all other subfamilies form well supported clades. We discuss the implications of this history on the evolution of morphological characters and ecological transitions (nearshore vs. offshore) within the slipper lobsters. Finally, we identify, through ancestral state character reconstructions, key morphological features diagnostic of the major clades of diversity within the Scyllaridae and relate this character evolution to current taxonomy and classification. Copyright © 2011 Elsevier Inc. All rights reserved.

Mitochondrial diversity and distribution of African green monkeys (chlorocebus gray, 1870).

PubMed

Haus, Tanja; Akom, Emmanuel; Agwanda, Bernard; Hofreiter, Michael; Roos, Christian; Zinner, Dietmar

2013-04-01

African green monkeys (Chlorocebus) represent a widely distributed and morphologically diverse primate genus in sub-Saharan Africa. Little attention has been paid to their genetic diversity and phylogeny. Based on morphological data, six species are currently recognized, but their taxonomy remains disputed. Here, we aim to characterize the mitochondrial (mt) DNA diversity, biogeography and phylogeny of African green monkeys. We analyzed the complete mitochondrial cytochrome b gene of 126 samples using feces from wild individuals and material from zoo and museum specimens with clear geographical provenance, including several type specimens. We found evidence for nine major mtDNA clades that reflect geographic distributions rather than taxa, implying that the mtDNA diversity of African green monkeys does not conform to existing taxonomic classifications. Phylogenetic relationships among clades could not be resolved suggesting a rapid early divergence of lineages. Several discordances between mtDNA and phenotype indicate that hybridization may have occurred in contact zones among species, including the threatened Bale monkey (Chlorocebus djamdjamensis). Our results provide both valuable data on African green monkeys' genetic diversity and evolution and a basis for further molecular studies on this genus. © 2013 Wiley Periodicals, Inc.

77 FR 4403 - Proposed Collection; Comment Request for Form 8832

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-27

... 8832, Entity Classification Election. DATES: Written comments should be received on or before March 27... INFORMATION: Title: Entity Classification Election. OMB Number: 1545-1516. Form Number: Form 8832. Abstract... its current classification must file Form 8832 to elect a classification. Current Actions: Changes...

DNA Barcoding the Medusozoa using mtCOI

NASA Astrophysics Data System (ADS)

Ortman, Brian D.; Bucklin, Ann; Pagès, Francesc; Youngbluth, Marsh

2010-12-01

The Medusozoa are a clade within the Cnidaria comprising the classes Hydrozoa, Scyphozoa, and Cubozoa. Identification of medusozoan species is challenging, even for taxonomic experts, due to their fragile forms and complex, morphologically-distinct life history stages. In this study 231 sequences for a portion of the mitochondrial Cytochrome Oxidase I (mtCOI) gene were obtained from 95 species of Medusozoans including; 84 hydrozoans (61 siphonophores, eight anthomedusae, four leptomedusae, seven trachymedusae, and four narcomedusae), 10 scyphozoans (three coronatae, four semaeostomae, two rhizostomae, and one stauromedusae), and one cubozoan. This region of mtCOI has been used as a DNA barcode (i.e., a molecular character for species recognition and discrimination) for a diverse array of taxa, including some Cnidaria. Kimura 2-parameter (K2P) genetic distances between sequence variants within species ranged from 0 to 0.057 (mean 0.013). Within the 13 genera for which multiple species were available, K2P distance between congeneric species ranged from 0.056 to 0.381. A cluster diagram generated by Neighbor Joining (NJ) using K2P distances reliably clustered all barcodes of the same species with ≥99% bootstrap support, ensuring accurate identification of species. Intra- and inter-specific variation of the mtCOI gene for the Medusozoa are appropriate for this gene to be used as a DNA barcode for species-level identification, but not for phylogenetic analysis or taxonomic classification of unknown sequences at higher taxonomic levels. This study provides a set of molecular tools that can be used to address questions of speciation, biodiversity, life-history, and population boundaries in the Medusozoa.

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.

Phylogenetic patterns of geographical and ecological diversification in the subgenus Drosophila.

PubMed

Morales-Hojas, Ramiro; Vieira, Jorge

2012-01-01

Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. Members of the subgenus Drosophila are distributed across the globe and show a large diversity of ecological niches. Furthermore, taxonomic classification of Drosophila includes the rank radiation, which refers to closely related species groups. Nevertheless, it has never been tested if these taxonomic radiations correspond to evolutionary radiations. Here we present a study of the patterns of diversification of Drosophila to test for increased diversification rates in relation to the geographic and ecological diversification processes. For this, we have estimated and dated a phylogeny of 218 species belonging to the major species groups of the subgenus. The obtained phylogenies are largely consistent with previous studies and indicate that the major groups appeared during the Oligocene/Miocene transition or early Miocene, characterized by a trend of climate warming with brief periods of glaciation. Ancestral reconstruction of geographic ranges and ecological resource use suggest at least two dispersals to the Neotropics from the ancestral Asiatic tropical disribution, and several transitions to specialized ecological resource use (mycophagous and cactophilic). Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. However, diversification analyses show no significant support for adaptive radiations as a result of geographic dispersal or ecological resource shift. Also, cactophily has not resulted in an increase in the diversification rate of the repleta and related groups. It is thus concluded that the taxonomic radiations do not correspond to adaptive radiations.

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.

Investigating bacterial populations in styrene-degrading biofilters by 16S rDNA tag pyrosequencing.

PubMed

Portune, Kevin J; Pérez, M Carmen; Álvarez-Hornos, F Javier; Gabaldón, Carmen

2015-01-01

Microbial biofilms are essential components in the elimination of pollutants within biofilters, yet still little is known regarding the complex relationships between microbial community structure and biodegradation function within these engineered ecosystems. To further explore this relationship, 16S rDNA tag pyrosequencing was applied to samples taken at four time points from a styrene-degrading biofilter undergoing variable operating conditions. Changes in microbial structure were observed between different stages of biofilter operation, and the level of styrene concentration was revealed to be a critical factor affecting these changes. Bacterial genera Azoarcus and Pseudomonas were among the dominant classified genera in the biofilter. Canonical correspondence analysis (CCA) and correlation analysis revealed that the genera Brevundimonas, Hydrogenophaga, and Achromobacter may play important roles in styrene degradation under increasing styrene concentrations. No significant correlations (P > 0.05) could be detected between biofilter operational/functional parameters and biodiversity measurements, although biological heterogeneity within biofilms and/or technical variability within pyrosequencing may have considerably affected these results. Percentages of selected bacterial taxonomic groups detected by fluorescence in situ hybridization (FISH) were compared to results from pyrosequencing in order to assess the effectiveness and limitations of each method for identifying each microbial taxon. Comparison of results revealed discrepancies between the two methods in the detected percentages of numerous taxonomic groups. Biases and technical limitations of both FISH and pyrosequencing, such as the binding of FISH probes to non-target microbial groups and lack of classification of sequences for defined taxonomic groups from pyrosequencing, may partially explain some differences between the two methods.

Is Homo sapiens polytypic? Human taxonomic diversity and its implications.

PubMed

Woodley, Michael A

2010-01-01

The term race is a traditional synonym for subspecies, however it is frequently asserted that Homo sapiens is monotypic and that what are termed races are nothing more than biological illusions. In this manuscript a case is made for the hypothesis that H. sapiens is polytypic, and in this way is no different from other species exhibiting similar levels of genetic and morphological diversity. First it is demonstrated that the four major definitions of race/subspecies can be shown to be synonymous within the context of the framework of race as a correlation structure of traits. Next the issue of taxonomic classification is considered where it is demonstrated that H. sapiens possesses high levels morphological diversity, genetic heterozygosity and differentiation (F(ST)) compared to many species that are acknowledged to be polytypic with respect to subspecies. Racial variation is then evaluated in light of the phylogenetic species concept, where it is suggested that the least inclusive monophyletic units exist below the level of species within H. sapiens indicating the existence of a number of potential human phylogenetic species; and the biological species concept, where it is determined that racial variation is too small to represent differentiation at the level of biological species. Finally the implications of this are discussed in the context of anthropology where an accurate picture of the sequence and timing of events during the evolution of human taxa are required for a complete picture of human evolution, and medicine, where a greater appreciation of the role played by human taxonomic differences in disease susceptibility and treatment responsiveness will save lives in the future.

A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies.

PubMed

Ramos, Vitor; Morais, João; Vasconcelos, Vitor M

2017-04-25

The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies.

A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies

PubMed Central

Ramos, Vitor; Morais, João; Vasconcelos, Vitor M.

2017-01-01

The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies. PMID:28440791

The unbridged gap between clinical diagnosis and contemporary research on aphasia: A short discussion on the validity and clinical utility of taxonomic categories.

PubMed

Kasselimis, Dimitrios S; Simos, Panagiotis G; Peppas, Christos; Evdokimidis, Ioannis; Potagas, Constantin

2017-01-01

Even if the traditional aphasia classification is continuously questioned by many scholars, it remains widely accepted among clinicians and included in textbooks as the gold standard. The present study aims to investigate the validity and clinical utility of this taxonomy. For this purpose, 65 left-hemisphere stroke patients were assessed and classified with respect to aphasia type based on performance on a Greek adaptation of the Boston Diagnostic Aphasia Examination. MRI and/or CT scans were obtained for each patient and lesions were identified and coded according to location. Results indicate that 26.5% of the aphasic profiles remained unclassified. More importantly, we failed to confirm the traditional lesion-to-syndrome correspondence for 63.5% of patients. Overall, our findings elucidate crucial vulnerabilities of the neo-associationist classification, and further support a deficit-rather than a syndrome-based approach. The issue of unclassifiable patients is also discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

Studying long 16S rDNA sequences with ultrafast-metagenomic sequence classification using exact alignments (Kraken).

PubMed

Valenzuela-González, Fabiola; Martínez-Porchas, Marcel; Villalpando-Canchola, Enrique; Vargas-Albores, Francisco

2016-03-01

Ultrafast-metagenomic sequence classification using exact alignments (Kraken) is a novel approach to classify 16S rDNA sequences. The classifier is based on mapping short sequences to the lowest ancestor and performing alignments to form subtrees with specific weights in each taxon node. This study aimed to evaluate the classification performance of Kraken with long 16S rDNA random environmental sequences produced by cloning and then Sanger sequenced. A total of 480 clones were isolated and expanded, and 264 of these clones formed contigs (1352 ± 153 bp). The same sequences were analyzed using the Ribosomal Database Project (RDP) classifier. Deeper classification performance was achieved by Kraken than by the RDP: 73% of the contigs were classified up to the species or variety levels, whereas 67% of these contigs were classified no further than the genus level by the RDP. The results also demonstrated that unassembled sequences analyzed by Kraken provide similar or inclusively deeper information. Moreover, sequences that did not form contigs, which are usually discarded by other programs, provided meaningful information when analyzed by Kraken. Finally, it appears that the assembly step for Sanger sequences can be eliminated when using Kraken. Kraken cumulates the information of both sequence senses, providing additional elements for the classification. In conclusion, the results demonstrate that Kraken is an excellent choice for use in the taxonomic assignment of sequences obtained by Sanger sequencing or based on third generation sequencing, of which the main goal is to generate larger sequences. Copyright © 2016 Elsevier B.V. All rights reserved.

Revisiting the taxonomical classification of Porcine Circovirus type 2 (PCV2): still a real challenge.

PubMed

Franzo, Giovanni; Cortey, Martí; Olvera, Alex; Novosel, Dinko; Castro, Alessandra Marnie Martins Gomes De; Biagini, Philippe; Segalés, Joaquim; Drigo, Michele

2015-08-28

PCV2 has emerged as one of the most devastating viral infections of swine farming, causing a relevant economic impact due to direct losses and control strategies expenses. Epidemiological and experimental studies have evidenced that genetic diversity is potentially affecting the virulence of PVC2. The growing number of PCV2 complete genomes and partial sequences available at GenBank questioned the accepted PCV2 classification. Nine hundred seventy five PCV2 complete genomes and 1,270 ORF2 sequences available from GenBank were subjected to recombination, PASC and phylogenetic analyses and results were used for comparison with previous classification scheme. The outcome of these analyses favors the recognition of four genotypes on the basis of ORF2 sequences, namely PCV2a, PCV2b, PCV2c and PCV2d-mPCV2b. To deal with the difficulty of founding an unambiguous classification and accounting the impossibility to define a p-distance cut-off, a set of reference sequences that could be used in further phylogenetic studies for PCV2 genotyping was established. Being aware that extensive phylogenetic analyses are time-consuming and often impracticable during routine diagnostic activity, ORF2 nucleotide positions adequately conserved in the reference sequences were identified and reported to allow a quick genotype differentiation. Globally, the present work provides an updated scenario of PCV2 genotypes distribution and, based on the limits of the previous classification criteria, proposes new rapid and effective schemes for differentiating the four defined PCV2 genotypes.

Taxonomic updates in Dolichandra Cham. (Bignonieae, Bignoniaceae)

PubMed Central

Fonseca, Luiz Henrique M.; Cabral, Simone Miranda; Agra, Maria de Fátima; Lohmann, Lúcia G.

2015-01-01

Abstract Dolichandra is a genus of lianas found in dry and wet Neotropical forests. The genus currently includes eight species and is well characterized by molecular and morphological synapomorphies. Here, Macfadyena hispida (DC.) Seemann is removed from synonomy with Dolichandra uncata (Andrews) L.G. Lohmann based on the presence of the hispid indument, vinaceus ovary, long fruits, and winged seeds. The combination Dolichandra hispida (DC.) L.H. Fonseca & L.G. Lohmann, comb. nov. is proposed, increasing the number of accepted species of Dolichandra to nine. A taxonomic key for all species of Dolichandra is presented. PMID:25878548

3122 Florence: Lightcurve Analysis and Preliminary Model

NASA Astrophysics Data System (ADS)

Franco, Lorenzo; Bacci, Paolo; Maestripieri, Martina; Baj, Giorgio; Galli, Gianni; Marchini, Alessandro; Noschese, Alfonso; Valvasori, Adriano; Caselli, Catia; Barbieri, Lorenzo; Facchini, Mauro

2018-04-01

Photometric observations of 3122 Florence were carried out on 12 nights between 2017 Aug 30 and Oct 6. This allowed us to determine a synodic period range from P = 2.3568 h ± 0.0002 to 2.3576 h ± 0.0002 with amplitude ranging from A = 0.22 to 0.16 mag. Multi-band photometric sessions and low resolution visible spectrum analysis shows a taxonomic class S, according to the SMASS II classification. Using lightcurve inversion method we also obtained a preliminary shape and spin axis model of (λ = 164° ± 15, β = -86° ± 5) with a sidereal period Psid = 2.3583 h ± 0.0005.

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.

Machine learning for predicting soil classes in three semi-arid landscapes

USGS Publications Warehouse

Brungard, Colby W.; Boettinger, Janis L.; Duniway, Michael C.; Wills, Skye A.; Edwards, Thomas C.

2015-01-01

Mapping the spatial distribution of soil taxonomic classes is important for informing soil use and management decisions. Digital soil mapping (DSM) can quantitatively predict the spatial distribution of soil taxonomic classes. Key components of DSM are the method and the set of environmental covariates used to predict soil classes. Machine learning is a general term for a broad set of statistical modeling techniques. Many different machine learning models have been applied in the literature and there are different approaches for selecting covariates for DSM. However, there is little guidance as to which, if any, machine learning model and covariate set might be optimal for predicting soil classes across different landscapes. Our objective was to compare multiple machine learning models and covariate sets for predicting soil taxonomic classes at three geographically distinct areas in the semi-arid western United States of America (southern New Mexico, southwestern Utah, and northeastern Wyoming). All three areas were the focus of digital soil mapping studies. Sampling sites at each study area were selected using conditioned Latin hypercube sampling (cLHS). We compared models that had been used in other DSM studies, including clustering algorithms, discriminant analysis, multinomial logistic regression, neural networks, tree based methods, and support vector machine classifiers. Tested machine learning models were divided into three groups based on model complexity: simple, moderate, and complex. We also compared environmental covariates derived from digital elevation models and Landsat imagery that were divided into three different sets: 1) covariates selected a priori by soil scientists familiar with each area and used as input into cLHS, 2) the covariates in set 1 plus 113 additional covariates, and 3) covariates selected using recursive feature elimination. Overall, complex models were consistently more accurate than simple or moderately complex models. Random forests (RF) using covariates selected via recursive feature elimination was consistently the most accurate, or was among the most accurate, classifiers between study areas and between covariate sets within each study area. We recommend that for soil taxonomic class prediction, complex models and covariates selected by recursive feature elimination be used. Overall classification accuracy in each study area was largely dependent upon the number of soil taxonomic classes and the frequency distribution of pedon observations between taxonomic classes. Individual subgroup class accuracy was generally dependent upon the number of soil pedon observations in each taxonomic class. The number of soil classes is related to the inherent variability of a given area. The imbalance of soil pedon observations between classes is likely related to cLHS. Imbalanced frequency distributions of soil pedon observations between classes must be addressed to improve model accuracy. Solutions include increasing the number of soil pedon observations in classes with few observations or decreasing the number of classes. Spatial predictions using the most accurate models generally agree with expected soil–landscape relationships. Spatial prediction uncertainty was lowest in areas of relatively low relief for each study area.

Analysis of hard coal quality for narrow size fraction under 20 mm

NASA Astrophysics Data System (ADS)

Niedoba, Tomasz; Pięta, Paulina

2018-01-01

The paper presents the results of an analysis of hard coal quality diversion in narrow size fraction by using taxonomic methods. Raw material samples were collected in selected mines of Upper Silesian Industrial Region and they were classified according to the Polish classification as types 31, 34.2 and 35. Then, each size fraction was characterized in terms of the following properties: density, ash content, calorific content, volatile content, total sulfur content and analytical moisture. As a result of the analysis it can be stated that the best quality in the entire range of the tested size fractions was the 34.2 coking coal type. At the same time, in terms of price parameters, high quality of raw material characterised the following size fractions: 0-6.3 mm of 31 energetic coal type and 0-3.15 mm of 35 coking coal type. The methods of grouping (Ward's method) and agglomeration (k-means method) have shown that the size fraction below 10 mm was characterized by higher quality in all the analyzed hard coal types. However, the selected taxonomic methods do not make it possible to identify individual size fraction or hard coal types based on chosen parameters.

DNA barcoding commercially important aquatic invertebrates of Turkey.

PubMed

Keskin, Emre; Atar, Hasan Hüseyin

2013-08-01

DNA barcoding was used in order to identify aquatic invertebrates sampled from fisheries bycatch and discards. A total of 440 unique cytochrome c oxidase sub unit I (COI) barcodes were generated for 22 species from three important phyla (Arthropoda, Cnidaria, and Mollusca). All the species were sequenced and submitted to GenBank and Barcode of Life Database (BOLD) databases using 654 bp-long fragment of mitochondrial COI gene. Two of them (Pontastacus leptodactylus and Rapana bezoar) were first records of the species for the BOLD database and six of them (Carcinus aestuarii, Loligo vulgaris, Melicertus kerathurus, Nephrops norvegicus, Scyllarides latus, and Scyllarus arctus) were first standard (>648 bp) COI barcode records for the GenBank database. COI barcodes were analyzed for nucleotide composition, nucleotide pair frequencies, and Kimura's two-parameter genetic distance. Mean genetic distance among species was found increasing at higher taxonomic levels. Neighbor-joining trees generated were congruent with morphometric-based taxonomic classification. Findings of this study clearly demonstrate that DNA barcodes could be used as an efficient molecular tool in identification of not only target species from fisheries but also bycatch and discard species, and so it could provide us leverage for a better understanding in monitoring and management of fisheries and biodiversity.

Brachiopod faunas after the end Ordovician mass extinction from South China: Testing ecological change through a major taxonomic crisis

NASA Astrophysics Data System (ADS)

Huang, Bing; Harper, David A. T.; Rong, Jiayu; Zhan, Renbin

2017-05-01

Classification of extinction events and their severity is generally based on taxonomic counts. The ecological impacts of such events have been categorized and prioritized but rarely tested with empirical data. The ecology of the end Ordovician extinction and subsequent biotic recovery is tracked through abundant and diverse brachiopod faunas in South China. The spatial and temporal ranges of some 6500 identified specimens, from 10 collections derived from six localities were investigated by network and cluster analyses, nonmetric multidimensional scaling and a species abundance model. Depth zonations and structure of brachiopod assemblages along an onshore-offshore gradient in the late Katian were similar to those in the latest Ordovician-earliest Silurian (post-extinction fauna). Within this ecological framework, deeper-water faunas are partly replaced by new taxa; siliciclastic substrates continued to be dominated by the more 'Ordovician' orthides and strophomenides, shallow-water carbonate environments hosted atrypides, athyridides and pentamerides, with the more typical Ordovician brachiopod fauna continuing to dominate until the late Rhuddanian. The end Ordovician extinctions tested the resilience of the brachiopod fauna without damage to its overall ecological structure; that commenced later at the end of the Rhuddanian.

Application of Taxonomic Modeling to Microbiota Data Mining for Detection of Helminth Infection in Global Populations.

PubMed

Torbati, Mahbaneh Eshaghzadeh; Mitreva, Makedonka; Gopalakrishnan, Vanathi

2016-12-01

Human microbiome data from genomic sequencing technologies is fast accumulating, giving us insights into bacterial taxa that contribute to health and disease. The predictive modeling of such microbiota count data for the classification of human infection from parasitic worms, such as helminths, can help in the detection and management across global populations. Real-world datasets of microbiome experiments are typically sparse, containing hundreds of measurements for bacterial species, of which only a few are detected in the bio-specimens that are analyzed. This feature of microbiome data produces the challenge of needing more observations for accurate predictive modeling and has been dealt with previously, using different methods of feature reduction. To our knowledge, integrative methods, such as transfer learning, have not yet been explored in the microbiome domain as a way to deal with data sparsity by incorporating knowledge of different but related datasets. One way of incorporating this knowledge is by using a meaningful mapping among features of these datasets. In this paper, we claim that this mapping would exist among members of each individual cluster, grouped based on phylogenetic dependency among taxa and their association to the phenotype. We validate our claim by showing that models incorporating associations in such a grouped feature space result in no performance deterioration for the given classification task. In this paper, we test our hypothesis by using classification models that detect helminth infection in microbiota of human fecal samples obtained from Indonesia and Liberia countries. In our experiments, we first learn binary classifiers for helminth infection detection by using Naive Bayes, Support Vector Machines, Multilayer Perceptrons, and Random Forest methods. In the next step, we add taxonomic modeling by using the SMART-scan module to group the data, and learn classifiers using the same four methods, to test the validity of the achieved groupings. We observed a 6% to 23% and 7% to 26% performance improvement based on the Area Under the receiver operating characteristic (ROC) Curve (AUC) and Balanced Accuracy (Bacc) measures, respectively, over 10 runs of 10-fold cross-validation. These results show that using phylogenetic dependency for grouping our microbiota data actually results in a noticeable improvement in classification performance for helminth infection detection. These promising results from this feasibility study demonstrate that methods such as SMART-scan can be utilized in the future for knowledge transfer from different but related microbiome datasets by phylogenetically-related functional mapping, to enable novel integrative biomarker discovery.

Global Coordination and Standardisation in Marine Biodiversity through the World Register of Marine Species (WoRMS) and Related Databases

PubMed Central

Bouchet, Philippe; Boxshall, Geoff; Fauchald, Kristian; Gordon, Dennis; Hoeksema, Bert W.; Poore, Gary C. B.; van Soest, Rob W. M.; Stöhr, Sabine; Walter, T. Chad; Vanhoorne, Bart; Decock, Wim

2013-01-01

The World Register of Marine Species is an over 90% complete open-access inventory of all marine species names. Here we illustrate the scale of the problems with species names, synonyms, and their classification, and describe how WoRMS publishes online quality assured information on marine species. Within WoRMS, over 100 global, 12 regional and 4 thematic species databases are integrated with a common taxonomy. Over 240 editors from 133 institutions and 31 countries manage the content. To avoid duplication of effort, content is exchanged with 10 external databases. At present WoRMS contains 460,000 taxonomic names (from Kingdom to subspecies), 368,000 species level combinations of which 215,000 are currently accepted marine species names, and 26,000 related but non-marine species. Associated information includes 150,000 literature sources, 20,000 images, and locations of 44,000 specimens. Usage has grown linearly since its launch in 2007, with about 600,000 unique visitors to the website in 2011, and at least 90 organisations from 12 countries using WoRMS for their data management. By providing easy access to expert-validated content, WoRMS improves quality control in the use of species names, with consequent benefits to taxonomy, ecology, conservation and marine biodiversity research and management. The service manages information on species names that would otherwise be overly costly for individuals, and thus minimises errors in the application of nomenclature standards. WoRMS' content is expanding to include host-parasite relationships, additional literature sources, locations of specimens, images, distribution range, ecological, and biological data. Species are being categorised as introduced (alien, invasive), of conservation importance, and on other attributes. These developments have a multiplier effect on its potential as a resource for biodiversity research and management. As a consequence of WoRMS, we are witnessing improved communication within the scientific community, and anticipate increased taxonomic efficiency and quality control in marine biodiversity research and management. PMID:23505408

Out of Africa: Phylogeny and biogeography of the widespread genus Acanthodactylus (Reptilia: Lacertidae).

PubMed

Tamar, Karin; Carranza, Salvador; Sindaco, Roberto; Moravec, Jiří; Trape, Jean-François; Meiri, Shai

2016-10-01

Acanthodactylus lizards are among the most diverse and widespread diurnal reptiles in the arid regions spanning from North Africa across to western India. Acanthodactylus constitutes the most species-rich genus in the family Lacertidae, with over 40 recognized species inhabiting a wide variety of dry habitats. The genus has seldom undergone taxonomic revisions, and although there are a number of described species and species-groups, their boundaries, as well as their interspecific relationships, remain largely unresolved. We constructed a multilocus phylogeny, combining data from two mitochondrial (12S, cytb) and three nuclear (MC1R, ACM4, c-mos) markers for 302 individuals belonging to 36 known species, providing the first large-scale time-calibrated molecular phylogeny of the genus. We evaluated phylogenetic relationships between and within species-groups, and assessed Acanthodactylus biogeography across its known range. Acanthodactylus cladogenesis is estimated to have originated in Africa due to vicariance and dispersal events from the Oligocene onwards. Radiation started with the separation into three clades: the Western and scutellatus clades largely distributed in North Africa, and the Eastern clade occurring mostly in south-west Asia. Most Acanthodactylus species diverged during the Miocene, possibly as a result of regional geological instability and climatic changes. We support most of the current taxonomic classifications and phylogenetic relationships, and provide genetic validity for most species. We reveal a new distinct blanfordii species-group, suggest new phylogenetic positions (A. hardyi, A. masirae), and synonymize several species and subspecies (A. lineomaculatus, A. boskianus khattensis and A. b. nigeriensis) with their phylogenetically closely-related species. We recommend a thorough systematic revision of taxa, such as A. guineensis, A. grandis, A. dumerilii, A. senegalensis and the pardalis and erythrurus species-groups, which exhibit high levels of intraspecific variability, and clear evidence of phylogenetic complexity. Copyright © 2016 Elsevier Inc. All rights reserved.

Global coordination and standardisation in marine biodiversity through the World Register of Marine Species (WoRMS) and related databases.

PubMed

Costello, Mark J; Bouchet, Philippe; Boxshall, Geoff; Fauchald, Kristian; Gordon, Dennis; Hoeksema, Bert W; Poore, Gary C B; van Soest, Rob W M; Stöhr, Sabine; Walter, T Chad; Vanhoorne, Bart; Decock, Wim; Appeltans, Ward

2013-01-01

The World Register of Marine Species is an over 90% complete open-access inventory of all marine species names. Here we illustrate the scale of the problems with species names, synonyms, and their classification, and describe how WoRMS publishes online quality assured information on marine species. Within WoRMS, over 100 global, 12 regional and 4 thematic species databases are integrated with a common taxonomy. Over 240 editors from 133 institutions and 31 countries manage the content. To avoid duplication of effort, content is exchanged with 10 external databases. At present WoRMS contains 460,000 taxonomic names (from Kingdom to subspecies), 368,000 species level combinations of which 215,000 are currently accepted marine species names, and 26,000 related but non-marine species. Associated information includes 150,000 literature sources, 20,000 images, and locations of 44,000 specimens. Usage has grown linearly since its launch in 2007, with about 600,000 unique visitors to the website in 2011, and at least 90 organisations from 12 countries using WoRMS for their data management. By providing easy access to expert-validated content, WoRMS improves quality control in the use of species names, with consequent benefits to taxonomy, ecology, conservation and marine biodiversity research and management. The service manages information on species names that would otherwise be overly costly for individuals, and thus minimises errors in the application of nomenclature standards. WoRMS' content is expanding to include host-parasite relationships, additional literature sources, locations of specimens, images, distribution range, ecological, and biological data. Species are being categorised as introduced (alien, invasive), of conservation importance, and on other attributes. These developments have a multiplier effect on its potential as a resource for biodiversity research and management. As a consequence of WoRMS, we are witnessing improved communication within the scientific community, and anticipate increased taxonomic efficiency and quality control in marine biodiversity research and management.

Automatic plankton image classification combining multiple view features via multiple kernel learning.

PubMed

Zheng, Haiyong; Wang, Ruchen; Yu, Zhibin; Wang, Nan; Gu, Zhaorui; Zheng, Bing

2017-12-28

Plankton, including phytoplankton and zooplankton, are the main source of food for organisms in the ocean and form the base of marine food chain. As the fundamental components of marine ecosystems, plankton is very sensitive to environment changes, and the study of plankton abundance and distribution is crucial, in order to understand environment changes and protect marine ecosystems. This study was carried out to develop an extensive applicable plankton classification system with high accuracy for the increasing number of various imaging devices. Literature shows that most plankton image classification systems were limited to only one specific imaging device and a relatively narrow taxonomic scope. The real practical system for automatic plankton classification is even non-existent and this study is partly to fill this gap. Inspired by the analysis of literature and development of technology, we focused on the requirements of practical application and proposed an automatic system for plankton image classification combining multiple view features via multiple kernel learning (MKL). For one thing, in order to describe the biomorphic characteristics of plankton more completely and comprehensively, we combined general features with robust features, especially by adding features like Inner-Distance Shape Context for morphological representation. For another, we divided all the features into different types from multiple views and feed them to multiple classifiers instead of only one by combining different kernel matrices computed from different types of features optimally via multiple kernel learning. Moreover, we also applied feature selection method to choose the optimal feature subsets from redundant features for satisfying different datasets from different imaging devices. We implemented our proposed classification system on three different datasets across more than 20 categories from phytoplankton to zooplankton. The experimental results validated that our system outperforms state-of-the-art plankton image classification systems in terms of accuracy and robustness. This study demonstrated automatic plankton image classification system combining multiple view features using multiple kernel learning. The results indicated that multiple view features combined by NLMKL using three kernel functions (linear, polynomial and Gaussian kernel functions) can describe and use information of features better so that achieve a higher classification accuracy.

Killer whale ecotypes: is there a global model?

PubMed

de Bruyn, P J N; Tosh, Cheryl A; Terauds, Aleks

2013-02-01

Killer whales, Orcinus orca, are top predators occupying key ecological roles in a variety of ecosystems and are one of the most widely distributed mammals on the planet. In consequence, there has been significant interest in understanding their basic biology and ecology. Long-term studies of Northern Hemisphere killer whales, particularly in the eastern North Pacific (ENP), have identified three ecologically distinct communities or ecotypes in that region. The success of these prominent ENP studies has led to similar efforts at clarifying the role of killer whale ecology in other regions, including Antarctica. In the Southern Hemisphere, killer whales present a range of behavioural, social and morphological characteristics to biologists, who often interpret this as evidence to categorize individuals or groups, and draw general ecological conclusions about these super-predators. Morphologically distinct forms (Type A, B, C, and D) occur in the Southern Ocean and studies of these different forms are often presented in conjunction with evidence for specialised ecology and behaviours. Here we review current knowledge of killer whale ecology and ecotyping globally and present a synthesis of existing knowledge. In particular, we highlight the complexity of killer whale ecology in the Southern Hemisphere and examine this in the context of comparatively well-studied Northern Hemisphere populations. We suggest that assigning erroneous or prefatory ecotypic status in the Southern Hemisphere could be detrimental to subsequent killer whale studies, because unsubstantiated characteristics may be assumed as a result of such classification. On this basis, we also recommend that ecotypic status classification for Southern Ocean killer whale morphotypes be reserved until more evidence-based ecological and taxonomic data are obtained. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

Alternative ways of representing Zapotec and Cuicatec folk classification of birds: a multidimensional model and its implications for culturally-informed conservation in Oaxaca, México.

PubMed

Alcántara-Salinas, Graciela; Ellen, Roy F; Valiñas-Coalla, Leopoldo; Caballero, Javier; Argueta-Villamar, Arturo

2013-12-09

We report on a comparative ethno-ornithological study of Zapotec and Cuicatec communities in Northern Oaxaca, Mexico that provided a challenge to some existing descriptions of folk classification. Our default model was the taxonomic system of ranks developed by Brent Berlin. Fieldwork was conducted in the Zapotec village of San Miguel Tiltepec and in the Cuicatec village of San Juan Teponaxtla, using a combination of ethnographic interviews and pile-sorting tests. Post-fieldwork, Principal Component Analysis using NTSYSpc V. 2.11f was applied to obtain pattern variation for the answers from different participants. Using language and pile-sorting data analysed through Principal Component Analysis, we show how both Zapotec and Cuicatec subjects place a particular emphasis on an intermediate level of classification.These categories group birds with non-birds using ecological and behavioral criteria, and violate a strict distinction between symbolic and mundane (or ‘natural’), and between ‘general-purpose’ and ‘single-purpose’ schemes. We suggest that shared classificatory knowledge embodying everyday schemes for apprehending the world of birds might be better reflected in a multidimensional model that would also provide a more realistic basis for developing culturally-informed conservation strategies.

Alternative ways of representing Zapotec and Cuicatec folk classification of birds: a multidimensional model and its implications for culturally-informed conservation in Oaxaca, México

PubMed Central

2013-01-01

Background We report on a comparative ethno-ornithological study of Zapotec and Cuicatec communities in Northern Oaxaca, Mexico that provided a challenge to some existing descriptions of folk classification. Our default model was the taxonomic system of ranks developed by Brent Berlin. Methods Fieldwork was conducted in the Zapotec village of San Miguel Tiltepec and in the Cuicatec village of San Juan Teponaxtla, using a combination of ethnographic interviews and pile-sorting tests. Post-fieldwork, Principal Component Analysis using NTSYSpc V. 2.11f was applied to obtain pattern variation for the answers from different participants. Results and conclusion Using language and pile-sorting data analysed through Principal Component Analysis, we show how both Zapotec and Cuicatec subjects place a particular emphasis on an intermediate level of classification. These categories group birds with non-birds using ecological and behavioral criteria, and violate a strict distinction between symbolic and mundane (or ‘natural’), and between ‘general-purpose’ and ‘single-purpose’ schemes. We suggest that shared classificatory knowledge embodying everyday schemes for apprehending the world of birds might be better reflected in a multidimensional model that would also provide a more realistic basis for developing culturally-informed conservation strategies. PMID:24321280

Cultures in psychiatric nosology: the CCMD-2-R and international classification of mental disorders.

PubMed

Lee, S

1996-12-01

This essay reviews the Chinese Classification of Mental Disorders, Second Edition, Revised (CCMD-2-R, 1995), by assuming the theoretical stance that symptom recognition, disease construction, and taxonomic strategy in psychiatry reflect, and are constrained by, the cultural norms and values as well as the political and economic organizations of the society in which they are embedded. The CCMD-2-R is an ethnomedical classification grounded in both symptomatology and etiology, in which Chinese psychiatrists seek to conform with international classifications on the one hand, and to sustain a nosology with Chinese cultural characteristics on the other. Although broad similarities between the ICD-10 and CCMD-2-R are evident, their blending is legitimately incomplete. Thus, the particular additions (e.g., travelling psychosis, qigong induced mental disorders), deletions (e.g., somatoform disorders, pathological gambling, a number of personality and sexual disorders), retentions (e.g., unipolar mania, neurosis, hysteria, homosexuality), and variations (e.g., depressive neurosis, neurasthenia) reveal not only the changing notions of illness but also the shifting social realities in contemporary China. The CCMD-2-R will be widely used by Chinese psychiatrists and should standardize diagnostic practice and facilitate research, but its impact on everyday clinical work and psychiatric training remains to be evaluated. For Western researchers, it is one avenue for achieving an understanding of the Chinese social world, and should usefully be contrasted with the ICD-10 and DSM-IV as the move towards an international nosology continues.

Visual Recognition Software for Binary Classification and Its Application to Spruce Pollen Identification

PubMed Central

Tcheng, David K.; Nayak, Ashwin K.; Fowlkes, Charless C.; Punyasena, Surangi W.

2016-01-01

Discriminating between black and white spruce (Picea mariana and Picea glauca) is a difficult palynological classification problem that, if solved, would provide valuable data for paleoclimate reconstructions. We developed an open-source visual recognition software (ARLO, Automated Recognition with Layered Optimization) capable of differentiating between these two species at an accuracy on par with human experts. The system applies pattern recognition and machine learning to the analysis of pollen images and discovers general-purpose image features, defined by simple features of lines and grids of pixels taken at different dimensions, size, spacing, and resolution. It adapts to a given problem by searching for the most effective combination of both feature representation and learning strategy. This results in a powerful and flexible framework for image classification. We worked with images acquired using an automated slide scanner. We first applied a hash-based “pollen spotting” model to segment pollen grains from the slide background. We next tested ARLO’s ability to reconstruct black to white spruce pollen ratios using artificially constructed slides of known ratios. We then developed a more scalable hash-based method of image analysis that was able to distinguish between the pollen of black and white spruce with an estimated accuracy of 83.61%, comparable to human expert performance. Our results demonstrate the capability of machine learning systems to automate challenging taxonomic classifications in pollen analysis, and our success with simple image representations suggests that our approach is generalizable to many other object recognition problems. PMID:26867017

TAXONOMY OF MEDICAL DEVICES IN THE LOGIC OF HEALTH TECHNOLOGY ASSESSMENT.

PubMed

Henschke, Cornelia; Panteli, Dimitra; Perleth, Matthias; Busse, Reinhard

2015-01-01

The suitability of general HTA methodology for medical devices is gaining interest as a topic of scientific discourse. Given the broad range of medical devices, there might be differences between groups of devices that impact both the necessity and the methods of their assessment. Our aim is to develop a taxonomy that provides researchers and policy makers with an orientation tool on how to approach the assessment of different types of medical devices. Several classifications for medical devices based on varying rationales for different regulatory and reporting purposes were analyzed in detail to develop a comprehensive taxonomic model. The taxonomy is based on relevant aspects of existing classification schemes incorporating elements of risk and functionality. Its 9 × 6 matrix distinguishes between the diagnostic or therapeutic nature of devices and considers whether the medical device is directly used by patients, constitutes part of a specific procedure, or can be used for a variety of procedures. We considered the relevance of different device categories in regard to HTA to be considerably variable, ranging from high to low. Existing medical device classifications cannot be used for HTA as they are based on different underlying logics. The developed taxonomy combines different device classification schemes used for different purposes. It aims at providing decision makers with a tool enabling them to consider device characteristics in detail across more than one dimension. The placement of device groups in the matrix can provide decision support on the necessity of conducting a full HTA.

Rapid identification and classification of Mycobacterium spp. using whole-cell protein barcodes with matrix assisted laser desorption ionization time of flight mass spectrometry in comparison with multigene phylogenetic analysis.

PubMed

Wang, Jun; Chen, Wen Feng; Li, Qing X

2012-02-24

The need of quick diagnostics and increasing number of bacterial species isolated necessitate development of a rapid and effective phenotypic identification method. Mass spectrometry (MS) profiling of whole cell proteins has potential to satisfy the requirements. The genus Mycobacterium contains more than 154 species that are taxonomically very close and require use of multiple genes including 16S rDNA for phylogenetic identification and classification. Six strains of five Mycobacterium species were selected as model bacteria in the present study because of their 16S rDNA similarity (98.4-99.8%) and the high similarity of the concatenated 16S rDNA, rpoB and hsp65 gene sequences (95.9-99.9%), requiring high identification resolution. The classification of the six strains by MALDI TOF MS protein barcodes was consistent with, but at much higher resolution than, that of the multi-locus sequence analysis of using 16S rDNA, rpoB and hsp65. The species were well differentiated using MALDI TOF MS and MALDI BioTyper™ software after quick preparation of whole-cell proteins. Several proteins were selected as diagnostic markers for species confirmation. An integration of MALDI TOF MS, MALDI BioTyper™ software and diagnostic protein fragments provides a robust phenotypic approach for bacterial identification and classification. Copyright © 2011 Elsevier B.V. All rights reserved.

[Review of current classification and terminology of vulvar disorders].

PubMed

Sláma, J

2012-08-01

To summarize current terminology and classification of vulvar disorders. Review article. Gynecologic oncology center, Department of Gynecology and Obstetrics, General Faculty Hospital and 1st Medical School of Charles University, Prague. Vulvar disorders include wide spectrum of different diagnoses. Multidisciplinary collaboration is frequently needed in diagnostical and therapeutical process. It is essential to use unified terminology using standard dermatological terms, and unified classification for comprehensible communication between different medical professions. Current classification, which is based on Clinical-pathological criteria, was established by International Society for the Study of Vulvovaginal Disease. Recently, there was introduced Clinical classification, which groups disorders according to main morphological finding. Adequate and unified classification and terminology are necessary for effective communication during the diagnostical process.

14 CFR 1203.501 - Applying derivative classification markings.

Code of Federal Regulations, 2011 CFR

2011-01-01

... INFORMATION SECURITY PROGRAM Derivative Classification § 1203.501 Applying derivative classification markings... classification decisions: (b) Verify the information's current level of classification so far as practicable...

14 CFR 1203.501 - Applying derivative classification markings.

Code of Federal Regulations, 2010 CFR

2010-01-01

... INFORMATION SECURITY PROGRAM Derivative Classification § 1203.501 Applying derivative classification markings... classification decisions: (b) Verify the information's current level of classification so far as practicable...

The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life on Earth

PubMed Central

2014-01-01

Abstract The Encyclopedia of Life (EOL, http://eol.org) aims to provide unprecedented global access to a broad range of information about life on Earth. It currently contains 3.5 million distinct pages for taxa and provides content for 1.3 million of those pages. The content is primarily contributed by EOL content partners (providers) that have a more limited geographic, taxonomic or topical scope. EOL aggregates these data and automatically integrates them based on associated scientific names and other classification information. EOL also provides interfaces for curation and direct content addition. All materials in EOL are either in the public domain or licensed under a Creative Commons license. In addition to the web interface, EOL is also accessible through an Application Programming Interface. In this paper, we review recent developments added for Version 2 of the web site and subsequent releases through Version 2.2, which have made EOL more engaging, personal, accessible and internationalizable. We outline the core features and technical architecture of the system. We summarize milestones achieved so far by EOL to present results of the current system implementation and establish benchmarks upon which to judge future improvements. We have shown that it is possible to successfully integrate large amounts of descriptive biodiversity data from diverse sources into a robust, standards-based, dynamic, and scalable infrastructure. Increasing global participation and the emergence of EOL-powered applications demonstrate that EOL is becoming a significant resource for anyone interested in biological diversity. PMID:24891832

A detailed phylogeny for the Methanomicrobiales

NASA Technical Reports Server (NTRS)

Rouviere, P.; Mandelco, L.; Winker, S.; Woese, C. R.

1992-01-01

The small subunit rRNA sequence of twenty archaea, members of the Methanomicrobiales, permits a detailed phylogenetic tree to be inferred for the group. The tree confirms earlier studies, based on far fewer sequences, in showing the group to be divided into two major clusters, temporarily designated the "methanosarcina" group and the "methanogenium" group. The tree also defines phylogenetic relationships within these two groups, which in some cases do not agree with the phylogenetic relationships implied by current taxonomic names--a problem most acute for the genus Methanogenium and its relatives. The present phylogenetic characterization provides the basis for a consistent taxonomic restructuring of this major methanogenic taxon.

taxonomic diversity and pest vulnerability in street tree assemblages

EPA Pesticide Factsheets

Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to what extent diversity reduces vulnerability to polyphagous (i.e. generalist) pests. Drawing on field data from seven communities in metropolitan Cincinnati, Ohio, USA, we tested the hypothesis that communities with higher diversity would exhibit lower vulnerability to the polyphagous Asian longhorned beetle, which currently threatens the region. Based on street tree compositions and the beetle??s host preferences, Asian longhorned beetle threatened up to 35.6% of individual street trees and 47.5% of the total basal area across the study area, but we did not see clear connections between taxonomic diversity and beetle vulnerability among study communities. For example, the city of Fairfield was among the least diverse communities but had the lowest proportion of trees vulnerable to Asian longhorned beetle, whereas the city of Wyoming exhibited high diversity and high vulnerability. On the other hand, Forest Park aligned with our original hypothesis, as it was characterised by low diversity and high vulnerability. Our results demonstrate that relatively high taxonomic diversity in street tree assemblages does not necessarily lead to reduced vulnerability to a polyphagous pest. Considering the threats posed by polyphagous pests, selecting a set of relatively pest resistant trees known to perform well in ur

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

PubMed

Mende, Daniel R; Letunic, Ivica; Huerta-Cepas, Jaime; Li, Simone S; Forslund, Kristoffer; Sunagawa, Shinichi; Bork, Peer

2017-01-04

The availability of microbial genomes has opened many new avenues of research within microbiology. This has been driven primarily by comparative genomics approaches, which rely on accurate and consistent characterization of genomic sequences. It is nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defined prokaryotic clades. Thus, we developed proGenomes, a resource that provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic clade. These genomes are assigned to 5306 consistent and accurate taxonomic species clusters based on previously established methodology. proGenomes also contains functional information for almost 80 million protein-coding genes, including a comprehensive set of general annotations and more focused annotations for carbohydrate-active enzymes and antibiotic resistance genes. Additionally, broad habitat information is provided for many genomes. All genomes and associated information can be downloaded by user-selected clade or multiple habitat-specific sets of representative genomes. We expect that the availability of high-quality genomes with comprehensive functional annotations will promote advances in clinical microbial genomics, functional evolution and other subfields of microbiology. proGenomes is available at http://progenomes.embl.de. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Cercosporoid fungi (Mycosphaerellaceae) 4. Species on dicots (Acanthaceae to Amaranthaceae).

PubMed

Braun, Uwe; Crous, Pedro W; Nakashima, Chiharu

2015-12-01

The present paper continues a series of comprehensive taxonomic treatments of cercosporoid fungi (formerly Cercospora s. lat.), belonging to the Mycosphaerellaceae (Ascomycota). The fourth contribution of this series initiates treatments of cercosporoid fungi on dicots and comprises species occurring on hosts belonging the the families Acanthaceae, Actinidiaceae, Adoxaceae, Aizoaceae, Altingiaceae, and Amaranthaceae. The species are described and illustrated in alphabetical order under the particular cercosporoid genera, supplemented by keys to the species concerned. A detailed introduction, a survey of currently recognised cercosporoid genera, a key to the genera concerned, and a discussion of taxonomically relevant characters were published in the first part of this series. The following taxonomic novelties are introduced: Cercospora blepharidicola nom. nov., C. celosiigena sp. nov., C. justiciae-adhatodae sp. nov., C. justiciigena nom. nov., C. sambucicola nom. nov., C. thunbergiigena nom. nov., Cercosporella pseudachyranthis comb. nov., Pseudocercospora cyathulae comb. nov., P. depazeoides comb. nov., P. varia var. viburni-sargentii var. nov., P. viburnicola sp. nov., P. viburni-erosi sp. nov., and P. viburni-nudi sp. nov.

Tephritid Integrative Taxonomy: Where We Are Now, with a Focus on the Resolution of Three Tropical Fruit Fly Species Complexes.

PubMed

Schutze, Mark K; Virgilio, Massimiliano; Norrbom, Allen; Clarke, Anthony R

2017-01-31

Accurate species delimitation underpins good taxonomy. Formalization of integrative taxonomy in the past decade has provided a framework for using multidisciplinary data to make species delimitation hypotheses more rigorous. We address the current state of integrative taxonomy by using as a case study an international project targeted at resolving three important tephritid species complexes: Bactrocera dorsalis complex, Anastrepha fraterculus complex, and Ceratitis FAR (C. fasciventris, C. anonae, C. rosa) complex. The integrative taxonomic approach has helped deliver significant advances in resolving these complexes: It has been used to identify some taxa as belonging to the same biological species as well as to confirm hidden cryptic diversity under a single taxonomic name. Nevertheless, the general application of integrative taxonomy has not been without issue, revealing challenges that must be considered when undertaking an integrative taxonomy project. Scrutiny of this international case study provides a unique opportunity to document lessons learned for the benefit of not only tephritid taxonomists, but also the wider taxonomic community.

Phylogenetic-based nomenclatural proposals for Ophiocordycipitaceae (Hypocreales) with new combinations in Tolypocladium.

PubMed

Quandt, C Alisha; Kepler, Ryan M; Gams, Walter; Araújo, João P M; Ban, Sayaka; Evans, Harry C; Hughes, David; Humber, Richard; Hywel-Jones, Nigel; Li, Zengzhi; Luangsa-Ard, J Jennifer; Rehner, Stephen A; Sanjuan, Tatiana; Sato, Hiroki; Shrestha, Bhushan; Sung, Gi-Ho; Yao, Yi-Jian; Zare, Rasoul; Spatafora, Joseph W

2014-06-01

Ophiocordycipitaceae is a diverse family comprising ecologically, economically, medicinally, and culturally important fungi. The family was recognized due to the polyphyly of the genus Cordyceps and the broad diversity of the mostly arthropod-pathogenic lineages of Hypocreales. The other two cordyceps-like families, Cordycipitaceae and Clavicipitaceae, will be revised taxonomically elsewhere. Historically, many species were placed in Cordyceps, but other genera have been described in this family as well, including several based on anamorphic features. Currently there are 24 generic names in use across both asexual and sexual life stages for species of Ophiocordycipitaceae. To reflect changes in Art. 59 in the International Code of Nomenclature for algae, fungi, and plants (ICN), we propose to protect and to suppress names within Ophiocordycipitaceae, and to present taxonomic revisions in the genus Tolypocladium, based on rigorous and extensively sampled molecular phylogenetic analyses. When approaching this task, we considered the principles of priority, monophyly, minimizing taxonomic revisions, and the practical utility of these fungi within the wider biological research community.

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.

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

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

Pyrosequencing of mcrA and Archaeal 16S rRNA Genes Reveals Diversity and Substrate Preferences of Methanogen Communities in Anaerobic Digesters

PubMed Central

Wilkins, David; Lu, Xiao-Ying; Shen, Zhiyong; Chen, Jiapeng

2014-01-01

Methanogenic archaea play a key role in biogas-producing anaerobic digestion and yet remain poorly taxonomically characterized. This is in part due to the limitations of low-throughput Sanger sequencing of a single (16S rRNA) gene, which in the past may have undersampled methanogen diversity. In this study, archaeal communities from three sludge digesters in Hong Kong and one wastewater digester in China were examined using high-throughput pyrosequencing of the methyl coenzyme M reductase (mcrA) and 16S rRNA genes. Methanobacteriales, Methanomicrobiales, and Methanosarcinales were detected in each digester, indicating that both hydrogenotrophic and acetoclastic methanogenesis was occurring. Two sludge digesters had similar community structures, likely due to their similar design and feedstock. Taxonomic classification of the mcrA genes suggested that these digesters were dominated by acetoclastic methanogens, particularly Methanosarcinales, while the other digesters were dominated by hydrogenotrophic Methanomicrobiales. The proposed euryarchaeotal order Methanomassiliicoccales and the uncultured WSA2 group were detected with the 16S rRNA gene, and potential mcrA genes for these groups were identified. 16S rRNA gene sequencing also recovered several crenarchaeotal groups potentially involved in the initial anaerobic digestion processes. Overall, the two genes produced different taxonomic profiles for the digesters, while greater methanogen richness was detected using the mcrA gene, supporting the use of this functional gene as a complement to the 16S rRNA gene to better assess methanogen diversity. A significant positive correlation was detected between methane production and the abundance of mcrA transcripts in digesters treating sludge and wastewater samples, supporting the mcrA gene as a biomarker for methane yield. PMID:25381241

The extinct river shark Glyphis pagoda from the Miocene of Myanmar and a review of the fossil record of the genus Glyphis (Carcharhiniformes: Carcharhinidae).

PubMed

Shimada, Kenshu; Egi, Naoko; Tsubamoto, Takehisa; Maung-Maung, Maung-Maung; Thaung-Htike, Thaung-Htike; Zin-Maung-Maung-Thein, Zin-Maung-Maung-Thein; Nishioka, Yuichiro; Sonoda, Teppei; Takai, Masanaru

2016-09-05

We redescribe an extinct river shark, Glyphis pagoda (Noetling), on the basis of 20 teeth newly collected from three different Miocene localities in Myanmar. One locality is a nearshore marine deposit (Obogon Formation) whereas the other two localities represent terrestrial freshwater deposits (Irrawaddy sediments), suggesting that G. pagoda from the Irrawaddy sediments was capable of tolerating low salinity like the extant Glyphis. Glyphis pagoda likely reached up to at least 185 cm in total body length and was probably piscivorous. The fossil species occurs in rocks of Myanmar and eastern and western India and stratigraphically ranges at least from the Lower Miocene (Aquitanian) to the lower Upper Miocene (mid-Tortonian). It has been classified under at least eight other genera to date, along with numerous taxonomic synonyms largely stemming from the lack of understanding of the heterodonty in extant Glyphis in the original description. Our literature review suggests that known Miocene shark faunas, particularly those in India, are manifested with unreliable taxonomic identifications and outdated classifications that warrant the need for a comprehensive taxonomic review in order to evaluate the evolutionary history and diversity pattern of Miocene shark faunas. The genus Glyphis has a roughly 23-million-year-long history, and its success may be related to the evolution of its low salinity tolerance. While extant Glyphis spp. are considered to be particularly vulnerable to habitat degradation and overfishing, the fossil record of G. pagoda provides renewed perspective on the natural history of the genus that can be taken into further consideration for conservation biology of the extant forms.

The Exploring Nature of Definitions and Classifications of Language Learning Strategies (LLSs) in the Current Studies of Second/Foreign Language Learning

ERIC Educational Resources Information Center

Fazeli, Seyed Hossein

2011-01-01

This study aims to explore the nature of definitions and classifications of Language Learning Strategies (LLSs) in the current studies of second/foreign language learning in order to show the current problems regarding such definitions and classifications. The present study shows that there is not a universal agreeable definition and…

Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources.

PubMed

Mao, Jin; Moore, Lisa R; Blank, Carrine E; Wu, Elvis Hsin-Hui; Ackerman, Marcia; Ranade, Sonali; Cui, Hong

2016-12-13

The large-scale analysis of phenomic data (i.e., full phenotypic traits of an organism, such as shape, metabolic substrates, and growth conditions) in microbial bioinformatics has been hampered by the lack of tools to rapidly and accurately extract phenotypic data from existing legacy text in the field of microbiology. To quickly obtain knowledge on the distribution and evolution of microbial traits, an information extraction system needed to be developed to extract phenotypic characters from large numbers of taxonomic descriptions so they can be used as input to existing phylogenetic analysis software packages. We report the development and evaluation of Microbial Phenomics Information Extractor (MicroPIE, version 0.1.0). MicroPIE is a natural language processing application that uses a robust supervised classification algorithm (Support Vector Machine) to identify characters from sentences in prokaryotic taxonomic descriptions, followed by a combination of algorithms applying linguistic rules with groups of known terms to extract characters as well as character states. The input to MicroPIE is a set of taxonomic descriptions (clean text). The output is a taxon-by-character matrix-with taxa in the rows and a set of 42 pre-defined characters (e.g., optimum growth temperature) in the columns. The performance of MicroPIE was evaluated against a gold standard matrix and another student-made matrix. Results show that, compared to the gold standard, MicroPIE extracted 21 characters (50%) with a Relaxed F1 score > 0.80 and 16 characters (38%) with Relaxed F1 scores ranging between 0.50 and 0.80. Inclusion of a character prediction component (SVM) improved the overall performance of MicroPIE, notably the precision. Evaluated against the same gold standard, MicroPIE performed significantly better than the undergraduate students. MicroPIE is a promising new tool for the rapid and efficient extraction of phenotypic character information from prokaryotic taxonomic descriptions. However, further development, including incorporation of ontologies, will be necessary to improve the performance of the extraction for some character types.

RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.

PubMed

Novichkov, Pavel S; Kazakov, Alexey E; Ravcheev, Dmitry A; Leyn, Semen A; Kovaleva, Galina Y; Sutormin, Roman A; Kazanov, Marat D; Riehl, William; Arkin, Adam P; Dubchak, Inna; Rodionov, Dmitry A

2013-11-01

Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches). RegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics. We significantly expanded a reference collection of manually curated regulons we introduced earlier. RegPrecise 3.0 provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties. Taxonomy-specific collections include 781 TF regulogs inferred in more than 160 genomes representing 14 taxonomic groups of Bacteria. TF-specific collections include regulogs for a selected subset of 40 TFs reconstructed across more than 30 taxonomic lineages. Novel collections of regulons operated by RNA regulatory elements (riboswitches) include near 400 regulogs inferred in 24 bacterial lineages. RegPrecise 3.0 provides four classifications of the reference regulons implemented as controlled vocabularies: 55 TF protein families; 43 RNA motif families; ~150 biological processes or metabolic pathways; and ~200 effectors or environmental signals. Genome-wide visualization of regulatory networks and metabolic pathways covered by the reference regulons are available for all studied genomes. A separate section of RegPrecise 3.0 contains draft regulatory networks in 640 genomes obtained by an conservative propagation of the reference regulons to closely related genomes. RegPrecise 3.0 gives access to the transcriptional regulons reconstructed in bacterial genomes. Analytical capabilities include exploration of: regulon content, structure and function; TF binding site motifs; conservation and variations in genome-wide regulatory networks across all taxonomic groups of Bacteria. RegPrecise 3.0 was selected as a core resource on transcriptional regulation of the Department of Energy Systems Biology Knowledgebase, an emerging software and data environment designed to enable researchers to collaboratively generate, test and share new hypotheses about gene and protein functions, perform large-scale analyses, and model interactions in microbes, plants, and their communities.

Genetic diversity of neotropical primates: phylogeny, population genetics, and animal models for infectious diseases.

PubMed

Moreira, M A M; Bonvicino, C R; Soares, M A; Seuánez, H N

2010-01-01

The classification of neotropical primates has been controversial, and different arrangements have been proposed based on disparate taxonomic criteria and on the traits selected for elucidating phylogenetic reconstructions, like morphologic characters, nuclear DNA and mitochondrial DNA. Population studies of some neotropical primates have been useful for assessing their extant genetic variability and for understanding their social structure and dynamics. Finally, neotropical primates have become valuable models for some human infectious deseases, especially for HIV studies related to viral resistance. In this review, we comment on these aspects that make neotropical primates a group of highly valuable species for basic and applied research. Copyright 2010 S. Karger AG, Basel.

The Ancient Evolutionary History of Polyomaviruses

PubMed Central

Buck, Christopher B.; Van Doorslaer, Koenraad; Peretti, Alberto; Geoghegan, Eileen M.; Tisza, Michael J.; An, Ping; Katz, Joshua P.; Pipas, James M.; McBride, Alison A.; Camus, Alvin C.; McDermott, Alexa J.; Dill, Jennifer A.; Delwart, Eric; Ng, Terry F. F.; Farkas, Kata; Austin, Charlotte; Kraberger, Simona; Davison, William; Pastrana, Diana V.; Varsani, Arvind

2016-01-01

Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae. PMID:27093155

A subgeneric classification of the genus Vaccinium and the metamorphosis of V. section Bracteata Nakai: more terrestrial and less epiphytic in habit, more continental and less insular in distribution.

PubMed

Vander Kloet, S P; Dickinson, T A

2009-05-01

The taxonomic integrity of Vaccinium section Bracteata sensu Sleumer was assessed using a variety of numerical measures on a data matrix created from 46 OTUs scored for 65 descriptors. These analyses supported a much restricted ambit for section Bracteata and the concomitant resurrection of section Nesococcus and section Euepigynium, a more cosmopolitan interpretation for section Eococcus and section Pyxothamnus as well as a new taxon, Vaccinium section Baccula-nigra Kloet, sect. nov. to accommodate V. fragile Franch. and its conspecifics. A key to all the sections as well as a brief description for each section is also provided.

The family Rhabdoviridae: Mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins

USGS Publications Warehouse

Dietzgen, Ralf G.; Kondo, Hideki; Goodin, Michael M.; Kurath, Gael; Vasilakis, Nikos

2017-01-01

The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes.

Diversity of large DNA viruses of invertebrates.

PubMed

Williams, Trevor; Bergoin, Max; van Oers, Monique M

2017-07-01

In this review we provide an overview of the diversity of large DNA viruses known to be pathogenic for invertebrates. We present their taxonomical classification and describe the evolutionary relationships among various groups of invertebrate-infecting viruses. We also indicate the relationships of the invertebrate viruses to viruses infecting mammals or other vertebrates. The shared characteristics of the viruses within the various families are described, including the structure of the virus particle, genome properties, and gene expression strategies. Finally, we explain the transmission and mode of infection of the most important viruses in these families and indicate, which orders of invertebrates are susceptible to these pathogens. Copyright © 2016 Elsevier Inc. All rights reserved.

Highly divergent cyclo-like virus in a great roundleaf bat (Hipposideros armiger) in Vietnam.

PubMed

Kemenesi, Gábor; Kurucz, Kornélia; Zana, Brigitta; Tu, Vuong Tan; Görföl, Tamás; Estók, Péter; Földes, Fanni; Sztancsik, Katalin; Urbán, Péter; Fehér, Enikő; Jakab, Ferenc

2017-08-01

Members of the viral family Circoviridae are increasingly recognized worldwide. Bats seem to be natural reservoirs or dietary-related dispensers of these viruses. Here, we report a distantly related member of the genus Cyclovirus detected in the faeces of a great roundleaf bat (Hipposideros armiger). Interestingly, the novel virus lacks a Circoviridae-specific stem-loop structure, although a Geminiviridae-like nonamer sequence was detected in the large intergenic region. Based on these differences and its phylogenetic position, we propose that our new virus represents a distant and highly divergent member of the genus Cyclovirus. However it is lacking several characteristics of members of the genus, which raises a challenge in its taxonomic classification.

Conservation genetics and species recovery

USGS Publications Warehouse

Pendleton, Ed; Vandergast, A.G.; King, T.L.

2008-01-01

Recent advances in molecular genetics have proven to be extremely useful in efforts to conserve imperiled species. Genetics data are used to identify appropriate units of management (e.g., populations, metapopulations), effective sizes of breeding populations, population mixing rates, and other variables. These data help managers make decisions about which populations to preserve, whether to move individuals from one site to another, how to breed species most effectively in captivity, and even, in some cases, what taxonomic classification is most appropriate. Many U.S. Geological Survey (USGS) Science Centers and Cooperative Fish and Wildlife Research Units have developed capabilities in genetics research. The two case studies that follow illustrate how USGS geneticists are assisting managers in recovering species on the brink.

Rapid quantification and taxonomic classification of environmentalDNA from both prokaryotic and eukaryotic origins using a microarray

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

DeSantis, Todd Z.; Stone, Carol E.; Murray, Sonya R.

2005-02-22

A microarray has been designed using 62,358 probes matched to both prokaryotic and eukaryotic small-subunit ribosomal RNA genes. The array categorized environmental DNA to specific phylogenetic clusters in under 9 h. To a background of DNA generated from natural outdoor aerosols, known quantities of rRNA gene copies from distinct organisms were added producing corresponding hybridization intensity scores that correlated well with their concentrations (r=0.917). Reproducible differences in microbial community composition were observed by altering the genomic DNA extraction method. Notably, gentle extractions produced peak intensities for Mycoplasmatales and Burkholderiales, whereas a vigorous disruption produced peak intensities for Vibrionales,Clostridiales, and Bacillales.

Taxonomic classification of soils using digital information from LANDSAT data. Huayllamarca and eucaliptus areas. M.S. Thesis - Bolivia Univ.

NASA Technical Reports Server (NTRS)

Quiroga, S. Q.

1977-01-01

The applicability of LANDSAT digital information to soil mapping is described. A compilation of all cartographic information and bibliography of the study area is made. LANDSAT MSS images on a scale of 1:250,000 are interpreted and a physiographic map with legend is prepared. The study area is inspected and a selection of the sample areas is made. A digital map of the different soil units is produced and the computer mapping units are checked against the soil units encountered in the field. The soil boundaries obtained by automatic mapping were not substantially changed by field work. The accuracy of the automatic mapping is rather high.

Traditional Knowledge and Nutritive Value of Indigenous Foods in the Oraon Tribal Community of Jharkhand: An Exploratory Cross-sectional Study

PubMed Central

Ghosh-Jerath, Suparna; Singh, Archna; Kamboj, Preeti; Goldberg, Gail; Magsumbol, Melina S.

2015-01-01

Traditional knowledge and nutritional value of indigenous foods of the Oraon tribal community in Jharkhand, India was explored. Focus group discussions were conducted with adult members to identify commonly consumed indigenous foods. Taxonomic classification and quantitative estimation of nutritive value were conducted in laboratories or utilized data from Indian food composition database. More than 130 varieties of indigenous foods were identified, many of which were rich sources of micronutrients like calcium, iron, vitamin A, and folic acid. Some were reported having medicinal properties. Utilization and ease of assimilation of indigenous foods into routine diets can be leveraged to address malnutrition in tribal communities. PMID:25902000

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.

Evolutionary and Taxonomic Implications of Variation in Nuclear Genome Size: Lesson from the Grass Genus Anthoxanthum (Poaceae)

PubMed Central

Chumová, Zuzana; Krejčíková, Jana; Mandáková, Terezie; Suda, Jan; Trávníček, Pavel

2015-01-01

The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x–18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus. PMID:26207824

Evolutionary and Taxonomic Implications of Variation in Nuclear Genome Size: Lesson from the Grass Genus Anthoxanthum (Poaceae).

PubMed

Chumová, Zuzana; Krejčíková, Jana; Mandáková, Terezie; Suda, Jan; Trávníček, Pavel

2015-01-01

The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x-18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus.

Generic revision and species classification of the Microdontinae (Diptera, Syrphidae)

PubMed Central

Reemer, Menno; Ståhls, Gunilla

2013-01-01

Abstract With 552 species group names available (excluding misspellings), the Microdontinae constitute the smallest of the three subfamilies of Syrphidae. Paradoxically, this subfamily is taxonomically the least organized of the three: 388 species names were previously classified in a single genus, Microdon Meigen, 1803. The present paper introduces a new generic classification of the Microdontinae, relying partly on the results of phylogenetic analyses of morphological and molecular data as published in other papers, and partly on examination of primary type specimens of 347 taxa, plus additional material, and original descriptions. A total number of 67 genus group names (excluding misspellings) are evaluated, redescribed, diagnosed and discussed, with several implications for their taxonomic status. Of these, 43 names are considered as valid genera, 7 as subgenera, 17 as synonyms. Two generic names (Ceratoconcha Simroth, 1907, Nothomicrodon Wheeler, 1924) are left unplaced, because they are known from immature stages only and cannot be reliably associated with taxa known from adults. The following 10 new genera are described by Reemer: Domodon, Heliodon, Laetodon, Menidon, Mermerizon, Metadon, Peradon, Piruwa, Sulcodon and Thompsodon. A key to all genera, subgenera and species groups is given. A total number of 26 new species are described in the following genera: Archimicrodon Hull, 1945, Ceratrichomyia Séguy, 1951, Domodon, Furcantenna Cheng, 2008, Heliodon, Indascia Keiser, 1958, Kryptopyga Hull, 1944, Masarygus Brèthes. 1908, Mermerizon, Metadon, Microdon, Paramixogaster Brunetti, 1923, Piruwa, Pseudomicrodon Hull, 1937, Rhopalosyrphus Giglio-Tos, 1891, and Thompsodon. New lectotypes are designated for Ceratrichomyia behara Séguy, 1951 and Microdon iheringi Bezzi, 1910. A total number of 267 new combinations of species and genera are proposed. New synonyms are proposed for 19 species group names. Three replacement names are introduced for primary and secondary junior homonyms: Microdon shirakii nom. n. (= Microdon tuberculatus Shiraki, 1968, primary homonym of Microdon tuberculatus de Meijere, 1913), Paramixogaster brunettii nom. n. (= Mixogaster vespiformis Brunetti, 1913, secondary homonym of Microdon vespiformis de Meijere, 1908), Paramixogaster sacki nom. n. (= Myxogaster variegata Sack, 1922, secondary homonym of Ceratophya variegata Walker, 1852). An attempt is made to classify all available species names into (sub)genera and species groups. The resulting classification comprises 454 valid species and 98 synonyms (excluding misspellings), of which 17 valid names and three synonyms are left unplaced. The paper concludes with a discussion on diagnostic characters of Microdontinae. PMID:23798897

Classification problems of Mount Kenya soils

NASA Astrophysics Data System (ADS)

Mutuma, Evans; Csorba, Ádám; Wawire, Amos; Dobos, Endre; Michéli, Erika

2017-04-01

Soil sampling on the agricultural lands covering 1200 square kilometers in the Eastern part of Mount Kenya was carried out to assess the status of soil organic carbon (SOC) as a soil fertility indicator, and to create an up-to-date soil classification map. The geology of the area consists of volcanic rocks and recent superficial deposits. The volcanic rocks are related to the Pliocene time; mainly: lahars, phonolites, tuffs, basalt and ashes. A total of 28 open profiles and 49 augered profiles with 269 samples were collected. The samples were analyzed for total carbon, organic carbon, particle size distribution, percent bases, cation exchange capacity and pH among other parameters. The objective of the study was to evaluate the variability of SOC in different Reference Soil Groups (RGS) and to compare the determined classification units with the KENSOTER database. Soil classification was performed based on the World Reference Base (WRB) for Soil Resources 2014. Based on the earlier surveys, geological and environmental setting, Nitisols were expected to be the dominant soils of the sampled area. However, this was not the case. The major differences to earlier survey data (KENSOTER database) are the presence of high activity clays (CEC value range 27.6 cmol/kg - 70 cmol/kg), high silt content (range 32.6 % - 52.4 %) and silt/clay ratio (range of 0.6 - 1.4) keeping these soils out of the Nitisols RSG. There was good accordance in the morphological features with the earlier survey but failed the silt/clay ratio criteria for Nitisols. This observation calls attention to set new classification criteria for Nitisols and other soils of warm, humid regions with variable rate of weathering to avoid difficulties in interpretation. To address the classification problem, this paper further discusses the taxonomic relationships between the studied soils. On the contrary most of the diagnostic elements (like the presence Umbric horizon, Vitric and Andic properties) and the some qualifiers (Humic, Dystric, Clayic, Skeletic, Leptic, etc) represent useful information for land use and management in the area.

A glimpse into the genetic basis of symbiosis between Hydrogenophaga and their helper strains in the biodegradation of 4-aminobenzenesulfonate

PubMed Central

Kim, Kangsan; Gan, Han Ming

2017-01-01

We report the whole genome sequences of Hydrogenophaga intermedia S1 and Agrobacterium radiobacter S2, the first reported bacterial co-culture capable of degrading 4-aminobenzenesulfonate (4-ABS), a recalcitrant industrial waste product. To gain insights into the genetic basis for the syntrophic interaction between this symbiotic pair and also another recently reported Hydrogenophaga associated co-culture, Hydrogenophaga sp. PBC and Ralstonia sp. PBA, we performed detailed genetic analysis of these four strains focusing on the metabolic pathways associated with biotin, para-aminobenzoic acid (pABA), and protocatechuate metabolism. Both assembled Hydrogenophaga draft genomes are missing a majority of the genetic components associated in the biosynthetic pathway of pABA and biotin. Interestingly, a fused pABA synthase was found in R. sp PBA but not in A. radiobacter S2. Furthermore, using whole genome data, the taxonomic classification of R. sp. PBA and A. radiobacter S2 (both previously inferred from 16S rRNA gene) was re-investigated, providing new evidence to propose for their re-classification at the genus and species level, respectively PMID:28775791

Evidentiary Reasoning in Diagnostic Classification Models

ERIC Educational Resources Information Center

Levy, Roy

2009-01-01

In "Unique Characteristics of Diagnostic Classification Models: A Comprehensive Review of the Current State-of-the-Art," Rupp and Templin (2008) undertake the ambitious task of providing a thorough portrait of the current state of diagnostic classification models (DCM). In this commentary, the author applauds Rupp and Templin for their…

Population Genetic Structure and Phylogeography of Camellia flavida (Theaceae) Based on Chloroplast and Nuclear DNA Sequences

PubMed Central

Wei, Su-Juan; Lu, Yong-Bin; Ye, Quan-Qing; Tang, Shao-Qing

2017-01-01

Camellia flavida is an endangered species of yellow camellia growing in limestone mountains in southwest China. The current classification of C. flavida into two varieties, var. flavida and var. patens, is controversial. We conducted a genetic analysis of C. flavida to determine its taxonomic structure. A total of 188 individual plants from 20 populations across the entire distribution range in southwest China were analyzed using two DNA fragments: a chloroplast DNA fragment from the small single copy region and a single-copy nuclear gene called phenylalanine ammonia-lyase (PAL). Sequences from both chloroplast and nuclear DNA were highly diverse; with high levels of genetic differentiation and restricted gene flow. This result can be attributed to the high habitat heterogeneity in limestone karst, which isolates C. flavida populations from each other. Our nuclear DNA results demonstrate that there are three differentiated groups within C. flavida: var. flavida 1, var. flavida 2, and var. patens. These genetic groupings are consistent with the morphological characteristics of the plants. We suggest that the samples included in this study constitute three taxa and the var. flavida 2 group is the genuine C. flavida. The three groups should be recognized as three management units for conservation concerns. PMID:28579991

Taxonomic revision of the Dasypus kappleri complex, with revalidations of Dasypus pastasae (Thomas, 1901) and Dasypus beniensis Lönnberg, 1942 (Cingulata, Dasypodidae).

PubMed

Feijó, Anderson; Cordeiro-Estrela, Pedro

2016-09-23

Dasypus kappleri is the largest species of the genus Dasypus and is restricted to the Amazonian rainforest biome. Over the last century, related taxa have been described and synonymized without comprehensive analyses, and the current classification involving two subspecies, Dasypus k. kappleri and Dasypus k. pastasae, has never been revised. The aim of this work is to clarify the taxonomy of Dasypus kappleri through integrative morphological and morphometric analyses. We examined 70 specimens housed in scientific collections as well as photographs of the type specimens of five nominal taxa. Three methodologies (discrete characters, linear and geometric morphometrics) were employed. All results converged on the recognition of three allopatric groups, each with diagnostic qualitative and quantitative traits, that we recognize as full species: Dasypus kappleri Krauss, 1862, occurs in the Guiana shield; Dasypus pastasae (Thomas, 1901) is distributed from the eastern Andes of Peru, Ecuador, Colombia, and Venezuela south of the Orinoco River into the western Brazilian Amazon; and Dasypus beniensis Lönnberg, 1942, occurs in the lowlands of Amazonian Brazil and Bolivia to the south of the Madre de Dios, Madeira, and lower Amazon rivers. This revision raises to nine the number of living species of Dasypus.

IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex

PubMed Central

Maccari, Giuseppe; Robinson, James; Ballingall, Keith; Guethlein, Lisbeth A.; Grimholt, Unni; Kaufman, Jim; Ho, Chak-Sum; de Groot, Natasja G.; Flicek, Paul; Bontrop, Ronald E.; Hammond, John A.; Marsh, Steven G. E.

2017-01-01

The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resource in its field, and this has led to an average of 1500 unique visitors and more than 5000 viewed pages per month. As the database has grown in size and complexity, it has created a number of challenges in maintaining and organizing information, particularly the need to standardize nomenclature and taxonomic classification, while incorporating new allele submissions. Here, we describe the latest database release, the IPD-MHC 2.0 and discuss planned developments. This release incorporates sequence updates and new tools that enhance database queries and improve the submission procedure by utilizing common tools that are able to handle the varied requirements of each MHC-group. PMID:27899604

Molecular systematics of Dendrobium (Orchidaceae, Dendrobieae) from mainland Asia based on plastid and nuclear sequences.

PubMed

Xiang, Xiao-Guo; Schuiteman, André; Li, De-Zhu; Huang, Wei-Chang; Chung, Shih-Wen; Li, Jian-Wu; Zhou, Hai-Lang; Jin, Wei-Tao; Lai, Yang-Jun; Li, Zhen-Yu; Jin, Xiao-Hua

2013-12-01

Dendrobium is one of the three largest genera and presents some of the most intricate taxonomic problems in the family Orchidaceae. Based on five DNA markers and a broad sampling of Dendrobium and its relatives from mainland Asia (109 species), our results indicate that mainland Asia Dendrobium is divided into eight clades (with two unplaced species) that form polytomies along the spine of the cladogram. Both Dendrobium and Epigeneium are well supported as monophyletic, whereas sect. Dendrobium, sect. Densiflora, sect. Breviflores, sect. Holochrysa, are paraphyletic/polyphyletic. Many ignored phylogenetic relationships, such as the one of major clades formed by D. jenkinsii and D. lindleyi (two members of sect. Densiflora), the Aphyllum group, the Devonianum group, the Catenatum group, the Crepidatum group, and the Dendrobium moniliforme complex are well supported by both molecular and morphological evidence. Based on our data, we propose to broaden sect. Dendrobium to include sect. Stuposa, sect. Breviflores, and sect. Holochrysa and to establish a new section to accommodate D. jenkinsii and D. lindleyi. Our results indicated that it is preferable to use a broad generic concept of Dendrobium and to pursue an improved infrageneric classification at sectional level, taking into account both morphology and current molecular findings. Copyright © 2013 Elsevier Inc. All rights reserved.

Modeling phytoplankton community in reservoirs. A comparison between taxonomic and functional groups-based models.

PubMed

Di Maggio, Jimena; Fernández, Carolina; Parodi, Elisa R; Diaz, M Soledad; Estrada, Vanina

2016-01-01

In this paper we address the formulation of two mechanistic water quality models that differ in the way the phytoplankton community is described. We carry out parameter estimation subject to differential-algebraic constraints and validation for each model and comparison between models performance. The first approach aggregates phytoplankton species based on their phylogenetic characteristics (Taxonomic group model) and the second one, on their morpho-functional properties following Reynolds' classification (Functional group model). The latter approach takes into account tolerance and sensitivity to environmental conditions. The constrained parameter estimation problems are formulated within an equation oriented framework, with a maximum likelihood objective function. The study site is Paso de las Piedras Reservoir (Argentina), which supplies water for consumption for 450,000 population. Numerical results show that phytoplankton morpho-functional groups more closely represent each species growth requirements within the group. Each model performance is quantitatively assessed by three diagnostic measures. Parameter estimation results for seasonal dynamics of the phytoplankton community and main biogeochemical variables for a one-year time horizon are presented and compared for both models, showing the functional group model enhanced performance. Finally, we explore increasing nutrient loading scenarios and predict their effect on phytoplankton dynamics throughout a one-year time horizon. Copyright © 2015 Elsevier Ltd. All rights reserved.

Qualitative analysis of the vaginal microbiota of healthy cattle and cattle with genital-tract disease.

PubMed

Rodrigues, N F; Kästle, J; Coutinho, T J D; Amorim, A T; Campos, G B; Santos, V M; Marques, L M; Timenetsky, J; de Farias, S T

2015-06-12

The microbial community of the reproductive appara-tus, when known, can provide information about the health of the host. Metagenomics has been used to characterize and obtain genetic infor-mation about microbial communities in various environments and can relate certain diseases with changes in this community composition. In this study, samples of vaginal surface mucosal secretions were col-lected from five healthy cows and five cows that showed symptoms of reproductive disorders. Following high-throughput sequencing of the isolated microbial DNA, data were processed using the Mothur soft-ware to remove low-quality sequences and chimeras, and released to the Ribosomal Database Project for classification of operational taxo-nomic units (OTUs). Local BLASTn was performed and results were loaded into the MEGAN program for viewing profiles and taxonomic microbial attributes. The control profile comprised a total of 15 taxa, with Bacteroides, Enterobacteriaceae, and Victivallis comprising the highest representation of OTUs; the reproductive disorder-positive profile comprised 68 taxa, with Bacteroides, Enterobacteriaceae, His-tophilus, Victivallis, Alistipes, and Coriobacteriaceae being the taxa with the most OTU representation. A change was observed in both the community composition as well as in the microbial attributes of the profiles, suggesting that a relationship might exist between the patho-gen and representative taxa, reflecting the production of metabolites to disease progression.

In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas.

PubMed

Tran, Phuong N; Savka, Michael A; Gan, Han Ming

2017-01-01

The genus Pseudomonas has one of the largest diversity of species within the Bacteria kingdom. To date, its taxonomy is still being revised and updated. Due to the non-standardized procedure and ambiguous thresholds at species level, largely based on 16S rRNA gene or conventional biochemical assay, species identification of publicly available Pseudomonas genomes remains questionable. In this study, we performed a large-scale analysis of all Pseudomonas genomes with species designation (excluding the well-defined P. aeruginosa ) and re-evaluated their taxonomic assignment via in silico genome-genome hybridization and/or genetic comparison with valid type species. Three-hundred and seventy-three pseudomonad genomes were analyzed and subsequently clustered into 145 distinct genospecies. We detected 207 erroneous labels and corrected 43 to the proper species based on Average Nucleotide Identity Multilocus Sequence Typing (MLST) sequence similarity to the type strain. Surprisingly, more than half of the genomes initially designated as Pseudomonas syringae and Pseudomonas fluorescens should be classified either to a previously described species or to a new genospecies. Notably, high pairwise average nucleotide identity (>95%) indicating species-level similarity was observed between P. synxantha-P. libanensis, P. psychrotolerans - P. oryzihabitans , and P. kilonensis- P. brassicacearum , that were previously differentiated based on conventional biochemical tests and/or genome-genome hybridization techniques.

Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016).

PubMed

Adams, Michael J; Lefkowitz, Elliot J; King, Andrew M Q; Harrach, Balázs; Harrison, Robert L; Knowles, Nick J; Kropinski, Andrew M; Krupovic, Mart; Kuhn, Jens H; Mushegian, Arcady R; Nibert, Max; Sabanadzovic, Sead; Sanfaçon, Hélène; Siddell, Stuart G; Simmonds, Peter; Varsani, Arvind; Zerbini, Francisco Murilo; Gorbalenya, Alexander E; Davison, Andrew J

2016-10-01

This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2016.Changes to virus taxonomy (the Universal Scheme of Virus Classification of the International Committee on Taxonomy of Viruses [ICTV]) now take place annually and are the result of a multi-stage process. In accordance with the ICTV Statutes ( http://www.ictvonline.org/statutes.asp ), proposals submitted to the ICTV Executive Committee (EC) undergo a review process that involves input from the ICTV Study Groups (SGs) and Subcommittees (SCs), other interested virologists, and the EC. After final approval by the EC, proposals are then presented for ratification to the full ICTV membership by publication on an ICTV web site ( http://www.ictvonline.org/ ) followed by an electronic vote. The latest set of proposals approved by the EC was made available on the ICTV website by January 2016 ( https://talk.ictvonline.org/files/proposals/ ). A list of these proposals was then emailed on 28 March 2016 to the 148 members of ICTV, namely the EC Members, Life Members, ICTV Subcommittee Members (including the SG chairs) and ICTV National Representatives. Members were then requested to vote on whether to ratify the taxonomic proposals (voting closed on 29 April 2016).

Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp.

PubMed Central

Mendes-Soares, Helena; Krishnan, Vandhana; Settles, Matthew L.; Ravel, Jacques; Brown, Celeste J.; Forney, Larry J.

2015-01-01

Although vaginal microbial communities of some healthy women have high proportions of Atopobium vaginae, the genus Atopobium is more commonly associated with bacterial vaginosis, a syndrome associated with an increased risk of adverse pregnancy outcomes and the transmission of sexually transmitted diseases. Genetic differences within Atopobium species may explain why single species can be associated with both health and disease. We used 16S rRNA gene sequences from previously published studies to explore the taxonomic diversity of the genus Atopobium in vaginal microbial communities of healthy women. Although A. vaginae was the species most commonly found, we also observed three other Atopobium species in the vaginal microbiota, one of which, A. parvulum, was not previously known to reside in the human vagina. Furthermore, we found several potential novel species of the genus Atopobium and multiple phylogenetic clades of A. vaginae. The diversity of Atopobium found in our study, which focused only on samples from healthy women, is greater than previously recognized, suggesting that analysis of samples from women with BV would yield even more diversity. Classification of microbes only to the genus level may thus obfuscate differences that might be important to better understand health or disease. PMID:25778779

Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches.

PubMed

Yahr, Rebecca; Schoch, Conrad L; Dentinger, Bryn T M

2016-09-05

The fungal kingdom is a hyperdiverse group of multicellular eukaryotes with profound impacts on human society and ecosystem function. The challenge of documenting and describing fungal diversity is exacerbated by their typically cryptic nature, their ability to produce seemingly unrelated morphologies from a single individual and their similarity in appearance to distantly related taxa. This multiplicity of hurdles resulted in the early adoption of DNA-based comparisons to study fungal diversity, including linking curated DNA sequence data to expertly identified voucher specimens. DNA-barcoding approaches in fungi were first applied in specimen-based studies for identification and discovery of taxonomic diversity, but are now widely deployed for community characterization based on sequencing of environmental samples. Collectively, fungal barcoding approaches have yielded important advances across biological scales and research applications, from taxonomic, ecological, industrial and health perspectives. A major outstanding issue is the growing problem of 'sequences without names' that are somewhat uncoupled from the traditional framework of fungal classification based on morphology and preserved specimens. This review summarizes some of the most significant impacts of fungal barcoding, its limitations, and progress towards the challenge of effective utilization of the exponentially growing volume of data gathered from high-throughput sequencing technologies.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

Notes on the genus Tunga (Siphonaptera: Tungidae) II – neosomes, morphology, classification, and other taxonomic notes

PubMed Central

Linardi, Pedro Marcos; Beaucournu, Jean-Claude; de Avelar, Daniel Moreira; Belaz, Sorya

2014-01-01

This review focuses on the neosomes, morphology, and taxonomy of adult species of the genus Tunga, complementing the previously published data on the phylogeny, ecology, and pathogenic role. Neosomes are structures formed after penetration of adult females into the skin of hosts resulting in significant enlargement, being the most characteristic and most frequently observed form in hosts. Neosomes can be differentiated by shape, measurements, and sites of attachment to principal hosts. The taxonomic value and morphometric data of the most widely used characteristics to separate species – such as frontal curvature, head chaetotaxy, preoral internal sclerotization, ventral and dorsal genal lobes, eyes, maxillary palps, fusion of pronotum and mesonotum, metacoxae, metatarsi chaetotaxy, spermatheca (females), manubrium, basimere, telomere, and phallosome (males) – are comparatively analyzed. The sexes, individual variations, undescribed species, higher taxa, as well as a proposal for division of the genus into two subgenera (Tunga and Brevidigita) are presented (as previously given by Wang). A key for females, males, and gravid females (neosomes) also is included for identifying the 13 known species. Data on host specificity and geographical distribution may also support the identification of Tunga species because some sand fleas and their hosts may have co-evolved. PMID:25514594

IRAS Low Resolution Spectra of Asteroids

NASA Technical Reports Server (NTRS)

Cohen, Martin; Walker, Russell G.

2002-01-01

Optical/near-infrared studies of asteroids are based on reflected sunlight and surface albedo variations create broad spectral features, suggestive of families of materials. There is a significant literature on these features, but there is very little work in the thermal infrared that directly probes the materials emitting on the surfaces of asteroids. We have searched for and extracted 534 thermal spectra of 245 asteroids from the original Dutch (Groningen) archive of spectra observed by the IRAS Low Resolution Spectrometer (LRS). We find that, in general, the observed shapes of the spectral continua are inconsistent with that predicted by the standard thermal model used by IRAS. Thermal models such as proposed by Harris (1998) and Harris et al.(1998) for the near-earth asteroids with the "beaming parameter" in the range of 1.0 to 1.2 best represent the observed spectral shapes. This implies that the IRAS Minor Planet Survey (IMPS, Tedesco, 1992) and the Supplementary IMPS (SIMPS, Tedesco, et al., 2002) derived asteroid diameters are systematically underestimated, and the albedos are overestimated. We have tentatively identified several spectral features that appear to be diagnostic of at least families of materials. The variation of spectral features with taxonomic class hints that thermal infrared spectra can be a valuable tool for taxonomic classification of asteroids.

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.

Multivariate analysis as a key tool in chemotaxonomy of brinjal eggplant, African eggplants and wild related species.

PubMed

Haliński, Łukasz P; Samuels, John; Stepnowski, Piotr

2017-12-01

The brinjal eggplant (Solanum melongena L.) is an important vegetable species worldwide, while African eggplants (S. aethiopicum L., S. macrocarpon L.) are indigenous vegetable species of local significance. Taxonomy of eggplants and their wild relatives is complicated and still unclear. Hence, the objective of the study was to clarify taxonomic position of cultivars and landraces of brinjal, its wild relatives and African eggplant species and their wild ancestors using chemotaxonomic markers and multivariate analysis techniques for data processing, with special attention paid to the recognition of markers characteristic for each group of the plants. The total of 34 accessions belonging to 9 species from genus Solanum L. were used in the study. Chemotaxonomic analysis was based on the profiles of cuticular n-alkanes and methylalkanes, obtained using gas chromatography-mass spectrometry and gas chromatography with flame ionization detector. Standard hierarchical cluster analysis (HCA) and principal component analysis (PCA) were used for the classification, while the latter and two-way HCA allowed to identify markers responsible for the clustering of the species. Cultivars, landraces and wild forms of S. melongena were practically identical in terms of their taxonomic position. The results confirmed high and statistically significant distinctiveness of all African eggplant species from the brinjal eggplant. The latter was characterized mostly by abundant long chain hydrocarbons in the range of 34-37 carbon atoms. The differences between both African eggplant species were, however, also statistically significant; S. aethiopicum displayed the highest contribution of 2-methylalkanes to the total cuticular hydrocarbons, while S. macrocarpon was characterized by elevated n-alkanes in the range of 25-32 carbon atoms. Wild ancestors of both African eggplant species were identical with their cultivated relatives. Concluding, high usefulness of the chemotaxonomic approach in classification of this important group of plants was confirmed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Integration of DNA barcoding approaches into aquatic bioassessments

EPA Science Inventory

The Clean Water Act directs states to protect water resources by developing criteria based in part on biological assessments of natural aquatic ecosystems. Current protocols can be limited by the availability of taxonomic expertise and concerns about precision and accuracy in mor...

Automated structural classification of lipids by machine learning.

PubMed

Taylor, Ryan; Miller, Ryan H; Miller, Ryan D; Porter, Michael; Dalgleish, James; Prince, John T

2015-03-01

Modern lipidomics is largely dependent upon structural ontologies because of the great diversity exhibited in the lipidome, but no automated lipid classification exists to facilitate this partitioning. The size of the putative lipidome far exceeds the number currently classified, despite a decade of work. Automated classification would benefit ongoing classification efforts by decreasing the time needed and increasing the accuracy of classification while providing classifications for mass spectral identification algorithms. We introduce a tool that automates classification into the LIPID MAPS ontology of known lipids with >95% accuracy and novel lipids with 63% accuracy. The classification is based upon simple chemical characteristics and modern machine learning algorithms. The decision trees produced are intelligible and can be used to clarify implicit assumptions about the current LIPID MAPS classification scheme. These characteristics and decision trees are made available to facilitate alternative implementations. We also discovered many hundreds of lipids that are currently misclassified in the LIPID MAPS database, strongly underscoring the need for automated classification. Source code and chemical characteristic lists as SMARTS search strings are available under an open-source license at https://www.github.com/princelab/lipid_classifier. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

UniEuk: Time to Speak a Common Language in Protistology!

PubMed

Berney, Cédric; Ciuprina, Andreea; Bender, Sara; Brodie, Juliet; Edgcomb, Virginia; Kim, Eunsoo; Rajan, Jeena; Parfrey, Laura Wegener; Adl, Sina; Audic, Stéphane; Bass, David; Caron, David A; Cochrane, Guy; Czech, Lucas; Dunthorn, Micah; Geisen, Stefan; Glöckner, Frank Oliver; Mahé, Frédéric; Quast, Christian; Kaye, Jonathan Z; Simpson, Alastair G B; Stamatakis, Alexandros; Del Campo, Javier; Yilmaz, Pelin; de Vargas, Colomban

2017-05-01

Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental '-omics' surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta-omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist -omics age to the fragile, centuries-old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community-based and expert-driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL-EBI, ensuring its broad use and long-term preservation as a reference taxonomy for eukaryotes. © 2017 The Author(s) Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.

Integrating and visualizing primary data from prospective and legacy taxonomic literature

PubMed Central

Agosti, Donat; Penev, Lyubomir; Sautter, Guido; Georgiev, Teodor; Catapano, Terry; Patterson, David; King, David; Pereira, Serrano; Vos, Rutger Aldo; Sierra, Soraya

2015-01-01

Abstract Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions. PMID:26023286

Bacterial community composition in the gut content of Lampetra japonica revealed by 16S rRNA gene pyrosequencing.

PubMed

Zuo, Yu; Xie, Wenfang; Pang, Yue; Li, Tiesong; Li, Qingwei; Li, Yingying

2017-01-01

The composition of the bacterial communities in the hindgut contents of Lampetrs japonica was surveyed by Illumina MiSeq of the 16S rRNA gene. An average of 32385 optimized reads was obtained from three samples. The rarefaction curve based on the operational taxonomic units tended to approach the asymptote. The rank abundance curve representing the species richness and evenness was calculated. The composition of microbe in six classification levels was also analyzed. Top 20 members in genera level were displayed as the classification tree. The abundance of microorganisms in different individuals was displayed as the pie charts at the branch nodes in the classification tree. The differences of top 50 genera in abundance between individuals of lamprey are displayed as a heatmap. The pairwise comparison of bacterial taxa abundance revealed that there are no significant differences of gut microbiota between three individuals of lamprey at a given rarefied depth. Also, the gut microbiota derived from L. japonica displays little similarity with other aquatic organism of Vertebrata after UPGMA analysis. The metabolic function of the bacterial communities was predicted through KEGG analysis. This study represents the first analysis of the bacterial community composition in the gut content of L. japonica. The investigation of the gut microbiota associated with L. japonica will broaden our understanding of this unique organism.

On Identifying Clusters Within the C-type Asteroids of the Sloan Digital Sky Survey

NASA Astrophysics Data System (ADS)

Poole, Renae; Ziffer, J.; Harvell, T.

2012-10-01

We applied AutoClass, a data mining technique based upon Bayesian Classification, to C-group asteroid colors in the Sloan Digital Sky Survey (SDSS). Previous taxonomic studies relied mostly on Principal Component Analysis (PCA) to differentiate asteroids within the C-group (e.g. B, G, F, Ch, Cg and Cb). AutoClass's advantage is that it calculates the most probable classification for us, removing the human factor from this part of the analysis. In our results, AutoClass divided the C-groups into two large classes and six smaller classes. The two large classes (n=4974 and 2033, respectively) display distinct regions with some overlap in color-vs-color plots. Each cluster's average spectrum is compared to 'typical' spectra of the C-group subtypes as defined by Tholen (1989) and each cluster's members are evaluated for consistency with previous taxonomies. Of the 117 asteroids classified as B-type in previous taxonomies, only 12 were found with SDSS colors that matched our criteria of having less than 0.1 magnitude error in u and 0.05 magnitude error in g, r, i, and z colors. Although this is a relatively small group, 11 of the 12 B-types were placed by AutoClass in the same cluster. By determining the C-group sub-classifications in the large SDSS database, this research furthers our understanding of the stratigraphy and composition of the main-belt.

Biodiversity of the Deep-Sea Continental Margin Bordering the Gulf of Maine (NW Atlantic): Relationships among Sub-Regions and to Shelf Systems

PubMed Central

Kelly, Noreen E.; Shea, Elizabeth K.; Metaxas, Anna; Haedrich, Richard L.; Auster, Peter J.

2010-01-01

Background In contrast to the well-studied continental shelf region of the Gulf of Maine, fundamental questions regarding the diversity, distribution, and abundance of species living in deep-sea habitats along the adjacent continental margin remain unanswered. Lack of such knowledge precludes a greater understanding of the Gulf of Maine ecosystem and limits development of alternatives for conservation and management. Methodology/Principal Findings We use data from the published literature, unpublished studies, museum records and online sources, to: (1) assess the current state of knowledge of species diversity in the deep-sea habitats adjacent to the Gulf of Maine (39–43°N, 63–71°W, 150–3000 m depth); (2) compare patterns of taxonomic diversity and distribution of megafaunal and macrofaunal species among six distinct sub-regions and to the continental shelf; and (3) estimate the amount of unknown diversity in the region. Known diversity for the deep-sea region is 1,671 species; most are narrowly distributed and known to occur within only one sub-region. The number of species varies by sub-region and is directly related to sampling effort occurring within each. Fishes, corals, decapod crustaceans, molluscs, and echinoderms are relatively well known, while most other taxonomic groups are poorly known. Taxonomic diversity decreases with increasing distance from the continental shelf and with changes in benthic topography. Low similarity in faunal composition suggests the deep-sea region harbours faunal communities distinct from those of the continental shelf. Non-parametric estimators of species richness suggest a minimum of 50% of the deep-sea species inventory remains to be discovered. Conclusions/Significance The current state of knowledge of biodiversity in this deep-sea region is rudimentary. Our ability to answer questions is hampered by a lack of sufficient data for many taxonomic groups, which is constrained by sampling biases, life-history characteristics of target species, and the lack of trained taxonomists. PMID:21124960

Functional and taxonomic dynamics of an electricity-consuming methane-producing microbial community.

PubMed

Bretschger, Orianna; Carpenter, Kayla; Phan, Tony; Suzuki, Shino; Ishii, Shun'ichi; Grossi-Soyster, Elysse; Flynn, Michael; Hogan, John

2015-11-01

The functional and taxonomic microbial dynamics of duplicate electricity-consuming methanogenic communities were observed over a 6 months period to characterize the reproducibility, stability and recovery of electromethanogenic consortia. The highest rate of methanogenesis was 0.72 mg-CH4/L/day, which occurred during the third month of enrichment when multiple methanogenic phylotypes and associated Desulfovibrionaceae phylotypes were present in the electrode-associated microbial community. Results also suggest that electromethanogenic microbial communities are very sensitive to electron donor-limiting open-circuit conditions. A 45 min exposure to open-circuit conditions induced an 87% drop in volumetric methane production rates. Methanogenic performance recovered after 4 months to a maximum value of 0.30 mg-CH4/L/day under set potential operation (-700 mV vs Ag/AgCl); however, current consumption and biomass production was variable over time. Long-term functional and taxonomic analyses from experimental replicates provide new knowledge toward understanding how to enrich electromethanogenic communities and operate bioelectrochemical systems for stable and reproducible performance. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

Taxonomic and ad hoc categorization within the two cerebral hemispheres.

PubMed

Shen, Yeshayahu; Aharoni, Bat-El; Mashal, Nira

2015-01-01

A typicality effect refers to categorization which is performed more quickly or more accurately for typical than for atypical members of a given category. Previous studies reported a typicality effect for category members presented in the left visual field/right hemisphere (RH), suggesting that the RH applies a similarity-based categorization strategy. However, findings regarding the typicality effect within the left hemisphere (LH) are less conclusive. The current study tested the pattern of typicality effects within each hemisphere for both taxonomic and ad hoc categories, using words presented to the left or right visual fields. Experiment 1 tested typical and atypical members of taxonomic categories as well as non-members, and Experiment 2 tested typical and atypical members of ad hoc categories as well as non-members. The results revealed a typicality effect in both hemispheres and in both types of categories. Furthermore, the RH categorized atypical stimuli more accurately than did the LH. Our findings suggest that both hemispheres rely on a similarity-based categorization strategy, but the coarse semantic coding of the RH seems to facilitate the categorization of atypical members.

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

PubMed Central

Sczyrba, Alexander; Hofmann, Peter; Belmann, Peter; Koslicki, David; Janssen, Stefan; Dröge, Johannes; Gregor, Ivan; Majda, Stephan; Fiedler, Jessika; Dahms, Eik; Bremges, Andreas; Fritz, Adrian; Garrido-Oter, Ruben; Jørgensen, Tue Sparholt; Shapiro, Nicole; Blood, Philip D.; Gurevich, Alexey; Bai, Yang; Turaev, Dmitrij; DeMaere, Matthew Z.; Chikhi, Rayan; Nagarajan, Niranjan; Quince, Christopher; Meyer, Fernando; Balvočiūtė, Monika; Hansen, Lars Hestbjerg; Sørensen, Søren J.; Chia, Burton K. H.; Denis, Bertrand; Froula, Jeff L.; Wang, Zhong; Egan, Robert; Kang, Dongwan Don; Cook, Jeffrey J.; Deltel, Charles; Beckstette, Michael; Lemaitre, Claire; Peterlongo, Pierre; Rizk, Guillaume; Lavenier, Dominique; Wu, Yu-Wei; Singer, Steven W.; Jain, Chirag; Strous, Marc; Klingenberg, Heiner; Meinicke, Peter; Barton, Michael; Lingner, Thomas; Lin, Hsin-Hung; Liao, Yu-Chieh; Silva, Genivaldo Gueiros Z.; Cuevas, Daniel A.; Edwards, Robert A.; Saha, Surya; Piro, Vitor C.; Renard, Bernhard Y.; Pop, Mihai; Klenk, Hans-Peter; Göker, Markus; Kyrpides, Nikos C.; Woyke, Tanja; Vorholt, Julia A.; Schulze-Lefert, Paul; Rubin, Edward M.; Darling, Aaron E.; Rattei, Thomas; McHardy, Alice C.

2018-01-01

In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions. PMID:28967888

Illustrated catalogue of Neotropical Ctenuchina, Euchromiina and Pericopina types (Lepidoptera, Erebidae, Arctiinae, Arctiini) described by Hans Zerny, with discussion on their taxonomic status.

PubMed

Pinheiro, L R; Gaal-Haszler, S

2015-03-03

The type material of 54 names of Ctenuchina, Euchromiina and Pericopina proposed by Hans Zerny are treated. Of these, the material belonging to 43 of the 54 names, represented by 118 specimens, are deposited at the Naturhistorisches Museum Wien (NHMW). The remaining are at the BMNH, NMNH, ZMHB or the ZSM, except for one of the species, which material was not traced. Comments on each name and its current taxonomic status, illustrations of holotypes and lectotypes, as well as information about their conservation status are provided. Lectotypes are designated for 23 of the taxa, and two new synonyms are proposed Eucyane variabilis flavofasciata and E. variabilis roseofasciata (=Hypocrita variabilis variabilis). Additionally, nine names have their taxonomic status changed: Correbia columbiana stat. nov., Autochloris jordani comb. nov., Chrostosoma exomelan comb. nov., C. flavothoracides comb. nov., C. pseudothia comb. nov., C. xanthomelan comb. nov., Ecdemus imbecillus comb. nov., Pseudomya clandestina comb. nov., and Uranophora felderi, comb. nov. Illustrations of the genitalia of some of the species are also provided.

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

The family Rhabdoviridae: mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins.

PubMed

Dietzgen, Ralf G; Kondo, Hideki; Goodin, Michael M; Kurath, Gael; Vasilakis, Nikos

2017-01-02

The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- and bipartite genomes. Copyright © 2016 Elsevier B.V. All rights reserved.

Classification of "Pseudomonas azotocolligans" Anderson 1955, 132, in the genus Sphingomonas as Sphingomonas trueperi sp. nov.

PubMed

Kämpfer, P; Denner, E B; Meyer, S; Moore, E R; Busse, H J

1997-04-01

"Pseudomonas azotocolligans" ATCC 12417T (T = type strain), which was described as a diazotrophic bacterium, was reinvestigated to clarify its taxonomic position. 16S ribosomal DNA sequence comparisons demonstrated that this strain clusters phylogenetically with species of the genus Sphingomonas and represents a new species. The results of investigations of the fatty acid patterns, polar lipid profiles, and quinone system supported this placement. The substrate utilization profile and biochemical characteristics displayed no obvious similarity to the characteristics of any previously described species of the genus Sphingomonas. The new name Sphingomonas trueperi is proposed on the basis of these results and previously published data for the G + C content of the genomic DNA and the polyamine pattern.

Second International Conference on Crimean-Congo Hemorrhagic Fever.

PubMed

Spengler, Jessica R; Bente, Dennis A; Bray, Mike; Burt, Felicity; Hewson, Roger; Korukluoglu, Gülay; Mirazimi, Ali; Weber, Friedemann; Papa, Anna

2018-02-01

The Second International Conference on Crimean-Congo Hemorrhagic Fever (CCHF) was held in Thessaloniki, Greece, from September 10-13, 2017, and brought together international public health professionals, clinicians, ecologists, and basic laboratory researchers. Nearly 100 participants, representing 24 countries and the World Health Organization (WHO), were in attendance. Meeting sessions covered the epidemiology of CCHF in humans; ticks and virus-tick interactions; wild and domestic animal hosts; molecular virology; taxonomic classification; pathogenesis and animal models; clinical aspects and diagnosis; clinical management and clinical trials; and disease prevention in humans. The concluding session focused on recent WHO recommendations for public health measures and future research. This report summarizes lectures by the invited speakers and highlights advances in the field. Copyright © 2017. Published by Elsevier B.V.

G-mode analysis of the reflection spectra of 84 asteroids.

NASA Astrophysics Data System (ADS)

Birlan, M.; Barucci, M. A.; Fulchignoni, M.

1996-01-01

A revised version of the G-mode multivariate statistics (Coradini et al. 1977) has been used to analyse a sample of 84 asteroids. This sample of asteroids is described by 29 variables, namely 23 colours between 0.9 and 2.35 microns obtained from the data base collected by Bell et al. (Private communication), 5 colors between 0.3 and 0.85 microns from the ECAS survey (Zellner et al. 1985) and the revised IRAS albedo (Tedesco et al. 1992). The G-mode method allows the user to obtain an automatic classification of the asteroids in spectrally homogeneous groups. The role of the IR colours in separating the various groups is outlined, particularly with regard to the fine subdivision of S and C taxonomical types.

Taxonomy and morphology of species of the genus Squalus Linnaeus, 1758 from the Southwestern Atlantic Ocean (Chondrichthyes: Squaliformes: Squalidae).

PubMed

Viana, Sarah T De F; Carvalho, Marcelo R De; Gomes, Ulisses L

2016-07-04

Squalus is a genus of reportedly cosmopolitan shark species that have a high taxonomic complexity due to difficulties in their morphological differentiation; many of its species need revision. Currently, there are 26 valid species of Squalus, which have been divided into three species-groups according to overall morphological similarity, the S. acanthias, S. megalops, and S. mitsukurii groups. Loss of type specimens, propagation of erroneous identifications in the literature, and difficulties in obtaining representative series for comparison are secondary challenges that have impeded a global taxonomic revision of the genus. This problem applies clearly to species from the Southwestern Atlantic Ocean, including species that occur off Brazil. Following a current global tendency, a regional taxonomic revision of Squalus was conducted in order to investigate which species are valid in the Southwestern Atlantic Ocean and provide diagnostic morphological characters that can be efficiently used for identifying species. Comparative detailed analysis of external (e.g. morphometrics, dentition, and color pattern) and skeletal morphology (primarily meristic data, neurocrania and claspers) of specimens of Squalus from the region revealed four new species that are herein described (S. albicaudus sp. nov., S. bahiensis sp. nov., S. lobularis sp. nov., and S. quasimodo sp. nov.), as well as S. acanthias, which is redescribed from the region based on new material. Comparisons are offered based on examinations of congeneric species; this work is part of a global systematic revision of Squalus.

A Novel Virus Detected in Papillomas and Carcinomas of the Endangered Western Barred Bandicoot (Perameles bougainville) Exhibits Genomic Features of both the Papillomaviridae and Polyomaviridae▿

PubMed Central

Woolford, Lucy; Rector, Annabel; Van Ranst, Marc; Ducki, Andrea; Bennett, Mark D.; Nicholls, Philip K.; Warren, Kristin S.; Swan, Ralph A.; Wilcox, Graham E.; O'Hara, Amanda J.

2007-01-01

Conservation efforts to prevent the extinction of the endangered western barred bandicoot (Perameles bougainville) are currently hindered by a progressively debilitating cutaneous and mucocutaneous papillomatosis and carcinomatosis syndrome observed in captive and wild populations. In this study, we detected a novel virus, designated the bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1), in lesional tissue from affected western barred bandicoots using multiply primed rolling-circle amplification and PCR with the cutaneotropic papillomavirus primer pairs FAP59/FAP64 and AR-L1F8/AR-L1R9. Sequencing of the BPCV1 genome revealed a novel prototype virus exhibiting genomic properties of both the Papillomaviridae and the Polyomaviridae. Papillomaviral properties included a large genome size (∼7.3 kb) and the presence of open reading frames (ORFs) encoding canonical L1 and L2 structural proteins. The genomic organization in which structural and nonstructural proteins were encoded on different strands of the double-stranded genome and the presence of ORFs encoding the nonstructural proteins large T and small t antigens were, on the other hand, typical polyomaviral features. BPCV1 may represent the first member of a novel virus family, descended from a common ancestor of the papillomaviruses and polyomaviruses recognized today. Alternatively, it may represent the product of ancient recombination between members of these two virus families. The discovery of this virus could have implications for the current taxonomic classification of Papillomaviridae and Polyomaviridae and can provide further insight into the evolution of these ancient virus families. PMID:17898069

Quantifying motivation with effort-based decision-making paradigms in health and disease.

PubMed

Chong, T T-J; Bonnelle, V; Husain, M

2016-01-01

Motivation can be characterized as a series of cost-benefit valuations, in which we weigh the amount of effort we are willing to expend (the cost of an action) in return for particular rewards (its benefits). Human motivation has traditionally been measured with self-report and questionnaire-based tools, but an inherent limitation of these methods is that they are unable to provide a mechanistic explanation of the processes underlying motivated behavior. A major goal of current research is to quantify motivation objectively with effort-based decision-making paradigms, by drawing on a rich literature from nonhuman animals. Here, we review this approach by considering the development of these paradigms in the laboratory setting over the last three decades, and their more recent translation to understanding choice behavior in humans. A strength of this effort-based approach to motivation is that it is capable of capturing the wide range of individual differences, and offers the potential to dissect motivation into its component elements, thus providing the basis for more accurate taxonomic classifications. Clinically, modeling approaches might provide greater sensitivity and specificity to diagnosing disorders of motivation, for example, in being able to detect subclinical disorders of motivation, or distinguish a disorder of motivation from related but separate syndromes, such as depression. Despite the great potential in applying effort-based paradigms to index human motivation, we discuss several caveats to interpreting current and future studies, and the challenges in translating these approaches to the clinical setting. © 2016 Elsevier B.V. All rights reserved.

A dated phylogeny of the papilionoid legume genus Canavalia reveals recent diversification by a pantropical liana lineage.

PubMed

Snak, Cristiane; Vatanparast, Mohammad; Silva, Christian; Lewis, Gwilym Peter; Lavin, Matt; Kajita, Tadashi; Queiroz, Luciano Paganucci de

2016-05-01

Canavalia is a pantropical legume genus of lianas comprising approximately 60 species distributed in a wide range of habitats. In the last taxonomic revision, the genus was divided into four subgenera: Canavalia (Pantropical), Catodonia (Neotropical, excepting one species also found in the Old World), Maunaloa (Hawaiian), and Wenderothia (Neotropical). In this study, we reconstructed the phylogeny of Canavalia using a broad taxon sampling and analyses of nuclear (ETS and ITS) and plastid markers (trnK/matK). We evaluated the infrageneric classification of the genus and investigated its biogeographical history using molecular dating analyses and ancestral area reconstructions. The phylogenetic analyses resolved subgenus Wenderothia as monophyletic. Subgenus Catodonia needs to be recircumscribed and the relationships between subgenera Canavalia and Maunaloa remain unclear. Canavalia arose during the Miocene with a mean stem age estimate of 13.8Ma and mean crown age estimate of 8.7Ma, and most extant species evolved during the Pleistocene. Several climatic and geological events are chronologically coincident with the divergence of the major clades of Canavalia (glacial/interglacial periods, Andes uplift and the formation of Pebas and post-Pebas systems, closure of the Isthmus of Panama, and change in the direction of ocean currents). Ancestral area reconstructions for the early divergence of the genus are equivocal, although, some evidence suggests Canavalia originated in the wet forests of South America and achieved its current pantropical distribution through recent transoceanic dispersal. The evolution of Canavalia is better explained by a series of several processes than by discrete historical events. Copyright © 2016 Elsevier Inc. All rights reserved.

Application of metagenomics technologies for antimicrobial resistance and food safety research and beyond

USDA-ARS?s Scientific Manuscript database

Current developments in the field of metagenomics in biological sciences have demonstrated the need and potential usefulness of taxonomical and functional analyses of meta-omics data generated by genomics, transcriptomics, proteomics, and metabolomics. This review will provide a general overview of...

Amphibian (Xenopus sp.) iodothyronine deiodinase production for screening of thyroid-disrupting chemicals

EPA Science Inventory

The U.S. EPA-MED amphibian thyroid group is currently screening chemicals for inhibition of human iodothyronine deiodinase activity as components of the thyroid system important in human development. Amphibians are a bellwether taxonomic group to gauge toxicity of chemicals in th...

Genetic variability of HEV isolates: inconsistencies of current classification.

PubMed

Oliveira-Filho, Edmilson F; König, Matthias; Thiel, Heinz-Jürgen

2013-07-26

Many HEV and HEV-like sequences have been reported during the last years, including isolates which may represent a number of potential new genera, new genotypes or new subtypes within the family Hepeviridae. Using the most common classification system, difficulties in the establishment of subtypes have been reported. Moreover the relevance of subtype classification for epidemiology can be questioned. In this study we have performed phylogenetic analyses based on whole capsid gene and complete HEV genomic sequences in order to evaluate the current classification of HEV at genotype and subtype levels. The results of our analyses modify the current taxonomy of genotype 3 and refine the established system for typing of HEV. In addition we suggest a classification for hepeviruses recently isolated from bats, ferrets, rats and wild boar. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures.

PubMed

Schloss, Patrick D; Handelsman, Jo

2006-10-01

The recent advent of tools enabling statistical inferences to be drawn from comparisons of microbial communities has enabled the focus of microbial ecology to move from characterizing biodiversity to describing the distribution of that biodiversity. Although statistical tools have been developed to compare community structures across a phylogenetic tree, we lack tools to compare the memberships and structures of two communities at a particular operational taxonomic unit (OTU) definition. Furthermore, current tests of community structure do not indicate the similarity of the communities but only report the probability of a statistical hypothesis. Here we present a computer program, SONS, which implements nonparametric estimators for the fraction and richness of OTUs shared between two communities.

32 CFR 1648.6 - Registrants transferred for classification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 32 National Defense 6 2014-07-01 2014-07-01 false Registrants transferred for classification. 1648... SYSTEM CLASSIFICATION BY LOCAL BOARD § 1648.6 Registrants transferred for classification. (a) Before a..., be transferred for classification to a local board nearer to his current address than is the local...

32 CFR 1648.6 - Registrants transferred for classification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 32 National Defense 6 2013-07-01 2013-07-01 false Registrants transferred for classification. 1648... SYSTEM CLASSIFICATION BY LOCAL BOARD § 1648.6 Registrants transferred for classification. (a) Before a..., be transferred for classification to a local board nearer to his current address than is the local...

32 CFR 1648.6 - Registrants transferred for classification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 6 2010-07-01 2010-07-01 false Registrants transferred for classification. 1648... SYSTEM CLASSIFICATION BY LOCAL BOARD § 1648.6 Registrants transferred for classification. (a) Before a..., be transferred for classification to a local board nearer to his current address than is the local...

32 CFR 1648.6 - Registrants transferred for classification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 32 National Defense 6 2011-07-01 2011-07-01 false Registrants transferred for classification. 1648... SYSTEM CLASSIFICATION BY LOCAL BOARD § 1648.6 Registrants transferred for classification. (a) Before a..., be transferred for classification to a local board nearer to his current address than is the local...

32 CFR 1648.6 - Registrants transferred for classification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 32 National Defense 6 2012-07-01 2012-07-01 false Registrants transferred for classification. 1648... SYSTEM CLASSIFICATION BY LOCAL BOARD § 1648.6 Registrants transferred for classification. (a) Before a..., be transferred for classification to a local board nearer to his current address than is the local...

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.

Microsporidian pathogens in European gypsy moth populations

Treesearch

Michael L. McManus; Leellen Solter

2003-01-01

The significance of microsporidian pathogens as mortality agents of gypsy moth (Lymantria dispar L.) in Europe frequently is overlooked. Collections of isolates from 10 different countries suggest that three genera and several biotypes are extant. It is important that the taxonomic placement and phylogeny of currently described genera and species be...

Overview of the taxonomy of zooxanthellate Scleractinia.

PubMed

Veron, John

2013-11-01

Coral taxonomy has entered a historical phase where nomenclatorial uncertainty is rapidly increasing. The fundamental cause is mandatory adherence to historical monographs that lack essential information of all sorts, and also to type specimens, if they exist at all, that are commonly unrecognizable fragments or are uncharacteristic of the species they are believed to represent. Historical problems, including incorrect subsequent type species designations, also create uncertainty for many well-established genera. The advent of in situ studies in the 1970s revealed these issues; now molecular technology is again changing the taxonomic landscape. The competing methodologies involved must be seen in context if they are to avoid becoming an additional basis for continuing nomenclatorial instability. To prevent this happening, the International Commission on Zoological Nomenclature (ICZN) will need to focus on rules that consolidate well-established nomenclature and allow for the designation of new type specimens that are unambiguous, and which include both skeletal material and soft tissue for molecular study. Taxonomic and biogeographic findings have now become linked, with molecular methodologies providing the capacity to re-visit past taxonomic decisions, and to extend both taxonomy and biogeography into the realm of evolutionary theory. It is proposed that most species will ultimately be seen as operational taxonomic units that are human rather than natural constructs, which in consequence will always have fuzzy morphological, genetic, and distribution boundaries. The pathway ahead calls for the integration of morphological and molecular taxonomies, and for website delivery of information that crosses current discipline boundaries.

The unholy trinity: taxonomy, species delimitation and DNA barcoding

PubMed Central

DeSalle, Rob; Egan, Mary G; Siddall, Mark

2005-01-01

Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this ‘DNA barcoding’ initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the ‘DNA barcoding’ initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the ‘DNA barcoding’ initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings—Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of ‘DNA barcoding’. PMID:16214748

The Results of Development of the Project ZOOINT and its Future Perspectives

NASA Astrophysics Data System (ADS)

Smirnov, I. S.; Lobanov, A. L.; Alimov, A. F.; Medvedev, S. G.; Golikov, A. A.

The work on a computerization of main processes of accumulation and analysis of the collection, expert and literary data on a systematics and faunistics of various taxa of animal (a basis of studying of a biological diversity) was started in the Zoological Institute in 1987. In 1991 the idea of creating of the software package, ZOOlogical INTegrated system (ZOOINT) was born. ZOOINT could provide a loading operation about collections and simultaneously would allow to analyze the accumulated data with the help of various queries. During execution, the project ZOOINT was transformed slightly and has given results a little bit distinguished from planned earlier, but even more valuable. In the Internet the site about the information retrieval system (IRS) ZOOINT was built also ( ZOOINT ). The implementation of remote access to the taxonomic information, with possibility to work with databases (DB) of the IRS ZOOINT in the on-line mode was scheduled. It has required not only innovation of computer park of the developers and users, but also mastering of new software: language HTML, operating system of Windows NT, and technology of Active Server Pages (ASP). One of the serious problems of creating of databases and the IRS on zoology is the problem of representation of hierarchical classification. Building the classifiers, specialized standard taxonomic databases, which have obtained the name ZOOCOD solved this problem. The lately magnified number of attempts of creating of taxonomic electronic lists, tables and DB has required development of some primary rules of unification of zoological systematic databases. These rules assume their application in institutes of the biological profile, in which the processes of a computerization are very slowly, and the building of databases is in the most rudimentary state. These some positions and the standards of construction of biological (taxonomic) databases should facilitate dialogue of the biologists, application in the near future of most advanced technologies of development of the DB (for example, usage of the XML platform) and, eventually, building of the modern information systems. The work on the project is carried out at support of the RFBR grant N 02-07-90217; programs "The Information system on a biodiversity of Russia" and Project N 15 "Antarctic Regions".

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

A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda)

PubMed Central

2013-01-01

Background The infraorder Anomura has long captivated the attention of evolutionary biologists due to its impressive morphological diversity and ecological adaptations. To date, 2500 extant species have been described but phylogenetic relationships at high taxonomic levels remain unresolved. Here, we reconstruct the evolutionary history—phylogeny, divergence times, character evolution and diversification—of this speciose clade. For this purpose, we sequenced two mitochondrial (16S and 12S) and three nuclear (H3, 18S and 28S) markers for 19 of the 20 extant families, using traditional Sanger and next-generation 454 sequencing methods. Molecular data were combined with 156 morphological characters in order to estimate the largest anomuran phylogeny to date. The anomuran fossil record allowed us to incorporate 31 fossils for divergence time analyses. Results Our best phylogenetic hypothesis (morphological + molecular data) supports most anomuran superfamilies and families as monophyletic. However, three families and eleven genera are recovered as para- and polyphyletic. Divergence time analysis dates the origin of Anomura to the Late Permian ~259 (224–296) MYA with many of the present day families radiating during the Jurassic and Early Cretaceous. Ancestral state reconstruction suggests that carcinization occurred independently 3 times within the group. The invasion of freshwater and terrestrial environments both occurred between the Late Cretaceous and Tertiary. Diversification analyses found the speciation rate to be low across Anomura, and we identify 2 major changes in the tempo of diversification; the most significant at the base of a clade that includes the squat-lobster family Chirostylidae. Conclusions Our findings are compared against current classifications and previous hypotheses of anomuran relationships. Many families and genera appear to be poly- or paraphyletic suggesting a need for further taxonomic revisions at these levels. A divergence time analysis provides key insights into the origins of major lineages and events and the timing of morphological (body form) and ecological (habitat) transitions. Living anomuran biodiversity is the product of 2 major changes in the tempo of diversification; our initial insights suggest that the acquisition of a crab-like form did not act as a key innovation. PMID:23786343