A comprehensive phylogenetic classification of the Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from members of the fungal taxonomic community. The classification includes 196 taxa, down to the level of order, of which 23 are described or are validated ...

... 2002)3742.0.CO;2 Phylogenetic Analysis of Morpho Butterflies (Nymphalidae, Morphinae): Implications for Classification and Natur...

Accurate classification systems based on evolution are imperative for biological investigations. The recent explosion of molecular phylogenetics has resulted in a much improved classification of angiosperms. More than five phylogenetic lineages have been recognized from Scrophulariaceae sensu ...

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 ...

Liatrinae is a small subtribe of Eupatorieae that occurs in North America with a center of generic-level diversity in the southeastern United States. Molecular phylogenetic data were sought to assess whether two monotypic genera, Garberia and Hartwrightia, are accurately placed in the subtribe, and to resolve questions of the generic-level ...

Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1) are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypes is helpful in surveillance, epidemiological analysis and detection of novel variants, e.g., circulating recombinant ...

Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1) are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypes is helpful in surveillance, epidemiological analysis and detection of novel variants, e.g., circulating recombinant ...

BackgroundPrevious 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 ...

As sequenced genomes become larger and sequencing becomes faster, there is a need to develop accurate automated genome comparison techniques and databases to facilitate derivation of genome functionality; identification of enzymes, putative operons, and metabolic pathways; and to derive phylogenetic classification of microbes. This ...

Metagenomics projects collect DNA from uncharacterized environments that may contain thousands of species per sample. One main challenge facing metagenomic analysis is phylogenetic classification of raw sequence reads into groups representing the same or similar taxa, a prerequisite for genome assembly and for analyzing the biological diversity of a ...

This study tests the hypothesis that phylogenetic classification can predict whether A. pullulans strains will produce useful levels of the commercial polysaccharide, pullulan, or the valuable enzyme, xylanase. To test this hypothesis, 19 strains of A. pullulans with previously described phenotypes...

... upper haustorium of Cuscuta L., Cassytha L., and Viscum L. Pp. 319�334 in Parasitic Fflowering plants, ... ...

BackgroundComputational analysis of metagenomes requires the taxonomical assignment of the genome contigs assembled from DNA reads of environmental samples. Because of the diverse nature of microbiomes, the length of the assemblies obtained can vary between a few hundred bp to a few hundred Kbp. Current taxonomic classification algorithms provide accurate ...

It is hard to accurately identify specific species of the Lactobacillus casei group using phenotypic techniques alone. Some strains of this species group are considered to be probiotic and are widely applied in the food industry. In this study, we compared the use of two phylogenetic markers, the 16S rRNA and dnaK genes, for species discrimination of the ...

Piroplasmosis was first described in raccoons (Procyon lotor) in 1926, and the official description of a small piroplasm as Babesia lotori was done in 1981. Babesia microti-like gene sequences have been characterized in raccoons in both North American and Japan. It is well documented that the microscopic appearance of piroplasms does not always accurately predict the genotype ...

Accurate phylogenetic reconstruction methods are inherently computationally heavy and therefore are limited to relatively small numbers of taxa. Supertree construction is the task of amalgamating small trees over partial sets into a big tree over the complete taxa set. The need for fast and accurate supertree methods has become crucial ...

The practice of classifying organisms into hierarchical groups originated with Aristotle and was codified into nearly immutable biological law by Linnaeus. The heart of taxonomy is the biological species, which forms the foundation for higher levels of classification. Whereas species have long been established among sexual eukaryotes, achieving a meaningful species concept for ...

Neural network techniques for multispectral image classification and spatial pattern detection are compared to the standard techniques of maximum-likelihood classification and spatial correlation. The neural network produced a more accurate classification...

This is a brief article from Molecular Biology and Evolution (2002) on classification of Wolbachia by molecular phylogenetics. The introduction to the paper provides an overview of previous phylogenetic analyses and classification of Wolbachia into supergroups. The authors use additional taxonomic sampling of two ...

SUMMARYClassification of viral sequences should be fast, objective, accurate, and reproducible. Most methods that classify sequences use either pairwise distances or phylogenetic relations, but cannot discern when a sequence is unclassifiable. The branching index (BI) combines distance and phylogeny methods to compute a ratio that quantifies how closely a ...

Accurate classification of HIV and the identification of recombinants, including precise breakpoint definitions, is of crucial importance for epidemiological monitoring and the design of potential drugs. Recently we developed jpHMM, a new method to detect recombinations in HIV-l genomes. jpHMM predicts phylogenetic recombination ...

... World: A Case of Conflicting Phylogenies. Systematic Botany 29:3, 702-715Online ... (2002) Aluminum Hyperaccumulation in Angiosperms: A Review of Its Phylogenetic ... ...

... species), no one has previously suggested a close relationship between these species. Only a long distance dispersal event or an ancient phylogenetic relationship could ... ...

... Classification of this page unclassified Classification of Abstract unclassified ... Armament Drive System � Elevation and Azimuth drives ... System Test ...

... positioning data on the order of one meter. Substrate Classification- To produce accurate maps of these areas we applied the RoxAnn substrate classification method...

Traditional methods of species classification and identification of the organism are based on morphological, physiological, biochemical, developmental and nutritional characteristics. Accurate assignment of taxonomic status to the new biologically active microbial isolates through existing bioinformatics methods is now very essential and also helpful in ...

Partial gyrA sequences were determined for twelve strains belonging to Bacillus amyloliquefaciens, B. atrophaeus, B. licheniformis, B. mojavensis, B. subtilis subsp. subtilis, B. subtilis subsp. spizizenii and B. vallismortis. The average nucleotide and translated amino acid similarities for the seven type strains were 83.7 and 95.1%, respectively, whereas the corresponding value for the 16S rRNA ...

In this study, we integrated a DNA barcoding project with an ecological survey on intertidal polychaete communities and investigated the utility of CO1 gene sequence as a DNA barcode for the classification of the intertidal polychaetes. Using 16S rDNA as a complementary marker and combining morphological and ecological characterization, some of dominant and common polychaete ...

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences ...

This is a book chapter on the genetics of Pythium to be published in a book titled "Oomycete Genetics and Genomics: Biology, Interactions with Plants and Animals, and Toolbox." It covers the basic taxonomic classification of species in the genus, the phylogenetic placements, and reviews the literatu...

... the deep divergences and potential effects of extensive RNA editing on phylogenetic reconstruction. Future directions for hornwort ... 2006Keywords: Anthocerotophyta, hornworts, Leiosporoceros, Phaeomegac...

... of this character and its taxonomic distribution. Although state 2 is said to be correlated with syndactyly (Hall, 1987), some ... ...

... that contains Cordylanthus rigidus (Benth.) Jeps. (Cordylanthus), Orthocarpus luteus Nutt. (Orthocarpus), and Casttlleja fissifolia L.f. (Casttlleja). ... C. capitatus Nutt. ex Benth, but not Orthocarpus...

... base insertion is shared by Orthilia secunda and Pyrola picta. Parsimony analysis of the matK1 data matrix (127 ... ...

... have been introduced elsewhere (e.g., the widespread Marrubium vulgare L. and Leonotis nepetifolia (L.) R. Br.). This ... ...

Contents: Biology of North American Tortoises: Introduction; Phylogenetic Systematics of North American Tortoises (Genus Gopherus): Evidence for Their Classification; Validity of the Tortoise Xerobates lepidocephalus Ottley and Velazques in Baja Californi...

Comparing bacterial 16S rDNA sequences to GenBank and other large public databases via BLAST often provides results of little use for identification and taxonomic assignment of the organisms of interest. The human microbiome, and in particular the oral microbiome, includes many taxa, and accurate identification of sequence data is essential for studies of these communities. ...

Comparing bacterial 16S rDNA sequences to GenBank and other large public databases via BLAST often provides results of little use for identification and taxonomic assignment of the organisms of interest. The human microbiome, and in particular the oral microbiome, includes many taxa, and accurate identification of sequence data is essential for studies of these communities. ...

Genome signatures are data vectors derived from the compositional statistics of DNA. The self-organizing map (SOM) is a neural network method for the conceptualisation of relationships within complex data, such as genome signatures. The various parameters of the SOM training phase are investigated for their effect on the accuracy of the resulting output map. It is concluded that larger SOMs, as ...

Human subjects term indicating a classification of research subjects into women and men. In some cases, gender cannot be accurately determined, e.g., for pooled blood samples. The classification of research subjects into women and men. In some cases, gender cannot be accurately determined (e.g., pooled blood ...

This exercise should be used to have students form their own classification of ferns by observing a variety of structural modifications in several ferns. The activity will give the students an understanding of some of the problems involved with phylogenetic classifications.

The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate species identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have ...

The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate species identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have ...

... individual classifiers forming the ensembles. Furthermore, some studies have shown that an ensemble could be as accurate ...

... at the same position but at different elevations. ... used for accurate Digital Elevation Model (DEM ... 24]) for unsupervised classification, distributed target ...

PurposeOcular infections caused by fungal organisms can cause significant ocular morbidity, particularly when diagnosis and treatment are delayed. Rapid and accurate identification of Fusarium species at the subgenus level using current diagnostic standards is timely and insensitive. The purpose of this study is to examine the usefulness of polymerase chain reaction (PCR) ...

... of morphological characteristics. However, this scheme has been criticized for not accurately reflecting evolutionary relationships within the ... the Indian Ocean from Africa. It has been said that the p...

Characters flagged as convergent based on newer molecular phylogenetic trees inform both practical identification and more esoteric classification. Nematode morphological characters such as lateral lines, bullae and laciniae are quite independent structures from those similarly named in other organi...

Rapidly growing number of sequenced genomes requires fast and accurate computational tools for analysis of different transposable elements (TEs). In this paper we focus on rapid and reliable procedure for classification of autonomous non-LTR retrotransposons based on alignment and clustering of their reverse transcriptase (RT) domains. Typically, the RT ...

The internal classification of the cosmopolitan and medically important genus Culex is thoroughly reviewed and updated to reflect the multitude of taxonomic changes and concepts which have been published since the classification was last compiled by Edwards in 1932. Both formal and informal taxa are included. The classification is ...

Information about the phylogenetic relationships of Plecoptera is summarized. The few characters supporting monophyly of the order are outlined. Several characters of possible significance for the search for the closest relatives of the stoneflies are discussed, but the sister-group of the order remains unknown. Numerous characters supporting the presently recognized ...

Sirococcus clavigignenti-juglandacearum (Sc-j), which causes a canker disease on butternut, is largely responsible for the decline of this tree in the United States and Canada. The original description of the species was based on anamorphic characters because the teleomorph is unknown. Recent phylogenetic investigations have found that Sc-j is not a member of the genus ...

BackgroundAriids or sea catfishes are one of the two otophysan fish families (out of about 67 families in four orders) that inhabit mainly marine and brackish waters (although some species occur strictly in fresh waters). The group includes over 150 species placed in ~29 genera and two subfamilies (Galeichthyinae and Ariinae). Despite their global distribution, ariids are largely restricted to the ...

BackgroundGibbons or small apes inhabit tropical and subtropical rain forests in Southeast Asia and adjacent regions, and are, next to great apes, our closest living relatives. With up to 16 species, gibbons form the most diverse group of living hominoids, but the number of taxa, their phylogenetic relationships and their phylogeography is controversial. To further the ...

� Canopy chemistry and spectroscopy offer insight into community assembly and ecosystem processes in high-diversity tropical forests, but phylogenetic and environmental factors controlling chemical traits underpinning spectral signatures remain poorly understood. � We measured 21 leaf chemical traits and spectroscopic signatures of 594 canopy individuals on high-fertility ...

DNA was extracted and the 18S ribosomal RNA gene was amplified and sequenced from the blood of 2 Pallas' cats (Otocolobus manul) infected with small intraerythrocytic piroplasms. Sequences of the parasite were found to be identical with that of a previously reported Cytauxzoon-like piroplasm from a Pallas' cat. Phylogenetic analyses of the parasite DNA sequences obtained from ...

A self-organizing map (SOM) was developed as a novel bioinformatics strategy for phylogenetic classification of sequence fragments obtained from pooled genome samples of uncultured microbes in environmental and clinical samples. This phylogenetic classification was possible without either orthologous sequence sets ...

The avian subfamily Tetraoninae (grouse and ptarmigan) is a Holarctic group in the order Galliformes distinguished by morphological adaptations to cold environments and behavioral traits associated with elaborate courtship. Here we investigate the relationships of 17 tetraonines and 12 other galliform species using mitochondrial 12S and ND2 sequence data. We found support for the recent ...

MOTIVATION: As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multispecies nucleotide sequence alignment to determine whether it is likely to ...

Motivation: As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multispecies nucleotide sequence alignment to determine whether it is likely to ...

Determining accurate phylogenetic relationships among the members of the woody Sonchus alliance presents challenges because of an insufficient level of molecular variation and the convergent evolution of similar morphological traits in island settings. To obtain a better resolved phylogeny and to test the potential role of hybridization and introgression, ...

The Fungi comprise a diverse kingdom of eukaryotes that are characterized by a typically filamentous but sometimes unicellular vegetative form, and heterotrophic, absorptive nutrition. Their simple morphologies and variable ecological strategies have confounded efforts to elucidate their limits, phylogenetic relationships, and diversity. Here we review progress in developing a ...

BackgroundWith current technology, vast amounts of data can be cheaply and efficiently produced in association studies, and to prevent data analysis to become the bottleneck of studies, fast and efficient analysis methods that scale to such data set sizes must be developed.ResultsWe present a fast method for accurate localisation of disease causing variants in high density ...

Traditionally, the classification of tumors has been based on morphology, or the tumor�s structure, but morphological classification cannot accurately predict biological behavior, prognosis, or response to treatment. In 1998, the NCI director issued an appeal, or Director�s Challenge, called �Toward a Molecular ...

One key difficulty with text classification learning algorithms is that they require many hand-labeled examples to learn accurately. This dissertation demonstrates that supervised learning algorithms that use a small number of labeled examples and many in...

robust signature set possible. Combine your training sites to create the weighted training site for each the unsupervised classification method, the software was instructed to create x number of clusters in x iterations that a accurate and complete set of class definitions are created. These classes are typically created

... risk assessment. Land cover classification of ASTER and Hyperion images is performed in a detailed nomenclature including ... accuracy of 85% for ASTER and 93% for Hyperion classification. Although Hyperi...

Accurate exposure classification tools are required to link exposure with health effects in epidemiological studies. Long-term, time-integrated exposure measures would be desirable to address the problem of developing appropriate residential childhood exposure classifications. ...

Accurate classification of diseases is imperative to the needs of physicians, researchers, vital statistics offices, hospitals, etc. It was felt that a review of coding rules that were not clearly defined in the ICD-9 was required in order to evaluate the...

Recent advances in sparse modeling and dictionary learning for discriminative applications show high potential for numerous classification tasks. In this paper, we show that highly accurate material classification from hyperspectral imagery (HSI) can be o...

A need exists in both the civilian and military communities for an automated seafloor classification system that can remotely and accurately estimate and map sediment properties for a number of seafloor engineering applications and for input to acoustic p...

A data fusion system with artificial neural networks (ANN) is used for fast and accurate classification of five earth surface conditions and surface changes, based on seven SSMI multichannel microwave satellite measurements. The measurements include brigh...

Early detection of breast cancer depends on the accurate classification of microcalcifications. We have developed a computer vision system that can classify microcalcifications objectively and consistently to aid radiologists in the diagnosis of breast ca...

Early detection of breast cancer depends on the accurate classification of microcalcifications. We have developed a computer vision system that can classify microcalcifications objectively and consistently to aid radiologists in the diagnosis of breast ca...

Early detection of breast cancer depends on the accurate classification of microcalcifications. We have developed a computer vision system that can classify microcalcifications objectively and consistently to aid radiologists in the diagnosis of breast ca...

... flexible classification functions also were the most accurate: neural networks (overall classification accuracy = 0.94) and mixture discriminant ... 2010Keywords: acoustic identification, Anabat, discrimi...

BackgroundProtein structure comparison is one of the most important problems in computational biology and plays a key role in protein structure prediction, fold family classification, motif finding, phylogenetic tree reconstruction and protein docking.ResultsWe propose a novel method to compare the protein structures in an accurate and ...

... composition, a 350-tree plot is needed. Short-column chromatographic analysis is acceptably accurate for rapid classification of ... ...

Key to Venice Inlet. One purpose of the USGS National Assessment of Coastal Change Project is to provide accurate representations of pre-storm ground ...

of mesothelioma and his predictions of the increasing incidence of this condition. This research has contributed has produced what turned out to be accurate forecasts of the incidence of mesothelioma in Britain

by means of time or frequency domain PSOLA (see e.g. [3]). A prerequisite is again an accurate estimate

... stated in the abstract, Light Detection and Ranging (LIDAR) data were used in this study "to compare ... heights, they could be accurately detected by using LIDAR classification in the wetlands where the ...

...classification of the employee; (ii) The date of the audiogram; (iii) The examiner's name; (iv) The date of the last acoustic or exhaustive calibration of the audiometer; (v) Accurate records of the measurements of the background sound...

The two diaporthalean fungi Anisogramma virgultorum and A. anomala are biotrophic parasites. Anisogramma virgultorum causes stromatal cankers on young shoots of birch and A. anomala infects young branches of Corylus avellana. Although previous classifications, based on morphological characteristics,...

Despite the familiarity and economic significance of Coccinellidae, the family has thus far escaped analysis by rigorous phylogenetic methods. As a result, the internal classification remains unstable and there is no framework with which to interpret evolutionary events within the family. Coccinel...

DR0079 from Deinococcus radiodurans Responses of Deinococcus radiodurans............................2-4-43 MS Lipton, HM Mottaz, and AK Schmid

Phylogenetic analysis of gene sequences has had a profound impact on understanding diversity and relationships among the yeasts, and the application of this information to development of a system of classification based on phylogeny has resulted in numerous changes of taxon names. Gene sequence ana...

Contents: New Phylogenetic Classification in Bacteria; Present and Future of the Study on Brain Functions; Comparison of chemical inactivation of salicylate 5-hydroxylase, m-hydroxybenzoate 6-hydroxylase, and p-hydroxybenzoate 3-hydroxylase from Rhodococc...

... in Appendix 2, and the taxon by character matrix is given in Appendix 3. Molecular Characters Collections were made from native populations and botanical gardens between 1995 and 1998. Fresh leaves were...

Pyraloidea, the third largest superfamily of the Lepidoptera, is comprised of two families - Pyralidae and Crambidae. The history of families previously placed in the Pyraloidea is discussed. The group now includes about 16,000 species worldwide. Morphologically, the superfamily is defined by a b...

... data sets were analyzed both separately and combined. Topological and data set incongruence were examined to determine ... incongruence rather than �soft.� The latter occurs when topological differences a...

... and E. A. Friar. 2000. Supraspecific classification of Eleocharis (Cyperaceae) revisited: evidence from the internal transcribed spacer ( ... ...

... and later generally supported by molecular studies (Mummenhoff & Koch, 1994; Mummenhoff et al., 1997a, b; Koch et al., 2001). Thus, it is unclear to ... broadly sampled molecular studies of Brassicaceae (...

... Li, and C. E. Schweitzer. 2007. A new family, genus, and species of crab (Crustacea, Decapoda, Brachyura) from the Upper Cretaceous (Campanian) of Manitoba, Canada. Canadian Journal of Earth Science 44:174...

... from cultivated barley only H. bogdanii has a tough (rarely fragile) rachis. The rachis of all other ... including the outgroup is always fragile, hence a tough rachis has been developed independently in ...

... model (MK1 model invokes equal forward and backward transition rates; Lewis, 2001a) and the �Asymmetrical Markov k-state ... model� (AsymmMK model in which �forward� and �backward� transition rates can be...

of feathers and flight + speciation and adaptive radiation September 22 Systematics, classification and phylogeny + the species concept + taxonomic characters and cladistics + convergent evolution + molecular phylogenetic techniques September 24 Avian structure and function I: feather structure and growth, types

... S.H., J.H. Wimsatt, and D.E. GREEN. Phylogenetic classification of the frog pathogen Amphibiothecum (Dermosporidium) ... 702-706. CONVERSE, K.A. and D.E. GREEN. Diseases of salamanders. 2005 Pages 118...

BackgroundMachine 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 ...

Phylogeny is deeply pertinent to evolutionary studies. Traits that perform a body function are expected to be strongly influenced by physical "requirements" of the function. We investigated if such traits exhibit phylogenetic signals, and, if so, how phylogenetic noises bias quantification of form-function relationships. A form-function system that is ...

The use of phylogenetic comparative methods in ecological research has advanced during the last twenty years, mainly due to accurate phylogenetic reconstructions based on molecular data and computational and statistical advances. We used phylogenetic correlograms and phylogenetic eigenvector ...

Some uses of monoclonal antibodies in bacteriology are discussed with emphasis on identification and classification of microorganisms. It is pointed out that monoclonal antibodies are useful in diagnostic purposes, i.e., identification of bacteria and bacterial antigens in unknowns and classification of new isolates. They are also important for studying ...

For almost a decade it has been acknowledged that the flowering plant dichotomy of monocotyledons and dicotyledons does not reflect the evolution of angiosperms. Despite this, conclusions in the field of chemosystematics are still drawn from, and rely on, non-phylogenetic botanical classifications such as those of Cronquist, Dahlgren and Takhtajan. In this ...

We introduce a model for simulating mutation of prokaryote DNA sequences. Using that model we can then evaluated traditional techniques like parsimony and maximum likelihood methods for computing phylogenetic relationships. We also use the model to mimic large scale genomic changes, and use this to evaluate multifractal and related information theory techniques which take into ...

not understand enough about phylogenetics to know that the first classification "Homo sapiens" falls under. For example, if a novice user tries to find "Homo sapiens" from the root of the tree, most novices would is "Eukaryota" . Therefore, a user can enter a portion of the path, for example "Homo sapiens", and get the path

A molecular phylogenetic analysis of 25 isolates of fish nodaviruses, the causative agents of viral nervous necrosis of marine fish, was performed based on the nucleotide sequences (427 bases) of the coat protein gene. These fish nodaviruses were classified into four clusters: tiger puffer nervous necrosis virus, striped jack nervous necrosis virus, berfin flounder nervous ...

A second species of the enigmatic lampyrid genus Oculogryphus is described and figured as Oculogryphus bicolorsp. n. from Vietnam. The definition of the genus is slightly modified with consideration of newly detected morphological variation from this species. According to a comprehensive phylogenetic analysis including nearly 80% of documented lampyrid genera, Oculogryphus is ...

There is a general assumption that eukaryote species are demarcated by morphological or genetic discontinuities. This stems from the idea that species are defined by the ability of individuals to mate and produce viable progeny. At the microscopic level, where organisms often proliferate more by asexual than sexual reproduction, this tidy classification system breaks down and ...

The mitochondrial DNA hypervariable segment I (HVS-I) is widely used in studies of human evolutionary genetics, and therefore accurate estimates of mutation rates among nucleotide sites in this region are essential. We have developed a novel maximum-likelihood methodology for estimating site-specific mutation rates from partial phylogenetic information, ...

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 ...

Reduction of soluble uranium U(VI) to less-soluble uranium U(IV) is a promising approach to minimize migration from contaminated aquifers. It is generally assumed that, under constant reducing conditions, U(IV) is stable and immobile; however, in a previous study, we documented reoxidation of U(IV) under continuous reducing conditions (Wan et al., Environ. Sci. Technol. 2005, 39:6162-6169). To ...

BackgroundRieske non-heme iron aromatic ring-hydroxylating oxygenases (RHOs) are multi-component enzyme systems that are remarkably diverse in bacteria isolated from diverse habitats. Since the first classification in 1990, there has been a need to devise a new classification scheme for these enzymes because many RHOs have been discovered, which do not ...

Orolingual tremors include tremors of the jaw, tongue, pharynx, and face. There is currently no accepted classification scheme for such tremors. A proper classification scheme for orolingual tremors should aid in providing more accurate diagnoses and permit future research studies assessing important aspects such as pathogenesis or ...

In this paper, an algorithm is developed for segmenting document images into four classes: background, photograph, text, and graph. Features used for classification are based on the distribution patterns of wavelet coefficients in high frequency bands. Two important attributes of the algorithm are its multiscale nature-it classifies an image at different resolutions ...

Virulent Newcastle Disease Virus (NDV) is endemic in Pakistan and is a major problem to their poultry industry. Since Newcastle Disease is highly contagious and clinically similar to the highly pathogenic avian influenza, accurate and rapid monitoring of an outbreak is very important. Additionally, ...

... not accurately detect it. We made audible and ultrasound recordings of the calling songs of a phylogenetically ... band. Keywords: acoustics, spectra, cricket, katydid, efficiency, sound, ultrasound, Gryl...

We have traced the evolution patterns of 2480 transmembrane transporters from five complete genome sequences spanning the entire Hemiascomycete phylum: Saccharomyces cerevisiae, Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, and Yarrowia lipolytica. The use of nonambiguous functional and phylogenetic criteria derived from the TCDB ...

PHYML Online is a web interface to PHYML, a software that implements a fast and accurate heuristic for estimating maximum likelihood phylogenies from DNA and protein sequences. This tool provides the user with a number of options, e.g. nonparametric bootstrap and estimation of various evolutionary parameters, in order to perform comprehensive phylogenetic ...

The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on ...

BackgroundRevised by Bond and Platnick in 2007, the trapdoor spider genus Myrmekiaphila comprises 11 species. Species delimitation and placement within one of three species groups was based on modifications of the male copulatory device. Because a phylogeny of the group was not available these species groups might not represent monophyletic lineages; species definitions likewise were untested ...

Phospholipid fatty acids (PLFA) have been widely used to characterize environmental microbial communities, generating community profiles that can distinguish phylogenetic or functional groups within the community. The poor specificity of organism groups with fatty acid biomarkers in the classic PLFA-microorganism associations is a confounding factor in many of the statistical ...

Phospholipid fatty acids (PLFA) have been widely used to characterize environmental microbial communities, generating community profiles that can distinguish phylogenetic or functional groups within the community. The poor specificity of organism groups with fatty acid biomarkers in the classic PLFA-microorganism associations is a confounding factor in many of the statistical ...

Spores of the myxozoan parasite Myxobolus turpisrotundus Zhang 2009 were observed for the first time bearing caudal appendages. Most spores had the typical Myxobolus spp. morphology, but approximately 10% of spores possessed a spore body that was slightly elongated with a short tail projecting from the spore valve. In other spores, the tail was much more clearly visible and elongate. The spore ...

Bioamines act as neurohormonal messengers through their binding to receptors which belong to the largest membrane protein family known so far: the seven spanning membrane receptors. This class of receptors transmits the effect of agonist binding to intracellular effectors by interacting with an intermediary G-protein. The diversity of receptor subtypes inside the protein family, observed in many ...

Human subjects term indicating a classification of research subjects into women and men. In some cases, gender cannot be accurately determined, e.g., for pooled blood samples. The classification of research subjects into women and men. In some cases, gender cannot be accurately determined (e.g., pooled blood ...

transducer pulse coded sonar system that performs target localisation in two dimensions and classificationOn-the-fly Classifying Sonar with Accurate Range and Bearing Estimation Lindsay Kleeman Intelligent second. 1 Introduction Sonar classification provides a fast means for determining geometric properties

& J. F. Ammirati (eds) Arctic and alpine mycology. University of Wash- ington Press, Seattle of agarics from nuclear gene sequences and basidiospore ultra- structure. Mycological Research 111: 1019 classification of the Fungi. Mycological Research 111: 509�47. Hibbett, D. S. & M. J. Donoghue. 1998. Integrating

This is an entry page for exploration of eukaryotic systematics. The primary feature of the page is a cladogram of eukaryotic lineages with links to information pages for each lineage. There is also a brief introduction to classification of eukaryotes, a link to a tutorial on phylogenetics and systematics, and links to other resources on eukaryotic biology ...

This page provides information on classification of archaea. There is an explanation of ribosomal DNA and its use in molecular phylogenetics, Carl Woese's discovery of the three kingdoms of life, and more recent work on classification of archaea. There is also a hyperlinked list of other resources on archaea and a bibliography of ...

This paper presents an overview of the current state of historical linguistics in Australian languages. Australian languages have been important in theoretical debates about the nature of language change and the possibilities for reconstruction and classification in areas of intensive diffusion. Here are summarized the most important outstanding questions for Australian ...

Xanthoparmelia conspersa 1 Xanthoparmelia protomatrae Xanthoparmelia stenophylla Xanthoparmelia subdiffluens Xanthoparmelia sublaevis Xanthoparmelia conspersa 1 Xanthoparmelia protomatrae Xanthoparmelia stenophylla stygia 2 Melanelia hepatizon Platismatia glauca 1 Platismatia glauca 2 Platismatia norvegica Omphalodium

BackgroundThe use of molecular genetic data in phylogenetic systematics has revolutionized this field of research in that several taxonomic groupings defined by traditional taxonomic approaches have been rejected by molecular data. The taxonomic classification of the oribatid mite group Circumdehiscentiae ("Higher Oribatida") is largely based on ...

Molecular sequences provide a rich source of data for inferring the phylogenetic relationships among species. However, recent work indicates that even an accurate multiple alignment of a large sequence set may yield an incorrect phylogeny and that the quality of the phylogenetic tree improves when the input consists only of the highly ...

The complete mitochondrial cytochrome oxidase II gene was sequenced from 17 black flies, representing 13 putative species, and used to infer phylogenetic relationships. A midge (Paratanytarsus sp.) and three mosquitoes (Aedes aegypti, Anopheles quadrimaculatus, and Culex quinquefasciatus) were used as outgroup taxa. All outgroup taxa were highly divergent from black flies. ...

Human immunodeficiency virus type-1 (HIV-1), hepatitis B and C and other rapidly evolving viruses are characterized by extremely high levels of genetic diversity. To facilitate diagnosis and the development of prevention and treatment strategies that efficiently target the diversity of these viruses, and other pathogens such as human T-lymphotropic virus type-1 (HTLV-1), human herpes virus type-8 ...

Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification�plants, animals, fungi, and protists�have been transformed through numerous permutations into the current system of six �supergroups.� The intent of the supergroup ...

Classification skills, so foundational to science, must be taught. While children have a passion and drive to organize and categorize their experiences, sometimes the way they organize them doesn't lead to a worthwhile or accurate scientific understanding. Just as putting a pencil in the hands of a child doesn't automatically teach them to write, having a ...

a large number of rules efficiently for classifica- tion. Many studies [1, 5] have indicated the inherent that CMAR in general has higher prediction accuracy than CBA [9] and C4.5 [10]. Second, to improve both. In this section, we develop methods to generate rules for classification. The second phase, classification

Incorporation of evidence from clinical research requires critical appraisal of its quality. Information retrieval systems can facilitate clinicians' judgments by automatically labeling retrieved citations with their strength of evidence categories. Preliminary results of such a text classification experiment involving MEDLINE citations show that a "bag of words" approach is ...

Text classification is the process of classifying documents into predefined categories based on their content. Existing supervised learning algorithms to automatically classify text need sufficient documents to learn accurately. This paper presents a new algorithm for text classification that requires fewer documents for training. ...

A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated ...

DNA barcoding shows enormous promise for the rapid identification of organisms at the species level. There has been much recent debate, however, about the need for longer barcode sequences, especially when these sequences are used to construct molecular phylogenies. Here, we have analysed a set of fungal mitochondrial sequences � of various lengths � and we have monitored the effect of ...

The study of genome rearrangement is much harder than the corresponding problems on DNA and protein sequences, because of the occurrences of numerous combinatorial structures. By explicitly exploring these combinatorial structures, the recently developed adequate subgraph theory shows that a family of these structures, adequate subgraphs, are informative in finding the optimal solutions to the ...

The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequences of these rearrangements. However, even simple models lead to NP-hard problems, particularly in the area of phylogenetic ...

Student understanding of biological representations has not been well studied. Yet, we know that to be efficient problem solvers in evolutionary biology and systematics, college students must develop expertise in thinking with a particular type of representation, phylogenetic trees. The purpose of this study was to understand how undergraduates make sense of ...