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1

Accurate phylogenetic classification of DNA fragments based onsequence composition  

SciTech Connect

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 sequence 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.

McHardy, Alice C.; Garcia Martin, Hector; Tsirigos, Aristotelis; Hugenholtz, Philip; Rigoutsos, Isidore

2006-05-01

2

Phylogenetics and classification of the pantropical fern family Lindsaeaceae  

E-print Network

Phylogenetics and classification of the pantropical fern family Lindsaeaceae SAMULI LEHTONEN1 for publication 2 June 2010 The classification and generic definition in the tropical­subtropical fern family, and c. 73% of the currently accepted species. The phylogenetic relationships of the lindsaeoid ferns

3

A higher-level phylogenetic classification of the Fungi  

Microsoft Academic Search

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 here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae,

David S. Hibbett; Manfred Binder; Joseph F. Bischoff; Meredith Blackwell; F. Cannon; Ove E. Eriksson; Sabine Huhndorf; Timothy James; Paul M. Kirk; Robert Lu Cking; H. Thorsten Lumbsch; François Lutzoni; P. Brandon Matheny; David J. McLaughlin; Martha J. Powell; Scott Redhead; Conrad L. Schoch; Joseph W. Spatafora; Joost A. Stalpers; Rytas Vilgalys; M. Catherine Aime; André Aptroot; Robert Bauer; Dominik Begerow; Gerald L. Benny; A Lisa; Pedro W. Crous; Yu-Cheng Dai; Walter Gams; David M. Geiser; Gareth W. Griffith; Cécile Gueidan; David L. Hawksworth; Geir Hestmark; Kentaro Hosaka; Richard A. Humber; Kevin D. Hyde; Joseph E. Ironside; Ko Ljalg; Cletus P. Kurtzman; Karl-Henrik Larsson; Robert Lichtwardt; Jolanta Mia Þ Dlikowska; Jolanta Mi?dlikowska; Andrew Miller; Jean-Marc Moncalvo; Sharon Mozley-Standridge; Franz Oberwinkler; Erast Parmasto; Valérie Reeb; Jack D. Rogers; Claude Roux; Leif Ryvarden; José Paulo Sampaio; Arthur Schüßler; Junta Sugiyama; R. Greg Thorn; Leif Tibell; Wendy A. Untereiner; Christopher Walker; Zheng Wang; Alex Weir; Michael Weiss; Merlin M. White; Katarina Winka; Yi-Jian Yao; Ning Zhang

2007-01-01

4

Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach  

PubMed Central

Supertree methods construct trees on a set of taxa (species) combining many smaller trees on the overlapping subsets of the entire set of taxa. A ‘quartet’ is an unrooted tree over taxa, hence the quartet-based supertree methods combine many -taxon unrooted trees into a single and coherent tree over the complete set of taxa. Quartet-based phylogeny reconstruction methods have been receiving considerable attentions in the recent years. An accurate and efficient quartet-based method might be competitive with the current best phylogenetic tree reconstruction methods (such as maximum likelihood or Bayesian MCMC analyses), without being as computationally intensive. In this paper, we present a novel and highly accurate quartet-based phylogenetic tree reconstruction method. We performed an extensive experimental study to evaluate the accuracy and scalability of our approach on both simulated and biological datasets. PMID:25117474

Reaz, Rezwana; Bayzid, Md. Shamsuzzoha; Rahman, M. Sohel

2014-01-01

5

Protein Classification Using Transductive Learning On Phylogenetic Profiles  

E-print Network

Protein Classification Using Transductive Learning On Phylogenetic Profiles Roger Craig and Li Liao Phylogenetic profiles of proteins - strings of ones and zeros encoding respectively the presence and absence of proteins in a group of genomes - have recently been used to identify homologous proteins and/or proteins

Liao, Li

6

A Functional-Phylogenetic Classification System for Transmembrane Solute Transporters  

PubMed Central

A comprehensive classification system for transmembrane molecular transporters has been developed and recently approved by the transport panel of the nomenclature committee of the International Union of Biochemistry and Molecular Biology. This system is based on (i) transporter class and subclass (mode of transport and energy coupling mechanism), (ii) protein phylogenetic family and subfamily, and (iii) substrate specificity. Almost all of the more than 250 identified families of transporters include members that function exclusively in transport. Channels (115 families), secondary active transporters (uniporters, symporters, and antiporters) (78 families), primary active transporters (23 families), group translocators (6 families), and transport proteins of ill-defined function or of unknown mechanism (51 families) constitute distinct categories. Transport mode and energy coupling prove to be relatively immutable characteristics and therefore provide primary bases for classification. Phylogenetic grouping reflects structure, function, mechanism, and often substrate specificity and therefore provides a reliable secondary basis for classification. Substrate specificity and polarity of transport prove to be more readily altered during evolutionary history and therefore provide a tertiary basis for classification. With very few exceptions, a phylogenetic family of transporters includes members that function by a single transport mode and energy coupling mechanism, although a variety of substrates may be transported, sometimes with either inwardly or outwardly directed polarity. In this review, I provide cross-referencing of well-characterized constituent transporters according to (i) transport mode, (ii) energy coupling mechanism, (iii) phylogenetic grouping, and (iv) substrates transported. The structural features and distribution of recognized family members throughout the living world are also evaluated. The tabulations should facilitate familial and functional assignments of newly sequenced transport proteins that will result from future genome sequencing projects. PMID:10839820

Saier, Milton H.

2000-01-01

7

Phylogenetic and functional classification of ATP-binding cassette (ABC) systems.  

PubMed

ATP binding cassette (ABC) systems constitute one of the most abundant superfamilies of proteins. They are involved in the transport of a wide variety of substances, but also in many cellular processes and in their regulation. In this paper, we made a comparative analysis of the properties of ABC systems and we provide a phylogenetic and functional classification. This analysis will be helpful to accurately annotate ABC systems discovered during the sequencing of the genome of living organisms and to identify the partners of the ABC ATPases. PMID:12370001

Bouige, Philippe; Laurent, David; Piloyan, Linda; Dassa, Elie

2002-10-01

8

The ABC of ABCS: a phylogenetic and functional classification of ABC systems in living organisms.  

PubMed

ATP binding cassette (ABC) systems constitute one of the most abundant superfamilies of proteins. They are involved not only in the transport of a wide variety of substances, but also in many cellular processes and in their regulation. In this paper, we made a comparative analysis of the properties of ABC systems and we provide a phylogenetic and functional classification. This analysis will be helpful to accurately annotate ABC systems discovered during the sequencing of the genome of living organisms and to identify the partners of the ABC ATPases. PMID:11421270

Dassa, E; Bouige, P

2001-01-01

9

Phylogenetic classification of Cordyceps and the clavicipitaceous fungi  

PubMed Central

Cordyceps, comprising over 400 species, was historically classified in the Clavicipitaceae, based on cylindrical asci, thickened ascus apices and filiform ascospores, which often disarticulate into part-spores. Cordyceps was characterized by the production of well-developed often stipitate stromata and an ecology as a pathogen of arthropods and Elaphomyces with infrageneric classifications emphasizing arrangement of perithecia, ascospore morphology and host affiliation. To refine the classification of Cordyceps and the Clavicipitaceae, the phylogenetic relationships of 162 taxa were estimated based on analyses consisting of five to seven loci, including the nuclear ribosomal small and large subunits (nrSSU and nrLSU), the elongation factor 1? (tef1), the largest and the second largest subunits of RNA polymerase II (rpb1 and rpb2), ?-tubulin (tub), and mitochondrial ATP6 (atp6). Our results strongly support the existence of three clavicipitaceous clades and reject the monophyly of both Cordyceps and Clavicipitaceae. Most diagnostic characters used in current classifications of Cordyceps (e.g., arrangement of perithecia, ascospore fragmentation, etc.) were not supported as being phylogenetically informative; the characters that were most consistent with the phylogeny were texture, pigmentation and morphology of stromata. Therefore, we revise the taxonomy of Cordyceps and the Clavicipitaceae to be consistent with the multi-gene phylogeny. The family Cordycipitaceae is validated based on the type of Cordyceps, C. militaris, and includes most Cordyceps species that possess brightly coloured, fleshy stromata. The new family Ophiocordycipitaceae is proposed based on Ophiocordyceps Petch, which we emend. The majority of species in this family produce darkly pigmented, tough to pliant stromata that often possess aperithecial apices. The new genus Elaphocordyceps is proposed for a subclade of the Ophiocordycipitaceae, which includes all species of Cordyceps that parasitize the fungal genus Elaphomyces and some closely related species that parasitize arthropods. The family Clavicipitaceae s. s. is emended and includes the core clade of grass symbionts (e.g., Balansia, Claviceps, Epichloë, etc.), and the entomopathogenic genus Hypocrella and relatives. In addition, the new genus Metacordyceps is proposed for Cordyceps species that are closely related to the grass symbionts in the Clavicipitaceae s. s. Metacordyceps includes teleomorphs linked to Metarhizium and other closely related anamorphs. Two new species are described, and lists of accepted names for species in Cordyceps, Elaphocordyceps, Metacordyceps and Ophiocordyceps are provided. PMID:18490993

Sung, Gi-Ho; Hywel-Jones, Nigel L.; Sung, Jae-Mo; Luangsa-ard, J. Jennifer; Shrestha, Bhushan; Spatafora, Joseph W.

2007-01-01

10

CPM: A Graph Pattern Matching Kernel with Diffusion for Accurate Graph Classification  

E-print Network

with Diffusion for Accurate Graph Classification Aaron Smalter, Jun Huan Department of Electrical Engineering databases search algorithms [17, 32, 40, 42], graph classification aims to construct accurate predictiveCPM: A Graph Pattern Matching Kernel with Diffusion for Accurate Graph Classification Aaron Smalter

Kansas, University of

11

Phylogenetic Classification of Prokaryotic and Eukaryotic Sir2-like Proteins  

Microsoft Academic Search

Sirtuins (Sir2-like proteins) are present in prokaryotes and eukaryotes. Here, two new human sirtuins (SIRT6 and SIRT7) are found to be similar to a particular subset of insect, nematode, plant, and protozoan sirtuins. Molecular phylogenetic analysis of 60 sirtuin conserved core domain sequences from a diverse array of organisms (including archaeans, bacteria, yeasts, plants, protozoans, and metazoans) shows that eukaryotic

Roy A. Frye

2000-01-01

12

Genetic diversity and phylogenetic classification of viral hemorrhagic septicemia virus (VHSV)  

E-print Network

Genetic diversity and phylogenetic classification of viral hemorrhagic septicemia virus (VHSV) B the genetic diversity of viral hemorrhagic septicemia virus (VHSV) and to gain insight into the molecular into a highly homogeneous genetic group, European isolates exhibited a higher genetic variability. Sub- grouping

Paris-Sud XI, Université de

13

Phylogenetic classification of Aureobasidium pullulans strains for production of pullulan and xylanase  

Technology Transfer Automated Retrieval System (TEKTRAN)

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...

14

The COG database: new developments in phylogenetic classification of proteins from complete genomes  

Microsoft Academic Search

The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http:\\/\\/www.ncbi.nlm.nih. gov\\/COG). In addition, a supplement to the COGs is available, in which proteins encoded

Roman L. Tatusov; Darren A. Natale; Igor V. Garkavtsev; Tatiana A. Tatusova; Uma T. Shankavaram; Bachoti S. Rao; Boris Kiryutin; M. Y. Galperin; Natalie D. Fedorova; Eugene V. Koonin

2001-01-01

15

Molecular phylogenetic perspectives for character classification and convergence: Framing some issues with nematode vulval appendages and telotylenchid tail termini  

Technology Transfer Automated Retrieval System (TEKTRAN)

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...

16

Phylogeny and phylogenetic classification of the antbirds, ovenbirds, woodcreepers, and allies (Aves: Passeriformes: Infraorder Furnariides)  

USGS Publications Warehouse

The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well-sampled higher-level phylogenetic studies. Using DNA sequence data from the nuclear RAG-1 and RAG-2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family-level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier studies in which discerning relationships at the base of the radiation was also difficult. In contrast, branch support for family-rank taxa and for many relationships within those clades was generally high. Our results support the Melanopareidae and Grallariidae as distinct from the Rhinocryptidae and Formicariidae, respectively. Within the Furnariides our data contradict some recent phylogenetic hypotheses and suggest that further study is needed to resolve these discrepancies. Of the few genera represented by multiple species, several were not monophyletic, indicating that additional systematic work remains within furnariine families and must include dense taxon sampling. We use this study as a basis for proposing a new phylogenetic classification for the group and in the process erect new family-group names for clades having high branch support across methods. ?? 2009 The Willi Hennig Society.

Moyle, R.G.; Chesser, R.T.; Brumfield, R.T.; Tello, J.G.; Marchese, D.J.; Cracraft, J.

2009-01-01

17

Exploiting Problem Domain Knowledge for Accurate Building Image Classification  

Microsoft Academic Search

\\u000a An approach for classification of building images through rule-based fuzzy inference is presented. It exploits rough matching\\u000a and problem domain knowledge to improve precision results. This approach uses knowledge representation based on a fuzzy reasoning\\u000a model for establishing a bridge between visual primitives and their interpretations.\\u000a \\u000a \\u000a Knowledge representation goes from low level to high level features. The knowledge is acquired

Andrés Dorado; Ebroul Izquierdo

2004-01-01

18

The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.  

PubMed

Eukaryotes and archaebacteria form the clade neomura and are sisters, as shown decisively by genes fragmented only in archaebacteria and by many sequence trees. This sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an alpha-proteobacterium, which also fail to account for numerous features shared specifically by eukaryotes and actinobacteria. I revise the phagotrophy theory of eukaryote origins by arguing that the essentially autogenous origins of most eukaryotic cell properties (phagotrophy, endomembrane system including peroxisomes, cytoskeleton, nucleus, mitosis and sex) partially overlapped and were synergistic with the symbiogenetic origin of mitochondria from an alpha-proteobacterium. These radical innovations occurred in a derivative of the neomuran common ancestor, which itself had evolved immediately prior to the divergence of eukaryotes and archaebacteria by drastic alterations to its eubacterial ancestor, an actinobacterial posibacterium able to make sterols, by replacing murein peptidoglycan by N-linked glycoproteins and a multitude of other shared neomuran novelties. The conversion of the rigid neomuran wall into a flexible surface coat and the associated origin of phagotrophy were instrumental in the evolution of the endomembrane system, cytoskeleton, nuclear organization and division and sexual life-cycles. Cilia evolved not by symbiogenesis but by autogenous specialization of the cytoskeleton. I argue that the ancestral eukaryote was uniciliate with a single centriole (unikont) and a simple centrosomal cone of microtubules, as in the aerobic amoebozoan zooflagellate Phalansterium. I infer the root of the eukaryote tree at the divergence between opisthokonts (animals, Choanozoa, fungi) with a single posterior cilium and all other eukaryotes, designated 'anterokonts' because of the ancestral presence of an anterior cilium. Anterokonts comprise the Amoebozoa, which may be ancestrally unikont, and a vast ancestrally biciliate clade, named 'bikonts'. The apparently conflicting rRNA and protein trees can be reconciled with each other and this ultrastructural interpretation if long-branch distortions, some mechanistically explicable, are allowed for. Bikonts comprise two groups: corticoflagellates, with a younger anterior cilium, no centrosomal cone and ancestrally a semi-rigid cell cortex with a microtubular band on either side of the posterior mature centriole; and Rhizaria [a new infrakingdom comprising Cercozoa (now including Ascetosporea classis nov.), Retaria phylum nov., Heliozoa and Apusozoa phylum nov.], having a centrosomal cone or radiating microtubules and two microtubular roots and a soft surface, frequently with reticulopodia. Corticoflagellates comprise photokaryotes (Plantae and chromalveolates, both ancestrally with cortical alveoli) and Excavata (a new protozoan infrakingdom comprising Loukozoa, Discicristata and Archezoa, ancestrally with three microtubular roots). All basal eukaryotic radiations were of mitochondrial aerobes; hydrogenosomes evolved polyphyletically from mitochondria long afterwards, the persistence of their double envelope long after their genomes disappeared being a striking instance of membrane heredity. I discuss the relationship between the 13 protozoan phyla recognized here and revise higher protozoan classification by updating as subkingdoms Lankester's 1878 division of Protozoa into Corticata (Excavata, Alveolata; with prominent cortical microtubules and ancestrally localized cytostome--the Parabasalia probably secondarily internalized the cytoskeleton) and Gymnomyxa [infrakingdoms Sarcomastigota (Choanozoa, Amoebozoa) and Rhizaria; both ancestrally with a non-cortical cytoskeleton of radiating singlet microtubules and a relatively soft cell surface with diffused feeding]. As the eukaryote root almost certainly lies within Gymnomyxa, probably among the Sarcomastigota, Corticata are derived. Following the single symbiogenetic origin of chloroplasts in a corticoflagellate host with cortical alveoli, this ancestral plant radiated

Cavalier-Smith, T

2002-03-01

19

Accurate Arrhythmia classification using auto-associative neural network.  

PubMed

Currently about one in eighteen of the American population suffer from cardiac Arrhythmias that lead to Coronary Heart Diseases and this rate is steadily increasing. An early monitoring and diagnosis of Arrhythmia based on Electrocardiogram signals can help in reducing mortality. This paper primarily focuses on the application of Auto Associative Neural Network as a new classification approach, which does not require feature extraction task. The weights of a trained Neural Network are stored as class representative models that results in high compression gain with respect to the size of training data. The evaluation of the proposed technique is tested on segmented ECG beats of four different classes of Arrhythmia excluding normal pattern. These beats have been extracted from the MIT/BIH Arrhythmia database and compared against the state-of-the art template matching technique such as Dynamic Time Warping. The proposed technique yields an average accuracy of more than 97% and a relative compression gain of above 90%. PMID:24110670

Chakroborty, Sandipan

2013-01-01

20

Phylogenetic Analysis and Classification of the Fungal bHLH Domain  

PubMed Central

The basic Helix-Loop-Helix (bHLH) domain is an essential highly conserved DNA-binding domain found in many transcription factors in all eukaryotic organisms. The bHLH domain has been well studied in the Animal and Plant Kingdoms but has yet to be characterized within Fungi. Herein, we obtained and evaluated the phylogenetic relationship of 490 fungal-specific bHLH containing proteins from 55 whole genome projects composed of 49 Ascomycota and 6 Basidiomycota organisms. We identified 12 major groupings within Fungi (F1–F12); identifying conserved motifs and functions specific to each group. Several classification models were built to distinguish the 12 groups and elucidate the most discerning sites in the domain. Performance testing on these models, for correct group classification, resulted in a maximum sensitivity and specificity of 98.5% and 99.8%, respectively. We identified 12 highly discerning sites and incorporated those into a set of rules (simplified model) to classify sequences into the correct group. Conservation of amino acid sites and phylogenetic analyses established that like plant bHLH proteins, fungal bHLH–containing proteins are most closely related to animal Group B. The models used in these analyses were incorporated into a software package, the source code for which is available at www.fungalgenomics.ncsu.edu. PMID:22114358

Sailsbery, Joshua K.; Atchley, William R.; Dean, Ralph A.

2012-01-01

21

Molecular Phylogenetic Evaluation of Classification and Scenarios of Character Evolution in Calcareous Sponges (Porifera, Class Calcarea)  

PubMed Central

Calcareous sponges (Phylum Porifera, Class Calcarea) are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU) rDNA and the almost complete large subunit (LSU) rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae) and Leucettidae and between Leucascandra (Jenkinidae) and Sycon carteri (Sycettidae). According to our results, the taxonomy of Calcarea is in desperate need of a thorough revision, which cannot be achieved by considering morphology alone or relying on a taxon sampling based on the current classification below the subclass level. PMID:22479395

Voigt, Oliver; Wülfing, Eilika; Wörheide, Gert

2012-01-01

22

Enhanced assessment of the wound-healing process by accurate multi-view tissue classification  

E-print Network

or surgical wounds and dermatological lesions. Moreover, wound care is expensive: according to a report to be drastically reduced, there is a growing demand for patients to be cared for at home;wound monitoring could1 Enhanced assessment of the wound-healing process by accurate multi-view tissue classification

Boyer, Edmond

23

Rapid phylogenetic and functional classification of short genomic fragments with signature peptides  

PubMed Central

Background Classification is difficult for shotgun metagenomics data from environments such as soils, where the diversity of sequences is high and where reference sequences from close relatives may not exist. Approaches based on sequence-similarity scores must deal with the confounding effects that inheritance and functional pressures exert on the relation between scores and phylogenetic distance, while approaches based on sequence alignment and tree-building are typically limited to a small fraction of gene families. We describe an approach based on finding one or more exact matches between a read and a precomputed set of peptide 10-mers. Results At even the largest phylogenetic distances, thousands of 10-mer peptide exact matches can be found between pairs of bacterial genomes. Genes that share one or more peptide 10-mers typically have high reciprocal BLAST scores. Among a set of 403 representative bacterial genomes, some 20 million 10-mer peptides were found to be shared. We assign each of these peptides as a signature of a particular node in a phylogenetic reference tree based on the RNA polymerase genes. We classify the phylogeny of a genomic fragment (e.g., read) at the most specific node on the reference tree that is consistent with the phylogeny of observed signature peptides it contains. Using both synthetic data from four newly-sequenced soil-bacterium genomes and ten real soil metagenomics data sets, we demonstrate a sensitivity and specificity comparable to that of the MEGAN metagenomics analysis package using BLASTX against the NR database. Phylogenetic and functional similarity metrics applied to real metagenomics data indicates a signal-to-noise ratio of approximately 400 for distinguishing among environments. Our method assigns ~6.6 Gbp/hr on a single CPU, compared with 25 kbp/hr for methods based on BLASTX against the NR database. Conclusions Classification by exact matching against a precomputed list of signature peptides provides comparable results to existing techniques for reads longer than about 300 bp and does not degrade severely with shorter reads. Orders of magnitude faster than existing methods, the approach is suitable now for inclusion in analysis pipelines and appears to be extensible in several different directions. PMID:22925230

2012-01-01

24

Accurate crop classification using hierarchical genetic fuzzy rule-based systems  

NASA Astrophysics Data System (ADS)

This paper investigates the effectiveness of an advanced classification system for accurate crop classification using very high resolution (VHR) satellite imagery. Specifically, a recently proposed genetic fuzzy rule-based classification system (GFRBCS) is employed, namely, the Hierarchical Rule-based Linguistic Classifier (HiRLiC). HiRLiC's model comprises a small set of simple IF-THEN fuzzy rules, easily interpretable by humans. One of its most important attributes is that its learning algorithm requires minimum user interaction, since the most important learning parameters affecting the classification accuracy are determined by the learning algorithm automatically. HiRLiC is applied in a challenging crop classification task, using a SPOT5 satellite image over an intensively cultivated area in a lake-wetland ecosystem in northern Greece. A rich set of higher-order spectral and textural features is derived from the initial bands of the (pan-sharpened) image, resulting in an input space comprising 119 features. The experimental analysis proves that HiRLiC compares favorably to other interpretable classifiers of the literature, both in terms of structural complexity and classification accuracy. Its testing accuracy was very close to that obtained by complex state-of-the-art classification systems, such as the support vector machines (SVM) and random forest (RF) classifiers. Nevertheless, visual inspection of the derived classification maps shows that HiRLiC is characterized by higher generalization properties, providing more homogeneous classifications that the competitors. Moreover, the runtime requirements for producing the thematic map was orders of magnitude lower than the respective for the competitors.

Topaloglou, Charalampos A.; Mylonas, Stelios K.; Stavrakoudis, Dimitris G.; Mastorocostas, Paris A.; Theocharis, John B.

2014-10-01

25

Evaluation of recA gene as a phylogenetic marker in the classification of dairy propionibacteria.  

PubMed

The aim of this study was to investigate the validity of recA gene as a molecular marker for the reliable discrimination and classification of dairy propionibacteria and the closely related species. Regions of the recA gene, varying in size between 613 and 677 nucleotides, were sequenced for Propionibacterium acidipropionici, P. cyclohexanicum, P. freudenreichii, P. jensenii, P. microaerophilum and P. thoenii using degenerate consensus primers constructed by aligning recA sequences of some actinobacteria. The 16S rRNA encoding genes for the type and reference strains of the species P. acidipropionici, P. jensenii and P. thoenii were also sequenced to remove ambiguous positions present in the current database reports, such to improve the classification scheme of reference. As found for other bacterial species, recA sequences permitted a better distinction among the dairy propionibacteria considered than 16S rRNA gene. However, the topology of phylogenetic trees constructed on the recA gene regions sequenced and their putative translations appeared rather different and less statistically valid than the 16S rRNA gene tree. In addition, the possibility of designing PCR-based identification and detection tests on the new recA sequences was demonstrated by assessing specific amplification protocols for P. cyclohexanicum and P. microaerophilum. PMID:16458468

Rossi, Franca; Dellaglio, Franco; Torriani, Sandra

2006-09-01

26

Phylogenetic classification at generic level in the absence of distinct phylogenetic patterns of phenotypical variation: a case study in graphidaceae (ascomycota).  

PubMed

Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed. PMID:23251515

Parnmen, Sittiporn; Lücking, Robert; Lumbsch, H Thorsten

2012-01-01

27

Enhanced assessment of the wound-healing process by accurate multiview tissue classification.  

PubMed

With the widespread use of digital cameras, freehand wound imaging has become common practice in clinical settings. There is however still a demand for a practical tool for accurate wound healing assessment, combining dimensional measurements and tissue classification in a single user-friendly system. We achieved the first part of this objective by computing a 3-D model for wound measurements using uncalibrated vision techniques. We focus here on tissue classification from color and texture region descriptors computed after unsupervised segmentation. Due to perspective distortions, uncontrolled lighting conditions and view points, wound assessments vary significantly between patient examinations. The main contribution of this paper is to overcome this drawback with a multiview strategy for tissue classification, relying on a 3-D model onto which tissue labels are mapped and classification results merged. The experimental classification tests demonstrate that enhanced repeatability and robustness are obtained and that metric assessment is achieved through real area and volume measurements and wound outline extraction. This innovative tool is intended for use not only in therapeutic follow-up in hospitals but also for telemedicine purposes and clinical research, where repeatability and accuracy of wound assessment are critical. PMID:20875969

Wannous, Hazem; Lucas, Yves; Treuillet, Sylvie

2011-02-01

28

Toward a stable classification of genera within the Entolomataceae: a phylogenetic re-evaluation of the Rhodocybe-Clitopilus clade.  

PubMed

Despite the recent molecular systematic analyses of the Entolomataceae (Agaricales, Basidiomycota), a robust classification of genera supported by morphological and phylogenetic evidence remains unresolved for this cosmopolitan family of pink-spored fungi. Here, a phylogenetic analysis for one of the two major clades (Rhodocybe-Clitopilus) was conducted using three nuclear protein-coding gene regions, the mitochondrial ATP synthase subunit 6 (atp6), the nuclear RNA polymerase subunit II (rpb2) and the nuclear translation elongation factor subunit 1-? (tef1). Five monophyletic groups are resolved with strong statistical support and a set of morphological features for delineation of genera is presented. In the revised classification proposed here, Clitopilus is retained, Rhodocybe is emended, two genera previously accepted as synonyms of Rhodocybe (Clitopilopsis and Rhodophana) are resurrected and Clitocella is described as new. PMID:24987124

Kluting, Kerri L; Baroni, Timothy J; Bergemann, Sarah E

2014-11-01

29

Phylogenetic classification of Bartonella species by comparing groEL sequences.  

PubMed

Bartonella is a bacterial genus classified in the alpha-Proteobacteria on the basis of 165 rDNA sequence comparison. The highly conserved heat-shock chaperonin protein, GroEL, has proved to be a valuable resolving tool to classify ten Bartonella species. The groEL gene was amplified and sequenced from ten Bartonella isolates: Bartonella alsatica, Bartonella vinsonii subsp. arupensis, Bartonella taylorii, Bartonella tribocorum, Bartonella birtlesii, Bartonella henselae Marseille (URLLY8), B. henselae (90-615), B. henselae (Fizz), B. henselae (CAL-1) and B. henselae (SA-2). Then, phylogenetic relationships were inferred between our isolates and eight other species and subspecies from the comparison of both 16S rDNA and groEL sequences using parsimony, neighbour-joining and maximum-likelihood methods. By using groEL sequences, the first reliable classification of most known Bartonella species and subspecies was established. Four strongly supported subgroups were distinguished: firstly, the two human pathogens B. henselae and Bartonella quintana; secondly, a cluster including four rodent isolates, Bartonella elizabethae, B. tribocorum, Bartonella grahamii and B. taylorii; thirdly, a cluster including the B. vinsonii subspecies (B. vinsonii subsp. vinsonii, arupensis and berkhoffii); and lastly, B. birtlesii and 'Bartonella weissi'. 'Bartonella washoensis', B. alsatica, Bartonella doshiae, Bartonella bacilliformis and Bartonella clarridgeiae did not reliably cluster with any other Bartonella species. In addition, the groEL gene was shown to be useful in subtyping six B. henselae isolates into three variants: Houston, Marseille and Fizz. PMID:11837299

Zeaiter, Zaher; Fournier, Pierre-Edouard; Ogata, Hiroyuki; Raoult, Didier

2002-01-01

30

Determining suitable image resolutions for accurate supervised crop classification using remote sensing data  

NASA Astrophysics Data System (ADS)

Mapping the spatial distribution of crops has become a fundamental input for agricultural production monitoring using remote sensing. However, the multi-temporality that is often necessary to accurately identify crops and to monitor crop growth generally comes at the expense of coarser observation supports, and can lead to increasingly erroneous class allocations caused by mixed pixels. For a given application like crop classification, the spatial resolution requirement (e.g. in terms of a maximum tolerable pixel size) differs considerably over different landscapes. To analyse the spatial resolution requirements for accurate crop identification via image classification, this study builds upon and extends a conceptual framework established in a previous work1. This framework allows defining quantitatively the spatial resolution requirements for crop monitoring based on simulating how agricultural landscapes, and more specifically the fields covered by a crop of interest, are seen by instruments with increasingly coarser resolving power. The concept of crop specific pixel purity, defined as the degree of homogeneity of the signal encoded in a pixel with respect to the target crop type, is used to analyse how mixed the pixels can be (as they become coarser), without undermining their capacity to describe the desired surface properties. In this case, this framework has been steered towards answering the question: "What is the spatial resolution requirement for crop identification via supervised image classification, in particular minimum and coarsest acceptable pixel sizes, and how do these requirements change over different landscapes?" The framework is applied over four contrasting agro-ecological landscapes in Middle Asia. Inputs to the experiment were eight multi-temporal images from the RapidEye sensor, the simulated pixel sizes range from 6.5 m to 396.5 m. Constraining parameters for crop identification were defined by setting thresholds for classification accuracy and uncertainty. Different types of crops display marked individuality regarding the pixel size requirements, depending on the spatial structures and cropping pattern in the sites. The coarsest acceptable pixel sizes and corresponding purities for the same type of crop were found to vary from site to site, and some crops could not be identified using pixels coarser than 200 m.

Löw, Fabian; Duveiller, Grégory

2013-10-01

31

Photometric brown-dwarf classification. I. A method to identify and accurately classify large samples of brown dwarfs without spectroscopy  

NASA Astrophysics Data System (ADS)

Aims: We present a method, named photo-type, to identify and accurately classify L and T dwarfs onto the standard spectral classification system using photometry alone. This enables the creation of large and deep homogeneous samples of these objects efficiently, without the need for spectroscopy. Methods: We created a catalogue of point sources with photometry in 8 bands, ranging from 0.75 to 4.6 ?m, selected from an area of 3344 deg2, by combining SDSS, UKIDSS LAS, and WISE data. Sources with 13.0 0.8, were then classified by comparison against template colours of quasars, stars, and brown dwarfs. The L and T templates, spectral types L0 to T8, were created by identifying previously known sources with spectroscopic classifications, and fitting polynomial relations between colour and spectral type. Results: Of the 192 known L and T dwarfs with reliable photometry in the surveyed area and magnitude range, 189 are recovered by our selection and classification method. We have quantified the accuracy of the classification method both externally, with spectroscopy, and internally, by creating synthetic catalogues and accounting for the uncertainties. We find that, brighter than J = 17.5, photo-type classifications are accurate to one spectral sub-type, and are therefore competitive with spectroscopic classifications. The resultant catalogue of 1157 L and T dwarfs will be presented in a companion paper.

Skrzypek, N.; Warren, S. J.; Faherty, J. K.; Mortlock, D. J.; Burgasser, A. J.; Hewett, P. C.

2015-02-01

32

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

PubMed Central

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

2010-01-01

33

Phylogenetic classification of the frog pathogen Amphibiothecum (Dermosporidium) penneri based on small ribosomal subunit sequencing  

USGS Publications Warehouse

We determined 1,600 base pairs of DNA sequence in the 18S small ribosomal subunit from two geographically distinct isolates of Dermosporidium penneri. Maximum likelihood and parsimony analysis of these sequences place D. penneri in the order Dermocystida of the class Mesomycetozoea. The 18S rRNA sequences from these two isolates only differ within a single region of 16 contiguous nucleotides. Based on the distant phylogenetic relationship of these organisms to Amphibiocystidium ranae and similarity to Sphaerothecum destruens we propose the organism be renamed Amphibiothecum penneri.

Feldman, S.H.; Wimsatt, J.H.; Green, D.E.

2005-01-01

34

Classification of the Indo-European Languages Using a Phylogenetic Network Approach  

Microsoft Academic Search

\\u000a Discovering the origin of the Indo-European (IE) language family is one of the most intensively studied problems in historical\\u000a linguistics. Gray and Atkinson (2003) inferred a phylogenetic tree (i.e., additive tree or X-tree, Barthelémy and Guénoche\\u000a 1991) of the IE family, using bayesian inference and rate-smoothing algorithms, based on the 87 Indo-European language data\\u000a set collected by Dyen et al.

Alix Boc; Anna Maria Di Sciullo; Vladimir Makarenkov

35

Toward a Phylogenetic Classification of Primates Based on DNA Evidence Complemented by Fossil Evidence  

Microsoft Academic Search

A highly resolved primate cladogram based on DNA evidence is congruent with extant and fossil osteological evidence. A provisional primate classification based on this cladogram and the time scale provided by fossils and the model of local molecular clocks has all named taxa represent clades and assigns the same taxonomic rank to those clades of roughly equivalent age. Order Primates

Morris Goodman; Calvin A. Porter; John Czelusniak; Scott L. Page; Horacio Schneider; Jeheskel Shoshani; Gregg Gunnell; Colin P. Groves

1998-01-01

36

Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life.  

PubMed Central

A symbiosis-based phylogeny leads to a consistent, useful classification system for all life. "Kingdoms" and "Domains" are replaced by biological names for the most inclusive taxa: Prokarya (bacteria) and Eukarya (symbiosis-derived nucleated organisms). The earliest Eukarya, anaerobic mastigotes, hypothetically originated from permanent whole-cell fusion between members of Archaea (e.g., Thermoplasma-like organisms) and of Eubacteria (e.g., Spirochaeta-like organisms). Molecular biology, life-history, and fossil record evidence support the reunification of bacteria as Prokarya while subdividing Eukarya into uniquely defined subtaxa: Protoctista, Animalia, Fungi, and Plantae. Images Fig. 1 PMID:8577716

Margulis, L

1996-01-01

37

Deceptive desmas: molecular phylogenetics suggests a new classification and uncovers convergent evolution of lithistid demosponges.  

PubMed

Reconciling the fossil record with molecular phylogenies to enhance the understanding of animal evolution is a challenging task, especially for taxa with a mostly poor fossil record, such as sponges (Porifera). 'Lithistida', a polyphyletic group of recent and fossil sponges, are an exception as they provide the richest fossil record among demosponges. Lithistids, currently encompassing 13 families, 41 genera and >300 recent species, are defined by the common possession of peculiar siliceous spicules (desmas) that characteristically form rigid articulated skeletons. Their phylogenetic relationships are to a large extent unresolved and there has been no (taxonomically) comprehensive analysis to formally reallocate lithistid taxa to their closest relatives. This study, based on the most comprehensive molecular and morphological investigation of 'lithistid' demosponges to date, corroborates some previous weakly-supported hypotheses, and provides novel insights into the evolutionary relationships of the previous 'order Lithistida'. Based on molecular data (partial mtDNA CO1 and 28S rDNA sequences), we show that 8 out of 13 'Lithistida' families belong to the order Astrophorida, whereas Scleritodermidae and Siphonidiidae form a separate monophyletic clade within Tetractinellida. Most lithistid astrophorids are dispersed between different clades of the Astrophorida and we propose to formally reallocate them, respectively. Corallistidae, Theonellidae and Phymatellidae are monophyletic, whereas the families Pleromidae and Scleritodermidae are polyphyletic. Family Desmanthidae is polyphyletic and groups within Halichondriidae - we formally propose a reallocation. The sister group relationship of the family Vetulinidae to Spongillida is confirmed and we propose here for the first time to include Vetulina into a new Order Sphaerocladina. Megascleres and microscleres possibly evolved and/or were lost several times independently in different 'lithistid' taxa, and microscleres might at least be four times more likely lost than megascleres. Desma spicules occasionally may have undergone secondary losses too. Our study provides a framework for further detailed investigations of this important demosponge group. PMID:25565279

Schuster, Astrid; Erpenbeck, Dirk; Pisera, Andrzej; Hooper, John; Bryce, Monika; Fromont, Jane; Wörheide, Gert

2015-01-01

38

Deceptive Desmas: Molecular Phylogenetics Suggests a New Classification and Uncovers Convergent Evolution of Lithistid Demosponges  

PubMed Central

Reconciling the fossil record with molecular phylogenies to enhance the understanding of animal evolution is a challenging task, especially for taxa with a mostly poor fossil record, such as sponges (Porifera). ‘Lithistida’, a polyphyletic group of recent and fossil sponges, are an exception as they provide the richest fossil record among demosponges. Lithistids, currently encompassing 13 families, 41 genera and >300 recent species, are defined by the common possession of peculiar siliceous spicules (desmas) that characteristically form rigid articulated skeletons. Their phylogenetic relationships are to a large extent unresolved and there has been no (taxonomically) comprehensive analysis to formally reallocate lithistid taxa to their closest relatives. This study, based on the most comprehensive molecular and morphological investigation of ‘lithistid’ demosponges to date, corroborates some previous weakly-supported hypotheses, and provides novel insights into the evolutionary relationships of the previous ‘order Lithistida’. Based on molecular data (partial mtDNA CO1 and 28S rDNA sequences), we show that 8 out of 13 ‘Lithistida’ families belong to the order Astrophorida, whereas Scleritodermidae and Siphonidiidae form a separate monophyletic clade within Tetractinellida. Most lithistid astrophorids are dispersed between different clades of the Astrophorida and we propose to formally reallocate them, respectively. Corallistidae, Theonellidae and Phymatellidae are monophyletic, whereas the families Pleromidae and Scleritodermidae are polyphyletic. Family Desmanthidae is polyphyletic and groups within Halichondriidae – we formally propose a reallocation. The sister group relationship of the family Vetulinidae to Spongillida is confirmed and we propose here for the first time to include Vetulina into a new Order Sphaerocladina. Megascleres and microscleres possibly evolved and/or were lost several times independently in different ‘lithistid’ taxa, and microscleres might at least be four times more likely lost than megascleres. Desma spicules occasionally may have undergone secondary losses too. Our study provides a framework for further detailed investigations of this important demosponge group. PMID:25565279

Schuster, Astrid; Erpenbeck, Dirk; Pisera, Andrzej; Hooper, John; Bryce, Monika; Fromont, Jane; Wörheide, Gert

2015-01-01

39

Phylogenetic analysis, genomic diversity and classification of M class gene segments of turkey reoviruses.  

PubMed

From 2011 to 2014, 13 turkey arthritis reoviruses (TARVs) were isolated from cases of swollen hock joints in 2-18-week-old turkeys. In addition, two isolates from similar cases of turkey arthritis were received from another laboratory. Eight turkey enteric reoviruses (TERVs) isolated from fecal samples of turkeys were also used for comparison. The aims of this study were to characterize turkey reovirus (TRV) based on complete M class genome segments and to determine genetic diversity within TARVs in comparison to TERVs and chicken reoviruses (CRVs). Nucleotide (nt) cut off values of 84%, 83% and 85% for the M1, M2 and M3 gene segments were proposed and used for genotype classification, generating 5, 7, and 3 genotypes, respectively. Using these nt cut off values, we propose M class genotype constellations (GCs) for avian reoviruses. Of the seven GCs, GC1 and GC3 were shared between the TARVs and TERVs, indicating possible reassortment between turkey and chicken reoviruses. The TARVs and TERVs were divided into three GCs, and GC2 was unique to TARVs and TERVs. The proposed new GC approach should be useful in identifying reassortant viruses, which may ultimately be used in the design of a universal vaccine against both chicken and turkey reoviruses. PMID:25655814

Mor, Sunil K; Marthaler, Douglas; Verma, Harsha; Sharafeldin, Tamer A; Jindal, Naresh; Porter, Robert E; Goyal, Sagar M

2015-03-23

40

Classification algorithms with multi-modal data fusion could accurately distinguish neuromyelitis optica from multiple sclerosis  

PubMed Central

Neuromyelitis optica (NMO) exhibits substantial similarities to multiple sclerosis (MS) in clinical manifestations and imaging results and has long been considered a variant of MS. With the advent of a specific biomarker in NMO, known as anti-aquaporin 4, this assumption has changed; however, the differential diagnosis remains challenging and it is still not clear whether a combination of neuroimaging and clinical data could be used to aid clinical decision-making. Computer-aided diagnosis is a rapidly evolving process that holds great promise to facilitate objective differential diagnoses of disorders that show similar presentations. In this study, we aimed to use a powerful method for multi-modal data fusion, known as a multi-kernel learning and performed automatic diagnosis of subjects. We included 30 patients with NMO, 25 patients with MS and 35 healthy volunteers and performed multi-modal imaging with T1-weighted high resolution scans, diffusion tensor imaging (DTI) and resting-state functional MRI (fMRI). In addition, subjects underwent clinical examinations and cognitive assessments. We included 18 a priori predictors from neuroimaging, clinical and cognitive measures in the initial model. We used 10-fold cross-validation to learn the importance of each modality, train and finally test the model performance. The mean accuracy in differentiating between MS and NMO was 88%, where visible white matter lesion load, normal appearing white matter (DTI) and functional connectivity had the most important contributions to the final classification. In a multi-class classification problem we distinguished between all of 3 groups (MS, NMO and healthy controls) with an average accuracy of 84%. In this classification, visible white matter lesion load, functional connectivity, and cognitive scores were the 3 most important modalities. Our work provides preliminary evidence that computational tools can be used to help make an objective differential diagnosis of NMO and MS. PMID:25610795

Eshaghi, Arman; Riyahi-Alam, Sadjad; Saeedi, Roghayyeh; Roostaei, Tina; Nazeri, Arash; Aghsaei, Aida; Doosti, Rozita; Ganjgahi, Habib; Bodini, Benedetta; Shakourirad, Ali; Pakravan, Manijeh; Ghana'ati, Hossein; Firouznia, Kavous; Zarei, Mojtaba; Azimi, Amir Reza; Sahraian, Mohammad Ali

2015-01-01

41

Photometric brown-dwarf classification. I. A method to identify and accurately classify large samples of brown dwarfs without spectroscopy  

E-print Network

Aims. We present a method, named photo-type, to identify and accurately classify L and T dwarfs onto the standard spectral classification system using photometry alone. This enables the creation of large and deep homogeneous samples of these objects efficiently, without the need for spectroscopy. Methods. We created a catalogue of point sources with photometry in 8 bands, ranging from 0.75 to 4.6 microns, selected from an area of 3344 deg^2, by combining SDSS, UKIDSS LAS, and WISE data. Sources with 13.0 0.8, were then classified by comparison against template colours of quasars, stars, and brown dwarfs. The L and T templates, spectral types L0 to T8, were created by identifying previously known sources with spectroscopic classifications, and fitting polynomial relations between colour and spectral type. Results. Of the 192 known L and T dwarfs with reliable photometry in the surveyed area and magnitude range, 189 are recovered by our selection and classification method. We have quantified the accuracy of th...

Skrzypek, Nathalie; Faherty, Jacqueline K; Mortlock, Daniel J; Burgasser, Adam J; Hewett, Paul C

2014-01-01

42

Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts  

PubMed Central

Background Distinction between true protein interactions and crystal packing contacts is important for structural bioinformatics studies to respond to the need of accurate classification of the rapidly increasing protein structures. There are many unannotated crystal contacts and there also exist false annotations in this rapidly expanding volume of data. Previous tools have been proposed to address this problem. However, challenging issues still remain, such as low performance when the training and test data contain mixed interfaces having diverse sizes of contact areas. Methods and results B factor is a measure to quantify the vibrational motion of an atom, a more relevant feature than interface size to characterize protein binding. We propose to use three features related to B factor for the classification between biological interfaces and crystal packing contacts. The first feature is the sum of the normalized B factors of the interfacial atoms in the contact area, the second is the average of the interfacial B factor per residue in the chain, and the third is the average number of interfacial atoms with a negative normalized B factor per residue in the chain. We investigate the distribution properties of these basic features and a compound feature on four datasets of biological binding and crystal packing, and on a protein binding-only dataset with known binding affinity. We also compare the cross-dataset classification performance of these features with existing methods and with a widely-used and the most effective feature interface area. The results demonstrate that our features outperform the interface area approach and the existing prediction methods remarkably for many tests on all of these datasets. Conclusions The proposed B factor related features are more effective than interface area to distinguish crystal packing from biological binding interfaces. Our computational methods have a potential for large-scale and accurate identification of biological interactions from the experimentally determined structural data stored at PDB which may have diverse interface sizes. PMID:25522196

2014-01-01

43

Number of signatures necessary for accurate classification. [for multispectral scanner data  

NASA Technical Reports Server (NTRS)

This paper presents a procedure for determining the number of signatures to use in classifying multispectral scanner data. A large initial set of signatures is obtained by clustering the training points within each category (such as 'wheat' or 'other') to be recognized. These clusters are then combined into broader signatures by a program that considers each pair of signatures within a category, combines the best pair in the light of certain criteria, saves the combined signature and repeats the procedure until there is one signature for each category. The result is a collection of sets of signatures, one set for each number between the number of initial clusters and the number of categories. With the aid of statistics such as an estimate of the probability of misclassification between categories, the user can choose the smallest set satisfying his requirements for classification accuracy.

Richardson, W.; Pentland, A.; Crane, R.; Horwitz, H.

1976-01-01

44

Detecting atheromatous plaques in the aortic arch or supra-aortic arteries for more accurate stroke subtype classification.  

PubMed

Introduction. To investigate the correlations of atheromatous plaques in the aortic arch or supra-aortic arteries with intracranial arterial stenosis and carotid plaques in stroke patients, and to determine whether taking these plaques into account will reduce the proportion of patients in the undetermined etiology group. Methods. We prospectively enrolled 308 ischemic stroke patients, whose clinical characteristics and A-S-C-O classifications were compared with analyses of intracranial arteries, carotid arteries, aortic arch, and supra-aortic arteries. Results. 125(40.6%) patients had plaques in the aortic arch or supra-aortic arteries, of which 106 (84.8%) had complex plaques. No correlations were observed between these plaques and carotid plaques (?p = 0.283) or intracranial arterial stenosis (?p = 0.097). After detecting the mobile thrombi in the aortic arch and supra-aortic arteries, the proportion of patients in the atherothrombosis group was increased from 33.8% to 55.5% (?p = 0.00), whereas the proportion of patients in stroke of undetermined etiology group was decreased from 19.2% to 11.0% (?p = 0.00). Discussion. Examining only the carotid and intracranial arteries may not provide adequate information about large arteries in stroke patients. Therefore, it would be better to include a search for relevant plaques in the aortic arch or supra-aortic arteries in modern stroke workup, for it may lead to more accurate stroke subtype classification and guide secondary prevention. PMID:24738734

Cui, Xiaoyang; Wu, Simiao; Zeng, Quantao; Xiao, Jiahe; Liu, Ming

2015-02-01

45

Novel exomphalos genetic mouse model: The importance of accurate phenotypic classification  

PubMed Central

Background Rodent models of abdominal wall defects (AWD) may provide insight into the pathophysiology of these conditions including gut dysfunction in gastroschisis, or pulmonary hypoplasia in exomphalos. Previously, a Scribble mutant mouse model (circletail) was reported to exhibit gastroschisis. We further characterise this AWD in Scribble knockout mice. Method Homozygous Scrib knockout mice were obtained from heterozygote matings. Fetuses were collected at E17.5–18.5 with intact amniotic membranes. Three mutants and two control fetuses were imaged by in amnio micro-MRI. Remaining fetuses were dissected, photographed and gut length/weight measured. Ileal specimens were stained for interstitial cells of Cajal (ICC), imaged using confocal microscopy and ICC quantified. Results 127 fetuses were collected, 15 (12%) exhibited AWD. Microdissection revealed 3 mutants had characteristic exomphalos phenotype with membrane-covered gut/liver herniation into the umbilical cord. A further 12 exhibited extensive AWD, with eviscerated abdominal organs and thin covering membrane (intact or ruptured). Micro-MRI confirmed these phenotypes. Gut was shorter and heavier in AWD group compared to controls but morphology/number of ICC was not different. Discussion The Scribble knockout fetus exhibits exomphalos (intact and ruptured), in contrast to the original published phenotype of gastroschisis. Detailed dissection of fetuses is essential ensuring accurate phenotyping and result reporting. PMID:24094954

Carnaghan, Helen; Roberts, Tom; Savery, Dawn; Norris, Francesca C.; McCann, Conor J.; Copp, Andrew J.; Scambler, Peter J.; Lythgoe, Mark F.; Greene, Nicholas D.; DeCoppi, Paolo; Burns, Alan J.; Pierro, Agustino; Eaton, Simon

2013-01-01

46

The use of small training sets containing mixed pixels for accurate hard image classification: Training on mixed spectral responses for classification by a SVM  

Microsoft Academic Search

The accuracy of a supervised image classification is a function of the training data used in its generation. It is, therefore, critical that the training stage of a supervised classification is designed to provide the necessary information. Guidance on the design of the training stage of a classification typically calls for the use of a large sample of randomly selected

Giles M. Foody; Ajay Mathur

2006-01-01

47

Phylogenetic Classification of Trichophyton mentagrophytes Complex Strains Based on DNA Sequences of Nuclear Ribosomal Internal Transcribed Spacer 1 Regions  

PubMed Central

Using internal transcribed spacer 1 (ITS1) region ribosomal DNA sequences from 37 stock strains and clinical isolates provisionally termed Trichophyton mentagrophytes complex in Japan, we demonstrated the mutual phylogenetic relationships of these strains. Members of this complex were classified into 3 ITS1-homologous groups and 13 ITS1-identical groups by their sequences. ITS1-homologous group I consists of Arthroderma vanbreuseghemii, T. mentagrophytes human isolates, and several strains of T. mentagrophytes animal isolates. Five strains of Arthroderma simii form a cluster comprising ITS1-homologous group II. The Americano-European and African races of Arthroderma benhamiae, T. mentagrophytes var. erinacei, and one strain of a T. mentagrophytes animal isolate constitute ITS1-homologous group III. According to the phylogenetic tree constructed with Trichophyton rubrum as an outgroup, ITS1-homologous groups I and II comprised a monophyletic cluster and ITS1-homologous group III constituted another cluster which was rather distant from the others in the complex. This system was applicable to the phylogenetic analysis of closely related strains. Using this technique, human and animal isolates of T. mentagrophytes were also clearly distinguishable from each other. PMID:9705405

Makimura, Koichi; Mochizuki, Takashi; Hasegawa, Atsuhiko; Uchida, Katsuhisa; Saito, Hiuga; Yamaguchi, Hideyo

1998-01-01

48

Comprehensive Phylogenetic Reconstructions of African Swine Fever Virus: Proposal for a New Classification and Molecular Dating of the Virus  

PubMed Central

African swine fever (ASF) is a highly lethal disease of domestic pigs caused by the only known DNA arbovirus. It was first described in Kenya in 1921 and since then many isolates have been collected worldwide. However, although several phylogenetic studies have been carried out to understand the relationships between the isolates, no molecular dating analyses have been achieved so far. In this paper, comprehensive phylogenetic reconstructions were made using newly generated, publicly available sequences of hundreds of ASFV isolates from the past 70 years. Analyses focused on B646L, CP204L, and E183L genes from 356, 251, and 123 isolates, respectively. Phylogenetic analyses were achieved using maximum likelihood and Bayesian coalescence methods. A new lineage-based nomenclature is proposed to designate 35 different clusters. In addition, dating of ASFV origin was carried out from the molecular data sets. To avoid bias, diversity due to positive selection or recombination events was neutralized. The molecular clock analyses revealed that ASFV strains currently circulating have evolved over 300 years, with a time to the most recent common ancestor (TMRCA) in the early 18th century. PMID:23936068

Michaud, Vincent; Randriamparany, Tantely; Albina, Emmanuel

2013-01-01

49

Increasing the data size to accurately reconstruct the phylogenetic relationships between nine subgroups of the Drosophila melanogaster species group (Drosophilidae, Diptera).  

PubMed

Previous phylogenetic analyses of the melanogaster species group have led to conflicting hypotheses concerning their relationship; therefore the addition of new sequence data is necessary to discover the phylogeny of this species group. Here we present new data derived from 17 genes and representing 48 species to reconstruct the phylogeny of the melanogaster group. A variety of statistical tests, as well as maximum likelihood mapping analysis, were performed to estimate data quality, suggesting that all genes had a high degree of contribution to resolve the phylogeny. Individual locus was analyzed using maximum likelihood (ML), and the concatenated dataset (12,988 bp) were analyzed using partitioned maximum likelihood (ML) and Bayesian analyses. Separated analysis produced various phylogenetic relationships, however, phylogenetic topologies from ML and Bayesian analysis based on concatenated dataset, at the subgroup level, were completely identical to each other with high levels of support. Our results recovered three major clades: the ananassae subgroup, followed by the montium subgroup, the melanogaster subgroup and the oriental subgroups form the third monophyletic clade, in which melanogaster (takahashii, suzukii) forms one subclade and ficusphila [eugracilis (elegans, rhopaloa)] forms another. However, more data are necessary to determine the phylogenetic position of Drosophila lucipennis which proved difficult to place. PMID:21985965

Yang, Yong; Hou, Zhuo-Cheng; Qian, Yuan-Huai; Kang, Han; Zeng, Qing-Tao

2012-01-01

50

DEFLATE compression algorithm corrects for overestimation of phylogenetic diversity by Grantham approach to single-nucleotide polymorphism classification.  

PubMed

Improvements in speed and cost of genome sequencing are resulting in increasing numbers of novel non-synonymous single nucleotide polymorphisms (nsSNPs) in genes known to be associated with disease. The large number of nsSNPs makes laboratory-based classification infeasible and familial co-segregation with disease is not always possible. In-silico methods for classification or triage are thus utilised. A popular tool based on multiple-species sequence alignments (MSAs) and work by Grantham, Align-GVGD, has been shown to underestimate deleterious effects, particularly as sequence numbers increase. We utilised the DEFLATE compression algorithm to account for expected variation across a number of species. With the adjusted Grantham measure we derived a means of quantitatively clustering known neutral and deleterious nsSNPs from the same gene; this was then used to assign novel variants to the most appropriate cluster as a means of binary classification. Scaling of clusters allows for inter-gene comparison of variants through a single pathogenicity score. The approach improves upon the classification accuracy of Align-GVGD while correcting for sensitivity to large MSAs. Open-source code and a web server are made available at https://github.com/aschlosberg/CompressGV. PMID:24828207

Schlosberg, Arran; Lam, Brian Y H; Yeo, Giles S H; Clifton-Bligh, Roderick J

2014-01-01

51

DEFLATE Compression Algorithm Corrects for Overestimation of Phylogenetic Diversity by Grantham Approach to Single-Nucleotide Polymorphism Classification  

PubMed Central

Improvements in speed and cost of genome sequencing are resulting in increasing numbers of novel non-synonymous single nucleotide polymorphisms (nsSNPs) in genes known to be associated with disease. The large number of nsSNPs makes laboratory-based classification infeasible and familial co-segregation with disease is not always possible. In-silico methods for classification or triage are thus utilised. A popular tool based on multiple-species sequence alignments (MSAs) and work by Grantham, Align-GVGD, has been shown to underestimate deleterious effects, particularly as sequence numbers increase. We utilised the DEFLATE compression algorithm to account for expected variation across a number of species. With the adjusted Grantham measure we derived a means of quantitatively clustering known neutral and deleterious nsSNPs from the same gene; this was then used to assign novel variants to the most appropriate cluster as a means of binary classification. Scaling of clusters allows for inter-gene comparison of variants through a single pathogenicity score. The approach improves upon the classification accuracy of Align-GVGD while correcting for sensitivity to large MSAs. Open-source code and a web server are made available at https://github.com/aschlosberg/CompressGV. PMID:24828207

Schlosberg, Arran; Lam, Brian Y. H.; Yeo, Giles S. H.; Clifton-Bligh, Roderick J.

2014-01-01

52

[Preliminary classification and phylogenetic relationship among Onchidiidae in China inferred from 18S rRNA partial sequence].  

PubMed

As a nutritious mollusk living in the intertidal zone, Onchidiidae has a significant value for biological research. Nine populations were collected from the costal areas such as Chongming (Shanghai), Ningde (Fujian), Haikou (Hainan) in this study. Through the study of anatomy and other methods to investigate the major category characteristics, the nine populations were preliminary classified. By sequencing segments of 18S rRNA gene and constructing phylogenetic trees using these nine populations and four other 18S rRNA gene sequences from GenBank, with Siphonaria as an outgroup, we analyzed the phylogeny of Onchidiidae in mainland China. The trees were used for discussing the relationship between the populations of the Onchidiidae in this study. The results showed that the southern coast has more populations than the northern coast in China. Besides two known species, Onchidium struma (JZH) and O. verruculatum (FJZ & HNZ), five new recorded species may exist: Onchidium(1), Platevindex(2), one Peronia(1) and Paraoncidium(1). The phylogenetic trees indicated that the nine populations can be divided into four subgroups, Peronia, Onchidium, Platevindex and Paraoncidium, and Peronia has the highest confidence level in clustering. Onchidium verruculatum (FJZ & HNZ) should be Peronia verruculata. PMID:20740699

Wu, Wen-Jian; Shen, Bin; Chen, Cheng; Shen, He-Ding; Wei, Luan-Luan; Wang, Ling; Li, Kai

2010-08-01

53

Phylogenetic relationships and classification of thiolases and thiolase-like proteins of Mycobacterium tuberculosis and Mycobacterium smegmatis.  

PubMed

Thiolases are enzymes involved in lipid metabolism. Thiolases remove the acetyl-CoA moiety from 3-ketoacyl-CoAs in the degradative reaction. They can also catalyze the reverse Claisen condensation reaction, which is the first step of biosynthetic processes such as the biosynthesis of sterols and ketone bodies. In human, six distinct thiolases have been identified. Each of these thiolases is different from the other with respect to sequence, oligomeric state, substrate specificity and subcellular localization. Four sequence fingerprints, identifying catalytic loops of thiolases, have been described. In this study genome searches of two mycobacterial species (Mycobacterium tuberculosis and Mycobacterium smegmatis), were carried out, using the six human thiolase sequences as queries. Eight and thirteen different thiolase sequences were identified in M. tuberculosis and M. smegmatis, respectively. In addition, thiolase-like proteins (one encoded in the Mtb and two in the Msm genome) were found. The purpose of this study is to classify these mostly uncharacterized thiolases and thiolase-like proteins. Several other sequences obtained by searches of genome databases of bacteria, mammals and the parasitic protist family of the Trypanosomatidae were included in the analysis. Thiolase-like proteins were also found in the trypanosomatid genomes, but not in those of mammals. In order to study the phylogenetic relationships at a high confidence level, additional thiolase sequences were included such that a total of 130 thiolases and thiolase-like protein sequences were used for the multiple sequence alignment. The resulting phylogenetic tree identifies 12 classes of sequences, each possessing a characteristic set of sequence fingerprints for the catalytic loops. From this analysis it is now possible to assign the mycobacterial thiolases to corresponding homologues in other kingdoms of life. The results of this bioinformatics analysis also show interesting differences between the distributions of M. tuberculosis and M. smegmatis thiolases over the 12 different classes. PMID:24825023

Anbazhagan, Padmanabhan; Harijan, Rajesh K; Kiema, Tiila R; Janardan, Neelanjana; Murthy, M R N; Michels, Paul A M; Juffer, André H; Wierenga, Rik K

2014-07-01

54

Two new species of Geodiscelis Michener & Rozen (Hymenoptera: Apoidea: Colletidae) with a phylogenetic analysis and subgeneric classification of the genus.  

PubMed

Two new species of the genus Geodiscelis are described: Geodiscelis nazcalinea Packer & Dumesh, sp. nov. from Peru (the first record of the genus from that country) and G. phisquiri Packer & Dumesh, sp. nov. from northern Chile. The new species are most closely related to G. longiceps, but differ primarily in having somewhat less elongate heads and in details of the male terminalia. A key to the five known species of the genus is provided as are the results of a phylogenetic analysis based upon 68 characters, and the genus is formally divided into three subgenera: Geodiscelis s. str. Michener and Rozen, Geodiscelis (Nazcoediscelis) Packer and Dumesh, subgenus nov. and Geodiscelis (Thaumoediscelis) Packer and Dumesh, subgenus nov. The two new species described herein belong to subgenus Geodiscelis (Nazcoediscelis). Figures of the most important characters are provided. Tiquilia sp. (Boraginaceae) is the probable floral host of both new species and it is suggested that all species are ground-nesters. Sexual dimorphism in an unusual character is recorded for G. thaumaskelos Packer.  PMID:25283109

Packer, Laurence; Dumesh, Sheila

2014-01-01

55

Accurate and universal delineation of prokaryotic species.  

PubMed

The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI (species identification tool; http://www.bork.embl.de/software/specI/), a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes. Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, >62% were resolved by literature support. PMID:23892899

Mende, Daniel R; Sunagawa, Shinichi; Zeller, Georg; Bork, Peer

2013-09-01

56

A non-contact method based on multiple signal classification algorithm to reduce the measurement time for accurately heart rate detection.  

PubMed

Non-contact methods for the assessment of vital signs are of great interest for specialists due to the benefits obtained in both medical and special applications, such as those for surveillance, monitoring, and search and rescue. This paper investigates the possibility of implementing a digital processing algorithm based on the MUSIC (Multiple Signal Classification) parametric spectral estimation in order to reduce the observation time needed to accurately measure the heart rate. It demonstrates that, by proper dimensioning the signal subspace, the MUSIC algorithm can be optimized in order to accurately assess the heart rate during an 8-28 s time interval. The validation of the processing algorithm performance was achieved by minimizing the mean error of the heart rate after performing simultaneous comparative measurements on several subjects. In order to calculate the error the reference value of heart rate was measured using a classic measurement system through direct contact. PMID:24007088

Bechet, P; Mitran, R; Munteanu, M

2013-08-01

57

CLASSIFICATION  

NSDL National Science Digital Library

Project Overview: Classification is grouping similar objects together. When you go into a grocery store, you see fresh fruits and vegetables, frozen food, cereal, and pet suplies in different aisles. Imagine how difficult life would be if you went into a store, and the aisles were not labeled to tell you where to find the items! You don't have to be a scientist to use classification! You use classification when you group your IPOD music into different genres and when you divide your dark colored clothing from light colors to do laundry. You might even use it to sort Halloween candy into 4 groups: chocolate candy, hard candy, chewy candy, and gum. The science of classification is called taxonomy. Taxonomy classifies organisms based on evolutionary relationships and describes and names organisms with a two-part name: genus and species. Scientists use taxonomy to identify unknown organisms by using books called field guides or by using taxonomic keys (also called dichomotous keys). Project Objective: As a class,you will be previewing and answering some questions about some classification resources to learn how to use a dichotomous key, how to key a specimen, and to help you write your own dichotomous key for school items. Project: Get a sheet of notebook paper and pencil and refer to the websites to find the answers to the questions. One way to classify objects is to create a "tree" to group similar objects together.Open hierarchical classfication of objects to the second page and find the diagram of common household objects. See how all the ...

Ballew, Mrs.

2010-10-17

58

16S Classifier: A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets  

PubMed Central

The diversity of microbial species in a metagenomic study is commonly assessed using 16S rRNA gene sequencing. With the rapid developments in genome sequencing technologies, the focus has shifted towards the sequencing of hypervariable regions of 16S rRNA gene instead of full length gene sequencing. Therefore, 16S Classifier is developed using a machine learning method, Random Forest, for faster and accurate taxonomic classification of short hypervariable regions of 16S rRNA sequence. It displayed precision values of up to 0.91 on training datasets and the precision values of up to 0.98 on the test dataset. On real metagenomic datasets, it showed up to 99.7% accuracy at the phylum level and up to 99.0% accuracy at the genus level. 16S Classifier is available freely at http://metagenomics.iiserb.ac.in/16Sclassifier and http://metabiosys.iiserb.ac.in/16Sclassifier. PMID:25646627

Chaudhary, Nikhil; Sharma, Ashok K.; Agarwal, Piyush; Gupta, Ankit; Sharma, Vineet K.

2015-01-01

59

Is the SIOP-2001 Classification of Renal Tumors of Childhood accurate with regard to prognosis? A problem revisited  

PubMed Central

Introduction The goal of this study was to analyze morbidity and mortality of Wilms’ tumor based on the revised SIOP-2001 classification. Material and methods Sixty-four patients with unilateral Wilms’ tumor, 33 girls (51.5%) and 31 boys (48.5%), aged 1 to 144 months (mean: 42.8 months) were treated between 1993 and 2009. All patients underwent multimodal therapy according to the SIOP protocols. The follow-up period ranged from 2 to 18 years (mean: 11.6 years). Results Thirty-three patients (51.6%) had intermediate-risk, 6 (9.4%) low-risk and 25 (39%) high-risk tumors. Stage I disease was diagnosed in 28 (43.7%), stage II in 19 (29.7%), stage III in 8 (12.5%) and stage IV in 9 patients (14.1%). Event-free survival (EFS) in the entire group was 78.1% and OS was 92.2%. The EFS in stage IV (44.4%) was significantly lower than in stage I (82.1%, p = 0.04), stage II (89.5%, p = 0.02) and in the entire group (78.1%, p = 0.04). Sixteen complications were observed in 14 children (21.9%); metastases in 7 cases (10.9%), 8 relapses (12.5%) and 5 deaths (7.8%). Blastemal (20/24 – 83.3%) and anaplastic (3/24 – 12.5%) subtypes were responsible for mortality in high-risk tumors (OS – 87.5%), while poorly differentiated epithelial (7/34 – 20.6%) and regressive (8/34 – 23.5%) subtypes decreased OS (94.1%) in the intermediate-risk tumors. Conclusions The results of our study show that epithelial and regressive subtypes were responsible for mortality in the intermediate-risk Wilms’ tumors. PMID:23056081

Taran, Katarzyna; M?ynarski, Wojciech; Sitkiewicz, Anna

2012-01-01

60

Phylogenetics of Crabronini, with a consideration of the evolution of predatory and nesting behaviors (Insecta: Hymenoptera: Crabronidae)  

E-print Network

......................................................................................................... 19 Classification, taxon sampling, and outgroup considerations.......................................... 19 Terminology and character selection ............................................................................. 20 Phylogenetic... analysis .................................................................................................... 20 Results ................................................................................................................................ 21...

Bennett, Daniel J.

2010-12-17

61

Phylogenetic analysis of Potentilla using DNA sequences of nuclear ribosomal internal transcribed spacers (ITS), and implications for the classification of Rosoideae ( Rosaceae )  

Microsoft Academic Search

The circumscription ofPotentilla has varied widely. To investigate the monophyly ofPotentilla and the phylogenetic relationships of associated genera we used nuclear ribosomal internal transcribed spacer (ITS) DNA sequences. Fourteen species ofPotentilla (sensuWolf 1908) were included, some of which represent proposed segregate genera (such asArgentina, Comarum, Drymocallis, Duchesnea, Pentaphylloides, andSibbaldiopsis), and 17 other genera ofRosoideae, usingPrunus as outgroup. Our most parsimonious

Torsten Eriksson; Michael J. Donoghue; Malin S. Hibbs

1998-01-01

62

GB Virus C/Hepatitis G Virus Groups and Subgroups: Classification by a Restriction Fragment Length Polymorphism Method Based on Phylogenetic Analysis of the 5? Untranslated Region  

PubMed Central

A phylogenetic tree based on 150 5? untranslated region sequences deposited in GenBank database allowed segregation of the sequences into three major groups, including two subgroups, i.e., 1, 2a, 2b, and 3, supported by bootstrap analysis. Restriction site analysis of these sequences predicted that HinfI and either AatII or AciI could be used for genomic typing with 99.4% accuracy. cDNA sequencing and subsequent alignment of 21 Argentine GB virus C/hepatitis G virus strains confirmed restriction fragment length polymorphism patterns theoretically predicted. This method may be useful for a rapid screening of samples when either epidemiological or transmission studies of this agent are carried out. PMID:10203483

Quarleri, J. F.; Mathet, V. L.; Feld, M.; Ferrario, D.; della Latta, M. P.; Verdun, R.; Sánchez, D. O.; Oubiña, J. R.

1999-01-01

63

Large-Scale Phylogenetic Classification of Fungal Chitin Synthases and Identification of a Putative Cell-Wall Metabolism Gene Cluster in Aspergillus Genomes  

PubMed Central

The cell wall is a protective and versatile structure distributed in all fungi. The component responsible for its rigidity is chitin, a product of chitin synthase (Chsp) enzymes. There are seven classes of chitin synthase genes (CHS) and the amount and type encoded in fungal genomes varies considerably from one species to another. Previous Chsp sequence analyses focused on their study as individual units, regardless of genomic context. The identification of blocks of conserved genes between genomes can provide important clues about the interactions and localization of chitin synthases. On the present study, we carried out an in silico search of all putative Chsp encoded in 54 full fungal genomes, encompassing 21 orders from five phyla. Phylogenetic studies of these Chsp were able to confidently classify 347 out of the 369 Chsp identified (94%). Patterns in the distribution of Chsp related to taxonomy were identified, the most prominent being related to the type of fungal growth. More importantly, a synteny analysis for genomic blocks centered on class IV Chsp (the most abundant and widely distributed Chsp class) identified a putative cell wall metabolism gene cluster in members of the genus Aspergillus, the first such association reported for any fungal genome. PMID:25148134

Pacheco-Arjona, Jose Ramon; Ramirez-Prado, Jorge Humberto

2014-01-01

64

Endometriosis fertility index score maybe more accurate for predicting the outcomes of in vitro fertilisation than r-AFS classification in women with endometriosis  

PubMed Central

Background Endometriosis is a common disease. The most widely used staging system of endometriosis is the revised American Fertility Society classification (r-AFS classification) which has limited predictive ability for pregnancy after surgery. The endometriosis fertility index (EFI) is used to predict fecundity after endometriosis surgery. This diagnostic accuracy study was designed to compare the predictive value of the EFI with that of the r-AFS classification for IVF outcomes in patients with endometriosis. Methods 199 women with endometriosis receiving IVF treatment after surgery were analysis. The EFI score and r-AFS classification in their ability to predict these IVF outcomes were compared in the same population. ROC curves were used to analyse the predictive values of the EFI and r-AFS indices for clinical pregnancy, and their accuracies were evaluated by sensitivity, specificity, and the Youden’s index. Results The Area Under the Curve (AUC) of the EFI score (AUC?=?0.641, Standard Error(SE)?=?0.039, P?=?0.001, 95% CI?=?0.564-0.717, cut-off score?=?6) was significantly larger than that of the r-AFS classification (AUC?=?0.445, SE?=?0.041, P?=?0.184, and 95% CI?=?0.364-0.526). The antral follicle count, oestradiol level on day of hCG, number of oocytes retrieved, number of oocytes fertilised, and number of cleaved embryos in the greater than or equal to 6 EFI score group was greater than that of the lower than or equal to 5 EFI score group, and the dose of gonadotropin of the greater than or equal to 6 EFI score group were less than that in the lower than or equal to 5 EFI score group. Implantation rate, clinical pregnancy rate, and cumulative pregnancy rate in the greater than or equal to 6 EFI score group were higher than in the lower than or equal to 5 EFI score group. Conclusions It suggests that the EFI has more predictive power for IVF outcomes in endometriosis patients than the r-AFS classification. The clinical pregnancy rate was higher in patients with EFI greater than or equal to 6 score than with EFI lower than or equal to 5 score. PMID:24330552

2013-01-01

65

A classification for extant ferns  

Microsoft Academic Search

We present a revised classification for extant ferns, with emphasis on ordinal and familial ranks, and a synop- sis of included genera. Our classification reflects recently published phylogenetic hypotheses based on both morphological and molecular data. Within our new classification, we recognize four monophyletic classes, 11 monophyletic orders, and 37 families, 32 of which are strongly supported as monophyletic. One

Alan R. Smith; Kathleen M. Pryer; Eric Schuettpelz; Petra Korall; Harald Schneider; Paul G. Wolf

2006-01-01

66

A preliminary phylogenetic analysis of the New World Helopini (Coleoptera, Tenebrionidae, Tenebrioninae) indicates the need for profound rearrangements of the classification  

PubMed Central

Abstract Helopini is a diverse tribe in the subfamily Tenebrioninae with a worldwide distribution. The New World helopine species have not been reviewed recently and several doubts emerge regarding their generic assignment as well as the naturalness of the tribe and subordinate taxa. To assess these questions, a preliminary cladistic analysis was conducted with emphasis on sampling the genera distributed in the New World, but including representatives from other regions. The parsimony analysis includes 30 ingroup species from America, Europe and Asia of the subtribes Helopina and Cylindrinotina, plus three outgroups, and 67 morphological characters. Construction of the matrix resulted in the discovery of morphological character states not previously reported for the tribe, particularly from the genitalia of New World species. A consensus of the 12 most parsimonious trees supports the monophyly of the tribe based on a unique combination of characters, including one synapomorphy. None of the subtribes or the genera of the New World represented by more than one species (Helops Fabricius, Nautes Pascoe and Tarpela Bates) were recovered as monophyletic. Helopina was recovered as paraphyletic in relation to Cylindrinotina. One Nearctic species of Helops and one Palearctic species of Tarpela (subtribe Helopina) were more closely related to species of Cylindrinotina. A relatively derived clade, mainly composed by Neotropical species, was found; it includes seven species of Tarpela, seven species of Nautes, and three species of Helops, two Nearctic and one Neotropical. Our results reveal the need to deeply re-evaluate the current classification of the tribe and subordinated taxa, but a broader taxon sampling and further character exploration is needed in order to fully recognize monophyletic groups at different taxonomic levels (from subtribes to genera). PMID:25009428

Cifuentes-Ruiz, Paulina; Zaragoza-Caballero, Santiago; Ochoterena-Booth, Helga; Morón, Miguel Ángel

2014-01-01

67

Phylogenetic Relationships of the Acanthocephala Inferred from 18S Ribosomal DNA Sequences  

Microsoft Academic Search

Phylogenetic relationships within the Acanthocephala have remained unresolved. Past systematic efforts have focused on creating classifications with little consideration of phylogenetic methods. The Acanthocephala are currently divided into three major taxonomic groups: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These groups are characterized by structural features in addition to the taxonomy and habitat of hosts parasitized. In this study the phylogenetic relationships of

James R. Garey; Steven A. Nadler

1998-01-01

68

Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier  

PubMed Central

Current methods to identify unknown insect (class Insecta) cytochrome c oxidase (COI barcode) sequences often rely on thresholds of distances that can be difficult to define, sequence similarity cut-offs, or monophyly. Some of the most commonly used metagenomic classification methods do not provide a measure of confidence for the taxonomic assignments they provide. The aim of this study was to use a naïve Bayesian classifier (Wang et al. Applied and Environmental Microbiology, 2007; 73: 5261) to automate taxonomic assignments for large batches of insect COI sequences such as data obtained from high-throughput environmental sequencing. This method provides rank-flexible taxonomic assignments with an associated bootstrap support value, and it is faster than the blast-based methods commonly used in environmental sequence surveys. We have developed and rigorously tested the performance of three different training sets using leave-one-out cross-validation, two field data sets, and targeted testing of Lepidoptera, Diptera and Mantodea sequences obtained from the Barcode of Life Data system. We found that type I error rates, incorrect taxonomic assignments with a high bootstrap support, were already relatively low but could be lowered further by ensuring that all query taxa are actually present in the reference database. Choosing bootstrap support cut-offs according to query length and summarizing taxonomic assignments to more inclusive ranks can also help to reduce error while retaining the maximum number of assignments. Additionally, we highlight gaps in the taxonomic and geographic representation of insects in public sequence databases that will require further work by taxonomists to improve the quality of assignments generated using any method.

Porter, Teresita M; Gibson, Joel F; Shokralla, Shadi; Baird, Donald J; Golding, G Brian; Hajibabaei, Mehrdad

2014-01-01

69

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering  

E-print Network

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IIIboj_996 105..121 THE ANGIOSPERM PHYLOGENY GROUP*1 1 Recommended citation: APG III (2009 KEYWORDS: angiosperm classification ­ phylogenetic classification ­ DNA phylogenetics ­ classification

Olmstead, Richard

70

Phylogenetic Models: Algebra and Evolution  

E-print Network

Phylogenetic Models: Algebra and Evolution Elizabeth S. Allman Dept. of Mathematics and Statistics evolutionary tree 2. sequence evolution probabilistic models on trees 3. phylogenetic ideals and varieties history. IMA -- Phylogenetic Models: Algebra and Evolution Slide 1 #12;For phylogenetic inference

Allman, Elizabeth S.

71

Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses  

PubMed Central

Background Cymbidium orchids, including some 50 species, are the famous flowers, and they possess high commercial value in the floricultural industry. Furthermore, the values of different orchids are great differences. However, species identification is very difficult. To a certain degree, chloroplast DNA sequence data are a versatile tool for species identification and phylogenetic implications in plants. Different chloroplast loci have been utilized for evaluating phylogenetic relationships at each classification level among plant species, including at the interspecies and intraspecies levels. However, there is no evidence that a short sequence can distinguish all plant species from each other in order to infer phylogenetic relationships. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. Results The complete nucleotide sequences of eight individuals from a total of five Cymbidium species’ chloroplast (cp) genomes were determined using Illumina sequencing technology of the total DNA via a combination of de novo and reference-guided assembly. The length of the Cymbidium cp genome is about 155 kb. The cp genomes contain 123 unique genes, and the IR regions contain 24 duplicates. Although the genomes, including genome structure, gene order and orientation, are similar to those of other orchids, they are not evolutionarily conservative. The cp genome of Cymbidium evolved moderately with more than 3% sequence divergence, which could provide enough information for phylogeny. Rapidly evolving chloroplast genome regions were identified and 11 new divergence hotspot regions were disclosed for further phylogenetic study and species identification in Orchidaceae. Conclusions Phylogenomic analyses were conducted using 10 complete chloroplast genomes from seven orchid species. These data accurately identified the individuals and established the phylogenetic relationships between the species. The results reveal that phylogenomics based on organelle genome sequencing lights the species identification—organelle-scale “barcodes”, and is also an effective approach for studying whole populations and phylogenetic characteristics of Cymbidium. PMID:23597078

2013-01-01

72

Phylogenetic Inference From Conserved sites Alignments  

SciTech Connect

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 conserved, motif regions of the alignment. This work introduces two methods of producing multiple alignments that include only the conserved regions of the initial alignment. The first method retains conserved motifs, whereas the second retains individual conserved sites in the initial alignment. Using parsimony analysis on a mitochondrial data set containing 19 species among which the phylogenetic relationships are widely accepted, both conserved alignment methods produce better phylogenetic trees than the complete alignment. Unlike any of the 19 inference methods used before to analyze this data, both methods produce trees that are completely consistent with the known phylogeny. The motif-based method employs far fewer alignment sites for comparable error rates. For a larger data set containing mitochondrial sequences from 39 species, the site-based method produces a phylogenetic tree that is largely consistent with known phylogenetic relationships and suggests several novel placements.

grundy, W.N.; Naylor, G.J.P.

1999-08-15

73

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction  

E-print Network

Recent sequencing and computing advances have enabled phylogenetic analyses to expand to both entire genomes and large clades, thus requiring more efficient and accurate methods designed specifically for the phylogenomic ...

Rasmussen, Matthew D.

74

Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae)  

PubMed Central

Background and Aims The Arecoideae is the largest and most diverse of the five subfamilies of palms (Arecaceae/Palmae), containing >50 % of the species in the family. Despite its importance, phylogenetic relationships among Arecoideae are poorly understood. Here the most densely sampled phylogenetic analysis of Arecoideae available to date is presented. The results are used to test the current classification of the subfamily and to identify priority areas for future research. Methods DNA sequence data for the low-copy nuclear genes PRK and RPB2 were collected from 190 palm species, covering 103 (96 %) genera of Arecoideae. The data were analysed using the parsimony ratchet, maximum likelihood, and both likelihood and parsimony bootstrapping. Key Results and Conclusions Despite the recovery of paralogues and pseudogenes in a small number of taxa, PRK and RPB2 were both highly informative, producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Simultaneous analyses of the combined data sets provided additional resolution and support. Two areas of incongruence between PRK and RPB2 were strongly supported by the bootstrap relating to the placement of tribes Chamaedoreeae, Iriarteeae and Reinhardtieae; the causes of this incongruence remain uncertain. The current classification within Arecoideae was strongly supported by the present data. Of the 14 tribes and 14 sub-tribes in the classification, only five sub-tribes from tribe Areceae (Basseliniinae, Linospadicinae, Oncospermatinae, Rhopalostylidinae and Verschaffeltiinae) failed to receive support. Three major higher level clades were strongly supported: (1) the RRC clade (Roystoneeae, Reinhardtieae and Cocoseae), (2) the POS clade (Podococceae, Oranieae and Sclerospermeae) and (3) the core arecoid clade (Areceae, Euterpeae, Geonomateae, Leopoldinieae, Manicarieae and Pelagodoxeae). However, new data sources are required to elucidate ambiguities that remain in phylogenetic relationships among and within the major groups of Arecoideae, as well as within the Areceae, the largest tribe in the palm family. PMID:21325340

Baker, William J.; Norup, Maria V.; Clarkson, James J.; Couvreur, Thomas L. P.; Dowe, John L.; Lewis, Carl E.; Pintaud, Jean-Christophe; Savolainen, Vincent; Wilmot, Tomas; Chase, Mark W.

2011-01-01

75

Phylogenetic relationships among cultivated Allium species from restriction enzyme analysis of the chloroplast genome  

Microsoft Academic Search

The genus Allium contains many economically important species, including the bulb onion, chive, garlic, Japanese bunching onion, and leek. Phylogenetic relationships among the cultivated alliums are not well understood, and taxonomic classifications are based on relatively few morphological characters. Chloroplast DNA is highly conserved and useful in determining phylogenetic relationships. The size of the chloroplast genome of Allium cepa was

M. J. Havey

1991-01-01

76

Fast and Accurate Face Recognition Using Support Vector Machines  

Microsoft Academic Search

The challenge of face recognition software is the rapid and accurate identification or classification of a query image, or set of query images, based on a set of known target images. Although Support Vector Machines (SVMs) are known to be accurate for the classification problem they are limited in this application by the time required for training which is dependent

K. E. Gates

2005-01-01

77

Phylogenetic analysis of the oriental-Palearctic-Afrotropical members of Anopheles (Culicidae: Diptera) based on nuclear rDNA and mitochondrial DNA characteristics.  

PubMed

The phylogenetic relationships of Anopheles spp. at the junction of Oriental, Palearctic, and Afrotropical regions in the Iranian plateau were investigated using molecular markers. A 711-bp mitochondrial DNA cytochrome oxidase C subunit I (COI) fragment and the entire second internal transcribed spacer (ITS2) region (286-576 bp) of the nuclear ribosomal DNA (rDNA-ITS2) were sequenced from 14 and 28 taxa, respectively. The analyses included 12 species within Anopheles and 4 within the Myzorhynchus Series of the subgenus Anopheles, 8 within Neocellia, 6 within Myzomyia, 3 within Paramyzomyia, and 1 within the Pyretophorus Series of the subgenus Cellia. The congruent tree topologies of both molecular markers strongly supported monophyly of subgenera Anopheles and Cellia. Phylogenetic trees constructed on the basis of ITS2 sequences could accurately categorize all of the series according to the classical taxonomy but could not distinguish Pyretophorus (Anopheles subpictus) from Paramyzomyia Series. Although sequence data of the COI region were available for only 14 species, the inferred trees revealed good classification among the series but could not show the monophyletic relationship of Cellia spp. Except for a few cases, the tree inferred from ITS2 sequences revealed the best classification for the species studied. The molecular data could significantly improve our understanding of the phylogenetic position of the taxa. PMID:25241686

Karimian, Fateh; Oshaghi, Mohammad Ali; Sedaghat, Mohammad Mahdi; Waterhouse, Robert M; Vatandoost, Hasan; Hanafi-Bojd, Ahmad Ali; Ravasan, Naseh Maleki; Chavshin, Ali Reza

2014-01-01

78

Journey into Phylogenetic Systematics  

NSDL National Science Digital Library

This straightforward and informative site from the Museum of Paleontology (UCMP) at the University of California at Berkeley offers an excellent introduction to Phylogenetic Systematics, the reconstruction of "the pattern of events that have led to the distribution and diversity of life." The site is organized into several sections, addressing "the philosophy, methodology, and implications of cladistic analysis." Descriptive summaries are made more useful with links to the UCMP Glossary of Phylogenetic Terms, and interested users may seek greater depth by linking directly to the UCMP's additional resources.

79

Canopy phylogenetic, chemical and spectral assembly in a lowland Amazonian forest.  

PubMed

• 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 Inceptisols and low-fertility Ultisols in a lowland Amazonian forest. The spectranomics approach, which explicitly connects phylogenetic, chemical and spectral patterns in tropical canopies, provided the basis for analysis. • Intracrown and intraspecific variation in chemical traits varied from 1.4 to 36.7% (median 9.3%), depending upon the chemical constituent. Principal components analysis showed that 14 orthogonal combinations were required to explain 95% of the variation among 21 traits, indicating the high dimensionality of canopy chemical signatures among taxa. Inceptisols and lianas were associated with high leaf nutrient concentrations and low concentrations of defense compounds. Independent of soils or plant habit, an average 70% (maximum 89%) of chemical trait variation was explained by taxonomy. At least 10 traits were quantitatively linked to remotely sensed signatures, which provided highly accurate species classification. • The results suggest that taxa found on fertile soils carry chemical portfolios with a deep evolutionary history, whereas taxa found on low-fertility soils have undergone trait evolution at the species level. Spectranomics provides a new connection between remote sensing and community assembly theory in high-diversity tropical canopies. PMID:21118261

Asner, Gregory P; Martin, Roberta E

2011-03-01

80

The revised classification of eukaryotes.  

PubMed

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information. PMID:23020233

Adl, Sina M; Simpson, Alastair G B; Lane, Christopher E; Lukeš, Julius; Bass, David; Bowser, Samuel S; Brown, Matthew W; Burki, Fabien; Dunthorn, Micah; Hampl, Vladimir; Heiss, Aaron; Hoppenrath, Mona; Lara, Enrique; Le Gall, Line; Lynn, Denis H; McManus, Hilary; Mitchell, Edward A D; Mozley-Stanridge, Sharon E; Parfrey, Laura W; Pawlowski, Jan; Rueckert, Sonja; Shadwick, Rueckert S; Shadwick, Laura; Schoch, Conrad L; Smirnov, Alexey; Spiegel, Frederick W

2012-09-01

81

Continental Paleobiogeography as Phylogenetic Evidence  

Microsoft Academic Search

Morphological convergence between members of clades isolated on different landmasses can mislead phylogenetic analyses, and can imply intercontinental dispersals that are unlikely given reconstructed paleogeography. It is argued here that paleobiogeographic data, like chronostratigraphic data, are relevant to the process of inferring phylogenetic relationships. In order to allow the dynamic history of continental paleogeography to influence phylogenetic analysis, a ?chronobiogeographic

James B. Rossie; Erik R. Seiffert

82

Reducing Distortion in Phylogenetic Networks  

Microsoft Academic Search

When multiple genes are used in a phylogenetic study, the result is often a collection of incompatible trees. Phylogenetic networks and super-networks can be employed to analyze and visualize the incom- patible signals in such a data set. In many situations, it is important to have control over the amount of imcompatibility that is represented in a phylogenetic network, for

Daniel H. Huson; Mike A. Steel; Jim Whitfield

2006-01-01

83

Charles Darwin, beetles and phylogenetics.  

PubMed

Here, we review Charles Darwin's relation to beetles and developments in coleopteran systematics in the last two centuries. Darwin was an enthusiastic beetle collector. He used beetles to illustrate different evolutionary phenomena in his major works, and astonishingly, an entire sub-chapter is dedicated to beetles in "The Descent of Man". During his voyage on the Beagle, Darwin was impressed by the high diversity of beetles in the tropics, and he remarked that, to his surprise, the majority of species were small and inconspicuous. However, despite his obvious interest in the group, he did not get involved in beetle taxonomy, and his theoretical work had little immediate impact on beetle classification. The development of taxonomy and classification in the late nineteenth and earlier twentieth century was mainly characterised by the exploration of new character systems (e.g. larval features and wing venation). In the mid-twentieth century, Hennig's new methodology to group lineages by derived characters revolutionised systematics of Coleoptera and other organisms. As envisioned by Darwin and Ernst Haeckel, the new Hennigian approach enabled systematists to establish classifications truly reflecting evolution. Roy A. Crowson and Howard E. Hinton, who both made tremendous contributions to coleopterology, had an ambivalent attitude towards the Hennigian ideas. The Mickoleit school combined detailed anatomical work with a classical Hennigian character evaluation, with stepwise tree building, comparatively few characters and a priori polarity assessment without explicit use of the outgroup comparison method. The rise of cladistic methods in the 1970s had a strong impact on beetle systematics. Cladistic computer programs facilitated parsimony analyses of large data matrices, mostly morphological characters not requiring detailed anatomical investigations. Molecular studies on beetle phylogeny started in the 1990s with modest taxon sampling and limited DNA data. This has changed dramatically. With very large data sets and high throughput sampling, phylogenetic questions can be addressed without prior knowledge of morphological characters. Nevertheless, molecular studies have not lead to the great breakthrough in beetle systematics--yet. Especially the phylogeny of the extremely species rich suborder Polyphaga remains incompletely resolved. Coordinated efforts of molecular workers and of morphologists using innovative techniques may lead to more profound insights in the near future. The final aim is to develop a well-founded phylogeny, which truly reflects the evolution of this immensely species rich group of organisms. PMID:19760277

Beutel, Rolf G; Friedrich, Frank; Leschen, Richard A B

2009-11-01

84

Charles Darwin, beetles and phylogenetics  

NASA Astrophysics Data System (ADS)

Here, we review Charles Darwin’s relation to beetles and developments in coleopteran systematics in the last two centuries. Darwin was an enthusiastic beetle collector. He used beetles to illustrate different evolutionary phenomena in his major works, and astonishingly, an entire sub-chapter is dedicated to beetles in “The Descent of Man”. During his voyage on the Beagle, Darwin was impressed by the high diversity of beetles in the tropics, and he remarked that, to his surprise, the majority of species were small and inconspicuous. However, despite his obvious interest in the group, he did not get involved in beetle taxonomy, and his theoretical work had little immediate impact on beetle classification. The development of taxonomy and classification in the late nineteenth and earlier twentieth century was mainly characterised by the exploration of new character systems (e.g. larval features and wing venation). In the mid-twentieth century, Hennig’s new methodology to group lineages by derived characters revolutionised systematics of Coleoptera and other organisms. As envisioned by Darwin and Ernst Haeckel, the new Hennigian approach enabled systematists to establish classifications truly reflecting evolution. Roy A. Crowson and Howard E. Hinton, who both made tremendous contributions to coleopterology, had an ambivalent attitude towards the Hennigian ideas. The Mickoleit school combined detailed anatomical work with a classical Hennigian character evaluation, with stepwise tree building, comparatively few characters and a priori polarity assessment without explicit use of the outgroup comparison method. The rise of cladistic methods in the 1970s had a strong impact on beetle systematics. Cladistic computer programs facilitated parsimony analyses of large data matrices, mostly morphological characters not requiring detailed anatomical investigations. Molecular studies on beetle phylogeny started in the 1990s with modest taxon sampling and limited DNA data. This has changed dramatically. With very large data sets and high throughput sampling, phylogenetic questions can be addressed without prior knowledge of morphological characters. Nevertheless, molecular studies have not lead to the great breakthrough in beetle systematics—yet. Especially the phylogeny of the extremely species rich suborder Polyphaga remains incompletely resolved. Coordinated efforts of molecular workers and of morphologists using innovative techniques may lead to more profound insights in the near future. The final aim is to develop a well-founded phylogeny, which truly reflects the evolution of this immensely species rich group of organisms.

Beutel, Rolf G.; Friedrich, Frank; Leschen, Richard A. B.

2009-11-01

85

PAL: Phylogenetic Analysis Library  

NSDL National Science Digital Library

Created by researchers at the Universities of Auckland (New Zealand) and Oxford (UK), PAL (Phylogenetic Analysis Library) is a Java library intended for use in molecular evolution and phylogenetics. PAL currently consists of thirteen packages with "ready-to-use objects" for reading/writing sequence alignments, distance matrices, and trees; substitution models for nucleotides and amino acids; efficient maximum-likelihood estimation of pairwise distances and tree branch lengths; numerous statistical tests; and options for constructing neighbor-joining and UPGMA trees; among many other features. The program may be downloaded as a .tar.gz or .hqx file, but users who are only interested in accessing the library and not in programming may want simply to download a user front end; conditions for use and instructions are included on-site.

86

Refuting phylogenetic relationships  

PubMed Central

Background Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account. Here we address this dimension in the context of concatenation approaches to phylogeny. Results We discuss some of the limits of a methodology restricted to verificationism, the philosophy on which gene concatenation practices generally rely. As an alternative, we describe a software which identifies and focuses on impossible or refuted relationships, through a simple analysis of bootstrap bipartitions, followed by multivariate statistical analyses. We show how refuting phylogenetic relationships could in principle facilitate systematics. We also apply our method to the study of two complex phylogenies: the phylogeny of the archaea and the phylogeny of the core of genes shared by all life forms. While many groups are rejected, our results left open a possible proximity of N. equitans and the Methanopyrales, of the Archaea and the Cyanobacteria, and as well the possible grouping of the Methanobacteriales/Methanoccocales and Thermosplasmatales, of the Spirochaetes and the Actinobacteria and of the Proteobacteria and firmicutes. Conclusion It is sometimes easier (and preferable) to decide which species do not group together than which ones do. When possible topologies are limited, identifying local relationships that are rejected may be a useful alternative to classical concatenation approaches aiming to find a globally resolved tree on the basis of weak phylogenetic markers. Reviewers This article was reviewed by Mark Ragan, Eugene V Koonin and J Peter Gogarten. PMID:16956399

Bucknam, James; Boucher, Yan; Bapteste, Eric

2006-01-01

87

Caminalcule Phylogenetic Exercise  

NSDL National Science Digital Library

To prepare students to think about the data, assumptions, and interpretations that are part of a phylogenetic analysis. This exercise comes in five parts. The first part is all of the data â all specimens and age dates for all specimens. This simulates the impossible â a complete fossil record. The second part has 10% of the specimens randomly removed (an imperfect fossil record), but all age information is provided for the 90% given. Similarly, the third and fourth parts have 20% (different 20%s) of the data randomly removed, and all information is provided for the 80% of remaining specimens (a more imperfect fossil record). The fifth part has dates only for the modern forms â all other dates are removed. This simulates the situation for a group lacking a fossil record or a situation where the fossil record is ignored. Depending on the class size, students either individually or in groups develop a phylogeny from their data prior to class time. In class we lay everything out on tables and compare and contrast the various phylogenies and in the process discuss many of the basic assumptions, practices, biases, etc. of phylogenetic reconstruction. You could make this more complex and have students code things into MacClade, Paup, etc.; however, I use this for the concepts of phylogenetic reconstruction only.

Bill Ausich

88

Quantitative developmental data in a phylogenetic framework.  

PubMed

Following the embryonic period of organogenesis, most development is allometric growth, which is thought to produce most of the evolutionary morphological divergence between related species. Bivariate or multivariate coefficients of allometry are used to describe quantitative developmental data and are comparable across taxa; as such, these coefficients are amenable to direct treatment in a phylogenetic framework. Mapping of actual allometric coefficients onto phylogenetic trees is supported on the basis of the evolving nature of growth programs and the type of character (continuous) that they represent. This procedure depicts evolutionary allometry accurately and allows for the generation of reliable reconstructions of ancestral allometry, as shown here with a previously published case study on rodent cranial ontogeny. Results reconstructed the signature allometric patterns of rodents to the root of the phylogeny, which could be traced back into a (minimum) Paleocene age. Both character and statistical dependence need to be addressed, so this approach can be integrated with phylogenetic comparative methods that deal with those issues. It is shown that, in this particular sample of rodents, common ancestry explains little allometric variation given the level of divergence present within, and convergence between, major rodent lineages. Furthermore, all that variation is independent of body mass. Thus, from an evolutionary perspective, allometry appears to have a strong functional and likely adaptive basis. PMID:25130201

Giannini, Norberto Pedro

2014-12-01

89

Classification 1: Classification Scheme  

NSDL National Science Digital Library

This lesson shows students that living things can be sorted into groups in many ways using various features to decide which things belong to which group and that classification schemes will vary with purpose. It is the first of a two-part series on classification. At this grade level, students should have the opportunity to learn about an increasing variety of living organisms, both the familiar and the exotic, and should become more precise in identifying similarities and differences among them. Firsthand observation of the living environment is essential for students to gain an understanding of the differences among organisms. This lesson is intended to supplement direct investigations made by students by using the Internet to expose them to a variety of living organisms, as well as encourage them to start developing classification schemes of their own.

90

A Multichannel Approach to Fingerprint Classification  

Microsoft Academic Search

Fingerprint classification provides an important indexing mechanism in a fingerprint database. An accurate and consistent classification can greatly reduce fingerprint matching time for a large database. We present a fingerprint classification algorithm which is able to achieve an accuracy better than previously reported in the literature. We classify fingerprints into five categories: whorl, right loop, left loop, arch, and tented

Anil K. Jain; Salil Prabhakar; Lin Hong

1999-01-01

91

Construct a phylogenetic tree  

NSDL National Science Digital Library

This web page will construct a phylogenetic tree of the creatures you select below. It will use the protein sequences of the protein cytochrome c from each of these organisms to construct the tree. Select the desired creatures from the lists below. To select more than one in the same list, hold down the apple key (on Macs); the control key (on PCs); on the Suns, you just click. If you want to clear your selections and start over, click the "Clear all selections" button. You must also choose one and only one outgroup organism so that your tree will have a root. This is especially important for the parsimony analysis. The outgroup organism should not be closely related to the other organisms. When you have made the selections you want, click the "calculate tree" button. Your request will then be processed. This may take a while, so please be patient.

Brian White

2012-06-28

92

Phylogenetic Incongruence in E. coli O104: Understanding the Evolutionary Relationships of Emerging Pathogens in the Face of Homologous Recombination  

PubMed Central

Escherichia coli O104:H4 was identified as an emerging pathogen during the spring and summer of 2011 and was responsible for a widespread outbreak that resulted in the deaths of 50 people and sickened over 4075. Traditional phenotypic and genotypic assays, such as serotyping, pulsed field gel electrophoresis (PFGE), and multilocus sequence typing (MLST), permit identification and classification of bacterial pathogens, but cannot accurately resolve relationships among genotypically similar but pathotypically different isolates. To understand the evolutionary origins of E. coli O104:H4, we sequenced two strains isolated in Ontario, Canada. One was epidemiologically linked to the 2011 outbreak, and the second, unrelated isolate, was obtained in 2010. MLST analysis indicated that both isolates are of the same sequence type (ST678), but whole-genome sequencing revealed differences in chromosomal and plasmid content. Through comprehensive phylogenetic analysis of five O104:H4 ST678 genomes, we identified 167 genes in three gene clusters that have undergone homologous recombination with distantly related E. coli strains. These recombination events have resulted in unexpectedly high sequence diversity within the same sequence type. Failure to recognize or adjust for homologous recombination can result in phylogenetic incongruence. Understanding the extent of homologous recombination among different strains of the same sequence type may explain the pathotypic differences between the ON2010 and ON2011 strains and help shed new light on the emergence of this new pathogen. PMID:22493677

Hao, Weilong; Allen, Vanessa G.; Jamieson, Frances B.; Low, Donald E.; Alexander, David C.

2012-01-01

93

Accurate GSM Indoor Localization  

Microsoft Academic Search

Accurate indoor localization has long been an objective of the ubiquitous computing research community, and numerous indoor lo- calization solutions based on 802.11, Bluetooth, ultrasound and infrared technologies have been proposed. This paper presents the first accurate GSM indoor localization system that achieves median accuracy of 5 me- ters in large multi-floor buildings. The key idea that makes accurate GSM-based

Veljo Otsason; Alex Varshavsky; Anthony Lamarca; Eyal De Lara

2005-01-01

94

Leaf Classification  

NSDL National Science Digital Library

The purpose of this resource is to develop a classification system for a set of objects and learn about hierarchical classification systems. Any set of objects, such as insects or rocks, may be used as well.

The GLOBE Program, University Corporation for Atmospheric Research (UCAR)

2003-08-01

95

Spectral classification  

NASA Astrophysics Data System (ADS)

Taxonomic classification of astronomically observed stellar objects is described in terms of spectral properties. Stars receive a classification containing a letter, number, and a Roman numeral, which relates the star to other stars of higher or lower Roman numerals. The citation indicates the stellar chromatic emission in relation to the wavelengths of other stars. Standards are chosen from the available objects detected. Various classification schemes such as the MK, HD, and the Barbier-Chalonge-Divan systems are defined, including examples of indexing differences. Details delineating the separations between classifications are discussed with reference to the information content in spectral and in photometric classification schemes. The parameters usually used for classification include the temperature, luminosity, reddening, binarity, rotation, magnetic field, and elemental abundance or composition. The inclusion of recently discovered extended wavelength characteristics in nominal classifications is outlined, together with techniques involved in automated classification.

Jaschek, C.

96

Phylogenetics and the Human Microbiome  

PubMed Central

The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work. PMID:25102857

Matsen, Frederick A.

2015-01-01

97

SIMULTANEOUS FAULT DETECTION AND CLASSIFICATION FOR SEMICONDUCTOR MANUFACTURING TOOLS  

E-print Network

SIMULTANEOUS FAULT DETECTION AND CLASSIFICATION FOR SEMICONDUCTOR MANUFACTURING TOOLS Brian E, accurate, and sensitive detection of equipment and process faults to maintain high process yields and rapid fault classification (diagnosis) of the cause to minimize tool downtime in semiconductor manufacturing

Boning, Duane S.

98

Contextual classification of multispectral image data: Approximate algorithm  

NASA Technical Reports Server (NTRS)

An approximation to a classification algorithm incorporating spatial context information in a general, statistical manner is presented which is computationally less intensive. Classifications that are nearly as accurate are produced.

Tilton, J. C. (principal investigator)

1980-01-01

99

Absolute Pitch in Boreal Chickadees and Humans: Exceptions that Test a Phylogenetic Rule  

ERIC Educational Resources Information Center

This research examined generality of the phylogenetic rule that birds discriminate frequency ranges more accurately than mammals. Human absolute pitch chroma possessors accurately tracked transitions between frequency ranges. Independent tests showed that they used note naming (pitch chroma) to remap the tones into ranges; neither possessors nor…

Weisman, Ronald G.; Balkwill, Laura-Lee; Hoeschele, Marisa; Moscicki, Michele K.; Bloomfield, Laurie L.; Sturdy, Christopher B.

2010-01-01

100

Plant photoreceptors: phylogenetic overview.  

PubMed

Plants possess photoreceptors to perceive light which controls most aspects of their lives. Three photoreceptor families are well characterized: cryptochromes (crys), phototropins (phots), and phytochromes (phys). Two putative families have been identified more recently: Zeitlupes (ZTLs) and UV-B photoreceptors (ULI). Using Arabidopsis thaliana and Oryza sativa photoreceptor sequences as references, we have searched for photoreceptor encoding genes in the major phyla of plant kingdom. For each photoreceptor family, using a phylogenetic tree based on the alignment of conserved amino acid sequences, we have tried to trace back the evolution and the emergence of the diverse photoreceptor ancestral sequences. The green alga Chlamydomonas contains one cry and one phot sequence, probably close to the corresponding ancestral sequences, and no phy-related sequence. The putative UV-B photoreceptors seem to be restricted to the Brassicacae. Except for mosses and ferns, which contain divergent photoreceptor numbers, the composition of the diverse photoreceptor families is conserved between species. A high conservation of the residues within domains is observed in each photoreceptor family. The complete phylogenic analysis of the photoreceptor families in plants has confirmed the existence of crucial evolutionary nodes between the major phyla. For each photoreceptor class, a major duplication occurred before the separation between Mono- and Eudicotyledons. This allowed postulating on the putative ancestral function of the photoreceptors. PMID:16170454

Lariguet, Patricia; Dunand, Christophe

2005-10-01

101

Phylogenetic Analysis of a Spontaneous Cocoa Bean Fermentation Metagenome Reveals New Insights into Its Bacterial and Fungal Community Diversity  

PubMed Central

This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly ?-Proteobacteria) and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni). Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques. PMID:22666442

Illeghems, Koen; De Vuyst, Luc; Papalexandratou, Zoi; Weckx, Stefan

2012-01-01

102

Quantum Simulation of Phylogenetic Trees  

E-print Network

Quantum simulations constructing probability tensors of biological multi-taxa in phylogenetic trees are proposed, in terms of positive trace preserving maps, describing evolving systems of quantum walks with multiple walkers. Basic phylogenetic models applying on trees of various topologies are simulated following appropriate decoherent quantum circuits. Quantum simulations of statistical inference for aligned sequences of biological characters are provided in terms of a quantum pruning map operating on likelihood operator observables, utilizing state-observable duality and measurement theory.

Demosthenes Ellinas; Peter Jarvis

2011-05-09

103

A hybrid learning algorithm for text classification  

E-print Network

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. Instead of using words, word relation i.e association rules from these words is used to derive feature set from preclassified text documents. The concept of Naive Bayes classifier is then used on derived features and finally only a single concept of Genetic Algorithm has been added for final classification. Experimental results show that the classifier build this way is more accurate than the existing text classification systems.

Kamruzzaman, S M

2010-01-01

104

Cyber-infrastructure for Fusarium (CiF): Three integrated platforms supporting strain identification, phylogenetics, comparative genomics, and knowledge sharing  

Technology Transfer Automated Retrieval System (TEKTRAN)

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 ...

105

Phylogenetic relationships of salangid fishes (Osmeridae, Salanginae) with comments on phylogenetic placement of the salangids based on mitochondrial DNA sequences.  

PubMed

We used partial DNA sequences of cytochrome b and 16S mitochondrial genes to determine the phylogenetic placement of salangid fishes and the generic relationships within the salangids. Our molecular data strongly support the monophyly of salangid fishes, the inclusion of salangids in the Osmeridae, and the sister group relationship between salangids and osmerids. Our analyses suggest that Plecoglossus can be separated from all the other salangids and osmerids. Mallotus and Hypomesus are clustered within Osmerinae, rather than allied with Salanginae. As regards the relationships within the salangids, our analyses are incongruent with all previous classification hypotheses. Our phylogenetic analyses support the sister group relationships between Protosalanx and Neosalanx, and between Salanx and Hemisalanx. More evidences show that Leucosoma is more closely related to the Salanx-Hemisalanx clade, while Salangichthys forms part of an unresolved basal polytomy. PMID:15737583

Fu, Cuizhang; Luo, Jing; Wu, Jihua; Andrés López, J; Zhong, Yang; Lei, Guangchun; Chen, Jiakuan

2005-04-01

106

Phylogenetic analysis under reticulate evolution.  

PubMed

The usual assumption that species have evolved from a common ancestor by a simple branching process--where each branch is genetically isolated--has been challenged by the observation of frequent hybridization between species in natural populations. In fact, most plant species are thought to have hybrid origins. This reticulate pattern of species evolution has posed problems in the definition of speciation and in phylogenetic reconstruction, especially when molecular data are used. As a result, hybridization has been largely treated as an evolutionary accident or statistical error in phylogenetic analysis. In this paper, I explicitly incorporate hybridization as an evolutionary occurrence and then conduct phylogenetic reconstruction. I first examine the reticulate evolution under a pure drift model, and then extend the theory to fit a mutation model. A least-squares method is developed for reconstructing a reticulate phylogeny using gene frequency data. The efficacy of the method under the pure drift model is verified via Monte Carlo simulations. PMID:10833196

Xu, S

2000-06-01

107

Interpreting the universal phylogenetic tree  

NASA Technical Reports Server (NTRS)

The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist.

Woese, C. R.

2000-01-01

108

Interpreting the universal phylogenetic tree  

PubMed Central

The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist. PMID:10900003

Woese, Carl R.

2000-01-01

109

Molecular identification and phylogenetic study of Demodex caprae.  

PubMed

The DNA barcode has been widely used in species identification and phylogenetic analysis since 2003, but there have been no reports in Demodex. In this study, to obtain an appropriate DNA barcode for Demodex, molecular identification of Demodex caprae based on mitochondrial cox1 was conducted. Firstly, individual adults and eggs of D. caprae were obtained for genomic DNA (gDNA) extraction; Secondly, mitochondrial cox1 fragment was amplified, cloned, and sequenced; Thirdly, cox1 fragments of D. caprae were aligned with those of other Demodex retrieved from GenBank; Finally, the intra- and inter-specific divergences were computed and the phylogenetic trees were reconstructed to analyze phylogenetic relationship in Demodex. Results obtained from seven 429-bp fragments of D. caprae showed that sequence identities were above 99.1% among three adults and four eggs. The intraspecific divergences in D. caprae, Demodex folliculorum, Demodex brevis, and Demodex canis were 0.0-0.9, 0.5-0.9, 0.0-0.2, and 0.0-0.5%, respectively, while the interspecific divergences between D. caprae and D. folliculorum, D. canis, and D. brevis were 20.3-20.9, 21.8-23.0, and 25.0-25.3, respectively. The interspecific divergences were 10 times higher than intraspecific ones, indicating considerable barcoding gap. Furthermore, the phylogenetic trees showed that four Demodex species gathered separately, representing independent species; and Demodex folliculorum gathered with canine Demodex, D. caprae, and D. brevis in sequence. In conclusion, the selected 429-bp mitochondrial cox1 gene is an appropriate DNA barcode for molecular classification, identification, and phylogenetic analysis of Demodex. D. caprae is an independent species and D. folliculorum is closer to D. canis than to D. caprae or D. brevis. PMID:25132566

Zhao, Ya-E; Cheng, Juan; Hu, Li; Ma, Jun-Xian

2014-10-01

110

Spectral classification  

Microsoft Academic Search

Taxonomic classification of astronomically observed stellar objects is described in terms of spectral properties. Stars receive a classification containing a letter, number, and a Roman numeral, which relates the star to other stars of higher or lower Roman numerals. The citation indicates the stellar chromatic emission in relation to the wavelengths of other stars. Standards are chosen from the available

C. Jaschek

1982-01-01

111

Fingerprint classification  

Microsoft Academic Search

A fingerprint classification algorithm is presented in this paper. Fingerprints are classified into five categories: arch, tented arch, left loop, right loop and whorl. The algorithm extracts singular points (cores and deltas) in a fingerprint image and performs classification based on the number and locations of the detected singular points. The classifier is invariant to rotation, translation and small amounts

Kalle Karu; Anil K. Jain

1996-01-01

112

Hubble Classification  

Microsoft Academic Search

A classification scheme for galaxies, devised in its original form in 1925 by Edwin P Hubble (1889-1953), and still widely used today. The Hubble classification recognizes four principal types of galaxy---elliptical, spiral, barred spiral and irregular---and arranges these in a sequence that is called the tuning-fork diagram....

P. Murdin

2000-01-01

113

Grading More Accurately  

ERIC Educational Resources Information Center

Grades matter. College grading systems, however, are often ad hoc and prone to mistakes. This essay focuses on one factor that contributes to high-quality grading systems: grading accuracy (or "efficiency"). I proceed in several steps. First, I discuss the elements of "efficient" (i.e., accurate) grading. Next, I present analytical results…

Rom, Mark Carl

2011-01-01

114

Integrating Classification and Association Rule Mining  

Microsoft Academic Search

Classification rule mining aims to discover a small set of rules in the database that forms an accurate classifier. Association rule mining finds all the rules existing in the database that satisfy some minimum support and minimum confidence constraints. For association rule mining, the target of discovery is not pre-determined, while for classification rule mining there is one and only

Bing Liu; Wynne Hsu; Yiming Ma

1998-01-01

115

A Phylogenetic Re-Analysis of Groupers with Applications for Ciguatera Fish Poisoning  

PubMed Central

Background Ciguatera fish poisoning (CFP) is a significant public health problem due to dinoflagellates. It is responsible for one of the highest reported incidence of seafood-borne illness and Groupers are commonly reported as a source of CFP due to their position in the food chain. With the role of recent climate change on harmful algal blooms, CFP cases might become more frequent and more geographically widespread. Since there is no appropriate treatment for CFP, the most efficient solution is to regulate fish consumption. Such a strategy can only work if the fish sold are correctly identified, and it has been repeatedly shown that misidentifications and species substitutions occur in fish markets. Methods We provide here both a DNA-barcoding reference for groupers, and a new phylogenetic reconstruction based on five genes and a comprehensive taxonomical sampling. We analyse the correlation between geographic range of species and their susceptibility to ciguatera accumulation, and the co-occurrence of ciguatoxins in closely related species, using both character mapping and statistical methods. Results Misidentifications were encountered in public databases, precluding accurate species identifications. Epinephelinae now includes only twelve genera (vs. 15 previously). Comparisons with the ciguatera incidences show that in some genera most species are ciguateric, but statistical tests display only a moderate correlation with the phylogeny. Atlantic species were rarely contaminated, with ciguatera occurrences being restricted to the South Pacific. Conclusions The recent changes in classification based on the reanalyses of the relationships within Epinephelidae have an impact on the interpretation of the ciguatera distribution in the genera. In this context and to improve the monitoring of fish trade and safety, we need to obtain extensive data on contamination at the species level. Accurate species identifications through DNA barcoding are thus an essential tool in controlling CFP since meal remnants in CFP cases can be easily identified with molecular tools. PMID:25093850

Schoelinck, Charlotte; Hinsinger, Damien D.; Dettaï, Agnès; Cruaud, Corinne; Justine, Jean-Lou

2014-01-01

116

Phylogenetic relationships among Maloideae species  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

117

Phylogenetic signals in morphometric data  

Microsoft Academic Search

Although many of the goals and concepts of qualitative morphological analysis and morphometrics are similar, systematists have largely rejected the use of morphometric methods in phylogenetic analysis on a variety of grounds. This review finds that (1) the concepts of a cladistic character and a morphometric vari- able are essentially identical, (2) morphometric methods can be instrumental in discovering and

Norman MacLeod

118

Accurate Unlexicalized Parsing  

Microsoft Academic Search

We demonstrate that an unlexicalized PCFG can parse much more accurately than previously shown, by making use of simple, linguistically motivated state splits, which break down false independence assumptions latent in a vanilla treebank grammar. Indeed, its performance of 86.36% (LP\\/LR F PCFG models, and surprisingly close to the current state-of-the-art. This result has potential uses beyond establishing a strong

Dan Klein; Christopher D. Manning

2003-01-01

119

Accurate Finite Difference Algorithms  

NASA Technical Reports Server (NTRS)

Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

Goodrich, John W.

1996-01-01

120

Increased Taxon Sampling Greatly Reduces Phylogenetic Error  

Microsoft Academic Search

Several authors have argued recently that extensive taxon sampling has a positive and important effect on the accuracy of phylogenetic estimates. However, other authors have argued that there is little beneét of extensive taxon sampling, and so phylogenetic problems can or should be reduced to a few exemplar taxa as a means of reducing the computational complexity of the phylogenetic

Derrick J. Zwickl; David M. Hillis

2002-01-01

121

Biomedical Image Classification with Random Subwindows and Decision Trees  

E-print Network

Biomedical Image Classification with Random Subwindows and Decision Trees Rapha¨el Mar´ee, Pierre a problem of biomedical image classification that involves the automatic classification of x-ray images that will be able to predict accurately the class of new, unseen images. In biomedical applications, such automatic

Wehenkel, Louis

122

Quartet-Net: A Quartet-Based Method to Reconstruct Phylogenetic Networks  

PubMed Central

Phylogenetic networks can model reticulate evolutionary events such as hybridization, recombination, and horizontal gene transfer. However, reconstructing such networks is not trivial. Popular character-based methods are computationally inefficient, whereas distance-based methods cannot guarantee reconstruction accuracy because pairwise genetic distances only reflect partial information about a reticulate phylogeny. To balance accuracy and computational efficiency, here we introduce a quartet-based method to construct a phylogenetic network from a multiple sequence alignment. Unlike distances that only reflect the relationship between a pair of taxa, quartets contain information on the relationships among four taxa; these quartets provide adequate capacity to infer a more accurate phylogenetic network. In applications to simulated and biological data sets, we demonstrate that this novel method is robust and effective in reconstructing reticulate evolutionary events and it has the potential to infer more accurate phylogenetic distances than other conventional phylogenetic network construction methods such as Neighbor-Joining, Neighbor-Net, and Split Decomposition. This method can be used in constructing phylogenetic networks from simple evolutionary events involving a few reticulate events to complex evolutionary histories involving a large number of reticulate events. A software called “Quartet-Net” is implemented and available at http://sysbio.cvm.msstate.edu/QuartetNet/. PMID:23493256

Yang, Jialiang; Grünewald, Stefan; Wan, Xiu-Feng

2013-01-01

123

Herbicide Classification  

NSDL National Science Digital Library

This lesson focuses on understanding the classification system intowhich herbicides are organized. Terms of classification, classificationhierachy, examples of classification and a brief overview of the eightmodes of action are all discussed in this lesson. Once this isunderstood it is much easier to grasp similar herbicides and know whythey may exhibit certain symptoms to weeds and plants alike.Objectives:1.Understand how herbicides are classified and why it is important for managing herbicide resistance2.Understand the Importance of classification and herbicides by mode of action rather than chemical family3.Be able to tell the difference between mode of action and site of action4.Be able to differentiate between herbicide families, modes of action, and sites of action5.Understand common name, trade names and sites of absorption

124

Phylogenetic diversity of nonmarine picocyanobacteria.  

PubMed

We studied the phylogenetic diversity of nonmarine picocyanobacteria broadening the sequence data set with 43 new sequences of the 16S rRNA gene. The sequences were derived from monoclonal strains isolated from four volcanic high-altitude athalassohaline lakes in Mexico, five glacial ultraoligotrophic North Patagonian lakes and six Italian lakes of glacial, volcanic and morenic origin. The new sequences fall into a number of both novel and previously described clades within the phylogenetic tree of 16S rRNA gene. The new cluster of Lake Nahuel Huapi (North Patagonia) forms a sister clade to the subalpine cluster II and the marine Synechococcus subcluster 5.2. Our finding of the novel clade of 'halotolerants' close to the marine subcluster 5.3 (Synechococcus RCC307) constitutes an important demonstration that euryhaline and marine strains affiliate closely. The intriguing results obtained shed new light on the importance of the nonmarine halotolerants in the phylogenesis of picocyanobacteria. PMID:23528076

Callieri, Cristiana; Coci, Manuela; Corno, Gianluca; Macek, Miroslav; Modenutti, Beatriz; Balseiro, Esteban; Bertoni, Roberto

2013-08-01

125

Point estimates in phylogenetic reconstructions  

PubMed Central

Motivation: The construction of statistics for summarizing posterior samples returned by a Bayesian phylogenetic study has so far been hindered by the poor geometric insights available into the space of phylogenetic trees, and ad hoc methods such as the derivation of a consensus tree makeup for the ill-definition of the usual concepts of posterior mean, while bootstrap methods mitigate the absence of a sound concept of variance. Yielding satisfactory results with sufficiently concentrated posterior distributions, such methods fall short of providing a faithful summary of posterior distributions if the data do not offer compelling evidence for a single topology. Results: Building upon previous work of Billera et al., summary statistics such as sample mean, median and variance are defined as the geometric median, Fréchet mean and variance, respectively. Their computation is enabled by recently published works, and embeds an algorithm for computing shortest paths in the space of trees. Studying the phylogeny of a set of plants, where several tree topologies occur in the posterior sample, the posterior mean balances correctly the contributions from the different topologies, where a consensus tree would be biased. Comparisons of the posterior mean, median and consensus trees with the ground truth using simulated data also reveals the benefits of a sound averaging method when reconstructing phylogenetic trees. Availability and implementation: We provide two independent implementations of the algorithm for computing Fréchet means, geometric medians and variances in the space of phylogenetic trees. TFBayes: https://github.com/pbenner/tfbayes, TrAP: https://github.com/bacak/TrAP. Contact: philipp.benner@mis.mpg.de PMID:25161244

Benner, Philipp; Ba?ák, Miroslav; Bourguignon, Pierre-Yves

2014-01-01

126

Phylogenetic Toric Varieties on Graphs  

E-print Network

. . . . . . . . . . . . . . . . . . 5 4. Toric varieties . . . . . . . . . . . . . . . . . . . . . . . . . 10 4.1. Toric varieties in weighted projective space . . . . . 11 4.2. Quotient of a toric variety by a subtorus . . . . . . 14 II PHYLOGENETIC MODELS ON TRIVALENT GRAPHS... Decomposition of a degree two element with all cycle edges of weight two . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 II.13 Typical generator of degree two and a decomposition of a degree two element with all cycle edges of weight one...

Buczynska, Weronika J.

2010-10-12

127

LABEL: Fast and Accurate Lineage Assignment with Assessment of H5N1 and H9N2 Influenza A Hemagglutinins  

PubMed Central

The evolutionary classification of influenza genes into lineages is a first step in understanding their molecular epidemiology and can inform the subsequent implementation of control measures. We introduce a novel approach called Lineage Assignment By Extended Learning (LABEL) to rapidly determine cladistic information for any number of genes without the need for time-consuming sequence alignment, phylogenetic tree construction, or manual annotation. Instead, LABEL relies on hidden Markov model profiles and support vector machine training to hierarchically classify gene sequences by their similarity to pre-defined lineages. We assessed LABEL by analyzing the annotated hemagglutinin genes of highly pathogenic (H5N1) and low pathogenicity (H9N2) avian influenza A viruses. Using the WHO/FAO/OIE H5N1 evolution working group nomenclature, the LABEL pipeline quickly and accurately identified the H5 lineages of uncharacterized sequences. Moreover, we developed an updated clade nomenclature for the H9 hemagglutinin gene and show a similarly fast and reliable phylogenetic assessment with LABEL. While this study was focused on hemagglutinin sequences, LABEL could be applied to the analysis of any gene and shows great potential to guide molecular epidemiology activities, accelerate database annotation, and provide a data sorting tool for other large-scale bioinformatic studies. PMID:24466291

Shepard, Samuel S.; Davis, C. Todd; Bahl, Justin; Rivailler, Pierre; York, Ian A.; Donis, Ruben O.

2014-01-01

128

Learning classification trees  

NASA Technical Reports Server (NTRS)

Algorithms for learning classification trees have had successes in artificial intelligence and statistics over many years. How a tree learning algorithm can be derived from Bayesian decision theory is outlined. This introduces Bayesian techniques for splitting, smoothing, and tree averaging. The splitting rule turns out to be similar to Quinlan's information gain splitting rule, while smoothing and averaging replace pruning. Comparative experiments with reimplementations of a minimum encoding approach, Quinlan's C4 and Breiman et al. Cart show the full Bayesian algorithm is consistently as good, or more accurate than these other approaches though at a computational price.

Buntine, Wray

1991-01-01

129

Phylogenetic inference of Indian malaria vectors from multilocus DNA sequences.  

PubMed

Inferences on the taxonomic positions, phylogenetic interrelationships and divergence time among closely related species of medical importance is essential to understand evolutionary patterns among species, and based on which, disease control measures could be devised. To this respect, malaria is one of the important mosquito borne diseases of tropical and sub-tropical parts of the globe. Taxonomic status of malaria vectors has been so far documented based on morphological, cytological and few molecular genetic features. However, utilization of multilocus DNA sequences in phylogenetic inferences are still in dearth. India contains one of the richest resources of mosquito species diversity but little molecular taxonomic information is available in Indian malaria vectors. We herewith utilized the whole genome sequence information of An. gambiae to amplify and sequence three orthologous nuclear genetic regions in six Indian malaria vector species (An. culicifacies, An. minimus, An. sundaicus, An. fluviatilis, An. annularis and An. stephensi). Further, we utilized the previously published DNA sequence information on the COII and ITS2 genes in all the six species, making the total number of loci to five. Multilocus molecular phylogenetic study of Indian anophelines and An. gambiae was conducted at each individual genetic region using Neighbour Joining (NJ), Maximum Likelihood (ML), Maximum Parsimony (MP) and Bayesian approaches. Although tree topologies with COII, and ITS2 genes were similar, for no other three genetic regions similar tree topologies were observed. In general, the reconstructed phylogenetic status of Indian malaria vectors follows the pattern based on morphological and cytological classifications that was reconfirmed with COII and ITS2 genetic regions. Further, divergence times based on COII gene sequences were estimated among the seven Anopheles species which corroborate the earlier hypothesis on the radiation of different species of the Anopheles genus during the late Cretaceous period. PMID:20435167

Dixit, Jyotsana; Srivastava, Hemlata; Sharma, Meenu; Das, Manoj K; Singh, O P; Raghavendra, K; Nanda, Nutan; Dash, Aditya P; Saksena, D N; Das, Aparup

2010-08-01

130

Accurate quantum chemical calculations  

NASA Technical Reports Server (NTRS)

An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

1989-01-01

131

Disk-Covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction  

Microsoft Academic Search

The evolutionary history of a set of species is represented by a phylogenetic tree, which is a rooted, leaf-labeled tree, where internal nodes represent ancestral species and the leaves rep- resent modern day species. Accurate (or even boundedly inaccurate) topology reconstructions of large and divergent trees from realistic length sequences have long been considered one of the major challenges in

Daniel H. Huson; Scott M. Nettles; Tandy J. Warnow

1999-01-01

132

TreeFam: a curated database of phylogenetic trees of animal gene families  

Microsoft Academic Search

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary his- 20 tory of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed align- ments and trees in a similar fashion to Pfam.

Heng Li; Avril Coghlan; Jue Ruan; Lachlan James M. Coin; Jean-karim Hériché; Lara Osmotherly; Ruiqiang Li; Tao Liu; Zhang Zhang; Lars Bolund; Gane Ka-shu Wong; Wei-mou Zheng; Paramvir Dehal; Jun Wang; Richard Durbin

2006-01-01

133

Mining associative classification rules with stock trading data - A GA-based method  

Microsoft Academic Search

Associative classifiers are a classification system based on associative classification rules. Although associative classification is more accurate than a traditional classification approach, it cannot handle numerical data and its relationships. Therefore, an ongoing research problem is how to build associative classifiers from numerical data. In this work, we focus on stock trading data with many numerical technical indicators, and the

Ya-Wen Chang Chien; Yen-Liang Chen

2010-01-01

134

Stellar Populations Classification  

E-print Network

Outline Stellar Populations Classification Surface photometry STRUCTURE OF GALAXIES 2. Stellar Populations, classification, surface photometry Piet van der Kruit Kapteyn Astronomical Institute University Populations, classification, surface photometry #12;Outline Stellar Populations Classification Surface

Kruit, Piet van der

135

Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus  

PubMed Central

The accurate diagnosis of diseases caused by pathogenic bacteria requires a stable species classification. Rhodococcus fascians is the only documented member of its ill-defined genus that is capable of causing disease on a wide range of agriculturally important plants. Comparisons of genome sequences generated from isolates of Rhodococcus associated with diseased plants revealed a level of genetic diversity consistent with them representing multiple species. To test this, we generated a tree based on more than 1700 homologous sequences from plant-associated isolates of Rhodococcus, and obtained support from additional approaches that measure and cluster based on genome similarities. Results were consistent in supporting the definition of new Rhodococcus species within clades containing phytopathogenic members. We also used the genome sequences, along with other rhodococcal genome sequences to construct a molecular phylogenetic tree as a framework for resolving the Rhodococcus genus. Results indicated that Rhodococcus has the potential for having 20 species and also confirmed a need to revisit the taxonomic groupings within Rhodococcus. PMID:25237311

Creason, Allison L.; Davis, Edward W.; Putnam, Melodie L.; Vandeputte, Olivier M.; Chang, Jeff H.

2014-01-01

136

Image Classification  

NSDL National Science Digital Library

In this exercise, students get experience with image classification. Images are an increasingly important source of information about land cover and land use over time because comparisons of historic and current images can provide an estimate of change in the landscape.

2008-10-14

137

Multisensor classification of sedimentary rocks  

NASA Technical Reports Server (NTRS)

A comparison is made between linear discriminant analysis and supervised classification results based on signatures from the Landsat TM, the Thermal Infrared Multispectral Scanner (TIMS), and airborne SAR, alone and combined into extended spectral signatures for seven sedimentary rock units exposed on the margin of the Wind River Basin, Wyoming. Results from a linear discriminant analysis showed that training-area classification accuracies based on the multisensor data were improved an average of 15 percent over TM alone, 24 percent over TIMS alone, and 46 percent over SAR alone, with similar improvement resulting when supervised multisensor classification maps were compared to supervised, individual sensor classification maps. When training area signatures were used to map spectrally similar materials in an adjacent area, the average classification accuracy improved 19 percent using the multisensor data over TM alone, 2 percent over TIMS alone, and 11 percent over SAR alone. It is concluded that certain sedimentary lithologies may be accurately mapped using a single sensor, but classification of a variety of rock types can be improved using multisensor data sets that are sensitive to different characteristics such as mineralogy and surface roughness.

Evans, Diane

1988-01-01

138

On-the-fly Classifying Sonar with Accurate Range and Bearing Estimation  

E-print Network

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

139

A second species of Oculogryphus (Coleoptera, Lampyridae), with notes on the phylogenetic affinities of the genus  

PubMed Central

Abstract A second species of the enigmatic lampyrid genus Oculogryphus is described and figured as Oculogryphus bicolor sp. 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 the putative sister group to Stenocladius s. str. within the paraphyletic group of Ototretinae-Ototretadrilinae.The classification of Stenocladius is briefly discussed in this context. PMID:21594065

Jeng, Ming-Luen; Branham, Marc A.; Engel, Michael S.

2011-01-01

140

Phylogenetic Origins of Brain Organisers  

PubMed Central

The regionalisation of the nervous system begins early in embryogenesis, concomitant with the establishment of the anteroposterior (AP) and dorsoventral (DV) body axes. The molecular mechanisms that drive axis induction appear to be conserved throughout the animal kingdom and may be phylogenetically older than the emergence of bilateral symmetry. As a result of this process, groups of patterning genes that are equally well conserved are expressed at specific AP and DV coordinates of the embryo. In the emerging nervous system of vertebrate embryos, this initial pattern is refined by local signalling centres, secondary organisers, that regulate patterning, proliferation, and axonal pathfinding in adjacent neuroepithelium. The main secondary organisers for the AP neuraxis are the midbrain-hindbrain boundary, zona limitans intrathalamica, and anterior neural ridge and for the DV neuraxis the notochord, floor plate, and roof plate. A search for homologous secondary organisers in nonvertebrate lineages has led to controversy over their phylogenetic origins. Based on a recent study in hemichordates, it has been suggested that the AP secondary organisers evolved at the base of the deuterostome superphylum, earlier than previously thought. According to this view, the lack of signalling centres in some deuterostome lineages is likely to reflect a secondary loss due to adaptive processes. We propose that the relative evolutionary flexibility of secondary organisers has contributed to a broader morphological complexity of nervous systems in different clades. PMID:24278699

Robertshaw, Ellen; Kiecker, Clemens

2012-01-01

141

Phylogenetic Conservatism in Plant Phenology  

NASA Technical Reports Server (NTRS)

Phenological events defined points in the life cycle of a plant or animal have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism the tendency for closely related species to share similar ecological and biological attributes in phenological traits across flowering plants. We aggregated published and unpublished data on timing of first flower and first leaf, encompassing 4000 species at 23 sites across the Northern Hemisphere. We reconstructed the phylogeny for the set of included species, first, using the software program Phylomatic, and second, from DNA data. We then quantified phylogenetic conservatism in plant phenology within and across sites. We show that more closely related species tend to flower and leaf at similar times. By contrasting mean flowering times within and across sites, however, we illustrate that it is not the time of year that is conserved, but rather the phenological responses to a common set of abiotic cues. Our findings suggest that species cannot be treated as statistically independent when modelling phenological responses.Closely related species tend to resemble each other in the timing of their life-history events, a likely product of evolutionarily conserved responses to environmental cues. The search for the underlying drivers of phenology must therefore account for species' shared evolutionary histories.

Davies, T. Jonathan; Wolkovich, Elizabeth M.; Kraft, Nathan J. B.; Salamin, Nicolas; Allen, Jenica M.; Ault, Toby R.; Betancourt, Julio L.; Bolmgren, Kjell; Cleland, Elsa E.; Cook, Benjamin I.; Crimmins, Theresa M.; Mazer, Susan J.; McCabe, Gregory J.; Pau, Stephanie; Regetz, Jim; Schwartz, Mark D.; Travers, Steven E.

2013-01-01

142

A phylogenetic model for understanding the effect of gene duplication on cancer progression  

PubMed Central

As biotechnology advances rapidly, a tremendous amount of cancer genetic data has become available, providing an unprecedented opportunity for understanding the genetic mechanisms of cancer. To understand the effects of duplications and deletions on cancer progression, two genomes (normal and tumor) were sequenced from each of five stomach cancer patients in different stages (I, II, III and IV). We developed a phylogenetic model for analyzing stomach cancer data. The model assumes that duplication and deletion occur in accordance with a continuous time Markov Chain along the branches of a phylogenetic tree attached with five extended branches leading to the tumor genomes. Moreover, coalescence times of the phylogenetic tree follow a coalescence process. The simulation study suggests that the maximum likelihood approach can accurately estimate parameters in the phylogenetic model. The phylogenetic model was applied to the stomach cancer data. We found that the expected number of changes (duplication and deletion) per gene for the tumor genomes is significantly higher than that for the normal genomes. The goodness-of-fit test suggests that the phylogenetic model with constant duplication and deletion rates can adequately fit the duplication data for the normal genomes. The analysis found nine duplicated genes that are significantly associated with stomach cancer. PMID:24371277

Ma, Qin; Reeves, Jaxk H.; Liberles, David A.; Yu, Lili; Chang, Zheng; Zhao, Jing; Cui, Juan; Xu, Ying; Liu, Liang

2014-01-01

143

ATV: display and manipulation of annotated phylogenetic trees ATV: display and manipulation of annotated phylogenetic trees  

E-print Network

ATV: display and manipulation of annotated phylogenetic trees 8/10/01 1 ATV: display and manipulation of annotated phylogenetic trees Christian M. Zmasek and Sean R. Eddy Howard Hughes Medical: {zmasek,eddy}@genetics.wustl.edu Key words: tree display, tree viewer, phylogenetic tree, java

Eddy, Sean

144

Molecular phylogenetics and character evolution of morphologically diverse groups, Dendrobium section Dendrobium and allies.  

PubMed

It is always difficult to construct coherent classification systems for plant lineages having diverse morphological characters. The genus Dendrobium, one of the largest genera in the Orchidaceae, includes ?1100 species, and enormous morphological diversification has hindered the establishment of consistent classification systems covering all major groups of this genus. Given the particular importance of species in Dendrobium section Dendrobium and allied groups as floriculture and crude drug genetic resources, there is an urgent need to establish a stable classification system. To clarify phylogenetic relationships in Dendrobium section Dendrobium and allied groups, we analysed the macromolecular characters of the group. Phylogenetic analyses of 210 taxa of Dendrobium were conducted on DNA sequences of internal transcribed spacer (ITS) regions of 18S-26S nuclear ribosomal DNA and the maturase-coding gene (matK) located in an intron of the plastid gene trnK using maximum parsimony and Bayesian methods. The parsimony and Bayesian analyses revealed 13 distinct clades in the group comprising section Dendrobium and its allied groups. Results also showed paraphyly or polyphyly of sections Amblyanthus, Aporum, Breviflores, Calcarifera, Crumenata, Dendrobium, Densiflora, Distichophyllae, Dolichocentrum, Holochrysa, Oxyglossum and Pedilonum. On the other hand, the monophyly of section Stachyobium was well supported. It was found that many of the morphological characters that have been believed to reflect phylogenetic relationships are, in fact, the result of convergence. As such, many of the sections that have been recognized up to this point were found to not be monophyletic, so recircumscription of sections is required. PMID:25107672

Takamiya, Tomoko; Wongsawad, Pheravut; Sathapattayanon, Apirada; Tajima, Natsuko; Suzuki, Shunichiro; Kitamura, Saki; Shioda, Nao; Handa, Takashi; Kitanaka, Susumu; Iijima, Hiroshi; Yukawa, Tomohisa

2014-01-01

145

The neuron classification problem.  

PubMed

A systematic account of neuron cell types is a basic prerequisite for determining the vertebrate nervous system global wiring diagram. With comprehensive lineage and phylogenetic information unavailable, a general ontology based on structure-function taxonomy is proposed and implemented in a knowledge management system, and a prototype analysis of select regions (including retina, cerebellum, and hypothalamus) presented. The supporting Brain Architecture Knowledge Management System (BAMS) Neuron ontology is online and its user interface allows queries about terms and their definitions, classification criteria based on the original literature and "Petilla Convention" guidelines, hierarchies, and relations-with annotations documenting each ontology entry. Combined with three BAMS modules for neural regions, connections between regions and neuron types, and molecules, the Neuron ontology provides a general framework for physical descriptions and computational modeling of neural systems. The knowledge management system interacts with other web resources, is accessible in both XML and RDF/OWL, is extendible to the whole body, and awaits large-scale data population requiring community participation for timely implementation. PMID:17582506

Bota, Mihail; Swanson, Larry W

2007-11-01

146

Selecting Species Traits for Biomonitoring Applications in light of Phylogenetic Relationships among Lotic Insects  

NASA Astrophysics Data System (ADS)

The use of species traits as indicators of environmental disturbance is being considered for biomonitoring programs globally. As such, methods to select relevant and informative traits for inclusion in biometrics need to be developed. In this research, we identified 20 traits of aquatic insects within six trait groups: morphology, mobility, life-history strategy, thermal tolerance, feeding guild and ecology (e.g., habitat preference). We constructed phylogenetic trees for 1) all lotic insect species of North America and 2) all Ephemeroptera, Plecoptera and Trichoptera species based on morphology- and molecular-based analyses and classifications. We then measured variability (i.e., plasticity) of the 20 traits and six trait groups across the two phylogenetic trees. Traits with higher degrees of plasticity indicated traits that were less phylogenetically constrained, and were considered informative for biomonitoring purposes. Thermal tolerance, rheophily, body size at maturity and feeding guild showed the highest plasticity across both phylogenetic trees. Two mobility traits, occurrence in drift and adult dispersal distance, showed moderate plasticity. By contrast, adult exiting ability, degree of attachment, adult lifespan and body shape showed low variability and were thus less informative. Plastic species traits that are less phylogenetically constrained may be most useful in detecting community change along environmental gradients.

Poff, N.; Vieira, N. K.; Simmons, M. P.; Olden, J. D.; Kondratieff, B. C.; Finn, D. S.

2005-05-01

147

Primate Classification  

NSDL National Science Digital Library

In this lesson students learn how classification of organisms is based on evolutionary relationships. They will also learn how primates are categorized, and how they are related. Students transfer examples (names) of primates from their location in an outline hierarchy of primate groups into a set of nested boxes reflecting that same hierarchy. A cladogram can then be drawn illustrating how these groups are related in an evolutionary way.

148

Mitochondrial Phylogenetics and Evolution of Mysticete Whales  

Microsoft Academic Search

The phylogenetic relationships among baleen whales (Order: Cetacea) remain uncertain despite extensive research in cetacean molecular phylogenetics and a potential morphological sample size of over 2 million animals harvested. Ques- tions remain regarding the number of species and the monophyly of genera, as well as higher order relationships. Here, we approach mysticete phylogeny with complete mitochondrial genome sequence analysis. We

Takeshi Sasaki; Masato Nikaido; Healy Hamilton; Mutsuo Goto; Hidehiro Kato; Naohisa Kanda; LUIS A. PASTENE; Ying Cao; R. EWAN FORDYCE; Masami Hasegawa; Norihiro Okada

2005-01-01

149

A Structural EM Algorithm for Phylogenetic Inference  

Microsoft Academic Search

A central task in the study of molecular evolution is the reconstruction of a phylogenetic tree from sequences of current-day taxa. The most established approach to tree reconstruction is maximum likelihood (ML) analysis. Unfortunately, searching for the maximum likelihood phylogenetic tree is computationally prohibitive for large data sets. In this paper, we describe a new algorithm that uses Structural EM

Nir Friedman; Matan Ninio; Itsik Pe'er; Tal Pupko

2002-01-01

150

Taxonomy, Phylogenetics, and Philip S. Ward  

E-print Network

Chapter 1 Taxonomy, Phylogenetics, and Evolution Philip S. Ward 1.1 Introduction Since their origin features of evolutionary history. Species-level taxonomy has advanced more fitfully than ant phylogenetics and features of their biology are dis- cussed. The state of species-level taxonomy is eval- uated

Ward, Philip S.

151

A Novel Approach for Compressing Phylogenetic Trees  

E-print Network

A Novel Approach for Compressing Phylogenetic Trees Suzanne J. Matthews, Seung-Jin Sul, and Tiffani,sulsj,tlw}@cse.tamu.edu Abstract. Phylogenetic trees are tree structures that depict relation- ships between organisms. Popular analysis techniques often produce large collections of candidate trees, which are expensive to store. We

Williams, Tiffani

152

Phylogenetic fields of species: cross-species patterns of phylogenetic structure and geographical coexistence  

PubMed Central

Differential coexistence among species underlies geographical patterns of biodiversity. Understanding such patterns has relied either on ecological or historical approaches applied separately. Recently, macroecology and community phylogenetics have tried to integrate both ecological and historical approaches. However, macroecology is mostly non-phylogenetic, whereas community phylogenetics is largely focused on local scales. Here, we propose a conceptual framework to link macroecology and community phylogenetics by exploring the evolutionary context of large-scale species coexistence, introducing the phylogenetic field concept. This is defined as the phylogenetic structure of species co-occurrence within a focal species' geographical range. We developed concepts and methods for analysing phylogenetic fields and applied them to study coexistence patterns of the bat family Phyllostomidae. Our analyses showed that phyllostomid bats coexist mostly with closely related species, revealing a north–south gradient from overdispersed to clustered phylogenetic fields. Patterns at different phylogenetic levels (i.e. all species versus close relatives only) presented the same gradient. Results support the tropical niche conservatism hypothesis, potentially mediated by higher speciation rates in the region of origin coupled with shared environmental preferences among species. The phylogenetic field approach enables species-based community phylogenetics, instead of those that are site-based, allowing the description of historical processes at more appropriate macroecological and biogeographic scales. PMID:23390100

Villalobos, Fabricio; Rangel, Thiago F.; Diniz-Filho, José Alexandre F.

2013-01-01

153

Revising angiotensinogen from phylogenetic and genetic variants perspectives.  

PubMed

Angiotensinogen (AGT) belongs to the serpin superfamily. It acts as the unique substrate of all angiotensin peptides, which generates a spectrum of angiotensin peptides in the renin-angiotensin system and regulates hypertension. This serpin belongs to the multiple member group V2 of the intron encoded vertebrate serpin classification. Despite huge advancements in the understanding of angiotensinogen based on biochemical properties and its roles in the RAS, phylogenetic history of AGT remains forgotten. To date, there is no comprehensive study illustrating the phylogenetic history of AGT. Herein, we investigated phylogenetic traits of AGT gene across vertebrates. Gene structures of AGT gene from selected ray-finned fishes varied in exon I and II with insertions of two novel introns in the core domain for ray-finned fishes at the position 77c and 233c. We that found AGT loci is conserved from lampreys to human and estimated to be older than 500 MY. By comparing AGT protein in 57 vertebrate genomes, we illustrated that the reactive center loop (RCL) of AGT protein became from inhibitory (in lampreys, GTEAKAETVVGIMPI†SMPPT) to non-inhibitory (in human, EREPTESTQQLNKPE†VLEVT) during period of 500 MY. We identified 690 AGT variants by analysis of 1092 human genomes with top three variation classes belongs to SNPs (89.7%), somatic SNVs (5.2%) and deletion (2.9%). There are 32 key residues out of 121 missense variants, which are deleterious for AGT protein, computed by combination of SIFT and PolyPhen V2 methods. These results may have clinical implications for understanding hypertension. PMID:24631685

Kumar, Abhishek; Sarde, Sandeep J; Bhandari, Anita

2014-04-01

154

SUNPLIN: Simulation with Uncertainty for Phylogenetic Investigations  

PubMed Central

Background Phylogenetic comparative analyses usually rely on a single consensus phylogenetic tree in order to study evolutionary processes. However, most phylogenetic trees are incomplete with regard to species sampling, which may critically compromise analyses. Some approaches have been proposed to integrate non-molecular phylogenetic information into incomplete molecular phylogenies. An expanded tree approach consists of adding missing species to random locations within their clade. The information contained in the topology of the resulting expanded trees can be captured by the pairwise phylogenetic distance between species and stored in a matrix for further statistical analysis. Thus, the random expansion and processing of multiple phylogenetic trees can be used to estimate the phylogenetic uncertainty through a simulation procedure. Because of the computational burden required, unless this procedure is efficiently implemented, the analyses are of limited applicability. Results In this paper, we present efficient algorithms and implementations for randomly expanding and processing phylogenetic trees so that simulations involved in comparative phylogenetic analysis with uncertainty can be conducted in a reasonable time. We propose algorithms for both randomly expanding trees and calculating distance matrices. We made available the source code, which was written in the C++ language. The code may be used as a standalone program or as a shared object in the R system. The software can also be used as a web service through the link: http://purl.oclc.org/NET/sunplin/. Conclusion We compare our implementations to similar solutions and show that significant performance gains can be obtained. Our results open up the possibility of accounting for phylogenetic uncertainty in evolutionary and ecological analyses of large datasets. PMID:24229408

2013-01-01

155

Phylogenetic Analysis of Mitochondrial Outer Membrane ?-Barrel Channels  

PubMed Central

Transport of molecules across mitochondrial outer membrane is pivotal for a proper function of mitochondria. The transport pathways across the membrane are formed by ion channels that participate in metabolite exchange between mitochondria and cytoplasm (voltage-dependent anion-selective channel, VDAC) as well as in import of proteins encoded by nuclear genes (Tom40 and Sam50/Tob55). VDAC, Tom40, and Sam50/Tob55 are present in all eukaryotic organisms, encoded in the nuclear genome, and have ?-barrel topology. We have compiled data sets of these protein sequences and studied their phylogenetic relationships with a special focus on the position of Amoebozoa. Additionally, we identified these protein-coding genes in Acanthamoeba castellanii and Dictyostelium discoideum to complement our data set and verify the phylogenetic position of these model organisms. Our analysis show that mitochondrial ?-barrel channels from Archaeplastida (plants) and Opisthokonta (animals and fungi) experienced many duplication events that resulted in multiple paralogous isoforms and form well-defined monophyletic clades that match the current model of eukaryotic evolution. However, in representatives of Amoebozoa, Chromalveolata, and Excavata (former Protista), they do not form clearly distinguishable clades, although they locate basally to the plant and algae branches. In most cases, they do not posses paralogs and their sequences appear to have evolved quickly or degenerated. Consequently, the obtained phylogenies of mitochondrial outer membrane ?-channels do not entirely reflect the recent eukaryotic classification system involving the six supergroups: Chromalveolata, Excavata, Archaeplastida, Rhizaria, Amoebozoa, and Opisthokonta. PMID:22155732

Wojtkowska, Ma?gorzata; J?kalski, Marcin; Pie?kowska, Joanna R.; Stobienia, Olgierd; Karachitos, Andonis; Przytycka, Teresa M.; Weiner, January; Kmita, Hanna; Maka?owski, Wojciech

2012-01-01

156

Molecular phylogenetics of the clover genus (Trifolium--Leguminosae).  

PubMed

Trifolium, the clover genus, is one of the largest genera of the legume family. We conducted parsimony and Bayesian phylogenetic analyses based on nuclear ribosomal DNA internal transcribed spacer and chloroplast trnL intron sequences obtained from 218 of the ca. 255 species of Trifolium, representatives from 11 genera of the vicioid clade, and an outgroup Lotus. We confirm the monophyly of Trifolium, and propose a new infrageneric classification of the genus based on the phylogenetic results. Incongruence between the nrDNA and cpDNA results suggests five to six cases of apparent hybrid speciation, and identifies the putative progenitors of the allopolyploids T. dubium, a widespread weed, and T. repens, the most commonly cultivated clover species. Character state reconstructions confirm 2n=16 as the ancestral chromosome number in Trifolium, and infer a minimum of 19 instances of aneuploidy and 22 of polyploidy in the genus. The ancestral life history is hypothesized to be annual in subgenus Chronosemium and equivocal in subgenus Trifolium. Transitions between the annual and perennial habit are common. Our results are consistent with a Mediterranean origin of the genus, probably in the Early Miocene. A single origin of all North and South American species is hypothesized, while the species of sub-Saharan Africa may originate from three separate dispersal events. PMID:16483799

Ellison, Nick W; Liston, Aaron; Steiner, Jeffrey J; Williams, Warren M; Taylor, Norman L

2006-06-01

157

Feature utility in polarimetric radar image classification  

NASA Technical Reports Server (NTRS)

The information content in polarimetric SAR images is examined, and the polarimetric image variables containing the information that is important to the classification of terrain features in the images are determined. It is concluded that accurate classification can be done when just over half of the image variables are retained. A reduction in image data dimensionality gives storage savings, and can lead to the improvement of classifier performance. In addition, it is shown that a simplified radar system with only phase-calibrated CO-POL or SINGLE TX channels can give classification performance which approaches that of a fully polarimetric radar.

Cumming, Ian G.; Van Zyl, Jakob J.

1989-01-01

158

Beach Classification  

NSDL National Science Digital Library

This activity provides students with an in-class practice of landscape interpretation using slides of beaches shown by the instructor. Students view a select number of slides and are asked to classify each beach shown using the Wright and Short Beach Classification: dissipative, reflexive, and intermediate by visually identifying landforms and processes of each beach type. The outcome of this activity is that students have practice identifying landforms and processes and applying their observations and interpretations of geomorphic features and processes for an applied purpose. Designed for a geomorphology course Has minimal/no quantitative component

Davis, Lisa

159

Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting  

PubMed Central

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the phylogenetic relationships among the sequences under study to make more accurate predictions. The program is guaranteed to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phylogenetic tree relating the input species. We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known. PMID:11997340

Blanchette, Mathieu; Tompa, Martin

2002-01-01

160

Accurate detection of demosaicing regularity for digital image forensics  

Microsoft Academic Search

In this paper, we propose a novel accurate detection framework of demosaicing regularity from different source images. The proposed framework first reversely classifies the demosaiced samples into several categories and then estimates the underlying demosaicing formulas for each category based on partial second-order derivative correlation models, which detect both the intrachannel and the cross-channel demosaicing correlation. An expectation-maximization reverse classification

Hong Cao; Alex C. Kot

2009-01-01

161

Machine learning for patient-adaptive ectopic beat classification  

E-print Network

Physicians require automated techniques to accurately analyze the vast amount of physiological data collected by continuous monitoring devices. In this thesis, we consider one analysis task in particular, the classification ...

Wiens, Jenna Marleau

2010-01-01

162

[Asthma classification].  

PubMed

Asthma, as chronic inflammatory disease, shows variations in clinical manifestations and the degree of airflow obstruction, so its severity may change over time in the same patient. The Global Initiative for Asthma (GINA) established a practical system of classification, considering clinical and functional aspects as frequency of diurnal and nocturnal respiratory symptoms and lung function, their combination allows for classifying asthma severity as intermittent and persistent ( mild, moderate and severe). Recently, it has been proposed to classify the asthma according to degree of control: controlled, partly controlled and uncontrolled. The parameters used in this system are: frequency of diurnal and nocturnal respiratory symptoms, activity limitation, use of rescue therapy, determining the forced expiratory volume in one second (FEV1) or peak expiratory flow (PEF) and the exacerbations. The patient's participation on the asthma classification has also been considered through the self application of asthma control questionnaire (ACT). Patients with high risk of death are classified in the group of difficult asthma control (ADC), requiring major and minor criteria to define it; the common denominator is the decontrol of the disease, high dose steroids and appropriate treatment previously established. Sort asthma with any of these systems, information about its impact on the patient's life and thus establish the recommended treatment schedule for each patient group. PMID:20873054

Salas Hernández, Jorge; Fernández Vega, Margarita; Almeida Arvizu, Victor Manuel

2009-01-01

163

Computational Prediction of Phylogenetically Conserved Sequence Motifs for Five Different Candidate Genes in Type II Diabetic Nephropathy  

PubMed Central

Background: Computational identification of phylogenetic motifs helps to understand the knowledge about known functional features that includes catalytic site, substrate binding epitopes, and protein-protein interfaces. Furthermore, they are strongly conserved among orthologs, indicating their evolutionary importance. The study aimed to analyze five candidate genes involved in type II diabetic nephropathy and to predict phylogenetic motifs from their corresponding orthologous protein sequences. Methods: AKR1B1, APOE, ENPP1, ELMO1 and IGFBP1 are the genes that have been identified as an important target for type II diabetic nephropathy through experimental studies. Their corresponding protein sequences, structures, orthologous sequences were retrieved from UniprotKB, PDB, and PHOG database respectively. Multiple sequence alignments were constructed using ClustalW and phylogenetic motifs were identified using MINER. The occurrence of amino acids in the obtained phylogenetic motifs was generated using WebLogo and false positive expectations were calculated against phylogenetic similarity. Results: In total, 17 phylogenetic motifs were identified from the five proteins and the residues such as glycine, leucine, tryptophan, aspartic acid were found in appreciable frequency whereas arginine identified in all the predicted PMs. The result implies that these residues can be important to the functional and structural role of the proteins and calculated false positive expectations implies that they were generally conserved in traditional sense. Conclusion: The prediction of phylogenetic motifs is an accurate method for detecting functionally important conserved residues. The conserved motifs can be used as a potential drug target for type II diabetic nephropathy. PMID:23113206

Sindhu, T; Rajamanikandan, S; Srinivasan, P

2012-01-01

164

Classification and knowledge  

NASA Technical Reports Server (NTRS)

Automated procedures to classify objects are discussed. The classification problem is reviewed, and the relation of epistemology and classification is considered. The classification of stellar spectra and of resolved images of galaxies is addressed.

Kurtz, Michael J.

1989-01-01

165

Remote Sensing Information Classification  

NASA Technical Reports Server (NTRS)

This viewgraph presentation reviews the classification of Remote Sensing data in relation to epidemiology. Classification is a way to reduce the dimensionality and precision to something a human can understand. Classification changes SCALAR data into NOMINAL data.

Rickman, Douglas L.

2008-01-01

166

Phylogenetic relationships of Chinese Adiantum based on five plastid markers.  

PubMed

Adiantum consists of about 150-200 species mostly with a pantropical distribution, yet the classifications of Adiantum have been based primarily on regional studies. Confounding the clarity of reconstructing the evolutionary history of Adiantum is that previous molecular phylogenetic studies suggest that a separate and distinctive clade, the vittarioids, may be derived from within Adiantum. Five plastid markers (atpA, atpB, rbcL, trnL-F and rps4-trnS) are employed to assess the monophyly of Adiantum, and construct the molecular phylogeny of Chinese Adiantum. Our analyses support the monophyly of Adiantum. All temperate Adiantum species form a clade nested within the pantropical grade, suggesting a tropical origin of Adiantum. Six main clades are supported within Chinese Adiantum, which are only partially consistent with Lin's classification of the genus. Series Caudata is polyphyletic with series Gravesiana nested within one subgroup of series Caudata. The prolonged whip-like stolon at the apex of the fronds is the defining character for series Caudata, but it may have evolved multiple times. Adiantum reniforme with the simple fronds is sister to series Venusta, which has a decompound lamina with many flabellate to cuneate segments. Series Veneri-capilliformia is not monophyletic, with A. capillus-veneris sister to series Flabellulata except for A. diaphanum, and A. edentulum sister to series Pedata. Series Flabellulata is biphyletic with A. diaphanum nested within the pantropical grade. The phylogeny suggests that convergent evolution in frond architecture has occurred in Adiantum. PMID:21809178

Lu, Jin-Mei; Wen, Jun; Lutz, Sue; Wang, Yi-Ping; Li, De-Zhu

2012-03-01

167

Evolutionary Trees and phylogenetics: An algebraic perspective  

E-print Network

. MBE (1988) 5:626-644. Gorilla AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCAT... Orangutan_Mac. Chimpanzee Human Gorilla Orangutan Gibbon Squirrel_Monkey Tarsier 0.1 Evolutionary trees and phylogenetics 6 sequences: Gorilla AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCAT... Orangutan

Allman, Elizabeth S.

168

Constructing phylogenetic trees using interacting pathways  

PubMed Central

Phylogenetic trees are used to represent evolutionary relationships among biological species or organisms. The construction of phylogenetic trees is based on the similarities or differences of their physical or genetic features. Traditional approaches of constructing phylogenetic trees mainly focus on physical features. The recent advancement of high-throughput technologies has led to accumulation of huge amounts of biological data, which in turn changed the way of biological studies in various aspects. In this paper, we report our approach of building phylogenetic trees using the information of interacting pathways. We have applied hierarchical clustering on two domains of organisms—eukaryotes and prokaryotes. Our preliminary results have shown the effectiveness of using the interacting pathways in revealing evolutionary relationships. PMID:23750081

Wan, Peng; Che, Dongsheng

2013-01-01

169

PHYLOGENETIC ANALYSIS VIA DC PROGRAMMING 1 ...  

E-print Network

The evolutionary history of species may be described by a phylogenetic tree whose ...... 12. S. E. Ellis and M. V. Nayakkankuppam. Primates. Human. Chimpanzee ... trees: uniqueness of the likelihood point, Journal of Molecular Evolution, 28.

2005-06-15

170

Endolithic Microbial Ecosystems: Molecular Phylogenetic Composition,  

E-print Network

support the principle that patterns of microbial diversity are governed by similar principles observed Endolithic Microbial Ecosystems: Molecular Phylogenetic Composition, Ecology and Geobiology of Philosophy Department of Molecular, Cellular and Developmental Biology 2005 #12;Endolithic Microbial

Pace, Norman

171

Distribution of phylogenetic diversity under random extinction  

E-print Network

Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this `future phylogenetic diversity' provides a measure of the impact of various extinction scenarios in biodiversity conservation. In this paper we study the distribution of future phylogenetic diversity under a simple model of extinction (a generalized `field of bullets' model). We show that the distribution of future phylogenetic diversity converges to a normal distribution as the number of species grows (under mild conditions, which are necessary). We also describe an algorithm to compute the distribution efficiently, provided the edge lengths are integral, and briefly outline the significance of our findings for biodiversity conservation.

Beata Faller; Fabio Pardi; Mike Steel

2007-08-02

172

Accurate Monitor 1.2  

NSDL National Science Digital Library

With many computer users developing their own Web sites, some of them may be interested in monitoring how search engines may be ranking their site. This latest edition of Accurate Monitor may prove useful, as it allows individuals to find the position of their Web site in search engines like Altavista and Google. Additionally, Accurate Monitor can generate advanced statistics and monitor plugins, along with providing a flexible interface system. This version of Accurate Monitor is compatible with all systems running Windows 95 and higher.

2003-01-01

173

What is the phylogenetic position of Cryptosporidium ?  

Microsoft Academic Search

The phylogenetic position of Cryptosporidium is elusive. Although previous studies based solely upon small-subunit (SSU) rRNA sequences suggested that the genus was an early emerging lineage among the Apicomplexa, bootstrap support for this placement was low. Here, the phylogenetic position of Cryptosporidium has been re-evaluated for SSU rRNA, fused SSU\\/large-subunit (LSU) rRNA and six protein sequences using traditional distance-based neighbour-joining,

Guan Zhu; Janet S. Keithly; Herve Philippe

2000-01-01

174

Genotypic Identification of Fusarium Species from Ocular Sources: Comparison to Morphologic Classification and Antifungal Sensitivity Testing (An AOS Thesis)  

PubMed Central

Purpose Ocular 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) analysis of the internal transcribed spacer (ITS) regions (ITS1, 5.8S, and ITS2) in detecting and differentiating Fusarium species from isolates of ocular infections, and to assess the correlation between the genotypic and morphologic classification. Methods Fifty-eight isolates from 52 patients diagnosed with Fusarium ocular infections were retrieved from storage at the Bascom Palmer Eye Institute’s ocular microbiology laboratory. Morphologic classification was determined at both a general and a reference microbiology laboratory. DNA was extracted and purified, and the ITS region was amplified and sequenced. Following DNA sequences, alignment and phylogenetic analysis were done. Susceptibility to antifungal drugs was measured according to the Clinical and Laboratory Standards Institute reference method. Results Sequence analysis demonstrated 15 unique sequences among the 58 isolates. The grouping showed that the 58 isolates were distributed among 4 main species complexes. At the species level, morphologic classification correlated with genotypic classification in 25% and 97% of the isolates in a general microbiology and a reference mycology laboratory, respectively. Conclusions The sequence variation within the ITS provides a sufficient quantitative basis for the development of a molecular diagnostic approach to the Fusarium pathogens isolated from ocular infections. Morphology based on microscopic and macroscopic observations yields inconsistent results, particularly at nonreference laboratories, emphasizing the need for a more reproducible test with less user-dependent variability. Fusarium solani tends to be more resistant to certain antifungals (azoles). PMID:19277239

Alfonso, Eduardo C.

2008-01-01

175

New contributions towards the understanding of the phylogenetic relationships among economically important fruit flies (Diptera: Tephritidae).  

PubMed

Fruit flies (Diptera: Tephritidae) are a species-rich and economically important group. The phylogenetic relationships among the many taxa are still to be fully resolved and the monophyly of several groups is still to be confirmed. This paper reports a study of the phylogenetic relationships among 23 economically important tephritid species (representing several major lineages of the family) which examines the sequence of a region of mitochondrial DNA encompassing the cytb, tRNA(Ser) and ND1 genes. Substitutions characteristic of particular taxa were found that could help classify members of the family at any developmental stage. The trees obtained by the maximum parsimony, neighbour joining and maximum likelihood methods were generally compatible with present morphological classification patterns. However, the data reveal some characteristics of the phylogenetic relationships of this family that do not agree with present classifications. The results support the probable non-monophyletic nature of the subfamily Trypetinae and suggest that Bactrocera cucurbitae (Coquillet) is more closely related to the genus Dacus than to other species of Bactrocera. PMID:16768816

Segura, M D; Callejas, C; Fernández, M P; Ochando, M D

2006-06-01

176

How does cognition evolve? Phylogenetic comparative psychology.  

PubMed

Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution. PMID:21927850

MacLean, Evan L; Matthews, Luke J; Hare, Brian A; Nunn, Charles L; Anderson, Rindy C; Aureli, Filippo; Brannon, Elizabeth M; Call, Josep; Drea, Christine M; Emery, Nathan J; Haun, Daniel B M; Herrmann, Esther; Jacobs, Lucia F; Platt, Michael L; Rosati, Alexandra G; Sandel, Aaron A; Schroepfer, Kara K; Seed, Amanda M; Tan, Jingzhi; van Schaik, Carel P; Wobber, Victoria

2012-03-01

177

Phylogenetic structure in tropical hummingbird communities.  

PubMed

How biotic interactions, current and historical environment, and biogeographic barriers determine community structure is a fundamental question in ecology and evolution, especially in diverse tropical regions. To evaluate patterns of local and regional diversity, we quantified the phylogenetic composition of 189 hummingbird communities in Ecuador. We assessed how species and phylogenetic composition changed along environmental gradients and across biogeographic barriers. We show that humid, low-elevation communities are phylogenetically overdispersed (coexistence of distant relatives), a pattern that is consistent with the idea that competition influences the local composition of hummingbirds. At higher elevations communities are phylogenetically clustered (coexistence of close relatives), consistent with the expectation of environmental filtering, which may result from the challenge of sustaining an expensive means of locomotion at high elevations. We found that communities in the lowlands on opposite sides of the Andes tend to be phylogenetically similar despite their large differences in species composition, a pattern implicating the Andes as an important dispersal barrier. In contrast, along the steep environmental gradient between the lowlands and the Andes we found evidence that species turnover is comprised of relatively distantly related species. The integration of local and regional patterns of diversity across environmental gradients and biogeographic barriers provides insight into the potential underlying mechanisms that have shaped community composition and phylogenetic diversity in one of the most species-rich, complex regions of the world. PMID:19805042

Graham, Catherine H; Parra, Juan L; Rahbek, Carsten; McGuire, Jimmy A

2009-11-17

178

Classification of the acanthocephala.  

PubMed

In 1985, Amin presented a new system for the classification of the Acanthocephala in Crompton and Nickol's (1985) book 'Biology of the Acanthocephala' and recognized the concepts of Meyer (1931, 1932, 1933) and Van Cleave (1936, 1941, 1947, 1948, 1949, 1951, 1952). This system became the standard for the taxonomy of this group and remains so to date. Many changes have taken place and many new genera and species, as well as higher taxa, have been described since. An updated version of the 1985 scheme incorporating new concepts in molecular taxonomy, gene sequencing and phylogenetic studies is presented. The hierarchy has undergone a total face lift with Amin's (1987) addition of a new class, Polyacanthocephala (and a new order and family) to remove inconsistencies in the class Palaeacanthocephala. Amin and Ha (2008) added a third order (and a new family) to the Palaeacanthocephala, Heteramorphida, which combines features from the palaeacanthocephalan families Polymorphidae and Heteracanthocephalidae. Other families and subfamilies have been added but some have been eliminated, e.g. the three subfamilies of Arythmacanthidae: Arhythmacanthinae Yamaguti, 1935; Neoacanthocephaloidinae Golvan, 1960; and Paracanthocephaloidinae Golvan, 1969. Amin (1985) listed 22 families, 122 genera and 903 species (4, 4 and 14 families; 13, 28 and 81 genera; 167, 167 and 569 species in Archiacanthocephala, Eoacanthocephala and Palaeacanthocephala, respectively). The number of taxa listed in the present treatment is 26 families (18% increase), 157 genera (29%), and 1298 species (44%) (4, 4 and 16; 18, 29 and 106; 189, 255 and 845, in the same order), which also includes 1 family, 1 genus and 4 species in the class Polyacanthocephala Amin, 1987, and 3 genera and 5 species in the fossil family Zhijinitidae. PMID:24261131

Amin, Omar M

2013-09-01

179

Phylogenetic relationships among subsurface microorganisms  

SciTech Connect

This report summarizes the progress made from 6/90--3/91 toward completion of our project, Phylogenetic Relationships among subsurface microorganisms. 16S rRNA was sequenced, and based on the sequence the SMCC isolates were assigned to preliminary groups. Microorganisms were obtained at various depths at the Savannah River Site, including the Surface (0 m), Congaree (91 m), and Middendorf (244 m, 259 m, 265 m). Sequence data from four isolates from the Congaree formation indicate these microorganisms can be divided into Pseudomonas spp. or Acinetobacter spp. Three 16S rRNA probes were synthesized based on sequence data. The synthesized probes were tested through in situ hybridization. Optimal conditions for in situ hybridization were determined. Because stability of RNA-DNA hybrids is dependent on hybridization stringency, related organisms can be differentiated using a single probe under different strigencies. The results of these hybridizations agree with results obtained by Balkwill and Reeves using restriction fragment length polymorphism analysis. The RNA content of a cell reflects its metabolic state. Cells which are starved for four days are not detectable with the homologous 16S rRNA probe. However, within 15 minutes of refeeding, detectable rRNA appeared. This suggests that organisms which are undetectable in environmental samples due to starvation may be detectable after addition of nutrients. Stepwise addition of specific nutrients could indicate which nutrients are rate limiting for growth. Preliminary experiments with soil samples from the Hanford Site indicate indigenous microorganisms can be detected by oligionucleotide probes. Further, using multiple probes based on universal sequences increases the number of organisms detected. Double label experiments, using a rhodamine-labelled oligionucleotide probe with free coumarin succinimidyl ester will allow simultaneous detection of total bacteria and specific 16S rRNA containing bacteria. 4 tabs. (MHB)

Nierzwicki-Bauer, S.A.

1991-01-01

180

Indel reliability in indel-based phylogenetic inference.  

PubMed

It is often assumed that it is unlikely that the same insertion or deletion (indel) event occurred at the same position in two independent evolutionary lineages, and thus, indel-based inference of phylogeny should be less subject to homoplasy compared with standard inference which is based on substitution events. Indeed, indels were successfully used to solve debated evolutionary relationships among various taxonomical groups. However, indels are never directly observed but rather inferred from the alignment and thus indel-based inference may be sensitive to alignment errors. It is hypothesized that phylogenetic reconstruction would be more accurate if it relied only on a subset of reliable indels instead of the entire indel data. Here, we developed a method to quantify the reliability of indel characters by measuring how often they appear in a set of alternative multiple sequence alignments. Our approach is based on the assumption that indels that are consistently present in most alternative alignments are more reliable compared with indels that appear only in a small subset of these alignments. Using simulated and empirical data, we studied the impact of filtering and weighting indels by their reliability scores on the accuracy of indel-based phylogenetic reconstruction. The new method is available as a web-server at http://guidance.tau.ac.il/RELINDEL/. PMID:25409663

Ashkenazy, Haim; Cohen, Ofir; Pupko, Tal; Huchon, Dorothée

2014-01-01

181

The ‘requirement of total evidence’ and its role in phylogenetic systematics  

Microsoft Academic Search

The question of whether or not to partition data for the purposes of inferring phylogenetic hypotheses remains controversial.\\u000a Opinions have been especially divided since Kluge's (1989, Systematic Zoology 38, 7–25) claim that data partitioning violates the requirement of total evidence (RTE). Unfortunately, advocacy for or against\\u000a the RTE has not been based on accurate portrayals of the requirement. The RTE

Kirk Fitzhugh

2006-01-01

182

rbcL sequence divergence and phylogenetic relationships in Saxifragaceae sensu lato.  

PubMed Central

Phylogenetic relationships are often poorly understood at higher taxonomic levels (family and above) despite intensive morphological analysis. An excellent example is Saxifragaceae sensu lato, which represents one of the major phylogenetic problems in angiosperms at higher taxonomic levels. As originally defined, the family is a heterogeneous assemblage of herbaceous and woody taxa comprising 15 subfamilies. Although more recent classifications fundamentally modified this scheme, little agreement exists regarding the circumscription, taxonomic rank, or relationships of these subfamilies. The recurrent discrepancies in taxonomic treatments of the Saxifragaceae prompted an investigation of the power of chloroplast gene sequences to resolve phylogenetic relationships within this family and between the Saxifragaceae and other major plant lineages. Sequence data from the gene rbcL (ribulose-1,5-bisphosphate carboxylase, large subunit) reveal that (i) Saxifragaceae sensu lato is at least paraphyletic, and probably polyphyletic, (ii) the genera Parnassia and Brexia are only distantly related to other members of Saxifragaceae, and (iii) representatives of the Solanaceae (subclass Asteridae) appear more closely related to Saxifragaceae (subclass Rosidase) than traditionally maintained. These data illustrate the value of chloroplast gene sequence data in resolving genetic, and hence phylogenetic, relationships among members of the most taxonomically complex groups. PMID:2352941

Soltis, D E; Soltis, P S; Clegg, M T; Durbin, M

1990-01-01

183

Phylogenetic Modeling of Heterogeneous Gene-Expression Microarray Data from Cancerous Specimens  

PubMed Central

Abstract The qualitative dimension of gene expression data and its heterogeneous nature in cancerous specimens can be accounted for by phylogenetic modeling that incorporates the directionality of altered gene expressions, complex patterns of expressions among a group of specimens, and data-based rather than specimen-based gene linkage. Our phylogenetic modeling approach is a double algorithmic technique that includes polarity assessment that brings out the qualitative value of the data, followed by maximum parsimony analysis that is most suitable for the data heterogeneity of cancer gene expression. We demonstrate that polarity assessment of expression values into derived and ancestral states, via outgroup comparison, reduces experimental noise; reveals dichotomously expressed asynchronous genes; and allows data pooling as well as comparability of intra- and interplatforms. Parsimony phylogenetic analysis of the polarized values produces a multidimensional classification of specimens into clades that reveal shared derived gene expressions (the synapomorphies); provides better assessment of ontogenic pathways and phyletic relatedness of specimens; efficiently utilizes dichotomously expressed genes; produces highly predictive class recognition; illustrates gene linkage and multiple developmental pathways; provides higher concordance between gene lists; and projects the direction of change among specimens. Further implication of this phylogenetic approach is that it may transform microarray into diagnostic, prognostic, and predictive tool. PMID:18699725

Abu-Asab, Mones S.; Chaouchi, Mohamed

2008-01-01

184

Inter-rater reliability of the EPUAP pressure ulcer classification system using photographs  

Microsoft Academic Search

BACKGROUND: Many classification systems for grading pressure ulcers are discussed in the literature. Correct identification and classification of a pressure ulcer is important for accurate reporting of the magnitude of the problem, and for timely prevention. The reliability of pressure ulcer classification systems has rarely been tested. AIMS AND OBJECTIVES: The purpose of this paper is to examine the inter-rater

Tom Defloor; Lisette Schoonhoven

2004-01-01

185

A statistical approach to root system classification  

PubMed Central

Plant root systems have a key role in ecology and agronomy. In spite of fast increase in root studies, still there is no classification that allows distinguishing among distinctive characteristics within the diversity of rooting strategies. Our hypothesis is that a multivariate approach for “plant functional type” identification in ecology can be applied to the classification of root systems. The classification method presented is based on a data-defined statistical procedure without a priori decision on the classifiers. The study demonstrates that principal component based rooting types provide efficient and meaningful multi-trait classifiers. The classification method is exemplified with simulated root architectures and morphological field data. Simulated root architectures showed that morphological attributes with spatial distribution parameters capture most distinctive features within root system diversity. While developmental type (tap vs. shoot-borne systems) is a strong, but coarse classifier, topological traits provide the most detailed differentiation among distinctive groups. Adequacy of commonly available morphologic traits for classification is supported by field data. Rooting types emerging from measured data, mainly distinguished by diameter/weight and density dominated types. Similarity of root systems within distinctive groups was the joint result of phylogenetic relation and environmental as well as human selection pressure. We concluded that the data-define classification is appropriate for integration of knowledge obtained with different root measurement methods and at various scales. Currently root morphology is the most promising basis for classification due to widely used common measurement protocols. To capture details of root diversity efforts in architectural measurement techniques are essential. PMID:23914200

Bodner, Gernot; Leitner, Daniel; Nakhforoosh, Alireza; Sobotik, Monika; Moder, Karl; Kaul, Hans-Peter

2013-01-01

186

Land classification and ecosystem classification.  

PubMed

Earth, the ecosphere, is a unified functional ecosystem. Ecological land classification (ELC) and regionalization divides and categorizes this unity into similar and dissimilar pieces-sectoral ecosystems - at various scales, in the interests of admiration and understanding. The recognition of land/water ecosystems in a hierarchy of sizes provides a rational base for the many-scaled problems of protection and careful exploitation in the fields of agriculture, forestry, wildlife and recreation. In forested terrain the protection of biodiversity, old growth forests, watersheds and wildlife habitat depends on spatial-temporal planning of forestry operations to maintain a preferred mosaic structure of local ecosystems within each ecological region. Without ecological understanding and a good ELC, this is impossible. Conceiving the world as comprising nested land/water ecosystems that are the source of life, elevates the role of Earth-as-context, an antidote to destructive anthropocentrism. PMID:24197992

Rowe, J S

1996-01-01

187

Characterization of a branch of the phylogenetic tree.  

PubMed

We use a combination of analytic models and computer simulations to gain insight into the dynamics of evolution. Our results suggest that certain interesting phenomena should eventually emerge from the fossil record. For example, there should be a "tortoise and hare effect": those genera with the smallest species death rate are likely to survive much longer than genera with large species birth and death rates. A complete characterization of the behavior of a branch of the phylogenetic tree corresponding to a genus and accurate mathematical representations of the various stages are obtained. We apply our results to address certain controversial issues that have arisen in paleontology such as the importance of punctuated equilibrium and whether unique Cambrian phyla have survived to the present. PMID:12623281

Samuel, Stuart A; Weng, Gezhi

2003-02-21

188

Characterization of a branch of the phylogenetic tree  

SciTech Connect

We use a combination of analytic models and computer simulations to gain insight into the dynamics of evolution. Our results suggest that certain interesting phenomena should eventually emerge from the fossil record. For example, there should be a ''tortoise and hare effect'': Those genera with the smallest species death rate are likely to survive much longer than genera with large species birth and death rates. A complete characterization of the behavior of a branch of the phylogenetic tree corresponding to a genus and accurate mathematical representations of the various stages are obtained. We apply our results to address certain controversial issues that have arisen in paleontology such as the importance of punctuated equilibrium and whether unique Cambrian phyla have survived to the present.

Samuel, Stuart A.; Weng, Gezhi

2003-04-11

189

Analysis of the peroxiredoxin family: using active-site structure and sequence information for global classification and residue analysis.  

PubMed

Peroxiredoxins (Prxs) are a widespread and highly expressed family of cysteine-based peroxidases that react very rapidly with H?O?, organic peroxides, and peroxynitrite. Correct subfamily classification has been problematic because Prx subfamilies are frequently not correlated with phylogenetic distribution and diverge in their preferred reductant, oligomerization state, and tendency toward overoxidation. We have developed a method that uses the Deacon Active Site Profiler (DASP) tool to extract functional-site profiles from structurally characterized proteins to computationally define subfamilies and to identify new Prx subfamily members from GenBank(nr). For the 58 literature-defined Prx test proteins, 57 were correctly assigned, and none were assigned to the incorrect subfamily. The >3500 putative Prx sequences identified were then used to analyze residue conservation in the active site of each Prx subfamily. Our results indicate that the existence and location of the resolving cysteine vary in some subfamilies (e.g., Prx5) to a greater degree than previously appreciated and that interactions at the A interface (common to Prx5, Tpx, and higher order AhpC/Prx1 structures) are important for stabilization of the correct active-site geometry. Interestingly, this method also allows us to further divide the AhpC/Prx1 into four groups that are correlated with functional characteristics. The DASP method provides more accurate subfamily classification than PSI-BLAST for members of the Prx family and can now readily be applied to other large protein families. PMID:21287625

Nelson, Kimberly J; Knutson, Stacy T; Soito, Laura; Klomsiri, Chananat; Poole, Leslie B; Fetrow, Jacquelyn S

2011-03-01

190

Analysis of the peroxiredoxin family: using active site structure and sequence information for global classification and residue analysis  

PubMed Central

Peroxiredoxins (Prxs) are a widespread and highly expressed family of cysteine-based peroxidases that react very rapidly with H2O2, organic peroxides, and peroxynitrite. Correct subfamily classification has been problematic since Prx subfamilies are frequently not correlated with phylogenetic distribution and diverge in their preferred reductant, oligomerization state, and tendency towards overoxidation. We have developed a method that uses the Deacon Active Site Profiler (DASP) tool to extract functional site profiles from structurally characterized proteins, to computationally define subfamilies, and to identify new Prx subfamily members from GenBank(nr). For the 58 literature-defined Prx test proteins, 57 were correctly assigned and none were assigned to the incorrect subfamily. The >3500 putative Prx sequences identified were then used to analyze residue conservation in the active site of each Prx subfamily. Our results indicate that the existence and location of the resolving cysteine varies in some subfamilies (e.g. Prx5) to a greater degree than previously appreciated and that interactions at the A interface (common to Prx5, Tpx and higher order AhpC/Prx1 structures) are important for stabilization of the correct active site geometry. Interestingly, this method also allows us to further divide the AhpC/Prx1 into four groups that are correlated with functional characteristics. The DASP method provides more accurate subfamily classification than PSI-BLAST for members of the Prx family and can now readily be applied to other large protein families. PMID:21287625

Nelson, Kimberly J.; Knutson, Stacy T.; Soito, Laura; Klomsiri, Chananat; Poole, Leslie B.; Fetrow, Jacquelyn S.

2010-01-01

191

Probabilistic Graphical Model Representation in Phylogenetics  

PubMed Central

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis–Hastings or Gibbs sampling of the posterior distribution. [Computation; graphical models; inference; modularization; statistical phylogenetics; tree plate.] PMID:24951559

Höhna, Sebastian; Heath, Tracy A.; Boussau, Bastien; Landis, Michael J.; Ronquist, Fredrik; Huelsenbeck, John P.

2014-01-01

192

Rationale and goals: Our understanding of the higher-level phylogenetic relationships of Fungi has advanced considerably in recent years. These advances have been  

E-print Network

Rationale and goals: Our understanding of the higher-level phylogenetic relationships of Fungi has in comprehensive classifications of fungi, including those in the Dictionary of the Fungi, GenBank, Myconet, the Tree of Life Web Project, the Mycota vol. VII, the Fungi chapter in the recent Assembling the Tree

Hibbett, David S.

193

Teaching Molecular Phylogenetics through Investigating a Real-World Phylogenetic Problem  

ERIC Educational Resources Information Center

A phylogenetics exercise is incorporated into the "Introduction to biocomputing" course, a junior-level course at Savannah State University. This exercise is designed to help students learn important concepts and practical skills in molecular phylogenetics through solving a real-world problem. In this application, students are required to identify…

Zhang, Xiaorong

2012-01-01

194

A Primer of Phylogenetic ProceduresA Primer of Phylogenetic Procedures THE UNIVERSITY OF KANSAS  

E-print Network

A Primer of Phylogenetic ProceduresA Primer of Phylogenetic Procedures THE UNIVERSITY OF KANSAS. R. BROOKS V. A. FUNK TTHEHE CCOMPLEATOMPLEAT CCLADISTLADIST #12;THE UNIVERSITY OF KANSAS MUSEUM) to Publications, Museum of Natural History, The University of Kansas, Lawrence, Kansas 66045-2454, USA. To order

Sikes, Derek S.

195

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

PubMed

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

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

2011-06-01

196

Evaluating Support for the Current Classification of Eukaryotic Diversity  

PubMed Central

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 system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature and is appearing in introductory biology textbooks. We evaluate the stability and support for the current six-supergroup classification of eukaryotes based on molecular genealogies. We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa. Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature. We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life. PMID:17194223

Parfrey, Laura Wegener; Barbero, Erika; Lasser, Elyse; Dunthorn, Micah; Bhattacharya, Debashish; Patterson, David J; Katz, Laura A

2006-01-01

197

A User's Guide to a Data Base of the Diversity of Pseudomonas syringae and Its Application to Classifying Strains in This Phylogenetic Complex  

PubMed Central

The Pseudomonas syringae complex is composed of numerous genetic lineages of strains from both agricultural and environmental habitats including habitats closely linked to the water cycle. The new insights from the discovery of this bacterial species in habitats outside of agricultural contexts per se have led to the revelation of a wide diversity of strains in this complex beyond what was known from agricultural contexts. Here, through Multi Locus Sequence Typing (MLST) of 216 strains, we identified 23 clades within 13 phylogroups among which the seven previously described P. syringae phylogroups were included. The phylogeny of the core genome of 29 strains representing nine phylogroups was similar to the phylogeny obtained with MLST thereby confirming the robustness of MLST-phylogroups. We show that phenotypic traits rarely provide a satisfactory means for classification of strains even if some combinations are highly probable in some phylogroups. We demonstrate that the citrate synthase (cts) housekeeping gene can accurately predict the phylogenetic affiliation for more than 97% of strains tested. We propose a list of cts sequences to be used as a simple tool for quickly and precisely classifying new strains. Finally, our analysis leads to predictions about the diversity of P. syringae that is yet to be discovered. We present here an expandable framework mainly based on cts genetic analysis into which more diversity can be integrated. PMID:25184292

Berge, Odile; Monteil, Caroline L.; Bartoli, Claudia; Chandeysson, Charlotte; Guilbaud, Caroline; Sands, David C.; Morris, Cindy E.

2014-01-01

198

A user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex.  

PubMed

The Pseudomonas syringae complex is composed of numerous genetic lineages of strains from both agricultural and environmental habitats including habitats closely linked to the water cycle. The new insights from the discovery of this bacterial species in habitats outside of agricultural contexts per se have led to the revelation of a wide diversity of strains in this complex beyond what was known from agricultural contexts. Here, through Multi Locus Sequence Typing (MLST) of 216 strains, we identified 23 clades within 13 phylogroups among which the seven previously described P. syringae phylogroups were included. The phylogeny of the core genome of 29 strains representing nine phylogroups was similar to the phylogeny obtained with MLST thereby confirming the robustness of MLST-phylogroups. We show that phenotypic traits rarely provide a satisfactory means for classification of strains even if some combinations are highly probable in some phylogroups. We demonstrate that the citrate synthase (cts) housekeeping gene can accurately predict the phylogenetic affiliation for more than 97% of strains tested. We propose a list of cts sequences to be used as a simple tool for quickly and precisely classifying new strains. Finally, our analysis leads to predictions about the diversity of P. syringae that is yet to be discovered. We present here an expandable framework mainly based on cts genetic analysis into which more diversity can be integrated. PMID:25184292

Berge, Odile; Monteil, Caroline L; Bartoli, Claudia; Chandeysson, Charlotte; Guilbaud, Caroline; Sands, David C; Morris, Cindy E

2014-01-01

199

Genomic Repeat Abundances Contain Phylogenetic Signal  

PubMed Central

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution. PMID:25261464

Dodsworth, Steven; Chase, Mark W.; Kelly, Laura J.; Leitch, Ilia J.; Macas, Ji?í; Novák, Petr; Piednoël, Mathieu; Weiss-Schneeweiss, Hanna; Leitch, Andrew R.

2015-01-01

200

Phylogenetic tree shapes resolve disease transmission patterns  

PubMed Central

Background and Objectives: Whole-genome sequencing is becoming popular as a tool for understanding outbreaks of communicable diseases, with phylogenetic trees being used to identify individual transmission events or to characterize outbreak-level overall transmission dynamics. Existing methods to infer transmission dynamics from sequence data rely on well-characterized infectious periods, epidemiological and clinical metadata which may not always be available, and typically require computationally intensive analysis focusing on the branch lengths in phylogenetic trees. We sought to determine whether the topological structures of phylogenetic trees contain signatures of the transmission patterns underlying an outbreak. Methodology: We use simulated outbreaks to train and then test computational classifiers. We test the method on data from two real-world outbreaks. Results: We show that different transmission patterns result in quantitatively different phylogenetic tree shapes. We describe topological features that summarize a phylogeny’s structure and find that computational classifiers based on these are capable of predicting an outbreak’s transmission dynamics. The method is robust to variations in the transmission parameters and network types, and recapitulates known epidemiology of previously characterized real-world outbreaks. Conclusions and implications: There are simple structural properties of phylogenetic trees which, when combined, can distinguish communicable disease outbreaks with a super-spreader, homogeneous transmission and chains of transmission. This is possible using genome data alone, and can be done during an outbreak. We discuss the implications for management of outbreaks. PMID:24916411

Colijn, Caroline; Gardy, Jennifer

2014-01-01

201

Prioritizing Populations for Conservation Using Phylogenetic Networks  

PubMed Central

In the face of inevitable future losses to biodiversity, ranking species by conservation priority seems more than prudent. Setting conservation priorities within species (i.e., at the population level) may be critical as species ranges become fragmented and connectivity declines. However, existing approaches to prioritization (e.g., scoring organisms by their expected genetic contribution) are based on phylogenetic trees, which may be poor representations of differentiation below the species level. In this paper we extend evolutionary isolation indices used in conservation planning from phylogenetic trees to phylogenetic networks. Such networks better represent population differentiation, and our extension allows populations to be ranked in order of their expected contribution to the set. We illustrate the approach using data from two imperiled species: the spotted owl Strix occidentalis in North America and the mountain pygmy-possum Burramys parvus in Australia. Using previously published mitochondrial and microsatellite data, we construct phylogenetic networks and score each population by its relative genetic distinctiveness. In both cases, our phylogenetic networks capture the geographic structure of each species: geographically peripheral populations harbor less-redundant genetic information, increasing their conservation rankings. We note that our approach can be used with all conservation-relevant distances (e.g., those based on whole-genome, ecological, or adaptive variation) and suggest it be added to the assortment of tools available to wildlife managers for allocating effort among threatened populations. PMID:24586451

Volkmann, Logan; Martyn, Iain; Moulton, Vincent; Spillner, Andreas; Mooers, Arne O.

2014-01-01

202

Genomic repeat abundances contain phylogenetic signal.  

PubMed

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution. PMID:25261464

Dodsworth, Steven; Chase, Mark W; Kelly, Laura J; Leitch, Ilia J; Macas, Ji?í; Novák, Petr; Piednoël, Mathieu; Weiss-Schneeweiss, Hanna; Leitch, Andrew R

2015-01-01

203

Threat Diversity Will Erode Mammalian Phylogenetic Diversity in the Near Future  

PubMed Central

To reduce the accelerating rate of phylogenetic diversity loss, many studies have searched for mechanisms that could explain why certain species are at risk, whereas others are not. In particular, it has been demonstrated that species might be affected by both extrinsic threat factors as well as intrinsic biological traits that could render a species more sensitive to extinction; here, we focus on extrinsic factors. Recently, the International Union for Conservation of Nature developed a new classification of threat types, including climate change, urbanization, pollution, agriculture and aquaculture, and harvesting/hunting. We have used this new classification to analyze two main factors that could explain the expected future loss of mammalian phylogenetic diversity: 1. differences in the type of threats that affect mammals and 2. differences in the number of major threats that accumulate for a single species. Our results showed that Cetartiodactyla, Diprotodontia, Monotremata, Perissodactyla, Primates, and Proboscidea could lose a high proportion of their current phylogenetic diversity in the coming decades. In contrast, Chiroptera, Didelphimorphia, and Rodentia could lose less phylogenetic diversity than expected if extinctions were random. Some mammalian clades, including Marsupiala, Chiroptera, and a subclade of Primates, are affected by particular threat types, most likely due solely to their geographic locations and associations with particular habitats. However, regardless of the geography, habitat, and taxon considered, it is not the threat type, but the threat diversity that determines the extinction risk for species and clades. Thus, some mammals might be randomly located in areas subjected to a large diversity of threats; they might also accumulate detrimental traits that render them sensitive to different threats, which is a characteristic that could be associated with large body size. Any action reducing threat diversity is expected to have a significant impact on future mammalian phylogeny. PMID:23029443

Jono, Clémentine M. A.; Pavoine, Sandrine

2012-01-01

204

The phylogenetic significance of colour patterns in marine teleost larvae  

PubMed Central

Ichthyologists, natural-history artists, and tropical-fish aquarists have described, illustrated, or photographed colour patterns in adult marine fishes for centuries, but colour patterns in marine fish larvae have largely been neglected. Yet the pelagic larval stages of many marine fishes exhibit subtle to striking, ephemeral patterns of chromatophores that warrant investigation into their potential taxonomic and phylogenetic significance. Colour patterns in larvae of over 200 species of marine teleosts, primarily from the western Caribbean, were examined from digital colour photographs, and their potential utility in elucidating evolutionary relationships at various taxonomic levels was assessed. Larvae of relatively few basal marine teleosts exhibit erythrophores, xanthophores, or iridophores (i.e. nonmelanistic chromatophores), but one or more of those types of chromatophores are visible in larvae of many basal marine neoteleosts and nearly all marine percomorphs. Whether or not the presence of nonmelanistic chromatophores in pelagic marine larvae diagnoses any major teleost taxonomic group cannot be determined based on the preliminary survey conducted, but there is a trend toward increased colour from elopomorphs to percomorphs. Within percomorphs, patterns of nonmelanistic chromatophores may help resolve or contribute evidence to existing hypotheses of relationships at multiple levels of classification. Mugilid and some beloniform larvae share a unique ontogenetic transformation of colour pattern that lends support to the hypothesis of a close relationship between them. Larvae of some tetraodontiforms and lophiiforms are strikingly similar in having the trunk enclosed in an inflated sac covered with xanthophores, a character that may help resolve the relationships of these enigmatic taxa. Colour patterns in percomorph larvae also appear to diagnose certain groups at the interfamilial, familial, intergeneric, and generic levels. Slight differences in generic colour patterns, including whether the pattern comprises xanthophores or erythrophores, often distinguish species. The homology, ontogeny, and possible functional significance of colour patterns in larvae are discussed. Considerably more investigation of larval colour patterns in marine teleosts is needed to assess fully their value in phylogenetic reconstruction. PMID:24039297

Baldwin, Carole C

2013-01-01

205

A Comprehensive Phylogenetic Analysis of Deadenylases  

PubMed Central

Deadenylases catalyze the shortening of the poly(A) tail at the messenger ribonucleic acid (mRNA) 3?-end in eukaryotes. Therefore, these enzymes influence mRNA decay, and constitute a major emerging group of promising anti-cancer pharmacological targets. Herein, we conducted full phylogenetic analyses of the deadenylase homologs in all available genomes in an effort to investigate evolutionary relationships between the deadenylase families and to identify invariant residues, which probably play key roles in the function of deadenylation across species. Our study includes both major Asp-Glu-Asp-Asp (DEDD) and exonuclease-endonuclease-phospatase (EEP) deadenylase superfamilies. The phylogenetic analysis has provided us with important information regarding conserved and invariant deadenylase amino acids across species. Knowledge of the phylogenetic properties and evolution of the domain of deadenylases provides the foundation for the targeted drug design in the pharmaceutical industry and modern exonuclease anti-cancer scientific research. PMID:24348009

Pavlopoulou, Athanasia; Vlachakis, Dimitrios; Balatsos, Nikolaos A.A.; Kossida, Sophia

2013-01-01

206

Comparative genomic analysis and phylogenetic position of Theileria equi  

PubMed Central

Background Transmission of arthropod-borne apicomplexan parasites that cause disease and result in death or persistent infection represents a major challenge to global human and animal health. First described in 1901 as Piroplasma equi, this re-emergent apicomplexan parasite was renamed Babesia equi and subsequently Theileria equi, reflecting an uncertain taxonomy. Understanding mechanisms by which apicomplexan parasites evade immune or chemotherapeutic elimination is required for development of effective vaccines or chemotherapeutics. The continued risk of transmission of T. equi from clinically silent, persistently infected equids impedes the goal of returning the U. S. to non-endemic status. Therefore comparative genomic analysis of T. equi was undertaken to: 1) identify genes contributing to immune evasion and persistence in equid hosts, 2) identify genes involved in PBMC infection biology and 3) define the phylogenetic position of T. equi relative to sequenced apicomplexan parasites. Results The known immunodominant proteins, EMA1, 2 and 3 were discovered to belong to a ten member gene family with a mean amino acid identity, in pairwise comparisons, of 39%. Importantly, the amino acid diversity of EMAs is distributed throughout the length of the proteins. Eight of the EMA genes were simultaneously transcribed. As the agents that cause bovine theileriosis infect and transform host cell PBMCs, we confirmed that T. equi infects equine PBMCs, however, there is no evidence of host cell transformation. Indeed, a number of genes identified as potential manipulators of the host cell phenotype are absent from the T. equi genome. Comparative genomic analysis of T. equi revealed the phylogenetic positioning relative to seven apicomplexan parasites using deduced amino acid sequences from 150 genes placed it as a sister taxon to Theileria spp. Conclusions The EMA family does not fit the paradigm for classical antigenic variation, and we propose a novel model describing the role of the EMA family in persistence. T. equi has lost the putative genes for host cell transformation, or the genes were acquired by T. parva and T. annulata after divergence from T. equi. Our analysis identified 50 genes that will be useful for definitive phylogenetic classification of T. equi and closely related organisms. PMID:23137308

2012-01-01

207

Accurate Replication in Genetic Programming  

Microsoft Academic Search

Abstract One characteristic tendency of genetic program - ming is the production of considerably larger trees than expected It has been suggested that this is related to the ability of individuals to replicate ac - curately In this paper we present theoretical anal - ysis which shows that, for certain specific cases, the pressure for accurate replication induces an increase

Nicholas Freitag Mcphee; Justin Darwin Miller

1995-01-01

208

Probabilistic graphical model representation in phylogenetics.  

PubMed

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution. PMID:24951559

Höhna, Sebastian; Heath, Tracy A; Boussau, Bastien; Landis, Michael J; Ronquist, Fredrik; Huelsenbeck, John P

2014-09-01

209

Phylogenetic diversity of phytopathogenic mycoplasmalike organisms.  

PubMed

By using specific primers, the 16S rRNA genes of Japanese mycoplasmalike organisms (MLOs) were amplified by polymerase chain reactions from MLO-enriched fractions of plants infected with each of six different MLOs. Each of the polymerase chain reaction fragments (length, 1,370 nucleotides) was directly sequenced in both strands by using 17 oligonucleotide primers. A phylogenetic tree constructed by using the sequence data showed that these Japanese MLOs are phylogenetically diverse microorganisms that fall into three groups, group I (onion yellows, tomato yellows, mulberry dwarf, and paulownia witches' broom MLOs), group II (tsuwabuki witches' broom MLO), and group III (rice yellow dwarf MLO). A high level of sequence homology (99%) between the Oenothera hookeri MLO and the severe strain of the western aster yellows MLO on the one hand and group I MLOs on the other indicates that the O. hookeri MLO and the severe strain of the western aster yellows MLO belong to group I and suggests that these MLOs, isolated from two geographically separated locations, descended from a very similar ancestor. Although group I contains phylogenetically identical MLOs, the organisms are transmitted by diverse insect vectors. The three MLO groups are more closely related to Acholeplasma laidlawii than to Mycoplasma gallisepticum. Thus, although MLOs are phylogenetically diverse, they are evolutionarily distant from other mollicutes. These data, together with other information (including phylogenetic relationships, vector specificity, plant-pathogenic properties, and habitat in plant phloem sieve tubes), suggest that MLOs could be classified into at least three phylogenetic groups (groups I through III). PMID:8347505

Namba, S; Oyaizu, H; Kato, S; Iwanami, S; Tsuchizaki, T

1993-07-01

210

Maximizing the Phylogenetic Diversity of Seed Banks.  

PubMed

Ex situ conservation efforts such as those of zoos, botanical gardens, and seed banks will form a vital complement to in situ conservation actions over the coming decades. It is therefore necessary to pay the same attention to the biological diversity represented in ex situ conservation facilities as is often paid to protected-area networks. Building the phylogenetic diversity of ex situ collections will strengthen our capacity to respond to biodiversity loss. Since 2000, the Millennium Seed Bank Partnership has banked seed from 14% of the world's plant species. We assessed the taxonomic, geographic, and phylogenetic diversity of the Millennium Seed Bank collection of legumes (Leguminosae). We compared the collection with all known legume genera, their known geographic range (at country and regional levels), and a genus-level phylogeny of the legume family constructed for this study. Over half the phylogenetic diversity of legumes at the genus level was represented in the Millennium Seed Bank. However, pragmatic prioritization of species of economic importance and endangerment has led to the banking of a less-than-optimal phylogenetic diversity and prioritization of range-restricted species risks an underdispersed collection. The current state of the phylogenetic diversity of legumes in the Millennium Seed Bank could be substantially improved through the strategic banking of relatively few additional taxa. Our method draws on tools that are widely applied to in situ conservation planning, and it can be used to evaluate and improve the phylogenetic diversity of ex situ collections. Maximizar la Riqueza Filogenética de los Bancos de Semillas. PMID:25196170

Griffiths, Kate E; Balding, Sharon T; Dickie, John B; Lewis, Gwilym P; Pearce, Tim R; Grenyer, Richard

2014-09-01

211

A molecular phylogenetic analysis of the Scarabaeinae (dung beetles).  

PubMed

The dung beetles (Scarabaeinae) include ca. 5000 species and exhibit a diverse array of morphologies and behaviors. This variation presumably reflects the adaptation to a diversity of food types and the different strategies used to avoid competition for vertebrate dung, which is the primary breeding environment for most species. The current classification gives great weight to the major behavioral types, separating the ball rollers and the tunnelers, but existing phylogenetic studies have been based on limited taxonomic or biogeographic sampling and have been contradictory. Here, we present a molecular phylogenetic analysis of 214 species of Scarabaeinae, representing all 12 traditionally recognized tribes and six biogeographical regions, using partial gene sequences from one nuclear (28S) and two mitochondrial (cox1, rrnL) genes. Length variation in 28S (588-621 bp) and rrnL (514-523 bp) was subjected to a thorough evaluation of alternative alignments, gap-coding methods, and tree searches using model-based (Bayesian and likelihood), maximum parsimony, and direct optimization analyses. The small-bodied, non-dung-feeding Sarophorus+Coptorhina were basal in all reconstructions. These were closely related to rolling Odontoloma+Dicranocara, suggesting an early acquisition of rolling behavior. Smaller tribes and most genera were monophyletic, while Canthonini and Dichotomiini each consisted of multiple paraphyletic lineages at hierarchical levels equivalent to the smaller tribes. Plasticity of rolling and tunneling was evidenced by a lack of monophyly (S-H test, p > 0.05) and several reversals within clades. The majority of previously unrecognized clades were geographical, including the well-supported Neotropical Phanaeini+Eucraniini, and a large Australian clade of rollers as well as tunneling Coptodactyla and Demarziella. Only three lineages, Gymnopleurini, Copris+Microcopris and Onthophagus, were widespread and therefore appear to be dispersive at a global scale. A reconstruction of biogeographical characters recovered 38-48 transitions between regions and an African origin for most lineages. Dispersal-vicariance analysis supported an African origin with links to all other regions and little back-migration. Our results provide a new synthesis of global-scale dung beetle evolution, demonstrating the great plasticity of behavioral and morphological traits and the importance of biogeographic distributions as the basis for a new classification. PMID:17656114

Monaghan, Michael T; Inward, Daegan J G; Hunt, Toby; Vogler, Alfried P

2007-11-01

212

A Novel Approach for Compressing Phylogenetic Trees  

Microsoft Academic Search

\\u000a Phylogenetic trees are tree structures that depict relationships between organisms. Popular analysis techniques often produce\\u000a large collections of candidate trees, which are expensive to store. We introduce TreeZip, a novel algorithm to compress phylogenetic\\u000a trees based on their shared evolutionary relationships. We evaluate TreeZip’s performance on fourteen tree collections ranging\\u000a from 2,505 trees on 328 taxa to 150,000 trees on

Suzanne J. Matthews; Seung-Jin Sul; Tiffani L. Williams

2010-01-01

213

Understanding phylogenetic incongruence: lessons from phyllostomid bats.  

PubMed

All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar-feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species-rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar-feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats. PMID:22891620

Dávalos, Liliana M; Cirranello, Andrea L; Geisler, Jonathan H; Simmons, Nancy B

2012-11-01

214

Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids  

PubMed Central

Background The Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids. Results The Vitis vinifera chloroplast genome is 160,928 bp in length, including a pair of inverted repeats of 26,358 bp that are separated by small and large single copy regions of 19,065 bp and 89,147 bp, respectively. The gene content and order of Vitis is identical to many other unrearranged angiosperm chloroplast genomes, including tobacco. Phylogenetic analyses using maximum parsimony and maximum likelihood were performed on DNA sequences of 61 protein-coding genes for two datasets with 28 or 29 taxa, including eight or nine taxa from four of the seven currently recognized major clades of rosids. Parsimony and likelihood phylogenies of both data sets provide strong support for the placement of Vitaceae as sister to the remaining rosids. However, the position of the Myrtales and support for the monophyly of the eurosid I clade differs between the two data sets and the two methods of analysis. In parsimony analyses, the inclusion of Gossypium is necessary to obtain trees that support the monophyly of the eurosid I clade. However, maximum likelihood analyses place Cucumis as sister to the Myrtales and therefore do not support the monophyly of the eurosid I clade. Conclusion Phylogenies based on DNA sequences from complete chloroplast genome sequences provide strong support for the position of the Vitaceae as the earliest diverging lineage of rosids. Our phylogenetic analyses support recent assertions that inadequate taxon sampling and incorrect model specification for concatenated multi-gene data sets can mislead phylogenetic inferences when using whole chloroplast genomes for phylogeny reconstruction. PMID:16603088

Jansen, Robert K; Kaittanis, Charalambos; Saski, Christopher; Lee, Seung-Bum; Tomkins, Jeffrey; Alverson, Andrew J; Daniell, Henry

2006-01-01

215

Ensemble sparse classification of Alzheimer's disease.  

PubMed

The high-dimensional pattern classification methods, e.g., support vector machines (SVM), have been widely investigated for analysis of structural and functional brain images (such as magnetic resonance imaging (MRI)) to assist the diagnosis of Alzheimer's disease (AD) including its prodromal stage, i.e., mild cognitive impairment (MCI). Most existing classification methods extract features from neuroimaging data and then construct a single classifier to perform classification. However, due to noise and small sample size of neuroimaging data, it is challenging to train only a global classifier that can be robust enough to achieve good classification performance. In this paper, instead of building a single global classifier, we propose a local patch-based subspace ensemble method which builds multiple individual classifiers based on different subsets of local patches and then combines them for more accurate and robust classification. Specifically, to capture the local spatial consistency, each brain image is partitioned into a number of local patches and a subset of patches is randomly selected from the patch pool to build a weak classifier. Here, the sparse representation-based classifier (SRC) method, which has shown to be effective for classification of image data (e.g., face), is used to construct each weak classifier. Then, multiple weak classifiers are combined to make the final decision. We evaluate our method on 652 subjects (including 198 AD patients, 225 MCI and 229 normal controls) from Alzheimer's Disease Neuroimaging Initiative (ADNI) database using MR images. The experimental results show that our method achieves an accuracy of 90.8% and an area under the ROC curve (AUC) of 94.86% for AD classification and an accuracy of 87.85% and an AUC of 92.90% for MCI classification, respectively, demonstrating a very promising performance of our method compared with the state-of-the-art methods for AD/MCI classification using MR images. PMID:22270352

Liu, Manhua; Zhang, Daoqiang; Shen, Dinggang

2012-04-01

216

Cirrhosis Classification Based on Texture Classification of Random Features  

PubMed Central

Accurate staging of hepatic cirrhosis is important in investigating the cause and slowing down the effects of cirrhosis. Computer-aided diagnosis (CAD) can provide doctors with an alternative second opinion and assist them to make a specific treatment with accurate cirrhosis stage. MRI has many advantages, including high resolution for soft tissue, no radiation, and multiparameters imaging modalities. So in this paper, multisequences MRIs, including T1-weighted, T2-weighted, arterial, portal venous, and equilibrium phase, are applied. However, CAD does not meet the clinical needs of cirrhosis and few researchers are concerned with it at present. Cirrhosis is characterized by the presence of widespread fibrosis and regenerative nodules in the hepatic, leading to different texture patterns of different stages. So, extracting texture feature is the primary task. Compared with typical gray level cooccurrence matrix (GLCM) features, texture classification from random features provides an effective way, and we adopt it and propose CCTCRF for triple classification (normal, early, and middle and advanced stage). CCTCRF does not need strong assumptions except the sparse character of image, contains sufficient texture information, includes concise and effective process, and makes case decision with high accuracy. Experimental results also illustrate the satisfying performance and they are also compared with typical NN with GLCM. PMID:24707317

Shao, Ying; Guo, Dongmei; Zheng, Yuanjie; Zhao, Zuowei; Qiu, Tianshuang

2014-01-01

217

A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.  

PubMed

The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach. PMID:24747130

Miadlikowska, Jolanta; Kauff, Frank; Högnabba, Filip; Oliver, Jeffrey C; Molnár, Katalin; Fraker, Emily; Gaya, Ester; Hafellner, Josef; Hofstetter, Valérie; Gueidan, Cécile; Otálora, Mónica A G; Hodkinson, Brendan; Kukwa, Martin; Lücking, Robert; Björk, Curtis; Sipman, Harrie J M; Burgaz, Ana Rosa; Thell, Arne; Passo, Alfredo; Myllys, Leena; Goward, Trevor; Fernández-Brime, Samantha; Hestmark, Geir; Lendemer, James; Lumbsch, H Thorsten; Schmull, Michaela; Schoch, Conrad L; Sérusiaux, Emmanuël; Maddison, David R; Arnold, A Elizabeth; Lutzoni, François; Stenroos, Soili

2014-10-01

218

Accurate models for EUV lithography  

Microsoft Academic Search

Accurate modeling of EUV Lithography is a mandatory step in driving the technology towards its foreseen insertion point for 22-16nm node patterning. The models are needed to correct EUV designs for imaging effects, and to understand and improve the CD fingerprint of the exposure tools. With a full-field EUV ADT from ASML now available in the IMEC cleanroom, wafer data

Eric Hendrickx; Gian F. Lorusso; Jiong Jiang; Luoqi Chen; Wei Liu; Eelco van Setten; Steve Hansen

2009-01-01

219

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach  

PubMed Central

Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology. PMID:25414723

Erickson, David L.; Jones, Frank A.; Swenson, Nathan G.; Pei, Nancai; Bourg, Norman A.; Chen, Wenna; Davies, Stuart J.; Ge, Xue-jun; Hao, Zhanqing; Howe, Robert W.; Huang, Chun-Lin; Larson, Andrew J.; Lum, Shawn K. Y.; Lutz, James A.; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D.; Fang-Sun, I.; Wright, S. Joseph; Wolf, Amy T.; Ye, W.; Xing, Dingliang; Zimmerman, Jess K.; Kress, W. John

2014-01-01

220

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach.  

PubMed

Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology. PMID:25414723

Erickson, David L; Jones, Frank A; Swenson, Nathan G; Pei, Nancai; Bourg, Norman A; Chen, Wenna; Davies, Stuart J; Ge, Xue-Jun; Hao, Zhanqing; Howe, Robert W; Huang, Chun-Lin; Larson, Andrew J; Lum, Shawn K Y; Lutz, James A; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D; Fang-Sun, I; Wright, S Joseph; Wolf, Amy T; Ye, W; Xing, Dingliang; Zimmerman, Jess K; Kress, W John

2014-01-01

221

Mitochondrial phylogenetics and evolution of mysticete whales.  

PubMed

The phylogenetic relationships among baleen whales (Order: Cetacea) remain uncertain despite extensive research in cetacean molecular phylogenetics and a potential morphological sample size of over 2 million animals harvested. Questions remain regarding the number of species and the monophyly of genera, as well as higher order relationships. Here, we approach mysticete phylogeny with complete mitochondrial genome sequence analysis. We determined complete mtDNA sequences of 10 extant Mysticeti species, inferred their phylogenetic relationships, and estimated node divergence times. The mtDNA sequence analysis concurs with previous molecular studies in the ordering of the principal branches, with Balaenidae (right whales) as sister to all other mysticetes base, followed by Neobalaenidae (pygmy right whale), Eschrichtiidae (gray whale), and finally Balaenopteridae (rorquals + humpback whale). The mtDNA analysis further suggests that four lineages exist within the clade of Eschrichtiidae + Balaenopteridae, including a sister relationship between the humpback and fin whales, and a monophyletic group formed by the blue, sei, and Bryde's whales, each of which represents a newly recognized phylogenetic relationship in Mysticeti. We also estimated the divergence times of all extant mysticete species, accounting for evolutionary rate heterogeneity among lineages. When the mtDNA divergence estimates are compared with the mysticete fossil record, several lineages have molecular divergence estimates strikingly older than indicated by paleontological data. We suggest this discrepancy reflects both a large amount of ancestral polymorphism and long generation times of ancestral baleen whale populations. PMID:15805012

Sasaki, Takeshi; Nikaido, Masato; Hamilton, Healy; Goto, Mutsuo; Kato, Hidehiro; Kanda, Naohisa; Pastene, Luis; Cao, Ying; Fordyce, R; Hasegawa, Masami; Okada, Norihiro

2005-02-01

222

Zen and the art of phylogenetic inference  

E-print Network

modification - `change', occurs within lineages by various processes, such as mutation, selection, genetic by the mosquito-borne West Nile virus. - phylogenetic trees have been used to date the origins of Indo- European on organismal diversity #12;Why is it all about information and the organization of that information? · Once we

Czygrinow, Andrzej

223

Molecular Phylogenetics of Mastodon and Tyrannosaurus rex  

Microsoft Academic Search

We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen alpha1(I) and alpha2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant

Chris L. Organ; Mary H. Schweitzer; Wenxia Zheng; Lisa M. Freimark; Lewis C. Cantley; John M. Asara

2008-01-01

224

Large-Scale Inference of Phylogenetic Trees  

E-print Network

Large-Scale Inference of Phylogenetic Trees Alexandros Stamatakis Institute of Computer Science Trees Alexandros Stamatakis As of July 1st 2006 Swiss Institute of Bioinformatics at Lausanne #12 Tree-of-life New insights in medical & biological research #12;© Alexandros Stamatakis, March 2006 7

Poirazi, Yiota

225

A phylogenetic system of Clavatoraceae (fossil Charophyta)  

Microsoft Academic Search

Using the cladistic method of Hennig a phylogenetic system of Clavatoraceae (fossil Charophyta) is proposed. A number of new combinations arise from this study.The family Clavatoraceae is composed of three monophyla: (1) the Atopocharoidae, which are defined by presenting a utricle with a radial symmetry formed by the superposition of two whorls of spine-shaped bracts and includes traditional members plus

C. Martín-Closas

1996-01-01

226

Sequence-Length Requirements for Phylogenetic Methods  

E-print Network

, and Tandy Warnow2 1 Department of Computer Science, University of New Mexico Albuquerque, NM 87131 moret simulations based on random birth-death trees, with controlled deviations from ultrametricity, to collect data on the "Tree of Life," is a big computational challenge. Indeed, such large-scale phylogenetic analysis

Moret, Bernard

227

MOLECULAR PHYLOGENETIC RELATIONSHIPS AMONG DIABROTICA SPECIES (ACCESSION NO. AF195195)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Corn rootworms of the genus Diabrotica (Coleoptera: Chrysomelidae) are the most serious pest of corn in midwestern United States. Despite their economic importance, phylogenetic relationships within the genus remain unclear. Phylogenetic analysis of five Diabrotica was undertaken using DNA sequences...

228

MOLECULAR PHYLOGENETIC RELATIONSHIPS AMONG DIABROTICA SPECIES (ACCESSION NO. AF195201)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Corn rootworms of the genus Diabrotica (Coleoptera: Chrysomelidae) are the most serious pest of corn in midwestern United States. Despite their economic importance, phylogenetic relationships within the genus remain unclear. Phylogenetic analysis of five Diabrotica was undertaken using DNA sequences...

229

MOLECULAR PHYLOGENETIC RELATIONSHIPS AMONG DIABROTICA SPECIES (ACCESSION NO. AF195202)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Corn rootworms of the genus Diabrotica (Coleoptera: Chrysomelidae) are the most serious pest of corn in midwestern United States. Despite their economic importance, phylogenetic relationships within the genus remain unclear. Phylogenetic analysis of five Diabrotica was undertaken using DNA sequences...

230

MOLECULAR PHYLOGENETIC RELATIONSHIPS AMONG DIABROTICA SPECIES (ACCESSION NO. AF195193)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Corn rootworms of the genus Diabrotica (Coleoptera: Chrysomelidae) are the most serious pest of corn in midwestern United States. Despite their economic importance, phylogenetic relationships within the genus remain unclear. Phylogenetic analysis of five Diabrotica was undertaken using DNA sequences...

231

MOLECULAR PHYLOGENETIC RELATIONSHIPS AMONG DIABROTICA SPECIES (ACCESSION NO. AF195199)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Corn rootworms of the genus Diabrotica (Coleoptera: Chrysomelidae) are the most serious pest of corn in midwestern United States. Despite their economic importance, phylogenetic relationships within the genus remain unclear. Phylogenetic analysis of five Diabrotica was undertaken using DNA sequences...

232

MOLECULAR PHYLOGENETIC RELATIONSHIPS AMONG DIABROTICA SPECIES (ACCESSION NO. AF195198)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Corn rootworms of the genus Diabrotica (Coleoptera: Chrysomelidae) are the most serious pest of corn in midwestern United States. Despite their economic importance, phylogenetic relationships within the genus remain unclear. Phylogenetic analysis of five Diabrotica was undertaken using DNA sequences...

233

Automatic classification of blank substrate defects  

NASA Astrophysics Data System (ADS)

Mask preparation stages are crucial in mask manufacturing, since this mask is to later act as a template for considerable number of dies on wafer. Defects on the initial blank substrate, and subsequent cleaned and coated substrates, can have a profound impact on the usability of the finished mask. This emphasizes the need for early and accurate identification of blank substrate defects and the risk they pose to the patterned reticle. While Automatic Defect Classification (ADC) is a well-developed technology for inspection and analysis of defects on patterned wafers and masks in the semiconductors industry, ADC for mask blanks is still in the early stages of adoption and development. Calibre ADC is a powerful analysis tool for fast, accurate, consistent and automatic classification of defects on mask blanks. Accurate, automated classification of mask blanks leads to better usability of blanks by enabling defect avoidance technologies during mask writing. Detailed information on blank defects can help to select appropriate job-decks to be written on the mask by defect avoidance tools [1][4][5]. Smart algorithms separate critical defects from the potentially large number of non-critical defects or false defects detected at various stages during mask blank preparation. Mechanisms used by Calibre ADC to identify and characterize defects include defect location and size, signal polarity (dark, bright) in both transmitted and reflected review images, distinguishing defect signals from background noise in defect images. The Calibre ADC engine then uses a decision tree to translate this information into a defect classification code. Using this automated process improves classification accuracy, repeatability and speed, while avoiding the subjectivity of human judgment compared to the alternative of manual defect classification by trained personnel [2]. This paper focuses on the results from the evaluation of Automatic Defect Classification (ADC) product at MP Mask Technology Center (MPMask). The Calibre ADC tool was qualified on production mask blanks against the manual classification. The classification accuracy of ADC is greater than 95% for critical defects with an overall accuracy of 90%. The sensitivity to weak defect signals and locating the defect in the images is a challenge we are resolving. The performance of the tool has been demonstrated on multiple mask types and is ready for deployment in full volume mask manufacturing production flow. Implementation of Calibre ADC is estimated to reduce the misclassification of critical defects by 60-80%.

Boettiger, Tom; Buck, Peter; Paninjath, Sankaranarayanan; Pereira, Mark; Ronald, Rob; Rost, Dan; Samir, Bhamidipati

2014-10-01

234

Multilocus phylogeny of the New-World mud turtles (Kinosternidae) supports the traditional classification of the group.  

PubMed

A goal of modern taxonomy is to develop classifications that reflect current phylogenetic relationships and are as stable as possible given the inherent uncertainties in much of the tree of life. Here, we provide an in-depth phylogenetic analysis, based on 14 nuclear loci comprising 10,305 base pairs of aligned sequence data from all but two species of the turtle family Kinosternidae, to determine whether recent proposed changes to the group's classification are justified and necessary. We conclude that those proposed changes were based on (1) mtDNA gene tree anomalies, (2) preliminary analyses that do not fully capture the breadth of geographic variation necessary to motivate taxonomic changes, and (3) changes in rank that are not motivated by non-monophyletic groups. Our recommendation, for this and other similar cases, is that taxonomic changes be made only when phylogenetic results that are statistically well-supported and corroborated by multiple independent lines of genetic evidence indicate that non-monophyletic groups are currently recognized and need to be corrected. We hope that other members of the phylogenetics community will join us in proposing taxonomic changes only when the strongest phylogenetic data demand such changes, and in so doing that we can move toward stable, phylogenetically informed classifications of lasting value. PMID:24704303

Spinks, Phillip Q; Thomson, Robert C; Gidi?, Müge; Bradley Shaffer, H

2014-07-01

235

Classification of pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in MEGAN  

PubMed Central

The classification of high-throughput sequencing data of protein-encoding genes is not as well established as for 16S rRNA. The objective of this work was to develop a simple and accurate method of classifying large datasets of pmoA sequences, a common marker for methanotrophic bacteria. A taxonomic system for pmoA was developed based on a phylogenetic analysis of available sequences. The taxonomy incorporates the known diversity of pmoA present in public databases, including both sequences from cultivated and uncultivated organisms. Representative sequences from closely related genes, such as those encoding the bacterial ammonia monooxygenase, were also included in the pmoA taxonomy. In total, 53 low-level taxa (genus-level) are included. Using previously published datasets of high-throughput pmoA amplicon sequence data, we tested two approaches for classifying pmoA: a naïve Bayesian classifier and BLAST. Classification of pmoA sequences based on BLAST analyses was performed using the lowest common ancestor (LCA) algorithm in MEGAN, a software program commonly used for the analysis of metagenomic data. Both the naïve Bayesian and BLAST methods were able to classify pmoA sequences and provided similar classifications; however, the naïve Bayesian classifier was prone to misclassifying contaminant sequences present in the datasets. Another advantage of the BLAST/LCA method was that it provided a user-interpretable output and enabled novelty detection at various levels, from highly divergent pmoA sequences to genus-level novelty. PMID:22558000

Dumont, Marc G.; Lüke, Claudia; Deng, Yongcui; Frenzel, Peter

2013-01-01

236

Cnidarian phylogenetic relationships as revealed by mitogenomics  

PubMed Central

Background Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia?+?Octocorallia) – cnidarians with a reproductive polyp and the absence of a medusa stage – and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) – cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. Results We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia?+?Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae?+?Coronatae], Acraspeda [Cubozoa?+?Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. Conclusions Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that the shared morphological characters in these groups are plesiomorphies, originated in the branch leading to Medusozoa. The expansion of mitogenomic data along with improvements in phylogenetic inference methods and use of additional nuclear markers will further enhance our understanding of the phylogenetic relationships and character evolution within Cnidaria. PMID:23302374

2013-01-01

237

Audio Segmentation and Classification  

E-print Network

Audio Segmentation and Classification Abdillahi Hussein Omar Kgs. Lyngby 2005 #12;Preface The work describes the work done on the development of an audio segmentation and classification system. Many existing works on audio classification deal with the problem of classifying known homogeneous audio segments

238

Chapter 7. Phylogenetic analysis Homework for chapter 7  

E-print Network

Chapter 7. Phylogenetic analysis Homework for chapter 7 Bioinformatics - Lecture 7 Louis Wehenkel - Bioinformatique (1/16) #12;Chapter 7. Phylogenetic analysis Homework for chapter 7 Chapter 7. Phylogenetic analysis On trees and evolution Inferring trees from data Homework for chapter 7 Louis Wehenkel GBIO0009

Wehenkel, Louis

239

Efficiency and Accuracy of Phylogenetic Trees for Large Sequence Datasets  

E-print Network

Efficiency and Accuracy of Phylogenetic Trees for Large Sequence Datasets Daniel Keymer, Stanford structuring the data in terms of evolutionary relationships as shown in a phylogenetic tree. However, the algorithms traditionally used to build phylogenetic trees often become overwhelmed as the number of sequences

240

Phylogenetic Species Recognition and Species Concepts in Fungi  

Microsoft Academic Search

Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology 31, 000–000. The operational species concept, i.e., the one used to recognize species, is contrasted to the theoretical species concept. A phylogenetic approach to recognize fungal species based on concordance of multiple gene genealogies is compared to those based on morphology and reproductive behavior. Examples where Phylogenetic Species

John W. Taylor; David J. Jacobson; Scott Kroken; Takao Kasuga; David M. Geiser; David S. Hibbett; Matthew C. Fisher

2000-01-01

241

A general species delimitation method with applications to phylogenetic placements  

PubMed Central

Motivation: Sequence-based methods to delimit species are central to DNA taxonomy, microbial community surveys and DNA metabarcoding studies. Current approaches either rely on simple sequence similarity thresholds (OTU-picking) or on complex and compute-intensive evolutionary models. The OTU-picking methods scale well on large datasets, but the results are highly sensitive to the similarity threshold. Coalescent-based species delimitation approaches often rely on Bayesian statistics and Markov Chain Monte Carlo sampling, and can therefore only be applied to small datasets. Results: We introduce the Poisson tree processes (PTP) model to infer putative species boundaries on a given phylogenetic input tree. We also integrate PTP with our evolutionary placement algorithm (EPA-PTP) to count the number of species in phylogenetic placements. We compare our approaches with popular OTU-picking methods and the General Mixed Yule Coalescent (GMYC) model. For de novo species delimitation, the stand-alone PTP model generally outperforms GYMC as well as OTU-picking methods when evolutionary distances between species are small. PTP neither requires an ultrametric input tree nor a sequence similarity threshold as input. In the open reference species delimitation approach, EPA-PTP yields more accurate results than de novo species delimitation methods. Finally, EPA-PTP scales on large datasets because it relies on the parallel implementations of the EPA and RAxML, thereby allowing to delimit species in high-throughput sequencing data. Availability and implementation: The code is freely available at www.exelixis-lab.org/software.html. Contact: Alexandros.Stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23990417

Zhang, Jiajie; Kapli, Paschalia; Pavlidis, Pavlos; Stamatakis, Alexandros

2013-01-01

242

Efficient and accurate fragmentation methods.  

PubMed

Conspectus Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131?000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, ?-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cut-off (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum mechanical calculations on fragment-fragment (dimer) interactions. The EFMO method is both more accurate and more computationally efficient than the most commonly used FMO implementation (FMO2), in which all dimers are explicitly included in the calculation. While the FMO2 method itself does not incorporate three-body interactions, such interactions are included in the EFMO method via the EFP self-consistent induction term. Several applications (ranging from clusters to proteins) of the three methods are discussed to demonstrate their efficacy. The EFMO method will be especially exciting once the analytic gradients have been completed, because this will allow geometry optimizations, the prediction of vibrational spectra, reaction path following, and molecular dynamics simulations using the method. PMID:24810424

Pruitt, Spencer R; Bertoni, Colleen; Brorsen, Kurt R; Gordon, Mark S

2014-09-16

243

Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos.  

PubMed

Fairy armadillos or pichiciegos (Xenarthra, Dasypodidae) are among the most elusive mammals. Due to their subterranean and nocturnal lifestyle, their basic biology and evolutionary history remain virtually unknown. Two distinct species with allopatric distributions are recognized: Chlamyphorus truncatus is restricted to central Argentina, while Calyptophractus retusus occurs in the Gran Chaco of Argentina, Paraguay, and Bolivia. To test their monophyly and resolve their phylogenetic affinities within armadillos, we obtained sequence data from modern and museum specimens for two mitochondrial genes (12S RNA [MT-RNR1] and NADH dehydrogenase 1 [MT-ND1]) and two nuclear exons (breast cancer 1 early onset exon 11 [BRCA1] and von Willebrand factor exon 28 [VWF]). Phylogenetic analyses provided a reference phylogeny and timescale for living xenarthran genera. Our results reveal monophyletic pichiciegos as members of a major armadillo subfamily (Chlamyphorinae). Their strictly fossorial lifestyle probably evolved as a response to the Oligocene aridification that occurred in South America after their divergence from Tolypeutinae around 32 million years ago (Mya). The ancient divergence date (?17Mya) for separation between the two species supports their taxonomic classification into distinct genera. The synchronicity with Middle Miocene marine incursions along the Paraná river basin suggests a vicariant origin for pichiciegos by the disruption of their ancestral range. Their phylogenetic distinctiveness and rarity in the wild argue in favor of high conservation priority. PMID:22122941

Delsuc, Frédéric; Superina, Mariella; Tilak, Marie-Ka; Douzery, Emmanuel J P; Hassanin, Alexandre

2012-02-01

244

DNA sequence support for a close phylogenetic relationship between some storks and New World vultures.  

PubMed Central

Nucleotide sequences from the mitochondrial cytochrome b gene were used to address a controversial suggestion that New World vultures are related more closely to storks than to Old World vultures. Phylogenetic analyses of 1-kb sequences from 18 relevant avian species indicate that the similarities in morphology and behavior between New World and Old World vultures probably manifest convergent adaptations associated with carrion-feeding, rather than propinquity of descent. Direct sequence evidence for a close phylogenetic alliance between at least some New World vultures and storks lends support to conclusions reached previously from DNA.DNA hybridization methods and detailed morphology-based appraisals, and it illustrates how mistaken assumptions of homology for organismal adaptations can compromise biological classifications. However, there was a lack of significant resolution for most other branches in the cytochrome b phylogenetic reconstructions. This irresolution is most likely attributable to a close temporal clustering of nodes, rather than to ceiling effects (mutational saturation) producing an inappropriate window of resolution for the cytochrome b sequences. Images PMID:8197203

Avise, J C; Nelson, W S; Sibley, C G

1994-01-01

245

Cloud field classification based on textural features  

NASA Technical Reports Server (NTRS)

An essential component in global climate research is accurate cloud cover and type determination. Of the two approaches to texture-based classification (statistical and textural), only the former is effective in the classification of natural scenes such as land, ocean, and atmosphere. In the statistical approach that was adopted, parameters characterizing the stochastic properties of the spatial distribution of grey levels in an image are estimated and then used as features for cloud classification. Two types of textural measures were used. One is based on the distribution of the grey level difference vector (GLDV), and the other on a set of textural features derived from the MaxMin cooccurrence matrix (MMCM). The GLDV method looks at the difference D of grey levels at pixels separated by a horizontal distance d and computes several statistics based on this distribution. These are then used as features in subsequent classification. The MaxMin tectural features on the other hand are based on the MMCM, a matrix whose (I,J)th entry give the relative frequency of occurrences of the grey level pair (I,J) that are consecutive and thresholded local extremes separated by a given pixel distance d. Textural measures are then computed based on this matrix in much the same manner as is done in texture computation using the grey level cooccurrence matrix. The database consists of 37 cloud field scenes from LANDSAT imagery using a near IR visible channel. The classification algorithm used is the well known Stepwise Discriminant Analysis. The overall accuracy was estimated by the percentage or correct classifications in each case. It turns out that both types of classifiers, at their best combination of features, and at any given spatial resolution give approximately the same classification accuracy. A neural network based classifier with a feed forward architecture and a back propagation training algorithm is used to increase the classification accuracy, using these two classes of features. Preliminary results based on the GLDV textural features alone look promising.

Sengupta, Sailes Kumar

1989-01-01

246

Classification of DNA sequences based on thermal melting profiles  

PubMed Central

A new classification scheme based on the melting profile of DNA sequences simulated thermal melting profiles. This method was applied in the classification of (a) several species of mammalian ­ ? globin and (b) ?­chain class II MHC genes. Comparison of the thermal melting profile with the molecular phylogenetic trees constructed using the sequences shows that the melting temperature based approach is able to reproduce most of the major features of the sequence based evolutionary tree. Melting profile method takes into account the inherent structure and dynamics of the DNA molecule, does not require sequence alignment prior to tree construction, and provides a means to verify the results experimentally. Therefore our results show that melting profile based classification of DNA sequences could be a useful tool for sequence analysis. PMID:21042401

Reese, Edward; Krishnan, Vishwanathan V

2010-01-01

247

Complete mitochondrial genomes elucidate phylogenetic relationships of the deep-sea octocoral families Coralliidae and Paragorgiidae  

NASA Astrophysics Data System (ADS)

In the past decade, molecular phylogenetic analyses of octocorals have shown that the current morphological taxonomic classification of these organisms needs to be revised. The latest phylogenetic analyses show that most octocorals can be divided into three main clades. One of these clades contains the families Coralliidae and Paragorgiidae. These families share several taxonomically important characters and it has been suggested that they may not be monophyletic; with the possibility of the Coralliidae being a derived branch of the Paragorgiidae. Uncertainty exists not only in the relationship of these two families, but also in the classification of the two genera that make up the Coralliidae, Corallium and Paracorallium. Molecular analyses suggest that the genus Corallium is paraphyletic, and it can be divided into two main clades, with the Paracorallium as members of one of these clades. In this study we sequenced the whole mitochondrial genome of five species of Paragorgia and of five species of Corallium to use in a phylogenetic analysis to achieve two main objectives; the first to elucidate the phylogenetic relationship between the Paragorgiidae and Coralliidae and the second to determine whether the genera Corallium and Paracorallium are monophyletic. Our results show that other members of the Coralliidae share the two novel mitochondrial gene arrangements found in a previous study in Corallium konojoi and Paracorallium japonicum; and that the Corallium konojoi arrangement is also found in the Paragorgiidae. Our phylogenetic reconstruction based on all the protein coding genes and ribosomal RNAs of the mitochondrial genome suggest that the Coralliidae are not a derived branch of the Paragorgiidae, but rather a monophyletic sister branch to the Paragorgiidae. While our manuscript was in review a study was published using morphological data and several fragments from mitochondrial genes to redefine the taxonomy of the Coralliidae. Paracorallium was subsumed into Corallium and the genus Hemicorallium was resurrected. This left two disjunct clades as Corallium, making that genus paraphyletic. One of the clades includes the type specimens of Corallium, indicating that clade should remain Corallium. For the other clade, we support the resurrection of the genus Pleurocorallium to fix the paraphyly of Corallium. Based on congruent phylogenies in both studies, the genus Pleurocorallium includes the species C. secundum, C. kishinouyei, C. konojoi, C. elatius, and C. niveum.

Figueroa, Diego F.; Baco, Amy R.

2014-01-01

248

Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling  

PubMed Central

Background Phylogenies are essential to many areas of biology, but phylogenetic methods may give incorrect estimates under some conditions. A potentially common scenario of this type is when few taxa are sampled and terminal branches for the sampled taxa are relatively long. However, the best solution in such cases (i.e., sampling more taxa versus more characters) has been highly controversial. A widespread assumption in this debate is that added taxa must be complete (no missing data) in order to save analyses from the negative impacts of limited taxon sampling. Here, we evaluate whether incomplete taxa can also rescue analyses under these conditions (empirically testing predictions from an earlier simulation study). Methodology/Principal Findings We utilize DNA sequence data from 16 vertebrate species with well-established phylogenetic relationships. In each replicate, we randomly sample 4 species, estimate their phylogeny (using Bayesian, likelihood, and parsimony methods), and then evaluate whether adding in the remaining 12 species (which have 50, 75, or 90% of their data replaced with missing data cells) can improve phylogenetic accuracy relative to analyzing the 4 complete taxa alone. We find that in those cases where sampling few taxa yields an incorrect estimate, adding taxa with 50% or 75% missing data can frequently (>75% of relevant replicates) rescue Bayesian and likelihood analyses, recovering accurate phylogenies for the original 4 taxa. Even taxa with 90% missing data can sometimes be beneficial. Conclusions We show that adding taxa that are highly incomplete can improve phylogenetic accuracy in cases where analyses are misled by limited taxon sampling. These surprising empirical results confirm those from simulations, and show that the benefits of adding taxa may be obtained with unexpectedly small amounts of data. These findings have important implications for the debate on sampling taxa versus characters, and for studies attempting to resolve difficult phylogenetic problems. PMID:22900065

Wiens, John J.; Tiu, Jonathan

2012-01-01

249

Phylogenetic networks with edge-disjoint recombination cycles  

NASA Astrophysics Data System (ADS)

Phylogenetic analysis is a branch of biology that establishes the evolutionary relationships between living organisms. The goal of phylogenetic analysis is to determine the order and approximate timing of speciation events in the evolution of a given set of species. Phylogenetic networks allow to represent evolutionary histories that include events like recombination and hybridization. In this paper, we introduce a class of phylogenetic networks called extended galled-trees in which recombination cycles share no edge. We show that the site consistency problem, which is NP-hard in general, can be solved in polynomial time for this class of phylogenetic networks.

Dubrova, Elena

2005-06-01

250

A phylogenetic analysis of Prunus and the Amygdaloideae (Rosaceae) using ITS sequences of nuclear ribosomal DNA.  

PubMed

The economically important plum or cherry genus (PRUNUS:) and the subfamily Amygdaloideae of the Rosaceae have a controversial taxonomic history due to the lack of a phylogenetic framework. Phylogenetic analysis using the ITS sequences of nuclear ribosomal DNA (nrDNA) was conducted to construct the evolutionary history and evaluate the historical classifications of PRUNUS: and the Amygdaloideae. The analyses suggest two major groups within the Amygdaloideae: (1) PRUNUS: s.l. (sensu lato) and MADDENIA:, and (2) EXOCHORDA:, Oemleria, and PRINSEPIA: The ITS phylogeny supports the recent treatment of including EXOCHORDA: (formerly in the Spiraeoideae) in the Amygdaloideae. MADDENIA: is found to be nested within PRUNUS: s.l. in the parsimony and distance analyses, but basal to PRUNUS: s.l. in the maximum likelihood analysis. Within PRUNUS:, two major groups are recognizable: (1) the AMYGDALUS:-PRUNUS: group, and (2) the CERASUS:-LAUROCERASUS:-PADUS: group. The clades in the ITS phylogeny are not congruent with most subgeneric groups in the widely used classification of PRUNUS: by Rehder. A broadly defined PRUNUS: is supported. PMID:11159135

Lee, S; Wen, J

2001-01-01

251

Phylogenetic analysis reveals the evolution and diversification of cyclins in eukaryotes.  

PubMed

Cyclins are a family of diverse proteins that play fundamental roles in regulating cell cycle progression in Eukaryotes. Cyclins have been identified from protists to higher Eukaryotes, while its evolution remains vague and the findings turn out controversial. Current classification of cyclins is mainly based on their functions, which may not be appropriate for the systematic evolutionary analysis. In this work, we performed comparative and phylogenetic analysis of cyclins to investigate their classification, origin and evolution. Cyclins originated in early Eukaryotes and evolved from protists to plants, fungi and animals. Based on the phylogenetic tree, cyclins can be divided into three major groups designated as the group I, II and III with different functions and features. Group I plays key roles in cell cycle, group II varied in actions are kingdom (plant, fungi and animal) specific, and group III functions in transcription regulation. Our results showed that the dominating cyclins (group I) diverged from protists to plants, fungi and animals, while divergence of the other cyclins (groups II and III) has occurred in protists. We also discussed the evolutionary relationships between cyclins and cyclin-dependent kinases (CDKs) and found that the cyclins have undergone divergence in protists before the divergence of animal CDKs. This reclassification and evolutionary analysis of cyclins might facilitate understanding eukaryotic cell cycle control. PMID:23261709

Ma, Zhaowu; Wu, Yuliang; Jin, Jialu; Yan, Jun; Kuang, Shuzhen; Zhou, Mi; Zhang, Yuexuan; Guo, An-Yuan

2013-03-01

252

Molecular phylogenetics of mastodon and Tyrannosaurus rex.  

PubMed

We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen alpha1(I) and alpha2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable. PMID:18436782

Organ, Chris L; Schweitzer, Mary H; Zheng, Wenxia; Freimark, Lisa M; Cantley, Lewis C; Asara, John M

2008-04-25

253

Wavelet Leader multifractal analysis for texture classification  

Microsoft Academic Search

ABSTRACT Image classification often relies on texture characterization. Yet texture characterization has so far rarely been based on a true 2D multifractal analysis. Recently, a 2D wavelet Leader based multifractal formalism,has been proposed. It allows to perform an accurate, complete and low computational and memory,costs multifractal characterization of textures in images. This contribution describes the first application of such a

Herwig Wendt; Patrice Abry; Stéphane Jaffard; Hui Ji; Zuowei Shen

2009-01-01

254

Astragalus (Fabaceae): A molecular phylogenetic perspective  

Microsoft Academic Search

Nucleotide sequences of the plastidmatK gene and nuclear rDNA internal transcribed spacer region were sampled fromAstragalus L. (Fabaceae), and its closest relatives within tribe Galegeae, to infer phylogenetic relationships and estimate ages of\\u000a diversification. Consistent with previous studies that emphasized sampling for nrDNA ITS primarily within either New World\\u000a or Old World species groups,Astragalus, with the exception of a few

Martin F. Wojciechowski

2005-01-01

255

The phylogenetic position of Udonella (Platyhelminthes) 1  

Microsoft Academic Search

Phylogenetic analysis of molecular data from complete 18S rRNA and partial 28S rRNA genes, of a variety of platyhelminths, places the enigmatic Udonella caligorum firmly as a monopisthocotylean monogenean. Both maximum parsimony and a modified distance measure, operating under a maximum likelihood model, gave identical solutions for each data set. These data further support morphological evidence from ultrastructural studies indicating

D. T. J. Littlewood; K. Rohde; K. A. Clough

1998-01-01

256

Accurate extraction of the News  

E-print Network

We propose a new scheme for extracting gravitational radiation from a characteristic numerical simulation of a spacetime. This method is similar in conception to our earlier work but analytical and numerical implementation is different. The scheme is based on direct transformation to the Bondi coordinates and the gravitational waves are extracted by calculating the Bondi news function in Bondi coordinates. The entire calculation is done in a way which will make the implementation easy when we use uniform Bondi angular grid at $\\mathcal I^+$. Using uniform Bondi grid for news calculation has added advantage that we have to solve only ordinary differential equations instead of partial differential equation. For the test problems this new scheme allows us to extract gravitational radiation much more accurately than the previous schemes.

Shrirang S. Deshingkar

2006-09-14

257

On numerically accurate finite element  

NASA Technical Reports Server (NTRS)

A general criterion for testing a mesh with topologically similar repeat units is given, and the analysis shows that only a few conventional element types and arrangements are, or can be made suitable for computations in the fully plastic range. Further, a new variational principle, which can easily and simply be incorporated into an existing finite element program, is presented. This allows accurate computations to be made even for element designs that would not normally be suitable. Numerical results are given for three plane strain problems, namely pure bending of a beam, a thick-walled tube under pressure, and a deep double edge cracked tensile specimen. The effects of various element designs and of the new variational procedure are illustrated. Elastic-plastic computation at finite strain are discussed.

Nagtegaal, J. C.; Parks, D. M.; Rice, J. R.

1974-01-01

258

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation  

PubMed Central

Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes. Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes. PMID:16754613

Roger, Andrew J; Hug, Laura A

2006-01-01

259

A Consistent Phylogenetic Backbone for the Fungi  

PubMed Central

The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. PMID:22114356

Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

2012-01-01

260

Security classification of information  

SciTech Connect

This document is the second of a planned four-volume work that comprehensively discusses the security classification of information. The main focus of Volume 2 is on the principles for classification of information. Included herein are descriptions of the two major types of information that governments classify for national security reasons (subjective and objective information), guidance to use when determining whether information under consideration for classification is controlled by the government (a necessary requirement for classification to be effective), information disclosure risks and benefits (the benefits and costs of classification), standards to use when balancing information disclosure risks and benefits, guidance for assigning classification levels (Top Secret, Secret, or Confidential) to classified information, guidance for determining how long information should be classified (classification duration), classification of associations of information, classification of compilations of information, and principles for declassifying and downgrading information. Rules or principles of certain areas of our legal system (e.g., trade secret law) are sometimes mentioned to .provide added support to some of those classification principles.

Quist, A.S.

1993-04-01

261

Recursive heuristic classification  

NASA Technical Reports Server (NTRS)

The author will describe a new problem-solving approach called recursive heuristic classification, whereby a subproblem of heuristic classification is itself formulated and solved by heuristic classification. This allows the construction of more knowledge-intensive classification programs in a way that yields a clean organization. Further, standard knowledge acquisition and learning techniques for heuristic classification can be used to create, refine, and maintain the knowledge base associated with the recursively called classification expert system. The method of recursive heuristic classification was used in the Minerva blackboard shell for heuristic classification. Minerva recursively calls itself every problem-solving cycle to solve the important blackboard scheduler task, which involves assigning a desirability rating to alternative problem-solving actions. Knowing these ratings is critical to the use of an expert system as a component of a critiquing or apprenticeship tutoring system. One innovation of this research is a method called dynamic heuristic classification, which allows selection among dynamically generated classification categories instead of requiring them to be prenumerated.

Wilkins, David C.

1994-01-01

262

Multiple sequence alignment: a major challenge to large-scale phylogenetics  

PubMed Central

Over the last decade, dramatic advances have been made in developing methods for large-scale phylogeny estimation, so that it is now feasible for investigators with moderate computational resources to obtain reasonable solutions to maximum likelihood and maximum parsimony, even for datasets with a few thousand sequences. There has also been progress on developing methods for multiple sequence alignment, so that greater alignment accuracy (and subsequent improvement in phylogenetic accuracy) is now possible through automated methods. However, these methods have not been tested under conditions that reflect properties of datasets confronted by large-scale phylogenetic estimation projects. In this paper we report on a study that compares several alignment methods on a benchmark collection of nucleotide sequence datasets of up to 78,132 sequences. We show that as the number of sequences increases, the number of alignment methods that can analyze the datasets decreases. Furthermore, the most accurate alignment methods are unable to analyze the very largest datasets we studied, so that only moderately accurate alignment methods can be used on the largest datasets. As a result, alignments computed for large datasets have relatively large error rates, and maximum likelihood phylogenies computed on these alignments also have high error rates. Therefore, the estimation of highly accurate multiple sequence alignments is a major challenge for Tree of Life projects, and more generally for large-scale systematics studies. PMID:21113338

Liu, Kevin; Linder, C. Randal; Warnow, Tandy

2011-01-01

263

Sparse representation for tumor classification based on feature extraction using latent low-rank representation.  

PubMed

Accurate tumor classification is crucial to the proper treatment of cancer. To now, sparse representation (SR) has shown its great performance for tumor classification. This paper conceives a new SR-based method for tumor classification by using gene expression data. In the proposed method, we firstly use latent low-rank representation for extracting salient features and removing noise from the original samples data. Then we use sparse representation classifier (SRC) to build tumor classification model. The experimental results on several real-world data sets show that our method is more efficient and more effective than the previous classification methods including SVM, SRC, and LASSO. PMID:24678505

Gan, Bin; Zheng, Chun-Hou; Zhang, Jun; Wang, Hong-Qiang

2014-01-01

264

Sparse Representation for Tumor Classification Based on Feature Extraction Using Latent Low-Rank Representation  

PubMed Central

Accurate tumor classification is crucial to the proper treatment of cancer. To now, sparse representation (SR) has shown its great performance for tumor classification. This paper conceives a new SR-based method for tumor classification by using gene expression data. In the proposed method, we firstly use latent low-rank representation for extracting salient features and removing noise from the original samples data. Then we use sparse representation classifier (SRC) to build tumor classification model. The experimental results on several real-world data sets show that our method is more efficient and more effective than the previous classification methods including SVM, SRC, and LASSO. PMID:24678505

Zheng, Chun-Hou; Zhang, Jun; Wang, Hong-Qiang

2014-01-01

265

Classification of earth terrain using polarimetric synthetic aperture radar images  

NASA Technical Reports Server (NTRS)

Supervised and unsupervised classification techniques are developed and used to classify the earth terrain components from SAR polarimetric images of San Francisco Bay and Traverse City, Michigan. The supervised techniques include the Bayes classifiers, normalized polarimetric classification, and simple feature classification using discriminates such as the absolute and normalized magnitude response of individual receiver channel returns and the phase difference between receiver channels. An algorithm is developed as an unsupervised technique which classifies terrain elements based on the relationship between the orientation angle and the handedness of the transmitting and receiving polariation states. It is found that supervised classification produces the best results when accurate classifier training data are used, while unsupervised classification may be applied when training data are not available.

Lim, H. H.; Swartz, A. A.; Yueh, H. A.; Kong, J. A.; Shin, R. T.; Van Zyl, J. J.

1989-01-01

266

The revised lung adenocarcinoma classification—an imaging guide  

PubMed Central

Advances in our understanding of the pathology, radiology and clinical behaviour of peripheral lung adenocarcinomas facilitated a more robust terminology and classification of these lesions. The International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society (IASLC/ATS/ERS) classification introduced new terminology to better reflect this heterogeneous group of adenocarcinomas formerly known as bronchoalveolar cell carcinoma (BAC). There is now a clear distinction between pre-invasive, minimally invasive and frankly invasive lesions. The radiographic appearance of these ranges from pure ground glass nodules to solid mass lesions. Radiologists must be aware of the new classification in order to work alongside multidisciplinary colleagues to allow accurate staging and treatment. This article reviews the new classification of lung adenocarcinomas. Management options of these lesions with particular focus on radiological implications of the new classification will be reviewed. PMID:25349704

Gardiner, Natasha; Jogai, Sanjay

2014-01-01

267

Intraregional classification of wine via ICP-MS elemental fingerprinting.  

PubMed

The feasibility of elemental fingerprinting in the classification of wines according to their provenance vineyard soil was investigated in the relatively small geographical area of a single wine district. Results for the Stellenbosch wine district (Western Cape Wine Region, South Africa), comprising an area of less than 1,000 km(2), suggest that classification of wines from different estates (120 wines from 23 estates) is indeed possible using accurate elemental data and multivariate statistical analysis based on a combination of principal component analysis, cluster analysis, and discriminant analysis. This is the first study to demonstrate the successful classification of wines at estate level in a single wine district in South Africa. The elements B, Ba, Cs, Cu, Mg, Rb, Sr, Tl and Zn were identified as suitable indicators. White and red wines were grouped in separate data sets to allow successful classification of wines. Correlation between wine classification and soil type distributions in the area was observed. PMID:24996361

Coetzee, P P; van Jaarsveld, F P; Vanhaecke, F

2014-12-01

268

Accurate models for EUV lithography  

NASA Astrophysics Data System (ADS)

Accurate modeling of EUV Lithography is a mandatory step in driving the technology towards its foreseen insertion point for 22-16nm node patterning. The models are needed to correct EUV designs for imaging effects, and to understand and improve the CD fingerprint of the exposure tools. With a full-field EUV ADT from ASML now available in the IMEC cleanroom, wafer data can be collected to calibrate accurate models and check if the existing modeling infrastructure can be extended to EUV lithography. As a first topic, we have measured the CD on wafer of a typical OPC dataset at different flare levels and modeled the evolution of wafer CD through flare, reticle CD, and pitch using Brion's Tachyon OPC engine. The modeling first requires the generation of a flare map using long-range kernels to model the EUV specific long-range flare. The accuracy of the flare map can be established independently from the CD measurements, by using the traditional disappearing pad test for flare determination (Kirk test). The flare map is then used as background intensity in the calibration of the traditional optical models with short-range kernels. For a structure set of 600 features and over a flare range of 4-6%, an rms fit value of 0.9nm was obtained. As a second aspect of the modeling, we have calibrated a full resist model to process window data. The full resist model is then used in a combination with experimental measurements of reticle CD, slit intensity uniformity, focal plane behavior, and EUV thick mask effects to model the evolution of wafer CD across the exposure field. The modeled evolution of CD across the exposure field was found to be a good match to the experimentally seen evolution of CD across the field, and confirms that the 4 factors mentioned above are main contributions to the CD uniformity across the field. As such the modeling work enables a better understanding of the errors contributing to CD variation across the field for EUV technology.

Hendrickx, Eric; Lorusso, Gian F.; Jiang, Jiong; Chen, Luoqi; Liu, Wei; Van Setten, Eelco; Hansen, Steve

2009-10-01

269

Photometric Classification of Supernovae  

NASA Astrophysics Data System (ADS)

Photometric classification of supernova cosmology samples currently depends on a limited number of core-collapse templates for both the classification and production of simulated test samples. We present the results of systematic template variations for both classification and simulation, using the sncosmo package to classify core-collapse supernovae simulated with the SNANA package. Our goal is to understand better the template uncertainties in future photometrically-classified supernova cosmology samples.

Zimmerman, Daniel; Cunningham, John; Kuhlmann, Steve; Gupta, Ravi; Kovacs, Eve; Spinka, Harold

2015-01-01

270

Biomarker Selection and Classification of “-Omics” Data Using a Two-Step Bayes Classification Framework  

PubMed Central

Identification of suitable biomarkers for accurate prediction of phenotypic outcomes is a goal for personalized medicine. However, current machine learning approaches are either too complex or perform poorly. Here, a novel two-step machine-learning framework is presented to address this need. First, a Naïve Bayes estimator is used to rank features from which the top-ranked will most likely contain the most informative features for prediction of the underlying biological classes. The top-ranked features are then used in a Hidden Naïve Bayes classifier to construct a classification prediction model from these filtered attributes. In order to obtain the minimum set of the most informative biomarkers, the bottom-ranked features are successively removed from the Naïve Bayes-filtered feature list one at a time, and the classification accuracy of the Hidden Naïve Bayes classifier is checked for each pruned feature set. The performance of the proposed two-step Bayes classification framework was tested on different types of -omics datasets including gene expression microarray, single nucleotide polymorphism microarray (SNParray), and surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) proteomic data. The proposed two-step Bayes classification framework was equal to and, in some cases, outperformed other classification methods in terms of prediction accuracy, minimum number of classification markers, and computational time. PMID:24106694

Assawamakin, Anunchai; Prueksaaroon, Supakit; Kulawonganunchai, Supasak; Shaw, Philip James; Varavithya, Vara; Ruangrajitpakorn, Taneth; Tongsima, Sissades

2013-01-01

271

New insights into myosin evolution and classification  

PubMed Central

Myosins are eukaryotic actin-dependent molecular motors important for a broad range of functions like muscle contraction, vision, hearing, cell motility, and host cell invasion of apicomplexan parasites. Myosin heavy chains consist of distinct head, neck, and tail domains and have previously been categorized into 18 different classes based on phylogenetic analysis of their conserved heads. Here we describe a comprehensive phylogenetic examination of many previously unclassified myosins, with particular emphasis on sequences from apicomplexan and other chromalveolate protists including the model organism Toxoplasma, the malaria parasite Plasmodium, and the ciliate Tetrahymena. Using different phylogenetic inference methods and taking protein domain architectures, specific amino acid polymorphisms, and organismal distribution into account, we demonstrate a hitherto unrecognized common origin for ciliate and apicomplexan class XIV myosins. Our data also suggest common origins for some apicomplexan myosins and class VI, for classes II and XVIII, for classes XII and XV, and for some microsporidian myosins and class V, thereby reconciling evolutionary history and myosin structure in several cases and corroborating the common coevolution of myosin head, neck, and tail domains. Six novel myosin classes are established to accommodate sequences from chordate metazoans (class XIX), insects (class XX), kinetoplastids (class XXI), and apicomplexans and diatom algae (classes XXII, XXIII, and XXIV). These myosin (sub)classes include sequences with protein domains (FYVE, WW, UBA, ATS1-like, and WD40) previously unknown to be associated with myosin motors. Regarding the apicomplexan “myosome,” we significantly update class XIV classification, propose a systematic naming convention, and discuss possible functions in these parasites. PMID:16505385

Foth, Bernardo J.; Goedecke, Marc C.; Soldati, Dominique

2006-01-01

272

38 CFR 4.46 - Accurate measurement.  

Code of Federal Regulations, 2010 CFR

...46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect to landmarks, should be insisted on. The use of a goniometer in the measurement of limitation of motion...

2010-07-01

273

Modularized evolution in archaeal methanogens phylogenetic forest.  

PubMed

Methanogens are methane-producing archaea that plays a key role in the global carbon cycle. To date, the evolutionary history of methanogens and closely related nonmethanogen species remains unresolved among studies conducted upon different genetic markers, attributing to horizontal gene transfers (HGTs). With an effort to decipher both congruent and conflicting evolutionary events, reconstruction of coevolved gene clusters and hierarchical structure in the archaeal methanogen phylogenetic forest, comprehensive evolution, and network analyses were performed upon 3,694 gene families from 41 methanogens and 33 closely related archaea. Our results show that 1) greater than 50% of genes are in topological dissonance with others; 2) the prevalent interorder HGTs, even for core genes, in methanogen genomes led to their scrambled phylogenetic relationships; 3) most methanogenesis-related genes have experienced at least one HGT; 4) greater than 20% of the genes in methanogen genomes were transferred horizontally from other archaea, with genes involved in cell-wall synthesis and defense system having been transferred most frequently; 5) the coevolution network contains seven statistically robust modules, wherein the central module has the highest average node strength and comprises a majority of the core genes; 6) different coevolutionary module genes boomed in different time and evolutionary lineage, constructing diversified pan-genome structures; 7) the modularized evolution is also closely related to the vertical evolution signals and the HGT rate of the genes. Overall, this study presented a modularized phylogenetic forest that describes a combination of complicated vertical and nonvertical evolutionary processes for methanogenic archaeal species. PMID:25502908

Li, Jun; Wong, Chi-Fat; Wong, Mabel Ting; Huang, He; Leung, Frederick C

2014-01-01

274

Phylogenetic Interrelationships of Ginglymodian Fishes (Actinopterygii: Neopterygii)  

PubMed Central

The Ginglymodi is one of the most common, though poorly understood groups of neopterygians, which includes gars, macrosemiiforms, and “semionotiforms.” In particular, the phylogenetic relationships between the widely distributed “semionotiforms,” and between them and other ginglymodians have been enigmatic. Here, the phylogenetic relationships between eight of the 11 “semionotiform” genera, five genera of living and fossil gars and three macrosemiid genera, are analysed through cladistic analysis, based on 90 morphological characters and 37 taxa, including 7 out-group taxa. The results of the analysis show that the Ginglymodi includes two main lineages: Lepisosteiformes and †Semionotiformes. The genera †Pliodetes, †Araripelepidotes, †Lepidotes, †Scheenstia, and †Isanichthys are lepisosteiforms, and not semionotiforms, as previously thought, and these taxa extend the stratigraphic range of the lineage leading to gars back up to the Early Jurassic. A monophyletic †Lepidotes is restricted to the Early Jurassic species, whereas the strongly tritoral species previously referred to †Lepidotes are referred to †Scheenstia. Other species previously referred to †Lepidotes represent other genera or new taxa. The macrosemiids are well nested within semionotiforms, together with †Semionotidae, here restricted to †Semionotus, and a new family including †Callipurbeckia n. gen. minor (previously referred to †Lepidotes), †Macrosemimimus, †Tlayuamichin, †Paralepidotus, and †Semiolepis. Due to the numerous taxonomic changes needed according to the phylogenetic analysis, this article also includes formal taxonomic definitions and diagnoses for all generic and higher taxa, which are new or modified. The study of Mesozoic ginglymodians led to confirm Patterson’s observation that these fishes show morphological affinities with both halecomorphs and teleosts. Therefore, the compilation of large data sets including the Mesozoic ginglymodians and the re-evaluation of several hypotheses of homology are essential to test the hypotheses of the Halecostomi vs. the Holostei, which is one of the major topics in the evolution of Mesozoic vertebrates and the origin of modern fish faunas. PMID:22808031

López-Arbarello, Adriana

2012-01-01

275

[Phylogenetic relationships of Amur sturgeon Acipenser schrenckii Brandt, 1869 based on 18S rDNA sequensing data].  

PubMed

The analysis of phylogenetic relationships based on 18S rDNA sequences of Amur sturgeon Acipenser schrenckii Brandt, 1869 with other acipenseriform species was performed in this study. Complete sequences (1746 b. p.) in seven individual clones of A. schrenckii 18S rRNA were determined. Mutation profile of Amur sturgeon 18S rDNA demonstrated high similarity with that of Lake Sturgeon A. fulvescens. Both presumably functional sequence and the specific mutation (insertion of adenine after position 658) of Amur sturgeon 18S rDNA were identified by structural-functional analyses. Phylogenetic reconstructions performed using different methods (NJ, MP, ML and Bayesian) support monophyly of the genus Acipenser and point to: 1) closer relationships Amur sturgeon with sterlet, than Baltic sturgeon, which is in agreement with Artyukhin's eco-morphological classification (Artyukhin, 1995, 2006); 2) sufficiently high differentiation between North-American (A. fulvescens) and Eurasian (A. schrenckii, A. ruthenus and A. sturio) sturgeons. PMID:19435281

Rozhkovan, K V; Chelomina, G N; Ivanov, S A

2009-01-01

276

Ultrametric networks: a new tool for phylogenetic analysis  

PubMed Central

Background The large majority of optimization problems related to the inference of distance?based trees used in phylogenetic analysis and classification is known to be intractable. One noted exception is found within the realm of ultrametric distances. The introduction of ultrametric trees in phylogeny was inspired by a model of evolution driven by the postulate of a molecular clock, now dismissed, whereby phylogeny could be represented by a weighted tree in which the sum of the weights of the edges separating any given leaf from the root is the same for all leaves. Both, molecular clocks and rooted ultrametric trees, fell out of fashion as credible representations of evolutionary change. At the same time, ultrametric dendrograms have shown good potential for purposes of classification in so far as they have proven to provide good approximations for additive trees. Most of these approximations are still intractable, but the problem of finding the nearest ultrametric distance matrix to a given distance matrix with respect to the L? distance has been long known to be solvable in polynomial time, the solution being incarnated in any minimum spanning tree for the weighted graph subtending to the matrix. Results This paper expands this subdominant ultrametric perspective by studying ultrametric networks, consisting of the collection of all edges involved in some minimum spanning tree. It is shown that, for a graph with n vertices, the construction of such a network can be carried out by a simple algorithm in optimal time O(n2) which is faster by a factor of n than the direct adaptation of the classical O(n3) paradigm by Warshall for computing the transitive closure of a graph. This algorithm, called UltraNet, will be shown to be easily adapted to compute relaxed networks and to support the introduction of artificial points to reduce the maximum distance between vertices in a pair. Finally, a few experiments will be discussed to demonstrate the applicability of subdominant ultrametric networks. Availability http://www.dei.unipd.it/~ciompin/main/Ultranet/Ultranet.html PMID:23497437

2013-01-01

277

Novel multi-sample scheme for inferring phylogenetic markers from whole genome tumor profiles  

PubMed Central

Computational cancer phylogenetics seeks to enumerate the temporal sequences of aberrations in tumor evolution, thereby delineating the evolution of possible tumor progression pathways, molecular subtypes and mechanisms of action. We previously developed a pipeline for constructing phylogenies describing evolution between major recurring cell types computationally inferred from whole-genome tumor profiles. The accuracy and detail of the phylogenies, however, depends on the identification of accurate, high-resolution molecular markers of progression, i.e., reproducible regions of aberration that robustly differentiate different subtypes and stages of progression. Here we present a novel hidden Markov model (HMM) scheme for the problem of inferring such phylogenetically significant markers through joint segmentation and calling of multi-sample tumor data. Our method classifies sets of genome-wide DNA copy number measurements into a partitioning of samples into normal (diploid) or amplified at each probe. It differs from other similar HMM methods in its design specifically for the needs of tumor phylogenetics, by seeking to identify robust markers of progression conserved across a set of copy number profiles. We show an analysis of our method in comparison to other methods on both synthetic and real tumor data, which confirms its effectiveness for tumor phylogeny inference and suggests avenues for future advances. PMID:24407301

Subramanian, Ayshwarya; Shackney, Stanley; Schwartz, Russell

2013-01-01

278

Best Practices for Data Sharing in Phylogenetic Research  

PubMed Central

As phylogenetic data becomes increasingly available, along with associated data on species’ genomes, traits, and geographic distributions, the need to ensure data availability and reuse become more and more acute. In this paper, we provide ten “simple rules” that we view as best practices for data sharing in phylogenetic research. These rules will help lead towards a future phylogenetics where data can easily be archived, shared, reused, and repurposed across a wide variety of projects. PMID:24987572

Cranston, Karen; Harmon, Luke J.; O'Leary, Maureen A.; Lisle, Curtis

2014-01-01

279

Phylogenetic tree construction based on 2D graphical representation  

NASA Astrophysics Data System (ADS)

A new approach based on the two-dimensional (2D) graphical representation of the whole genome sequence [Bo Liao, Chem. Phys. Lett., 401(2005) 196.] is proposed to analyze the phylogenetic relationships of genomes. The evolutionary distances are obtained through measuring the differences among the 2D curves. The fuzzy theory is used to construct phylogenetic tree. The phylogenetic relationships of H5N1 avian influenza virus illustrate the utility of our approach.

Liao, Bo; Shan, Xinzhou; Zhu, Wen; Li, Renfa

2006-04-01

280

CTEP Simplified Disease Classification Overview  

Cancer.gov

CTEP Simplified Disease Classification Overview The CTEP Simplified Disease Classification (CTEP SDC) v1.0 is a restructured, more intuitive classification of diseases, designed to meet the needs of CTEP while still allowing reporting based on the

281

Engineering rock mass classifications  

Microsoft Academic Search

This book is a reference on rock mass classification, consolidating into one handy source information widely scattered through the literature. Includes new, unpublished material and case histories. Presents the fundamental concepts of classification schemes and critically appraises their practical application in industrial projects such as tunneling and mining.

Z. T. Bieniawski

1989-01-01

282

Robotic Rock Classification and  

E-print Network

Robotic Rock Classification and Autonomous Exploration Liam Pedersen #12;Acknowledgements for me to spend three summers at NASA's Ames Research Center working with him on rock classification to himself, a marvelous spectrometer with which to study rocks in Antarctica. Dr. Bill Cassidy's unstinting

Shamos, Michael I.

283

Security classification of information  

Microsoft Academic Search

This document is the second of a planned four-volume work that comprehensively discusses the security classification of information. The main focus of Volume 2 is on the principles for classification of information. Included herein are descriptions of the two major types of information that governments classify for national security reasons (subjective and objective information), guidance to use when determining whether

Quist

1993-01-01

284

Classification Oliver Gray  

E-print Network

Classification of N = 2 minimal models Oliver Gray What is a CFT? Classifying modular invariant of the N = 2 Virasoro unitary minimal models Oliver Gray Universit¨at Augsburg 17th December 2008 First Cuban Congress #12;Classification of N = 2 minimal models Oliver Gray What is a CFT? Classifying modular

Gasparim, Elizabeth

285

Library Classification 2020  

ERIC Educational Resources Information Center

In this article the author explores how a new library classification system might be designed using some aspects of the Dewey Decimal Classification (DDC) and ideas from other systems to create something that works for school libraries in the year 2020. By examining what works well with the Dewey Decimal System, what features should be carried…

Harris, Christopher

2013-01-01

286

Classification of Hypersensitivity Pneumonitis  

Microsoft Academic Search

Background: Regardless of the causative antigen, hypersensitivity pneumonitis (HP) is usually classified as ‘acute’, ‘subacute’ or ‘chronic’. Considerable confusion still surrounds this classification because there are no widely accepted criteria to distinguish the various stages. The objective of this study wasto determine whether the current classification of HP truly reflects categories of patients with distinct clinical features. Methods: Data obtained

Yves Lacasse; Moises Selman; Ulrich Costabel; Jean-Charles Dalphin; Ferran Morell; Riitta Erkinjuntti-Pekkanen; Nestor L. Mueller; Thomas V. Colby; Mark Schuyler; Valérie Jomphe; Yvon Cormier

2009-01-01

287

PHYLOGENY AND CLASSIFICATION OF FINLAYA AND ALLIED TAXA (DIPTERA: CULICIDAE: AEDINI) BASED ON MORPHOLOGICAL DATA FROM ALL LIFE STAGES  

Technology Transfer Automated Retrieval System (TEKTRAN)

The phylogenetic relationships and generic assignments of ‘Finlaya’ and related taxa of uncertain taxonomic position in the classification of Aedini proposed by Reinert et al. (2004) are explored using 232 characters from eggs, fourth-instar larvae, pupae, adults and immature habitat coded for 116 e...

288

Phylogenetic relationships among Opisthobranchia (Mollusca: Gastropoda) based on mitochondrial  

E-print Network

Phylogenetic relationships among Opisthobranchia (Mollusca: Gastropoda) based on mitochondrial cox relationships among 37 species representing seven main lineages within Opisthobranchia (Mollusca: Gastropoda

Zardoya, Rafael

289

Phylogenetic relationships of Mesoamerican spider monkeys (Ateles geoffroyi): Molecular evidence suggests the need for a revised taxonomy.  

PubMed

Mesoamerican spider monkeys (Ateles geoffroyi sensu lato) are widely distributed from Mexico to northern Colombia. This group of primates includes many allopatric forms with morphologically distinct pelage color and patterning, but its taxonomy and phylogenetic history are poorly understood. We explored the genetic relationships among the different forms of Mesoamerican spider monkeys using mtDNA sequence data, and we offer a new hypothesis for the evolutionary history of the group. We collected up to ?800bp of DNA sequence data from hypervariable region 1 (HV1) of the control region, or D-loop, of the mitochondrion for multiple putative subspecies of Ateles geoffroyi sensu lato. Both maximum likelihood and Bayesian reconstructions, using Ateles paniscus as an outgroup, showed that (1) A. fusciceps and A. geoffroyi form two different monophyletic groups and (2) currently recognized subspecies of A. geoffroyi are not monophyletic. Within A. geoffroyi, our phylogenetic analysis revealed little concordance between any of the classifications proposed for this taxon and their phylogenetic relationships, therefore a new classification is needed for this group. Several possible clades with recent divergence times (1.7-0.8Ma) were identified within Ateles geoffroyi sensu lato. Some previously recognized taxa were not separated by our data (e.g., A. g. vellerosus and A. g. yucatanensis), while one distinct clade had never been described as a different evolutionary unit based on pelage or geography (Ateles geoffroyi ssp. indet. from El Salvador). Based on well-supported phylogenetic relationships, our results challenge previous taxonomic arrangements for Mesoamerican spider monkeys. We suggest a revised arrangement based on our data and call for a thorough taxonomic revision of this group. PMID:25451800

Morales-Jimenez, Alba Lucia; Cortés-Ortiz, Liliana; Di Fiore, Anthony

2015-01-01

290

Classification of Access Network Types: Ethernet, Wireless LAN, ADSL, Cable Modem or Dialup?  

E-print Network

Classification of Access Network Types: Ethernet, Wireless LAN, ADSL, Cable Modem or Dialup? Wei of Massachusetts, Amherst, MA 01003 Abstract--Ethernet, wireless LAN, ADSL, cable modem and di- alup are common access networks, but have dramatically differ- ent characteristics. Fast and accurate classification

Massachusetts at Amherst, University of

291

Multiclass Cancer Classification Using Semisupervised Ellipsoid ARTMAP and Particle Swarm Optimization with Gene Expression Data  

Microsoft Academic Search

It is crucial for cancer diagnosis and treatment to accurately identify the site of origin of a tumor. With the emergence and rapid advancement of DNA microarray technologies, constructing gene expression profiles for different cancer types has already become a promising means for cancer classification. In addition to research on binary classification such as normal versus tumor samples, which attracts

Rui Xu; Georgios C. Anagnostopoulos; Donald C. Wunsch

2007-01-01

292

Comparison of feature selection and classification for MALDI-MS data  

Microsoft Academic Search

INTRODUCTION: In the classification of Mass Spectrometry (MS) proteomics data, peak detection, feature selection, and learning classifiers are critical to classification accuracy. To better understand which methods are more accurate when classifying data, some publicly available peak detection algorithms for Matrix assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) data were recently compared; however, the issue of different feature selection methods

Qingzhong Liu; Andrew H Sung; Mengyu Qiao; Zhongxue Chen; Jack Y Yang; Mary Qu Yang; Xudong Huang; Youping Deng

2009-01-01

293

A Comparative Study of Feature Selection Methods for Probabilistic Neural Networks in Cancer Classification  

Microsoft Academic Search

Accurate diagnosis and classification is the key issue for the optimal treatment of cancer patients. Several studies demonstrate that cancer classification can be estimated with high accuracy, sensitivity and specificity from microarray-based gene expression profiling using artificial neural networks. In this paper, a comprehensive study was undertaken to investigate the capability of the probabilistic neural networks (PNN) associated with a

Chenn-jung Huang; Wei-chen Liao

2003-01-01

294

Land cover classification in the Argentine Pampas using multi-temporal Landsat TM data  

Microsoft Academic Search

The objective of this study was to explore the use of multi-temporal Landsat TM data from the same growing season for the classification of land cover types in the south-western portion of the Argentine Pampas. Investigations were made on how many dates are necessary to obtain an accurate classification and, given a fixed number of dates, which is the particular

J. P. Guerschman; J. M. Paruelo; C. Di Bella; M. C. Giallorenzi; F. Pacin

2003-01-01

295

Horny sponges and their affairs: on the phylogenetic relationships of keratose sponges.  

PubMed

The demosponge orders Dictyoceratida and Dendroceratida are historically assigned to the keratose (or "horny") sponges, which are mostly devoid of primary skeletal elements, but possess an elaborate skeleton of organic fibres instead. This paucity of complex mineral skeletal elements makes their unambiguous classification and phylogenetic reconstruction based on morphological features difficult. Here we present the most comprehensive molecular phylogeny to date for the Dendroceratida, Dictyoceratida, and also other sponge orders that largely lack a mineral skeleton or skeletal elements at all (i.e. Verongida, Halisarcida, Chondrosida), based on independent mitochondrial and nuclear markers. We used molecular data to validate the coherence of all recognised orders, families and subfamilies that are currently defined using morphological characteristics. We discussed the significance of morphological and chemotaxonomic characters for keratose sponges, and suggested adapted definitions for the classification of dendroceratid, dictyoceratid, and verongid higher taxa. Also, we found that chondrosid sponges are non-monophyletic with respect to Halisarcida. Verongida and Dendroceratida were monophyletic, however most of their classically recognised families were not recovered. This indicated that the current distinction between dendritic and mesh-like fibre skeletons is not significant at this level of classification. Dysideidae were found to be the sister-group to the remaining Dictyoceratida. Irciniidae formed a distinct clade, however Thorectidae and Spongiidae could not be separated with the molecular markers used. Finally, we are establishing the name Verongimorpha for the clade combining verongid, chondrosid and halisarcid taxa and readjust the content of its sister-clade Keratosa. PMID:22406528

Erpenbeck, Dirk; Sutcliffe, Patricia; Cook, Steve de C; Dietzel, Andreas; Maldonado, Manuel; van Soest, Rob W M; Hooper, John N A; Wörheide, Gert

2012-06-01

296

Improving the analysis of phylogenetic data.  

PubMed

Methods of phylogenetic analysis are presented that result in corrections of highly biased data sets, particularly those in which there are great differences between mutation and/or substitution rates from one nucleotide site to another along a DNA sequence. Two approaches are discussed. In the first, pairwise comparisons of a set of sequences are used to determine whether the most recent substitutions take place at the sites that are most polymorphic--that is, where the mutational "hot spots" are located. In the second, a "topiary pruning" method is used to remove selectively the bases in the data set that are most likely to occupy these hot spots and therefore to result in homoplastic substitutions. The two methods combined yield new and substantially older estimates of the time at which the mitochondrial Eve lived, and increase the likelihood that she lived in Africa. In these data, transversions provide a more satisfactory yardstick for phylogenetic analysis than transitions, because there is no detectable tendency for transversions to occur at mutational hot spots. PMID:8867842

Wills, C

1996-03-01

297

Posterior predictive Bayesian phylogenetic model selection.  

PubMed

We present two distinctly different posterior predictive approaches to Bayesian phylogenetic model selection and illustrate these methods using examples from green algal protein-coding cpDNA sequences and flowering plant rDNA sequences. The Gelfand-Ghosh (GG) approach allows dissection of an overall measure of model fit into components due to posterior predictive variance (GGp) and goodness-of-fit (GGg), which distinguishes this method from the posterior predictive P-value approach. The conditional predictive ordinate (CPO) method provides a site-specific measure of model fit useful for exploratory analyses and can be combined over sites yielding the log pseudomarginal likelihood (LPML) which is useful as an overall measure of model fit. CPO provides a useful cross-validation approach that is computationally efficient, requiring only a sample from the posterior distribution (no additional simulation is required). Both GG and CPO add new perspectives to Bayesian phylogenetic model selection based on the predictive abilities of models and complement the perspective provided by the marginal likelihood (including Bayes Factor comparisons) based solely on the fit of competing models to observed data. PMID:24193892

Lewis, Paul O; Xie, Wangang; Chen, Ming-Hui; Fan, Yu; Kuo, Lynn

2014-05-01

298

Phylogenetically-Informed Priorities for Amphibian Conservation  

PubMed Central

The amphibian decline and extinction crisis demands urgent action to prevent further large numbers of species extinctions. Lists of priority species for conservation, based on a combination of species’ threat status and unique contribution to phylogenetic diversity, are one tool for the direction and catalyzation of conservation action. We describe the construction of a near-complete species-level phylogeny of 5713 amphibian species, which we use to create a list of evolutionarily distinct and globally endangered species (EDGE list) for the entire class Amphibia. We present sensitivity analyses to test the robustness of our priority list to uncertainty in species’ phylogenetic position and threat status. We find that both sources of uncertainty have only minor impacts on our ‘top 100‘ list of priority species, indicating the robustness of the approach. By contrast, our analyses suggest that a large number of Data Deficient species are likely to be high priorities for conservation action from the perspective of their contribution to the evolutionary history. PMID:22952807

Isaac, Nick J. B.; Redding, David W.; Meredith, Helen M.; Safi, Kamran

2012-01-01

299

Phylogenetic diversity of Mesorhizobium in chickpea.  

PubMed

Crop domestication, in general, has reduced genetic diversity in cultivated gene pool of chickpea (Cicer arietinum) as compared with wild species (C. reticulatum, C. bijugum). To explore impact of domestication on symbiosis, 10 accessions of chickpeas, including 4 accessions of C. arietinum, and 3 accessions of each of C. reticulatum and C. bijugum species, were selected and DNAs were extracted from their nodules. To distinguish chickpea symbiont, preliminary sequences analysis was attempted with 9 genes (16S rRNA, atpD, dnaJ, glnA, gyrB, nifH, nifK, nodD and recA) of which 3 genes (gyrB, nifK and nodD) were selected based on sufficient sequence diversity for further phylogenetic analysis. Phylogenetic analysis and sequence diversity for 3 genes demonstrated that sequences from C. reticulatum were more diverse. Nodule occupancy by dominant symbiont also indicated that C. reticulatum (60 percent) could have more various symbionts than cultivated chickpea (80 percent). The study demonstrated that wild chickpeas (C. reticulatum) could be used for selecting more diverse symbionts in the field conditions and it implies that chickpea domestication affected symbiosis negatively in addition to reducing genetic diversity. PMID:24845514

Kim, Dong Hyun; Kaashyap, Mayank; Rathore, Abhishek; Das, Roma R; Parupalli, Swathi; Upadhyaya, Hari D; Gopalakrishnan, S; Gaur, Pooran M; Singh, Sarvjeet; Kaur, Jagmeet; Yasin, Mohammad; Varshney, Rajeev K

2014-06-01

300

Face shape differs in phylogenetically related populations.  

PubMed

3D analysis of facial morphology has delineated facial phenotypes in many medical conditions and detected fine grained differences between typical and atypical patients to inform genotype-phenotype studies. Next-generation sequencing techniques have enabled extremely detailed genotype-phenotype correlative analysis. Such comparisons typically employ control groups matched for age, sex and ethnicity and the distinction between ethnic categories in genotype-phenotype studies has been widely debated. The phylogenetic tree based on genetic polymorphism studies divides the world population into nine subpopulations. Here we show statistically significant face shape differences between two European Caucasian populations of close phylogenetic and geographic proximity from the UK and The Netherlands. The average face shape differences between the Dutch and UK cohorts were visualised in dynamic morphs and signature heat maps, and quantified for their statistical significance using both conventional anthropometry and state of the art dense surface modelling techniques. Our results demonstrate significant differences between Dutch and UK face shape. Other studies have shown that genetic variants influence normal facial variation. Thus, face shape difference between populations could reflect underlying genetic difference. This should be taken into account in genotype-phenotype studies and we recommend that in those studies reference groups be established in the same population as the individuals who form the subject of the study. PMID:24398794

Hopman, Saskia M J; Merks, Johannes H M; Suttie, Michael; Hennekam, Raoul C M; Hammond, Peter

2014-11-01

301

A phylogenetic analysis of the phylum Fibrobacteres.  

PubMed

Members of the phylum Fibrobacteres are highly efficient cellulolytic bacteria, best known for their role in rumen function and as potential sources of novel enzymes for bioenergy applications. Despite being key members of ruminants and other digestive microbial communities, our knowledge of this phylum remains incomplete, as much of our understanding is focused on two recognized species, Fibrobacter succinogenes and F. intestinalis. As a result, we lack insights regarding the environmental niche, host range, and phylogenetic organization of this phylum. Here, we analyzed over 1000 16S rRNA Fibrobacteres sequences available from public databases to establish a phylogenetic framework for this phylum. We identify both species- and genus-level clades that are suggestive of previously unknown taxonomic relationships between Fibrobacteres in addition to their putative lifestyles as host-associated or free-living. Our results shed light on this poorly understood phylum and will be useful for elucidating the function, distribution, and diversity of these bacteria in their niches. PMID:23759599

Jewell, Kelsea A; Scott, Jarrod J; Adams, Sandra M; Suen, Garret

2013-09-01

302

Social engagement and attachment: a phylogenetic perspective.  

PubMed

This article focuses on the importance of social engagement and the behavioral and neurophysiological mechanisms that allow individuals to reduce psychological and physical distance. A model of social engagement derived from the Polyvagal Theory is presented. The model emphasizes phylogeny as an organizing principle and includes the following points: (1) there are well-defined neural circuits to support social engagement behaviors and the defensive strategies of fight, flight, and freeze; (2) these neural circuits form a phylogenetically organized hierarchy; (3) without being dependent on conscious awareness, the nervous system evaluates risk in the environment and regulates the expression of adaptive behavior to match the neuroception of a safe, dangerous, or life-threatening environment; (4) social engagement behaviors and the benefits of the physiological states associated with social support require a neuroception of safety; (5) social behaviors associated with nursing, reproduction, and the formation of strong pair bonds require immobilization without fear; and (6) immobilization without fear is mediated by a co-opting of the neural circuit regulating defensive freezing behaviors through the involvement of oxytocin, a neuropeptide in mammals involved in the formation of social bonds. The model provides a phylogenetic interpretation of the neural mechanisms mediating the behavioral and physiological features associated with stress and several psychiatric disorders. PMID:14998870

Porges, Stephen W

2003-12-01

303

Locating evolutionary precursors on a phylogenetic tree.  

PubMed

Conspicuous innovations in the history of life are often preceded by more cryptic genetic and developmental precursors. In many cases, these appear to be associated with recurring origins of very similar traits in close relatives (parallelisms) or striking convergences separated by deep time (deep homologies). Although the phylogenetic distribution of gain and loss of traits hints strongly at the existence of such precursors, no models of trait evolution currently permit inference about their location on a tree. Here we develop a new stochastic model, which explicitly captures the dependency implied by a precursor and permits estimation of precursor locations. We apply it to the evolution of extrafloral nectaries (EFNs), an ecologically significant trait mediating a widespread mutualism between plants and ants. In legumes, a species-rich clade with morphologically diverse EFNs, the precursor model fits the data on EFN occurrences significantly better than conventional models. The model generates explicit hypotheses about the phylogenetic location of hypothetical precursors, which may help guide future studies of molecular genetic pathways underlying nectary position, development, and function. PMID:23206146

Marazzi, Brigitte; Ané, Cécile; Simon, Marcelo F; Delgado-Salinas, Alfonso; Luckow, Melissa; Sanderson, Michael J

2012-12-01

304

Francolin phylogenetics: molecular, morphobehavioral, and combined evidence.  

PubMed

The phylogenetics of francolins (Francolinus species) were reassessed by obtaining 660 bp of sequence of the mitochondrial DNA (mtDNA) cytochrome b gene from 20 species, the Common Quail Coturnix coturnix africana, and the Madagascar Partridge Margaroperdix madagarensis. Published sequences of the Japanese Quail C. c. japonica, Alectoris partridges, and the Junglefowl Gallus gallus were also included. Separate analysis of the 200 phylogenetically informative cytochrome b characters and the 25 informative morphobehavioral characters, as well as a combined analysis of molecular and morphobehavioral data, do not support francolin monophyly but provide strong evidence for two previously suggested clades--the quail-francolins (or partridges) and the partridge-francolins (pheasants/francolins). The quail-francolin clade comprises three groups of African francolins and three Asian species that were previously considered more closely related to the partridge-francolins. The partridge-francolin clade, which includes four groups of African francolins, forms a sister group to the Coturnix quails, the Madagascar Partridge, and the Alectoris partridges. The molecular data suggest that the two francolin clades diverged approximately 3-6 MYA. Climatic fluctuations of the past 2.5 MYA may have led to the diversification of the ecologically different francolin species groups and speciation within them. PMID:9562983

Bloomer, P; Crowe, T M

1998-04-01

305

PhyloFinder: An intelligent search engine for phylogenetic tree databases  

Microsoft Academic Search

BACKGROUND: Bioinformatic tools are needed to store and access the rapidly growing phylogenetic data. These tools should enable users to identify existing phylogenetic trees containing a specified taxon or set of taxa and to compare a specified phylogenetic hypothesis to existing phylogenetic trees. RESULTS: PhyloFinder is an intelligent search engine for phylogenetic databases that we have implemented using trees from

Duhong Chen; J Gordon Burleigh; Mukul S Bansal; David Fernández-Baca

2008-01-01

306

Progressive Classification Using Support Vector Machines  

NASA Technical Reports Server (NTRS)

An algorithm for progressive classification of data, analogous to progressive rendering of images, makes it possible to compromise between speed and accuracy. This algorithm uses support vector machines (SVMs) to classify data. An SVM is a machine learning algorithm that builds a mathematical model of the desired classification concept by identifying the critical data points, called support vectors. Coarse approximations to the concept require only a few support vectors, while precise, highly accurate models require far more support vectors. Once the model has been constructed, the SVM can be applied to new observations. The cost of classifying a new observation is proportional to the number of support vectors in the model. When computational resources are limited, an SVM of the appropriate complexity can be produced. However, if the constraints are not known when the model is constructed, or if they can change over time, a method for adaptively responding to the current resource constraints is required. This capability is particularly relevant for spacecraft (or any other real-time systems) that perform onboard data analysis. The new algorithm enables the fast, interactive application of an SVM classifier to a new set of data. The classification process achieved by this algorithm is characterized as progressive because a coarse approximation to the true classification is generated rapidly and thereafter iteratively refined. The algorithm uses two SVMs: (1) a fast, approximate one and (2) slow, highly accurate one. New data are initially classified by the fast SVM, producing a baseline approximate classification. For each classified data point, the algorithm calculates a confidence index that indicates the likelihood that it was classified correctly in the first pass. Next, the data points are sorted by their confidence indices and progressively reclassified by the slower, more accurate SVM, starting with the items most likely to be incorrectly classified. The user can halt this reclassification process at any point, thereby obtaining the best possible result for a given amount of computation time. Alternatively, the results can be displayed as they are generated, providing the user with real-time feedback about the current accuracy of classification.

Wagstaff, Kiri; Kocurek, Michael

2009-01-01

307

Conservation biology of Malagasy strepsirhines: a phylogenetic approach.  

PubMed

The phylogenetic diversity of extant lemurs represents one of the most important but least studied aspects of the conservation biology of primates. The phylogenetic diversity of a species is inversely proportional to the relative number and closeness of its phylogenetic relatives. Phylogenetic diversity can then be used to determine conservation priorities for specific biogeographic regions. Although Malagasy strepsirhines represent the highest phylogenetic diversity among primates at the global level, there are few phylogenetic data on species-specific and regional conservation plans for lemurs in Madagascar. Therefore, in this paper the following questions are addressed for extant lemurs: 1) how does the measure of taxonomic uniqueness used by Mittermeier et al. (1992 Lemurs of Madagascar; Gland, Switzerland: IUCN) equate with an index of phylogenetic diversity, 2) what are the regional conservation priorities based on analyses of phylogenetic diversity in extant lemurs, and 3) what conservation recommendations can be made based on analyses of phylogenetic diversity in lemurs? Taxonomic endemicity standardized weight (TESW) indices of phylogenetic diversity were used to determine the evolutionary component of biodiversity and to prioritize regions for conserving lemur taxa. TESW refers to the standardization of phylogenetic diversity indices for widespread taxa and endemicity of species. The phylogenetic data came from recent genetic studies of Malagasy strepsirhines at the species level. Lemur species were assigned as being either present or absent in six biogeographic regions. TESW indices were combined with data on lemur complementarity and protected areas to assign conservation priorities at the regional level. Although there were no overall differences between taxonomic ranks and phylogenetic rankings, there were significant differences for the top-ranked taxa. The phylogenetic component of lemur diversity is greatest for Daubentonia madagascariensis, Allocebus trichotis, Lepilemur septentrionalis, Indri indri, and Mirza coquereli. Regional conservation priorities are highest for lemurs that range into northeast humid forests and western dry forests. Expansion of existing protected areas in these regions may provide the most rapid method for preserving lemurs. In the long term, new protected areas must be created because there are lemur species that: 1) are not found in existing protected areas, 2) exist only in one or two protected areas, and 3) are still being discovered outside the current network of protected areas. Data on the population dynamics and feeding ecology of phylogenetically important species are needed to ensure that protected areas adequately conserve lemur populations in Madagascar. PMID:16365858

Lehman, Shawn M

2006-06-01

308

Overview of Hierarchical Models for Hyperspectral Image Classification Yuliya Tarabalka  

E-print Network

Overview of Hierarchical Models for Hyperspectral Image Classification Yuliya Tarabalka INRIA, AYIN team 06902 Sophia Antipolis, France yuliya.tarabalka@inria.fr Abstract Hyperspectral imaging enables the correlations between spa- tially adjacent pixels for accurate image analysis. This paper provides an overview

Boyer, Edmond

309

Reproducibility of single-beam acoustic seabed classification  

Microsoft Academic Search

Single-beam acoustic seabed classification continues to be a popular method for mapping seabeds and their sediments. Modern methods can generate maps of acoustic classes that are useful and reasonably accurate. Research toward improved methods continues. A continuing impediment to this research is ranking the accuracy of maps produced by new methods. Non-acoustic data, or ground truth, is usually sparse compared

Art Gleason; Jon Preston; Steve Bloomer

2009-01-01

310

A multilevel neural network model for density volumes classification  

Microsoft Academic Search

The accurate detection of tissue density variation in CT\\/MRI brain datasets can be useful for analysing and monitoring pathologies with slight differences. In fact, the objective knowledge of density distribution can be related to anatomical structures and therefore the process of monitoring illness and its treatment can be improved. In this paper, we present an approach for the classification of

Sergio Di Bona; Gabriele Pieri; Ovidio Salvetti

2001-01-01

311

Machine Learning Based Encrypted Traffic Classification: Identifying SSH and Skype  

E-print Network

be extremely accurate when the payload is not encrypted. However, encrypted applications such as SSH (Secure communication. Indeed, covering a collection of such dif- ferent encrypted behavior makes it difficultMachine Learning Based Encrypted Traffic Classification: Identifying SSH and Skype Riyad Alshammari

Zincir-Heywood, Nur

312

Solving Imbalanced Classification Problems with Support Vector Machines  

Microsoft Academic Search

The Support Vector Machine (SVM) is a pow- erful learning mechanism and promising results have been obtained in the field of medical diagnostics and text- categorization. However, successful applications to busi- ness oriented classification problems are still limited. Most real world data sets exhibit vast class imbalances and an accurate identification of the economical relevant minority class is a major

Stefan Lessmann

2004-01-01

313

A molecular phylogeny and classification of Bignoniaceae.  

PubMed

Bignoniaceae are woody, trees, shrubs, and lianas found in all tropical floras of the world with lesser representation in temperate regions. Phylogenetic analyses of chloroplast sequences (rbcL, ndhF, trnL-F) were undertaken to infer evolutionary relationships in Bignoniaceae and to revise its classification. Eight clades are recognized as tribes (Bignonieae, Catalpeae, Coleeae, Crescentieae, Jacarandeae, Oroxyleae, Tecomeae, Tourrettieae); additional inclusive clades are named informally. Jacarandeae and Catalpeae are resurrected; the former is sister to the rest of the family, and the latter occupies an unresolved position within the "core" Bignoniaceae. Tribe Eccremocarpeae is included in Tourrettieae. Past classifications recognized a large Tecomeae, but this tribe is paraphyletic with respect to all other tribes. Here Tecomeae are reduced to a clade of approximately 12 genera with a worldwide distribution in both temperate and tropical ecosystems. Two large clades, Bignonieae and Crescentiina, account for over 80% of the species in the family. Coleeae and Crescentieae are each included in larger clades, the Paleotropical alliance and Tabebuia alliance, respectively; each alliance includes a grade of taxa assigned to the traditional Tecomeae. Parsimony inference suggests that the family originated in the neotropics, with at least five dispersal events leading to the Old World representatives. PMID:21622359

Olmstead, Richard G; Zjhra, Michelle L; Lohmann, Lúcia G; Grose, Susan O; Eckert, Andrew J

2009-09-01

314

Estimating classification images with generalized linear and additive models  

PubMed Central

Conventional approaches to modeling classification image data can be described in terms of a standard linear model (LM). We show how the problem can be characterized as a Generalized Linear Model (GLM) with a Bernoulli distribution. We demonstrate via simulation that this approach is more accurate in estimating the underlying template in the absence of internal noise. With increasing internal noise, however, the advantage of the GLM over the LM decreases and GLM is no more accurate than LM. We then introduce the Generalized Additive Model (GAM), an extension of GLM that can be used to estimate smooth classification images adaptively. We show that this approach is more robust to the presence of internal noise and, finally, we demonstrate that GAM is readily adapted to estimation of higher-order (nonlinear) classification images and to testing their significance. PMID:19146276

Knoblauch, Kenneth; Maloney, Laurence T.

2008-01-01

315

Novel Accurate Bacterial Discrimination by MALDI-Time-of-Flight MS Based on Ribosomal Proteins Coding in S10-spc-alpha Operon at Strain Level S10-GERMS  

NASA Astrophysics Data System (ADS)

Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is one of the most widely used mass-based approaches for bacterial identification and classification because of the simple sample preparation and extremely rapid analysis within a few minutes. To establish the accurate MALDI-TOF MS bacterial discrimination method at strain level, the ribosomal subunit proteins coded in the S 10-spc-alpha operon, which encodes half of the ribosomal subunit protein and is highly conserved in eubacterial genomes, were selected as reliable biomarkers. This method, named the S10-GERMS method, revealed that the strains of genus Pseudomonas were successfully identified and discriminated at species and strain levels, respectively; therefore, the S10-GERMS method was further applied to discriminate the pathovar of P. syringae. The eight selected biomarkers (L24, L30, S10, S12, S14, S16, S17, and S19) suggested the rapid discrimination of P. syringae at the strain (pathovar) level. The S10-GERMS method appears to be a powerful tool for rapid and reliable bacterial discrimination and successful phylogenetic characterization. In this article, an overview of the utilization of results from the S10-GERMS method is presented, highlighting the characterization of the Lactobacillus casei group and discrimination of the bacteria of genera Bacillus and Sphingopyxis despite only two and one base difference in the 16S rRNA gene sequence, respectively.

Tamura, Hiroto; Hotta, Yudai; Sato, Hiroaki

2013-08-01

316

[Classification of glomerulopathies].  

PubMed

Glomerular diseases may be classified as acute or chronic, primary or secondary, hereditary or acquired, proliferative or non-proliferative etc. The most commonly used is the classification according to the histopathological finding. For certain types of glomerulonephritides histopathological image, as well as clinical presentation, may vary widely. A while ago there was no classification based on the pathogenesis of certain types of glomerular diseases. However, as scientists ellucidate the underlying pathogenetic mechanism, current classifications change. The latter is best shown at the example of membranoproliferative glomerulonephritis. PMID:25327007

Jelakovi?, Bojan; Cori?, Marijana; Kos, Jelena; Zivko, Marijana; Dika, Zivka; Laganovi?, Mario

2014-01-01

317

Mineral Classification Exercise  

NSDL National Science Digital Library

This exercise is designed to help students think about the properties of minerals that are most useful for mineral classification and identification. Students are given a set of minerals and asked to come up with a hierarchical classification scheme (a "key") that can be used to identify different mineral species. They compare their results with the products of other groups. They test the various schemes by applying them to unknown samples. While doing this exercise, the students develop observational and interpretational skill. They also begin to think about the nature of classification systems.

Perkins, Dexter

318

Phylogenetic identification of lateral genetic transfer events  

PubMed Central

Background Lateral genetic transfer can lead to disagreements among phylogenetic trees comprising sequences from the same set of taxa. Where topological discordance is thought to have arisen through genetic transfer events, tree comparisons can be used to identify the lineages that may have shared genetic information. An 'edit path' of one or more transfer events can be represented with a series of subtree prune and regraft (SPR) operations, but finding the optimal such set of operations is NP-hard for comparisons between rooted trees, and may be so for unrooted trees as well. Results Efficient Evaluation of Edit Paths (EEEP) is a new tree comparison algorithm that uses evolutionarily reasonable constraints to identify and eliminate many unproductive search avenues, reducing the time required to solve many edit path problems. The performance of EEEP compares favourably to that of other algorithms when applied to strictly bifurcating trees with specified numbers of SPR operations. We also used EEEP to recover edit paths from over 19 000 unrooted, incompletely resolved protein trees containing up to 144 taxa as part of a large phylogenomic study. While inferred protein trees were far more similar to a reference supertree than random trees were to each other, the phylogenetic distance spanned by random versus inferred transfer events was similar, suggesting that real transfer events occur most frequently between closely related organisms, but can span large phylogenetic distances as well. While most of the protein trees examined here were very similar to the reference supertree, requiring zero or one edit operations for reconciliation, some trees implied up to 40 transfer events within a single orthologous set of proteins. Conclusion Since sequence trees typically have no implied root and may contain unresolved or multifurcating nodes, the strategy implemented in EEEP is the most appropriate for phylogenomic analyses. The high degree of consistency among inferred protein trees shows that vertical inheritance is the dominant pattern of evolution, at least for the set of organisms considered here. However, the edit paths inferred using EEEP suggest an important role for genetic transfer in the evolution of microbial genomes as well. PMID:16472400

Beiko, Robert G; Hamilton, Nicholas

2006-01-01

319

Identifying optimal incomplete phylogenetic data sets from sequence databases  

E-print Network

Identifying optimal incomplete phylogenetic data sets from sequence databases Changhui Yan a,b , J a new method for identifying optimal incomplete data sets from large sequence databases based databases to identify useful phylogenetic data sets with a specified amount of missing data while

Sanderson, Mike

320

Constructing Evolutionary/Phylogenetic Trees 2 broad categories  

E-print Network

Constructing Evolutionary/Phylogenetic Trees · 2 broad categories: ­ Distance-based methods-Distance Trees Additive distance trees are edge-weighted trees, with distance between leaf nodes are exactly 114/4/06 #12;Constructing Evolutionary/Phylogenetic Trees · 2 broad categories: ­ Distance

Narasimhan, Giri

321

Constructing Evolutionary/Phylogenetic Trees 2 broad categories  

E-print Network

Constructing Evolutionary/Phylogenetic Trees · 2 broad categories: ­ Distance-based methods are edge-weighted trees, with distance between leaf nodes are exactly equal to length of path between nodes/Phylogenetic Trees · 2 broad categories: ­ Distance-based methods · Ultrametric · Additive: ­ UPGMA ­ Transformed

Narasimhan, Giri

322

Student Interpretations of Phylogenetic Trees in an Introductory Biology Course  

ERIC Educational Resources Information Center

Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa…

Dees, Jonathan; Momsen, Jennifer L.; Niemi, Jarad; Montplaisir, Lisa

2014-01-01

323

Using Decision Trees to Study the Convergence of Phylogenetic Analyses  

E-print Network

Using Decision Trees to Study the Convergence of Phylogenetic Analyses Grant Brammer and Tiffani L. Williams Abstract-- In this paper, we explore the novel use of deci- sion trees to study the convergence properties of phylogenetic analyses. A decision learning tree is constructed from the evolutionary

Williams, Tiffani

324

BLAST-EXPLORER helps you building datasets for phylogenetic analysis  

Microsoft Academic Search

BACKGROUND: The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database

Alexis Dereeper; Stephane Audic; Jean-Michel Claverie; Guillaume Blanc

2010-01-01

325

Nuclear mitochondrial DNA: an Achilles' heel of molecular systematics, phylogenetics,  

E-print Network

Nuclear mitochondrial DNA: an Achilles' heel of molecular systematics, phylogenetics-like DNA (numt) has been found in a variety of insect species. In this work, our objective was to create. This led us to infer that M. capixaba has numts. A phylogenetic analysis which included COI sequences

326

Land use/cover classification in the Brazilian Amazon using satellite images  

PubMed Central

Land use/cover classification is one of the most important applications in remote sensing. However, mapping accurate land use/cover spatial distribution is a challenge, particularly in moist tropical regions, due to the complex biophysical environment and limitations of remote sensing data per se. This paper reviews experiments related to land use/cover classification in the Brazilian Amazon for a decade. Through comprehensive analysis of the classification results, it is concluded that spatial information inherent in remote sensing data plays an essential role in improving land use/cover classification. Incorporation of suitable textural images into multispectral bands and use of segmentation-based method are valuable ways to improve land use/cover classification, especially for high spatial resolution images. Data fusion of multi-resolution images within optical sensor data is vital for visual interpretation, but may not improve classification performance. In contrast, integration of optical and radar data did improve classification performance when the proper data fusion method was used. Of the classification algorithms available, the maximum likelihood classifier is still an important method for providing reasonably good accuracy, but nonparametric algorithms, such as classification tree analysis, has the potential to provide better results. However, they often require more time to achieve parametric optimization. Proper use of hierarchical-based methods is fundamental for developing accurate land use/cover classification, mainly from historical remotely sensed data. PMID:24353353

Lu, Dengsheng; Batistella, Mateus; Li, Guiying; Moran, Emilio; Hetrick, Scott; Freitas, Corina da Costa; Dutra, Luciano Vieira; Sant’Anna, Sidnei João Siqueira

2013-01-01

327

Accurate indel prediction using paired-end short reads  

PubMed Central

Background One of the major open challenges in next generation sequencing (NGS) is the accurate identification of structural variants such as insertions and deletions (indels). Current methods for indel calling assign scores to different types of evidence or counter-evidence for the presence of an indel, such as the number of split read alignments spanning the boundaries of a deletion candidate or reads that map within a putative deletion. Candidates with a score above a manually defined threshold are then predicted to be true indels. As a consequence, structural variants detected in this manner contain many false positives. Results Here, we present a machine learning based method which is able to discover and distinguish true from false indel candidates in order to reduce the false positive rate. Our method identifies indel candidates using a discriminative classifier based on features of split read alignment profiles and trained on true and false indel candidates that were validated by Sanger sequencing. We demonstrate the usefulness of our method with paired-end Illumina reads from 80 genomes of the first phase of the 1001 Genomes Project ( http://www.1001genomes.org) in Arabidopsis thaliana. Conclusion In this work we show that indel classification is a necessary step to reduce the number of false positive candidates. We demonstrate that missing classification may lead to spurious biological interpretations. The software is available at: http://agkb.is.tuebingen.mpg.de/Forschung/SV-M/. PMID:23442375

2013-01-01

328

Drug classification: science, politics, both or neither?  

PubMed

Governments currently classify illicit drugs for various purposes: to guide courts in the sentencing of convicted violators of drug control laws, to prioritize targets of prevention measures and to educate the public about relative risks of the various drugs. It has been proposed that classification should be conducted by scientists and drug experts rather than by politicians, so that it will reflect only accurate factual knowledge of drug effects and risks rather than political biases. Although this is an appealing goal, it is inherently impossible because rank-ordering of the drugs inevitably requires value judgements concerning the different types of harm. Such judgements, even by scientists, depend upon subjective personal criteria and not only upon scientific facts. Moreover, classification that is meant to guide the legal system in controlling dangerous drug use can function only if it is in harmony with the values and sentiments of the public. In some respects, politicians may be better attuned to public attitudes and wishes, and to what policies the public will support, than are scientific experts. The problems inherent in such drug classification are illustrated by the examples of cannabis and of salvinorin A. They raise the question as to whether the classification process really serves any socially beneficial purpose. PMID:20148796

Kalant, Harold

2010-07-01

329

An updated traditional classification of inguinal hernias.  

PubMed

The traditional classification of inguinal hernias is the most widely used system today; however, it does not categorize all inguinal hernias nor their levels of complexity. The named systems of Gilbert, Nyhus, and Schumpelick are reviewed, and their common features are analyzed. A simple updating of the traditional classification along with the use of common modifiers creates a system that is all-inclusive and easy to use for data registries. The traditional classification of inguinal hernias (indirect, direct, and femoral) has withstood the test of time for almost 150 years. In this interval, inguinal hernia repairs have experienced significant evolution from simple ligation of the sac or suturing of the muscular defect to improved primary tissue repairs (e.g., Bassini, McVay, Shouldice) based upon better anatomic principles. Also during the past 30 years, two major revolutions in operative repairs have occurred. First, there is the use of mesh and, second, its placement laparoscopically. As a consequence, hernia surgeons today must choose among multiple competing operative techniques. No one operative technique has proven to be best for all inguinal hernias. Also different levels of complexity and severity exist among inguinal hernias, and thus it is essential that we accurately classify the various inguinal hernias, such that we surgeons can provide the best operative solution for each patient. As Fitzgibbons [1] states, "The primary purpose of a classification for any disease is to stratify for severity so that reasonable comparisons can be made between various treatment strategies." PMID:15221644

Zollinger, Robert M

2004-12-01

330

Phylogenetic relationships in genus Geopora (Pyronemataceae, Pezizales)  

Microsoft Academic Search

Species delimitation in the genus Geopora (Pyronemataceae) is complicated because of small number of differentiating characters, values of which tend to overlap among\\u000a the species. Current classification relies mainly on size and shape of ascospores and fruit-bodies, position of the apothecia\\u000a in the ground and length of excipular hairs. We measured ascospores in ca. 90 Geopora specimens. Sequences of internal

H. Tamm; K. Põldmaa; B. Kullman

2010-01-01

331

Predicting rates of interspecific interaction from phylogenetic trees.  

PubMed

Integrating phylogenetic information can potentially improve our ability to explain species' traits, patterns of community assembly, the network structure of communities, and ecosystem function. In this study, we use mathematical models to explore the ecological and evolutionary factors that modulate the explanatory power of phylogenetic information for communities of species that interact within a single trophic level. We find that phylogenetic relationships among species can influence trait evolution and rates of interaction among species, but only under particular models of species interaction. For example, when interactions within communities are mediated by a mechanism of phenotype matching, phylogenetic trees make specific predictions about trait evolution and rates of interaction. In contrast, if interactions within a community depend on a mechanism of phenotype differences, phylogenetic information has little, if any, predictive power for trait evolution and interaction rate. Together, these results make clear and testable predictions for when and how evolutionary history is expected to influence contemporary rates of species interaction. PMID:25349102

Nuismer, Scott L; Harmon, Luke J

2015-01-01

332

Open Reading Frame Phylogenetic Analysis on the Cloud  

PubMed Central

Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. PMID:23671843

2013-01-01

333

Open reading frame phylogenetic analysis on the cloud.  

PubMed

Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. PMID:23671843

Hung, Che-Lun; Lin, Chun-Yuan

2013-01-01

334

Using Phylogenetic, Functional and Trait Diversity to Understand Patterns of Plant Community Productivity  

E-print Network

Using Phylogenetic, Functional and Trait Diversity to Understand Patterns of Plant Community decades of research showing that increasing plant diversity results in greater community productivity has approach, and 7) a phylogenetic diversity measure, summing phylogenetic branch lengths connecting community

Minnesota, University of

335

The Shapley value of phylogenetic trees.  

PubMed

Every weighted tree corresponds naturally to a cooperative game that we call a tree game; it assigns to each subset of leaves the sum of the weights of the minimal subtree spanned by those leaves. In the context of phylogenetic trees, the leaves are species and this assignment captures the diversity present in the coalition of species considered. We consider the Shapley value of tree games and suggest a biological interpretation. We determine the linear transformation M that shows the dependence of the Shapley value on the edge weights of the tree, and we also compute a null space basis of M. Both depend on the split counts of the tree. Finally, we characterize the Shapley value on tree games by four axioms, a counterpart to Shapley's original theorem on the larger class of cooperative games. We also include a brief discussion of the core of tree games. PMID:17805545

Haake, Claus-Jochen; Kashiwada, Akemi; Su, Francis Edward

2008-04-01

336

Phylogenetic analysis of new plant myosin sequences.  

PubMed

We have sampled a large number of plant taxa, ranging from brown algae to angiosperms, for the presence of myosin sequences. Using phylogenetic analysis, we show that all but two of the new plant myosin sequences fall into two of three preexisting myosin classes. We identified two outlying sequences, which do not fall into any preexisting myosin class. Additionally, all genomic sequences encoding class XI myosins contain an intron in the region studied, suggesting that this genomic region has been conserved over at least 1 billion years of plant evolution. With these data, we can rapidly and consistently classify partial myosin sequences from plants. Our data show that plant myosins do not have clear orthologues in other kingdoms, providing interesting insights into the diversification of myosins. PMID:14562966

Bezanilla, Magdalena; Horton, Amy C; Sevener, Heather C; Quatrano, Ralph S

2003-08-01

337

Inferring Phylogenetic Networks from Gene Order Data  

PubMed Central

Existing algorithms allow us to infer phylogenetic networks from sequences (DNA, protein or binary), sets of trees, and distance matrices, but there are no methods to build them using the gene order data as an input. Here we describe several methods to build split networks from the gene order data, perform simulation studies, and use our methods for analyzing and interpreting different real gene order datasets. All proposed methods are based on intermediate data, which can be generated from genome structures under study and used as an input for network construction algorithms. Three intermediates are used: set of jackknife trees, distance matrix, and binary encoding. According to simulations and case studies, the best intermediates are jackknife trees and distance matrix (when used with Neighbor-Net algorithm). Binary encoding can also be useful, but only when the methods mentioned above cannot be used. PMID:24069602

Morozov, Alexey Anatolievich; Galachyants, Yuri Pavlovich; Likhoshway, Yelena Valentinovna

2013-01-01

338

Dating human cultural capacity using phylogenetic principles  

PubMed Central

Humans have genetically based unique abilities making complex culture possible; an assemblage of traits which we term “cultural capacity”. The age of this capacity has for long been subject to controversy. We apply phylogenetic principles to date this capacity, integrating evidence from archaeology, genetics, paleoanthropology, and linguistics. We show that cultural capacity is older than the first split in the modern human lineage, and at least 170,000 years old, based on data on hyoid bone morphology, FOXP2 alleles, agreement between genetic and language trees, fire use, burials, and the early appearance of tools comparable to those of modern hunter-gatherers. We cannot exclude that Neanderthals had cultural capacity some 500,000 years ago. A capacity for complex culture, therefore, must have existed before complex culture itself. It may even originated long before. This seeming paradox is resolved by theoretical models suggesting that cultural evolution is exceedingly slow in its initial stages. PMID:23648831

Lind, J.; Lindenfors, P.; Ghirlanda, S.; Lidén, K.; Enquist, M.

2013-01-01

339

Evolution of rbcL among Lathyrus and Kupicha's classification.  

PubMed

Phylogenetic relationships in the Lathyrus genus were examined using cpDNA data, particularly data attributed to the "barcode" rbcL gene to construct a possible evolutionary scenario. Plant barcoding can be used to differentiate between species within a genus and to conserve DNA within the same species. We assessed the phylogeny of 29 species of Lathyrus using maximum parsimony, maximum likelihood and unweighted pair-group method and arithmetic mean. The classifications did not agree with current morphological and basic Lathyrus classification. Lathyrus belinensis is a new species that was not described by Kupicha; according to rbcL analysis, the species belongs in the Lathyrus genus. Additionally, the genus Lathyrus has undergone a rapid population expansion as indicated by neutral selection indices. PMID:25366764

Marghali, S; Zitouna, N; Gharbi, M; Fadhlaoui, I; Trifi-Farah, N

2014-01-01

340

Phylogenetic analysis and temporal diversification of mosquitoes (Diptera: Culicidae) based on nuclear genes and morphology  

PubMed Central

Background Phylogenetic analyses provide a framework for examining the evolution of morphological and molecular diversity, interpreting patterns in biogeography, and achieving a stable classification. The generic and suprageneric relationships within mosquitoes (Diptera: Culicidae) are poorly resolved, making these subjects difficult to address. Results We carried out maximum parsimony and maximum likelihood, including Bayesian, analyses on a data set consisting of six nuclear genes and 80 morphological characters to assess their ability to resolve relationships among 25 genera. We also estimated divergence times based on sequence data and fossil calibration points, using Bayesian relaxed clock methods. Strong support was recovered for the basal position and monophyly of the subfamily Anophelinae and the tribes Aedini and Sabethini of subfamily Culicinae. Divergence times for major culicid lineages date to the early Cretaceous. Conclusions Deeper relationships within the family remain poorly resolved, suggesting the need for additional taxonomic sampling. Our results support the notion of rapid radiations early in the diversification of mosquitoes. PMID:20028549

2009-01-01

341

Application of COI sequences in studies of phylogenetic relationships among 40 Apionidae species.  

PubMed

The systematics of the family Apionidae, as well as the superfamily Curculionoidea, is currently in a state of flux. The comparative analyses of COI sequences from our studies shed some light on the systematics of these weevils. To study the relationship among the organisms of the family Apionidae, we determined the COI sequences of representatives of 23 species and 15 genera, i.e., Apion, Betulapion, Catapion, Ceratapion, Cyanapion, Eutrichapion, Exapion, Hemitrichapion, Holotrichapion, Ischnopterapion, Protapion, Pseudoperapion, Psudoprotapion, Pseudostenapion, and Stenopterapion. Then, they were compared with the COI sequences of 19 species and eight genera from GenBank (Aspidapion, Ceratapion, Exapion, Ischnopterapion, Lepidapion, Omphalapion, Oxystoma, and Protapion). The phylogenetic relationships inferred from molecular data are similar to the classification system developed by Alonso-Zarazaga and Lyal ( 1999 ), with some exceptions within the tribe Oxystomatini, and genera Ceratapion and Exapion. PMID:22934614

Ptaszy?ska, Aneta A; ??towski, Jacek; Gnat, Sebastian; Ma?ek, Wanda

2012-01-01

342

Application of COI Sequences in Studies of Phylogenetic Relationships Among 40 Apionidae Species  

PubMed Central

The systematics of the family Apionidae, as well as the superfamily Curculionoidea, is currently in a state of flux. The comparative analyses of COI sequences from our studies shed some light on the systematics of these weevils. To study the relationship among the organisms of the family Apionidae, we determined the COI sequences of representatives of 23 species and 15 genera, i.e., Apion, Betulapion, Catapion, Ceratapion, Cyanapion, Eutrichapion, Exapion, Hemitrichapion, Holotrichapion, Ischnopterapion, Protapion, Pseudoperapion, Psudoprotapion, Pseudostenapion, and Stenopterapion. Then, they were compared with the COI sequences of 19 species and eight genera from GenBank (Aspidapion, Ceratapion, Exapion, Ischnopterapion, Lepidapion, Omphalapion, Oxystoma, and Protapion). The phylogenetic relationships inferred from molecular data are similar to the classification system developed by Alonso-Zarazaga and Lyal (1999), with some exceptions within the tribe Oxystomatini, and genera Ceratapion and Exapion. PMID:22934614

Ptaszy?ska, Aneta A.; ??towski, Jacek; Gnat, Sebastian; Ma?ek, Wanda

2012-01-01

343

A higher-level phylogenetic classification of the Fungi David S. HIBBETTa,  

E-print Network

of Medicine, National Center for Biotechnology Information, 45 Center Drive, Bethesda, MD 20892-6510, USA c, The Netherlands o Botanical Institute, University of Tu¨bingen, Auf der Morgenstelle 1, D-72076 Tu¨bingen, Germany

Lutzoni, François M.

344

Dental characters of the Quaternary tapirs in China, their significance in classification and phylogenetic assessment  

Microsoft Academic Search

Most of the Quaternary tapir fossils from China are isolated teeth. The purpose of this paper is to identify them and to extract systematic and evolutionary information from them. Based on morphology and W\\/L ratio, isolated teeth can be identified successfully. On the whole, the identification of P1, M3 and P2 is believed to be reliable, while it is difficult

Haowen Tong

2005-01-01

345

A phylogenetic approach to mapping cell fate.  

PubMed

Recent, surprising, and controversial discoveries have challenged conventional concepts regarding the origins and plasticity of stem cells, and their contributions to tissue regeneration, and highlight just how little is known about mammalian development in comparison to simpler model organisms. In the case of the transparent worm, Caenorhabditis elegans, Sulston and colleagues used a microscope to record the birth and death of every cell during its life, and the compilation of this "fate map" represents a milestone achievement of developmental biology. Determining a fate map for mammals or other higher organisms is more complicated because they are opaque, take a long time to mature, and have a tremendous number of cells. Consequently, fate mapping experiments have relied on tagging a progenitor cell with a dye or genetic marker in order to later identify its descendants. This approach, however, extracts little information because it demonstrates that a population of cells, all having inherited the same label, shares a common ancestor, but it does not reveal how cells in that population are related to one another. To avoid that problem, as well as technical limitations of current methods for mapping cell fate, we, and others, have developed a new strategy for retrospectively deriving cell fate maps by using phylogenetics to infer the order in which somatic mutations have arisen in the genomes of individual cells during development in multicellular organisms. DNA replication inevitably introduces mutations, particularly at repetitive sequences, every time a cell divides. It is thus possible to deduce the history of cell divisions by cataloging somatic mutations and phylogenetically reconstructing cell lineage. This approach has the potential to produce a complete mammalian cell fate map that, in principle, could describe the developmental lineage of any cell and help resolve outstanding questions of stem cell biology, tissue repair and maintenance, and aging. PMID:17498550

Salipante, Stephen J; Horwitz, Marshall S

2007-01-01

346

Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution  

PubMed Central

Background The scientific literature contains many examples where DNA sequence analyses have been used to provide definitive answers to phylogenetic problems that traditional (non-DNA based) approaches alone have failed to resolve. One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments. Results In this study we report the first complete mitochondrial genome sequences of the extinct ice-age woolly rhinoceros (Coelodonta antiquitatis), and the threatened Javan (Rhinoceros sondaicus), Sumatran (Dicerorhinus sumatrensis), and black (Diceros bicornis) rhinoceroses. In combination with the previously published mitochondrial genomes of the white (Ceratotherium simum) and Indian (Rhinoceros unicornis) rhinoceroses, this data set putatively enables reconstruction of the rhinoceros phylogeny. While the six species cluster into three strongly supported sister-pairings: (i) The black/white, (ii) the woolly/Sumatran, and (iii) the Javan/Indian, resolution of the higher-level relationships has no statistical support. The phylogenetic signal from individual genes is highly diffuse, with mixed topological support from different genes. Furthermore, the choice of outgroup (horse vs tapir) has considerable effect on reconstruction of the phylogeny. The lack of resolution is suggestive of a hard polytomy at the base of crown-group Rhinocerotidae, and this is supported by an investigation of the relative branch lengths. Conclusion Satisfactory resolution of the rhinoceros phylogeny may not be achievable without additional analyses of substantial amounts of nuclear DNA. This study provides a compelling demonstration that, in spite of substantial sequence length, there are significant limitations with single-locus phylogenetics. We expect further examples of this to appear as next-generation, large-scale sequencing of complete mitochondrial genomes becomes commonplace in evolutionary studies. "The human factor in classification is nowhere more evident than in dealing with this superfamily (Rhinocerotoidea)." G. G. Simpson (1945) PMID:19432984

Willerslev, Eske; Gilbert, M Thomas P; Binladen, Jonas; Ho, Simon YW; Campos, Paula F; Ratan, Aakrosh; Tomsho, Lynn P; da Fonseca, Rute R; Sher, Andrei; Kuznetsova, Tatanya V; Nowak-Kemp, Malgosia; Roth, Terri L; Miller, Webb; Schuster, Stephan C

2009-01-01

347

Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes  

PubMed Central

Background Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. Methodology/Principal Findings We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A well-supported clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. Conclusions/Significance These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets. PMID:23372644

Hill, Malcolm S.; Hill, April L.; Lopez, Jose; Peterson, Kevin J.; Pomponi, Shirley; Diaz, Maria C.; Thacker, Robert W.; Adamska, Maja; Boury-Esnault, Nicole; Cárdenas, Paco; Chaves-Fonnegra, Andia; Danka, Elizabeth; De Laine, Bre-Onna; Formica, Dawn; Hajdu, Eduardo; Lobo-Hajdu, Gisele; Klontz, Sarah; Morrow, Christine C.; Patel, Jignasa; Picton, Bernard; Pisani, Davide; Pohlmann, Deborah; Redmond, Niamh E.; Reed, John; Richey, Stacy; Riesgo, Ana; Rubin, Ewelina; Russell, Zach; Rützler, Klaus; Sperling, Erik A.; di Stefano, Michael; Tarver, James E.; Collins, Allen G.

2013-01-01

348

Molecular phylogenetics, species diversity, and biogeography of the Andean lizards of the genus Proctoporus (Squamata: Gymnophthalmidae).  

PubMed

The family Gymnophthalmidae comprises ca. 220 described species of Neotropical lizards distributed from southern Mexico to Argentina. It includes 36 genera, among them Proctoporus, which contains six currently recognized species occurring across the yungas forests and wet montane grasslands of the Amazonian versant of the Andes from central Peru to central Bolivia. Here, we investigate the phylogenetic relationships and species limits of Proctoporus and closely related taxa by analyzing 2121 base pairs of mitochondrial (12S, 16S, and ND4) and nuclear (c-mos) genes. Our taxon sampling of 92 terminals includes all currently recognized species of Proctoporus and 15 additional species representing the most closely related groups to the genus. Maximum parsimony, maximum likelihood and Bayesian phylogenetic analyses recovered a congruent, fully resolved, and strongly supported hypothesis of relationships that challenges previous phylogenetic hypotheses and classifications, and biogeographic scenarios. Our main results are: (i) discovery of a strongly supported clade that includes all species of Proctoporus and within which are nested the monotypic Opipeuter xestus (a genus that we consider a junior synonym of Proctoporus), and two species of Euspondylus, that are therefore transferred to Proctoporus; (ii) the paraphyly of Proctoporus bolivianus with respect to P. subsolanus, which is proposed as a junior synonym of P. bolivianus; (iii) the detection of seven divergent and reciprocally monophyletic lineages (five of them previously assigned to P. bolivianus) that are considered confirmed candidate species, which implies that more candidate species are awaiting formal description and naming than currently recognized species in the genus; (iv) rejection of the hypothesis that Proctoporus diversified following a south to north pattern parallel to the elevation of the Andes; (v) species diversity in Proctoporus is the result of in situ diversification through vicariance in the grasslands of the high Andes, with at least five dispersals contributing to montane forest species. PMID:22982151

Goicoechea, Noemí; Padial, José M; Chaparro, Juan C; Castroviejo-Fisher, Santiago; De la Riva, Ignacio

2012-12-01

349

Gait Analysis for Classification  

E-print Network

This thesis describes a representation of gait appearance for the purpose of person identification and classification. This gait representation is based on simple localized image features such as moments extracted from ...

Lee, Lily

2003-06-26

350

Gait analysis for classification  

E-print Network

This thesis describes a representation of gait appearance for the purpose of person identification and classification. This gait representation is based on simple localized image features such as moments extracted from ...

Lee, Lily, 1971-

2002-01-01

351

2000 Mathematics Subject Classification  

NSDL National Science Digital Library

The proposed revision of the 1991 edition of the Mathematics Subject Classification, MSC2000, was officially announced at the upcoming International Congress of Mathematicians in Berlin (August 24, 1998). MSC2000 is a collaborative effort between the editors of Mathematical Review and Zentralblatt fur Mathematik, two journals that review mathematics literature. Mathematical Reviews is a publication of the American Mathematical Society (AMS) (discussed in the July 14, 1995 issue of the Scout Report). The 1991 edition of the MSC (linked to from the MSC2000 site) contains "over 5,000 two-, three-, and five-digit classifications, each corresponding to a discipline of mathematics." The MSC2000 classification scheme is browseable; the 1991 edition has both browse and search functionality. Application of the new classification scheme will begin in the year 2000.

352

Proteomic applications of automated GPCR classification.  

PubMed

The G-protein coupled receptor (GPCR) superfamily fulfils various metabolic functions and interacts with a diverse range of ligands. There is a lack of sequence similarity between the six classes that comprise the GPCR superfamily. Moreover, most novel GPCRs found have low sequence similarity to other family members which makes it difficult to infer properties from related receptors. Many different approaches have been taken towards developing efficient and accurate methods for GPCR classification, ranging from motif-based systems to machine learning as well as a variety of alignment-free techniques based on the physiochemical properties of their amino acid sequences. This review describes the inherent difficulties in developing a GPCR classification algorithm and includes techniques previously employed in this area. PMID:17639603

Davies, Matthew N; Gloriam, David E; Secker, Andrew; Freitas, Alex A; Mendao, Miguel; Timmis, Jon; Flower, Darren R

2007-08-01

353

Classification of Variable Stars Using Thick-Pen Transform Method  

NASA Astrophysics Data System (ADS)

A suitable classification of variable stars is an important task for understanding galaxy structure and evaluating stellar evolution. Most traditional approaches for classification have used various features of variable stars such as period, amplitude, color index, and Fourier coefficients. Recently, by focusing only on the light curve shape, Deb and Singh proposed a classification method based on multivariate principal component analysis (PCA). They applied the PCA method to light curves and compared its results with those obtained by Fourier coefficients. In this article, we propose a new procedure based on the thick-pen transform for obtaining accurate information on the light curve shape as well as for improving the accuracy of classification. The proposed method is applied to the data sets of variable stars from the Stellar Astrophysics and Research on Exoplanets (STARE) project and a small number of stars from Massive Compact Halo Objects (MACHO).

Park, M.; Oh, H.-S.; Kim, D.

2013-04-01

354

A Syntactic Classification based Web Page Ranking Algorithm  

E-print Network

The existing search engines sometimes give unsatisfactory search result for lack of any categorization of search result. If there is some means to know the preference of user about the search result and rank pages according to that preference, the result will be more useful and accurate to the user. In the present paper a web page ranking algorithm is being proposed based on syntactic classification of web pages. Syntactic Classification does not bother about the meaning of the content of a web page. The proposed approach mainly consists of three steps: select some properties of web pages based on user's demand, measure them, and give different weightage to each property during ranking for different types of pages. The existence of syntactic classification is supported by running fuzzy c-means algorithm and neural network classification on a set of web pages. The change in ranking for difference in type of pages but for same query string is also being demonstrated.

Mukhopadhyay, Debajyoti; Kim, Young-Chon

2011-01-01

355

Land Cover Classification Using ALOS Imagery For Penang, Malaysia  

NASA Astrophysics Data System (ADS)

This paper presents the potential of integrating optical and radar remote sensing data to improve automatic land cover mapping. The analysis involved standard image processing, and consists of spectral signature extraction and application of a statistical decision rule to identify land cover categories. A maximum likelihood classifier is utilized to determine different land cover categories. Ground reference data from sites throughout the study area are collected for training and validation. The land cover information was extracted from the digital data using PCI Geomatica 10.3.2 software package. The variations in classification accuracy due to a number of radar imaging processing techniques are studied. The relationship between the processing window and the land classification is also investigated. The classification accuracies from the optical and radar feature combinations are studied. Our research finds that fusion of radar and optical significantly improved classification accuracies. This study indicates that the land cover/use can be mapped accurately by using this approach.

Sim, C. K.; Abdullah, K.; MatJafri, M. Z.; Lim, H. S.

2014-02-01

356

Occupational Classification System Manual  

NSDL National Science Digital Library

Researchers may gain insight into the Bureau of Labor Statistics and Census Bureau occupational codes via the Occupational Classification System Manual (OCSM). A list of Major Occupation Group titles (MOGs) is provided as well as links to the Census Occupation Index--an alphabetical list of approximately 30,000 occupational titles. Further guidance in locating the proper occupation classification for research queries is outlined in the articles "Using the OCSM" and "Using the Census Index."

357

Classification for pulsars  

NASA Astrophysics Data System (ADS)

A new classification system for pulsars is proposed whereby 373 sample pulsars are divided into four natural groups by three gaps in the p vs p(dot) diagram. The validity of this classification is supported by a stepwise discriminant analysis. The first three classes correspond to the evolutionary stages based on the magnetic-decay model, and the fourth consists of millisecond pulsars which have gone through the accreting process in binary systems.

Li, Zong-Yun; Ding, Yue-Rong

1992-06-01

358

Classification for pulsars.  

NASA Astrophysics Data System (ADS)

A classification system for pulsars is presented. In the diagram p vs. p? three gaps divide 373 sample pulsars into four natural groups. The stepwise discriminant analysis of the sample indicates that this classification is reasonable. The first three classes correspond to the evolutionary stages based on the magnetic-decay model and the fourth consists of millisecond pulsars which have gone through their accreting process in binary systems.

Li, Zong-Yun; Ding, Yue-Rong

1992-06-01

359

GALSVM: Automated Morphology Classification  

NASA Astrophysics Data System (ADS)

GALSVM is IDL software for automated morphology classification. It was specially designed for high redshift data but can be used at low redshift as well. It analyzes morphologies of galaxies based on a particular family of learning machines called support vector machines. The method can be seen as a generalization of the classical CAS classification but with an unlimited number of dimensions and non-linear boundaries between decision regions. It is fully automated and consequently well adapted to large cosmological surveys.

Huertas-Company, Marc

2013-04-01

360

Potato Chip Classification  

NSDL National Science Digital Library

This activity introduces the structure and function of a dichotomous key, in preparation for student identification of plant and animal specimens. It also reinforces the idea that there are many possible answers in science. Students will be able to classify specimens (in this case, potato chips) according to observable characteristics, prepare a key showing their classification system, use their key to identify a specimen, and recognize the validity of classmates' classification systems.

1998-01-01

361

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

PubMed

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.The ISME Journal advance online publication, 24 October 2014; doi:10.1038/ismej.2014.208. PMID:25343514

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

2014-10-24

362

Is horizontal transmission really a problem for phylogenetic comparative methods? A simulation study using continuous cultural traits  

PubMed Central

Phylogenetic comparative methods (PCMs) provide a potentially powerful toolkit for testing hypotheses about cultural evolution. Here, we build on previous simulation work to assess the effect horizontal transmission between cultures has on the ability of both phylogenetic and non-phylogenetic methods to make inferences about trait evolution. We found that the mode of horizontal transmission of traits has important consequences for both methods. Where traits were horizontally transmitted separately, PCMs accurately reported when trait evolution was not correlated even at the highest levels of horizontal transmission. By contrast, linear regression analyses often incorrectly concluded that traits were correlated. Where simulated trait evolution was not correlated and traits were horizontally transmitted as a pair, both methods inferred increased levels of positive correlation with increasing horizontal transmission. Where simulated trait evolution was correlated, increasing rates of separate horizontal transmission led to decreasing levels of inferred correlation for both methods, but increasing rates of paired horizontal transmission did not. Furthermore, the PCM was also able to make accurate inferences about the ancestral state of traits. These results suggest that under certain conditions, PCMs can be robust to the effects of horizontal transmission. We discuss ways that future work can investigate the mode and tempo of horizontal transmission of cultural traits. PMID:21041214

Currie, Thomas E.; Greenhill, Simon J.; Mace, Ruth

2010-01-01

363

Target Recognition of Software Research about Machine System of Accurately Spraying  

Microsoft Academic Search

\\u000a The software is used modularity and qeneric idea, realize target recognition and accurately spraying, it consist of five modules:\\u000a module of image process, module of identifing the crop from the background of elaphic, module of target recognition and classification\\u000a of treatment, module of intelligent decision-making and helpness. Image process is made of distortion adjustment,gray strengthen,\\u000a neighbourhoods average, histogram equalization and

Yan Shi; Chunmei Zhang; Maogang Li; Haibo Yuan

2010-01-01

364

Extrahepatic biliary cancer: New staging classification  

PubMed Central

Tumor staging defines the point in the natural history of the malignancy when the diagnosis is made. The most common staging system for cancer is the tumor, node, metastases classification. Staging of cancers provides useful parameters in the determination of the extent of disease and prognosis. Cholangiocarcinoma are rare and refers to cancers that arise from the biliary epithelium. These tumors can occur anywhere along the biliary tree. These tumors have been previously divided into extrahepatic and intrahepatic lesions. Until recently the extrahepatic bile duct tumors have been considered as a single entity per American Joint Commission on Cancer (AJCC) staging classification. The most recent changes to the AJCC classification of bile duct cancers divide the tumors into two major categories: proximal and distal tumors. This practical classification is based on anatomy and surgical management. High quality cross-sectional computed tomography (CT) and/or magnetic resonance (MR) imaging of the abdomen are essential information to accurately stage this tumors. Imaging plays an important role in diagnosis, localization, staging and optimal management of cholangiocarcinoma. For example, it helps to localize the tumor to either perihilar or distal bile duct, both of which have different management. Further, it helps to accurately stage the disease and identify the presence of significant nodal and distant metastasis, which may preclude surgery. Also, it helps to identify the extent of local invasion, which has a major impact on the management. For example, extensive involvement of hepatic duct reaching up to second-order biliary radicals or major vascular encasement of portal vein or hepatic arteries precludes curative surgery and patient may be managed by palliative therapy. Further, imaging helps to identify any anatomical variations in the hepatic arterial or venous circulation and biliary ductal system, which is vital information for surgical planning. This review presents relevant clinical presentation and imaging acquisition and presentation for the accurate staging classification of bile duct tumors based on the new AJCC criteria. This will be performed with the assistance of anatomical diagrams and representative CT and MR images. The image interpretation must include all relevant imaging information for optimum staging. Detailed recommendations on the items required on the radiology report will be presented. PMID:22937214

Ganeshan, Dhakshinamoorthy; Moron, Fanny E; Szklaruk, Janio

2012-01-01

365

Phylogenetic signal in primate behaviour, ecology and life history  

PubMed Central

Examining biological diversity in an explicitly evolutionary context has been the subject of research for several decades, yet relatively recent advances in analytical techniques and the increasing availability of species-level phylogenies, have enabled scientists to ask new questions. One such approach is to quantify phylogenetic signal to determine how trait variation is correlated with the phylogenetic relatedness of species. When phylogenetic signal is high, closely related species exhibit similar traits, and this biological similarity decreases as the evolutionary distance between species increases. Here, we first review the concept of phylogenetic signal and suggest how to measure and interpret phylogenetic signal in species traits. Second, we quantified phylogenetic signal in primates for 31 variables, including body mass, brain size, life-history, sexual selection, social organization, diet, activity budget, ranging patterns and climatic variables. We found that phylogenetic signal varies extensively across and even within trait categories. The highest values are exhibited by brain size and body mass, moderate values are found in the degree of territoriality and canine size dimorphism, while low values are displayed by most of the remaining variables. Our results have important implications for the evolution of behaviour and ecology in primates and other vertebrates. PMID:23569289

Kamilar, Jason M.; Cooper, Natalie

2013-01-01

366

Enumerating all maximal frequent subtrees in collections of phylogenetic trees  

PubMed Central

Background A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events. Results We give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/. Conclusions Our computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees. PMID:25061474

2014-01-01

367

Phylogeny and Classification of the Trapdoor Spider Genus Myrmekiaphila: An Integrative Approach to Evaluating Taxonomic Hypotheses  

PubMed Central

Background Revised 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 hypotheses. The purpose of this study is to reconstruct the phylogeny of Myrmekiaphila species using molecular data to formally test the delimitation of species and species-groups. We seek to refine a set of established systematic hypotheses by integrating across molecular and morphological data sets. Methods and Findings Phylogenetic analyses comprising Bayesian searches were conducted for a mtDNA matrix composed of contiguous 12S rRNA, tRNA-val, and 16S rRNA genes and a nuclear DNA matrix comprising the glutamyl and prolyl tRNA synthetase gene each consisting of 1348 and 481 bp, respectively. Separate analyses of the mitochondrial and nuclear genome data and a concatenated data set yield M. torreya and M. millerae paraphyletic with respect to M. coreyi and M. howelli and polyphyletic fluviatilis and foliata species groups. Conclusions Despite the perception that molecular data present a solution to a crisis in taxonomy, studies like this demonstrate the efficacy of an approach that considers data from multiple sources. A DNA barcoding approach during the species discovery process would fail to recognize at least two species (M. coreyi and M. howelli) whereas a combined approach more accurately assesses species diversity and illuminates speciation pattern and process. Concomitantly these data also demonstrate that morphological characters likewise fail in their ability to recover monophyletic species groups and result in an unnatural classification. Optimizations of these characters demonstrate a pattern of “Dollo evolution” wherein a complex character evolves only once but is lost multiple times throughout the group's history. PMID:20856873

Bailey, Ashley L.; Brewer, Michael S.; Hendrixson, Brent E.; Bond, Jason E.

2010-01-01

368

A re-evaluation of phylogenetic relationships within reed warblers (Aves: Acrocephalidae) based on eight molecular loci and ISSR profiles.  

PubMed

Acrocephalidae is the most monomorphic family among passerines and has seen a long history of different classifications and successive revisions. In this study, we evaluated the phylogenetic relationships among 35 species of Acrocephalidae based on DNA sequences from five nuclear loci (MB, ODC, LDH, FIB5 and RAG-1), three mitochondrial genes (CYB, ND2 and COI) and genomic fingerprinting with ISSR-PCR. We could improve the resolution of phylogenetic relationships among many species, but despite the use of 6280 nucleotides, some deep-level relationships remain enigmatic. Lack of nodal support at some branches may be the result of rapid radiation. The last common ancestor of this family dated for the Middle Miocene (14 MYA). In agreement with previous studies, we recovered the major clades of Acrocephalus, Iduna (except I. aedon), Hippolais, Nesillas and Calamonastides. We accept the current taxonomic position of Calamonastides gracilirostris as a monotypic genus and the inclusion of Iduna natalensis and I. similis within Iduna but phylogenetic analyses based on mitochondrial and nuclear genes as well as ISSR profiles did not support the position of I. aedon in Iduna. Therefore, we resurrect the former genus Phragamaticola for this species in order to avoid paraphyletic clades. PMID:24910156

Arbabi, Tayebeh; Gonzalez, Javier; Wink, Michael

2014-09-01

369

Nuclear and cpDNA sequences combined provide strong inference of higher phylogenetic relationships in the phlox family (Polemoniaceae).  

PubMed

Members of the phlox family (Polemoniaceae) serve as useful models for studying various evolutionary and biological processes. Despite its biological importance, no family-wide phylogenetic estimate based on multiple DNA regions with complete generic sampling is available. Here, we analyze one nuclear and five chloroplast DNA sequence regions (nuclear ITS, chloroplast matK, trnL intron plus trnL-trnF intergeneric spacer, and the trnS-trnG, trnD-trnT, and psbM-trnD intergenic spacers) using parsimony and Bayesian methods, as well as assessments of congruence and long branch attraction, to explore phylogenetic relationships among 84 ingroup species representing all currently recognized Polemoniaceae genera. Relationships inferred from the ITS and concatenated chloroplast regions are similar overall. A combined analysis provides strong support for the monophyly of Polemoniaceae and subfamilies Acanthogilioideae, Cobaeoideae, and Polemonioideae. Relationships among subfamilies, and thus for the precise root of Polemoniaceae, remain poorly supported. Within the largest subfamily, Polemonioideae, four clades corresponding to tribes Polemonieae, Phlocideae, Gilieae, and Loeselieae receive strong support. The monogeneric Polemonieae appears sister to Phlocideae. Relationships within Polemonieae, Phlocideae, and Gilieae are mostly consistent between analyses and data permutations. Many relationships within Loeselieae remain uncertain. Overall, inferred phylogenetic relationships support a higher-level classification for Polemoniaceae proposed in 2000. PMID:18621551

Johnson, Leigh A; Chan, Lauren M; Weese, Terri L; Busby, Lisa D; McMurry, Samuel

2008-09-01

370

Phylogeny and classification of Prunus sensu lato (Rosaceae).  

PubMed

The classification of the economically important genus Prunus L. sensu lato (s.l.) is controversial due to the high levels of convergent or the parallel evolution of morphological characters. In the present study, phylogenetic analyses of fifteen main segregates of Prunus s.l. represented by eighty-four species were conducted with maximum parsimony and Bayesian approaches using twelve chloroplast regions (atpB-rbcL, matK, ndhF, psbA-trnH, rbcL, rpL16, rpoC1, rps16, trnS-G, trnL, trnL-F and ycf1) and three nuclear genes (ITS, s6pdh and SbeI) to explore their infrageneric relationships. The results of these analyses were used to develop a new, phylogeny-based classification of Prunus s.l. Our phylogenetic reconstructions resolved three main clades of Prunus s.l. with strong supports. We adopted a broad-sensed genus, Prunus, and recognised three subgenera corresponding to the three main clades: subgenus Padus, subgenus Cerasus and subgenus Prunus. Seven sections of subgenus Prunus were recognised. The dwarf cherries, which were previously assigned to subgenus Cerasus, were included in this subgenus Prunus. One new section name, Prunus L. subgenus Prunus section Persicae (T. T. Yü & L. T. Lu) S. L. Zhou and one new species name, Prunus tianshanica (Pojarkov) S. Shi, were proposed. PMID:23945216

Shi, Shuo; Li, Jinlu; Sun, Jiahui; Yu, Jing; Zhou, Shiliang

2013-11-01

371

Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison  

PubMed Central

Background Perturbations in intestinal microbiota composition have been associated with a variety of gastrointestinal tract-related diseases. The alleviation of symptoms has been achieved using treatments that alter the gastrointestinal tract microbiota toward that of healthy individuals. Identifying differences in microbiota composition through the use of 16S rRNA gene hypervariable tag sequencing has profound health implications. Current computational methods for comparing microbial communities are usually based on multiple alignments and phylogenetic inference, making them time consuming and requiring exceptional expertise and computational resources. As sequencing data rapidly grows in size, simpler analysis methods are needed to meet the growing computational burdens of microbiota comparisons. Thus, we have developed a simple, rapid, and accurate method, independent of multiple alignments and phylogenetic inference, to support microbiota comparisons. Results We create a metric, called compression-based distance (CBD) for quantifying the degree of similarity between microbial communities. CBD uses the repetitive nature of hypervariable tag datasets and well-established compression algorithms to approximate the total information shared between two datasets. Three published microbiota datasets were used as test cases for CBD as an applicable tool. Our study revealed that CBD recaptured 100% of the statistically significant conclusions reported in the previous studies, while achieving a decrease in computational time required when compared to similar tools without expert user intervention. Conclusion CBD provides a simple, rapid, and accurate method for assessing distances between gastrointestinal tract microbiota 16S hypervariable tag datasets. PMID:23617892

2013-01-01

372

Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets  

PubMed Central

Phylogenetic research is often stymied by selection of a marker that leads to poor phylogenetic resolution despite considerable cost and effort. Profiles of phylogenetic informativeness provide a quantitative measure for prioritizing gene sampling to resolve branching order in a particular epoch. To evaluate the utility of these profiles, we analyzed phylogenomic data sets from metazoans, fungi, and mammals, thus encompassing diverse time scales and taxonomic groups. We also evaluated the utility of profiles created based on simulated data sets. We found that genes selected via their informativeness dramatically outperformed haphazard sampling of markers. Furthermore, our analyses demonstrate that the original phylogenetic informativeness method can be extended to trees with more than four taxa. Thus, although the method currently predicts phylogenetic signal without specifically accounting for the misleading effects of stochastic noise, it is robust to the effects of homoplasy. The phylogenetic informativeness rankings obtained will allow other researchers to select advantageous genes for future studies within these clades, maximizing return on effort and investment. Genes identified might also yield efficient experimental designs for phylogenetic inference for many sister clades and outgroup taxa that are closely related to the diverse groups of organisms analyzed. PMID:23878813

López-Giráldez, Francesc; Moeller, Andrew H.; Townsend, Jeffrey P.

2013-01-01

373

Scalable metagenomic taxonomy classification using a reference genome database  

PubMed Central

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

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

2013-01-01

374

Phylogenetic biodiversity assessment based on systematic nomenclature.  

PubMed

Biodiversity assessment demands objective measures, because ultimately conservation decisions must prioritize the use of limited resources for preserving taxa. The most general framework for the objective assessment of conservation worth are those that assess evolutionary distinctiveness, e.g. Genetic (Crozier 1992) and Phylogenetic Diversity (Faith 1992), and Evolutionary History (Nee & May 1997). These measures all attempt to assess the conservation worth of any scheme based on how much of the encompassing phylogeny of organisms is preserved. However, their general applicability is limited by the small proportion of taxa that have been reliably placed in a phylogeny. Given that phylogenizaton of many interesting taxa or important is unlikely to occur soon, we present a framework for using taxonomy as a reasonable surrogate for phylogeny. Combining this framework with exhaustive searches for combinations of sites containing maximal diversity, we provide a proof-of-concept for assessing conservation schemes for systematized but un-phylogenised taxa spread over a series of sites. This is illustrated with data from four studies, on North Queensland flightless insects (Yeates et al. 2002), ants from a Florida Transect (Lubertazzi & Tschinkel 2003), New England bog ants (Gotelli & Ellison 2002) and a simulated distribution of the known New Zealand Lepidosauria (Daugherty et al. 1994). The results support this approach, indicating that species, genus and site numbers predict evolutionary history, to a degree depending on the size of the data set. PMID:19325850

Crozier, Ross H; Dunnett, Lisa J; Agapow, Paul-Michael

2005-01-01

375

Pareto-optimal phylogenetic tree reconciliation  

PubMed Central

Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. Results: We address this problem by giving an efficient algorithm for computing Pareto-optimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies. Availability and implementation: Our Python tools are freely available at www.cs.hmc.edu/?hadas/xscape. Contact: mukul@engr.uconn.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24932009

Libeskind-Hadas, Ran; Wu, Yi-Chieh; Bansal, Mukul S.; Kellis, Manolis

2014-01-01

376

Recursive algorithms for phylogenetic tree counting  

PubMed Central

Background In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying prior distributions. When all samples come from the same time point and no prior information available on divergence times, the tree counting problem is easy. However, when fossil evidence is used in the inference to constrain the tree or data are sampled serially, new tree spaces arise and counting the number of trees is more difficult. Results We describe an algorithm that is polynomial in the number of sampled individuals for counting of resolutions of a constraint tree assuming that the number of constraints is fixed. We generalise this algorithm to counting resolutions of a fully ranked constraint tree. We describe a quadratic algorithm for counting the number of possible fully ranked trees on n sampled individuals. We introduce a new type of tree, called a fully ranked tree with sampled ancestors, and describe a cubic time algorithm for counting the number of such trees on n sampled individuals. Conclusions These algorithms should be employed for Bayesian Markov chain Monte Carlo inference when fossil data are included or data are serially sampled. PMID:24164709

2013-01-01

377

Phylogenetic analysis of pbp genes in treponemes  

PubMed Central

Background ?-Lactamases are the main cause of bacterial resistance to penicillin, cephalosporins, and related ?-lactam compounds. The presence of the novel penicillin-binding protein (pbp) Tp47 in Treponema pallidum has been reported to be a well-known mechanism for turnover of b-lactam antibiotics. Although, T. pallidum remains sensitive to penicillin, clinically significant resistance to macrolides has emerged in many developing countries. The genome sequence of T. pallidum has shown the presence of genes encoding pbp, but there are no current reports of the presence of mobile plasmids. Methods The phylogenetic analysis is used to study the diversity of chromosomal pbp genes and its relatedness to Tp47 in Treponema species. Results In our study, genes encoding penicillin-binding proteins that showed significant similarity to each other appeared in separate clusters. Conclusion Tp47 showed no substantial similarity to other ?-lactamases in treponemes. The relatedness of Treponema denticola to other treponemes, including T. pallidum, and the reported presence of natural mobile antibiotic determinants highlight the importance of investigating the diversity of pbp genes in Treponema species. This will lead to a greater understanding of its potential to develop additional antibiotic resistance via horizontal gene transfer that could seriously compromise the treatment and control of syphilis. PMID:23330059

Chadha, Tejpreet; Trindade, Adão Alexandre

2013-01-01

378

The phylogenetic profile of mast cells.  

PubMed

Mast cells (MCs) are tissue-based immune cells that participate to both innate and adaptive immunities as well as to tissue-remodelling processes. Their evolutionary history appears as a fascinating process, whose outline we can only partly reconstruct according to current remnant evidence. MCs have been identified in all vertebrate classes, and a cell population with the overall characteristics of higher vertebrate MCs is identifiable even in the most evolutionarily advanced fish species. In invertebrates, cells related to vertebrate MCs have been recognized in ascidians, a class of urochordates which appeared approximately 500 million years ago. These comprise the granular hemocyte with intermediate characteristics of basophils and MCs and the "test cell" (see below). Both types of cells contain histamine and heparin, and provide defensive functions. The test cell releases tryptase after stimulation with compound 48/80. A leukocyte ancestor operating in the context of a primitive local innate immunity probably represents the MC phylogenetic progenitor. This cell was likely involved in phagocytic and killing activity against pathogens and operated as a general inducer of inflammation. This early type of defensive cell possibly expressed concomitant tissue-reparative functions. With the advent of recombinase activating gene (RAG)-mediated adaptive immunity in the Cambrian era, some 550 million years ago, and the emergence of early vertebrates, MC progenitors differentiated towards a more complex cellular entity. Early MCs probably appeared in the last common ancestor we shared with hagfish, lamprey, and sharks about 450-500 million years ago. PMID:25388242

Crivellato, Enrico; Travan, Luciana; Ribatti, Domenico

2015-01-01

379

Sequence-based molecular phylogenetics and phylogeography of the American box turtles (Terrapene spp.) with support from DNA barcoding.  

PubMed

The classification of the American box turtles (Terrapene spp.) has remained enigmatic to systematists. Previous comprehensive phylogenetic studies focused primarily on morphology. The goal of this study was to re-assess the classification of Terrapene spp. by obtaining DNA sequence data from a broad geographic range and from all four recognized species and 11 subspecies within the genus. Tissue samples were obtained for all taxa except for Terrapene nelsoni klauberi. DNA was extracted, and the mitochondrial DNA (mtDNA) cytochrome b (Cytb) and nuclear DNA (nucDNA) glyceraldehyde-3-phosphate-dehydrogenase (GAPD) genes were amplified via polymerase chain reaction and sequenced. In addition, the mtDNA gene commonly used for DNA barcoding (cytochrome oxidase c subunit I; COI) was amplified and sequenced to calculate pairwise percent DNA sequence divergence comparisons for each Terrapene taxon. The sequence data were analyzed using maximum likelihood and Bayesian phylogenetic inference, a molecular clock, AMOVAs, SAMOVAs, haplotype networks, and pairwise percent sequence divergence comparisons. Terrapene carolina mexicana and T. c. yucatana formed a monophyletic clade with T. c. triunguis, and this clade was paraphyletic to the rest of T. carolina. Terrapene ornata ornata and T. o. luteola lacked distinction phylogenetically, and Terrapene nelsoni was confirmed to be the sister taxon of T. ornata. Terrapene c. major, T. c. bauri, and Terrapene coahuila were not well resolved for some of the analyses. The DNA barcoding results indicated that all taxa were different species (>2% sequence divergence) except for T. c. triunguis - T. c. mexicana and T. o. ornata - T. o. luteola. The results suggest that T. c. triunguis should be elevated to species status (Terrapene mexicana), and mexicana and yucatana should be included in this group as subspecies. In addition, T. o. ornata and T. o. luteola should not be considered separate subspecies. The DNA barcoding data support these recommended taxonomic revisions. Because conservation efforts are typically species-based, these results will be important for facilitating successful conservation management strategies. PMID:23523575

Martin, Bradley T; Bernstein, Neil P; Birkhead, Roger D; Koukl, Jim F; Mussmann, Steven M; Placyk, John S

2013-07-01

380

Classification of mental disorders*  

PubMed Central

One of the fundamental difficulties in devising a classification of mental disorders is the lack of agreement among psychiatrists regarding the concepts upon which it should be based: diagnoses can rarely be verified objectively and the same or similar conditions are described under a confusing variety of names. This situation militates against the ready exchange of ideas and experiences and hampers progress. As a first step towards remedying this state of affairs, the author of the article below has undertaken a critical survey of existing classifications. He shows how some of the difficulties created by lack of knowledge regarding pathology and etiology may be overcome by the use of “operational definitions” and outlines the basic principles on which he believes a generally acceptable international classification might be constructed. If this can be done it should lead to a greater measure of agreement regarding the value of specific treatments for mental disorders and greatly facilitate a broad epidemiological approach to psychiatric research. PMID:13834299

Stengel, E.

1959-01-01

381

Commission 45: Spectral Classification  

NASA Astrophysics Data System (ADS)

This report gives an update of developments (since the last General Assembly at Prague) in the areas that are of relevance to the commission. In addition to numerous papers, a new monograph entitled Stellar Spectral Classification with Richard Gray and Chris Corbally as leading authors will be published by Princeton University Press as part of their Princeton Series in Astrophysics in April 2009. This book is an up-to-date and encyclopedic review of stellar spectral classification across the H-R diagram, including the traditional MK system in the blue-violet, recent extensions into the ultraviolet and infrared, the newly defined L-type and T-type spectral classes, as well as spectral classification of carbon stars, S-type stars, white dwarfs, novae, supernovae and Wolf-Rayet stars.

Giridhar, Sunetra; Gray, Richard O.; Corbally, Christopher J.; Bailer-Jones, Coryn A. L.; Eyer, Laurent; Irwin, Michael J.; Kirkpatrick, J. Davy; Majewski, Steven; Minniti, Dante; Nordström, Birgitta

382

Subordinate-level object classification reexamined.  

PubMed

The classification of a table as round rather than square, a car as a Mazda rather than a Ford, a drill bit as 3/8-inch rather than 1/4-inch, and a face as Tom have all been regarded as a single process termed "subordinate classification." Despite the common label, the considerable heterogeneity of the perceptual processing required to achieve such classifications requires, minimally, a more detailed taxonomy. Perceptual information relevant to subordinate-level shape classifications can be presumed to vary on continua of (a) the type of distinctive information that is present, nonaccidental or metric, (b) the size of the relevant contours or surfaces, and (c) the similarity of the to-be-discriminated features, such as whether a straight contour has to be distinguished from a contour of low curvature versus high curvature. We consider three, relatively pure cases. Case 1 subordinates may be distinguished by a representation, a geon structural description (GSD), specifying a nonaccidental characterization of an object's large parts and the relations among these parts, such as a round table versus a square table. Case 2 subordinates are also distinguished by GSDs, except that the distinctive GSDs are present at a small scale in a complex object so the location and mapping of the GSDs are contingent on an initial basic-level classification, such as when we use a logo to distinguish various makes of cars. Expertise for Cases 1 and 2 can be easily achieved through specification, often verbal, of the GSDs. Case 3 subordinates, which have furnished much of the grist for theorizing with "view-based" template models, require fine metric discriminations. Cases 1 and 2 account for the overwhelming majority of shape-based basic- and subordinate-level object classifications that people can and do make in their everyday lives. These classifications are typically made quickly, accurately, and with only modest costs of viewpoint changes. Whereas the activation of an array of multiscale, multiorientation filters, presumed to be at the initial stage of all shape processing, may suffice for determining the similarity of the representations mediating recognition among Case 3 subordinate stimuli (and faces), Cases 1 and 2 require that the output of these filters be mapped to classifiers that make explicit the nonaccidental properties, parts, and relations specified by the GSDs. PMID:10472199

Biederman, I; Subramaniam, S; Bar, M; Kalocsai, P; Fiser, J

1999-01-01

383

Remote balance weighs accurately amid high radiation  

NASA Technical Reports Server (NTRS)

Commercial beam-type balance, modified and outfitted with electronic controls and digital readout, can be remotely controlled for use in high radiation environments. This allows accurate weighing of breeder-reactor fuel pieces when they are radioactively hot.

Eggenberger, D. N.; Shuck, A. B.

1969-01-01

384

Mill profiler machines soft materials accurately  

NASA Technical Reports Server (NTRS)

Mill profiler machines bevels, slots, and grooves in soft materials, such as styrofoam phenolic-filled cores, to any desired thickness. A single operator can accurately control cutting depths in contour or straight line work.

Rauschl, J. A.

1966-01-01

385

Accurate capacitive metrology for atomic force microscopy  

E-print Network

This thesis presents accurate capacitive sensing metrology designed for a prototype atomic force microscope (AFM) originally developed in the MIT Precision Motion Control Lab. The capacitive measurements use a set of ...

Mazzeo, Aaron D. (Aaron David), 1979-

2005-01-01

386

BRDF Slices: Accurate Adaptive Anisotropic Appearance Acquisition  

E-print Network

' & $ % BRDF Slices: Accurate Adaptive Anisotropic Appearance Acquisition Jir´i Filip1 Radom´ir V´avra {filipj,vavra,haindl,zid,krupimik}@utia.cas.cz, havran@fel.cvut.cz We introduce unique publicly available

Havran, Vlastimil

387

Determination of Highly Accurate Heats of Formation  

NASA Technical Reports Server (NTRS)

Two approaches for directly computing a molecular heat of formation based on sophisticated ab initio electronic structure theory axe discussed and example calculations are presented for several molecules of interest in atmospheric chemistry including HNO and CICN. The accuracy of these approaches for a small subset of the molecules is demonstrated by comparison to very accurate experimental data. A third approach for evaluating accurate heats of formation consists of combining experimental and theoretical data. The potential for this method to provide reliable thermochemical data on many molecules using accurate experimental beats of formation for only a small number of species is demonstrated by giving accurate (Delta)H(sup 0, sub f) quantities for a host of fluorine, chlorine, and bromine oxide and nitrogen oxide compounds. Potential pitfalls in all three approaches are discussed.

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1996-01-01

388

Obtaining Maximal Concatenated Phylogenetic Data Sets from Large Sequence Databases  

E-print Network

Obtaining Maximal Concatenated Phylogenetic Data Sets from Large Sequence Databases Michael J of tree reconstruction, phylogeneticists are extracting increasingly large multigene data sets from permits all such data sets to be obtained in reasonable computing times even for large numbers

Sanderson, Mike

389

A Survey of Combinatorial Methods for Phylogenetic Networks  

PubMed Central

The evolutionary history of a set of species is usually described by a rooted phylogenetic tree. Although it is generally undisputed that bifurcating speciation events and descent with modifications are major forces of evolution, there is a growing belief that reticulate events also have a role to play. Phylogenetic networks provide an alternative to phylogenetic trees and may be more suitable for data sets where evolution involves significant amounts of reticulate events, such as hybridization, horizontal gene transfer, or recombination. In this article, we give an introduction to the topic of phylogenetic networks, very briefly describing the fundamental concepts and summarizing some of the most important combinatorial methods that are available for their computation. PMID:21081312

Huson, Daniel H.; Scornavacca, Celine

2011-01-01

390

RESEARCH Open Access Tree-average distances on certain phylogenetic  

E-print Network

-child. Keywords: digraph, distance, metric, hybrid, network, tree-child, normal network, phylogeny 1 Introduction]. See also the recent book [5]. There are many methods to reconstruct phylogenetic trees from

Willson, Stephen J.

391

Phylogenetic and functional diversity in large carnivore assemblages.  

PubMed

Large terrestrial carnivores are important ecological components and prominent flagship species, but are often extinction prone owing to a combination of biological traits and high levels of human persecution. This study combines phylogenetic and functional diversity evaluations of global and continental large carnivore assemblages to provide a framework for conservation prioritization both between and within assemblages. Species-rich assemblages of large carnivores simultaneously had high phylogenetic and functional diversity, but species contributions to phylogenetic and functional diversity components were not positively correlated. The results further provide ecological justification for the largest carnivore species as a focus for conservation action, and suggests that range contraction is a likely cause of diminishing carnivore ecosystem function. This study highlights that preserving species-rich carnivore assemblages will capture both high phylogenetic and functional diversity, but that prioritizing species within assemblages will involve trade-offs between optimizing contemporary ecosystem function versus the evolutionary potential for future ecosystem performance. PMID:23576787

Dalerum, F

2013-06-01

392

Phylogenetic diversity in cadmium : phosphorus ratio regulation by marine phytoplankton  

E-print Network

Phylogenetic diversity in cadmium : phosphorus ratio regulation by marine phytoplankton Z. V Abstract We examined the effect of irradiance and growth rate on cadmium : phosphorus ratio in five species

393

PieTree drawing phylogenetic trees and ancestral state reconstructions  

E-print Network

PieTree drawing phylogenetic trees and ancestral state reconstructions PieTree Release 0.4 Emma E Dependencies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 PieTree.2 Input tree file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2

Goldberg, Emma

394

Position: Postdoctoral Research Associate Position Available in Honey Bee Phylogenetics  

E-print Network

Position: Postdoctoral Research Associate Position Available in Honey Bee Phylogenetics Date Available: immediately Location: Honey Bee Research and Extension Laboratory (HBREL) Department's research in the area of honey bee ecology and conservation. Additionally, the successful candidate

Ferrara, Katherine W.

395

Disturbance drives phylogenetic community structure in coastal dune vegetation  

E-print Network

Disturbance drives phylogenetic community structure in coastal dune vegetation Background Coastal dunes are a globally distributed ecosystem characterized by strong internal gradients in disturbance plant community assembly, but their relative importance in coastal dunes is not well elucidated. We

Schierup, Mikkel Heide

396

Trees from trees: construction of phylogenetic supertrees using clann.  

PubMed

Supertree methods combine multiple phylogenetic trees to produce the overall best "supertree." They can be used to combine phylogenetic information from datasets only partially overlapping and from disparate sources (like molecular and morphological data), or to break down problems thought to be computationally intractable. Some of the longest standing phylogenetic conundrums are now being brought to light using supertree approaches. We describe the most widely used supertree methods implemented in the software program "clann" and provide a step by step tutorial for investigating phylogenetic information and reconstructing the best supertree. Clann is freely available for Windows, Mac and Unix/Linux operating systems under the GNU public licence at (http://bioinf.nuim.ie/software/clann). PMID:19378143

Creevey, Christopher J; McInerney, James O

2009-01-01

397

Comparisons of neural networks to standard techniques for image classification and correlation  

NASA Technical Reports Server (NTRS)

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 than maximum-likelihood of a Landsat scene of Tucson, Arizona. Some of the errors in the maximum-likelihood classification are illustrated using decision region and class probability density plots. As expected, the main drawback to the neural network method is the long time required for the training stage. The network was trained using several different hidden layer sizes to optimize both the classification accuracy and training speed, and it was found that one node per class was optimal. The performance improved when 3x3 local windows of image data were entered into the net. This modification introduces texture into the classification without explicit calculation of a texture measure. Larger windows were successfully used for the detection of spatial features in Landsat and Magellan synthetic aperture radar imagery.

Paola, Justin D.; Schowengerdt, Robert A.

1994-01-01

398

Study on the Technology and Method of Land Cover Classification for Geographic National Conditions Surveying  

NASA Astrophysics Data System (ADS)

Land Cover is the basis of geographic national conditions monitoring, extracting land cover information timely and accurately has become one of important tasks in the geographic national conditions surveying project. For the current situation of complex land cover type and large amount of data, there has emerged various new classification techniques and methods. However, the big difficult of classification?the large amount of data, the heavy workload of post-editing and other factors have seriously hampered the progress of the project. In this paper, it chooses high-resolution remote sensing image as original data, comprehensivly elaborates present research situation of oriented land cover classification. By the systematical analysis and summary of the basic and key problems of the land cover classification technology, relying on the geographic national information classification and standard system, discusses the available methods preliminarily to improve the accuracy of land cover classification which based on geographic national conditions surveying.

Jia, Y.; Li, H. T.; Gu, H. Y.; Han, Y. S.

2013-07-01

399

[Systemic vasculitides classification].  

PubMed

Systemic vasculitides are inflammatory diseases of blood vessels of various sizes, which mechanisms are different according to diseases. Classification can be made according to vessel size, histology and pathogenesis. Giant cell arteritis comprises Horton's disease and Takayasu's arteritis. Different mechanisms have been individualized in the group of necrotizing vasculitides: some are associated with ANCA and other to immune complexes. Other mechanisms have not been yet identified. One of the major purposes of classification is to describe adequately diseases and their outcome, then to treat them appropriately. PMID:22884126

Guillevin, Loïc; Terrier, Benjamin

2012-10-01

400

Classification of intraocular tuberculosis.  

PubMed

Abstract Tuberculosis in the TB endemic countries commonly manifests in the eye as tuberculous uveitis. There is a wide spectrum of the clinical manifestations of intraocular tuberculosis (IOTB). For want of any gold standard diagnostic tests or diagnostic criteria, the estimates of IOTB prevalence have varied greatly. None of the previously suggested guidelines for diagnosis of IOTB have been validated. We give definitions of clinical signs and diagnostic tests that have been used in the literature. Based on these, we propose a classification of IOTB comprising "confirmed IOTB," "probable IOTB," and "possible IOTB." This of necessity needs consensus among experts before carrying out studies to validate this classification. PMID:25314361

Gupta, Amod; Sharma, Aman; Bansal, Reema; Sharma, Kusum

2015-02-01

401

Accurate Parental Classification of Overweight Adolescents' Weight Status: Does It Matter?  

Microsoft Academic Search

OBJECTIVE.Our goal was to explore whether parents of overweight adolescents who recognize that their children are overweight engage in behaviors that are likely to help their adolescents with long-term weight management. METHODS.The study population included overweight adolescents (BMI 85th percen- tile) who participated in Project EAT (Eating Among Teens) I (1999) and II (2004) and their parents who were interviewed

Dianne Neumark-Sztainer; Melanie Wall; Patricia van den Berg

2010-01-01

402

Can Procalcitonin Be an Accurate Diagnostic Marker for the Classification of Diabetic Foot Ulcers?  

PubMed Central

Background: The differentiation of infected diabetic foot ulcers (IDFU) from non infected diabetic foot ulcers (NIDFU) is a challenging issue for clinicians. Objectives: Recently, procalcitonin (PCT) was introduced as a remarkable inflammatory marker. We aimed to evaluate the accuracy of PCT in comparison to other inflammatory markers for distinguishing IDFU from NIDFU. Materials and Methods: We evaluated PCT serum level as a marker of bacterial infection in patients with diabetic foot ulcers. Sixty patients with diabetic foot ulcers were consecutively enrolled in the study. A total of 30 patients were clinically identified as IDFU by an expert clinician, taking as criteria for purulent discharges or at least two of manifestations of inflammation including warmth, redness, swelling and pain. Results: Procalcitonin, white blood cells (WBCs), erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP), were found significantly higher in the IDFU group compared to the NIDFU group. The best cut-off value, sensitivity and specificity were 40.5 mm/h, 90% and 94% for ESR, 7.1 mg/dL, 80% and 74% for CRP, 0.21, 70% and 74% for PCT, and 7.7×109/L, 66% and 67% for WBCs, respectively. The area under the receiver operating characteristic curve for ESR was the greatest (0.967; P < 0.001), followed by CRP (0.871; P < 0.001), PCT (0.729; P < 0.001), and finally WBCs (0.721; P = 0.001). Conclusions: These results suggest that PCT can be a diagnostic marker in combination with other markers like ESR and CRP to distinguish infected from non-infected foot ulcers, when clinical manifestations are un specific. Additional research is needed before the routine usage of PCT to better define the role of PCT in IDFU. PMID:24696696

Jonaidi Jafari, Nematollah; Safaee Firouzabadi, Mahdi; Izadi, Morteza; Safaee Firouzabadi, Mohammad Sadegh; Saburi, Amin

2014-01-01

403

An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree  

Microsoft Academic Search

Given the mitochondrial gene orders and the phylogenetic relationship of a set of unichromosomal taxa, we study the problem\\u000a of finding a plausible and parsimonious assignment of genomic rearrangement events to the edges of the given phylogenetic\\u000a tree. An algorithm called algorithm TreeREx (tree rearrangement explorer) is proposed for solving this problem heuristically. TreeREx is based on an extended version

Matthias Bernt; Daniel Merkle; Martin Middendorf

2008-01-01

404

Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals.  

PubMed

One of the fundamental problems in bioinformatics is phylogenetic tree reconstruction, which can be used for classifying living organisms into different taxonomic clades. The classical approach to this problem is based on a marker such as 16S ribosomal RNA. Since evolutionary events like genomic rearrangements are not included in reconstructions of phylogenetic trees based on single genes, much effort has been made to find other characteristics for phylogenetic reconstruction in recent years. With the increasing availability of completely sequenced genomes, gene order can be considered as a new solution for this problem. In the present work, we applied maximal common intervals (MCIs) in two or more genomes to infer their distance and to reconstruct their evolutionary relationship. Additionally, measures based on uncommon segments (UCS's), i.e., those genomic segments which are not detected as part of any of the MCIs, are also used for phylogenetic tree reconstruction. We applied these two types of measures for reconstructing the phylogenetic tree of 63 prokaryotes with known COG (clusters of orthologous groups) families. Similarity between the MCI-based (resp. UCS-based) reconstructed phylogenetic trees and the phylogenetic tree obtained from NCBI taxonomy browser is as high as 93.1% (resp. 94.9%). We show that in the case of this diverse dataset of prokaryotes, tree reconstruction based on MCI and UCS outperforms most of the currently available methods based on gene orders, including breakpoint distance and DCJ. We additionally tested our new measures on a dataset of 13 closely-related bacteria from the genus Prochlorococcus. In this case, distances like rearrangement distance, breakpoint distance and DCJ proved to be useful, while our new measures are still appropriate for phylogenetic reconstruction. PMID:25195150

Heydari, Mahdi; Marashi, Sayed-Amir; Tusserkani, Ruzbeh; Sadeghi, Mehdi

2014-10-01

405

Phylogenetic Analysis of Reptilian Hemoglobins: Trees, Rates, and Divergences  

Microsoft Academic Search

.   Phylogenetic relationships among reptiles were examined using previously published and newly determined hemoglobin sequences.\\u000a Trees reconstructed from these sequences using maximum-parsimony, neighbor-joining, and maximum-likelihood algorithms were\\u000a compared with a phylogenetic tree of Amniota, which was assembled on the basis of published morphological data. All analyses differentiated ? chains into ?A and ?D types, which are present in all reptiles

Thomas A. Gorr; Barbara K. Mable; Traute Kleinschmidt

1998-01-01

406

Algorithms for Hyperspectral Signature Classification in Non-resolved Object Characterization Using Tabular Nearest Neighbor Encoding  

NASA Astrophysics Data System (ADS)

Accurate spectral signature classification is key to the nonimaging detection and recognition of spaceborne objects. In classical hyperspectral recognition applications, signature classification accuracy depends on accurate spectral endmember determination [1]. However, in selected target recognition (ATR) applications, it is possible to circumvent the endmember detection problem by employing a Bayesian classifier. Previous approaches to Bayesian classification of spectral signatures have been rule- based, or predicated on a priori parameterized information obtained from offline training, as in the case of neural networks [1,2]. Unfortunately, class separation and classifier refinement results in these methods tends to be suboptimal, and the number of signatures that can be accurately classified often depends linearly on the number of inputs. This can lead to potentially significant classification errors in the presence of noise or densely interleaved signatures. In this paper, we present an emerging technology for nonimaging spectral signature classfication based on a highly accurate but computationally efficient search engine called Tabular Nearest Neighbor Encoding (TNE) [3]. Based on prior results, TNE can optimize its classifier performance to track input nonergodicities, as well as yield measures of confidence or caution for evaluation of classification results. Unlike neural networks, TNE does not have a hidden intermediate data structure (e.g., the neural net weight matrix). Instead, TNE generates and exploits a user-accessible data structure called the agreement map (AM), which can be manipulated by Boolean logic operations to effect accurate classifier refinement algorithms. This allows the TNE programmer or user to determine parameters for classification accuracy, and to mathematically analyze the signatures for which TNE did not obtain classification matches. This dual approach to analysis (i.e., correct vs. incorrect classification) has been shown to significantly strengthen analysis of classifier performance in support of classifier optimization. We show that AM-based classification can be modified to include dynamic tracking of input statistical changes, to achieve accurate signature classification in the presence of noise, closely spaced or interleaved signatures, and simulated optical distortions. In particular, we examine two critical cases: (1) classification of multiple closely spaced signatures that are difficult to separate using distance measures, and (2) classification of materials in simulated hyperspectral images of spaceborne satellites. In each case, test data are derived from a NASA database of space material signatures. Additional analysis pertains to computational complexity and noise sensitivity, which are superior to Bayesian techniques based on classical neural networks.

Schmalz, M.; Key, G.

407

Noise-Tolerant Hyperspectral Signature Classification in Unresolved Object Detection with Adaptive Tabular Nearest Neighbor Encoding  

NASA Astrophysics Data System (ADS)

Accurate spectral signature classification is a crucial step in the nonimaging detection and recognition of spaceborne objects. In classical hyperspectral recognition applications, especially where linear mixing models are employed, signature classification accuracy depends on accurate spectral endmember discrimination. In selected target recognition (ATR) applications, previous non-adaptive techniques for signature classification have yielded class separation and classifier refinement results that tend to be suboptimal. In practice, the number of signatures accurately classified often depends linearly on the number of inputs. This can lead to potentially severe classification errors in the presence of noise or densely interleaved signatures. In this paper, we present an enhancement of an emerging technology for nonimaging spectral signature classification based on a highly accurate, efficient search engine called Tabular Nearest Neighbor Encoding (TNE). Adaptive TNE can optimize its classifier performance to track input nonergodicities and yield measures of confidence or caution for evaluation of classification results. Unlike neural networks, TNE does not have a hidden intermediate data structure (e.g., a neural net weight matrix). Instead, TNE generates and exploits a user-accessible data structure called the agreement map (AM), which can be manipulated by Boolean logic operations to effect accurate classifier refinement through programmable algorithms. The open architecture and programmability of TNE's pattern-space (AM) processing allows a TNE developer to determine the qualitative and quantitative reasons for classification accuracy, as well as characterize in detail the signatures for which TNE does not obtain classification matches, and why such mis-matches occur. In this study AM-based classification has been modified to partially compensate for input statistical changes, in response to performance metrics such as probability of correct classification (Pd) and rate of false detections (Rfa). Adaptive TNE can thus achieve accurate signature classification in the presence of time-varying noise, closely spaced or interleaved signatures, and imaging system optical distortions. We analyze classification accuracy of closely spaced spectral signatures adapted from a NASA database of space material signatures. Additional analysis pertains to computational complexity and noise sensitivity, which are superior to non-adaptive TNE or Bayesian techniques based on classical neural networks.

Schmalz, M.; Key, G.

408

Mathematics Subject Classification 2000 Mathematics Subject Classification 2000 (MSC2000)  

E-print Network

. The areas covered by Sections 90 and 92 have been reorganized into Sections 90, 91 and 92. Sections 90B contributions in different areas, the primary classification should cover the "most important" among themMathematics Subject Classification 2000 Mathematics Subject Classification 2000 (MSC2000

409

PERSPECTIVE Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time  

Microsoft Academic Search

A key challenge in ecological research is to integrate data from different scales to evaluate the ecological and evolutionary mechanisms that influence current patterns of biological diversity. We build on recent attempts to incorporate phylogenetic information into traditional diversity analyses and on existing research on beta diversity and phylogenetic community ecology. Phylogenetic beta diversity (phylobetadiversity) measures the phylogenetic distance among

Catherine H. Graham

2008-01-01

410

A recursive segmentation and classification scheme for improving segmentation accuracy and detection rate in real-time machine vision applications  

Microsoft Academic Search

The segmentation accuracy is shown to be a critical factor in detection rate improvement. With accurate segmentation, results are easier to interpret, and classification performance is better. Therefore, it is required to have a performance measure for segmentation evaluation. However, a number of restrictions limit using existing segmentation performance measures. A recursive segmentation and classification scheme is proposed to improve

Yuhira Ding; George J. Vachtsevanos; Yinchuan Zhang; Y. Wardi

2002-01-01

411

CBMF W4761 (Computational Genomics) Spring 2003 5/9/2003 Feature Selection with Exponential Model for Classification on  

E-print Network

of the obstacles to cancer treatment is to diagnose accurately and to target specific therapy for distinct tumor science, from cancer classification to prognostic prediction and from tissue development to therapeutic methods development. It's especially useful in cancer study to include classification and etiology

Hsu, Winston H.

412

Acoustic Classification with Single-Beam Echosounders: Processing Methods and Theory for Isolating Effects of the Seabed on Echoes  

Microsoft Academic Search

Analyzing the details of echoes from single-beam sounders is well established as a basis for seabed classification. Both echo shape and amplitude are analyzed to make maps of seabed sediment classes. For accurate acoustic classification of the seabed, the echoes should be influenced only by properties of the seabed. This paper surveys methods to remove artifacts caused by water depth,

Ben R. Biffard; Jon M. Preston; N. Ross Chapman

2007-01-01

413

Biomedical Image Classification with Random Subwindows and Decision Trees Raphael Maree, Pierre Geurts, Justus Piater, and Louis Wehenkel  

E-print Network

Biomedical Image Classification with Random Subwindows and Decision Trees Rapha¨el Mar´ee, Pierre Abstract In this paper, we address a problem of biomedical image classification that involves the automatic is to build a model that will be able to predict accurately the class of new, unseen images. Biomedical

Wehenkel, Louis

414

An Intuitive, Informative, and Most Balanced Representation of Phylogenetic Topologies  

PubMed Central

The recent explosion in the availability of genetic sequence data has made large-scale phylogenetic inference routine in many life sciences laboratories. The outcomes of such analyses are, typically, a variety of candidate phylogenetic relationships or tree topologies, even when the power of genome-scale data is exploited. Because much phylogenetic information must be buried in such topology distributions, it is important to reveal that information as effectively as possible; however, existing methods need to adopt complex structures to represent such information. Hence, researchers, in particular those not experts in evolutionary studies, sometimes hesitate to adopt these methods and much phylogenetic information could be overlooked and wasted. In this paper, we propose the centroid wheel tree representation, which is an informative representation of phylogenetic topology distributions, and which can be readily interpreted even by nonexperts. Furthermore, we mathematically prove this to be the most balanced representation of phylogenetic topologies and efficiently solvable in the framework of the traveling salesman problem, for which very sophisticated program packages are available. This theoretically and practically superior representation should aid biologists faced with abundant data. The centroid representation introduced here is fairly general, so it can be applied to other fields that are characterized by high-dimensional solution spaces and large quantities of noisy data. The software is implemented in Java and available via http://cwt.cb.k.u-tokyo.ac.jp/. PMID:20817714

Iwasaki, Wataru; Takagi, Toshihisa

2010-01-01

415

Classification: Arbitrary or Not?  

NSDL National Science Digital Library

In this lesson students working in teams classify furniture, share their categories and rationales, then note how their different schemes vary arbitrarily. They then see how living organisms are classified, and note how these groupings are natural, nearly always reflecting the same ancestral relationships in nested hierarchies, regardless of the deeper criteria. Such patterns are revealed with a look at several phylogenetic trees of primates. Finally, teachers are encouraged to give their students lab experience collecting data from a variety of primate characteristics (skulls, chromosomes, and hemoglobin), to see for themselves the congruency of those data sets.

416

ECOLOGICAL CLASSIFICATION ISSUES AND RESEARCH  

EPA Science Inventory

Purposes and need for ecological classification will be discussed. Some brief examples will highlight regional and watershed approaches, general issues of extrapolation and classification helpful to monitoring/assessment design for larger aquatic systems, and some specific concep...

417

Work Classification in Ancient Times.  

ERIC Educational Resources Information Center

The divisions of labor and the classifications of work in ancient times are described, and an early four-part classification based on the "Bhagavad Gita" is compared with that of the present "Dictionary of Occupational Titles." (Author)

Hopke, William

1979-01-01

418

28 CFR 17.26 - Derivative classification.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 2010-07-01 false Derivative classification. 17.26 Section...Classified Information § 17.26 Derivative classification. (a) Persons...classification guides. (b) Persons who apply derivative classification markings shall...

2010-07-01

419

32 CFR 644.426 - Classification.  

Code of Federal Regulations, 2010 CFR

...the special acts, classification will be coordinated with the interested Federal agency. The classification will be recorded on ENG Form 1825 (Real Property Classification), with sufficient information to justify the classification. Surplus property may...

2010-07-01

420

Nominated Texture Based Cervical Cancer Classification  

PubMed Central

Accurate classification of Pap smear images becomes the challenging task in medical image processing. This can be improved in two ways. One way is by selecting suitable well defined specific features and the other is by selecting the best classifier. This paper presents a nominated texture based cervical cancer (NTCC) classification system which classifies the Pap smear images into any one of the seven classes. This can be achieved by extracting well defined texture features and selecting best classifier. Seven sets of texture features (24 features) are extracted which include relative size of nucleus and cytoplasm, dynamic range and first four moments of intensities of nucleus and cytoplasm, relative displacement of nucleus within the cytoplasm, gray level cooccurrence matrix, local binary pattern histogram, tamura features, and edge orientation histogram. Few types of support vector machine (SVM) and neural network (NN) classifiers are used for the classification. The performance of the NTCC algorithm is tested and compared to other algorithms on public image database of Herlev University Hospital, Denmark, with 917 Pap smear images. The output of SVM is found to be best for the most of the classes and better results for the remaining classes. PMID:25649913

Mariarputham, Edwin Jayasingh; Stephen, Allwin

2015-01-01

421

Fast Image Texture Classification Using Decision Trees  

NASA Technical Reports Server (NTRS)

Texture analysis would permit improved autonomous, onboard science data interpretation for adaptive navigation, sampling, and downlink decisions. These analyses would assist with terrain analysis and instrument placement in both macroscopic and microscopic image data products. Unfortunately, most state-of-the-art texture analysis demands computationally expensive convolutions of filters involving many floating-point operations. This makes them infeasible for radiation- hardened computers and spaceflight hardware. A new method approximates traditional texture classification of each image pixel with a fast decision-tree classifier. The classifier uses image features derived from simple filtering operations involving integer arithmetic. The texture analysis method is therefore amenable to implementation on FPGA (field-programmable gate array) hardware. Image features based on the "integral image" transform produce descriptive and efficient texture descriptors. Training the decision tree on a set of training data yields a classification scheme that produces reasonable approximations of optimal "texton" analysis at a fraction of the computational cost. A decision-tree learning algorithm employing the traditional k-means criterion of inter-cluster variance is used to learn tree structure from training data. The result is an efficient and accurate summary of surface morphology in images. This work is an evolutionary advance that unites several previous algorithms (k-means clustering, integral images, decision trees) and applies them to a new problem domain (morphology analysis for autonomous science during remote exploration). Advantages include order-of-magnitude improvements in runtime, feasibility for FPGA hardware, and significant improvements in texture classification accuracy.

Thompson, David R.

2011-01-01

422

Anatomical Brain Images Alone Can Accurately Diagnose Chronic Neuropsychiatric Illnesses  

PubMed Central

Objective Diagnoses using imaging-based measures alone offer the hope of improving the accuracy of clinical diagnosis, thereby reducing the costs associated with incorrect treatments. Previous attempts to use brain imaging for diagnosis, however, have had only limited success in diagnosing patients who are independent of the samples used to derive the diagnostic algorithms. We aimed to develop a classification algorithm that can accurately diagnose chronic, well-characterized neuropsychiatric illness in single individuals, given the availability of sufficiently precise delineations of brain regions across several neural systems in anatomical MR images of the brain. Methods We have developed an automated method to diagnose individuals as having one of various neuropsychiatric illnesses using only anatomical MRI scans. The method employs a semi-supervised learning algorithm that discovers natural groupings of brains based on the spatial patterns of variation in the morphology of the cerebral cortex and other brain regions. We used split-half and leave-one-out cross-validation analyses in large MRI datasets to assess the reproducibility and diagnostic accuracy of those groupings. Results In MRI datasets from persons with Attention-Deficit/Hyperactivity Disorder, Schizophrenia, Tourette Syndrome, Bipolar Disorder, or persons at high or low familial risk for Major Depressive Disorder, our method discriminated with high specificity and nearly perfect sensitivity the brains of persons who had one specific neuropsychiatric disorder from the brains of healthy participants and the brains of persons who had a different neuropsychiatric disorder. Conclusions Although the classification algorithm presupposes the availability of precisely delineated brain regions, our findings suggest that patterns of morphological variation across brain surfaces, extracted from MRI scans alone, can successfully diagnose the presence of chronic neuropsychiatric disorders. Extensions of these methods are likely to provide biomarkers that will aid in identifying biological subtypes of those disorders, predicting disease course, and individualizing treatments for a wide range of neuropsychiatric illnesses. PMID:23236384

Bansal, Ravi; Staib, Lawrence H.; Laine, Andrew F.; Hao, Xuejun; Xu, Dongrong; Liu, Jun; Weissman, Myrna; Peterson, Bradley S.

2012-01-01

423

Phylogenetic and structural studies of a novel equine papillomavirus identified from aural plaques.  

PubMed

Papillomaviruses (PVs) infect a wide range of animal species and show great genetic diversity. To date, excluding equine sarcoids, only three species of PVs were identified associated with lesions in horses: Equus caballus papillomavirus 1 (EcPV1-cutaneous), EcPV2 (genital) and EcPV3 (aural plaques). In this study, we identified a novel equine PV from aural plaques, which we designated EcPV4. Cutaneous samples from horses with lesions that were microscopically diagnosed as aural plaques were subjected to DNA extraction, ampli