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Sample records for accurate phylogenetic classification

  1. Accurate phylogenetic classification of DNA fragments based onsequence composition

    SciTech Connect

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

    2006-05-01

    Metagenome studies have retrieved vast amounts of sequenceout of a variety of environments, leading to novel discoveries and greatinsights into the uncultured microbial world. Except for very simplecommunities, diversity makes sequence assembly and analysis a verychallenging problem. To understand the structure a 5 nd function ofmicrobial communities, a taxonomic characterization of the obtainedsequence fragments is highly desirable, yet currently limited mostly tothose sequences that contain phylogenetic marker genes. We show that forclades at the rank of domain down to genus, sequence composition allowsthe very accurate phylogenetic 10 characterization of genomic sequence.We developed a composition-based classifier, PhyloPythia, for de novophylogenetic 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.

  2. Accurate phylogenetic classification of variable-length DNA fragments

    E-print Network

    Cai, Long

    kb of training sequence for the creation of accurate models of sample-specific populations and can shown promise in the characterization of low-complexity commu- nities, and for the dominant organisms

  3. 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

  4. Protein Classification Using Transductive Learning On Phylogenetic Profiles

    E-print Network

    Liao, Li

    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

  5. A functional-phylogenetic classification system for transmembrane solute transporters.

    PubMed

    Saier, M H

    2000-06-01

    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

  6. Novel animal papillomavirus sequences and accurate phylogenetic placement.

    PubMed

    Mengual-Chuliá, Beatriz; García-Pérez, Raquel; Gottschling, Marc; Nindl, Ingo; Bravo, Ignacio G

    2012-12-01

    All amniotes are probably infected by specific papillomaviruses (PVs), but knowledge about PV diversity remains sparse. An insufficient taxon sampling, and a focus on humans as hosts, may perturb phylogenetic analyses leading to wrong conclusions about PV evolution. We performed a systematic approach to explore the diversity of PVs combining rolling circle amplification with the use of "universal" primers to search for the presence of novel PV sequences in animal samples. We communicate 12 sequences putatively corresponding to novel PVs gained from 10 host species in eight mammal families: Bovidae, Canidae, Cervidae, Equidae, Hominidae, Phocoenidae, Procyonidae and Pteropodidae. The phylogenetic position of the new sequences was inferred with an evolutionary placement algorithm under a Maximum Likelihood framework using a pre-computed, well-resolved tree constructed with the E1-E2-L1 gene sequences as a backbone. The new sequences were phylogenetically diverse and could be respectively placed with confidence within all four PV crown groups. The prevailing presence of sequences from the crown groups Alpha+Omikron-PVs and Beta+Xi-PVs may correspond to an increased viral diversity in these taxa, or rather reflect a combination of anthropocentric bias and preferential amplification from commonly used "universal" primers. Our results combined with literature data support the view that the number and diversity of animal PVs is overwhelmingly large. PMID:22960206

  7. A higher-level phylogenetic classification of the Fungi.

    PubMed

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

    2007-05-01

    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, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella. PMID:17572334

  8. Phylogenetic classification of Cordyceps and the clavicipitaceous fungi

    PubMed Central

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

    2007-01-01

    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

  9. Accurate molecular classification of cancer using simple rules

    PubMed Central

    Wang, Xiaosheng; Gotoh, Osamu

    2009-01-01

    Background One intractable problem with using microarray data analysis for cancer classification is how to reduce the extremely high-dimensionality gene feature data to remove the effects of noise. Feature selection is often used to address this problem by selecting informative genes from among thousands or tens of thousands of genes. However, most of the existing methods of microarray-based cancer classification utilize too many genes to achieve accurate classification, which often hampers the interpretability of the models. For a better understanding of the classification results, it is desirable to develop simpler rule-based models with as few marker genes as possible. Methods We screened a small number of informative single genes and gene pairs on the basis of their depended degrees proposed in rough sets. Applying the decision rules induced by the selected genes or gene pairs, we constructed cancer classifiers. We tested the efficacy of the classifiers by leave-one-out cross-validation (LOOCV) of training sets and classification of independent test sets. Results We applied our methods to five cancerous gene expression datasets: leukemia (acute lymphoblastic leukemia [ALL] vs. acute myeloid leukemia [AML]), lung cancer, prostate cancer, breast cancer, and leukemia (ALL vs. mixed-lineage leukemia [MLL] vs. AML). Accurate classification outcomes were obtained by utilizing just one or two genes. Some genes that correlated closely with the pathogenesis of relevant cancers were identified. In terms of both classification performance and algorithm simplicity, our approach outperformed or at least matched existing methods. Conclusion In cancerous gene expression datasets, a small number of genes, even one or two if selected correctly, is capable of achieving an ideal cancer classification effect. This finding also means that very simple rules may perform well for cancerous class prediction. PMID:19874631

  10. Optimal selection of mother wavelet for accurate infant cry classification.

    PubMed

    Saraswathy, J; Hariharan, M; Nadarajaw, Thiyagar; Khairunizam, Wan; Yaacob, Sazali

    2014-06-01

    Wavelet theory is emerging as one of the prevalent tool in signal and image processing applications. However, the most suitable mother wavelet for these applications is still a relative question mark amongst researchers. Selection of best mother wavelet through parameterization leads to better findings for the analysis in comparison to random selection. The objective of this article is to compare the performance of the existing members of mother wavelets and to select the most suitable mother wavelet for accurate infant cry classification. Optimal wavelet is found using three different criteria namely the degree of similarity of mother wavelets, regularity of mother wavelets and accuracy of correct recognition during classification processes. Recorded normal and pathological infant cry signals are decomposed into five levels using wavelet packet transform. Energy and entropy features are extracted at different sub bands of cry signals and their effectiveness are tested with four supervised neural network architectures. Findings of this study expound that, the Finite impulse response based approximation of Meyer is the best wavelet candidate for accurate infant cry classification analysis. PMID:24691930

  11. Toward a phylogenetic classification of the Leotiomycetes based on rDNA data Zheng Wang1

    E-print Network

    Hibbett, David S.

    Toward a phylogenetic classification of the Leotiomycetes based on rDNA data Zheng Wang1 Department rDNA regions (SSU+LSU+5.8S rDNA). A dataset was prepared with rDNA sequences data from 108 isolates cinerea, and between species of Bulgaria and Phadidiopycnis. Sequence data of rDNA regions

  12. A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution.

    PubMed

    Clement, Wendy L; Arakaki, Mónica; Sweeney, Patrick W; Edwards, Erika J; Donoghue, Michael J

    2014-06-13

    • Premise of the study: Despite recent progress, significant uncertainties remain concerning relationships among early-branching lineages within Viburnum (Adoxaceae), prohibiting a new classification and hindering studies of character evolution and the increasing use of Viburnum in addressing a wide range of ecological and evolutionary questions. We hoped to resolve these issues by sequencing whole plastid genomes for representative species and combining these with molecular data previously obtained from an expanded taxon sample.• Methods: We performed paired-end Illumina sequencing of plastid genomes of 22 Viburnum species and combined these data with a 10-gene data set to infer phylogenetic relationships for 113 species. We used the results to devise a comprehensive phylogenetic classification and to analyze the evolution of eight morphological characters that vary among early-branching lineages.• Key results: With greatly increased levels of confidence in most of the early branches, we propose a phylogenetic classification of Viburnum, providing formal phylogenetic definitions for 30 clades, including 13 with names recognized under the International Code of Nomenclature for Algae, Fungi, and Plants, eight with previously proposed informal names, and nine newly proposed names for major branches. Our parsimony reconstructions of bud structure, leaf margins, inflorescence form, ruminate endosperm, extrafloral nectaries, glandular trichomes, palisade anatomy, and pollen exine showed varying levels of homoplasy, but collectively provided morphological support for some, though not all, of the major clades.• Conclusions: Our study demonstrates the value of next-generation plastid sequencing, the ease of creating a formal phylogenetic classification, and the utility of such a system in describing patterns of character evolution. PMID:24928633

  13. Automatic classification and accurate size measurement of blank mask defects

    NASA Astrophysics Data System (ADS)

    Bhamidipati, Samir; Paninjath, Sankaranarayanan; Pereira, Mark; Buck, Peter

    2015-07-01

    A blank mask and its preparation stages, such as cleaning or resist coating, play an important role in the eventual yield obtained by using it. Blank mask defects' impact analysis directly depends on the amount of available information such as the number of defects observed, their accurate locations and sizes. Mask usability qualification at the start of the preparation process, is crudely based on number of defects. Similarly, defect information such as size is sought to estimate eventual defect printability on the wafer. Tracking of defect characteristics, specifically size and shape, across multiple stages, can further be indicative of process related information such as cleaning or coating process efficiencies. At the first level, inspection machines address the requirement of defect characterization by detecting and reporting relevant defect information. The analysis of this information though is still largely a manual process. With advancing technology nodes and reducing half-pitch sizes, a large number of defects are observed; and the detailed knowledge associated, make manual defect review process an arduous task, in addition to adding sensitivity to human errors. Cases where defect information reported by inspection machine is not sufficient, mask shops rely on other tools. Use of CDSEM tools is one such option. However, these additional steps translate into increased costs. Calibre NxDAT based MDPAutoClassify tool provides an automated software alternative to the manual defect review process. Working on defect images generated by inspection machines, the tool extracts and reports additional information such as defect location, useful for defect avoidance[4][5]; defect size, useful in estimating defect printability; and, defect nature e.g. particle, scratch, resist void, etc., useful for process monitoring. The tool makes use of smart and elaborate post-processing algorithms to achieve this. Their elaborateness is a consequence of the variety and complexity of defects encountered. The variety arises due to factors such as defect nature, size, shape and composition; and the optical phenomena occurring around the defect. This paper focuses on preliminary characterization results, in terms of classification and size estimation, obtained by Calibre MDPAutoClassify tool on a variety of mask blank defects. It primarily highlights the challenges faced in achieving the results with reference to the variety of defects observed on blank mask substrates and the underlying complexities which make accurate defect size measurement an important and challenging task.

  14. Accurate mobile malware detection and classification in the cloud.

    PubMed

    Wang, Xiaolei; Yang, Yuexiang; Zeng, Yingzhi

    2015-01-01

    As the dominator of the Smartphone operating system market, consequently android has attracted the attention of s malware authors and researcher alike. The number of types of android malware is increasing rapidly regardless of the considerable number of proposed malware analysis systems. In this paper, by taking advantages of low false-positive rate of misuse detection and the ability of anomaly detection to detect zero-day malware, we propose a novel hybrid detection system based on a new open-source framework CuckooDroid, which enables the use of Cuckoo Sandbox's features to analyze Android malware through dynamic and static analysis. Our proposed system mainly consists of two parts: anomaly detection engine performing abnormal apps detection through dynamic analysis; signature detection engine performing known malware detection and classification with the combination of static and dynamic analysis. We evaluate our system using 5560 malware samples and 6000 benign samples. Experiments show that our anomaly detection engine with dynamic analysis is capable of detecting zero-day malware with a low false negative rate (1.16 %) and acceptable false positive rate (1.30 %); it is worth noting that our signature detection engine with hybrid analysis can accurately classify malware samples with an average positive rate 98.94 %. Considering the intensive computing resources required by the static and dynamic analysis, our proposed detection system should be deployed off-device, such as in the Cloud. The app store markets and the ordinary users can access our detection system for malware detection through cloud service. PMID:26543718

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

    E-print Network

    Kansas, University of

    patterns from a graph database. We then map subgraphs to graphs in the graph database and use a process we 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

  16. 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...

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

    USGS Publications Warehouse

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

    2009-01-01

    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.

  18. Classification of Phylogenetic Profiles for Protein Function Prediction: An SVM Approach

    NASA Astrophysics Data System (ADS)

    Kotaru, Appala Raju; Joshi, Ramesh C.

    Predicting the function of an uncharacterized protein is a major challenge in post-genomic era due to problems complexity and scale. Having knowledge of protein function is a crucial link in the development of new drugs, better crops, and even the development of biochemicals such as biofuels. Recently numerous high-throughput experimental procedures have been invented to investigate the mechanisms leading to the accomplishment of a protein’s function and Phylogenetic profile is one of them. Phylogenetic profile is a way of representing a protein which encodes evolutionary history of proteins. In this paper we proposed a method for classification of phylogenetic profiles using supervised machine learning method, support vector machine classification along with radial basis function as kernel for identifying functionally linked proteins. We experimentally evaluated the performance of the classifier with the linear kernel, polynomial kernel and compared the results with the existing tree kernel. In our study we have used proteins of the budding yeast saccharomyces cerevisiae genome. We generated the phylogenetic profiles of 2465 yeast genes and for our study we used the functional annotations that are available in the MIPS database. Our experiments show that the performance of the radial basis kernel is similar to polynomial kernel is some functional classes together are better than linear, tree kernel and over all radial basis kernel outperformed the polynomial kernel, linear kernel and tree kernel. In analyzing these results we show that it will be feasible to make use of SVM classifier with radial basis function as kernel to predict the gene functionality using phylogenetic profiles.

  19. A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs

    PubMed Central

    Huang, Yong; Gu, Xun

    2007-01-01

    Background Phylogenetically related miRNAs (miRNA families) convey important information of the function and evolution of miRNAs. Due to the special sequence features of miRNAs, pair-wise sequence identity between miRNA precursors alone is often inadequate for unequivocally judging the phylogenetic relationships between miRNAs. Most of the current methods for miRNA classification rely heavily on manual inspection and lack measurements of the reliability of the results. Results In this study, we designed an analysis pipeline (the Phylogeny-Bootstrap-Cluster (PBC) pipeline) to identify miRNA families based on branch stability in the bootstrap trees derived from overlapping genome-wide miRNA sequence sets. We tested the PBC analysis pipeline with the miRNAs from six animal species, H. sapiens, M. musculus, G. gallus, D. rerio, D. melanogaster, and C. elegans. The resulting classification was compared with the miRNA families defined in miRBase. The two classifications were largely consistent. Conclusion The PBC analysis pipeline is an efficient method for classifying large numbers of heterogeneous miRNA sequences. It requires minimum human involvement and provides measurements of the reliability of the classification results. PMID:17341314

  20. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.

    PubMed

    Cavalier-Smith, T

    2002-03-01

    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

  1. Use of Spoligotyping for Accurate Classification of Recurrent Tuberculosis

    PubMed Central

    Warren, R. M.; Streicher, E. M.; Charalambous, S.; Churchyard, G.; van der Spuy, G. D.; Grant, A. D.; van Helden, P. D.; Victor, T. C.

    2002-01-01

    The spoligotyping method has become an important tool for the tracking of Mycobacterium tuberculosis strains in different epidemiological settings. In this study, we demonstrate the ability of the spoligotyping technique to accurately determine the pathogenetic mechanism of recurrent disease. This methodology has advantages over conventional restriction fragment length polymorphism methods which may be useful in large- scale intervention studies. PMID:12354898

  2. Phylogenetic Classification of Protozoa Based on the Structure of the Linker Domain in the Bifunctional Enzyme, Dihydrofolate

    E-print Network

    Richardson, David

    Phylogenetic Classification of Protozoa Based on the Structure of the Linker Domain a number of protozoa in two distinct and dissimilar structural fami- lies corresponding to two evolutionary- sification and evolutionary progression of the protozoa (2­5). It is thought that many eukaryotic taxa arose

  3. Fast and Accurate Gene Prediction by Decision Tree Classification , Jeffrey Shih-Chieh Chu2

    E-print Network

    Wang, Ke

    Fast and Accurate Gene Prediction by Decision Tree Classification Rong She1 , Jeffrey Shih Department of Molecular Biology and Biochemistry, Simon Fraser University, Canada. Abstract Gene prediction and are still evolving. In this paper, we present a novel gene prediction method that is both fast and ac

  4. Phylogenetic Classification at Generic Level in the Absence of Distinct Phylogenetic Patterns of Phenotypical Variation: A Case Study in Graphidaceae (Ascomycota)

    PubMed Central

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

    2012-01-01

    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

  5. Accurate crop classification using hierarchical genetic fuzzy rule-based systems

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    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.

  6. Towards a Formal Genealogical Classification of the Lezgian Languages (North Caucasus): Testing Various Phylogenetic Methods on Lexical Data

    PubMed Central

    Kassian, Alexei

    2015-01-01

    A lexicostatistical classification is proposed for 20 languages and dialects of the Lezgian group of the North Caucasian family, based on meticulously compiled 110-item wordlists, published as part of the Global Lexicostatistical Database project. The lexical data have been subsequently analyzed with the aid of the principal phylogenetic methods, both distance-based and character-based: Starling neighbor joining (StarlingNJ), Neighbor joining (NJ), Unweighted pair group method with arithmetic mean (UPGMA), Bayesian Markov chain Monte Carlo (MCMC), Unweighted maximum parsimony (UMP). Cognation indexes within the input matrix were marked by two different algorithms: traditional etymological approach and phonetic similarity, i.e., the automatic method of consonant classes (Levenshtein distances). Due to certain reasons (first of all, high lexicographic quality of the wordlists and a consensus about the Lezgian phylogeny among Caucasologists), the Lezgian database is a perfect testing area for appraisal of phylogenetic methods. For the etymology-based input matrix, all the phylogenetic methods, with the possible exception of UMP, have yielded trees that are sufficiently compatible with each other to generate a consensus phylogenetic tree of the Lezgian lects. The obtained consensus tree agrees with the traditional expert classification as well as some of the previously proposed formal classifications of this linguistic group. Contrary to theoretical expectations, the UMP method has suggested the least plausible tree of all. In the case of the phonetic similarity-based input matrix, the distance-based methods (StarlingNJ, NJ, UPGMA) have produced the trees that are rather close to the consensus etymology-based tree and the traditional expert classification, whereas the character-based methods (Bayesian MCMC, UMP) have yielded less likely topologies. PMID:25719456

  7. DNA barcode analysis: a comparison of phylogenetic and statistical classification methods

    PubMed Central

    Austerlitz, Frederic; David, Olivier; Schaeffer, Brigitte; Bleakley, Kevin; Olteanu, Madalina; Leblois, Raphael; Veuille, Michel; Laredo, Catherine

    2009-01-01

    Background DNA barcoding aims to assign individuals to given species according to their sequence at a small locus, generally part of the CO1 mitochondrial gene. Amongst other issues, this raises the question of how to deal with within-species genetic variability and potential transpecific polymorphism. In this context, we examine several assignation methods belonging to two main categories: (i) phylogenetic methods (neighbour-joining and PhyML) that attempt to account for the genealogical framework of DNA evolution and (ii) supervised classification methods (k-nearest neighbour, CART, random forest and kernel methods). These methods range from basic to elaborate. We investigated the ability of each method to correctly classify query sequences drawn from samples of related species using both simulated and real data. Simulated data sets were generated using coalescent simulations in which we varied the genealogical history, mutation parameter, sample size and number of species. Results No method was found to be the best in all cases. The simplest method of all, "one nearest neighbour", was found to be the most reliable with respect to changes in the parameters of the data sets. The parameter most influencing the performance of the various methods was molecular diversity of the data. Addition of genetically independent loci - nuclear genes - improved the predictive performance of most methods. Conclusion The study implies that taxonomists can influence the quality of their analyses either by choosing a method best-adapted to the configuration of their sample, or, given a certain method, increasing the sample size or altering the amount of molecular diversity. This can be achieved either by sequencing more mtDNA or by sequencing additional nuclear genes. In the latter case, they may also have to modify their data analysis method. PMID:19900297

  8. Molecular and morphological data supporting phylogenetic reconstruction of the genus Goniothalamus (Annonaceae), including a reassessment of previous infrageneric classifications

    PubMed Central

    Tang, Chin Cheung; Thomas, Daniel C.; Saunders, Richard M.K.

    2015-01-01

    Data is presented in support of a phylogenetic reconstruction of the species-rich early-divergent angiosperm genus Goniothalamus (Annonaceae) (Tang et al., Mol. Phylogenetic Evol., 2015) [1], inferred using chloroplast DNA (cpDNA) sequences. The data includes a list of primers for amplification and sequencing for nine cpDNA regions: atpB-rbcL, matK, ndhF, psbA-trnH, psbM-trnD, rbcL, trnL-F, trnS-G, and ycf1, the voucher information and molecular data (GenBank accession numbers) of 67 ingroup Goniothalamus accessions and 14 outgroup accessions selected from across the tribe Annoneae, and aligned data matrices for each gene region. We also present our Bayesian phylogenetic reconstructions for Goniothalamus, with information on previous infrageneric classifications superimposed to enable an evaluation of monophyly, together with a taxon-character data matrix (with 15 morphological characters scored for 66 Goniothalamus species and seven other species from the tribe Annoneae that are shown to be phylogenetically correlated). PMID:26286044

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

    NASA Astrophysics Data System (ADS)

    Löw, Fabian; Duveiller, Grégory

    2013-10-01

    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.

  10. GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics

    PubMed Central

    Smalter, Aaron; Huan, Jun (Luke); Jia, Yi; Lushington, Gerald

    2011-01-01

    Graph data mining is an active research area. Graphs are general modeling tools to organize information from heterogeneous sources and have been applied in many scientific, engineering, and business fields. With the fast accumulation of graph data, building highly accurate predictive models for graph data emerges as a new challenge that has not been fully explored in the data mining community. In this paper, we demonstrate a novel technique called graph pattern diffusion (GPD) kernel. Our idea is to leverage existing frequent pattern discovery methods and to explore the application of kernel classifier (e.g., support vector machine) in building highly accurate graph classification. In our method, we first identify all frequent patterns from a graph database. We then map subgraphs to graphs in the graph database and use a process we call “pattern diffusion” to label nodes in the graphs. Finally, we designed a graph alignment algorithm to compute the inner product of two graphs. We have tested our algorithm using a number of chemical structure data. The experimental results demonstrate that our method is significantly better than competing methods such as those kernel functions based on paths, cycles, and subgraphs. PMID:20431140

  11. Concomitant Medical Conditions and Therapies Preclude Accurate Classification of Children With Severe or Severe Complicated Clostridium difficile Infection.

    PubMed

    Kociolek, Larry K; Patel, Sameer J; Shulman, Stanford T; Gerding, Dale N

    2015-12-01

    Severe and severe complicated Clostridium difficile infections (SCDI/SCCDI) were retrospectively assessed in a pediatric cohort. Underlying medical conditions and concomitant medical therapy preclude accurate classification of children with SCDI/SCCDI, using current CDI severity definitions. Revised CDI definitions in children should focus on more objective, age-appropriate, and CDI-specific markers of severity. PMID:26582882

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

    USGS Publications Warehouse

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

    2005-01-01

    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.

  13. Molecular phylogenetic relationships and a revised classification of the subfamily Ericoideae (Ericaceae).

    PubMed

    Gillespie, Emily; Kron, Kathleen

    2010-07-01

    Subfamily Ericoideae (Ericaceae) includes 19 genera in five recognized tribes. Relationships involving the deepest nodes have been difficult to resolve, limiting the potential for further cladistic studies within the Ericoideae. The current study analyses six molecular markers using Bayesian, Maximum Likelihood and Maximum Parsimony methods to improve phylogenetic resolution within the Ericoideae. Two large clades were discovered. One clade includes the Phyllodoceae and Bejaria. The sister clade includes the Empetreae+Diplarche, Ericeae, Rhodoreae, and a clade comprised of Bryanthus and Ledothamnus. The current study improves upon the resolution of the phylogeny of the Ericoideae, particularly demonstrating support for the deepest nodes. Based on these results, we propose to retain the Ericeae, expand the Phyllodoceae to include Bejaria, expand the Empetreae to include Diplarche, retain the Rhodoreae (without Diplarche), dismantle the Bejarieae, and construct a new tribe, Bryantheae (Bryanthus and Ledothamnus). PMID:20193767

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

    PubMed Central

    Margulis, L

    1996-01-01

    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

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

    NASA Technical Reports Server (NTRS)

    Margulis, L.

    1996-01-01

    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.

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

    PubMed

    Margulis, L

    1996-02-01

    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. PMID:8577716

  17. Assignment of Calibration Information to Deeper Phylogenetic Nodes is More Effective in Obtaining Precise and Accurate Divergence Time Estimates.

    PubMed

    Mello, Beatriz; Schrago, Carlos G

    2014-01-01

    Divergence time estimation has become an essential tool for understanding macroevolutionary events. Molecular dating aims to obtain reliable inferences, which, within a statistical framework, means jointly increasing the accuracy and precision of estimates. Bayesian dating methods exhibit the propriety of a linear relationship between uncertainty and estimated divergence dates. This relationship occurs even if the number of sites approaches infinity and places a limit on the maximum precision of node ages. However, how the placement of calibration information may affect the precision of divergence time estimates remains an open question. In this study, relying on simulated and empirical data, we investigated how the location of calibration within a phylogeny affects the accuracy and precision of time estimates. We found that calibration priors set at median and deep phylogenetic nodes were associated with higher precision values compared to analyses involving calibration at the shallowest node. The results were independent of the tree symmetry. An empirical mammalian dataset produced results that were consistent with those generated by the simulated sequences. Assigning time information to the deeper nodes of a tree is crucial to guarantee the accuracy and precision of divergence times. This finding highlights the importance of the appropriate choice of outgroups in molecular dating. PMID:24855333

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

    PubMed Central

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

    2015-01-01

    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

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

    PubMed

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

    2015-03-23

    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

  20. Towards a phylogenetic generic classification of Thelypteridaceae: Additional sampling suggests alterations of neotropical taxa and further study of paleotropical genera.

    PubMed

    Almeida, Thaís Elias; Hennequin, Sabine; Schneider, Harald; Smith, Alan R; Batista, João Aguiar Nogueira; Ramalho, Aline Joseph; Proite, Karina; Salino, Alexandre

    2016-01-01

    Thelypteridaceae is one of the largest fern families, having about 950 species and a cosmopolitan distribution but with most species occurring in tropical and subtropical regions. Its generic classification remains controversial, with different authors recognizing from one up to 32 genera. Phylogenetic relationships within the family have not been exhaustively studied, but previous studies have confirmed the monophyly of the lineage. Thus far, sampling has been inadequate for establishing a robust hypothesis of infrafamilial relationships within the family. In order to understand phylogenetic relationships within Thelypteridaceae and thus to improve generic reclassification, we expand the molecular sampling, including new samples of Old World taxa and, especially, many additional neotropical representatives. We also explore the monophyly of exclusively or mostly neotropical genera Amauropelta, Goniopteris, Meniscium, and Steiropteris. Our sampling includes 68 taxa and 134 newly generated sequences from two plastid genomic regions (rps4-trnS and trnL-trnF), plus 73 rps4 and 72 trnL-trnF sequences from GenBank. These data resulted in a concatenated matrix of 1980 molecular characters for 149 taxa. The combined data set was analyzed using maximum parsimony and bayesian inference of phylogeny. Our results are consistent with the general topological structure found in previous studies, including two main lineages within the family: phegopteroid and thelypteroid. The thelypteroid lineage comprises two clades; one of these included the segregates Metathelypteris, Coryphopteris, and Amauropelta (including part of Parathelypteris), whereas the other comprises all segregates of Cyclosorus s.l., such as Goniopteris, Meniscium, and Steiropteris (including Thelypteris polypodioides, previously incertae sedis). The three mainly neotropical segregates were found to be monophyletic but nested in a broadly defined Cyclosorus. The fourth mainly neotropical segregate, Amauropelta, was found to include species considered to be part of Parathelypteris. In Old World thelypteroids, which correspond to nearly half the diversity in the family, an increase in sampling is still needed to resolve relationships and circumscription of genera, particularly in the christelloid clade (i.e., Amphineuron, Chingia, Christella, Pneumatopteris, Pronephrium, and Sphaerostephanos). Based on currently available knowledge, we propose the recognition of 16 genera in the family. PMID:26400101

  1. Highly Accurate Classification of Watson-Crick Basepairs on Termini of Single DNA Molecules

    PubMed Central

    Winters-Hilt, Stephen; Vercoutere, Wenonah; DeGuzman, Veronica S.; Deamer, David; Akeson, Mark; Haussler, David

    2003-01-01

    We introduce a computational method for classification of individual DNA molecules measured by an ?-hemolysin channel detector. We show classification with better than 99% accuracy for DNA hairpin molecules that differ only in their terminal Watson-Crick basepairs. Signal classification was done in silico to establish performance metrics (i.e., where train and test data were of known type, via single-species data files). It was then performed in solution to assay real mixtures of DNA hairpins. Hidden Markov Models (HMMs) were used with Expectation/Maximization for denoising and for associating a feature vector with the ionic current blockade of the DNA molecule. Support Vector Machines (SVMs) were used as discriminators, and were the focus of off-line training. A multiclass SVM architecture was designed to place less discriminatory load on weaker discriminators, and novel SVM kernels were used to boost discrimination strength. The tuning on HMMs and SVMs enabled biophysical analysis of the captured molecule states and state transitions; structure revealed in the biophysical analysis was used for better feature selection. PMID:12547778

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

    PubMed

    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

    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

  3. A comprehensive multilocus phylogeny of the Neotropical cotingas (Cotingidae, Aves) with a comparative evolutionary analysis of breeding system and plumage dimorphism and a revised phylogenetic classification.

    PubMed

    Berv, Jacob S; Prum, Richard O

    2014-12-01

    The Neotropical cotingas (Cotingidae: Aves) are a group of passerine birds that are characterized by extreme diversity in morphology, ecology, breeding system, and behavior. Here, we present a comprehensive phylogeny of the Neotropical cotingas based on six nuclear and mitochondrial loci (?7500 bp) for a sample of 61 cotinga species in all 25 genera, and 22 species of suboscine outgroups. Our taxon sample more than doubles the number of cotinga species studied in previous analyses, and allows us to test the monophyly of the cotingas as well as their intrageneric relationships with high resolution. We analyze our genetic data using a Bayesian species tree method, and concatenated Bayesian and maximum likelihood methods, and present a highly supported phylogenetic hypothesis. We confirm the monophyly of the cotingas, and present the first phylogenetic evidence for the relationships of Phibalura flavirostris as the sister group to Ampelion and Doliornis, and the paraphyly of Lipaugus with respect to Tijuca. In addition, we resolve the diverse radiations within the Cotinga, Lipaugus, Pipreola, and Procnias genera. We find no support for Darwin's (1871) hypothesis that the increase in sexual selection associated with polygynous breeding systems drives the evolution of color dimorphism in the cotingas, at least when analyzed at a broad categorical scale. Finally, we present a new comprehensive phylogenetic classification of all cotinga species. PMID:25234241

  4. Phylogenetic classification of Escherichia coli O26 strains from human, animals, and environmental origins using nucleotide polymorphisms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Shiga toxin-producing Escherichia coli (STEC) O26 strains are food-borne pathogens that were recently classified as adulterants in certain beef products. Little is known about their genetic diversity, including whether or not phylogenetic subtypes within the serogroup vary in their assoc...

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

    PubMed Central

    Michaud, Vincent; Randriamparany, Tantely; Albina, Emmanuel

    2013-01-01

    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

  6. Classification

    ERIC Educational Resources Information Center

    Clary, Renee; Wandersee, James

    2013-01-01

    In this article, Renee Clary and James Wandersee describe the beginnings of "Classification," which lies at the very heart of science and depends upon pattern recognition. Clary and Wandersee approach patterns by first telling the story of the "Linnaean classification system," introduced by Carl Linnacus (1707-1778), who is…

  7. A species independent universal bio-detection microarray for pathogen forensics and phylogenetic classification of unknown microorganisms

    PubMed Central

    2011-01-01

    Background The ability to differentiate a bioterrorist attack or an accidental release of a research pathogen from a naturally occurring pandemic or disease event is crucial to the safety and security of this nation by enabling an appropriate and rapid response. It is critical in samples from an infected patient, the environment, or a laboratory to quickly and accurately identify the precise pathogen including natural or engineered variants and to classify new pathogens in relation to those that are known. Current approaches for pathogen detection rely on prior genomic sequence information. Given the enormous spectrum of genetic possibilities, a field deployable, robust technology, such as a universal (any species) microarray has near-term potential to address these needs. Results A new and comprehensive sequence-independent array (Universal Bio-Signature Detection Array) was designed with approximately 373,000 probes. The main feature of this array is that the probes are computationally derived and sequence independent. There is one probe for each possible 9-mer sequence, thus 49 (262,144) probes. Each genome hybridized on this array has a unique pattern of signal intensities corresponding to each of these probes. These signal intensities were used to generate an un-biased cluster analysis of signal intensity hybridization patterns that can easily distinguish species into accepted and known phylogenomic relationships. Within limits, the array is highly sensitive and is able to detect synthetically mixed pathogens. Examples of unique hybridization signal intensity patterns are presented for different Brucella species as well as relevant host species and other pathogens. These results demonstrate the utility of the UBDA array as a diagnostic tool in pathogen forensics. Conclusions This pathogen detection system is fast, accurate and can be applied to any species. Hybridization patterns are unique to a specific genome and these can be used to decipher the identity of a mixed pathogen sample and can separate hosts and pathogens into their respective phylogenomic relationships. This technology can also differentiate between different species and classify genomes into their known clades. The development of this technology will result in the creation of an integrated biomarker-specific bio-signature, multiple select agent specific detection system. PMID:21672191

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

    NASA Astrophysics Data System (ADS)

    Bechet, P.; Mitran, R.; Munteanu, M.

    2013-08-01

    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.

  9. Cetacean morbilliviruses are phylogenetically divergent.

    PubMed

    van de Bildt, M W G; Kuiken, T; Osterhaus, A D M E

    2005-03-01

    We performed a phylogenetic comparison of porpoise morbillivirus (PMV) and dolphin morbillivirus (DMV) isolates from porpoises and dolphins respectively according to criteria adopted by the World Health Organization for the phylogenetic comparison of measles viruses. PMV and DMV were more divergent than the most distantly related measles virus strains, thus challenging the classification of PMV and DMV as two strains of a single species, cetacean morbillivirus. PMID:15747165

  10. Phylogenetic Status of an Unrecorded Species of Curvularia, C. spicifera, Based on Current Classification System of Curvularia and Bipolaris Group Using Multi Loci

    PubMed Central

    Jeon, Sun Jeong; Nguyen, Thi Thuong Thuong

    2015-01-01

    A seed-borne fungus, Curvularia sp. EML-KWD01, was isolated from an indigenous wheat seed by standard blotter method. This fungus was characterized based on the morphological characteristics and molecular phylogenetic analysis. Phylogenetic status of the fungus was determined using sequences of three loci: rDNA internal transcribed spacer, large ribosomal subunit, and glyceraldehyde 3-phosphate dehydrogenase gene. Multi loci sequencing analysis revealed that this fungus was Curvularia spicifera within Curvularia group 2 of family Pleosporaceae. PMID:26539036

  11. Fast, Simple and Accurate Handwritten Digit Classification by Training Shallow Neural Network Classifiers with the ‘Extreme Learning Machine’ Algorithm

    PubMed Central

    McDonnell, Mark D.; Tissera, Migel D.; Vladusich, Tony; van Schaik, André; Tapson, Jonathan

    2015-01-01

    Recent advances in training deep (multi-layer) architectures have inspired a renaissance in neural network use. For example, deep convolutional networks are becoming the default option for difficult tasks on large datasets, such as image and speech recognition. However, here we show that error rates below 1% on the MNIST handwritten digit benchmark can be replicated with shallow non-convolutional neural networks. This is achieved by training such networks using the ‘Extreme Learning Machine’ (ELM) approach, which also enables a very rapid training time (? 10 minutes). Adding distortions, as is common practise for MNIST, reduces error rates even further. Our methods are also shown to be capable of achieving less than 5.5% error rates on the NORB image database. To achieve these results, we introduce several enhancements to the standard ELM algorithm, which individually and in combination can significantly improve performance. The main innovation is to ensure each hidden-unit operates only on a randomly sized and positioned patch of each image. This form of random ‘receptive field’ sampling of the input ensures the input weight matrix is sparse, with about 90% of weights equal to zero. Furthermore, combining our methods with a small number of iterations of a single-batch backpropagation method can significantly reduce the number of hidden-units required to achieve a particular performance. Our close to state-of-the-art results for MNIST and NORB suggest that the ease of use and accuracy of the ELM algorithm for designing a single-hidden-layer neural network classifier should cause it to be given greater consideration either as a standalone method for simpler problems, or as the final classification stage in deep neural networks applied to more difficult problems. PMID:26262687

  12. Fast, Simple and Accurate Handwritten Digit Classification by Training Shallow Neural Network Classifiers with the 'Extreme Learning Machine' Algorithm.

    PubMed

    McDonnell, Mark D; Tissera, Migel D; Vladusich, Tony; van Schaik, André; Tapson, Jonathan

    2015-01-01

    Recent advances in training deep (multi-layer) architectures have inspired a renaissance in neural network use. For example, deep convolutional networks are becoming the default option for difficult tasks on large datasets, such as image and speech recognition. However, here we show that error rates below 1% on the MNIST handwritten digit benchmark can be replicated with shallow non-convolutional neural networks. This is achieved by training such networks using the 'Extreme Learning Machine' (ELM) approach, which also enables a very rapid training time (? 10 minutes). Adding distortions, as is common practise for MNIST, reduces error rates even further. Our methods are also shown to be capable of achieving less than 5.5% error rates on the NORB image database. To achieve these results, we introduce several enhancements to the standard ELM algorithm, which individually and in combination can significantly improve performance. The main innovation is to ensure each hidden-unit operates only on a randomly sized and positioned patch of each image. This form of random 'receptive field' sampling of the input ensures the input weight matrix is sparse, with about 90% of weights equal to zero. Furthermore, combining our methods with a small number of iterations of a single-batch backpropagation method can significantly reduce the number of hidden-units required to achieve a particular performance. Our close to state-of-the-art results for MNIST and NORB suggest that the ease of use and accuracy of the ELM algorithm for designing a single-hidden-layer neural network classifier should cause it to be given greater consideration either as a standalone method for simpler problems, or as the final classification stage in deep neural networks applied to more difficult problems. PMID:26262687

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

    PubMed Central

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

    2012-01-01

    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

  14. 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

    2013-01-01

    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

  15. Phylogenetic Models: Algebra and Evolution

    E-print Network

    Allman, Elizabeth S.

    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

  16. Directional biases in phylogenetic structure quantification: a Mediterranean case study

    PubMed Central

    Molina-Venegas, Rafael; Roquet, Cristina

    2014-01-01

    Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, using a large plant community and elevational dataset, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure; and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well-resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that sensitivity of phylogenetic structure measures to low phylogenetic resolution can strongly differ depending on phylogenetic tree shape. PMID:25076812

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

    PubMed Central

    2013-01-01

    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

  18. PHYLOGENETIC RELATIONSHIPS AND CLASSIFICATION OF DIDELPHID MARSUPIALS,

    E-print Network

    WORLD METATHERIAN MAMMALS ROBERT S. VOSS Department of Mammalogy American Museum of Natural History University of Minnesota BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY Number 322, 177 pp., 54 figures, 18 tables Issued June 30, 2009 Copyright E American Museum of Natural History 2009 ISSN 0003-0090 #12

  19. Phylogenetic system and zoogeography of the Plecoptera.

    PubMed

    Zwick, P

    2000-01-01

    Information about the phylogenetic relationships of Plecoptera is summarized. The few characters supporting monophyly of the order are outlined. Several characters of possible significance for the search for the closest relatives of the stoneflies are discussed, but the sister-group of the order remains unknown. Numerous characters supporting the presently recognized phylogenetic system of Plecoptera are presented, alternative classifications are discussed, and suggestions for future studies are made. Notes on zoogeography are appended. The order as such is old (Permian fossils), but phylogenetic relationships and global distribution patterns suggest that evolution of the extant suborders started with the breakup of Pangaea. There is evidence of extensive recent speciation in all parts of the world. PMID:10761594

  20. Phylogenetic Inference From Conserved sites Alignments

    SciTech Connect

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

    1999-08-15

    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.

  1. Phylogenetic Trees From Sequences

    NASA Astrophysics Data System (ADS)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  2. Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae)

    PubMed Central

    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

    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

  3. A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

    E-print Network

    Rasmussen, Matthew D.

    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 ...

  4. The phylogenetic likelihood library.

    PubMed

    Flouri, T; Izquierdo-Carrasco, F; Darriba, D; Aberer, A J; Nguyen, L-T; Minh, B Q; Von Haeseler, A; Stamatakis, A

    2015-03-01

    We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2-10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www.libpll.org under the GNU General Public License (GPL). PMID:25358969

  5. The Phylogenetic Likelihood Library

    PubMed Central

    Flouri, T.; Izquierdo-Carrasco, F.; Darriba, D.; Aberer, A.J.; Nguyen, L.-T.; Minh, B.Q.; Von Haeseler, A.; Stamatakis, A.

    2015-01-01

    We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2–10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www.libpll.org under the GNU General Public License (GPL). PMID:25358969

  6. [Analysis phylogenetic relationship of Gynostemma (Cucurbitaceae)].

    PubMed

    Qin, Shuang-shuang; Li, Hai-tao; Wang, Zhou-yong; Cui, Zhan-hu; Yu, Li-ying

    2015-05-01

    The sequences of ITS, matK, rbcL and psbA-trnH of 9 Gynostemma species or variety including 38 samples were compared and analyzed by molecular phylogeny method. Hemsleya macrosperma was designated as outgroup. The MP and NJ phylogenetic tree of Gynostemma was built based on ITS sequence, the results of PAUP phylogenetic analysis showed the following results: (1) The eight individuals of G. pentaphyllum var. pentaphyllum were not supported as monophyletic in the strict consensus trees and NJ trees. (2) It is suspected whether G. longipes and G. laxum should be classified as the independent species. (3)The classification of subgenus units of Gynostemma plants is supported. PMID:26323129

  7. Host specificity and phylogenetic relationships of chicken and turkey parvoviruses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous reports indicate that the newly discovered chicken parvoviruses (ChPV) and turkey parvoviruses (TuPV) are very similar to each other, yet they represent different species within a new genus of Parvoviridae. Currently, strain classification is based on the phylogenetic analysis of a 561 bas...

  8. Phylogenetic reconstruction of the wolf spiders (Araneae: Lycosidae) using sequences from the 12S rRNA, 28S rRNA, and NADH1 genes: implications for classification, biogeography, and the evolution of web building behavior.

    PubMed

    Murphy, Nicholas P; Framenau, Volker W; Donnellan, Stephen C; Harvey, Mark S; Park, Yung-Chul; Austin, Andrew D

    2006-03-01

    Current knowledge of the evolutionary relationships amongst the wolf spiders (Araneae: Lycosidae) is based on assessment of morphological similarity or phylogenetic analysis of a small number of taxa. In order to enhance the current understanding of lycosid relationships, phylogenies of 70 lycosid species were reconstructed by parsimony and Bayesian methods using three molecular markers; the mitochondrial genes 12S rRNA, NADH1, and the nuclear gene 28S rRNA. The resultant trees from the mitochondrial markers were used to assess the current taxonomic status of the Lycosidae and to assess the evolutionary history of sheet-web construction in the group. The results suggest that a number of genera are not monophyletic, including Lycosa, Arctosa, Alopecosa, and Artoria. At the subfamilial level, the status of Pardosinae needs to be re-assessed, and the position of a number of genera within their respective subfamilies is in doubt (e.g., Hippasa and Arctosa in Lycosinae and Xerolycosa, Aulonia and Hygrolycosa in Venoniinae). In addition, a major clade of strictly Australasian taxa may require the creation of a new subfamily. The analysis of sheet-web building in Lycosidae revealed that the interpretation of this trait as an ancestral state relies on two factors: (1) an asymmetrical model favoring the loss of sheet-webs and (2) that the suspended silken tube of Pirata is directly descended from sheet-web building. Paralogous copies of the nuclear 28S rRNA gene were sequenced, confounding the interpretation of the phylogenetic analysis and suggesting that a cautionary approach should be taken to the further use of this gene for lycosid phylogenetic analysis. PMID:16503280

  9. Molecular phylogenetics before sequences

    PubMed Central

    Ragan, Mark A; Bernard, Guillaume; Chan, Cheong Xin

    2014-01-01

    From 1971 to 1985, Carl Woese and colleagues generated oligonucleotide catalogs of 16S/18S rRNAs from more than 400 organisms. Using these incomplete and imperfect data, Carl and his colleagues developed unprecedented insights into the structure, function, and evolution of the large RNA components of the translational apparatus. They recognized a third domain of life, revealed the phylogenetic backbone of bacteria (and its limitations), delineated taxa, and explored the tempo and mode of microbial evolution. For these discoveries to have stood the test of time, oligonucleotide catalogs must carry significant phylogenetic signal; they thus bear re-examination in view of the current interest in alignment-free phylogenetics based on k-mers. Here we consider the aims, successes, and limitations of this early phase of molecular phylogenetics. We computationally generate oligonucleotide sets (e-catalogs) from 16S/18S rRNA sequences, calculate pairwise distances between them based on D2 statistics, compute distance trees, and compare their performance against alignment-based and k-mer trees. Although the catalogs themselves were superseded by full-length sequences, this stage in the development of computational molecular biology remains instructive for us today. PMID:24572375

  10. Charles Darwin, beetles and phylogenetics

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

    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.

  11. Charles Darwin, beetles and phylogenetics.

    PubMed

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

    2009-11-01

    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

  12. ClassyFlu: Classification of Influenza A Viruses with Discriminatively Trained Profile-HMMs

    PubMed Central

    Van der Auwera, Sandra; Bulla, Ingo; Ziller, Mario; Pohlmann, Anne; Harder, Timm; Stanke, Mario

    2014-01-01

    Accurate and rapid characterization of influenza A virus (IAV) hemagglutinin (HA) and neuraminidase (NA) sequences with respect to subtype and clade is at the basis of extended diagnostic services and implicit to molecular epidemiologic studies. ClassyFlu is a new tool and web service for the classification of IAV sequences of the HA and NA gene into subtypes and phylogenetic clades using discriminatively trained profile hidden Markov models (HMMs), one for each subtype or clade. ClassyFlu merely requires as input unaligned, full-length or partial HA or NA DNA sequences. It enables rapid and highly accurate assignment of HA sequences to subtypes H1–H17 but particularly focusses on the finer grained assignment of sequences of highly pathogenic avian influenza viruses of subtype H5N1 according to the cladistics proposed by the H5N1 Evolution Working Group. NA sequences are classified into subtypes N1–N10. ClassyFlu was compared to semiautomatic classification approaches using BLAST and phylogenetics and additionally for H5 sequences to the new “Highly Pathogenic H5N1 Clade Classification Tool” (IRD-CT) proposed by the Influenza Research Database. Our results show that both web tools (ClassyFlu and IRD-CT), although based on different methods, are nearly equivalent in performance and both are more accurate and faster than semiautomatic classification. A retraining of ClassyFlu to altered cladistics as well as an extension of ClassyFlu to other IAV genome segments or fragments thereof is undemanding. This is exemplified by unambiguous assignment to a distinct cluster within subtype H7 of sequences of H7N9 viruses which emerged in China early in 2013 and caused more than 130 human infections. http://bioinf.uni-greifswald.de/ClassyFlu is a free web service. For local execution, the ClassyFlu source code in PERL is freely available. PMID:24404173

  13. ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.

    PubMed

    Van der Auwera, Sandra; Bulla, Ingo; Ziller, Mario; Pohlmann, Anne; Harder, Timm; Stanke, Mario

    2014-01-01

    Accurate and rapid characterization of influenza A virus (IAV) hemagglutinin (HA) and neuraminidase (NA) sequences with respect to subtype and clade is at the basis of extended diagnostic services and implicit to molecular epidemiologic studies. ClassyFlu is a new tool and web service for the classification of IAV sequences of the HA and NA gene into subtypes and phylogenetic clades using discriminatively trained profile hidden Markov models (HMMs), one for each subtype or clade. ClassyFlu merely requires as input unaligned, full-length or partial HA or NA DNA sequences. It enables rapid and highly accurate assignment of HA sequences to subtypes H1-H17 but particularly focusses on the finer grained assignment of sequences of highly pathogenic avian influenza viruses of subtype H5N1 according to the cladistics proposed by the H5N1 Evolution Working Group. NA sequences are classified into subtypes N1-N10. ClassyFlu was compared to semiautomatic classification approaches using BLAST and phylogenetics and additionally for H5 sequences to the new "Highly Pathogenic H5N1 Clade Classification Tool" (IRD-CT) proposed by the Influenza Research Database. Our results show that both web tools (ClassyFlu and IRD-CT), although based on different methods, are nearly equivalent in performance and both are more accurate and faster than semiautomatic classification. A retraining of ClassyFlu to altered cladistics as well as an extension of ClassyFlu to other IAV genome segments or fragments thereof is undemanding. This is exemplified by unambiguous assignment to a distinct cluster within subtype H7 of sequences of H7N9 viruses which emerged in China early in 2013 and caused more than 130 human infections. http://bioinf.uni-greifswald.de/ClassyFlu is a free web service. For local execution, the ClassyFlu source code in PERL is freely available. PMID:24404173

  14. Phylogenetic systematics of microorganisms inhabiting thermal environments.

    PubMed

    Lebedinsky, A V; Chernyh, N A; Bonch-Osmolovskaya, E A

    2007-12-01

    Thermal habitats harbor specialized communities of thermophilic microorganisms, primarily prokaryotes. This review considers modern systematics of prokaryotes and the place of thermophilic archaea and bacteria in it. Among the existing hierarchical classifications of prokaryotes, the bulk of attention is given to the one accepted in the current second edition of "Bergey's Manual of Systematic Bacteriology", which is primarily based on 16S rRNA phylogeny and phenotypic properties of the organisms. Analysis of the genomics data shows that they on the whole agree with the 16S rRNA-based system, although revealing the significance of the evolutionary role of lateral transfer, duplication, and loss of genes. According to the classification elaborated in the current edition of "Bergey's Manual", the prokaryotes currently culturable under laboratory conditions are distributed among 26 phyla, two of which belong to the domain Archaea and 24 to the domain Bacteria. Six phyla contain exclusively thermophiles, and eleven phyla contain thermophiles along with mesophiles, thermophiles being usually separated phylogenetically and representing high-level taxa (classes, orders). In light of the data on the topology of the 16S rRNA-based phylogenetic tree and some other data, this review discusses the probable hyperthermophilic nature of the universal common ancestor. PMID:18205614

  15. A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset Luay Nakhleh Tandy Warnow

    E-print Network

    Evans, Steven N.

    A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset Luay Nakhleh Tandy Warnow Dept the dataset, we study the consequences for phylogenetic reconstruction of restricting the data to lexical datasets that use only lexical characters being probably less accurate than analyses based upon datasets

  16. The revised classification of eukaryotes

    PubMed Central

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

    2012-01-01

    This revision of the classification of eukaryotes, which updates that of Adl et al. (2005), 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

  17. Phylogenetic comparative methods complement discriminant function analysis in ecomorphology.

    PubMed

    Barr, W Andrew; Scott, Robert S

    2014-04-01

    In ecomorphology, Discriminant Function Analysis (DFA) has been used as evidence for the presence of functional links between morphometric variables and ecological categories. Here we conduct simulations of characters containing phylogenetic signal to explore the performance of DFA under a variety of conditions. Characters were simulated using a phylogeny of extant antelope species from known habitats. Characters were modeled with no biomechanical relationship to the habitat category; the only sources of variation were body mass, phylogenetic signal, or random "noise." DFA on the discriminability of habitat categories was performed using subsets of the simulated characters, and Phylogenetic Generalized Least Squares (PGLS) was performed for each character. Analyses were repeated with randomized habitat assignments. When simulated characters lacked phylogenetic signal and/or habitat assignments were random, <5.6% of DFAs and <8.26% of PGLS analyses were significant. When characters contained phylogenetic signal and actual habitats were used, 33.27 to 45.07% of DFAs and <13.09% of PGLS analyses were significant. False Discovery Rate (FDR) corrections for multiple PGLS analyses reduced the rate of significance to <4.64%. In all cases using actual habitats and characters with phylogenetic signal, correct classification rates of DFAs exceeded random chance. In simulations involving phylogenetic signal in both predictor variables and predicted categories, PGLS with FDR was rarely significant, while DFA often was. In short, DFA offered no indication that differences between categories might be explained by phylogenetic signal, while PGLS did. As such, PGLS provides a valuable tool for testing the functional hypotheses at the heart of ecomorphology. PMID:24382658

  18. Community Phylogenetics: Assessing Tree Reconstruction Methods and the Utility of DNA Barcodes

    PubMed Central

    Boyle, Elizabeth E.; Adamowicz, Sarah J.

    2015-01-01

    Studies examining phylogenetic community structure have become increasingly prevalent, yet little attention has been given to the influence of the input phylogeny on metrics that describe phylogenetic patterns of co-occurrence. Here, we examine the influence of branch length, tree reconstruction method, and amount of sequence data on measures of phylogenetic community structure, as well as the phylogenetic signal (Pagel’s ?) in morphological traits, using Trichoptera larval communities from Churchill, Manitoba, Canada. We find that model-based tree reconstruction methods and the use of a backbone family-level phylogeny improve estimations of phylogenetic community structure. In addition, trees built using the barcode region of cytochrome c oxidase subunit I (COI) alone accurately predict metrics of phylogenetic community structure obtained from a multi-gene phylogeny. Input tree did not alter overall conclusions drawn for phylogenetic signal, as significant phylogenetic structure was detected in two body size traits across input trees. As the discipline of community phylogenetics continues to expand, it is important to investigate the best approaches to accurately estimate patterns. Our results suggest that emerging large datasets of DNA barcode sequences provide a vast resource for studying the structure of biological communities. PMID:26110886

  19. A revision of infrageneric classification in Astelia Banks & Sol. ex R.Br. (Asteliaceae)

    PubMed Central

    Birch, Joanne L.

    2015-01-01

    Abstract Systematic investigations and phylogenetic analyses have indicated that Astelia, as currently circumscribed, is paraphyletic, with Collospermum nested within it. Further, Astelia subgenus Astelia is polyphyletic, and Astelia subgenera Asteliopsis and Tricella are paraphyletic, as currently circumscribed. Revision of the subgeneric classification of Astelia is warranted to ensure classification accurately reflects the evolutionary history of these taxa. Collospermum is relegated to synonymy within Astelia. Astelia is dioecious or polygamodioecious, with a superior ovary, anthers dorsi- or basifixed, pistillodes or pistils that have a single short or poorly defined style, a 3 lobed stigma, and fleshy uni- or trilocular fruit with funicular hairs that are poorly to well developed. Astelia subgenus Collospermum (Skottsb.) Birch is described. A key to Astelia sections is provided. Astelia hastata Colenso, Astelia montana Seem., and Astelia microsperma Colenso pro parte are resurrected and the new combination Astelia samoense (Skottsb.) Birch, comb. nov. is made. PMID:26312037

  20. Phylogenetic trees in bioinformatics

    SciTech Connect

    Burr, Tom L

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  1. Phylogenetic and Biogeographic Analysis of Sphaerexochine Trilobites

    PubMed Central

    Congreve, Curtis R.; Lieberman, Bruce S.

    2011-01-01

    Background Sphaerexochinae is a speciose and widely distributed group of cheirurid trilobites. Their temporal range extends from the earliest Ordovician through the Silurian, and they survived the end Ordovician mass extinction event (the second largest mass extinction in Earth history). Prior to this study, the individual evolutionary relationships within the group had yet to be determined utilizing rigorous phylogenetic methods. Understanding these evolutionary relationships is important for producing a stable classification of the group, and will be useful in elucidating the effects the end Ordovician mass extinction had on the evolutionary and biogeographic history of the group. Methodology/Principal Findings Cladistic parsimony analysis of cheirurid trilobites assigned to the subfamily Sphaerexochinae was conducted to evaluate phylogenetic patterns and produce a hypothesis of relationship for the group. This study utilized the program TNT, and the analysis included thirty-one taxa and thirty-nine characters. The results of this analysis were then used in a Lieberman-modified Brooks Parsimony Analysis to analyze biogeographic patterns during the Ordovician-Silurian. Conclusions/Significance The genus Sphaerexochus was found to be monophyletic, consisting of two smaller clades (one composed entirely of Ordovician species and another composed of Silurian and Ordovician species). By contrast, the genus Kawina was found to be paraphyletic. It is a basal grade that also contains taxa formerly assigned to Cydonocephalus. Phylogenetic patterns suggest Sphaerexochinae is a relatively distinctive trilobite clade because it appears to have been largely unaffected by the end Ordovician mass extinction. Finally, the biogeographic analysis yields two major conclusions about Sphaerexochus biogeography: Bohemia and Avalonia were close enough during the Silurian to exchange taxa; and during the Ordovician there was dispersal between Eastern Laurentia and the Yangtze block (South China) and between Eastern Laurentia and Avalonia. PMID:21738632

  2. [Foundations of the new phylogenetics].

    PubMed

    Pavlinov, I Ia

    2004-01-01

    Evolutionary idea is the core of the modern biology. Due to this, phylogenetics dealing with historical reconstructions in biology takes a priority position among biological disciplines. The second half of the 20th century witnessed growth of a great interest to phylogenetic reconstructions at macrotaxonomic level which replaced microevolutionary studies dominating during the 30s-60s. This meant shift from population thinking to phylogenetic one but it was not revival of the classical phylogenetics; rather, a new approach emerged that was baptized The New Phylogenetics. It arose as a result of merging of three disciplines which were developing independently during 60s-70s, namely cladistics, numerical phyletics, and molecular phylogenetics (now basically genophyletics). Thus, the new phylogenetics could be defined as a branch of evolutionary biology aimed at elaboration of "parsimonious" cladistic hypotheses by means of numerical methods on the basis of mostly molecular data. Classical phylogenetics, as a historical predecessor of the new one, emerged on the basis of the naturphilosophical worldview which included a superorganismal idea of biota. Accordingly to that view, historical development (the phylogeny) was thought an analogy of individual one (the ontogeny) so its most basical features were progressive parallel developments of "parts" (taxa), supplemented with Darwinian concept of monophyly. Two predominating traditions were diverged within classical phylogenetics according to a particular interpretation of relation between these concepts. One of them (Cope, Severtzow) belittled monophyly and paid most attention to progressive parallel developments of morphological traits. Such an attitude turned this kind of phylogenetics to be rather the semogenetics dealing primarily with evolution of structures and not of taxa. Another tradition (Haeckel) considered both monophyletic and parallel origins of taxa jointly: in the middle of 20th century it was split into phylistics (Rasnitsyn's term; close to Simpsonian evolutionary taxonomy) belonging rather to the classical realm, and Hennigian cladistics that pays attention to origin of monophyletic taxa exclusively. In early of the 20th century, microevolutionary doctrine became predominating in evolutionary studies. Its core is the population thinking accompanied by the phenetic one based on equation of kinship to overall similarity. They were connected to positivist philosophy and hence were characterized by reductionism at both ontological and epistemological levels. It led to fall of classical phylogenetics but created the prerequisites for the new phylogenetics which also appeared to be full of reductionism. The new rise of phylogenetic (rather than tree) thinking during the last third of the 20th century was caused by lost of explanatory power of population one and by development of the new worldview and new epistemological premises. That new worldview is based on the synergetic (Prigoginian) model of development of non-equilibrium systems: evolution of the biota, a part of which is phylogeny, is considered as such a development. At epistemological level, the principal premise appeared to be fall of positivism which was replaced by post-positivism argumentation schemes. Input of cladistics into new phylogenetics is twofold. On the one hand, it reduced phylogeny to cladistic history lacking any adaptivist interpretation and presuming minimal evolution model. From this it followed reduction of kinship relation to sister-group relation lacking any reference to real time scale and to ancestor-descendant relation. On the other hand, cladistics elaborated methodology of phylogenetic reconstructions based on the synapomorphy principle, the outgroup concept became its part. The both inputs served as premises of incorporation of both numerical techniques and molecular data into phylogenetic reconstruction. Numerical phyletics provided the new phylogenetics with easily manipulated algorithms of cladogram construing and thus made phylogenetic reconstructions o

  3. Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods.

    PubMed

    Stadler, Tanja; Bonhoeffer, Sebastian

    2013-03-19

    Host population structure has a major influence on epidemiological dynamics. However, in particular for sexually transmitted diseases, quantitative data on population contact structure are hard to obtain. Here, we introduce a new method that quantifies host population structure based on phylogenetic trees, which are obtained from pathogen genetic sequence data. Our method is based on a maximum-likelihood framework and uses a multi-type branching process, under which each host is assigned to a type (subpopulation). In a simulation study, we show that our method produces accurate parameter estimates for phylogenetic trees in which each tip is assigned to a type, as well for phylogenetic trees in which the type of the tip is unknown. We apply the method to a Latvian HIV-1 dataset, quantifying the impact of the intravenous drug user epidemic on the heterosexual epidemic (known tip states), and identifying superspreader dynamics within the men-having-sex-with-men epidemic (unknown tip states). PMID:23382421

  4. Phylogenetics and the Human Microbiome

    PubMed Central

    Matsen, Frederick A.

    2015-01-01

    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

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

    ERIC Educational Resources Information Center

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

    2010-01-01

    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…

  6. Quantum Simulation of Phylogenetic Trees

    E-print Network

    Demosthenes Ellinas; Peter Jarvis

    2011-05-09

    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.

  7. First phylogenetic analyses of galaxy evolution

    E-print Network

    Didier Fraix-Burnet

    2005-01-03

    The Hubble tuning fork diagram, based on morphology, has always been the preferred scheme for classification of galaxies and is still the only one originally built from historical/evolutionary relationships. At the opposite, biologists have long taken into account the parenthood links of living entities for classification purposes. Assuming branching evolution of galaxies as a "descent with modification", we show that the concepts and tools of phylogenetic systematics widely used in biology can be heuristically transposed to the case of galaxies. This approach that we call "astrocladistics" has been first applied to Dwarf Galaxies of the Local Group and provides the first evolutionary galaxy tree. The cladogram is sufficiently solid to support the existence of a hierarchical organization in the diversity of galaxies, making it possible to track ancestral types of galaxies. We also find that morphology is a summary of more fundamental properties. Astrocladistics applied to cosmology simulated galaxies can, unsurprisingly, reconstruct the correct "genealogy". It reveals evolutionary lineages, divergences from common ancestors, character evolution behaviours and shows how mergers organize galaxy diversity. Application to real normal galaxies is in progress. Astrocladistics opens a new way to analyse galaxy evolution and a path towards a new systematics of galaxies.

  8. Phylogenetic lineages in Pseudocercospora

    PubMed Central

    Crous, P.W.; Braun, U.; Hunter, G.C.; Wingfield, M.J.; Verkley, G.J.M.; Shin, H.-D.; Nakashima, C.; Groenewald, J.Z.

    2013-01-01

    Pseudocercospora is a large cosmopolitan genus of plant pathogenic fungi that are commonly associated with leaf and fruit spots as well as blights on a wide range of plant hosts. They occur in arid as well as wet environments and in a wide range of climates including cool temperate, sub-tropical and tropical regions. Pseudocercospora is now treated as a genus in its own right, although formerly recognised as either an anamorphic state of Mycosphaerella or having mycosphaerella-like teleomorphs. The aim of this study was to sequence the partial 28S nuclear ribosomal RNA gene of a selected set of isolates to resolve phylogenetic generic limits within the Pseudocercospora complex. From these data, 14 clades are recognised, six of which cluster in Mycosphaerellaceae. Pseudocercospora s. str. represents a distinct clade, sister to Passalora eucalypti, and a clade representing the genera Scolecostigmina, Trochophora and Pallidocercospora gen. nov., taxa formerly accommodated in the Mycosphaerella heimii complex and characterised by smooth, pale brown conidia, as well as the formation of red crystals in agar media. Other clades in Mycosphaerellaceae include Sonderhenia, Microcyclosporella, and Paracercospora. Pseudocercosporella resides in a large clade along with Phloeospora, Miuraea, Cercospora and Septoria. Additional clades represent Dissoconiaceae, Teratosphaeriaceae, Cladosporiaceae, and the genera Xenostigmina, Strelitziana, Cyphellophora and Thedgonia. The genus Phaeomycocentrospora is introduced to accommodate Mycocentrospora cantuariensis, primarily distinguished from Pseudocercospora based on its hyaline hyphae, broad conidiogenous loci and hila. Host specificity was considered for 146 species of Pseudocercospora occurring on 115 host genera from 33 countries. Partial nucleotide sequence data for three gene loci, ITS, EF-1?, and ACT suggest that the majority of these species are host specific. Species identified on the basis of host, symptomatology and general morphology, within the same geographic region, frequently differed phylogenetically, indicating that the application of European and American names to Asian taxa, and vice versa, was often not warranted. Taxonomic novelties: New genera - Pallidocercospora Crous, Phaeomycocentrospora Crous, H.D. Shin & U. Braun; New species - Cercospora eucommiae Crous, U. Braun & H.D. Shin, Microcyclospora quercina Crous & Verkley, Pseudocercospora ampelopsis Crous, U. Braun & H.D. Shin, Pseudocercospora cercidicola Crous, U. Braun & C. Nakash., Pseudocercospora crispans G.C. Hunter & Crous, Pseudocercospora crocea Crous, U. Braun, G.C. Hunter & H.D. Shin, Pseudocercospora haiweiensis Crous & X. Zhou, Pseudocercospora humulicola Crous, U. Braun & H.D. Shin, Pseudocercospora marginalis G.C. Hunter, Crous, U. Braun & H.D. Shin, Pseudocercospora ocimi-basilici Crous, M.E. Palm & U. Braun, Pseudocercospora plectranthi G.C. Hunter, Crous, U. Braun & H.D. Shin, Pseudocercospora proteae Crous, Pseudocercospora pseudostigmina-platani Crous, U. Braun & H.D. Shin, Pseudocercospora pyracanthigena Crous, U. Braun & H.D. Shin, Pseudocercospora ravenalicola G.C. Hunter & Crous, Pseudocercospora rhamnellae G.C. Hunter, H.D. Shin, U. Braun & Crous, Pseudocercospora rhododendri-indici Crous, U. Braun & H.D. Shin, Pseudocercospora tibouchinigena Crous & U. Braun, Pseudocercospora xanthocercidis Crous, U. Braun & A. Wood, Pseudocercosporella koreana Crous, U. Braun & H.D. Shin; New combinations - Pallidocercospora acaciigena (Crous & M.J. Wingf.) Crous & M.J. Wingf., Pallidocercospora crystallina (Crous & M.J. Wingf.) Crous & M.J. Wingf., Pallidocercospora heimii (Crous) Crous, Pallidocercospora heimioides (Crous & M.J. Wingf.) Crous & M.J. Wingf., Pallidocercospora holualoana (Crous, Joanne E. Taylor & M.E. Palm) Crous, Pallidocercospora konae (Crous, Joanne E. Taylor & M.E. Palm) Crous, Pallidoocercospora irregulariramosa (Crous & M.J. Wingf.) Crous & M.J. Wingf., Phaeomycocentrospora cantuariensis (E.S. Salmon & Wormald) Crous, H.D. Shin & U. Braun, Pseudocercospora hakeae (U. Braun & Cr

  9. Molecular phylogenetics and evolutionary history of ariid catfishes revisited: a comprehensive sampling

    PubMed Central

    Betancur-R, Ricardo

    2009-01-01

    Background Ariids or sea catfishes are one of the two otophysan fish families (out of about 67 families in four orders) that inhabit mainly marine and brackish waters (although some species occur strictly in fresh waters). The group includes over 150 species placed in ~29 genera and two subfamilies (Galeichthyinae and Ariinae). Despite their global distribution, ariids are largely restricted to the continental shelves due in part to their specialized reproductive behavior (i.e., oral incubation). Thus, among marine fishes, ariids offer an excellent opportunity for inferring historical biogeographic scenarios. Phylogenetic hypotheses available for ariids have focused on restricted geographic areas and comprehensive phylogenies are still missing. This study inferred phylogenetic hypotheses for 123 ariid species in 28 genera from different biogeographic provinces using both mitochondrial and nuclear sequences (up to ~4 kb). Results While the topologies obtained support the monophyly of basal groups, up to ten genera validated in previous morphological studies were incongruent with the molecular topologies. New World ariines were recovered as paraphyletic and Old World ariines were grouped into a well-supported clade that was further divided into subclades mainly restricted to major Gondwanan landmasses. A general area cladogram derived from the area cladograms of ariines and three other fish groups was largely congruent with the geological area cladogram of Gondwana. Nonetheless, molecular clock estimations provided variable results on the timing of ariine diversification (~105-41 mya). Conclusion This study provides the most comprehensive phylogeny of sea catfishes to date and highlights the need for re-assessment of their classification. While from a topological standpoint the evolutionary history of ariines is mostly congruent with vicariance associated with the sequence of events during Gondwanan fragmentation, ambiguous divergence time estimations hinders assessing the vicariant hypothesis on a temporal framework. Further examination of ariid fossils might provide the basis for more accurate inferences on the timing of ariine diversification. PMID:19627593

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

    PubMed Central

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

    2012-01-01

    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

  11. 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 ...

  12. Two issues in archaeological phylogenetics: taxon construction and outgroup selection.

    PubMed

    O'Brien, Michael J; Lyman, R Lee; Saab, Youssef; Saab, Elias; Darwent, John; Glover, Daniel S

    2002-03-21

    Cladistics is widely used in biology and paleobiology to construct phylogenetic hypotheses, but rarely has it been applied outside those disciplines. There is, however, no reason to suppose that cladistics is not applicable to anything that evolves by cladogenesis and produces a nested hierarchy of taxa. This includes cultural phenomena such as languages and tools recovered from archaeological contexts. Two methodological issues assume primacy in attempts to extend cladistics to archaeological materials: the construction of analytical taxa and the selection of appropriate outgroups. In biology the species is the primary taxonomic unit used, irrespective of the debates that have arisen in phylogenetic theory over the nature of species. Also in biology the phylogenetic history of a group of taxa usually is well enough known that an appropriate taxon can be selected as an outgroup. No analytical unit parallel to the species exists in archaeology, and thus taxa have to be constructed specifically for phylogenetic analysis. One method of constructing taxa is paradigmatic classification, which defines classes (taxa) on the basis of co-occurring, unweighted character states. Once classes have been created, a form of occurrence seriation-an archaeological method based on the theory of cultural transmission and heritability-offers an objective basis for selecting an outgroup. PMID:12051970

  13. Molecular identification of hepatitis B virus genotypes/subgenotypes: Revised classification hurdles and updated resolutions

    PubMed Central

    Pourkarim, Mahmoud Reza; Amini-Bavil-Olyaee, Samad; Kurbanov, Fuat; Van Ranst, Marc; Tacke, Frank

    2014-01-01

    The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the high genetic variability of HBV, the virus can be categorized into different HBV genotypes and subgenotypes, which considerably differ with respect to geographical distribution, transmission routes, disease progression, responses to antiviral therapy or vaccination, and clinical outcome measures such as cirrhosis or hepatocellular carcinoma. However, HBV (sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods. Thus, an accurate, holistic and dynamic classification system is essential. In this review article, we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification. Analyzing full-length genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system. Careful attention must be paid to all aspects of phylogenetic analysis, such as bootstrapping values and meeting the necessary thresholds for (sub)genotyping. Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel. As many of these strains were misclassified due to genetic differences resulting from recombination, we propose the term “recombino-subgenotype”. Moreover, immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV (sub)genotypes. We therefore suggest the term “immigro-subgenotype” to distinguish exotic (sub)genotypes from native ones. We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis, diagnosis and treatment. PMID:24966586

  14. An Analytical Method For Multi-class Molecular Cancer Classification

    E-print Network

    Poggio, Tomaso

    . Introduction The accurate classification of human cancer is an important component of modern cancer treatmentAn Analytical Method For Multi-class Molecular Cancer Classification Ryan Rifkin # & , Sayan-wise classification problems using such global gene expression patterns. However, classification across multiple

  15. Map Classification

    ERIC Educational Resources Information Center

    Larsgaard, Mary

    1973-01-01

    Although map classification may seem a somewhat esoteric subject, at least to those who are not map librarians, the enterprising searcher for map classification schemes can find a goodly number from which to choose. (30 references) (Author)

  16. A phylogenetic analysis of the myxobacteria: basis for their classification

    NASA Technical Reports Server (NTRS)

    Shimkets, L.; Woese, C. R.

    1992-01-01

    The primary sequence and secondary structural features of the 16S rRNA were compared for 12 different myxobacteria representing all the known cultivated genera. Analysis of these data show the myxobacteria to form a monophyletic grouping consisting of three distinct families, which lies within the delta subdivision of the purple bacterial phylum. The composition of the families is consistent with differences in cell and spore morphology, cell behavior, and pigment and secondary metabolite production but is not correlated with the morphological complexity of the fruiting bodies. The Nannocystis exedens lineage has evolved at an unusually rapid pace and its rRNA shows numerous primary and secondary structural idiosyncrasies.

  17. Phylogenetic Studies and Modern Classification of the Pyraloidea (Lepidoptera)

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  18. Molecular identification and phylogenetic study of Demodex caprae.

    PubMed

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

    2014-10-01

    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

  19. Host Specificity and Phylogenetic Relationships of Chicken and Turkey Parvoviruses.

    PubMed

    Zsak, Laszlo; Cha, Ra Mi; Li, Fenglan; Day, J Michael

    2015-03-01

    Inoculation of specific-pathogen-free chickens and turkeys with five chicken parvoviruses (ChPV) and five turkey parvoviruses (TuPV) resulted in productive virus replication only in the homologous host species. A phylogenetic tree based on nucleotide sequences of the VP1 gene segment revealed a host-specific clustering of the virus strains. These results suggest that the VP1 gene plays an essential role in host specificity of ChPV and TuPV strains and could be a relevant target sequence for strain classification. PMID:26292551

  20. Phylogenetics of Hydroidolina (Hydrozoa: Cnidaria)

    E-print Network

    Cartwright, Paulyn; Evans, Nathaniel Michael; Dunn, Casey W.; Marques, Antonio C.; Miglietta, Maria Pia; Schuchert, Peter; Collins, Allen G.

    2008-05-08

    . In an effort to further clarify hydroidolinan relationships, we performed phylogenetic analyses on 97 hydroidolinan taxa, using DNA sequences from partial mitochondrial 16S rDNA, nearly complete nuclear 18S rDNA and nearly complete nuclear 28S rDNA. Our...

  1. Phylogenetic Relationships Among Lepidium Papilliferum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous phylogenetic analyses of Lepidium included only a few acessions of L. montanum, L. flavum, and L. fremontii to represent western North Amrican species. Two additional species endemic to southwest Idaho have posed both taxonomic and conservation questions regarding their species status. Le...

  2. Phylogenetic relationships of sugarcane fungi

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The phylogenetic positions of Puccinia spp. infecting sugarcane (a complex hybrid of Saccharum spp.) was determined using 42 newly generated rust sequences and 25 sequences from Genbank. Rust specimens on sugarcane were collected from 161 locations in 25 countries and identified based on light micro...

  3. CRUSTACEAN ISSUES ] 3 Decapod Crustacean Phylogenetics

    E-print Network

    Alwes, Frederike

    CRUSTACEAN ISSUES ] 3 II %. m Decapod Crustacean Phylogenetics edited by Joel W. Martin, Keith A. Crandall, and Darryl L. Felder £\\ CRC Press J Taylor & Francis Group #12;Decapod Crustacean Phylogenetics to infringe. Library of Congress Cataloging-iii-Publication Data Decapod crustacean phylogenetics / editors

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

    PubMed Central

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

    2014-01-01

    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

  5. Phylogenetic assignment of Mycobacterium tuberculosis Beijing clinical isolates in Japan by maximum a posteriori estimation.

    PubMed

    Seto, Junji; Wada, Takayuki; Iwamoto, Tomotada; Tamaru, Aki; Maeda, Shinji; Yamamoto, Kaori; Hase, Atsushi; Murakami, Koichi; Maeda, Eriko; Oishi, Akira; Migita, Yuji; Yamamoto, Taro; Ahiko, Tadayuki

    2015-10-01

    Intra-species phylogeny of Mycobacterium tuberculosis has been regarded as a clue to estimate its potential risk to develop drug-resistance and various epidemiological tendencies. Genotypic characterization of variable number of tandem repeats (VNTR), a standard tool to ascertain transmission routes, has been improving as a public health effort, but determining phylogenetic information from those efforts alone is difficult. We present a platform based on maximum a posteriori (MAP) estimation to estimate phylogenetic information for M. tuberculosis clinical isolates from individual profiles of VNTR types. This study used 1245 M. tuberculosis clinical isolates obtained throughout Japan for construction of an MAP estimation formula. Two MAP estimation formulae, classification of Beijing family and other lineages, and classification of five Beijing sublineages (ST11/26, STK, ST3, and ST25/19 belonging to the ancient Beijing subfamily and modern Beijing subfamily), were created based on 24 loci VNTR (24Beijing-VNTR) profiles and phylogenetic information of the isolates. Recursive estimation based on the formulae showed high concordance with their authentic phylogeny by multi-locus sequence typing (MLST) of the isolates. The formulae might further support phylogenetic estimation of the Beijing lineage M. tuberculosis from the VNTR genotype with various geographic backgrounds. These results suggest that MAP estimation can function as a reliable probabilistic process to append phylogenetic information to VNTR genotypes of M. tuberculosis independently, which might improve the usage of genotyping data for control, understanding, prevention, and treatment of TB. PMID:26220897

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

    PubMed Central

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

    2013-01-01

    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

  7. Functional Basis of Microorganism Classification

    PubMed Central

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

    2015-01-01

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

  8. Phylogenetic positions of RH blood group-related genes in cyclostomes.

    PubMed

    Suzuki, Akinori; Endo, Kouhei; Kitano, Takashi

    2014-06-10

    The RH gene family in vertebrates consists of four major genes (RH, RHAG, RHBG, and RHCG). They are thought to have emerged in the common ancestor of vertebrates after two rounds of whole genome duplication (2R-WGD). To analyze the detailed phylogenetic relationships within the RH gene family, we determined three types of cDNA sequence that belong to the RH gene family in lamprey (Lethenteron reissneri) and designated them as RHBG-like, RHCG-like1, and RHCG-like2. Phylogenetic analyses clearly showed that RHCG-like1 and RHCG-like2 genes, which were probably duplicated in the lamprey lineage, are orthologs of gnathostome RHCG. In contrast, the clear phylogenetic position of the RHBG-like gene could not be obtained. Probably some convergent events for cyclostome RHBG-like genes prevented the accurate identification of their phylogenetic positions. PMID:24720951

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

    PubMed Central

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

    2015-01-01

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

  10. Multiple Sparse Representations Classification

    PubMed Central

    Plenge, Esben; Klein, Stefan S.; Niessen, Wiro J.; Meijering, Erik

    2015-01-01

    Sparse representations classification (SRC) is a powerful technique for pixelwise classification of images and it is increasingly being used for a wide variety of image analysis tasks. The method uses sparse representation and learned redundant dictionaries to classify image pixels. In this empirical study we propose to further leverage the redundancy of the learned dictionaries to achieve a more accurate classifier. In conventional SRC, each image pixel is associated with a small patch surrounding it. Using these patches, a dictionary is trained for each class in a supervised fashion. Commonly, redundant/overcomplete dictionaries are trained and image patches are sparsely represented by a linear combination of only a few of the dictionary elements. Given a set of trained dictionaries, a new patch is sparse coded using each of them, and subsequently assigned to the class whose dictionary yields the minimum residual energy. We propose a generalization of this scheme. The method, which we call multiple sparse representations classification (mSRC), is based on the observation that an overcomplete, class specific dictionary is capable of generating multiple accurate and independent estimates of a patch belonging to the class. So instead of finding a single sparse representation of a patch for each dictionary, we find multiple, and the corresponding residual energies provides an enhanced statistic which is used to improve classification. We demonstrate the efficacy of mSRC for three example applications: pixelwise classification of texture images, lumen segmentation in carotid artery magnetic resonance imaging (MRI), and bifurcation point detection in carotid artery MRI. We compare our method with conventional SRC, K-nearest neighbor, and support vector machine classifiers. The results show that mSRC outperforms SRC and the other reference methods. In addition, we present an extensive evaluation of the effect of the main mSRC parameters: patch size, dictionary size, and sparsity level. PMID:26177106

  11. How Accurate is Psychiatry?

    ERIC Educational Resources Information Center

    Greenburg, Joel

    1977-01-01

    The problems that plague psychiatry; such as poor diagnoses, inappropriate treatment, and outdated resources are detailed. A new, more accurate, Diagnostic and Statistical Manual of Mental Disorders (DSM III) to be adopted in 1978 may alleviate many improper diagnoses and treatments. (BT)

  12. Phycas: software for Bayesian phylogenetic analysis.

    PubMed

    Lewis, Paul O; Holder, Mark T; Swofford, David L

    2015-05-01

    Phycas is open source, freely available Bayesian phylogenetics software written primarily in C++ but with a Python interface. Phycas specializes in Bayesian model selection for nucleotide sequence data, particularly the estimation of marginal likelihoods, central to computing Bayes Factors. Marginal likelihoods can be estimated using newer methods (Thermodynamic Integration and Generalized Steppingstone) that are more accurate than the widely used Harmonic Mean estimator. In addition, Phycas supports two posterior predictive approaches to model selection: Gelfand-Ghosh and Conditional Predictive Ordinates. The General Time Reversible family of substitution models, as well as a codon model, are available, and data can be partitioned with all parameters unlinked except tree topology and edge lengths. Phycas provides for analyses in which the prior on tree topologies allows polytomous trees as well as fully resolved trees, and provides for several choices for edge length priors, including a hierarchical model as well as the recently described compound Dirichlet prior, which helps avoid overly informative induced priors on tree length. PMID:25577605

  13. On the nature of global classification

    PubMed Central

    Wheelis, Mark L.; Kandler, Otto; Woese, Carl R.

    1992-01-01

    Molecular sequencing technology has brought biology into the era of global (universal) classification. Methodologically and philosophically, global classification differs significantly from traditional, local classificagtion. The need for uniformity requires that higher level taxa be defined on the molecular level in terms of universally homologous functions. A global classification should reflect both principal dimentions of the evolutionary process: genealogical relationship and quality and extent of divergence within a group. The ultimate purpose of a global classification is not simply information storage and retrieval; such a system should also as an heuristic representation of the evolutionary paradigm that exerts a directing influence on the course of biology. The global system envisioned allows paraphyletic taxa. To retain maximal phylogenetic information in these cases, minor notational amendments in existing taxonomic conventions should be adopted. PMID:11537862

  14. [A new method of determining ages: chronological classification].

    PubMed

    Gubry, P

    1983-01-01

    Two methods of determining ages, the historical calendar method and the classification method, are compared using data for Chad from the UDEAC-TCHAD demographic survey. Complementary processing shows that the classification method is more accurate for those born in villages, while the historical method is more accurate for those born elsewhere. (summary in ENG) PMID:12265466

  15. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    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.

  16. Identifying optimal incomplete phylogenetic data sets from sequence databases.

    PubMed

    Yan, Changhui; Burleigh, J Gordon; Eulenstein, Oliver

    2005-06-01

    We introduce a new method for identifying optimal incomplete data sets from large sequence databases based on the graph theoretic concept of alpha-quasi-bicliques. The quasi-biclique method searches large sequence databases to identify useful phylogenetic data sets with a specified amount of missing data while maintaining the necessary amount of overlap among genes and taxa. The utility of the quasi-biclique method is demonstrated on large simulated sequence databases and on a data set of green plant sequences from GenBank. The quasi-biclique method greatly increases the taxon and gene sampling in the data sets while adding only a limited amount of missing data. Furthermore, under the conditions of the simulation, data sets with a limited amount of missing data often produce topologies nearly as accurate as those built from complete data sets. The quasi-biclique method will be an effective tool for exploiting sequence databases for phylogenetic information and also may help identify critical sequences needed to build large phylogenetic data sets. PMID:15878123

  17. Phylogenetic Signal Dissection Identifies the Root of Starfishes

    PubMed Central

    Feuda, Roberto; Smith, Andrew B.

    2015-01-01

    Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors - Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution – have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented. PMID:25955729

  18. Phylogenetic signal dissection identifies the root of starfishes.

    PubMed

    Feuda, Roberto; Smith, Andrew B

    2015-01-01

    Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors--Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution--have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented. PMID:25955729

  19. BIODIVERSITY Phylogenetic patterns differ for native and

    E-print Network

    Davies, Kendi

    BIODIVERSITY RESEARCH Phylogenetic patterns differ for native and exotic plant communities across Biodiversity, biological invasions, community assembly, ecophylogenetic diversity, invasion, phylobetadiversity

  20. Phylogenetic Conservatism in Plant Phenology

    NASA Technical Reports Server (NTRS)

    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

    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.

  1. TAXON 59 (2) April 2010: 538558Nickrent & al. Classification of Santalales INTRODUCTION

    E-print Network

    dePamphilis, Claude

    It has been over one decade since the emergence of the first classification of flowering plants based.e., the application of a molecular phylogenetic approach to one of the major angiosperm clades: Santalales. This study. The classification in Schultze-Motel (1964) essentially followed the treatment in Die natürlichen Pflanzenfamilien

  2. Assessing statistical reliability of phylogenetic trees via a speedy double bootstrap method.

    PubMed

    Ren, Aizhen; Ishida, Takashi; Akiyama, Yutaka

    2013-05-01

    Evaluating the reliability of estimated phylogenetic trees is of critical importance in the field of molecular phylogenetics, and for other endeavors that depend on accurate phylogenetic reconstruction. The bootstrap method is a well-known computational approach to phylogenetic tree assessment, and more generally for assessing the reliability of statistical models. However, it is known to be biased under certain circumstances, calling into question the accuracy of the method. Several advanced bootstrap methods have been developed to achieve higher accuracy, one of which is the double bootstrap approach, but the computational burden of this method has precluded its application to practical problems of phylogenetic tree selection. We address this issue by proposing a simple method called the speedy double bootstrap, which circumvents the second-tier resampling step in the regular double bootstrap approach. We also develop an implementation of the regular double bootstrap for comparison with our speedy method. The speedy double bootstrap suffers no significant loss of accuracy compared with the regular double bootstrap, while performing calculations significantly more rapidly (at minimum around 371 times faster, based on analysis of mammalian mitochondrial amino acid sequences and 12S and 16S rRNA genes). Our method thus enables, for the first time, the practical application of the double bootstrap technique in the context of molecular phylogenetics. The approach can also be used more generally for model selection problems wherever the maximum likelihood criterion is used. PMID:23485916

  3. Propionibacterium acnes Types I and II Represent Phylogenetically Distinct Groups

    PubMed Central

    McDowell, Andrew; Valanne, Susanna; Ramage, Gordon; Tunney, Michael M.; Glenn, Josephine V.; McLorinan, Gregory C.; Bhatia, Ajay; Maisonneuve, Jean-Francois; Lodes, Michael; Persing, David H.; Patrick, Sheila

    2005-01-01

    Although two phenotypes of the opportunistic pathogen Propionibacterium acnes (types I and II) have been described, epidemiological investigations of their roles in different infections have not been widely reported. Using immunofluorescence microscopy with monoclonal antibodies (MAbs) QUBPa1 and QUBPa2, specific for types I and II, respectively, we investigated the prevalences of the two types among 132 P. acnes isolates. Analysis of isolates from failed prosthetic hip implants (n = 40) revealed approximately equal numbers of type I and II organisms. Isolates from failed prosthetic hip-associated bone (n = 6) and tissue (n = 38) samples, as well as isolates from acne (n = 22), dental infections (n = 8), and skin removed during surgical incision (n = 18) were predominately of type I. A total of 11 (8%) isolates showed atypical MAb labeling and could not be conclusively identified. Phylogenetic analysis of P. acnes by nucleotide sequencing revealed the 16S rRNA gene to be highly conserved between types I and II. In contrast, sequence analysis of recA and a putative hemolysin gene (tly) revealed significantly greater type-specific polymorphisms that corresponded to phylogenetically distinct cluster groups. All 11 isolates with atypical MAb labeling were identified as type I by sequencing. Within the recA and tly phylogenetic trees, nine of these isolates formed a cluster distinct from other type I organisms, suggesting a further phylogenetic subdivision within type I. Our study therefore demonstrates that the phenotypic differences between P. acnes types I and II reflect deeper differences in their phylogeny. Furthermore, nucleotide sequencing provides an accurate method for identifying the type status of P. acnes isolates. PMID:15634990

  4. HIV classification using coalescent theory

    SciTech Connect

    Zhang, Ming; Letiner, Thomas K; Korber, Bette T

    2008-01-01

    Algorithms for subtype classification and breakpoint detection of HIV-I sequences are based on a classification system of HIV-l. Hence, their quality highly depend on this system. Due to the history of creation of the current HIV-I nomenclature, the current one contains inconsistencies like: The phylogenetic distance between the subtype B and D is remarkably small compared with other pairs of subtypes. In fact, it is more like the distance of a pair of subsubtypes Robertson et al. (2000); Subtypes E and I do not exist any more since they were discovered to be composed of recombinants Robertson et al. (2000); It is currently discussed whether -- instead of CRF02 being a recombinant of subtype A and G -- subtype G should be designated as a circulating recombination form (CRF) nd CRF02 as a subtype Abecasis et al. (2007); There are 8 complete and over 400 partial HIV genomes in the LANL-database which belong neither to a subtype nor to a CRF (denoted by U). Moreover, the current classification system is somehow arbitrary like all complex classification systems that were created manually. To this end, it is desirable to deduce the classification system of HIV systematically by an algorithm. Of course, this problem is not restricted to HIV, but applies to all fast mutating and recombining viruses. Our work addresses the simpler subproblem to score classifications of given input sequences of some virus species (classification denotes a partition of the input sequences in several subtypes and CRFs). To this end, we reconstruct ancestral recombination graphs (ARG) of the input sequences under restrictions determined by the given classification. These restritions are imposed in order to ensure that the reconstructed ARGs do not contradict the classification under consideration. Then, we find the ARG with maximal probability by means of Markov Chain Monte Carlo methods. The probability of the most probable ARG is interpreted as a score for the classification. To our knowledge, this particular problem was not addressed up to now. The software package Lamarc Kuhner et al. (2000) allows for sampling ARGs, but it assumes that recombination events only involve one breakpoint. However, in HIV recombinants usually have more than one breakpoint. Moreover, Lamarc does not perform an explicit breakpoint detection, but tries to find them by chance. Although this approach is suitable for most situations, it will not lead to satisfying results in case of highly recombining viruses with multiple breakpoints.

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

    PubMed Central

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

    2014-01-01

    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

  6. Learning classification trees

    NASA Technical Reports Server (NTRS)

    Buntine, Wray

    1991-01-01

    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.

  7. An Introduction to Phylogenetics Bret Larget

    E-print Network

    Payseur, Bret

    and of Statistics University of Wisconsin--Madison January 27, 2010 1 / 54 Modern Phylogenetics Phylogenies for forensic purposes. Phylogenetics is being used increasingly in comparative genomics and study of geneDirect - Full Size Image Page 1 of 2http://www.sciencedirect.com/science

  8. A Novel Approach for Compressing Phylogenetic Trees

    E-print Network

    Williams, Tiffani

    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

  9. RESEARCH Open Access Reconciling taxonomy and phylogenetic

    E-print Network

    Matsen, Frederick A. "Erick"

    RESEARCH Open Access Reconciling taxonomy and phylogenetic inference: formalism and algorithms: Although taxonomy is often used informally to evaluate the results of phylogenetic inference and the root that solves a "subcoloring" problem to express the difference between a taxonomy and a phylogeny at a given

  10. Phylogenetic Reconstruction from Gene-Order and

    E-print Network

    Moret, Bernard

    Foundation, IBM Corp. ­ p. #12;Overview · Gene-Order Data vs. Sequence Data · Phylogenetic ReconstructionPhylogenetic Reconstruction from Gene-Order and Gene-Content Data Bernard M.E. Moret ¡ ¢£ ¤¥ ¡§¦ ¨© ¢¦ ¨Department of Computer Science University of New Mexico ­ p. #12;Acknowledgments · Main collaborators: David

  11. Molecular and Morphological Analyses Reveal Phylogenetic Relationships of Stingrays Focusing on the Family Dasyatidae (Myliobatiformes)

    PubMed Central

    Lim, Kean Chong; Lim, Phaik-Eem; Chong, Ving Ching; Loh, Kar-Hoe

    2015-01-01

    Elucidating the phylogenetic relationships of the current but problematic Dasyatidae (Order Myliobatiformes) was the first priority of the current study. Here, we studied three molecular gene markers of 43 species (COI gene), 33 species (ND2 gene) and 34 species (RAG1 gene) of stingrays to draft out the phylogenetic tree of the order. Nine character states were identified and used to confirm the molecularly constructed phylogenetic trees. Eight or more clades (at different hierarchical level) were identified for COI, ND2 and RAG1 genes in the Myliobatiformes including four clades containing members of the present Dasyatidae, thus rendering the latter non-monophyletic. The uncorrected p-distance between these four ‘Dasytidae’ clades when compared to the distance between formally known families confirmed that these four clades should be elevated to four separate families. We suggest a revision of the present classification, retaining the Dasyatidae (Dasyatis and Taeniurops species) but adding three new families namely, Neotrygonidae (Neotrygon and Taeniura species), Himanturidae (Himantura species) and Pastinachidae (Pastinachus species). Our result indicated the need to further review the classification of Dasyatis microps. By resolving the non-monophyletic problem, the suite of nine character states enables the natural classification of the Myliobatiformes into at least thirteen families based on morphology. PMID:25867639

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

    PubMed

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

    2015-10-01

    Recent developments in sequencing technology have given rise to a large number of studies that assess bacterial diversity and community structure in termite and cockroach guts based on large amplicon libraries of 16S rRNA genes. Although these studies have revealed important ecological and evolutionary patterns in the gut microbiota, classification of the short sequence reads is limited by the taxonomic depth and resolution of the reference databases used in the respective studies. Here, we present a curated reference database for accurate taxonomic analysis of the bacterial gut microbiota of dictyopteran insects. The Dictyopteran gut microbiota reference Database (DictDb) is based on the Silva database but was significantly expanded by the addition of clones from 11 mostly unexplored termite and cockroach groups, which increased the inventory of bacterial sequences from dictyopteran guts by 26%. The taxonomic depth and resolution of DictDb was significantly improved by a general revision of the taxonomic guide tree for all important lineages, including a detailed phylogenetic analysis of the Treponema and Alistipes complexes, the Fibrobacteres, and the TG3 phylum. The performance of this first documented version of DictDb (v. 3.0) using the revised taxonomic guide tree in the classification of short-read libraries obtained from termites and cockroaches was highly superior to that of the current Silva and RDP databases. DictDb uses an informative nomenclature that is consistent with the literature also for clades of uncultured bacteria and provides an invaluable tool for anyone exploring the gut community structure of termites and cockroaches. PMID:26283320

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

    NASA Astrophysics Data System (ADS)

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

    2005-05-01

    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.

  14. SUNPLIN: Simulation with Uncertainty for Phylogenetic Investigations

    PubMed Central

    2013-01-01

    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

  15. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

    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.

  16. Synopsis of Trichosanthes (Cucurbitaceae) based on recent molecular phylogenetic data

    PubMed Central

    de Boer, Hugo J.; Thulin, Mats

    2012-01-01

    Abstract The snake gourd genus, Trichosanthes, is the largest genus in the Cucurbitaceae family, with over 90 species. Recent molecular phylogenetic data have indicated that the genus Gymnopetalum is to be merged with Trichosanthes to maintain monophyly. A revised infrageneric classification of Trichosanthes including Gymnopetalum is proposed with two subgenera, (I) subg. Scotanthus comb. nov. and (II) subg. Trichosanthes, eleven sections, (i) sect. Asterospermae, (ii) sect. Cucumeroides, (iii) sect. Edulis, (iv) sect. Foliobracteola, (v) sect. Gymnopetalum, (vi) sect. Involucraria, (vii) sect. Pseudovariifera sect. nov., (viii) sect. Villosae stat. nov., (ix) sect. Trichosanthes, (x) sect. Tripodanthera, and (xi) sect. Truncata. A synopsis of Trichosanthes with the 91 species recognized here is presented, including four new combinations, Trichosanthes orientalis, Trichosanthes tubiflora, Trichosanthes scabra var. pectinata, Trichosanthes scabra var. penicaudii, and a clarified nomenclature of Trichosanthes costata and Trichosanthes scabra. PMID:22645411

  17. Phylogenetic Relationships of American Willows (Salix L., Salicaceae)

    PubMed Central

    Lauron-Moreau, Aurélien; Pitre, Frédéric E.; Argus, George W.; Labrecque, Michel; Brouillet, Luc

    2015-01-01

    Salix L. is the largest genus in the family Salicaceae (450 species). Several classifications have been published, but taxonomic subdivision has been under continuous revision. Our goal is to establish the phylogenetic structure of the genus using molecular data on all American willows, using three DNA markers. This complete phylogeny of American willows allows us to propose a biogeographic framework for the evolution of the genus. Material was obtained for the 122 native and introduced willow species of America. Sequences were obtained from the ITS (ribosomal nuclear DNA) and two plastid regions, matK and rbcL. Phylogenetic analyses (parsimony, maximum likelihood, Bayesian inference) were performed on the data. Geographic distribution was mapped onto the tree. The species tree provides strong support for a division of the genus into two subgenera, Salix and Vetrix. Subgenus Salix comprises temperate species from the Americas and Asia, and their disjunction may result from Tertiary events. Subgenus Vetrix is composed of boreo-arctic species of the Northern Hemisphere and their radiation may coincide with the Quaternary glaciations. Sixteen species have ambiguous positions; genetic diversity is lower in subg. Vetrix. A molecular phylogeny of all species of American willows has been inferred. It needs to be tested and further resolved using other molecular data. Nonetheless, the genus clearly has two clades that have distinct biogeographic patterns. PMID:25880993

  18. Phylogenetic relationships of American willows (Salix L., Salicaceae).

    PubMed

    Lauron-Moreau, Aurélien; Pitre, Frédéric E; Argus, George W; Labrecque, Michel; Brouillet, Luc

    2015-01-01

    Salix L. is the largest genus in the family Salicaceae (450 species). Several classifications have been published, but taxonomic subdivision has been under continuous revision. Our goal is to establish the phylogenetic structure of the genus using molecular data on all American willows, using three DNA markers. This complete phylogeny of American willows allows us to propose a biogeographic framework for the evolution of the genus. Material was obtained for the 122 native and introduced willow species of America. Sequences were obtained from the ITS (ribosomal nuclear DNA) and two plastid regions, matK and rbcL. Phylogenetic analyses (parsimony, maximum likelihood, Bayesian inference) were performed on the data. Geographic distribution was mapped onto the tree. The species tree provides strong support for a division of the genus into two subgenera, Salix and Vetrix. Subgenus Salix comprises temperate species from the Americas and Asia, and their disjunction may result from Tertiary events. Subgenus Vetrix is composed of boreo-arctic species of the Northern Hemisphere and their radiation may coincide with the Quaternary glaciations. Sixteen species have ambiguous positions; genetic diversity is lower in subg. Vetrix. A molecular phylogeny of all species of American willows has been inferred. It needs to be tested and further resolved using other molecular data. Nonetheless, the genus clearly has two clades that have distinct biogeographic patterns. PMID:25880993

  19. Phylogenetic Relationships Matter: Antifungal Susceptibility among Clinically Relevant Yeasts

    PubMed Central

    Schmalreck, A. F.; Becker, K.; Fegeler, W.; Czaika, V.; Ulmer, H.; Lass-Flörl, C.

    2014-01-01

    The objective of this study was 2-fold: to evaluate whether phylogenetically closely related yeasts share common antifungal susceptibility profiles (ASPs) and whether these ASPs can be predicted from phylogeny. To address this question, 9,627 yeast strains were collected and tested for their antifungal susceptibility. Isolates were reidentified by considering recent changes in taxonomy and nomenclature. A phylogenetic (PHYLO) code based on the results of multilocus sequence analyses (large-subunit rRNA, small-subunit rRNA, translation elongation factor 1?, RNA polymerase II subunits 1 and 2) and the classification of the cellular neutral sugar composition of coenzyme Q and 18S ribosomal DNA was created to group related yeasts into PHYLO groups. The ASPs were determined for fluconazole, itraconazole, and voriconazole in each PHYLO group. The majority (95%) of the yeast strains were Ascomycetes. After reclassification, a total of 23 genera and 54 species were identified, resulting in an increase of 64% of genera and a decrease of 5% of species compared with the initial identification. These taxa were assigned to 17 distinct PHYLO groups (Ascomycota, n = 13; Basidiomycota, n = 4). ASPs for azoles were similar among members of the same PHYLO group and different between the various PHYLO groups. Yeast phylogeny may be an additional tool to significantly enhance the assessment of MIC values and to predict antifungal susceptibility, thereby more rapidly initiating appropriate patient management. PMID:24366735

  20. Neuromuscular disease classification system

    NASA Astrophysics Data System (ADS)

    Sáez, Aurora; Acha, Begoña; Montero-Sánchez, Adoración; Rivas, Eloy; Escudero, Luis M.; Serrano, Carmen

    2013-06-01

    Diagnosis of neuromuscular diseases is based on subjective visual assessment of biopsies from patients by the pathologist specialist. A system for objective analysis and classification of muscular dystrophies and neurogenic atrophies through muscle biopsy images of fluorescence microscopy is presented. The procedure starts with an accurate segmentation of the muscle fibers using mathematical morphology and a watershed transform. A feature extraction step is carried out in two parts: 24 features that pathologists take into account to diagnose the diseases and 58 structural features that the human eye cannot see, based on the assumption that the biopsy is considered as a graph, where the nodes are represented by each fiber, and two nodes are connected if two fibers are adjacent. A feature selection using sequential forward selection and sequential backward selection methods, a classification using a Fuzzy ARTMAP neural network, and a study of grading the severity are performed on these two sets of features. A database consisting of 91 images was used: 71 images for the training step and 20 as the test. A classification error of 0% was obtained. It is concluded that the addition of features undetectable by the human visual inspection improves the categorization of atrophic patterns.

  1. Subject Classification.

    ERIC Educational Resources Information Center

    Thompson, Gayle; And Others

    Three newspaper librarians described how they manage the files of newspaper clippings which are a necessary part of their collections. The development of a new subject classification system for the clippings files was outlined. The new subject headings were based on standard subject heading lists and on local need. It was decided to use a computer…

  2. Multisensor classification of sedimentary rocks

    NASA Technical Reports Server (NTRS)

    Evans, Diane

    1988-01-01

    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.

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

    E-print Network

    Sekercioglu, Y. Ahmet

    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

  4. Evolutionary models of phylogenetic trees.

    PubMed Central

    Pinelis, Iosif

    2003-01-01

    The most widely used evolutionary model for phylogenetic trees is the equal-rates Markov (ERM) model. A problem is that the ERM model predicts less imbalance than observed for trees inferred from real data; in fact, the observed imbalance tends to fall between the values predicted by the ERM model and those predicted by the proportional-to-distinguishable-arrangements (PDA) model. Here, a continuous multi-rate (MR) family of evolutionary models is presented which contains entire subfamilies corresponding to both the PDA and ERM models. Furthermore, this MR family covers an entire range from 'completely balanced' to 'completely unbalanced' models. In particular, the MR family contains other known evolutionary models. The MR family is very versatile and virtually free of assumptions on the character of evolution; yet it is highly susceptible to rigorous analyses. In particular, such analyses help to uncover adaptability, quasi-stabilization and prolonged stasis as major possible causes of the imbalance. However, the MR model is functionally simple and requires only three parameters to reproduce the observed imbalance. PMID:12965036

  5. Phylogenetic mapping of bacterial morphology

    NASA Technical Reports Server (NTRS)

    Siefert, J. L.; Fox, G. E.

    1998-01-01

    The availability of a meaningful molecular phylogeny for bacteria provides a context for examining the historical significance of various developments in bacterial evolution. Herein, the classical morphological descriptions of selected members of the domain Bacteria are mapped upon the genealogical ancestry deduced from comparison of small-subunit rRNA sequences. For the species examined in this study, a distinct pattern emerges which indicates that the coccus shape has arisen and accumulated independently multiple times in separate lineages and typically survived as a persistent end-state morphology. At least two other morphologies persist but have evolved only once. This study demonstrates that although bacterial morphology is not useful in defining bacterial phylogeny, it is remarkably consistent with that phylogeny once it is known. An examination of the experimental evidence available for morphogenesis as well as microbial fossil evidence corroborates these findings. It is proposed that the accumulation of persistent morphologies is a result of the biophysical properties of peptidoglycan and their genetic control, and that an evolved body-plan strategy based on peptidoglycan may have been a fate-sealing step in the evolution of Bacteria. More generally, this study illustrates that significant evolutionary insights can be obtained by examining biological and biochemical data in the context of a reliable phylogenetic structure.

  6. Ebolavirus classification based on natural vectors.

    PubMed

    Zheng, Hui; Yin, Changchuan; Hoang, Tung; He, Rong Lucy; Yang, Jie; Yau, Stephen S-T

    2015-06-01

    According to the WHO, ebolaviruses have resulted in 8818 human deaths in West Africa as of January 2015. To better understand the evolutionary relationship of the ebolaviruses and infer virulence from the relationship, we applied the alignment-free natural vector method to classify the newest ebolaviruses. The dataset includes three new Guinea viruses as well as 99 viruses from Sierra Leone. For the viruses of the family of Filoviridae, both genus label classification and species label classification achieve an accuracy rate of 100%. We represented the relationships among Filoviridae viruses by Unweighted Pair Group Method with Arithmetic Mean (UPGMA) phylogenetic trees and found that the filoviruses can be separated well by three genera. We performed the phylogenetic analysis on the relationship among different species of Ebolavirus by their coding-complete genomes and seven viral protein genes (glycoprotein [GP], nucleoprotein [NP], VP24, VP30, VP35, VP40, and RNA polymerase [L]). The topology of the phylogenetic tree by the viral protein VP24 shows consistency with the variations of virulence of ebolaviruses. The result suggests that VP24 be a pharmaceutical target for treating or preventing ebolaviruses. PMID:25803489

  7. Phylogenetic inference under varying proportions of indel-induced alignment gaps

    PubMed Central

    Dwivedi, Bhakti; Gadagkar, Sudhindra R

    2009-01-01

    Background The effect of alignment gaps on phylogenetic accuracy has been the subject of numerous studies. In this study, we investigated the relationship between the total number of gapped sites and phylogenetic accuracy, when the gaps were introduced (by means of computer simulation) to reflect indel (insertion/deletion) events during the evolution of DNA sequences. The resulting (true) alignments were subjected to commonly used gap treatment and phylogenetic inference methods. Results (1) In general, there was a strong – almost deterministic – relationship between the amount of gap in the data and the level of phylogenetic accuracy when the alignments were very "gappy", (2) gaps resulting from deletions (as opposed to insertions) contributed more to the inaccuracy of phylogenetic inference, (3) the probabilistic methods (Bayesian, PhyML & "ML?, " a method implemented in DNAML in PHYLIP) performed better at most levels of gap percentage when compared to parsimony (MP) and distance (NJ) methods, with Bayesian analysis being clearly the best, (4) methods that treat gapped sites as missing data yielded less accurate trees when compared to those that attribute phylogenetic signal to the gapped sites (by coding them as binary character data – presence/absence, or as in the ML? method), and (5) in general, the accuracy of phylogenetic inference depended upon the amount of available data when the gaps resulted from mainly deletion events, and the amount of missing data when insertion events were equally likely to have caused the alignment gaps. Conclusion When gaps in an alignment are a consequence of indel events in the evolution of the sequences, the accuracy of phylogenetic analysis is likely to improve if: (1) alignment gaps are categorized as arising from insertion events or deletion events and then treated separately in the analysis, (2) the evolutionary signal provided by indels is harnessed in the phylogenetic analysis, and (3) methods that utilize the phylogenetic signal in indels are developed for distance methods too. When the true homology is known and the amount of gaps is 20 percent of the alignment length or less, the methods used in this study are likely to yield trees with 90–100 percent accuracy. PMID:19698168

  8. Endolithic Microbial Ecosystems: Molecular Phylogenetic Composition,

    E-print Network

    Pace, Norman

    . Photosynthesis-based endolithic communities inhabit the outer millimeters to centimeters of rocks exposed been popularly considered geological evidence for oxygenic photosynthesis. Here I present the first stromatolites cannot be taken alone as evidence for oxygenic photosynthesis. Phylogenetic and statistical

  9. Distribution of phylogenetic diversity under random extinction

    E-print Network

    Beata Faller; Fabio Pardi; Mike Steel

    2007-08-02

    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.

  10. Pareto-optimal phylogenetic tree reconciliation

    E-print Network

    Libeskind-Hadas, Ran

    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 ...

  11. Phylogenetic structure in tropical hummingbird communities

    PubMed Central

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

    2009-01-01

    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

  12. How does cognition evolve? Phylogenetic comparative psychology

    PubMed Central

    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

    2014-01-01

    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

  13. Phylogenetic relationships of Chinese Adiantum based on five plastid markers.

    PubMed

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

    2012-03-01

    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

  14. Phylogenetic Distribution of Fungal Sterols

    PubMed Central

    Weete, John D.; Abril, Maritza; Blackwell, Meredith

    2010-01-01

    Background Ergosterol has been considered the “fungal sterol” for almost 125 years; however, additional sterol data superimposed on a recent molecular phylogeny of kingdom Fungi reveals a different and more complex situation. Methodology/Principal Findings The interpretation of sterol distribution data in a modern phylogenetic context indicates that there is a clear trend from cholesterol and other ?5 sterols in the earliest diverging fungal species to ergosterol in later diverging fungi. There are, however, deviations from this pattern in certain clades. Sterols of the diverse zoosporic and zygosporic forms exhibit structural diversity with cholesterol and 24-ethyl -?5 sterols in zoosporic taxa, and 24-methyl sterols in zygosporic fungi. For example, each of the three monophyletic lineages of zygosporic fungi has distinctive major sterols, ergosterol in Mucorales, 22-dihydroergosterol in Dimargaritales, Harpellales, and Kickxellales (DHK clade), and 24-methyl cholesterol in Entomophthorales. Other departures from ergosterol as the dominant sterol include: 24-ethyl cholesterol in Glomeromycota, 24-ethyl cholest-7-enol and 24-ethyl-cholesta-7,24(28)-dienol in rust fungi, brassicasterol in Taphrinales and hypogeous pezizalean species, and cholesterol in Pneumocystis. Conclusions/Significance Five dominant end products of sterol biosynthesis (cholesterol, ergosterol, 24-methyl cholesterol, 24-ethyl cholesterol, brassicasterol), and intermediates in the formation of 24-ethyl cholesterol, are major sterols in 175 species of Fungi. Although most fungi in the most speciose clades have ergosterol as a major sterol, sterols are more varied than currently understood, and their distribution supports certain clades of Fungi in current fungal phylogenies. In addition to the intellectual importance of understanding evolution of sterol synthesis in fungi, there is practical importance because certain antifungal drugs (e.g., azoles) target reactions in the synthesis of ergosterol. These findings also invalidate use of ergosterol as an indicator of biomass of certain fungal taxa (e.g., Glomeromycota). Data from this study are available from the Assembling the Fungal Tree of Life (AFTOL) Structural and Biochemical Database: http://aftol.umn.edu. PMID:20526375

  15. TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

    PubMed Central

    Chang, Jia-Ming; Di Tommaso, Paolo; Lefort, Vincent; Gascuel, Olivier; Notredame, Cedric

    2015-01-01

    This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. The evaluation can be used to identify the aligned positions most likely to contain structurally analogous residues and also most likely to support an accurate phylogenetic reconstruction. The TCS scoring scheme has been shown to be accurate predictor of structural alignment correctness among commonly used methods. It has also been shown to outperform common filtering schemes like Gblocks or trimAl when doing MSA post-processing prior to phylogenetic tree reconstruction. The web server is available from http://tcoffee.crg.cat/tcs. PMID:25855806

  16. TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.

    PubMed

    Chang, Jia-Ming; Di Tommaso, Paolo; Lefort, Vincent; Gascuel, Olivier; Notredame, Cedric

    2015-07-01

    This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. The evaluation can be used to identify the aligned positions most likely to contain structurally analogous residues and also most likely to support an accurate phylogenetic reconstruction. The TCS scoring scheme has been shown to be accurate predictor of structural alignment correctness among commonly used methods. It has also been shown to outperform common filtering schemes like Gblocks or trimAl when doing MSA post-processing prior to phylogenetic tree reconstruction. The web server is available from http://tcoffee.crg.cat/tcs. PMID:25855806

  17. Characterization of a branch of the phylogenetic tree

    SciTech Connect

    Samuel, Stuart A.; Weng, Gezhi

    2003-04-11

    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.

  18. Characterization of a branch of the phylogenetic tree.

    PubMed

    Samuel, Stuart A; Weng, Gezhi

    2003-02-21

    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

  19. Soil classifications systems review. Final report

    SciTech Connect

    1997-11-01

    Systems used to classify soils are discussed and compared. Major types of classification systems that are reviewed include natural systems, technical systems, the FAO/UNESCO world soil map, soil survey map units, and numerical taxonomy. Natural Classification systems discussed in detail are the United States system, Soil Taxonomy, and the Russian and Canadian systems. Included in the section on technical classification systems are reviews on the AASHO and Unified (ASTM) classification systems. The review of soil classification systems was conducted to establish improved availability of accurate ground thermal conductivity and other heat transfer related properties information. These data are intended to help in the design of closed-loop ground heat exchange systems.

  20. Feature utility in polarimetric radar image classification

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

    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.

  1. Caller behaviour classification using computational intelligence methods.

    PubMed

    Patel, Pretesh B; Marwala, Tshilidzi

    2010-02-01

    A classification system that accurately categorizes caller interaction within Interactive Voice Response systems is essential in determining caller behaviour. Field and call performance classifier for pay beneficiary application are developed. Genetic Algorithms, Multi-Layer Perceptron neural network, Radial Basis Function neural network, Fuzzy Inference Systems and Support Vector Machine computational intelligent techniques were considered in this research. Exceptional results were achieved. Classifiers with accuracy values greater than 90% were developed. The preferred models for field 'Say amount', 'Say confirmation' and call performance classification are the ensemble of classifiers. However, the Multi-Layer Perceptron classifiers performed the best in field 'Say account' and 'Select beneficiary' classification. PMID:20180256

  2. Probabilistic Graphical Model Representation in Phylogenetics

    PubMed Central

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

    2014-01-01

    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

  3. Teaching Molecular Phylogenetics through Investigating a Real-World Phylogenetic Problem

    ERIC Educational Resources Information Center

    Zhang, Xiaorong

    2012-01-01

    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…

  4. Phylogenetic generalised dissimilarity modelling: a new approach to analysing and predicting spatial turnover in the phylogenetic

    E-print Network

    Keogh, Scott

    spatial turnover in the phylogenetic composition of communities Dan F. Rosauer, Simon Ferrier, Kristen J National Univ., Canberra, ACT 0200, Australia. Compared to species turnover, patterns of phylogenetic turnover provide extra information about the spatial structure of biodiversity, for example providing more

  5. Protein classification artificial neural system.

    PubMed Central

    Wu, C.; Whitson, G.; McLarty, J.; Ermongkonchai, A.; Chang, T. C.

    1992-01-01

    A neural network classification method is developed as an alternative approach to the large database search/organization problem. The system, termed Protein Classification Artificial Neural System (ProCANS), has been implemented on a Cray supercomputer for rapid superfamily classification of unknown proteins based on the information content of the neural interconnections. The system employs an n-gram hashing function that is similar to the k-tuple method for sequence encoding. A collection of modular back-propagation networks is used to store the large amount of sequence patterns. The system has been trained and tested with the first 2,148 of the 8,309 entries of the annotated Protein Identification Resource protein sequence database (release 29). The entries included the electron transfer proteins and the six enzyme groups (oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases), with a total of 620 superfamilies. After a total training time of seven Cray central processing unit (CPU) hours, the system has reached a predictive accuracy of 90%. The classification is fast (i.e., 0.1 Cray CPU second per sequence), as it only involves a forward-feeding through the networks. The classification time on a full-scale system embedded with all known superfamilies is estimated to be within 1 CPU second. Although the training time will grow linearly with the number of entries, the classification time is expected to remain low even if there is a 10-100-fold increase of sequence entries. The neural database, which consists of a set of weight matrices of the networks, together with the ProCANS software, can be ported to other computers and made available to the genome community. The rapid and accurate superfamily classification would be valuable to the organization of protein sequence databases and to the gene recognition in large sequencing projects. PMID:1304365

  6. Genomic repeat abundances contain phylogenetic signal.

    PubMed

    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

    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

  7. Genomic Repeat Abundances Contain Phylogenetic Signal

    PubMed Central

    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

    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

  8. Prioritizing Populations for Conservation Using Phylogenetic Networks

    PubMed Central

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

    2014-01-01

    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

  9. Prioritizing populations for conservation using phylogenetic networks.

    PubMed

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

    2014-01-01

    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

  10. Worldwide phylogenetic relationship of avian poxviruses

    USGS Publications Warehouse

    Gyuranecz, Miklós; Foster, Jeffrey T.; Dán, Ádám; Ip, Hon S.; Egstad, Kristina F.; Parker, Patricia G.; Higashiguchi, Jenni M.; Skinner, Michael A.; Höfle, Ursula; Kreizinger, Zsuzsa; Dorrestein, Gerry M.; Solt, Szabolcs; Sós, Endre; Kim, Young Jun; Uhart, Marcela; Pereda, Ariel; González-Hein, Gisela; Hidalgo, Hector; Blanco, Juan-Manuel; Erdélyi, Károly

    2013-01-01

    Poxvirus infections have been found in 230 species of wild and domestic birds worldwide in both terrestrial and marine environments. This ubiquity raises the question of how infection has been transmitted and globally dispersed. We present a comprehensive global phylogeny of 111 novel poxvirus isolates in addition to all available sequences from GenBank. Phylogenetic analysis of Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we have expanded the analyses to include a second locus (DNA polymerase gene), allowing for a more robust phylogenetic framework, finer genetic resolution within specific groups and the detection of potential recombination. Our phylogenetic results reveal several major features of avipoxvirus evolution and ecology and propose an updated avipoxvirus taxonomy, including three novel subclades. The characterization of poxviruses from 57 species of birds in this study extends the current knowledge of their host range and provides the first evidence of the phylogenetic effect of genetic recombination of avipoxviruses. The repeated occurrence of avian family or order-specific grouping within certain clades (e.g. starling poxvirus, falcon poxvirus, raptor poxvirus, etc.) indicates a marked role of host adaptation, while the sharing of poxvirus species within prey-predator systems emphasizes the capacity for cross-species infection and limited host adaptation. Our study provides a broad and comprehensive phylogenetic analysis of the Avipoxvirus genus, an ecologically and environmentally important viral group, to formulate a genome sequencing strategy that will clarify avipoxvirus taxonomy.

  11. Worldwide Phylogenetic Relationship of Avian Poxviruses

    PubMed Central

    Foster, Jeffrey T.; Dán, Ádám; Ip, Hon S.; Egstad, Kristina F.; Parker, Patricia G.; Higashiguchi, Jenni M.; Skinner, Michael A.; Höfle, Ursula; Kreizinger, Zsuzsa; Dorrestein, Gerry M.; Solt, Szabolcs; Sós, Endre; Kim, Young Jun; Uhart, Marcela; Pereda, Ariel; González-Hein, Gisela; Hidalgo, Hector; Blanco, Juan-Manuel; Erdélyi, Károly

    2013-01-01

    Poxvirus infections have been found in 230 species of wild and domestic birds worldwide in both terrestrial and marine environments. This ubiquity raises the question of how infection has been transmitted and globally dispersed. We present a comprehensive global phylogeny of 111 novel poxvirus isolates in addition to all available sequences from GenBank. Phylogenetic analysis of the Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we expanded the analyses to include a second locus (DNA polymerase gene), allowing for a more robust phylogenetic framework, finer genetic resolution within specific groups, and the detection of potential recombination. Our phylogenetic results reveal several major features of avipoxvirus evolution and ecology and propose an updated avipoxvirus taxonomy, including three novel subclades. The characterization of poxviruses from 57 species of birds in this study extends the current knowledge of their host range and provides the first evidence of the phylogenetic effect of genetic recombination of avipoxviruses. The repeated occurrence of avian family or order-specific grouping within certain clades (e.g., starling poxvirus, falcon poxvirus, raptor poxvirus, etc.) indicates a marked role of host adaptation, while the sharing of poxvirus species within prey-predator systems emphasizes the capacity for cross-species infection and limited host adaptation. Our study provides a broad and comprehensive phylogenetic analysis of the Avipoxvirus genus, an ecologically and environmentally important viral group, to formulate a genome sequencing strategy that will clarify avipoxvirus taxonomy. PMID:23408635

  12. Hyperspectral image classification for mapping agricultural tillage practices

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An efficient classification framework for mapping agricultural tillage practice using hyperspectral remote sensing imagery is proposed, which has the potential to be implemented practically to provide rapid, accurate, and objective surveying data for precision agricultural management and appraisal f...

  13. Machine learning for patient-adaptive ectopic beat classification

    E-print Network

    Wiens, Jenna Marleau

    2010-01-01

    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 ...

  14. 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

    Hibbett, David S.

    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

  15. The phylogenetic significance of colour patterns in marine teleost larvae

    PubMed Central

    Baldwin, Carole C

    2013-01-01

    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

  16. Construction of the Platform for Phylogenetic Analysis

    NASA Astrophysics Data System (ADS)

    Meng, Zhen; Lin, Xiaoguang; He, Xing; Gao, Yanping; Liu, Hongmei; Liu, Yong; Zhou, Yuanchun; Li, Jianhui; Chen, Zhiduan; Zhang, Shouzhou; Li, Yong

    Based on discussing the history of advancement to building the tree of life using genetic and genomic information, effective strategies and methods for the construction of the tree of life, this paper carried out business process analysis and application design. It implements a phylogenetic analysis platform for the land plants based on this analysis. The platform extracts molecular data from the international public databases in batch, which is automated acquisition, cleaning function for users to understand the situation of peer data. The process of phylogenetic reconstruction includes several public modes and tools, such as batch extraction, multiple sequence alignment, cleaning & editing, tree reconstruction, phylogeny evaluation and visualization. All these procedures demand a number of interactive interfaces for phylogenetic tree automatic generation and decision-making aids experiment.

  17. Remote Sensing Information Classification

    NASA Technical Reports Server (NTRS)

    Rickman, Douglas L.

    2008-01-01

    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.

  18. Classification of Support Needs in a Residential Setting

    ERIC Educational Resources Information Center

    Riches, Vivienne Catherine

    2003-01-01

    A supports classification and assessment system is required in residential settings that enables accurate classification and resource allocation in the context of limited resources. In developing such a system, the American Association on Mental Retardation intensities of supports framework was used and consultation with all stakeholders resulted…

  19. 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

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

    2014-01-01

    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

  20. Classification of the acanthocephala.

    PubMed

    Amin, Omar M

    2013-09-01

    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

  1. Trends and concepts in fern classification

    PubMed Central

    Christenhusz, Maarten J. M.; Chase, Mark W.

    2014-01-01

    Background and Aims Throughout the history of fern classification, familial and generic concepts have been highly labile. Many classifications and evolutionary schemes have been proposed during the last two centuries, reflecting different interpretations of the available evidence. Knowledge of fern structure and life histories has increased through time, providing more evidence on which to base ideas of possible relationships, and classification has changed accordingly. This paper reviews previous classifications of ferns and presents ideas on how to achieve a more stable consensus. Scope An historical overview is provided from the first to the most recent fern classifications, from which conclusions are drawn on past changes and future trends. The problematic concept of family in ferns is discussed, with a particular focus on how this has changed over time. The history of molecular studies and the most recent findings are also presented. Key Results Fern classification generally shows a trend from highly artificial, based on an interpretation of a few extrinsic characters, via natural classifications derived from a multitude of intrinsic characters, towards more evolutionary circumscriptions of groups that do not in general align well with the distribution of these previously used characters. It also shows a progression from a few broad family concepts to systems that recognized many more narrowly and highly controversially circumscribed families; currently, the number of families recognized is stabilizing somewhere between these extremes. Placement of many genera was uncertain until the arrival of molecular phylogenetics, which has rapidly been improving our understanding of fern relationships. As a collective category, the so-called ‘fern allies’ (e.g. Lycopodiales, Psilotaceae, Equisetaceae) were unsurprisingly found to be polyphyletic, and the term should be abandoned. Lycopodiaceae, Selaginellaceae and Isoëtaceae form a clade (the lycopods) that is sister to all other vascular plants, whereas the whisk ferns (Psilotaceae), often included in the lycopods or believed to be associated with the first vascular plants, are sister to Ophioglossaceae and thus belong to the fern clade. The horsetails (Equisetaceae) are also members of the fern clade (sometimes inappropriately called ‘monilophytes’), but, within that clade, their placement is still uncertain. Leptosporangiate ferns are better understood, although deep relationships within this group are still unresolved. Earlier, almost all leptosporangiate ferns were placed in a single family (Polypodiaceae or Dennstaedtiaceae), but these families have been redefined to narrower more natural entities. Conclusions Concluding this paper, a classification is presented based on our current understanding of relationships of fern and lycopod clades. Major changes in our understanding of these families are highlighted, illustrating issues of classification in relation to convergent evolution and false homologies. Problems with the current classification and groups that still need study are pointed out. A summary phylogenetic tree is also presented. A new classification in which Aspleniaceae, Cyatheaceae, Polypodiaceae and Schizaeaceae are expanded in comparison with the most recent classifications is presented, which is a modification of those proposed by Smith et al. (2006, 2008) and Christenhusz et al. (2011). These classifications are now finding a wider acceptance and use, and even though a few amendments are made based on recently published results from molecular analyses, we have aimed for a stable family and generic classification of ferns. PMID:24532607

  2. Support Vector Machine Classification Trees.

    PubMed

    de Boves Harrington, Peter

    2015-11-01

    Proteomic and metabolomic studies based on chemical profiling require powerful classifiers to model accurately complex collections of data. Support vector machines (SVMs) are advantageous in that they provide a maximum margin of separation for the classification hyperplane. A new method for constructing classification trees, for which the branches comprise SVMs, has been devised. The novel feature is that the distribution of the data objects is used to determine the SVM encoding. The variance and covariance of the data objects are used for determining the bipolar encoding required for the SVM. The SVM that yields the lowest entropy of classification becomes the branch of the tree. The SVM-tree classifier has the added advantage that nonlinearly separable data may be accurately classified without optimization of the cost parameter C or searching for a correct higher dimensional kernel transform. It compares favorably to a regularized linear discriminant analysis, SVMs in a one against all multiple classifier, and a fuzzy rule-building expert system, a tree classifier with a fuzzy margin of separation. SVMs offer a speed advantage, especially for data sets that have more measurements than objects. PMID:26461495

  3. Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry

    PubMed Central

    Jia, Rui Zong; Zhang, Rong Juan; Wei, Qing; Chen, Wen Feng; Cho, Il Kyu; Chen, Wen Xin; Li, Qing X

    2015-01-01

    Mass spectrometry (MS) has been widely used for specific, sensitive and rapid analysis of proteins and has shown a high potential for bacterial identification and characterization. Type strains of four species of rhizobia and Escherichia coli DH5? were employed as reference bacteria to optimize various parameters for identification and classification of species of rhizobia by matrix-assisted laser desorption/ionization time-of-flight MS (MALDI TOF MS). The parameters optimized included culture medium states (liquid or solid), bacterial growth phases, colony storage temperature and duration, and protein data processing to enhance the bacterial identification resolution, accuracy and reliability. The medium state had little effects on the mass spectra of protein profiles. A suitable sampling time was between the exponential phase and the stationary phase. Consistent protein mass spectral profiles were observed for E. coli colonies pre-grown for 14 days and rhizobia for 21 days at 4°C or 21°C. A dendrogram of 75 rhizobial strains of 4 genera was constructed based on MALDI TOF mass spectra and the topological patterns agreed well with those in the 16S rDNA phylogenetic tree. The potential of developing a mass spectral database for all rhizobia species was assessed with blind samples. The entire process from sample preparation to accurate identification and classification of species required approximately one hour. PMID:26500417

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

    PubMed Central

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

    2010-01-01

    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

  5. Draft genome sequences for the obligate bacterial predators Bacteriovorax spp. of four phylogenetic clusters

    PubMed Central

    2015-01-01

    Bacteriovorax is the halophilic genus of the obligate bacterial predators, Bdellovibrio and like organisms. The predators are known for their unique biphasic life style in which they search for and attack their prey in the free living phase; penetrate, grow, multiply and lyse the prey in the intraperiplasmic phase. Bacteriovorax isolates representing four phylogenetic clusters were selected for genomic sequencing. Only one type strain genome has been published so far from the genus Bacteriovorax. We report the genomes from non-type strains isolated from aquatic environments. Here we describe and compare the genomic features of the four strains, together with the classification and annotation. PMID:26203326

  6. Sequence exploration reveals information bias among molecular markers used in phylogenetic reconstruction for Colletotrichum species.

    PubMed

    Rampersad, Sephra N; Hosein, Fazeeda N; Carrington, Christine Vf

    2014-01-01

    The Colletotrichum gloeosporioides species complex is among the most destructive fungal plant pathogens in the world, however, identification of isolates of quarantine importance to the intra-specific level is confounded by a number of factors that affect phylogenetic reconstruction. Information bias and quality parameters were investigated to determine whether nucleotide sequence alignments and phylogenetic trees accurately reflect the genetic diversity and phylogenetic relatedness of individuals. Sequence exploration of GAPDH, ACT, TUB2 and ITS markers indicated that the query sequences had different patterns of nucleotide substitution but were without evidence of base substitution saturation. Regions of high entropy were much more dispersed in the ACT and GAPDH marker alignments than for the ITS and TUB2 markers. A discernible bimodal gap in the genetic distance frequency histograms was produced for the ACT and GAPDH markers which indicated successful separation of intra- and inter-specific sequences in the data set. Overall, analyses indicated clear differences in the ability of these markers to phylogenetically separate individuals to the intra-specific level which coincided with information bias. PMID:25392785

  7. Phylogenetic signal in amphibian sensitivity to copper sulfate relative to experimental temperature.

    PubMed

    Chiari, Ylenia; Glaberman, Scott; Serén, Nina; Carretero, Miguel A; Capellini, Isabella

    2015-04-01

    The release of large quantities of chemicals into the environment represents a major source of environmental disturbance. In recent years, the focus of ecotoxicology has shifted from describing the effects of chemical contaminants on individual species to developing more integrated approaches for predicting and evaluating long term effects of chemicals across species and ecosystems. Traditional ecotoxicology is typically based on data of sensitivity to a contaminant of a few surrogate species and often considers little variability in chemical sensitivity within and among taxonomic groups. This approach assumes that evolutionary history and phylogenetic relatedness among species have little or no impact on species' sensitivity to chemical compounds. Few studies have tested this assumption. Using phylogenetic comparative methods and published data for amphibians, we show that sensitivity to copper sulfate, a commonly used pesticide, exhibits a strong phylogenetic signal when controlling for experimental temperature. Our results indicate that evolutionary history needs to be accounted for to make accurate predictions of amphibian sensitivity to this contaminant under different temperature scenarios. Since physiological and metabolic traits showing high phylogenetic signal likely underlie variation in species sensitivity to chemical stressors, future studies should evaluate and predict species vulnerability to pollutants using evolutionarily informed approaches. PMID:26214907

  8. The Independent Evolution Method Is Not a Viable Phylogenetic Comparative Method

    PubMed Central

    2015-01-01

    Phylogenetic comparative methods (PCMs) use data on species traits and phylogenetic relationships to shed light on evolutionary questions. Recently, Smaers and Vinicius suggested a new PCM, Independent Evolution (IE), which purportedly employs a novel model of evolution based on Felsenstein’s Adaptive Peak Model. The authors found that IE improves upon previous PCMs by producing more accurate estimates of ancestral states, as well as separate estimates of evolutionary rates for each branch of a phylogenetic tree. Here, we document substantial theoretical and computational issues with IE. When data are simulated under a simple Brownian motion model of evolution, IE produces severely biased estimates of ancestral states and changes along individual branches. We show that these branch-specific changes are essentially ancestor-descendant or “directional” contrasts, and draw parallels between IE and previous PCMs such as “minimum evolution”. Additionally, while comparisons of branch-specific changes between variables have been interpreted as reflecting the relative strength of selection on those traits, we demonstrate through simulations that regressing IE estimated branch-specific changes against one another gives a biased estimate of the scaling relationship between these variables, and provides no advantages or insights beyond established PCMs such as phylogenetically independent contrasts. In light of our findings, we discuss the results of previous papers that employed IE. We conclude that Independent Evolution is not a viable PCM, and should not be used in comparative analyses. PMID:26683838

  9. Flying Insect Classification with Inexpensive Yanping Chen

    E-print Network

    Zordan, Victor

    with large scale experiments, as measured both by the number of insects and the number of species consideredFlying Insect Classification with Inexpensive Sensors Yanping Chen Department of Computer Science, noninvasive sensors to accurately classify flying insects would have significant implications

  10. 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...

  11. Simulated annealing in the search for phylogenetic trees 

    E-print Network

    Barker, Daniel

    2000-07-18

    I investigate use of the simulated annealing heuristic to seek phylogenetic trees judged optimal according to the principle of parsimony. I begin by looking into the central data structure in phylogenetic research, the ...

  12. 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...

  13. MOLECULAR PHYLOGENETIC RELATIONSHIPS AMONG DIABROTICA SPECIES (ACCESSION NO. AF195196)

    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...

  14. Fly pollination in Ceropegia (Apocynaceae: Asclepiadoideae): biogeographic and phylogenetic perspectives

    E-print Network

    Chittka, Lars

    Fly pollination in Ceropegia (Apocynaceae: Asclepiadoideae): biogeographic and phylogenetic-shaped flowers that temporarily trap pollinators. The taxo- nomic diversity of pollinators, biogeographic and phylogenetic patterns of pollinator exploitation, and the level of specificity of interactions were assessed

  15. 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...

  16. 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...

  17. MOLECULAR PHYLOGENETIC RELATIONSHIPS AMONG DIABROTICA SPECIES (ACCESSION NO. AF195197)

    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...

  18. 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...

  19. 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...

  20. Phylogenetic relationships of the North American chorus frogs (Pseudacris: Hylidae)

    E-print Network

    Phylogenetic relationships of the North American chorus frogs (Pseudacris: Hylidae) Emily C We examined phylogenetic relationships of the North American chorus frogs (Pseudacris: Hylidae) from regilla and cadaverina, (2) a Fat Frog Clade including ornata, streckeri, and illi- noensis, (3

  1. Multilocus phylogenetic analysis of the genus Aeromonas.

    PubMed

    Martinez-Murcia, Antonio J; Monera, Arturo; Saavedra, M Jose; Oncina, Remedios; Lopez-Alvarez, Monserrate; Lara, Erica; Figueras, M Jose

    2011-05-01

    A broad multilocus phylogenetic analysis (MLPA) of the representative diversity of a genus offers the opportunity to incorporate concatenated inter-species phylogenies into bacterial systematics. Recent analyses based on single housekeeping genes have provided coherent phylogenies of Aeromonas. However, to date, a multi-gene phylogenetic analysis has never been tackled. In the present study, the intra- and inter-species phylogenetic relationships of 115 strains representing all Aeromonas species described to date were investigated by MLPA. The study included the independent analysis of seven single gene fragments (gyrB, rpoD, recA, dnaJ, gyrA, dnaX, and atpD), and the tree resulting from the concatenated 4705 bp sequence. The phylogenies obtained were consistent with each other, and clustering agreed with the Aeromonas taxonomy recognized to date. The highest clustering robustness was found for the concatenated tree (i.e. all Aeromonas species split into 100% bootstrap clusters). Both possible chronometric distortions and poor resolution encountered when using single-gene analysis were buffered in the concatenated MLPA tree. However, reliable phylogenetic species delineation required an MLPA including several "bona fide" strains representing all described species. PMID:21353754

  2. Quantifying MCMC exploration of phylogenetic tree space.

    PubMed

    Whidden, Chris; Matsen, Frederick A

    2015-05-01

    In order to gain an understanding of the effectiveness of phylogenetic Markov chain Monte Carlo (MCMC), it is important to understand how quickly the empirical distribution of the MCMC converges to the posterior distribution. In this article, we investigate this problem on phylogenetic tree topologies with a metric that is especially well suited to the task: the subtree prune-and-regraft (SPR) metric. This metric directly corresponds to the minimum number of MCMC rearrangements required to move between trees in common phylogenetic MCMC implementations. We develop a novel graph-based approach to analyze tree posteriors and find that the SPR metric is much more informative than simpler metrics that are unrelated to MCMC moves. In doing so, we show conclusively that topological peaks do occur in Bayesian phylogenetic posteriors from real data sets as sampled with standard MCMC approaches, investigate the efficiency of Metropolis-coupled MCMC (MCMCMC) in traversing the valleys between peaks, and show that conditional clade distribution (CCD) can have systematic problems when there are multiple peaks. PMID:25631175

  3. Quantifying MCMC Exploration of Phylogenetic Tree Space

    PubMed Central

    Whidden, Chris; Matsen, Frederick A.

    2015-01-01

    In order to gain an understanding of the effectiveness of phylogenetic Markov chain Monte Carlo (MCMC), it is important to understand how quickly the empirical distribution of the MCMC converges to the posterior distribution. In this article, we investigate this problem on phylogenetic tree topologies with a metric that is especially well suited to the task: the subtree prune-and-regraft (SPR) metric. This metric directly corresponds to the minimum number of MCMC rearrangements required to move between trees in common phylogenetic MCMC implementations. We develop a novel graph-based approach to analyze tree posteriors and find that the SPR metric is much more informative than simpler metrics that are unrelated to MCMC moves. In doing so, we show conclusively that topological peaks do occur in Bayesian phylogenetic posteriors from real data sets as sampled with standard MCMC approaches, investigate the efficiency of Metropolis-coupled MCMC (MCMCMC) in traversing the valleys between peaks, and show that conditional clade distribution (CCD) can have systematic problems when there are multiple peaks. PMID:25631175

  4. Sequence-Length Requirements for Phylogenetic Methods

    E-print Network

    Moret, Bernard

    simulations based on random birth-death trees, with controlled deviations from ultrametricity, to collect dataSequence-Length Requirements for Phylogenetic Methods Bernard M.E. Moret1 , Usman Roshan2 reconstruction method (DCMNJ+MP) based on disk-covering and the maximum parsimony cri- terion. We use extensive

  5. Phylogenetic and phylogenomic overview of the Polyporales.

    PubMed

    Binder, Manfred; Justo, Alfredo; Riley, Robert; Salamov, Asaf; Lopez-Giraldez, Francesc; Sjökvist, Elisabet; Copeland, Alex; Foster, Brian; Sun, Hui; Larsson, Ellen; Larsson, Karl-Henrik; Townsend, Jeffrey; Grigoriev, Igor V; Hibbett, David S

    2013-01-01

    We present a phylogenetic and phylogenomic overview of the Polyporales. The newly sequenced genomes of Bjerkandera adusta, Ganoderma sp., and Phlebia brevispora are introduced and an overview of 10 currently available Polyporales genomes is provided. The new genomes are 39 500 000-49 900 00 bp and encode for 12 910-16 170 genes. We searched available genomes for single-copy genes and performed phylogenetic informativeness analyses to evaluate their potential for phylogenetic systematics of the Polyporales. Phylogenomic datasets (25, 71, 356 genes) were assembled for the 10 Polyporales species with genome data and compared with the most comprehensive dataset of Polyporales to date (six-gene dataset for 373 taxa, including taxa with missing data). Maximum likelihood and Bayesian phylogenetic analyses of genomic datasets yielded identical topologies, and the corresponding clades also were recovered in the 373-taxa dataset although with different support values in some datasets. Three previously recognized lineages of Polyporales, antrodia, core polyporoid and phlebioid clades, are supported in most datasets, while the status of the residual polyporoid clade remains uncertain and certain taxa (e.g. Gelatoporia, Grifola, Tyromyces) apparently do not belong to any of the major lineages of Polyporales. The most promising candidate single-copy genes are presented, and nodes in the Polyporales phylogeny critical for the suprageneric taxonomy of the order are identified and discussed. PMID:23935031

  6. Dating human cultural capacity using phylogenetic principles

    E-print Network

    Lindenfors, Patrik

    Dating human cultural capacity using phylogenetic principles J. Lind1,2 , P. Lindenfors1,2 , S. Ghirlanda1,3 , K. Lide´n1,4 & M. Enquist1,2 1 Centre for the Study of Cultural Evolution, Stockholm based unique abilities making complex culture possible; an assemblage of traits which we term ``cultural

  7. Probabilistic Graphical Model Representation in Phylogenetics

    E-print Network

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

    2014-06-20

    .permissions@oup.com DOI:10.1093/sysbio/syu039 Advance Access publication June 20, 2014 Probabilistic Graphical Model Representation in Phylogenetics SEBASTIAN HÖHNA1,2,?, TRACY A. HEATH3,4, BASTIEN BOUSSAU3,5, MICHAEL J. LANDIS3, FREDRIK RONQUIST6, AND JOHN P. HUELSENBECK...

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

    PubMed Central

    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

    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

  9. Integrating Classification and Association Rule Mining Bing Liu Wynne Hsu Yiming Ma

    E-print Network

    Illinois at Chicago, University of

    Classification rule mining and association rule mining are two important data mining techniques. ClassificationIntegrating Classification and Association Rule Mining Bing Liu Wynne Hsu Yiming Ma Department a small set of rules in the database that forms an accurate classifier. Association rule mining finds all

  10. Terrain classification for a UGV

    NASA Astrophysics Data System (ADS)

    Sarwal, Alok; Baker, Chris; Rosenblum, Mark

    2005-05-01

    This work addresses the issue of Terrain Classification that can be applied for path planning for an Unmanned Ground Vehicle (UGV) platform. We are interested in classification of features such as rocks, bushes, trees and dirt roads. Currently, the data is acquired from a color camera mounted on the UGV as we can add range data from a second sensor in the future. The classification is accomplished by first, coarse segmenting a frame and then refining the initial segmentations through a convenient user interface. After the first frame, temporal information is exploited to improve the quality of the image segmentation and help classification adapt to changes due to ambient lighting, shadows, and scene changes as the platform moves. The Mean Shift Classifier algorithm provides segmentation of the current frame data. We have tested the above algorithms with four sequence of frames acquired in an environment with terrain representative of the type we expect to see in the field. A comparison of the results from this algorithm was done with accurate manually-segmented (ground-truth) data, for each frame in the sequence.

  11. Evaluating Support for the Current Classification of Eukaryotic Diversity

    PubMed Central

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

    2006-01-01

    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

  12. Spectral-spatial hyperspectral classification based on multi-center SAM and MRF

    NASA Astrophysics Data System (ADS)

    Tang, Bo; Liu, Zhi; Xiao, Xiaoyan; Nie, Mingyu; Chang, Jun; Jiang, Wei; Li, Xiaomei; Zheng, Chengyun

    2015-09-01

    In this paper, a novel framework for an accurate spectral-spatial classification of hyperspectral images is proposed to address nonlinear classification problems. The algorithm is based on the spectral angle mapper (SAM), which is achieved by introducing the multi-center model and Markov random fields (MRF) into a probabilistic decision framework to obtain an accurate classification. Experimental comparisons between several traditional classification methods and the proposed MSAM-MRF algorithm have demonstrated that the performance of the proposed MSAM-MRF algorithm outperforms the traditional classification algorithms.

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

    PubMed Central

    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; Sérusiaux, Emmanuël; Maddison, David R.; Arnold, A. Elizabeth; Lutzoni, François; Stenroos, Soili

    2014-01-01

    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

  14. Cnidarian phylogenetic relationships as revealed by mitogenomics

    PubMed Central

    2013-01-01

    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

  15. Mathematical Framework for Phylogenetic Birth-And-Death Models

    E-print Network

    Csürös, Miklós

    Mathematical Framework for Phylogenetic Birth-And-Death Models Mikl´os Csur¨os Istv´an Mikl´os February 5, 2009 Abstract A phylogenetic birth-and-death model is a probabilistic graphical model for a so genome evo- lution. Here we describe the mathematical formalism for phylogenetic birth-and-death models

  16. MATHEMATICAL AND COMPUTATIONAL LINGUISTICS PROJECT N.4 SYNTACTIC PHYLOGENETIC TREES

    E-print Network

    Marcolli, Matilde

    MATHEMATICAL AND COMPUTATIONAL LINGUISTICS PROJECT N.4 SYNTACTIC PHYLOGENETIC TREES CS101/MA191 for instance the collection of papers in [1]. Mostly, the computational reconstructions of linguistic CLASS WINTER 2015, MATILDE MARCOLLI 1. Linguistic Phylogenetic Trees The reconstruction of phylogenetic

  17. Introduction 1.1 Genealogical and Phylogenetic and Networks

    E-print Network

    California at Davis, University of

    Chapter 1 Introduction 1.1 Genealogical and Phylogenetic and Networks "All DNA is recombinant DNA be represented as a tree. [42]" Genealogical and Phylogenetic Networks are graph-theoretic models of evo- lution that go beyond Phylogenetic Trees, the traditional representation of evo- lutionary history. Genealogical

  18. Phylogenetic analyses of ecological communities using DNA barcode data.

    PubMed

    Swenson, Nathan G

    2012-01-01

    Ecologists and conservation biologists are increasingly focusing on quantifying the phylogenetic component of biodiversity in order to inform basic and applied research. A major obstacle of this approach in tropical ecosystems has been the difficulty of generating high-quality phylogenetic trees for the vast numbers of species in these systems. Phylogenetic trees inferred from DNA barcodes hold the potential to overcome this obstacle. Here, I present a methodological framework for analyzing the phylogenetic alpha and beta diversity of ecological communities using a phylogenetic tree. The analytical approach is presented using the freely available and widely used software platform "R". PMID:22684968

  19. Accurate photometric redshift probability density estimation - method comparison and application

    NASA Astrophysics Data System (ADS)

    Rau, Markus Michael; Seitz, Stella; Brimioulle, Fabrice; Frank, Eibe; Friedrich, Oliver; Gruen, Daniel; Hoyle, Ben

    2015-10-01

    We introduce an ordinal classification algorithm for photometric redshift estimation, which significantly improves the reconstruction of photometric redshift probability density functions (PDFs) for individual galaxies and galaxy samples. As a use case we apply our method to CFHTLS galaxies. The ordinal classification algorithm treats distinct redshift bins as ordered values, which improves the quality of photometric redshift PDFs, compared with non-ordinal classification architectures. We also propose a new single value point estimate of the galaxy redshift, which can be used to estimate the full redshift PDF of a galaxy sample. This method is competitive in terms of accuracy with contemporary algorithms, which stack the full redshift PDFs of all galaxies in the sample, but requires orders of magnitude less storage space. The methods described in this paper greatly improve the log-likelihood of individual object redshift PDFs, when compared with a popular neural network code (ANNZ). In our use case, this improvement reaches 50 per cent for high-redshift objects (z ? 0.75). We show that using these more accurate photometric redshift PDFs will lead to a reduction in the systematic biases by up to a factor of 4, when compared with less accurate PDFs obtained from commonly used methods. The cosmological analyses we examine and find improvement upon are the following: gravitational lensing cluster mass estimates, modelling of angular correlation functions and modelling of cosmic shear correlation functions.

  20. Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships

    PubMed Central

    2014-01-01

    Background Camellia is an economically and phylogenetically important genus in the family Theaceae. Owing to numerous hybridization and polyploidization, it is taxonomically and phylogenetically ranked as one of the most challengingly difficult taxa in plants. Sequence comparisons of chloroplast (cp) genomes are of great interest to provide a robust evidence for taxonomic studies, species identification and understanding mechanisms that underlie the evolution of the Camellia species. Results The eight complete cp genomes and five draft cp genome sequences of Camellia species were determined using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. The Camellia cp genomes exhibited typical circular structure that was rather conserved in genomic structure and the synteny of gene order. Differences of repeat sequences, simple sequence repeats, indels and substitutions were further examined among five complete cp genomes, representing a wide phylogenetic diversity in the genus. A total of fifteen molecular markers were identified with more than 1.5% sequence divergence that may be useful for further phylogenetic analysis and species identification of Camellia. Our results showed that, rather than functional constrains, it is the regional constraints that strongly affect sequence evolution of the cp genomes. In a substantial improvement over prior studies, evolutionary relationships of the section Thea were determined on basis of phylogenomic analyses of cp genome sequences. Conclusions Despite a high degree of conservation between the Camellia cp genomes, sequence variation among species could still be detected, representing a wide phylogenetic diversity in the genus. Furthermore, phylogenomic analysis was conducted using 18 complete cp genomes and 5 draft cp genome sequences of Camellia species. Our results support Chang’s taxonomical treatment that C. pubicosta may be classified into sect. Thea, and indicate that taxonomical value of the number of ovaries should be reconsidered when classifying the Camellia species. The availability of these cp genomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the phylogeny of the genus Camellia. PMID:25001059

  1. Phylogenetic and Biological Significance of Evolutionary Elements from Metazoan Mitochondrial Genomes

    PubMed Central

    Yuan, Jianbo; Zhu, Qingming; Liu, Bin

    2014-01-01

    The evolutionary history of living species is usually inferred through the phylogenetic analysis of molecular and morphological information using various mathematical models. New challenges in phylogenetic analysis are centered mostly on the search for accurate and efficient methods to handle the huge amounts of sequence data generated from newer genome sequencing. The next major challenge is the determination of relationships between the evolution of structural elements and their functional implementation, which is largely ignored in previous analyses. Here, we described the discovery of structural elements in metazoan mitochondrial genomes, termed key K-strings, that can serve as a basis for phylogenetic tree construction. Although comprising only a small fraction (0.73%) of all K-strings, these key K-strings are pivotal to the tree construction because they allow for a significant reduction in the computational time required to construct phylogenetic trees, and more importantly, they make significant improvement to the results of phylogenetic inference. The trees constructed from the key K-strings were consistent overall to our current view of metazoan phylogeny and exhibited a more rational topology than the trees constructed by using other conventional methods. Surprisingly, the key K-strings tended to accumulate in the conserved regions of the original sequences, which were most likely due to strong selection pressure. Furthermore, the special structural features of the key K-strings should have some potential applications in the study of the structures and functions relationship of proteins and in the determination of evolutionary trajectory of species. The novelty and potential importance of key K-strings lead us to believe that they are essential evolutionary elements. As such, they may play important roles in the process of species evolution and their physical existence. Further studies could lead to discoveries regarding the relationship between evolution and processes of speciation. PMID:24465405

  2. Molecular phylogenetics and historical biogeography amid shifting continents in the cockles and giant clams (Bivalvia: Cardiidae).

    PubMed

    Herrera, Nathanael D; Ter Poorten, Jan Johan; Bieler, Rüdiger; Mikkelsen, Paula M; Strong, Ellen E; Jablonski, David; Steppan, Scott J

    2015-12-01

    Reconstructing historical biogeography of the marine realm is complicated by indistinct barriers and, over deeper time scales, a dynamic landscape shaped by plate tectonics. Here we present the most extensive examination of model-based historical biogeography among marine invertebrates to date. We conducted the largest phylogenetic and molecular clock analyses to date for the bivalve family Cardiidae (cockles and giant clams) with three unlinked loci for 110 species representing 37 of the 50 genera. Ancestral ranges were reconstructed using the dispersal-extinction-cladogenesis (DEC) method with a time-stratified paleogeographic model wherein dispersal rates varied with shifting tectonics. Results were compared to previous classifications and the extensive paleontological record. Six of the eight prior subfamily groupings were found to be para- or polyphyletic. Cardiidae originated and subsequently diversified in the tropical Indo-Pacific starting in the Late Triassic. Eastern Atlantic species were mainly derived from the tropical Indo-Mediterranean region via the Tethys Sea. In contrast, the western Atlantic fauna was derived from Indo-Pacific clades. Our phylogenetic results demonstrated greater concordance with geography than did previous phylogenies based on morphology. Time-stratifying the DEC reconstruction improved the fit and was highly consistent with paleo-ocean currents and paleogeography. Lastly, combining molecular phylogenetics with a rich and well-documented fossil record allowed us to test the accuracy and precision of biogeographic range reconstructions. PMID:26234273

  3. mtDNA Diversity and Phylogenetic State of Korean Cattle Breed, Chikso

    PubMed Central

    Kim, Jae-Hwan; Byun, Mi Jeong; Kim, Myung-Jick; Suh, Sang Won; Ko, Yeoung-Gyu; Lee, Chang Woo; Jung, Kyoung-Sub; Kim, Eun Sung; Yu, Dae Jung; Kim, Woo Hyun; Choi, Seong-Bok

    2013-01-01

    In order to analyze the genetic diversity and phylogenetic status of the Korean Chikso breed, we determined sequences of mtDNA cytochrome b (cyt b) gene and performed phylogenetic analysis using 239 individuals from 5 Chikso populations. Five non-synonymous mutations of a total of 15 polymorphic sites were identified among 239 cyt b coding sequences. Thirteen haplotypes were defined, and haplotype diversity was 0.4709 ranging from 0.2577 to 0.6114. Thirty-five haplotypes (C1–C35) were classified among 9 Asia and 3 European breeds. C2 was a major haplotype that contained 206 sequences (64.6%) from all breeds used. C3–C13 haplotypes were Chikso-specific haplotypes. C1 and C2 haplotypes contained 80.5% of cyt b sequences of Hanwoo, Yanbian, Zaosheng and JB breeds. In phylogenetic analyses, the Chikso breed was contained into B. taurus lineage and was genetically more closely related to two Chinese breeds than to Korean brown cattle, Hanwoo. These results suggest that Chikso and Hanwoo have a genetic difference based on the mtDNA cyt b gene as well as their coat color, sufficient for classification as a separate breed. PMID:25049772

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

    PubMed Central

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

    1994-01-01

    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

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

    PubMed

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

    2014-07-01

    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

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

    NASA Astrophysics Data System (ADS)

    Figueroa, Diego F.; Baco, Amy R.

    2014-01-01

    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.

  7. Strategy Guideline: Accurate Heating and

    E-print Network

    (HVAC) Mechanical Contractors · HVAC System Designers · Builders · House Remodelers. This guide can, as the first step of HVAC system design. Accurate load calculations have a direct impact on energy efficiency of the iterative HVAC design procedure, as a full HVAC design involves much more than just the load calculation

  8. SYSTEMS BIOLOGY Accurate information transmission

    E-print Network

    Tsimring, Lev S.

    SYSTEMS BIOLOGY Accurate information transmission through dynamic biochemical signaling networks) and variability in cellular states (extrinsic noise) degrade information transmitted through signaling networks-induced information loss. In the extracellular signal­regulated kinase (ERK), calcium (Ca2+ ), and nuclear factor

  9. Morphological Phylogenetics in the Genomic Age.

    PubMed

    Lee, Michael S Y; Palci, Alessandro

    2015-10-01

    Evolutionary trees underpin virtually all of biology, and the wealth of new genomic data has enabled us to reconstruct them with increasing detail and confidence. While phenotypic (typically morphological) traits are becoming less important in reconstructing evolutionary trees, they still serve vital and unique roles in phylogenetics, even for living taxa for which vast amounts of genetic information are available. Morphology remains a powerful independent source of evidence for testing molecular clades, and - through fossil phenotypes - the primary means for time-scaling phylogenies. Morphological phylogenetics is therefore vital for transforming undated molecular topologies into dated evolutionary trees. However, if morphology is to be employed to its full potential, biologists need to start scrutinising phenotypes in a more objective fashion, models of phenotypic evolution need to be improved, and approaches for analysing phenotypic traits and fossils together with genomic data need to be refined. PMID:26439355

  10. Molecular phylogenetics of mastodon and Tyrannosaurus rex.

    PubMed

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

    2008-04-25

    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

  11. [It is normal for classification approaches to be diverse].

    PubMed

    Pavlinov, I Ia

    2003-01-01

    It is asserted that the postmodern concept of science, unlike the classical ideal, presumes necessary existence of various classification approaches (schools) in taxonomy, each corresponding to a particular aspect of consideration of the "taxic reality". They are set up by diversity of initial epistemological and ontological backgrounds which fix in a certain way a) fragments of that reality allowable for investigation, and b) allowable methods of exploration of the fragments being fixed. It makes it possible to define a taxonomic school as a unity of the above backgrounds together with consideration aspect delimited by them. Two extreme positions of these backgrounds could be recognized in recent taxonomic thought. One of them follows the scholastic tradition of elaboration of a formal and, hence, universal classificatory method ("new typology", numerical phenetics, pattern cladistics). Another one asserts dependence of classificatory approach on the judgment of the nature of taxic reality (natural philosophy, evolutionary schools of taxonomy). Some arguments are put forward in favor of significant impact of evolutionary thinking onto the theory of modern taxonomy. This impact is manifested by the correspondence principle which makes classificatory algorithms (and hence resulting classifications) depending onto initial assumptions about causes of taxic diversity. It is asserted that criteria of "quality" of both classifications proper and classificatory methods can be correctly formulated within the framework of a particular consideration aspect only. For any group of organisms, several particular classifications are rightful to exist, each corresponding to a particular consideration aspect. These classifications could not be arranged along the "better-worse" scale, as they reflect different fragments of the taxic reality. Their mutual interpretation depends on degree of compatibility of background assumptions and of the tasks being resolved. Extensionally, classifications are compatible as much as they coincide by context and hierarchical structure of included taxa. Intentionally, typological classifications are compatible if included taxa are comparable by their diagnoses, while phylogenetic classifications are compatible if the included taxa are ascribed monophyletic status. A brief consideration is given to the "new phylogenetics" (= "genophyletics") as to a classificatory approach aimed at elaboration of parsimonious phylogenetic hypotheses based on molecular biology data and employing numerical methods of cladistic analysis. This approach is shown to borrows some phenetic ideas and revives scholastic principle of unified classificatory basis. It is supposed that, in a time, biological classification would get escaping from plethora of positivistic ideas (including those being developed by nowaday cladistics) and would assimilate (revive) more actively holistic worldview. PMID:14524225

  12. The paracladistic approach to phylogenetic taxonomy

    E-print Network

    Carter, Joseph G.; Altaba, Cristian R.; Anderson, Laurie; Campbell, David; Fang, Zongjie; Harries, Peter; Skelton, Peter W.

    2015-04-30

    –4. Lamy, É. 1911. Mission dans l’Antarctique dirigée par le Dr. Charcot (1908–1910), collections recueilles par M. le Dr. Jacques Liouville. Pélécy- podes. Museum National d’Histoire Naturelle, Bulletin 16(7):388–394. Linnaeus, Carolus A. 1767. Caroli a..., in all three molecular phylogenetic analyses. However, all three molecular analyses place Nuculana pella (Linnaeus, 1767) in the smaller subclade, apart from other members of its genus, and two of the molecular analyses (not Fig. 1) resolve...

  13. A phylogenetic analysis of Aquifex pyrophilus

    NASA Technical Reports Server (NTRS)

    Burggraf, S.; Olsen, G. J.; Stetter, K. O.; Woese, C. R.

    1992-01-01

    The 16S rRNA of the bacterion Aquifex pyrophilus, a microaerophilic, oxygen-reducing hyperthermophile, has been sequenced directly from the the PCR amplified gene. Phylogenetic analyses show the Aq. pyrophilus lineage to be probably the deepest (earliest) in the (eu)bacterial tree. The addition of this deep branching to the bacterial tree further supports the argument that the Bacteria are of thermophilic ancestry.

  14. Phylogenetic relationships among Staphylococcus species and refinement of cluster groups based on multilocus data

    PubMed Central

    2012-01-01

    Background Estimates of relationships among Staphylococcus species have been hampered by poor and inconsistent resolution of phylogenies based largely on single gene analyses incorporating only a limited taxon sample. As such, the evolutionary relationships and hierarchical classification schemes among species have not been confidently established. Here, we address these points through analyses of DNA sequence data from multiple loci (16S rRNA gene, dnaJ, rpoB, and tuf gene fragments) using multiple Bayesian and maximum likelihood phylogenetic approaches that incorporate nearly all recognized Staphylococcus taxa. Results We estimated the phylogeny of fifty-seven Staphylococcus taxa using partitioned-model Bayesian and maximum likelihood analysis, as well as Bayesian gene-tree species-tree methods. Regardless of methodology, we found broad agreement among methods that the current cluster groups require revision, although there was some disagreement among methods in resolution of higher order relationships. Based on our phylogenetic estimates, we propose a refined classification for Staphylococcus with species being classified into 15 cluster groups (based on molecular data) that adhere to six species groups (based on phenotypic properties). Conclusions Our findings are in general agreement with gene tree-based reports of the staphylococcal phylogeny, although we identify multiple previously unreported relationships among species. Our results support the general importance of such multilocus assessments as a standard in microbial studies to more robustly infer relationships among recognized and newly discovered lineages. PMID:22950675

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

    PubMed

    Lee, S; Wen, J

    2001-01-01

    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

  16. Phylogenetic and Biogeographic Analysis of Sphaerexochine Trilobites

    E-print Network

    Congreve, Curtis Raymond; Lieberman, Bruce S.

    2011-06-01

    for producing a stable classification of the group, and will be useful in elucidating the effects the end Ordovician mass extinction had on the evolutionary and biogeographic history of the group. Methodology/Principal Findings: Cladistic parsimony analysis...

  17. New substitution models for rooting phylogenetic trees

    PubMed Central

    Williams, Tom A.; Heaps, Sarah E.; Cherlin, Svetlana; Nye, Tom M. W.; Boys, Richard J.; Embley, T. Martin

    2015-01-01

    The root of a phylogenetic tree is fundamental to its biological interpretation, but standard substitution models do not provide any information on its position. Here, we describe two recently developed models that relax the usual assumptions of stationarity and reversibility, thereby facilitating root inference without the need for an outgroup. We compare the performance of these models on a classic test case for phylogenetic methods, before considering two highly topical questions in evolutionary biology: the deep structure of the tree of life and the root of the archaeal radiation. We show that all three alignments contain meaningful rooting information that can be harnessed by these new models, thus complementing and extending previous work based on outgroup rooting. In particular, our analyses exclude the root of the tree of life from the eukaryotes or Archaea, placing it on the bacterial stem or within the Bacteria. They also exclude the root of the archaeal radiation from several major clades, consistent with analyses using other rooting methods. Overall, our results demonstrate the utility of non-reversible and non-stationary models for rooting phylogenetic trees, and identify areas where further progress can be made. PMID:26323766

  18. Phylogenetic stochastic mapping without matrix exponentiation.

    PubMed

    Irvahn, Jan; Minin, Vladimir N

    2014-09-01

    Phylogenetic stochastic mapping is a method for reconstructing the history of trait changes on a phylogenetic tree relating species/organism carrying the trait. State-of-the-art methods assume that the trait evolves according to a continuous-time Markov chain (CTMC) and works well for small state spaces. The computations slow down considerably for larger state spaces (e.g., space of codons), because current methodology relies on exponentiating CTMC infinitesimal rate matrices-an operation whose computational complexity grows as the size of the CTMC state space cubed. In this work, we introduce a new approach, based on a CTMC technique called uniformization, which does not use matrix exponentiation for phylogenetic stochastic mapping. Our method is based on a new Markov chain Monte Carlo (MCMC) algorithm that targets the distribution of trait histories conditional on the trait data observed at the tips of the tree. The computational complexity of our MCMC method grows as the size of the CTMC state space squared. Moreover, in contrast to competing matrix exponentiation methods, if the rate matrix is sparse, we can leverage this sparsity and increase the computational efficiency of our algorithm further. Using simulated data, we illustrate advantages of our MCMC algorithm and investigate how large the state space needs to be for our method to outperform matrix exponentiation approaches. We show that even on the moderately large state space of codons our MCMC method can be significantly faster than currently used matrix exponentiation methods. PMID:24918812

  19. Phylogenetic Stochastic Mapping Without Matrix Exponentiation

    PubMed Central

    Irvahn, Jan; Minin, Vladimir N.

    2014-01-01

    Abstract Phylogenetic stochastic mapping is a method for reconstructing the history of trait changes on a phylogenetic tree relating species/organism carrying the trait. State-of-the-art methods assume that the trait evolves according to a continuous-time Markov chain (CTMC) and works well for small state spaces. The computations slow down considerably for larger state spaces (e.g., space of codons), because current methodology relies on exponentiating CTMC infinitesimal rate matrices—an operation whose computational complexity grows as the size of the CTMC state space cubed. In this work, we introduce a new approach, based on a CTMC technique called uniformization, which does not use matrix exponentiation for phylogenetic stochastic mapping. Our method is based on a new Markov chain Monte Carlo (MCMC) algorithm that targets the distribution of trait histories conditional on the trait data observed at the tips of the tree. The computational complexity of our MCMC method grows as the size of the CTMC state space squared. Moreover, in contrast to competing matrix exponentiation methods, if the rate matrix is sparse, we can leverage this sparsity and increase the computational efficiency of our algorithm further. Using simulated data, we illustrate advantages of our MCMC algorithm and investigate how large the state space needs to be for our method to outperform matrix exponentiation approaches. We show that even on the moderately large state space of codons our MCMC method can be significantly faster than currently used matrix exponentiation methods. PMID:24918812

  20. DNA barcoding and phylogenetic relationships in Anatidae.

    PubMed

    Huang, Zuhao; Yang, Chengzhong; Ke, Dianhua

    2016-03-01

    Mitochondrial cytochrome c oxidase subunit I (COI) has been used as a powerful marker in a variety of phylogenetic studies. According to studies of bird species, the 694-bp sequence of the mitochondrial gene encoding COI is extremely useful for species identification and phylogeny. In the present study, we analyzed the COI barcodes of 79 species from 26 genera belonging to the Anatidae family. Sixty-six species (83.54%) of the species were identified correctly from their DNA barcodes. The remaining 13 species shared barcodes sequences with closely related species. Kimura two-parameter (K2P) distances were calculated between barcodes. The average genetic distance between species was 41 times higher compared to the average genetic distance within species. Neighbor-joining method was used to construct a phylogenetic tree, which grouped all of the genera into three divergent clades. Dendrocygna and Nomonyx?+?Oxyura were identified as early offshoots of the Anatidae. All the remaining taxa fell into two clades that correspond to the two subfamilies Anserinae and Anatiane. Based on our results, DNA barcoding is an effective molecular tool for Anatidae species identification and phylogenetic inference. PMID:24938090

  1. A Consistent Phylogenetic Backbone for the Fungi

    PubMed Central

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

    2012-01-01

    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

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

    PubMed Central

    Roger, Andrew J; Hug, Laura A

    2006-01-01

    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

  3. High-accurate and noise-tolerant texture descriptor

    NASA Astrophysics Data System (ADS)

    Akoushideh, Alireza; Mazloom-Nezhad Maybodi, Babak

    2015-02-01

    In this paper, we extend pyramid transform domain approach on local binary pattern (PLBP) to make a high-accurate and noise-tolerant texture descriptor. We combine PLBP information of sub-band images, which are attained using wavelet transform, in different resolution and make some new descriptors. Multi-level and -resolution LBP(MPR_LBP), multi-level and -band LBP (MPB_LBP), and multi-level, -band and -resolution LBP (MPBR_LBP) are our proposed descriptors that are applied to unsupervised classification of texture images on Outex, UIUC, and Scene-13 data sets. Experimental results show that the proposed descriptors not only demonstrate acceptable texture classification accuracy with significantly lower feature length, but also they are more noise-robustness to a number of recent state-of-the-art LBP extensions.

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

    PubMed Central

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

    2013-01-01

    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

  5. Association of Virulence Genotype with Phylogenetic Background in Comparison to Different Seropathotypes of Shiga Toxin-Producing Escherichia coli Isolates

    PubMed Central

    Girardeau, Jean Pierre; Dalmasso, Alessandra; Bertin, Yolande; Ducrot, Christian; Bord, Séverine; Livrelli, Valérie; Vernozy-Rozand, Christine; Martin, Christine

    2005-01-01

    The distribution of virulent factors (VFs) in 287 Shiga toxin-producing Escherichia coli (STEC) strains that were classified according to Karmali et al. into five seropathotypes (M. A. Karmali, M. Mascarenhas, S. Shen, K. Ziebell, S. Johnson, R. Reid-Smith, J. Isaac-Renton, C. Clark, K. Rahn, and J. B. Kaper, J. Clin. Microbiol. 41:4930-4940, 2003) was investigated. The associations of VFs with phylogenetic background were assessed among the strains in comparison with the different seropathotypes. The phylogenetic analysis showed that STEC strains segregated mainly in phylogenetic group B1 (70%) and revealed the substantial prevalence (19%) of STEC belonging to phylogenetic group A (designated STEC-A). The presence of virulent clonal groups in seropathotypes that are associated with disease and their absence from seropathotypes that are not associated with disease support the concept of seropathotype classification. Although certain VFs (eae, stx2-EDL933, stx2-vha, and stx2-vhb) were concentrated in seropathotypes associated with disease, others (astA, HPI, stx1c, and stx2-NV206) were concentrated in seropathotypes that are not associated with disease. Taken together with the observation that the STEC-A group was exclusively composed of strains lacking eae recovered from seropathotypes that are not associated with disease, the “atypical” virulence pattern suggests that STEC-A strains comprise a distinct category of STEC strains. A practical benefit of our phylogenetic analysis of STEC strains is that phylogenetic group A status appears to be highly predictive of “nonvirulent” seropathotypes. PMID:16333104

  6. Cirrhosis Classification Based on Texture Classification of Random Features

    PubMed Central

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

    2014-01-01

    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

  7. Cirrhosis classification based on texture classification of random features.

    PubMed

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

    2014-01-01

    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

  8. Phylogenetic relationships and the evolution of BMP4 in triggerfishes and filefishes (Balistoidea).

    PubMed

    McCord, Charlene L; Westneat, Mark W

    2016-01-01

    The triggerfishes (family Balistidae) and filefishes (family Monacanthidae) comprise a charismatic superfamily (Balistoidea) within the diverse order Tetraodontiformes. This group of largely marine fishes occupies an impressive ecological range across the world's oceans, and is well known for its locomotor and feeding diversity, unusual body shapes, small genome size, and ecological and economic importance. In order to investigate the evolutionary history of these important fish families, we used multiple phylogenetic methods to analyze molecular data from 86 species spanning the extant biodiversity of Balistidae and Monacanthidae. In addition to three gene regions that have been used extensively in phylogenetic analyses, we include sequence data for two mitochondrial regions, two nuclear markers, and the growth factor gene bmp4, which is involved with cranial development. Phylogenetic analyses strongly support the monophyly of the superfamily Balistoidea, the sister-family relationship of Balistidae and Monacanthidae, as well as three triggerfish and four filefish clades that are well resolved. A new classification for the Balistidae is proposed based on phylogenetic groups. Bayesian topology, as well as the timing of major cladogenesis events, is largely congruent with previous hypotheses of balistid phylogeny. However, we present a novel topology for major clades in the filefish family that illustrate the genera Aluterus and Stephanolepis are more closely related than previously posited. Molecular rates suggest a Miocene and Oligocene origin for the families Balistidae and Monacanthidae, respectively, and significant divergence of species in both families within the past 5million years. A second key finding of this study is that, relative to the other protein-coding gene regions in our DNA supermatrix, bmp4 shows a rapid accumulation of both synonymous and non-synonymous substitutions, especially within the family Monacanthidae. Overall substitution patterns in bmp4 support the hypothesis of stabilizing selection during the evolutionary history of regulatory genes, with a small number of isolated examples of accelerated non-synonymous changes detected in our phylogeny. PMID:26408967

  9. Acute pancreatitis: international classification and nomenclature.

    PubMed

    Bollen, T L

    2016-02-01

    The incidence of acute pancreatitis (AP) is increasing and it is associated with a major healthcare concern. New insights in the pathophysiology, better imaging techniques, and novel treatment options for complicated AP prompted the update of the 1992 Atlanta Classification. Updated nomenclature for pancreatic collections based on imaging criteria is proposed. Adoption of the newly Revised Classification of Acute Pancreatitis 2012 by radiologists should help standardise reports and facilitate accurate conveyance of relevant findings to referring physicians involved in the care of patients with AP. This review will clarify the nomenclature of pancreatic collections in the setting of AP. PMID:26602933

  10. Hydrometor classification from 2 dimensional videodisdrometer data

    NASA Astrophysics Data System (ADS)

    Grazioli, J.; Tuia, D.; Monhart, S.; Schneebeli, M.; Raupach, T.; Berne, A.

    2014-02-01

    This paper presents a hydrometeor classification technique based on two-dimensional video disdrometer (2DVD) data. The method provides an estimate of the dominant hydrometeor type falling over time intervals of 60 s during precipitation, using as input the statistical behavior of a set of particle descriptors, calculated for each particle image. The employed supervised algorithm is a support vector machine (SVM), trained over precipitation time steps labeled by visual inspection. In this way, 8 dominant hydrometeor classes could be discriminated. The algorithm achieves accurate classification performances, with median overall accuracies (Cohen's K) of 90% (0.88), and with accuracies higher than 84% for each hydrometeor class.

  11. Automatic classification of blank substrate defects

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    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%.

  12. Gallstone Classification in Western Countries.

    PubMed

    Cariati, Andrea

    2015-12-01

    In order to compare gallstone disease data from India and Asian countries with Western countries, it is fundamental to follow a common gallstone classification. Gallstone disease has afflicted humans since the time of Egyptian kings, and gallstones have been found during autopsies on mummies. Gallstone prevalence in adult population ranges from 10 to 15 %. Gallstones in Western countries are distinguished into the following classes: cholesterol gallstones that contain more than 50 % of cholesterol (nearly 75 % of gallstones) and pigment gallstones that contain less than 30 % of cholesterol by weight, which can be subdivided into black pigment gallstones and brown pigment gallstones. It has been shown that ultrastructural analysis with scanning electron microscopy is useful in the classification and study of pigment gallstones. Moreover, x-ray diffractometry analysis and infrared spectroscopy of gallstones are of fundamental importance for an accurate stone analysis. An accurate study of gallstones is useful to understand gallstone pathogenesis. In fact, bacteria are not important in cholesterol gallstone nucleation and growth, but they are important in brown pigment gallstone formation. On the contrary, calcium bilirubinate is fundamental in black pigment gallstone formation and probably also plays an important role in cholesterol gallstone nucleation and growth. PMID:26730029

  13. Shower Classification Software

    NASA Astrophysics Data System (ADS)

    Zloczewski, K.; Wisniewski, M.; Lelit, M.; Polakowski, K.

    2009-06-01

    We describe the Shower Classification Software (SCS) which makes an automatic shower classification of plotted meteors. This tool is developed to help observers make shower classification procedure fast and allows them to check calculations done by hand. The programme is available for Linux and Windows operating systems and can be obtained from http://www.pkim.org/?q=pl/scs.

  14. Government Classification: An Overview.

    ERIC Educational Resources Information Center

    Brown, Karen M.

    Classification of government documents (confidential, secret, top secret) is a system used by the executive branch to, in part, protect national security and foreign policy interests. The systematic use of classification markings with precise definitions was established during World War I, and since 1936 major changes in classification have…

  15. An updated evolutionary classification of CRISPR-Cas systems.

    PubMed

    Makarova, Kira S; Wolf, Yuri I; Alkhnbashi, Omer S; Costa, Fabrizio; Shah, Shiraz A; Saunders, Sita J; Barrangou, Rodolphe; Brouns, Stan J J; Charpentier, Emmanuelle; Haft, Daniel H; Horvath, Philippe; Moineau, Sylvain; Mojica, Francisco J M; Terns, Rebecca M; Terns, Michael P; White, Malcolm F; Yakunin, Alexander F; Garrett, Roger A; van der Oost, John; Backofen, Rolf; Koonin, Eugene V

    2015-11-01

    The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized. PMID:26411297

  16. The Impact of Plant Enemies Shows a Phylogenetic Signal

    PubMed Central

    Gilbert, Gregory S.; Briggs, Heather M.; Magarey, Roger

    2015-01-01

    The host ranges of plant pathogens and herbivores are phylogenetically constrained, so that closely related plant species are more likely to share pests and pathogens. Here we conducted a reanalysis of data from published experimental studies to test whether the severity of host-enemy interactions follows a similar phylogenetic signal. The impact of herbivores and pathogens on their host plants declined steadily with phylogenetic distance from the most severely affected focal hosts. The steepness of this phylogenetic signal was similar to that previously measured for binary-response host ranges. Enemy behavior and development showed similar, but weaker phylogenetic signal, with oviposition and growth rates declining with evolutionary distance from optimal hosts. Phylogenetic distance is an informative surrogate for estimating the likely impacts of a pest or pathogen on potential plant hosts, and may be particularly useful in early assessing risk from emergent plant pests, where critical decisions must be made with incomplete host records. PMID:25893581

  17. Impacts of Terraces on Phylogenetic Inference.

    PubMed

    Sanderson, Michael J; McMahon, Michelle M; Stamatakis, Alexandros; Zwickl, Derrick J; Steel, Mike

    2015-09-01

    Terraces are sets of trees with precisely the same likelihood or parsimony score, which can be induced by missing sequences in partitioned multi-locus phylogenetic data matrices. The potentially large set of trees on a terrace can be characterized by enumeration algorithms or consensus methods that exploit the pattern of partial taxon coverage in the data, independent of the sequence data themselves. Terraces can add ambiguity and complexity to phylogenetic inference, particularly in settings where inference is already challenging: data sets with many taxa and relatively few loci. In this article we present five new findings about terraces and their impacts on phylogenetic inference. First, we clarify assumptions about partitioning scheme model parameters that are necessary for the existence of terraces. Second, we explore the dependence of terrace size on partitioning scheme and indicate how to find the partitioning scheme associated with the largest terrace containing a given tree. Third, we highlight the impact of terrace size on bootstrap estimates of confidence limits in clades, and characterize the surprising result that the bootstrap proportion for a clade, as it is usually calculated, can be entirely determined by the frequency of bipartitions on a terrace, with some bipartitions receiving high support even when incorrect. Fourth, we dissect some effects of prior distributions of edge lengths on the computed posterior probabilities of clades on terraces, to understand an example in which long edges "attract" each other in Bayesian inference. Fifth, we describe how assuming relationships between edge-lengths of different loci, as an attempt to avoid terraces, can also be problematic when taxon coverage is partial, specifically when heterotachy is present. Finally, we discuss strategies for remediation of some of these problems. One promising approach finds a minimal set of taxa which, when deleted from the data matrix, reduces the size of a terrace to a single tree. PMID:25999395

  18. Phylogenetic tree construction based on 2D graphical representation

    NASA Astrophysics Data System (ADS)

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

    2006-04-01

    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.

  19. Best Practices for Data Sharing in Phylogenetic Research

    PubMed Central

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

    2014-01-01

    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

  20. MINER: software for phylogenetic motif identification

    PubMed Central

    La, David; Livesay, Dennis R.

    2005-01-01

    MINER is web-based software for phylogenetic motif (PM) identification. PMs are sequence regions (fragments) that conserve the overall familial phylogeny. PMs have been shown to correspond to a wide variety of catalytic regions, substrate-binding sites and protein interfaces, making them ideal functional site predictions. The MINER output provides an intuitive interface for interactive PM sequence analysis and structural visualization. The web implementation of MINER is freely available at . Source code is available to the academic community on request. PMID:15980467

  1. Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

    PubMed Central

    Broughton, Richard E.; Betancur-R., Ricardo; Li, Chenhong; Arratia, Gloria; Ortí, Guillermo

    2013-01-01

    Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a full sample of all bony fishes. Here we conducted a comprehensive phylogenetic study on a broad taxonomic sample of 61 actinopterygian and sarcopterygian lineages (with a chondrichthyan outgroup) using a molecular data set of 21 independent loci. These data yielded a resolved phylogenetic hypothesis for extant Osteichthyes, including 1) reciprocally monophyletic Sarcopterygii and Actinopterygii, as currently understood, with polypteriforms as the first diverging lineage within Actinopterygii; 2) a monophyletic group containing gars and bowfin (= Holostei) as sister group to teleosts; and 3) the earliest diverging lineage among teleosts being Elopomorpha, rather than Osteoglossomorpha. Relaxed-clock dating analysis employing a set of 24 newly applied fossil calibrations reveals divergence times that are more consistent with paleontological estimates than previous studies. Establishing a new phylogenetic pattern with accurate divergence dates for bony fishes illustrates several areas where the fossil record is incomplete and provides critical new insights on diversification of this important vertebrate group. PMID:23788273

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

    PubMed Central

    Subramanian, Ayshwarya; Shackney, Stanley; Schwartz, Russell

    2013-01-01

    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

  3. Strong phylogenetic signals and phylogenetic niche conservatism in ecophysiological traits across divergent lineages of Magnoliaceae

    PubMed Central

    Liu, Hui; Xu, Qiuyuan; He, Pengcheng; Santiago, Louis S.; Yang, Keming; Ye, Qing

    2015-01-01

    The early diverged Magnoliaceae shows a historical temperate-tropical distribution among lineages indicating divergent evolution, yet which ecophysiological traits are phylogenetically conserved, and whether these traits are involved in correlated evolution remain unclear. Integrating phylogeny and 20 ecophysiological traits of 27 species, from the four largest sections of Magnoliaceae, we tested the phylogenetic signals of these traits and the correlated evolution between trait pairs. Phylogenetic niche conservatism (PNC) in water-conducting and nutrient-use related traits was identified, and correlated evolution of several key functional traits was demonstrated. Among the three evergreen sections of tropical origin, Gwillimia had the lowest hydraulic-photosynthetic capacity and the highest drought tolerance compared with Manglietia and Michelia. Contrastingly, the temperate centred deciduous section, Yulania, showed high rates of hydraulic conductivity and photosynthesis at the cost of drought tolerance. This study elucidated the regulation of hydraulic and photosynthetic processes in the temperate-tropical adaptations for Magnoliaceae species, which led to strong phylogenetic signals and PNC in ecophysiological traits across divergent lineages of Magnoliaceae. PMID:26179320

  4. Strong phylogenetic signals and phylogenetic niche conservatism in ecophysiological traits across divergent lineages of Magnoliaceae.

    PubMed

    Liu, Hui; Xu, Qiuyuan; He, Pengcheng; Santiago, Louis S; Yang, Keming; Ye, Qing

    2015-01-01

    The early diverged Magnoliaceae shows a historical temperate-tropical distribution among lineages indicating divergent evolution, yet which ecophysiological traits are phylogenetically conserved, and whether these traits are involved in correlated evolution remain unclear. Integrating phylogeny and 20 ecophysiological traits of 27 species, from the four largest sections of Magnoliaceae, we tested the phylogenetic signals of these traits and the correlated evolution between trait pairs. Phylogenetic niche conservatism (PNC) in water-conducting and nutrient-use related traits was identified, and correlated evolution of several key functional traits was demonstrated. Among the three evergreen sections of tropical origin, Gwillimia had the lowest hydraulic-photosynthetic capacity and the highest drought tolerance compared with Manglietia and Michelia. Contrastingly, the temperate centred deciduous section, Yulania, showed high rates of hydraulic conductivity and photosynthesis at the cost of drought tolerance. This study elucidated the regulation of hydraulic and photosynthetic processes in the temperate-tropical adaptations for Magnoliaceae species, which led to strong phylogenetic signals and PNC in ecophysiological traits across divergent lineages of Magnoliaceae. PMID:26179320

  5. Abstract-This paper deals to the suitability of Complexity Measure of ECG signals for the classification of cardiac

    E-print Network

    Ayesta, Urtzi

    for the classification of cardiac arrhythmia's. Applying this algorithm to data from the MIT- BIH database a very poorView and C++ software. Keywords ­ Biomedical Signal Processing, Arrhythmia Classification. I. INTRODUCTION causes depends mainly on rapid detection and accurate classification of these arrhythmia's. Conventional

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

    E-print Network

    Zardoya, Rafael

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

  7. Phylogenetic analysis with the iPlant discovery environment.

    PubMed

    Matasci, Naim; McKay, Sheldon

    2013-06-01

    The iPlant Collaborative's Discovery Environment is a unified Web portal to many bioinformatics applications and analytical workflows, including various methods of phylogenetic analysis. This unit describes example protocols for phylogenetic analyses, starting at sequence retrieval from the GenBank sequence database, through to multiple sequence alignment inference and visualization of phylogenetic trees. Methods for extracting smaller sub-trees from very large phylogenies, and the comparative method of continuous ancestral character state reconstruction based on observed morphology of extant species related to their phylogenetic relationships, are also presented. PMID:23749754

  8. PHYLOGENETIC RELATIONSHIPS AMONG THE ASIAN TORTOISES OF THE GENUS INDOTESTUDO

    E-print Network

    Shaffer, H. Bradley

    PHYLOGENETIC RELATIONSHIPS AMONG THE ASIAN TORTOISES OF THE GENUS INDOTESTUDO (REPTILIA: TESTUDINES-inclusive tortoise genus Testudo, placing elongata, forstenii and travancorica in the subgenus Indotestudo

  9. Ultrametric networks: a new tool for phylogenetic analysis

    PubMed Central

    2013-01-01

    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

  10. AGN Zoo and Classifications of Active Galaxies

    NASA Astrophysics Data System (ADS)

    Mickaelian, Areg M.

    2015-07-01

    We review the variety of Active Galactic Nuclei (AGN) classes (so-called "AGN zoo") and classification schemes of galaxies by activity types based on their optical emission-line spectrum, as well as other parameters and other than optical wavelength ranges. A historical overview of discoveries of various types of active galaxies is given, including Seyfert galaxies, radio galaxies, QSOs, BL Lacertae objects, Starbursts, LINERs, etc. Various kinds of AGN diagnostics are discussed. All known AGN types and subtypes are presented and described to have a homogeneous classification scheme based on the optical emission-line spectra and in many cases, also other parameters. Problems connected with accurate classifications and open questions related to AGN and their classes are discussed and summarized.

  11. FastDTW: Toward Accurate Dynamic Time Warping in Linear Time and Space

    E-print Network

    Chan, Philip K.

    FastDTW: Toward Accurate Dynamic Time Warping in Linear Time and Space Stan Salvador and Philip}@cs.fit.edu ABSTRACT The dynamic time warping (DTW) algorithm is able to find the optimal alignment between two time series. It is often used to determine time series similarity, classification, and to find corresponding

  12. Phylogenetic relationships among megabats, microbats, and primates.

    PubMed

    Mindell, D P; Dick, C W; Baker, R J

    1991-11-15

    We present 744 nucleotide base positions from the mitochondrial 12S rRNA gene and 236 base positions from the mitochondrial cytochrome oxidase subunit I gene for a microbat, Brachyphylla cavernarum, and a megabat, Pteropus capestratus, in phylogenetic analyses with homologous DNA sequences from Homo sapiens, Mus musculus (house mouse), and Gallus gallus (chicken). We use information on evolutionary rate differences for different types of sequence change to establish phylogenetic character weights, and we consider alternative rRNA alignment strategies in finding that this mtDNA data set clearly supports bat monophyly. This result is found despite variations in outgroup used, gap coding scheme, and order of input for DNA sequences in multiple alignment bouts. These findings are congruent with morphological characters including details of wing structure as well as cladistic analyses of amino acid sequences for three globin genes and indicate that neurological similarities between megabats and primates are due to either retention of primitive characters or to convergent evolution rather than to inheritance from a common ancestor. This finding also indicates a single origin for flight among mammals. PMID:1658803

  13. A Distance Measure for Genome Phylogenetic Analysis

    NASA Astrophysics Data System (ADS)

    Cao, Minh Duc; Allison, Lloyd; Dix, Trevor

    Phylogenetic analyses of species based on single genes or parts of the genomes are often inconsistent because of factors such as variable rates of evolution and horizontal gene transfer. The availability of more and more sequenced genomes allows phylogeny construction from complete genomes that is less sensitive to such inconsistency. For such long sequences, construction methods like maximum parsimony and maximum likelihood are often not possible due to their intensive computational requirement. Another class of tree construction methods, namely distance-based methods, require a measure of distances between any two genomes. Some measures such as evolutionary edit distance of gene order and gene content are computational expensive or do not perform well when the gene content of the organisms are similar. This study presents an information theoretic measure of genetic distances between genomes based on the biological compression algorithm expert model. We demonstrate that our distance measure can be applied to reconstruct the consensus phylogenetic tree of a number of Plasmodium parasites from their genomes, the statistical bias of which would mislead conventional analysis methods. Our approach is also used to successfully construct a plausible evolutionary tree for the ?-Proteobacteria group whose genomes are known to contain many horizontally transferred genes.

  14. Entropy-based approach for selecting informative regions in the L1 gene of bovine papillomavirus for phylogenetic inference and primer design.

    PubMed

    Batista, M V A; Freitas, A C; Balbino, V Q

    2013-01-01

    Bovine papillomaviruses (BPVs) cause many benign and malignant lesions in cattle and other animals. Twelve BPV types have been identified so far, and several putative novel BPV types have been detected based on the analysis of L1 gene fragments, generated by FAP59/64 and MY11/09 primers. Phylogenetic trees are important in studies that describe novel BPV types. However, topological mistakes could be a problem in such studies. Therefore, we made use of entropy to find phylogenetic informative regions in the BPV L1 gene sequences from all 12 BPVs. Six data sets were created and phylogenetically compared to each other using neighbor-joining and maximum likelihood methods of phylogenetic tree reconstruction. We found two major regions in the L1 gene, using an entropy-based approach, which selects regions with low information complexity. More robust phylogenetic trees were obtained with these regions, when compared to the ones obtained with FAP59/64 and MY11/09 primers. More robust phylogenetic trees are important to accurately position novel BPV types, subtypes and variants. We conclude that an entropy-based approach is a good methodology for selecting regions of the L1 gene of BPVs that could be used to design more specific and sensitive degenerate primers, for the development of improved diagnostic methods. PMID:23420364

  15. Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference

    PubMed Central

    2011-01-01

    Background Model violations constitute the major limitation in inferring accurate phylogenies. Characterizing properties of the data that are not being correctly handled by current models is therefore of prime importance. One of the properties of protein evolution is the variation of the relative rate of substitutions across sites and over time, the latter is the phenomenon called heterotachy. Its effect on phylogenetic inference has recently obtained considerable attention, which led to the development of new models of sequence evolution. However, thus far focus has been on the quantitative heterogeneity of the evolutionary process, thereby overlooking more qualitative variations. Results We studied the importance of variation of the site-specific amino-acid substitution process over time and its possible impact on phylogenetic inference. We used the CAT model to define an infinite mixture of substitution processes characterized by equilibrium frequencies over the twenty amino acids, a useful proxy for qualitatively estimating the evolutionary process. Using two large datasets, we show that qualitative changes in site-specific substitution properties over time occurred significantly. To test whether this unaccounted qualitative variation can lead to an erroneous phylogenetic tree, we analyzed a concatenation of mitochondrial proteins in which Cnidaria and Porifera were erroneously grouped. The progressive removal of the sites with the most heterogeneous CAT profiles across clades led to the recovery of the monophyly of Eumetazoa (Cnidaria+Bilateria), suggesting that this heterogeneity can negatively influence phylogenetic inference. Conclusion The time-heterogeneity of the amino-acid replacement process is therefore an important evolutionary aspect that should be incorporated in future models of sequence change. PMID:21235782

  16. Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

    PubMed Central

    Gao, Beile

    2012-01-01

    Summary: The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria. PMID:22390973

  17. Recursive heuristic classification

    NASA Technical Reports Server (NTRS)

    Wilkins, David C.

    1994-01-01

    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.

  18. Security classification of information

    SciTech Connect

    Quist, A.S.

    1993-04-01

    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.

  19. Finding single copy genes out of sequenced genomes for multilocus phylogenetics in non-model fungi.

    PubMed

    Feau, Nicolas; Decourcelle, Thibaut; Husson, Claude; Desprez-Loustau, Marie-Laure; Dutech, Cyril

    2011-01-01

    Historically, fungal multigene phylogenies have been reconstructed based on a small number of commonly used genes. The availability of complete fungal genomes has given rise to a new wave of model organisms that provide large number of genes potentially useful for building robust gene genealogies. Unfortunately, cross-utilization of these resources to study phylogenetic relationships in the vast majority of non-model fungi (i.e. "orphan" species) remains an unexamined question. To address this problem, we developed a method coupled with a program named "PHYLORPH" (PHYLogenetic markers for ORPHans). The method screens fungal genomic databases (107 fungal genomes fully sequenced) for single copy genes that might be easily transferable and well suited for studies at low taxonomic levels (for example, in species complexes) in non-model fungal species. To maximize the chance to target genes with informative regions, PHYLORPH displays a graphical evaluation system based on the estimation of nucleotide divergence relative to substitution type. The usefulness of this approach was tested by developing markers in four non-model groups of fungal pathogens. For each pathogen considered, 7 to 40% of the 10-15 best candidate genes proposed by PHYLORPH yielded sequencing success. Levels of polymorphism of these genes were compared with those obtained for some genes traditionally used to build fungal phylogenies (e.g. nuclear rDNA, ?-tubulin, ?-actin, Elongation factor EF-1?). These genes were ranked among the best-performing ones and resolved accurately taxa relationships in each of the four non-model groups of fungi considered. We envision that PHYLORPH will constitute a useful tool for obtaining new and accurate phylogenetic markers to resolve relationships between closely related non-model fungal species. PMID:21533204

  20. Detecting Adaptive Evolution in Phylogenetic Comparative Analysis Using the Ornstein-Uhlenbeck Model.

    PubMed

    Cressler, Clayton E; Butler, Marguerite A; King, Aaron A

    2015-11-01

    Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and more detailed evolutionary hypotheses, including adaptive hypotheses with multiple selective optima and hypotheses with rate variation within and across lineages. The statistical performance of these sophisticated models has received relatively little systematic attention, however. We conducted an extensive simulation study to quantify the statistical properties of a class of models toward the simpler end of the spectrum that model phenotypic evolution using Ornstein-Uhlenbeck processes. We focused on identifying where, how, and why these methods break down so that users can apply them with greater understanding of their strengths and weaknesses. Our analysis identifies three key determinants of performance: a discriminability ratio, a signal-to-noise ratio, and the number of taxa sampled. Interestingly, we find that model-selection power can be high even in regions that were previously thought to be difficult, such as when tree size is small. On the other hand, we find that model parameters are in many circumstances difficult to estimate accurately, indicating a relative paucity of information in the data relative to these parameters. Nevertheless, we note that accurate model selection is often possible when parameters are only weakly identified. Our results have implications for more sophisticated methods inasmuch as the latter are generalizations of the case we study. PMID:26115662

  1. Exploration of phylogenetic data using a global sequence analysis method

    PubMed Central

    Chapus, Charles; Dufraigne, Christine; Edwards, Scott; Giron, Alain; Fertil, Bernard; Deschavanne, Patrick

    2005-01-01

    Background Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets. Results Here we explore the phylogenetic signal present in molecular data by genomic signatures, defined as the set of frequencies of short oligonucleotides present in DNA sequences. Although violating many of the standard assumptions of traditional phylogenetic analyses – in particular explicit statements of homology inherent in character matrices – the use of the signature does permit the analysis of very long sequences, even those that are unalignable, and is therefore most useful in cases where alignment is questionable. We compare the results obtained by traditional phylogenetic methods to those inferred by the signature method for two genes: RAG1, which is easily alignable, and 18S RNA, where alignments are often ambiguous for some regions. We also apply this method to a multigene data set of 33 genes for 9 bacteria and one archea species as well as to the whole genome of a set of 16 ?-proteobacteria. In addition to delivering phylogenetic results comparable to traditional methods, the comparison of signatures for the sequences involved in the bacterial example identified putative candidates for horizontal gene transfers. Conclusion The signature method is therefore a fast tool for exploring phylogenetic data, providing not only a pretreatment for discovering new sequence relationships, but also for identifying cases of sequence evolution that could confound traditional phylogenetic analysis. PMID:16280081

  2. Student Interpretations of Phylogenetic Trees in an Introductory Biology Course

    ERIC Educational Resources Information Center

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

    2014-01-01

    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…

  3. The impact of multiple protein sequence alignment on phylogenetic estimation.

    PubMed

    Wang, Li-San; Leebens-Mack, Jim; Kerr Wall, P; Beckmann, Kevin; dePamphilis, Claude W; Warnow, Tandy

    2011-01-01

    Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will phylogenetic reconstructions. Over the last decade or so, new multiple sequence alignment methods have been developed to improve comparative analyses of protein structure, but these new methods have not been typically used in phylogenetic analyses. In this paper, we report on a simulation study that we performed to evaluate the consequences of using these new multiple sequence alignment methods in terms of the resultant phylogenetic reconstruction. We find that while alignment accuracy is positively correlated with phylogenetic accuracy, the amount of improvement in phylogenetic estimation that results from an improved alignment can range from quite small to substantial. We observe that phylogenetic accuracy is most highly correlated with alignment accuracy when sequences are most difficult to align, and that variation in alignment accuracy can have little impact on phylogenetic accuracy when alignment error rates are generally low. We discuss these observations and implications for future work. PMID:21566256

  4. Genes order and phylogenetic reconstruction: application to #Proteobacteria

    E-print Network

    Chauve, Cedric

    Genes order and phylogenetic reconstruction: application to #­Proteobacteria Guillaume Blin Notes in Bioinformatics, pages 11--20, 2005. 1 #12; Genes order and phylogenetic reconstruction reconstruction based on gene order for whole genomes. We define three genomic distances between whole genomes

  5. Using Decision Trees to Study the Convergence of Phylogenetic Analyses

    E-print Network

    Williams, Tiffani

    Using Decision Trees to Study the Convergence of Phylogenetic Analyses Grant Brammer and Tiffani L properties of phylogenetic analyses. A decision learning tree is constructed from the evolutionary. Then, we use the depth of a decision tree as a technique to measure how distinct the runs are from each

  6. Primate molecular phylogenetics in a genomic era Nelson Ting

    E-print Network

    Ting, Nelson

    and Evolution, 335 Pacific Hall, 5289 University of Oregon Eugene, OR 97403, USA a r t i c l e i n f o Article Goodman founded the journal Molecular Phylogenetics and Evolution as a forum where scientists could phylogenetics demonstrates that consensus methods might pro- vide a false sense of support at certain nodes

  7. A geometric approach to support vector machine (SVM) classification.

    PubMed

    Mavroforakis, Michael E; Theodoridis, Sergios

    2006-05-01

    The geometric framework for the support vector machine (SVM) classification problem provides an intuitive ground for the understanding and the application of geometric optimization algorithms, leading to practical solutions of real world classification problems. In this work, the notion of "reduced convex hull" is employed and supported by a set of new theoretical results. These results allow existing geometric algorithms to be directly and practically applied to solve not only separable, but also nonseparable classification problems both accurately and efficiently. As a practical application of the new theoretical results, a known geometric algorithm has been employed and transformed accordingly to solve nonseparable problems successfully. PMID:16722171

  8. Predicting rates of interspecific interaction from phylogenetic trees.

    PubMed

    Nuismer, Scott L; Harmon, Luke J

    2015-01-01

    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

  9. Open reading frame phylogenetic analysis on the cloud.

    PubMed

    Hung, Che-Lun; Lin, Chun-Yuan

    2013-01-01

    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

  10. Open Reading Frame Phylogenetic Analysis on the Cloud

    PubMed Central

    2013-01-01

    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

  11. Exoribonuclease superfamilies: structural analysis and phylogenetic distribution

    PubMed Central

    Zuo, Yuhong; Deutscher, Murray P.

    2001-01-01

    Exoribonucleases play an important role in all aspects of RNA metabolism. Biochemical and genetic analyses in recent years have identified many new RNases and it is now clear that a single cell can contain multiple enzymes of this class. Here, we analyze the structure and phylogenetic distribution of the known exoribonucleases. Based on extensive sequence analysis and on their catalytic properties, all of the exoribonucleases and their homologs have been grouped into six superfamilies and various subfamilies. We identify common motifs that can be used to characterize newly-discovered exoribonucleases, and based on these motifs we correct some previously misassigned proteins. This analysis may serve as a useful first step for developing a nomenclature for this group of enzymes. PMID:11222749

  12. Phylogenetic and Ontogenetic View of Erythroblastic Islands

    PubMed Central

    Giger, Katie M.; Kalfa, Theodosia A.

    2015-01-01

    Erythroblastic islands are a hallmark of mammalian erythropoiesis consisting of a central macrophage surrounded by and interacting closely with the maturing erythroblasts. The macrophages are thought to serve many functions such as supporting erythroblast proliferation, supplying iron for hemoglobin, promoting enucleation, and clearing the nuclear debris; moreover, inhibition of erythroblastic island formation is often detrimental to erythropoiesis. There is still much not understood about the role that macrophages and microenvironment play in erythropoiesis and insights may be gleaned from a comparative analysis with erythropoietic niches in nonmammalian vertebrates which, unlike mammals, have erythrocytes that retain their nucleus. The phylogenetic development of erythroblastic islands in mammals in which the erythrocytes are anucleate underlines the importance of the macrophage in erythroblast enucleation. PMID:26557707

  13. Inferring Phylogenetic Networks from Gene Order Data

    PubMed Central

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

    2013-01-01

    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

  14. The Shapley value of phylogenetic trees.

    PubMed

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

    2008-04-01

    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

  15. Consistency between molecular phylogeny and morphological classification of the Salix matsudana Koidz. complex (Salicaceae).

    PubMed

    Du, S H; Wang, Z S; Li, Y X; Wang, D S; Zhang, J G

    2015-01-01

    The morphological species concept is based on morpho-logical traits, which are often subject to subjectivity or artifact. Molecular evidence is needed to test the reliability of morphological classification of taxa that are controversial and to provide appropriate taxonomic de-limitation. In this study, we used 15 single-copy nuclear loci and 2 chloroplast fragments to verify the morphological classification of the Salix matsudana Koidz. complex using phylogenetic approaches. Complete sequence alignment showed slight diversification in nuclear sequences and no variety in chloroplast DNA fragments. Phylogenetic trees revealed a monophyletic group consisting of all individuals of S. matsudana and 2 clades within this group, with a 100% bootstrap support value and 1.00 posterior probability. The topology of the phylogenetic trees was highly consistent with the morphological classification of the S. matsudana complex. Verifying the genetic background of these classification units based on remarkable morphological differences will provide a foundation for future studies of Salix and the breeding of new horticultural varieties. PMID:26345798

  16. Ultrahighly accurate 3D profilometer

    NASA Astrophysics Data System (ADS)

    Tsutsumi, Hideki; Yoshizumi, Keiichi; Takeuchi, Hiroyuki

    2005-02-01

    We have developed an Ultrahigh-Accurate 3-D Profilometer (UA3P), which, using a new, in-house-developed atomic force probe, has an accuracy of 10 nm. It is capable of measuring corners as small as 2 micro meter in radius and can cover an area up to 400 x 400 x 90 (mm), providing a powerful boost to nano-level processing. A commercial product was introduced in 1994. Examples of the key components made possible by this technology include aspherical lenses (used for a Blu-ray Disc device, a next-generation DVD, digital cameras, cellular phones, optical communications), free form lenses (used for frennel lens common to CD and DVD, laser printer lens, multi focus glass lens, cubic phase plate to extend depth of focus), gigabit semiconductor wafers, hard discs, air conditioner scroll vanes, DVC cylinders. The premiere ultra high-precision three-dimensional profilometer delivers superb performance using a variety of micro-measurements for a wide range of applications.

  17. Human Papillomavirus Type 16 Genetic Variants: Phylogeny and Classification Based on E6 and LCR

    PubMed Central

    Gheit, Tarik; Franceschi, Silvia; Vignat, Jerome; Burk, Robert D.; Sylla, Bakary S.; Tommasino, Massimo; Clifford, Gary M.

    2012-01-01

    Naturally occurring genetic variants of human papillomavirus type 16 (HPV16) are common and have previously been classified into 4 major lineages; European-Asian (EAS), including the sublineages European (EUR) and Asian (As), African 1 (AFR1), African 2 (AFR2), and North-American/Asian-American (NA/AA). We aimed to improve the classification of HPV16 variant lineages by using a large resource of HPV16-positive cervical samples collected from geographically diverse populations in studies on HPV and/or cervical cancer undertaken by the International Agency for Research on Cancer. In total, we sequenced the entire E6 genes and long control regions (LCRs) of 953 HPV16 isolates from 27 different countries worldwide. Phylogenetic analyses confirmed previously described variant lineages and subclassifications. We characterized two new sublineages within each of the lineages AFR1 and AFR2 that are robustly classified using E6 and/or the LCR. We could differentiate previously identified AA1, AA2, and NA sublineages, although they could not be distinguished by E6 alone, requiring the LCR for correct phylogenetic classification. We thus provide a classification system for HPV16 genomes based on 13 and 32 phylogenetically distinguishing positions in E6 and the LCR, respectively, that distinguish nine HPV16 variant sublineages (EUR, As, AFR1a, AFR1b, AFR2a, AFR2b, NA, AA1, and AA2). Ninety-seven percent of all 953 samples fitted this classification perfectly. Other positions were frequently polymorphic within one or more lineages but did not define phylogenetic subgroups. Such a standardized classification of HPV16 variants is important for future epidemiological and biological studies of the carcinogenic potential of HPV16 variant lineages. PMID:22491459

  18. Phylogenetic analysis of Gossypium L. using restriction fragment length polymorphism of repeated sequences.

    PubMed

    Zhang, Meiping; Rong, Ying; Lee, Mi-Kyung; Zhang, Yang; Stelly, David M; Zhang, Hong-Bin

    2015-10-01

    Cotton is the world's leading textile fiber crop and is also grown as a bioenergy and food crop. Knowledge of the phylogeny of closely related species and the genome origin and evolution of polyploid species is significant for advanced genomics research and breeding. We have reconstructed the phylogeny of the cotton genus, Gossypium L., and deciphered the genome origin and evolution of its five polyploid species by restriction fragment analysis of repeated sequences. Nuclear DNA of 84 accessions representing 35 species and all eight genomes of the genus were analyzed. The phylogenetic tree of the genus was reconstructed using the parsimony method on 1033 polymorphic repeated sequence restriction fragments. The genome origin of its polyploids was determined by calculating the diploid-polyploid restriction fragment correspondence (RFC). The tree is consistent with the morphological classification, genome designation and geographic distribution of the species at subgenus, section and subsection levels. Gossypium lobatum (D7) was unambiguously shown to have the highest RFC with the D-subgenomes of all five polyploids of the genus, while the common ancestor of Gossypium herbaceum (A1) and Gossypium arboreum (A2) likely contributed to the A-subgenomes of the polyploids. These results provide a comprehensive phylogenetic tree of the cotton genus and new insights into the genome origin and evolution of its polyploid species. The results also further demonstrate a simple, rapid and inexpensive method suitable for phylogenetic analysis of closely related species, especially congeneric species, and the inference of genome origin of polyploids that constitute over 70 % of flowering plants. PMID:25877517

  19. TIME-INTEGRATED EXPOSURE MEASURES TO IMPROVE THE PREDICTIVE POWER OF EXPOSURE CLASSIFICATION FOR EPIDEMIOLOGIC STUDIES

    EPA Science Inventory

    Accurate exposure classification tools are required to link exposure with health effects in epidemiological studies. Although long-term integrated exposure measurements are a critical component of exposure assessment, the ability to include these measurements into epidemiologic...

  20. INVENTORY AND CLASSIFICATION OF GREAT LAKES COASTAL WETLANDS FOR MONITORING AND ASSESSMENT AT LARGE SPATIAL SCALES

    EPA Science Inventory

    Monitoring aquatic resources for regional assessments requires an accurate and comprehensive inventory of the resource and useful classification of exosystem similarities. Our research effort to create an electronic database and work with various ways to classify coastal wetlands...

  1. Identification of two phylogenetic lineages of equine hepacivirus and high prevalence in Brazil.

    PubMed

    Figueiredo, Andreza Soriano; Lampe, Elisabeth; do Espírito-Santo, Márcia Paschoal; Mello, Francisco Campello do Amaral; de Almeida, Fernando Queiroz; de Lemos, Elba Regina Sampaio; Godoi, Tatianne Leme Oliveira Santos; Dimache, Luana Avila Giorgia; Dos Santos, Debora Regina Lopes; Villar, Livia Melo

    2015-12-01

    Non-primate hepacivirus (NPHV), as described in horses, is the virus most genetically related to hepatitis C virus (HCV). Although detected worldwide, limited data on genomic variability and distribution of NPHV are available in Latin America. The aim of this study was to investigate the genetic diversity and prevalence of equine NPHV in Brazil. Thirteen percent of 202 equines from three Brazilian states were positive for NPHV genome by reverse transcriptase PCR. Nucleotide sequences of the partial NS5B genome presented the greatest diversity described to date (25.6%), which is comparable to the upper limit of diversity for HCV subtype classification for the same region. Phylogenetic analysis revealed that Brazilian NPHV sequences along with isolates worldwide form two strongly supported clades (pp?=?1.0) suggesting the existence of two distinct lineages. PMID:26545848

  2. Mayaro virus: complete nucleotide sequence and phylogenetic relationships with other alphaviruses.

    PubMed

    Lavergne, Anne; de Thoisy, Benoît; Lacoste, Vincent; Pascalis, Hervé; Pouliquen, Jean-François; Mercier, Véronique; Tolou, Hugues; Dussart, Philippe; Morvan, Jacques; Talarmin, Antoine; Kazanji, Mirdad

    2006-05-01

    Mayaro (MAY) virus is a member of the genus Alphavirus in the family Togaviridae. Alphaviruses are distributed throughout the world and cause a wide range of diseases in humans and animals. Here, we determined the complete nucleotide sequence of MAY from a viral strain isolated from a French Guianese patient. The deduced MAY genome was 11,429 nucleotides in length, excluding the 5' cap nucleotide and 3' poly(A) tail. Nucleotide and amino acid homologies, as well as phylogenetic analyses of the obtained sequence confirmed that MAY is not a recombinant virus and belongs to the Semliki Forest complex according to the antigenic complex classification. Furthermore, analyses based on the E1 region revealed that MAY is closely related to Una virus, the only other South American virus clustering with the Old World viruses. On the basis of our results and of the alphaviruses diversity and pathogenicity, we suggest that alphaviruses may have an Old World origin. PMID:16343676

  3. Comparative phylogenetic study of Stichotrichia (Alveolata: Ciliophora: Spirotrichea) based on 18S-rDNA sequences.

    PubMed

    Paiva, T S; Borges, B N; Harada, M L; Silva-Neto, I D

    2009-01-01

    Since molecular phylogenies of stichotrich ciliates started to be published, some remarkable contradictions to morphology-based classifications have been reported, such as the Convergent Evolution of Urostylids and Uroleptids (CEUU) hypothesis, the Halteria paradox, the polyphyly of Oxytricha and of Stichotrichia. We hypothesized the internal phylogeny of 18S-rDNA from 53 morphological species of stichotrichs and their relationships with Hypotrichia and Oligotrichia using parsimony and neighbor-joining methods, including new data from Pseudouroleptus caudatus and Strongylidium pseudocrassum. Competing phylogenetic scenarios were compared using statistical tests, and the results suggest the reconsideration of both CEUU and the position of Halteria among flexible-body oxytrichids. The polyphyly of Oxytricha was not rejected and the monophyly of Stichotrichia was accepted based on parsimony analysis if Pseudoamphisiella is considered an external (discocephalid related) taxon. PMID:19291871

  4. Improved Surgical Site Infection (SSI) rate through accurately assessed surgical wounds

    PubMed Central

    John, Honeymol; Nimeri, Abdelrahman; ELLAHHAM, SAMER

    2015-01-01

    Sheikh Khalifa Medical City's (SKMC) Surgery Institute was identified as a high outlier in Surgical Site Infections (SSI) based on the American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) - Semi-Annual Report (SAR) in January 2012. The aim of this project was to improve SSI rates through accurate wound classification. We identified SSI rate reduction as a performance improvement and safety priority at SKMC, a tertiary referral center. We used the American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) best practice guidelines as a guide. ACS NSQIP is a clinical registry that provides risk-adjusted clinical outcome reports every six months. The rates of SSI are reported in an observed/expected ratio. The expected ratio is calculated based on the risk factors of the patients which include wound classification. We established a multidisciplinary SSI taskforce. The members of the SSI taskforce included the ACS NSQIP team members, quality, surgeons, nurses, infection control, IT, pharmacy, microbiology, and it was chaired by a colorectal surgeon. The taskforce focused on five areas: pre-op showering and hair removal, skin antisepsis, prophylactic antibiotics, peri-operative maintenance of glycaemia, and normothermia. We planned audits to evaluate our wound classification and our SSI rates based on the SAR. Our expected SSI rates in general surgery and the whole department were 2.52% and 1.70% respectively, while our observed SSI rates were 4.68% and 3.57% respectively, giving us a high outlier status with an odd's ratio of 1.72 and 2.03. Wound classifications were identified as an area of concern. For example, wound classifications were preoperatively selected based on the default wound classification of the booked procedure in the Electronic Medical Record (EMR) which led to under classifying wounds in many occasions. A total of 998 cases were reviewed, our rate of incorrect wound classification assignment was 36%, and the worst rates were in appendectomies (97%). Over time our incorrect wound classification decreased down to 22%, while at the same time our actual SSI wound occurrences per month and our odds ratio of SSI in the department have decreased an average of six to three per month. We followed the best practice guidelines of the ACS NSQIP. Accurate assessment of wound classification is necessary to make sure the expected SSI rates are not falsely high if wounds are under-classified. The present study shows that accurate wound classification in contaminated and dirty wounds can lead to lower odds ratio of SSI.

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

    PubMed Central

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

    2010-01-01

    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

  6. Phylogenetic relationships of the phasianidae reveals possible non-pheasant taxa.

    PubMed

    Bush, K L; Strobeck, C

    2003-01-01

    The phylogenetic relationships of 21 pheasant and 6 non-pheasant species were determined using nucleotide sequences from the mitochondrial cytochrome b gene. Maximum parsimony and maximum likelihood analysis were used to try to resolve the phylogenetic relationships within Phasianidae. Both the degree of resolution and strength of support are improved over previous studies due to the testing of a number of species from multiple pheasant genera, but several major ambiguities persist. Polyplectron bicalcaratum (grey peacock pheasant) is shown not to be a pheasant. Alternatively, it appears ancestral to either the partridges or peafowl. Pucrasia macrolopha macrolopha (koklass) and Gallus gallus (red jungle fowl) both emerge as non-pheasant genera. Monophyly of the pheasant group is challenged if Pucrasia macrolopha macrolopha and Gallus gallus are considered to be pheasants. The placement of Catreus wallichii (cheer) within the pheasants also remains undetermined, as does the cause for the great sequence divergence in Chrysolophus pictus obscurus (black-throated golden). These results suggest that alterations in taxonomic classifications may be required for some pheasant species and genera. PMID:14691314

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

    PubMed Central

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

    2015-01-01

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

  8. Phylogenetic Relationships in Bupleurum (Apiaceae) Based on Nuclear Ribosomal DNA ITS Sequence Data

    PubMed Central

    NEVES, SUSANA S.; WATSON, MARK F.

    2004-01-01

    • Backgroud and Aims The genus Bupleurum has long been recognized as a natural group, but its infrageneric classification is controversial and has not yet been studied in the light of sequence data. • Methods Phylogenetic relationships among 32 species (35 taxa) of the genus Bupleurum were investigated by comparative sequencing of the ITS region of the 18–26S nuclear ribosomal DNA repeat. Exemplar taxa from all currently accepted sections and subsections of the genus were included, along with outgroups from four other early branching Apioideae genera (Anginon, Heteromorpha, Physospermum and Pleurospermum). • Key Results Phylogenies generated by maximum parsimony, maximum likelihood, and neighbour?joining methods show similar topologies, demonstrating monophyly of Bupleurum and the division of the genus into two major clades. This division is also supported by analysis of the 5.8S coding sequence alone. The first branching clade is formed by all the species of the genus with pinnate?reticulate veined leaves and B. rigidum with a unique type of leaf venation. The other major clade includes the remaining species studied, all of which have more or less parallel?veined leaves. • Conclusions These phylogenetic results do not agree with any previous classifications of the genus. Molecular data also suggest that the endemic Macaronesian species B. salicifolium is a neoendemic, as the sequence divergence between the populations in Madeira and Canary Islands, and closer mainland relatives in north?west Africa is small. All endemic north?west African taxa are included in a single unresolved but well?supported clade, and the low nucleotide variation of ITS suggests a recent radiation within this group. The only southern hemisphere species, B. mundii (southern Africa), is shown to be a neoendemic, apparently closely related to B. falcatum, a Eurasian species. PMID:14980972

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

    PubMed

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

    2015-05-01

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

  10. 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

  11. Phylogenetic structure of angiosperm communities during tropical forest succession

    PubMed Central

    Letcher, Susan G.

    2010-01-01

    The phylogenetic structure of ecological communities can shed light on assembly processes, but the focus of phylogenetic structure research thus far has been on mature ecosystems. Here, I present the first investigation of phylogenetic community structure during succession. In a replicated chronosequence of 30 sites in northeastern Costa Rica, I found strong phylogenetic overdispersion at multiple scales: species present at local sites were a non-random assemblage, more distantly related than chance would predict. Phylogenetic overdispersion was evident when comparing the species present at each site with the regional species pool, the species pool found in each age category to the regional pool or the species present at each site to the pool of species found in sites of that age category. Comparing stem size classes within each age category, I found that during early succession, phylogenetic overdispersion is strongest in small stems. Overdispersion strengthens and spreads into larger size classes as succession proceeds, corroborating an existing model of forest succession. This study is the first evidence that succession leaves a distinct signature in the phylogenetic structure of communities. PMID:19801375

  12. Enumerating all maximal frequent subtrees in collections of phylogenetic trees

    PubMed Central

    2014-01-01

    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

  13. Student Interpretations of Phylogenetic Trees in an Introductory Biology Course

    PubMed Central

    Dees, Jonathan; Niemi, Jarad; Montplaisir, Lisa

    2014-01-01

    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 relatedness on phylogenetic trees, to measure the prevalence of correct taxa-relatedness interpretations, and to determine how student reasoning and correctness change in response to instruction and over time. Counting synapomorphies and nodes between taxa were the most common forms of incorrect reasoning, which presents a pedagogical dilemma concerning labeled synapomorphies on phylogenetic trees. Students also independently generated an alternative form of correct reasoning using monophyletic groups, the use of which decreased in popularity over time. Approximately half of all students were able to correctly interpret taxa relatedness on phylogenetic trees, and many memorized correct reasoning without understanding its application. Broad initial instruction that allowed students to generate inferences on their own contributed very little to phylogenetic tree understanding, while targeted instruction on evolutionary relationships improved understanding to some extent. Phylogenetic trees, which can directly affect student understanding of evolution, appear to offer introductory biology instructors a formidable pedagogical challenge. PMID:25452489

  14. The best of both worlds: Phylogenetic eigenvector regression and mapping

    PubMed Central

    Diniz, José Alexandre Felizola; Villalobos, Fabricio; Bini, Luis Mauricio

    2015-01-01

    Eigenfunction analyses have been widely used to model patterns of autocorrelation in time, space and phylogeny. In a phylogenetic context, Diniz-Filho et al. (1998) proposed what they called Phylogenetic Eigenvector Regression (PVR), in which pairwise phylogenetic distances among species are submitted to a Principal Coordinate Analysis, and eigenvectors are then used as explanatory variables in regression, correlation or ANOVAs. More recently, a new approach called Phylogenetic Eigenvector Mapping (PEM) was proposed, with the main advantage of explicitly incorporating a model-based warping in phylogenetic distance in which an Ornstein-Uhlenbeck (O-U) process is fitted to data before eigenvector extraction. Here we compared PVR and PEM in respect to estimated phylogenetic signal, correlated evolution under alternative evolutionary models and phylogenetic imputation, using simulated data. Despite similarity between the two approaches, PEM has a slightly higher prediction ability and is more general than the original PVR. Even so, in a conceptual sense, PEM may provide a technique in the best of both worlds, combining the flexibility of data-driven and empirical eigenfunction analyses and the sounding insights provided by evolutionary models well known in comparative analyses. PMID:26500445

  15. Investigating the performance of AIC in selecting phylogenetic models.

    PubMed

    Jhwueng, Dwueng-Chwuan; Huzurbazar, Snehalata; O'Meara, Brian C; Liu, Liang

    2014-08-01

    The popular likelihood-based model selection criterion, Akaike's Information Criterion (AIC), is a breakthrough mathematical result derived from information theory. AIC is an approximation to Kullback-Leibler (KL) divergence with the derivation relying on the assumption that the likelihood function has finite second derivatives. However, for phylogenetic estimation, given that tree space is discrete with respect to tree topology, the assumption of a continuous likelihood function with finite second derivatives is violated. In this paper, we investigate the relationship between the expected log likelihood of a candidate model, and the expected KL divergence in the context of phylogenetic tree estimation. We find that given the tree topology, AIC is an unbiased estimator of the expected KL divergence. However, when the tree topology is unknown, AIC tends to underestimate the expected KL divergence for phylogenetic models. Simulation results suggest that the degree of underestimation varies across phylogenetic models so that even for large sample sizes, the bias of AIC can result in selecting a wrong model. As the choice of phylogenetic models is essential for statistical phylogenetic inference, it is important to improve the accuracy of model selection criteria in the context of phylogenetics. PMID:24867284

  16. The best of both worlds: Phylogenetic eigenvector regression and mapping.

    PubMed

    Diniz, José Alexandre Felizola; Villalobos, Fabricio; Bini, Luis Mauricio

    2015-01-01

    Eigenfunction analyses have been widely used to model patterns of autocorrelation in time, space and phylogeny. In a phylogenetic context, Diniz-Filho et al. (1998) proposed what they called Phylogenetic Eigenvector Regression (PVR), in which pairwise phylogenetic distances among species are submitted to a Principal Coordinate Analysis, and eigenvectors are then used as explanatory variables in regression, correlation or ANOVAs. More recently, a new approach called Phylogenetic Eigenvector Mapping (PEM) was proposed, with the main advantage of explicitly incorporating a model-based warping in phylogenetic distance in which an Ornstein-Uhlenbeck (O-U) process is fitted to data before eigenvector extraction. Here we compared PVR and PEM in respect to estimated phylogenetic signal, correlated evolution under alternative evolutionary models and phylogenetic imputation, using simulated data. Despite similarity between the two approaches, PEM has a slightly higher prediction ability and is more general than the original PVR. Even so, in a conceptual sense, PEM may provide a technique in the best of both worlds, combining the flexibility of data-driven and empirical eigenfunction analyses and the sounding insights provided by evolutionary models well known in comparative analyses. PMID:26500445

  17. Classification Oliver Gray

    E-print Network

    Gasparim, Elizabeth

    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

  18. 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

  19. Library Classification 2020

    ERIC Educational Resources Information Center

    Harris, Christopher

    2013-01-01

    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…

  20. SEGMENTATION OF NEURONS BASED ON ONE-CLASS CLASSIFICATION Paul Hernandez-Herrera1

    E-print Network

    Papadakis, Manos

    SEGMENTATION OF NEURONS BASED ON ONE-CLASS CLASSIFICATION Paul Hernandez-Herrera1 , Manos Papadakis In this paper, we propose a novel one-class classification method to segment neurons. First, a new criterion ability to accurately and robustly segment neurons. 1. INTRODUCTION Neurons are the main part

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

    E-print Network

    Lutzoni, François M.

    , Joseph F. BISCHOFFb , Meredith BLACKWELLc , Paul F. CANNONd , Ove E. ERIKSSONe , Sabine HUHNDORFf PARMASTOah , Vale´rie REEBg , Jack D. ROGERSai , Claude ROUXaj , Leif RYVARDENak , Jose´ Paulo SAMPAIOal , Arthur SCHU¨ ßLERam , Junta SUGIYAMAan , R. Greg THORNao , Leif TIBELLap , Wendy A. UNTEREINERaq

  2. Disentangling the phylogenetic and ecological components of spider phenotypic variation.

    PubMed

    Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

    2014-01-01

    An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure. PMID:24651264

  3. Disentangling the Phylogenetic and Ecological Components of Spider Phenotypic Variation

    PubMed Central

    Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

    2014-01-01

    An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure. PMID:24651264

  4. 2-Stage Classification Modeling

    Energy Science and Technology Software Center (ESTSC)

    1994-11-01

    CIRCUIT2.4 is used to design optimum two-stage classification configurations and operating conditions for energy conservation. It permits simulation of five basic grinding-classification circuits, including one single-stage and four two-stage classification arrangements. Hydrocyclones, spiral classifiers, and sieve band screens can be simulated, and the user may choose the combination of devices for the flowsheet simulation. In addition, the user may select from four classification modeling methods to achieve the goals of a simulation project using themore »most familiar concepts. Circuit performance is modeled based on classification parameters or equipment operating conditions. A modular approach was taken in designing the program, which allows future addition of other models with relatively minor changes.« less

  5. 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)

    Tamura, Hiroto; Hotta, Yudai; Sato, Hiroaki

    2013-08-01

    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.

  6. Phylogenetic analysis of fungal heterotrimeric G protein-encoding genes and their expression during dimorphism in Mucor circinelloides.

    PubMed

    Valle-Maldonado, Marco Iván; Jácome-Galarza, Irvin Eduardo; Díaz-Pérez, Alma Laura; Martínez-Cadena, Guadalupe; Campos-García, Jesús; Ramírez-Díaz, Martha Isela; Reyes-De la Cruz, Homero; Riveros-Rosas, Héctor; Díaz-Pérez, César; Meza-Carmen, Víctor

    2015-12-01

    In fungi, heterotrimeric G proteins are key regulators of biological processes such as mating, virulence, morphology, among others. Mucor circinelloides is a model organism for many biological processes, and its genome contains the largest known repertoire of genes that encode putative heterotrimeric G protein subunits in the fungal kingdom: twelve G? (McGpa1-12), three G? (McGpb1-3), and three G? (McGpg1-3). Phylogenetic analysis of fungal G? showed that they are divided into four distinct groups as reported previously. Fungal G? and G? are also divided into four phylogenetic groups, and to our understanding this is the first report of a phylogenetic classification for fungal G? and G? subunits. Almost all genes that encode putative heterotrimeric G subunits in M. circinelloides are differentially expressed during dimorphic growth, except for McGpg1 (G?) that showed very low mRNA levels at all developmental stages. Moreover, several of the subunits are expressed in a similar pattern and at the same level, suggesting that they constitute discrete complexes. For example, McGpb3 (G?), and McGpg2 (G?), are co-expressed during mycelium growth, and McGpa1, McGpb2, and McGpg2, are co-expressed during yeast development. These findings provide the conceptual framework to study the biological role of these genes during M. circinelloides morphogenesis. PMID:26615741

  7. Progressive Classification Using Support Vector Machines

    NASA Technical Reports Server (NTRS)

    Wagstaff, Kiri; Kocurek, Michael

    2009-01-01

    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.

  8. Phylogeny and classification of the Catantopidae at the tribal level (Orthoptera, Acridoidea)

    PubMed Central

    Li, Baoping; Liu, Zhiwei; Zheng, Zhe-Min

    2011-01-01

    Abstract The grasshopper family Catantopidae is a well-known group, whose members include some of the most notorious agricultural pests. The existing classifications of the family are mostly utilitarian rather than being based on phylogenetic analysis and therefore unable to provide the stability desired for such an economically important group. In the present study, we present the first comprehensive phylogenetic analysis of the family based on morphology. By extensively sampling from the Chinese fauna, we included in the present analysis multiple representatives of each of the previously recognized tribes in the family. In total, we examined 94 genera represented by 240 species and evaluated 116 characters, including 84 for external morphology and 32 for male genitalia. The final matrix consists of 86 ingroup taxa and 88 characters. Our phylogenetic analyses resulted in a high resolution of the basal relationships of the family while showed considerable uncertainty about the relationships among some crown taxa. We further evaluated the usefulness of morphological characters in phylogeny reconstruction of the catantopids by examining character fit to the shortest trees found, and contrary to previous suggestions, our results suggest that genitalia characters are not as informative as external morphology in inferring higher-level relationship. We further suggest that earlier classification systems of grasshoppers in general and Catantopidae in particular most probably consist of many groups that are not natural due the heavy reliance on genitalia features and need to be revised in the light of future phylogenetic studies. Finally, we outlined a tentative classification scheme based on the results of our phylogenetic analysis. PMID:22287899

  9. Interpretation of bootstrap values in phylogenetic analysis.

    PubMed

    Wiesemüller, Bernhard; Rothe, Hartmut

    2006-06-01

    Bootstrap Analysis is a common tool in cladistics, and consequently many authors tend to believe that it could be close to a test of monophyly. In fact, it is only a procedure to calculate the redundancy of a certain character pattern among taxa. To demonstrate this, we set up a study with questionable data: Four skulls of great apes and humans were digitally photographed, and the pixels' brightness values were simply transformed to a one-zero-matrix, which was then used to calculate a Wagner tree with PHYLIP. As a rule, the higher the resolution of the photos is, the higher are the bootstrap values of supported taxa (and the lower are the bootstrap values of non-supported data). Redundancy of intertaxic information might indeed be an indicator of phylogenetic relationship, but can also be due to other reasons, like functional-adaptive needs in morphology, or semantic needs in a DNA-code. As a result, we tend to believe that high bootstrap values are actually less important than low ones. It is safer, based on a low bootstrap value, to claim that a certain taxon is not well supported by certain data. Therefore, we recommend discussions of low bootstrap values in future publications. PMID:16850767

  10. Ultrastructure, biology, and phylogenetic relationships of kinorhyncha.

    PubMed

    Neuhaus, Birger; Higgins, Robert P

    2002-07-01

    The article summarizes current knowledge mainly about the (functional) morphology and ultrastructure, but also about the biology, development, and evolution of the Kinorhyncha. The Kinorhyncha are microscopic, bilaterally symmetrical, exclusively free-living, benthic, marine animals and ecologically part of the meiofauna. They occur throughout the world from the intertidal to the deep sea, generally in sediments but sometimes associated with plants or other animals. From adult stages 141 species are known, but 38 species have been described from juvenile stages. The trunk is arranged into 11 segments as evidenced by cuticular plates, sensory spots, setae or spines, nervous system, musculature, and subcuticular glands. The ultrastructure of several organ systems and the postembryonic development are known for very few species. Almost no data are available about the embryology and only a single gene has been sequenced for a single species. The phylogenetic relationships within Kinorhyncha are unresolved. Priapulida, Loricifera, and Kinorhyncha are grouped together as Scalidophora, but arguments are found for every possible sistergroup relationship within this taxon. The recently published Ecdysozoa hypothesis suggests a closer relationship of the Scalidophora, Nematoda, Nematomorpha, Tardigrada, Onychophora, and Arthropoda. PMID:21708758

  11. Preprocessing remotely-sensed data for efficient analysis and classification

    SciTech Connect

    Kelly, P.M.; White, J.M.

    1993-01-01

    Interpreting remotely-sensed data typically requires expensive, specialized computing machinery capable of storing and manipulating large amounts of data quickly. In this paper, we present a method for accurately analyzing and categorizing remotely-sensed data on much smaller, less expensive platforms. Data size is reduced in such a way an efficient, interactive method of data classification.

  12. Preprocessing remotely-sensed data for efficient analysis and classification

    SciTech Connect

    Kelly, P.M.; White, J.M.

    1993-02-01

    Interpreting remotely-sensed data typically requires expensive, specialized computing machinery capable of storing and manipulating large amounts of data quickly. In this paper, we present a method for accurately analyzing and categorizing remotely-sensed data on much smaller, less expensive platforms. Data size is reduced in such a way an efficient, interactive method of data classification.

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

    PubMed

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

    2014-07-01

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

  14. Phylogenetic MCMC algorithms are misleading on mixtures of trees.

    PubMed

    Mossel, Elchanan; Vigoda, Eric

    2005-09-30

    Markov chain Monte Carlo (MCMC) algorithms play a critical role in the Bayesian approach to phylogenetic inference. We present a theoretical analysis of the rate of convergence of many of the widely used Markov chains. For N characters generated from a uniform mixture of two trees, we prove that the Markov chains take an exponentially long (in N) number of iterations to converge to the posterior distribution. Nevertheless, the likelihood plots for sample runs of the Markov chains deceivingly suggest that the chains converge rapidly to a unique tree. Our results rely on novel mathematical understanding of the log-likelihood function on the space of phylogenetic trees. The practical implications of our work are that Bayesian MCMC methods can be misleading when the data are generated from a mixture of trees. Thus, in cases of data containing potentially conflicting phylogenetic signals, phylogenetic reconstruction should be performed separately on each signal. PMID:16195459

  15. Short Communication Phylogenetic relationships among iguanian lizards using alternative

    E-print Network

    Schulte, Jim

    facilitate resolution of several longstanding phylogenetic issues across taxa such as land plants (Soltis et neither supported nor rejected (Schulte et al., 1998). Monophyly of the primarily New World clade

  16. Phylogenetic assessment of filoviruses: how many lineages of Marburg virus?

    E-print Network

    Peterson, A. Townsend; Holder, Mark T.

    2012-07-01

    Filoviruses have to date been considered as consisting of one diverse genus (Ebola viruses) and one undifferentiated genus (Marburg virus). We reconsider this idea by means of detailed phylogenetic analyses of sequence data available...

  17. Phylogenetic and Functional Biomakers as Indicators of Bacterial

    E-print Network

    Hazen, Terry

    Phylogenetic and Functional Biomakers as Indicators of Bacterial Community Responses to Mixed distributions each predicted different relationships among the sites, and comparisons of Euclidean distances (1). In addition, many disturbed sites contain multiple contaminants that can complicate treatment

  18. Refining Regulatory Networks through Phylogenetic Transfer of Information

    E-print Network

    Moret, Bernard

    Refining Regulatory Networks through Phylogenetic Transfer of Information Xiuwei Zhang and Bernard M.E. Moret Abstract--The experimental determination of transcriptional regulatory networks and associated inference algorithms, designed to improve the inference of regulatory networks for a family

  19. Large-scale analysis of phylogenetic search behavior 

    E-print Network

    Park, Hyun Jung

    2009-05-15

    Phylogenetic analysis is used in all branches of biology by inferring evolutionary trees. Applications include designing more effective drugs, tracing the transmission of deadly viruses, and guiding conservation and biodiversity efforts. Most...

  20. Markov invariants, plethysms, and phylogenetics (the long version)

    E-print Network

    J. G. Sumner; M. A. Charleston; L. S. Jermiin; P. D. Jarvis

    2008-07-22

    We explore model based techniques of phylogenetic tree inference exercising Markov invariants. Markov invariants are group invariant polynomials and are distinct from what is known in the literature as phylogenetic invariants, although we establish a commonality in some special cases. We show that the simplest Markov invariant forms the foundation of the Log-Det distance measure. We take as our primary tool group representation theory, and show that it provides a general framework for analysing Markov processes on trees. From this algebraic perspective, the inherent symmetries of these processes become apparent, and focusing on plethysms, we are able to define Markov invariants and give existence proofs. We give an explicit technique for constructing the invariants, valid for any number of character states and taxa. For phylogenetic trees with three and four leaves, we demonstrate that the corresponding Markov invariants can be fruitfully exploited in applied phylogenetic studies.

  1. Asperisporium and Pantospora (Mycosphaerellaceae): epitypifications and phylogenetic placement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The species-rich family Mycosphaerellaceae contains considerable morphological diversity and includes numerous anamorphic genera, many of which are economically important plant pathogens. Recent revisions and phylogenetic research have resulted in taxonomic instability. Ameliorating this problem req...

  2. Phylogenetic invariants for the general Markov model of sequence mutation.

    PubMed

    Allman, Elizabeth S; Rhodes, John A

    2003-12-01

    A phylogenetic invariant for a model of biological sequence evolution along a phylogenetic tree is a polynomial that vanishes on the expected frequencies of base patterns at the terminal taxa. While the use of these invariants for phylogenetic inference has long been of interest, explicitly constructing such invariants has been problematic. We construct invariants for the general Markov model of kappa-base sequence evolution on an n-taxon tree, for any kappa and n. The method depends primarily on the observation that certain matrices defined in terms of expected pattern frequencies must commute, and yields many invariants of degree kappa+1, regardless of the value of n. We define strong and parameter-strong sets of invariants, and prove several theorems indicating that the set of invariants produced here has these properties on certain sets of possible pattern frequencies. Thus our invariants may be sufficient for phylogenetic applications. PMID:14583169

  3. Phylogenetic analysis of hostsymbiont specificity and codivergence in bioluminescent symbioses

    E-print Network

    McFall-Ngai, Margaret

    Phylogenetic analysis of host­symbiont specificity and codivergence in bioluminescent symbioses Accepted 3 January 2007 Abstract Several groups of marine fishes and squids form mutualistic bioluminescent that bioluminescent symbioses are tightly coupled associations that might involve coevolutionary interactions

  4. RESEARCH ARTICLE Open Access Phylogenetic relationships among Staphylococcus

    E-print Network

    Parkinson, Christopher L.

    RESEARCH ARTICLE Open Access Phylogenetic relationships among Staphylococcus species and refinement of relationships among Staphylococcus species have been hampered by poor and inconsistent resolution of phylogenies approaches that incorporate nearly all recognized Staphylococcus taxa. Results: We estimated the phylogeny

  5. Obtaining Maximal Concatenated Phylogenetic Data Sets from Large Sequence Databases

    E-print Network

    Sanderson, Michael J.

    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

  6. Using models of nucleotide evolution to build phylogenetic trees.

    PubMed

    Bos, David H; Posada, David

    2005-01-01

    Molecular phylogenetics and its applications are popular and useful tools for making comparative investigations in genetics; however, estimating phylogenetic trees is not always straightforward. Some phylogenetic estimators use an explicit model of nucleotide evolution to estimate evolutionary parameters such as branch lengths and tree topology. There are many models to choose from, and use of the optimal model for a particular data set is important to avoid a loss of power and accuracy in phylogenetic estimations. Here, we review some molecular evolutionary forces and the parameters included in some common models of evolution used to interpret resulting patterns of molecular variation. We present some statistical methods of selecting a particular model of nucleotide evolution, and provide an empirical example of model selection. Statistical model selection strikes a balance between the bias introduced by some models and the increased variance of parameter estimates that results from using other models. PMID:15572070

  7. INTRODUCTION Recent phylogenetic studies have revealed a basal

    E-print Network

    Schuettpelz, Eric

    INTRODUCTION Recent phylogenetic studies have revealed a basal dichotomy within vascular plants, separating the lyco- phytes (less than 1% of extant vascular plants) from the euphyllophytes (Fig. 1 phylogeny depicting relationships of major vascular plant lineages. Topology summarizes the results

  8. Phylogenetic and functional diversity in large carnivore assemblages

    PubMed Central

    Dalerum, F.

    2013-01-01

    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

  9. A common tendency for phylogenetic overdispersion in mammalian assemblages

    PubMed Central

    Cooper, Natalie; Rodríguez, Jesús; Purvis, Andy

    2008-01-01

    Competition has long been proposed as an important force in structuring mammalian communities. Although early work recognized that competition has a phylogenetic dimension, only with recent increases in the availability of phylogenies have true phylogenetic investigations of mammalian community structure become possible. We test whether the phylogenetic structure of 142 assemblages from three mammalian clades (New World monkeys, North American ground squirrels and Australasian possums) shows the imprint of competition. The full set of assemblages display a highly significant tendency for members to be more distantly related than expected by chance (phylogenetic overdispersion). The overdispersion is also significant within two of the clades (monkeys and squirrels) separately. This is the first demonstration of widespread overdispersion in mammal assemblages and implies an important role for either competition between close relatives where traits are conserved, habitat filtering where distant relatives share convergent traits, or both. PMID:18508747

  10. MINI REVIEW Tempo and mode in evolution: phylogenetic inertia, adaptation

    E-print Network

    Saltzman, Wendy

    MINI REVIEW Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods S. Rectilinear trends were part of the dynamics (tempo) of evolution, and not associated with phyletic stasis

  11. Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics.

    PubMed

    Andújar, Carmelo; Arribas, Paula; Ruzicka, Filip; Crampton-Platt, Alex; Timmermans, Martijn J T N; Vogler, Alfried P

    2015-07-01

    High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well-supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer-mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well-understood ecosystems, and will propel both theoretical and applied soil science. PMID:25865150

  12. Phylogenetic relationships of rhizobia based on citrate synthase gene sequences.

    PubMed

    Hernández-Lucas, Ismael; Rogel-Hernández, Marco Antonio; Segovia, Lorenzo; Rojas-Jiménez, Keilor; Martínez-Romero, Esperanza

    2004-11-01

    Partial nucleotide sequences of the citrate synthase (gltA) gene from different rhizobia genera were determined. Tree topologies based on this housekeeping gene were similar to that obtained using 16S rRNA sequences. However gltA appeared to be more reliable at determining phylogenetic relationships of closely related taxa. We propose gltA sequences as an additional tool to be used in molecular phylogenetic studies. PMID:15612628

  13. SVM texture classification for tropical vegetation mapping

    NASA Astrophysics Data System (ADS)

    Chabrier, Sebastien; Stoll, Benoit; Goujon, Jean-Baptiste

    2012-11-01

    Nowadays, remote sensing is an essential science in French Polynesia because of its extended territory and the remoteness of its 120 islands. There is a strong need to study the vegetation cover and its evolution (biodiversity threat, invasive species, etc.). A growing satellite images database has been acquired throughout, giving access to very high resolution optical images such as Quickbird data. These data allow accessing the vegetation canopy spectral and contextual information, texture classification has proved to be an efficient tool to map the complex vegetation found in tropical regions. The main goal of this paper is to propose an optimized SVM multispectral-texture classification method for tropical vegetation mapping. One of the texture computation drawbacks is the window treatment size, which is related to the largest texture element size. In complex tropical vegetation cover, this parameter leads to very small ground truth learning database, inducing a significant degradation of the classifications accuracy. We propose to increase the thumbnail numbers using an under-sampling method, optimizing the size and the number of the thumbnails. The other drawback is the high dimensionality of the problem when dealing with multispectral textures. We thus propose to rank and select the most pertinent textures attributes in order to reduce the dimensionality without reducing the classification accuracy. We first introduce the study context, before exposing preliminary studies on tuning the SVM learning method. The adapted method is then accurately exposed and the interesting experimental results as well as a sample of applications are presented before to conclude.

  14. Randomized clustering forests for image classification.

    PubMed

    Moosmann, Frank; Nowak, Eric; Jurie, Frederic

    2008-09-01

    Some of the most effective recent methods for content-based image classification work by quantizing image descriptors, and accumulating histograms of the resulting visual word codes. Large numbers of descriptors and large codebooks are required for good results and this becomes slow using k-means. We introduce Extremely Randomized Clustering Forests ensembles of randomly created clustering trees and show that they provide more accurate results, much faster training and testing, and good resistance to background clutter. Second, an efficient image classification method is proposed. It combines ERC-Forests and saliency maps very closely with the extraction of image information. For a given image, a classifier builds a saliency map online and uses it to classify the image. We show in several state-of-the-art image classification tasks that this method can speed up the classification process enormously. Finally, we show that the proposed ERC-Forests can also be used very successfully for learning distance between images. The distance computation algorithm consists of learning the characteristic differences between local descriptors sampled from pairs of same or different objects. These differences are vector quantized by ERC-Forests and the similarity measure is computed from this quantization. The similarity measure has been evaluated on four very different datasets and always outperforms the state-of-the-art competitive approaches. PMID:18617720

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

    PubMed Central

    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

    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

  16. Phylogenetic relationships among hadal amphipods of the Superfamily Lysianassoidea: Implications for taxonomy and biogeography

    NASA Astrophysics Data System (ADS)

    Ritchie, H.; Jamieson, A. J.; Piertney, S. B.

    2015-11-01

    Amphipods of the superfamily Lysianassoidea are ubiquitous at hadal depths (>6000 m) and therefore are an ideal model group for investigating levels of endemism and the drivers of speciation in deep ocean trenches. The taxonomic classification of hadal amphipods is typically based on conventional morphological traits but it has been suggested that convergent evolution, phenotypic plasticity, intra-specific variability and ontogenetic variation may obscure the ability to robustly diagnose taxa and define species. Here we use phylogenetic analysis of DNA sequence variation at two mitochondrial (COI and 16S rDNA) and one nuclear (18S rDNA) regions at to examine the evolutionary relationships among 25 putative amphipod species representing 14 genera and 11 families that were sampled from across seven hadal trenches. We identify several instances where species, genera and families do not resolve monophyletic clades, highlighting incongruence between the current taxonomic classification and the molecular phylogeny for this group. Our data also help extend and resolve the known biogeographic distributions for the different species, such as identifying the co-occurrence of Hirondellea dubia and Hirondellea gigas in the Mariana trench.

  17. Resident-invader phylogenetic relatedness, not resident phylogenetic diversity, controls community invasibility.

    PubMed

    Tan, Jiaqi; Pu, Zhichao; Ryberg, Wade A; Jiang, Lin

    2015-07-01

    A central goal of invasion biology is to elucidate mechanisms regulating community invasibility. Darwin's naturalization hypothesis, one of the oldest hypotheses in invasion biology, emphasizes the importance of phylogenetic relatedness (PR) between resident and invader species for predicting invasibility. Alternatively, a recent extension of the diversity-invasibility hypothesis predicts that phylogenetic diversity (PD) of resident communities influences invasibility. Neither of these hypotheses has undergone rigorous experimental testing, and the relative contributions of PR and PD to community invasibility are unknown, in part because their effects tend to be confounded with each other. Here we consider both perspectives together by independently manipulating PR and PD in laboratory bacterial assemblages. We found that, although invader abundance decreased significantly as PR increased, it was unaffected by PD. Likewise, we found that resident-invader functional similarity, not functional diversity of resident communities, was a significant predictor of invader abundance. Nevertheless, invader abundance was better predicted by PR than by functional similarity. These results highlight the importance of considering species evolutionary relationships, especially the PR between resident and invader species, for the prediction, prevention, and management of biological invasions. PMID:26098339

  18. Proteomic applications of automated GPCR classification.

    PubMed

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

    2007-08-01

    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

  19. Permutation Tests for Classification

    E-print Network

    Mukherjee, Sayan

    2003-08-28

    We introduce and explore an approach to estimating statistical significance of classification accuracy, which is particularly useful in scientific applications of machine learning where high dimensionality of the data and ...

  20. Gait analysis for classification

    E-print Network

    Lee, Lily, 1971-

    2002-01-01

    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 ...

  1. Gait Analysis for Classification

    E-print Network

    Lee, Lily

    2003-06-26

    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 ...

  2. Molecular phylogenetics of Caenogastropoda (Gastropoda: Mollusca).

    PubMed

    Colgan, D J; Ponder, W F; Beacham, E; Macaranas, J

    2007-03-01

    Caenogastropoda is the dominant group of marine gastropods in terms of species numbers, diversity of habit and habitat and ecological importance. This paper reports the first comprehensive multi-gene phylogenetic study of the group. Data were collected from up to six genes comprising parts of 18S rRNA, 28S rRNA (five segments), 12S rRNA, cytochrome c oxidase subunit I, histone H3 and elongation factor 1alpha. The alignment has a combined length of 3995 base positions for 36 taxa, comprising 29 Caenogastropoda representing all of its major lineages and seven outgroups. Maximum parsimony, maximum likelihood and Bayesian analyses were conducted. The results generally support monophyly of Caenogastropoda and Hypsogastropoda (Caenogastropoda excepting Architaenioglossa, Cerithioidea and Campanilioidea). Within Hypsogastropoda, maximum likelihood and Bayesian analyses identified a near basal clade of nine or 10 families lacking an anterior inhalant siphon, and Cerithiopsidae s.l. (representing Triphoroidea), where the siphon is probably derived independently from other Hypsogastropoda. The asiphonate family Eatoniellidae was usually included in the clade but was removed in one Bayesian analysis. Of the two other studied families lacking a siphon, the limpet-shaped Calyptraeidae was associated with this group in some analyses, but the tent-shaped Xenophoridae was generally associated with the siphonate Strombidae. The other studied hypsogastropods with an anterior inhalant siphon include nine families, six of which are Neogastropoda, the only traditional caenogastropod group above the superfamily-level with strong morphological support. The hypotheses that Neogastropoda are monophyletic and that the group occupies a derived position within Hypsogastropoda are both contradicted, but weakly, by the molecular analyses. Despite the addition of large amounts of new molecular data, many caenogastropod lineages remain poorly resolved or unresolved in the present analyses, possibly due to a rapid radiation of the Hypsogastropoda following the Permian-Triassic extinction during the early Mesozoic. PMID:17127080

  3. Improvement of the classification system for wheelchair rugby: athlete priorities.

    PubMed

    Altmann, Viola C; Hart, Anne L; van Limbeek, Jacques; Vanlandewijck, Yves C

    2014-10-01

    A representative sample (N=302) of the wheelchair rugby population responded to a survey about the classification system based on prioritized items by International Wheelchair Rugby Federation members. Respondents stated, "The classification system is accurate but needs adjustments" (56%), "Any athlete with tetraequivalent impairment should be allowed to compete" (72%), "Athletes with cerebral palsy and other coordination impairments should be classified with a system different than the current one" (75%), and "The maximal value for trunk should be increased from 1.0 to 1.5" (67%). A minority stated, "Wheelchair rugby should only be open to spinal cord injury and other neurological conditions" (36%) and "There should be a 4.0 class" (33%). Results strongly indicated that athletes and stakeholders want adjustments to the classification system in two areas: a focus on evaluation of athletes with impairments other than loss of muscle power caused by spinal cord injury and changes in classification of trunk impairment. PMID:25211483

  4. Periscope video ship classification

    NASA Astrophysics Data System (ADS)

    Sadjadi, Firooz A.; OSullivan, Jack

    1996-05-01

    Automatic classification of surface ships by means of imaging sensors through the submarine's periscope is of interest to the naval underwater warfare center of the US Navy. In this paper we discuss a testbed designed for periscope video ship classification based on model-based automatic target recognition paradigm, will present the performance results for the application of some of the existing algorithms and will present a sequential tree based technique for ship recognition.

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

    PubMed Central

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

    2010-01-01

    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

  6. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment.

    PubMed

    Lartillot, Nicolas; Rodrigue, Nicolas; Stubbs, Daniel; Richer, Jacques

    2013-07-01

    Modeling across site variation of the substitution process is increasingly recognized as important for obtaining more accurate phylogenetic reconstructions. Both finite and infinite mixture models have been proposed and have been shown to significantly improve on classical single-matrix models. Compared with their finite counterparts, infinite mixtures have a greater expressivity. However, they are computationally more challenging. This has resulted in practical compromises in the design of infinite mixture models. In particular, a fast but simplified version of a Dirichlet process model over equilibrium frequency profiles implemented in PhyloBayes has often been used in recent phylogenomics studies, while more refined model structures, more realistic and empirically more fit, have been practically out of reach. We introduce a message passing interface version of PhyloBayes, implementing the Dirichlet process mixture models as well as more classical empirical matrices and finite mixtures. The parallelization is made efficient thanks to the combination of two algorithmic strategies: a partial Gibbs sampling update of the tree topology and the use of a truncated stick-breaking representation for the Dirichlet process prior. The implementation shows close to linear gains in computational speed for up to 64 cores, thus allowing faster phylogenetic reconstruction under complex mixture models. PhyloBayes MPI is freely available from our website www.phylobayes.org. PMID:23564032

  7. Evaluating nuclear protein-coding genes for phylogenetic utility in beetles.

    PubMed

    Wild, Alexander L; Maddison, David R

    2008-09-01

    Although nuclear protein-coding genes have proven broadly useful for phylogenetic inference, relatively few such genes are regularly employed in studies of Coleoptera, the most diverse insect order. We increase the number of loci available for beetle systematics by developing protocols for three genes previously unused in beetles (alpha-spectrin, RNA polymerase II and topoisomerase I) and by refining protocols for five genes already in use (arginine kinase, CAD, enolase, PEPCK and wingless). We evaluate the phylogenetic performance of each gene in a Bayesian framework against a presumably known test phylogeny. The test phylogeny covers 31 beetle specimens and two outgroup taxa of varying age, including three of the four extant beetle suborders and a denser sampling in Adephaga and in the carabid genus Bembidion. All eight genes perform well for Cenozoic divergences and accurately separate closely related species within Bembidion, but individual genes differ markedly in accuracy over the older Mesozoic and Permian divergences. The concatenated data reconstruct the test phylogeny with high support in both Bayesian and parsimony analyses, indicating that combining data from multiple nuclear loci will be a fruitful approach for assembling the beetle tree of life. PMID:18644735

  8. Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria?

    PubMed

    Ruhsam, Markus; Rai, Hardeep S; Mathews, Sarah; Ross, T Gregory; Graham, Sean W; Raubeson, Linda A; Mei, Wenbin; Thomas, Philip I; Gardner, Martin F; Ennos, Richard A; Hollingsworth, Peter M

    2015-09-01

    Obtaining accurate phylogenies and effective species discrimination using a small standardized set of plastid genes is challenging in evolutionarily young lineages. Complete plastid genome sequencing offers an increasingly easy-to-access source of characters that helps address this. The usefulness of this approach, however, depends on the extent to which plastid haplotypes track morphological species boundaries. We have tested the power of complete plastid genomes to discriminate among multiple accessions of 11 of 13 New Caledonian Araucaria species, an evolutionarily young lineage where the standard DNA barcoding approach has so far failed and phylogenetic relationships have remained elusive. Additionally, 11 nuclear gene regions were Sanger sequenced for all accessions to ascertain the success of species discrimination using a moderate number of nuclear genes. Overall, fewer than half of the New Caledonian Araucaria species with multiple accessions were monophyletic in the plastid or nuclear trees. However, the plastid data retrieved a phylogeny with a higher resolution compared to any previously published tree of this clade and supported the monophyly of about twice as many species and nodes compared to the nuclear data set. Modest gains in discrimination thus are possible, but using complete plastid genomes or a small number of nuclear genes in DNA barcoding may not substantially raise species discriminatory power in many evolutionarily young lineages. The big challenge therefore remains to develop techniques that allow routine access to large numbers of nuclear markers scaleable to thousands of individuals from phylogenetically disparate sample sets. PMID:25611173

  9. Supernova Photometric Lightcurve Classification

    NASA Astrophysics Data System (ADS)

    Zaidi, Tayeb; Narayan, Gautham

    2016-01-01

    This is a preliminary report on photometric supernova classification. We first explore the properties of supernova light curves, and attempt to restructure the unevenly sampled and sparse data from assorted datasets to allow for processing and classification. The data was primarily drawn from the Dark Energy Survey (DES) simulated data, created for the Supernova Photometric Classification Challenge. This poster shows a method for producing a non-parametric representation of the light curve data, and applying a Random Forest classifier algorithm to distinguish between supernovae types. We examine the impact of Principal Component Analysis to reduce the dimensionality of the dataset, for future classification work. The classification code will be used in a stage of the ANTARES pipeline, created for use on the Large Synoptic Survey Telescope alert data and other wide-field surveys. The final figure-of-merit for the DES data in the r band was 60% for binary classification (Type I vs II).Zaidi was supported by the NOAO/KPNO Research Experiences for Undergraduates (REU) Program which is funded by the National Science Foundation Research Experiences for Undergraduates Program (AST-1262829).

  10. Phylogeny and classification of Prunus sensu lato (Rosaceae).

    PubMed

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

    2013-11-01

    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

  11. Free classification of American English dialects by native and non-native listeners

    PubMed Central

    Clopper, Cynthia G.; Bradlow, Ann R.

    2009-01-01

    Most second language acquisition research focuses on linguistic structures, and less research has examined the acquisition of sociolinguistic patterns. The current study explored the perceptual classification of regional dialects of American English by native and non-native listeners using a free classification task. Results revealed similar classification strategies for the native and non-native listeners. However, the native listeners were more accurate overall than the non-native listeners. In addition, the non-native listeners were less able to make use of constellations of cues to accurately classify the talkers by dialect. However, the non-native listeners were able to attend to cues that were either phonologically or sociolinguistically relevant in their native language. These results suggest that non-native listeners can use information in the speech signal to classify talkers by regional dialect, but that their lack of signal-independent cultural knowledge about variation in the second language leads to less accurate classification performance. PMID:20161400

  12. The complete mitochondrial genome and phylogenetic analysis of the giant panda (Ailuropoda melanoleuca).

    PubMed

    Peng, Rui; Zeng, Bo; Meng, Xiuxiang; Yue, Bisong; Zhang, Zhihe; Zou, Fangdong

    2007-08-01

    The complete mitochondrial genome sequence of the giant panda, Ailuropoda melanoleuca, was determined by the long and accurate polymerase chain reaction (LA-PCR) with conserved primers and primer walking sequence methods. The complete mitochondrial DNA is 16,805 nucleotides in length and contains two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and one control region. The total length of the 13 protein-coding genes is longer than the American black bear, brown bear and polar bear by 3 amino acids at the end of ND5 gene. The codon usage also followed the typical vertebrate pattern except for an unusual ATT start codon, which initiates the NADH dehydrogenase subunit 5 (ND5) gene. The molecular phylogenetic analysis was performed on the sequences of 12 concatenated heavy-strand encoded protein-coding genes, and suggested that the giant panda is most closely related to bears. PMID:17499457

  13. Accurate estimation of sigma(exp 0) using AIRSAR data

    NASA Technical Reports Server (NTRS)

    Holecz, Francesco; Rignot, Eric

    1995-01-01

    During recent years signature analysis, classification, and modeling of Synthetic Aperture Radar (SAR) data as well as estimation of geophysical parameters from SAR data have received a great deal of interest. An important requirement for the quantitative use of SAR data is the accurate estimation of the backscattering coefficient sigma(exp 0). In terrain with relief variations radar signals are distorted due to the projection of the scene topography into the slant range-Doppler plane. The effect of these variations is to change the physical size of the scattering area, leading to errors in the radar backscatter values and incidence angle. For this reason the local incidence angle, derived from sensor position and Digital Elevation Model (DEM) data must always be considered. Especially in the airborne case, the antenna gain pattern can be an additional source of radiometric error, because the radar look angle is not known precisely as a result of the the aircraft motions and the local surface topography. Consequently, radiometric distortions due to the antenna gain pattern must also be corrected for each resolution cell, by taking into account aircraft displacements (position and attitude) and position of the backscatter element, defined by the DEM data. In this paper, a method to derive an accurate estimation of the backscattering coefficient using NASA/JPL AIRSAR data is presented. The results are evaluated in terms of geometric accuracy, radiometric variations of sigma(exp 0), and precision of the estimated forest biomass.

  14. Neural Network Classification of Stellar Spectra

    NASA Astrophysics Data System (ADS)

    Bailer-Jones, C. A. L.

    1997-08-01

    The MK classification system as first proposed in 1943 by Morgan, Keenan & Kellman (1943) has been an important tool in stellar and galactic astrophysics. Currently, MK classification is a useful approach to obtaining general information on stellar spectra and selecting stars for further study. However, the existing manual methods of obtaining classifications are slow, making it infeasible for them to be applied to the vast numbers of spectra which will be obtained in future spectral surveys. In this project I investigate the application of artificial neural networks to the automation of MK spectral classification. For the purposes of this project, I digitized and reduced 100 objective prism plates taken from the Michigan Spectral Survey (Houk 1994). Using software I developed, I extracted a set of over 5000 spectra at a resolution of ~3 AA covering the wavelength range 3800-5200 AA (Bailer-Jones, Irwin & von Hippel 1997a). These spectra were used in conjunction with their two-dimensional classifications listed in Michigan Henry Draper Catalogue (Houk & Smith-Moore 1988 and references therein) to develop supervised neural network classifiers. I show that neural networks can give accurate spectral type classifications (1 sigma = 0.82 subtypes, sigmaRMS = 1.09 subtypes) across the full range of spectral types present in the database (B2-M7); I show also that the networks yield correct luminosity classes for over 95% of both dwarfs and giants with a high degree of confidence (Bailer-Jones, Irwin & von Hippel 1997b). The high level of reproducibility of neural network classifications is demonstrated and an analysis of the effect of the complexity of the neural network on its classifications is given. For the purposes of many analyses, stellar spectra contain a large amount of redundant (correlated) information. I investigate the application of Principal Components Analysis (PCA) to the optimal compression of spectra. I show that PCA can compress the spectra by a factor of over 30 whilst retaining more than 95% of the variance in the data set. Furthermore, this compression leads to no decrease in classifier performance, indicating that the PCA compression from 820 to 25 components results in no significant loss of relevant information. I also demonstrate how PCA acts as a filter of noise and bogus features in a spectrum and can be used to identify unusual spectra. The ultimate goal of stellar classification should be a physical parameterization of the stars. I examine the application of neural networks to the problem of obtaining physical parameters (Teff, log g etc.) directly from an observed spectrum, by training a neural network on synthetic spectra and then applying it to observed spectra (Bailer-Jones et al. 1997). By determining physical parameters in this way, any assumptions and limitations of an intermediate classification scheme are avoided. However, I have used the effective temperature (Teff) inferred by the networks to produce an accurate calibration of the MK system for dwarf, giant and sub-giant stars, based on the set of 5000 observed spectra. This calibration agrees well with a number of calibrations published in the literature. It is demonstrated through the metallicity dependence of the derived temperature calibration that the neural networks are sensitive to the metallicity features in the observed spectra. With further work it is likely that neural networks will be able to determine metallicity reliably using only the optical stellar spectrum.

  15. Accurate histological terminology for small intestine carcinoid tumors

    PubMed Central

    Pusiol, Teresa; Morini, Alice; Piscioli, Irene; Scialpi, Michele

    2013-01-01

    The recent WHO Classification of Tumours of the Digestive System reflects the views of a Working Group that convened for an Editorial and Consensus Conference at the International Agency for Research on Cancer (IARC), Lyon, 10 December 2009 [1]. In this classification, the “neuroendocrine neoplasms of the small intestine” include neuroendocrine tumor (NET), neuroendocrine carcinoma (NEC), mixed adenoneuroendocrine carcinoma, EC cell, serotonin-producing NET, gangliocytic paraganglioma, gastrinoma, L cell, glucagon-like peptide-producing, PP/PYY-producing NETs, and somostatin-producing NET. “Carcinoid tumor” is the generic term traditionally applied to low-grade malignant neoplasms originating from the diffuse endocrine system exclusive of the pancreas and the thyroid C-cell, a term being progressively replaced by “well-differentiated (neuro)endocrine tumors/carcinomas”. It is now acknowledged that they represent a group of related neoplasms, not single pathologic entity. In the WHO classification, the NET includes NET G1 and NET G2, and the term “carcinoid” is used as a synonym of NET G1. We believed that the term “carcinoid tumor” is generic; consequently, the term should be avoided. We have read with great interest the paper by Lee et al. – “Multiple carcinoid tumor of the small intestine preoperatively diagnosed by double-balloon endoscopy” [2]. In the paper, Lee et al. wrote: “Histologic examination of the biopsy sample obtained by endoscopy confirmed the diagnosis of a carcinoid tumor. The tumor was composed of small uniform epithelial cells, which stained positively for chromogranin A and synaptophysin.” We believe that the histological diagnosis of carcinoid tumor is not correct. The description is typical of NET G1, according to the new WHO classification. The authors wrote: “These small tumors were diagnosed as carcinoid tumors by endoscopic findings, whereas histologic examination could not make this diagnosis… Microscopically, the tumors were composed of small uniform epithelial cells which stained positively for chromogranin A and synaptophysin. Furthermore, the largest tumor had invaded the muscularis propria. MIB-1 index was less than 1%.” It is evident that histological diagnosis was not reported. In conclusion, accurate histological diagnosis is necessary for the evaluation of treatment impact in the management of neuroendocrine tumors of the small intestine. PMID:23507937

  16. Molecular characterization and phylogenetics of Fennoscandian cowpox virus isolates based on the p4c and atip genes

    PubMed Central

    2014-01-01

    Background Cowpox virus (CPXV), a rodent-borne Orthopoxvirus (OPV) that is indigenous to Eurasia can infect humans, cattle, felidae and other animals. Molecular characterization of CPXVs isolated from different geographic locations is important for the understanding of their biology, geographic distribution, classification and evolution. Our aim was to characterize CPXVs isolated from Fennoscandia on the basis of A-type inclusion (ATI) phenotype, restriction fragment length polymorphism (RFLP) profiles of atip gene fragment amplicon, and phylogenetic tree topology in conjunction with the patristic and genetic distances based on full length DNA sequence of the atip and p4c genes. Methods ATI phenotypes were determined by transmission electron microcopy and RFLP profiles were obtained by restriction enzyme digestion of the atip gene fragment PCR product. A 6.2 kbp region spanning the entire atip and p4c genes of Fennoscandian CPXV isolates was amplified and sequenced. The phylogenetic affinity of Fennoscandian CPXV isolates to OPVs isolated from other geographic regions was determined on the basis of the atip and p4c genes. Results Fennoscandian CPXV isolates encoded full length atip and p4c genes. They produce wild type V+ ATI except for CPXV-No-H2. CPXVs were resolved into six and seven species clusters based on the phylogeny of the atip and p4c genes respectively. The CPXVs isolated from Fennoscandia were grouped into three distinct clusters that corresponded to isolates from Norway, Sweden and Finland. Conclusion CPXV is a polyphyletic assemblage of six or seven distinct clusters and the current classification in which CPXVs are united as one single species should be re-considered. Our results are of significance to the classification and evolution of OPVs. PMID:24972911

  17. SUMAC: Constructing Phylogenetic Supermatrices and Assessing Partially Decisive Taxon Coverage

    PubMed Central

    Freyman, William A.

    2015-01-01

    The amount of phylogenetically informative sequence data in GenBank is growing at an exponential rate, and large phylogenetic trees are increasingly used in research. Tools are needed to construct phylogenetic sequence matrices from GenBank data and evaluate the effect of missing data. Supermatrix Constructor (SUMAC) is a tool to data-mine GenBank, construct phylogenetic supermatrices, and assess the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. SUMAC calculates a novel metric, Missing Sequence Decisiveness Scores (MSDS), which measures how much each individual missing sequence contributes to the decisiveness of the matrix. MSDS can be used to compare supermatrices and prioritize the acquisition of new sequence data. SUMAC constructs supermatrices either through an exploratory clustering of all GenBank sequences within a taxonomic group or by using guide sequences to build homologous clusters in a more targeted manner. SUMAC assembles supermatrices for any taxonomic group recognized in GenBank and is optimized to run on multicore computer systems by parallelizing multiple stages of operation. SUMAC is implemented as a Python package that can run as a stand-alone command-line program, or its modules and objects can be incorporated within other programs. SUMAC is released under the open source GPLv3 license and is available at https://github.com/wf8/sumac. PMID:26648681

  18. Testing and quantifying phylogenetic signals and homoplasy in morphometric data.

    PubMed

    Klingenberg, Christian Peter; Gidaszewski, Nelly A

    2010-05-01

    The relationship between morphometrics and phylogenetic analysis has long been controversial. Here we propose an approach that is based on mapping morphometric traits onto phylogenies derived from other data and thus avoids the pitfalls encountered by previous studies. This method treats shape as a single, multidimensional character. We propose a test for the presence of a phylogenetic signal in morphometric data, which simulates the null hypothesis of the complete absence of phylogenetic structure by permutation of the shape data among the terminal taxa. We also propose 2 measures of the fit of morphometric data to the phylogeny that are direct extensions of the consistency index and retention index used in traditional cladistics. We apply these methods to a small study of the evolution of wing shape in the Drosophila melanogaster subgroup, for which a very strongly supported phylogeny is available. This case study reveals a significant phylogenetic signal and a relatively low degree of homoplasy. Despite the low homoplasy, the shortest tree computed from landmark data on wing shape is inconsistent with the well-supported phylogenetic tree from molecular data, underscoring that morphometric data may not provide reliable information for inferring phylogeny. PMID:20525633

  19. Global patterns and drivers of phylogenetic structure in island floras.

    PubMed

    Weigelt, Patrick; Kissling, W Daniel; Kisel, Yael; Fritz, Susanne A; Karger, Dirk Nikolaus; Kessler, Michael; Lehtonen, Samuli; Svenning, Jens-Christian; Kreft, Holger

    2015-01-01

    Islands are ideal for investigating processes that shape species assemblages because they are isolated and have discrete boundaries. Quantifying phylogenetic assemblage structure allows inferences about these processes, in particular dispersal, environmental filtering and in-situ speciation. Here, we link phylogenetic assemblage structure to island characteristics across 393 islands worldwide and 37,041 vascular plant species (representing angiosperms overall, palms and ferns). Physical and bioclimatic factors, especially those impeding colonization and promoting speciation, explained more variation in phylogenetic structure of angiosperms overall (49%) and palms (52%) than of ferns (18%). The relationships showed different or contrasting trends among these major plant groups, consistent with their dispersal- and speciation-related traits and climatic adaptations. Phylogenetic diversity was negatively related to isolation for palms, but unexpectedly it was positively related to isolation for angiosperms overall. This indicates strong dispersal filtering for the predominantly large-seeded, animal-dispersed palm family whereas colonization from biogeographically distinct source pools on remote islands likely drives the phylogenetic structure of angiosperm floras. We show that signatures of dispersal limitation, environmental filtering and in-situ speciation differ markedly among taxonomic groups on islands, which sheds light on the origin of insular plant diversity. PMID:26198002

  20. Global patterns and drivers of phylogenetic structure in island floras

    PubMed Central

    Weigelt, Patrick; Daniel Kissling, W.; Kisel, Yael; Fritz, Susanne A.; Karger, Dirk Nikolaus; Kessler, Michael; Lehtonen, Samuli; Svenning, Jens-Christian; Kreft, Holger

    2015-01-01

    Islands are ideal for investigating processes that shape species assemblages because they are isolated and have discrete boundaries. Quantifying phylogenetic assemblage structure allows inferences about these processes, in particular dispersal, environmental filtering and in-situ speciation. Here, we link phylogenetic assemblage structure to island characteristics across 393 islands worldwide and 37,041 vascular plant species (representing angiosperms overall, palms and ferns). Physical and bioclimatic factors, especially those impeding colonization and promoting speciation, explained more variation in phylogenetic structure of angiosperms overall (49%) and palms (52%) than of ferns (18%). The relationships showed different or contrasting trends among these major plant groups, consistent with their dispersal- and speciation-related traits and climatic adaptations. Phylogenetic diversity was negatively related to isolation for palms, but unexpectedly it was positively related to isolation for angiosperms overall. This indicates strong dispersal filtering for the predominantly large-seeded, animal-dispersed palm family whereas colonization from biogeographically distinct source pools on remote islands likely drives the phylogenetic structure of angiosperm floras. We show that signatures of dispersal limitation, environmental filtering and in-situ speciation differ markedly among taxonomic groups on islands, which sheds light on the origin of insular plant diversity. PMID:26198002

  1. On how many fundamental kinds of cells are present on Earth: looking for phylogenetic traits that would allow the identification of the primary lines of descent.

    PubMed

    Di Giulio, Massimo

    2014-06-01

    The phylogenetic analyses as far as the identification of the number of domains of life is concerned have not reached a clear conclusion. In the attempt to improve this circumstance, I introduce the concept that the amino acids codified in the genetic code might be of markers with outstanding phylogenetic power. In particular, I hypothesise the existence of a biosphere populated, for instance, by three groups of organisms having different genetic codes because codifying at least a different amino acid. Evidently, these amino acids would mark the proteins that are present in the three groups of organisms in an unambiguous way. Therefore, in essence, this mark would not be other than the one that we usually try to make in the phylogenetic analyses in which we transform the protein sequences in phylogenetic trees, for the purpose to identify, for example, the domains of life. Indeed, this mark would allow to classify proteins without performing phylogenetic analyses because proteins belonging to a group of organisms would be recognisable as marked in a natural way by at least a different amino acid among the diverse groups of organisms. This conceptualisation answers the question of how many fundamental kinds of cells have evolved from the Last Universal Common Ancestor (LUCA), as the genetic code has unique proprieties that make the codified amino acids excellent phylogenetic markers. The presence of the formyl-methionine only in proteins of bacteria would mark them and would identify these as domain of life. On the other hand, the presence of pyrrolysine in the genetic code of the euryarchaeota would identify them such as another fundamental kind of cell evolved from the LUCA. Overall, the phylogenetic distribution of formyl-methionine and pyrrolysine would identify at least two domains of life--Bacteria and Archaea--but their number might be actually four; that is to say, Bacteria, Euryarchaeota, archeobacteria that are not euryarchaeota and Eukarya. The usually accepted domains of life represented by Bacteria, Archaea and Eukarya are not compatible with the phylogenetic distribution of these two amino acids and therefore this last classification might be mistaken. PMID:24916656

  2. Target classification strategies

    NASA Astrophysics Data System (ADS)

    Schachter, Bruce J.

    2015-05-01

    Target classification algorithms have generally kept pace with developments in the academic and commercial sectors since the 1970s. However, most recently, investment into object classification by internet companies and various Human Brain Projects have far outpaced that of the defense sector. Implications are noteworthy. There are some unique characteristics of the military classification problem. Target classification is not solely an algorithm design problem, but is part of a larger system design task. The design flows down from a concept of operations (ConOps) and key performance parameters (KPPs). Inputs are image and/or signal data and time-synchronized metadata. The operation is real-time. The implementation minimizes size, weight and power (SWaP). The output must be conveyed to a time-strapped operator who understands the rules of engagement. It is assumed that the adversary is actively trying to defeat recognition. The target list is often mission dependent, not necessarily a closed set, and may change on a daily basis. It is highly desirable to obtain sufficiently comprehensive training and testing data sets, but costs of doing so are very high and data on certain target types are scarce. The training data may not be representative of battlefield conditions suggesting the avoidance of highly tuned designs. A number of traditional and emerging target classification strategies are reviewed in the context of the military target problem.

  3. An improved model for whole genome phylogenetic analysis by Fourier transform.

    PubMed

    Yin, Changchuan; Yau, Stephen S-T

    2015-10-01

    DNA sequence similarity comparison is one of the major steps in computational phylogenetic studies. The sequence comparison of closely related DNA sequences and genomes is usually performed by multiple sequence alignments (MSA). While the MSA method is accurate for some types of sequences, it may produce incorrect results when DNA sequences undergone rearrangements as in many bacterial and viral genomes. It is also limited by its computational complexity for comparing large volumes of data. Previously, we proposed an alignment-free method that exploits the full information contents of DNA sequences by Discrete Fourier Transform (DFT), but still with some limitations. Here, we present a significantly improved method for the similarity comparison of DNA sequences by DFT. In this method, we map DNA sequences into 2-dimensional (2D) numerical sequences and then apply DFT to transform the 2D numerical sequences into frequency domain. In the 2D mapping, the nucleotide composition of a DNA sequence is a determinant factor and the 2D mapping reduces the nucleotide composition bias in distance measure, and thus improving the similarity measure of DNA sequences. To compare the DFT power spectra of DNA sequences with different lengths, we propose an improved even scaling algorithm to extend shorter DFT power spectra to the longest length of the underlying sequences. After the DFT power spectra are evenly scaled, the spectra are in the same dimensionality of the Fourier frequency space, then the Euclidean distances of full Fourier power spectra of the DNA sequences are used as the dissimilarity metrics. The improved DFT method, with increased computational performance by 2D numerical representation, can be applicable to any DNA sequences of different length ranges. We assess the accuracy of the improved DFT similarity measure in hierarchical clustering of different DNA sequences including simulated and real datasets. The method yields accurate and reliable phylogenetic trees and demonstrates that the improved DFT dissimilarity measure is an efficient and effective similarity measure of DNA sequences. Due to its high efficiency and accuracy, the proposed DFT similarity measure is successfully applied on phylogenetic analysis for individual genes and large whole bacterial genomes. PMID:26151589

  4. 5 CFR 9901.221 - Classification requirements.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 2010-01-01 false Classification requirements. 9901.221...Personnel DEPARTMENT OF DEFENSE HUMAN RESOURCES MANAGEMENT AND...PERSONNEL SYSTEM (NSPS) Classification Classification Process § 9901.221...

  5. 5 CFR 9901.221 - Classification requirements.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 2011-01-01 false Classification requirements. 9901.221...Personnel DEPARTMENT OF DEFENSE HUMAN RESOURCES MANAGEMENT AND...PERSONNEL SYSTEM (NSPS) Classification Classification Process § 9901.221...

  6. Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region

    PubMed Central

    NIE, BIN; ZHANG, GUANGJIONG; GUO, YONGCAN; LI, QINGFENG; LIU, JINBO; TU, ZHIGUANG

    2015-01-01

    The classification of hepatitis C virus (HCV) genotypes is of clinical importance as it may help to predict drug therapy responses and estimate treatment duration. The classical method of HCV subgenotype classification is whole genome sequencing (WGS). However, the high cost and time-consuming nature of WGS limits its usage in clinical practice. A number of studies have been conducted to confirm whether specific regions of HCV could replace WGS in the classification of HCV subgenotypes. In the present study, we used the HCV database to select HCV sequences from different countries. The neighbor-joining method was used to construct phylogenetic trees based on different regions of HCV (core, E1, E2 and NS5B), to confirm which region could replace WGS in subgenotype classification. Our results indicated that the core, E1 and E2 regions could not be used to classify the HCV subgenotype correctly (core failed to recognize subgenotypes c and a, E1 failed to discriminate between subgenotypes a and b, and E2 failed to identify subgenotypes a and c). The NS5B region provided the correct subgenotype classification. The HCV samples (n=153) collected from patients in Sichuan province, (Southwest China) were sequenced and classified based on the NS5B region. The results indicated that the major subgenotype of HCV in patients from Sichuan was 1b (51.6%, n=79); other subgenotypes included 3b (30.1%, n=46), 3a (7.8%, n=12), 6a (8.5%, n=13), 2a (n=2) and 6n (n=1). The data from our analysis may prove to be helpful in future epidemiological investigations of HCV, and may aid in the prevention and clinical treatment of HCV. PMID:26311523

  7. Classification of mental disorders*

    PubMed Central

    Stengel, E.

    1959-01-01

    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

  8. Phylogenetic evidence for inter-typic recombination in the emergence of human enterovirus 71 subgenotypes

    PubMed Central

    Yoke-Fun, Chan; AbuBakar, Sazaly

    2006-01-01

    Background Human enterovirus 71 (EV-71) is a common causative agent of hand, foot and mouth disease (HFMD). In recent years, the virus has caused several outbreaks with high numbers of deaths and severe neurological complications. Several new EV-71 subgenotypes were identified from these outbreaks. The mechanisms that contributed to the emergence of these subgenotypes are unknown. Results Six EV-71 isolates from an outbreak in Malaysia, in 1997, were sequenced completely. These isolates were identified as EV-71 subgenotypes, B3, B4 and C2. A phylogenetic tree that correlated well with the present enterovirus classification scheme was established using these full genome sequences and all other available full genome sequences of EV-71 and human enterovirus A (HEV-A). Using the 5' UTR, P2 and P3 genomic regions, however, isolates of EV-71 subgenotypes B3 and C4 segregated away from other EV-71 subgenotypes into a cluster together with coxsackievirus A16 (CV-A16/G10) and EV-71 subgenotype C2 clustered with CV-A8. Results from the similarity plot analyses supported the clustering of these isolates with other HEV-A. In contrast, at the same genomic regions, a CV-A16 isolate, Tainan5079, clustered with EV-71. This suggests that amongst EV-71 and CV-A16, only the structural genes were conserved. The 3' end of the virus genome varied and consisted of sequences highly similar to various HEV-A viruses. Numerous recombination crossover breakpoints were identified within the non-structural genes of some of these newer EV-71 subgenotypes. Conclusion Phylogenetic evidence obtained from analyses of the full genome sequence supports the possible occurrence of inter-typic recombination involving EV-71 and various HEV-A, including CV-A16, the most common causal agent of HFMD. It is suggested that these recombination events played important roles in the emergence of the various EV-71 subgenotypes. PMID:16939656

  9. Phylogenetic Relationships of Citrus and Its Relatives Based on matK Gene Sequences

    PubMed Central

    Penjor, Tshering; Uehara, Miki; Ide, Manami; Matsumoto, Natsumi; Matsumoto, Ryoji

    2013-01-01

    The genus Citrus includes mandarin, orange, lemon, grapefruit and lime, which have high economic and nutritional value. The family Rutaceae can be divided into 7 subfamilies, including Aurantioideae. The genus Citrus belongs to the subfamily Aurantioideae. In this study, we sequenced the chloroplast matK genes of 135 accessions from 22 genera of Aurantioideae and analyzed them phylogenetically. Our study includes many accessions that have not been examined in other studies. The subfamily Aurantioideae has been classified into 2 tribes, Clauseneae and Citreae, and our current molecular analysis clearly discriminate Citreae from Clauseneae by using only 1 chloroplast DNA sequence. Our study confirms previous observations on the molecular phylogeny of Aurantioideae in many aspects. However, we have provided novel information on these genetic relationships. For example, inconsistent with the previous observation, and consistent with our preliminary study using the chloroplast rbcL genes, our analysis showed that Feroniella oblata is not nested in Citrus species and is closely related with Feronia limonia. Furthermore, we have shown that Murraya paniculata is similar to Merrillia caloxylon and is dissimilar to Murraya koenigii. We found that “true citrus fruit trees” could be divided into 2 subclusters. One subcluster included Citrus, Fortunella, and Poncirus, while the other cluster included Microcitrus and Eremocitrus. Compared to previous studies, our current study is the most extensive phylogenetic study of Citrus species since it includes 93 accessions. The results indicate that Citrus species can be classified into 3 clusters: a citron cluster, a pummelo cluster, and a mandarin cluster. Although most mandarin accessions belonged to the mandarin cluster, we found some exceptions. We also obtained the information on the genetic background of various species of acid citrus grown in Japan. Because the genus Citrus contains many important accessions, we have comprehensively discussed the classification of this genus. PMID:23638116

  10. A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis

    PubMed Central

    2015-01-01

    Background Biological nitrogen fixation, with an emphasis on the legume-rhizobia symbiosis, is a key process for agriculture and the environment, allowing the replacement of nitrogen fertilizers, reducing water pollution by nitrate as well as emission of greenhouse gases. Soils contain numerous strains belonging to the bacterial genus Bradyrhizobium, which establish symbioses with a variety of legumes. However, due to the high conservation of Bradyrhizobium 16S rRNA genes - considered as the backbone of the taxonomy of prokaryotes - few species have been delineated. The multilocus sequence analysis (MLSA) methodology, which includes analysis of housekeeping genes, has been shown to be promising and powerful for defining bacterial species, and, in this study, it was applied to Bradyrhizobium, species, increasing our understanding of the diversity of nitrogen-fixing bacteria. Description Classification of bacteria of agronomic importance is relevant to biodiversity, as well as to biotechnological manipulation to improve agricultural productivity. We propose the construction of an online database that will provide information and tools using MLSA to improve phylogenetic and taxonomic characterization of Bradyrhizobium, allowing the comparison of genomic sequences with those of type and representative strains of each species. Conclusion A database for the taxonomic and phylogenetic identification of the Bradyrhizobium, genus, using MLSA, will facilitate the use of biological data available through an intuitive web interface. Sequences stored in the on-line database can be compared with multiple sequences of other strains with simplicity and agility through multiple alignment algorithms and computational routines integrated into the database. The proposed database and software tools are available at http://mlsa.cnpso.embrapa.br, and can be used, free of charge, by researchers worldwide to classify Bradyrhizobium, strains; the database and software can be applied to replicate the experiments presented in this study as well as to generate new experiments. The next step will be expansion of the database to include other rhizobial species. PMID:26040196

  11. Developing and applying heterogeneous phylogenetic models with XRate.

    PubMed

    Westesson, Oscar; Holmes, Ian

    2012-01-01

    Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate 's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate 's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART. PMID:22693624

  12. A phylogenetic overview of the antrodia clade (Basidiomycota, Polyporales).

    PubMed

    Ortiz-Santana, Beatriz; Lindner, Daniel L; Miettinen, Otto; Justo, Alfredo; Hibbett, David S

    2013-01-01

    Phylogenetic relationships among members of the antrodia clade were investigated with molecular data from two nuclear ribosomal DNA regions, LSU and ITS. A total of 123 species representing 26 genera producing a brown rot were included in the present study. Three DNA datasets (combined LSU-ITS dataset, LSU dataset, ITS dataset) comprising sequences of 449 isolates were evaluated with three different phylogenetic analyses (maximum likelihood, maximum parsimony, Bayesian inference). We present a phylogenetic overview of the five main groups recovered: the fibroporia, laetiporus, postia, laricifomes and core antrodia groups. Not all of the main groups received strong support in the analyses, requiring further research. We were able to identify a number of well supported clades within the main groups. PMID:23935025

  13. Community structure of a microbial mat: The phylogenetic dimension

    USGS Publications Warehouse

    Risatti, J.B.; Capman, W.C.; Stahl, D.A.

    1994-01-01

    Traditional studies of microbial communities are incomplete because of the inability to identify and quantify all contributing populations. In the present study, we directly determine the abundance and distribution of sulfate-reducing bacterial populations in a microbial mat community by using hybridization probes complementary to the 16S-like rRNAs of major phylogenetic groups. Most of the major groups were found in this single community, distributed for the most part in nonoverlapping depth intervals of the mat. The reflection of the phylogenetic structure in the community structure suggests that those species making up the major phylogenetic groups perform specific interrelated metabolic functions in the community. Comparison of population profiles to previously observed rates of sulfate reduction suggests there are additional populations of sulfate-reducing bacteria both within the photooxic zone and deeper in the mat.

  14. Genetic and phylogenetic characterization of novel bocaparvovirus infecting chimpanzee.

    PubMed

    Brožová, Kristýna; Hrazdilová, Kristýna; Slaninková, Eva; Modrý, David; ?erný, Ji?í; Celer, Vladimír

    2016-01-01

    Primate bocaparvoviruses were first described in 2005, since then further human and gorilla bocaparvoviruses have been identified. To uncover diversity of non-human primates' bocaparvoviruses, their phylogenetic relationship and potential to cross the host species barrier, we tested 153 fecal samples from 17 captive primate species. The only one captive female of central chimpanzee (coded CPZh2) has been identified as bocaparvovirus positive. Based on the full genome phylogenetic analyses, CPZh2 strain shows close relationship to HBoV3 and GBoV. Further recombination analysis confirmed expected mosaic origin of CPZh2 strain. According the phylogenetic position, following the ICTV recommendations, we propose a novel genotype within the Primate bocaparvovirus 1 species infecting chimpanzee. PMID:26616676

  15. Electromechanical flowmeter accurately monitors fluid flow

    NASA Technical Reports Server (NTRS)

    Grant, D. J.

    1965-01-01

    Electromechanical flowmeter remotely and accurately monitors the flow rate and total volume of a transparent liquid discharged from a dispensing system. A dual dispensing tube system provides a relative reference level which permits compensation for temperature variations.

  16. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...the measurement of limitation of motion is indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be accurately measured and reported. [41 FR 11294, Mar. 18,...

  17. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...the measurement of limitation of motion is indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be accurately measured and reported. [41 FR 11294, Mar. 18,...

  18. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...the measurement of limitation of motion is indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be accurately measured and reported. [41 FR 11294, Mar. 18,...

  19. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...the measurement of limitation of motion is indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be accurately measured and reported. [41 FR 11294, Mar. 18,...

  20. Accurate capacitive metrology for atomic force microscopy

    E-print Network

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

    2005-01-01

    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 ...

  1. Understanding the Code: keeping accurate records.

    PubMed

    Griffith, Richard

    2015-10-01

    In his continuing series looking at the legal and professional implications of the Nursing and Midwifery Council's revised Code of Conduct, Richard Griffith discusses the elements of accurate record keeping under Standard 10 of the Code. This article considers the importance of accurate record keeping for the safety of patients and protection of district nurses. The legal implications of records are explained along with how district nurses should write records to ensure these legal requirements are met. PMID:26418404

  2. Spatial Pattern Classification for More Accurate Forecasting of Variable Energy Resources

    NASA Astrophysics Data System (ADS)

    Novakovskaia, E.; Hayes, C.; Collier, C.

    2014-12-01

    The accuracy of solar and wind forecasts is becoming increasingly essential as grid operators continue to integrate additional renewable generation onto the electric grid. Forecast errors affect rate payers, grid operators, wind and solar plant maintenance crews and energy traders through increases in prices, project down time or lost revenue. While extensive and beneficial efforts were undertaken in recent years to improve physical weather models for a broad spectrum of applications these improvements have generally not been sufficient to meet the accuracy demands of system planners. For renewables, these models are often used in conjunction with additional statistical models utilizing both meteorological observations and the power generation data. Forecast accuracy can be dependent on specific weather regimes for a given location. To account for these dependencies it is important that parameterizations used in statistical models change as the regime changes. An automated tool, based on an artificial neural network model, has been developed to identify different weather regimes as they impact power output forecast accuracy at wind or solar farms. In this study, improvements in forecast accuracy were analyzed for varying time horizons for wind farms and utility-scale PV plants located in different geographical regions.

  3. Using minimum DNA marker loci for accurate population classification in rice (Oryza sativa L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using few DNA markers to classify genetic background of a germplasm pool will help breeders make a quick decision while saving time and resources. WHICHLOCI is a computer program that selects the best combination of loci for population assignment through empiric analysis of molecular marker data. Th...

  4. Post-Mortem evaluation of amyloid-dopamine terminal positron emission tomography dementia classifications.

    PubMed

    Albin, Roger L; Fisher-Hubbard, Amanda; Shanmugasundaram, Krithika; Koeppe, Robert A; Burke, James F; Camelo-Piragua, Sandra; Lieberman, Andrew P; Giordani, Bruno; Frey, Kirk A

    2015-11-01

    Clinical classification of early dementia and mild cognitive impairment (MCI) is imprecise. We reported previously that molecular imaging classification of early dementia and MCI with dual amyloid and dopamine terminal positron emission tomography differs significantly from expert clinical classification. We now report pathological diagnoses in a substantial subset of our previously imaged subjects. Among 36 subjects coming to autopsy, imaging classifications and pathological diagnosis were concordant in 33 cases (??=?0.85). This approach enhanced specificity of Alzheimer's disease diagnosis. The strong concordance of imaging-based classifications and pathological diagnoses suggests that this imaging approach will be useful in establishing more accurate and convenient classification biomarkers for dementia research. Ann Neurol 2015;78:Ann Neurol 2015;78:679-696. PMID:26183692

  5. Improved Hierarchical Optimization-Based Classification of Hyperspectral Images Using Shape Analysis

    NASA Technical Reports Server (NTRS)

    Tarabalka, Yuliya; Tilton, James C.

    2012-01-01

    A new spectral-spatial method for classification of hyperspectral images is proposed. The HSegClas method is based on the integration of probabilistic classification and shape analysis within the hierarchical step-wise optimization algorithm. First, probabilistic support vector machines classification is applied. Then, at each iteration two neighboring regions with the smallest Dissimilarity Criterion (DC) are merged, and classification probabilities are recomputed. The important contribution of this work consists in estimating a DC between regions as a function of statistical, classification and geometrical (area and rectangularity) features. Experimental results are presented on a 102-band ROSIS image of the Center of Pavia, Italy. The developed approach yields more accurate classification results when compared to previously proposed methods.

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

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

    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.

  7. Mammalian phylogenetic diversity-area relationships at a continental scale

    PubMed Central

    Mazel, Florent; Renaud, Julien; Guilhaumon, François; Mouillot, David; Gravel, Dominique; Thuiller, Wilfried

    2015-01-01

    In analogy to the species-area relationship (SAR), one of the few laws in Ecology, the phylogenetic diversity-area relationship (PDAR) describes the tendency of phylogenetic diversity (PD) to increase with area. Although investigating PDAR has the potential to unravel the underlying processes shaping assemblages across spatial scales and to predict PD loss through habitat reduction, it has been little investigated so far. Focusing on PD has noticeable advantages compared to species richness (SR) since PD also gives insights on processes such as speciation/extinction, assembly rules and ecosystem functioning. Here we investigate the universality and pervasiveness of the PDAR at continental scale using terrestrial mammals as study case. We define the relative robustness of PD (compared to SR) to habitat loss as the area between the standardized PDAR and standardized SAR (i.e. standardized by the diversity of the largest spatial window) divided by the area under the standardized SAR only. This metric quantifies the relative increase of PD robustness compared to SR robustness. We show that PD robustness is higher than SR robustness but that it varies among continents. We further use a null model approach to disentangle the relative effect of phylogenetic tree shape and non random spatial distribution of evolutionary history on the PDAR. We find that for most spatial scales and for all continents except Eurasia, PDARs are not different from expected by a model using only the observed SAR and the shape of the phylogenetic tree at continental scale. Interestingly, we detect a strong phylogenetic structure of the Eurasian PDAR that can be predicted by a model that specifically account for a finer biogeographical delineation of this continent. In conclusion, the relative robustness of PD to habitat loss compared to species richness is determined by the phylogenetic tree shape but also depends on the spatial structure of PD. PMID:26649401

  8. Phylogenetic community structure: temporal variation in fish assemblage

    PubMed Central

    Santorelli, Sergio; Magnusson, William; Ferreira, Efrem; Caramaschi, Erica; Zuanon, Jansen; Amadio, Sidnéia

    2014-01-01

    Hypotheses about phylogenetic relationships among species allow inferences about the mechanisms that affect species coexistence. Nevertheless, most studies assume that phylogenetic patterns identified are stable over time. We used data on monthly samples of fish from a single lake over 10 years to show that the structure in phylogenetic assemblages varies over time and conclusions depend heavily on the time scale investigated. The data set was organized in guild structures and temporal scales (grouped at three temporal scales). Phylogenetic distance was measured as the mean pairwise distances (MPD) and as mean nearest-neighbor distance (MNTD). Both distances were based on counts of nodes. We compared the observed values of MPD and MNTD with values that were generated randomly using null model independent swap. A serial runs test was used to assess the temporal independence of indices over time. The phylogenetic pattern in the whole assemblage and the functional groups varied widely over time. Conclusions about phylogenetic clustering or dispersion depended on the temporal scales. Conclusions about the frequency with which biotic processes and environmental filters affect the local assembly do not depend only on taxonomic grouping and spatial scales. While these analyzes allow the assertion that all proposed patterns apply to the fish assemblages in the floodplain, the assessment of the relative importance of these processes, and how they vary depending on the temporal scale and functional group studied, cannot be determined with the effort commonly used. It appears that, at least in the system that we studied, the assemblages are forming and breaking continuously, resulting in various phylogeny-related structures that makes summarizing difficult. PMID:25360256

  9. Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum.

    PubMed

    Field, Ashley R; Testo, Weston; Bostock, Peter D; Holtum, Joseph A M; Waycott, Michelle

    2016-01-01

    The generic classification of huperzioid Lycopodiaceae was tested using Bayesian inference and Maximum likelihood phylogenetic analyses of DNA sequences from four chloroplast loci for 119 taxa and optimisation of 29 morphological characteristics onto the phylogeny. Consistent with previous studies, the subfamilies Lycopodioideae and Huperzioideae are monophyletic and diagnosable by synapomorphies that correlate with differences in their life-histories. Within the Huperzioideae, the monophyly of the widely adopted genus Huperzia (excl. Phylloglossum) is poorly supported. Three clades of huperzioid Lycopodiaceae were recovered in all analyses of molecular data: Phylloglossum drummondii, Huperzia sensu stricto and Phlegmariurus sensu lato. These clades are strongly supported by morphological characters, including differences in spores, gametophytes, sporophyte macro-morphology, as well as growth habit and life-histories. Our findings indicate that either a one-genus (Huperzia s.l.) or a three-genus (Phylloglossum, Huperzia s.s. and Phlegmariurus s.l.) classification of huperzioid Lycopods are equally supported by molecular evidence, but a two-genus system (Huperzia s.l.+Phylloglossum) is not. We recommend recognising three genera in the huperzioid Lycopodiaceae, as this classification best reflects evolutionary, ecological, and morphological divergence within the lineage. PMID:26493224

  10. AUTOMATIC MIXED PIXEL CLASSIFICATION (AMPC): UNSUPERVISED MIXED PIXEL CLASSIFICATION

    E-print Network

    Chang, Chein-I

    subpixel detection discussed in Chapters 5-6 AMPC can be also categorized into unsupervised mixed pixel13 AUTOMATIC MIXED PIXEL CLASSIFICATION (AMPC): UNSUPERVISED MIXED PIXEL CLASSIFICATION The automatic mixed pixel classification (AMPC) considered in this chapter is fully computer automated and can

  11. TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata

    PubMed Central

    Pirrung, Meg; Kennedy, Ryan; Caporaso, J. Gregory; Stombaugh, Jesse; Wendel, Doug; Knight, Rob

    2011-01-01

    Motivation: Microbial community profiling is a highly active area of research, but tools that facilitate visualization of phylogenetic trees and associated environmental data have not kept up with the increasing quantity of data generated in these studies. Results: TopiaryExplorer supports the visualization of very large phylogenetic trees, including features such as the automated coloring of branches by environmental data, manipulation of trees and incorporation of per-tip metadata (e.g. taxonomic labels). Availability: http://topiaryexplorer.sourceforge.net Contact: rob.knight@colorado.edu PMID:21903626

  12. caret: Classification and Regression Training

    NASA Astrophysics Data System (ADS)

    Kuhn, Max

    2015-05-01

    caret (Classification And REgression Training) provides functions for training and plotting classification and regression models. It contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality.

  13. Fast Image Texture Classification Using Decision Trees

    NASA Technical Reports Server (NTRS)

    Thompson, David R.

    2011-01-01

    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.

  14. Nominated texture based cervical cancer classification.

    PubMed

    Mariarputham, Edwin Jayasingh; Stephen, Allwin

    2015-01-01

    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

  15. An accurate method of extracting fat droplets in liver images for quantitative evaluation

    NASA Astrophysics Data System (ADS)

    Ishikawa, Masahiro; Kobayashi, Naoki; Komagata, Hideki; Shinoda, Kazuma; Yamaguchi, Masahiro; Abe, Tokiya; Hashiguchi, Akinori; Sakamoto, Michiie

    2015-03-01

    The steatosis in liver pathological tissue images is a promising indicator of nonalcoholic fatty liver disease (NAFLD) and the possible risk of hepatocellular carcinoma (HCC). The resulting values are also important for ensuring the automatic and accurate classification of HCC images, because the existence of many fat droplets is likely to create errors in quantifying the morphological features used in the process. In this study we propose a method that can automatically detect, and exclude regions with many fat droplets by using the feature values of colors, shapes and the arrangement of cell nuclei. We implement the method and confirm that it can accurately detect fat droplets and quantify the fat droplet ratio of actual images. This investigation also clarifies the effective characteristics that contribute to accurate detection.

  16. 28 CFR 17.26 - Derivative classification.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...2011-07-01 2011-07-01 false Derivative classification. 17.26 Section...Classified Information § 17.26 Derivative classification. (a) Persons...classification guides. (b) Persons who apply derivative classification markings shall...

  17. 28 CFR 17.26 - Derivative classification.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...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...

  18. Trophic phylogenetics: evolutionary influences on body size, feeding, and species associations in grassland arthropods.

    PubMed

    Lind, Eric M; Vincent, John B; Weiblen, George D; Cavender-Bares, Jeannine; Borer, Elizabeth T

    2015-04-01

    Contemporary animal-plant interactions such as herbivory are widely understood to be shaped by evolutionary history. Yet questions remain about the role of plant phylogenetic diversity in generating and maintaining herbivore diversity, and whether evolutionary relatedness of producers might predict the composition of consumer communities. We tested for evidence of evolutionary associations among arthropods and the plants on which they were found, using phylogenetic analysis of naturally occurring arthropod assemblages sampled from a plant-diversity manipulation experiment. Considering phylogenetic relationships among more than 900 arthropod consumer taxa and 29 plant species in the experiment, we addressed several interrelated questions. First, our results support the hypothesis that arthropod functional traits such as body size and trophic role are phylogenetically conserved in community ecological samples. Second, herbivores tended to cooccur with closer phylogenetic relatives than would be expected at random, whereas predators and parasitoids did not show phylogenetic association patterns. Consumer specialization, as measured by association through time with monocultures of particular host plant species, showed significant phylogenetic signal, although the. strength of this association varied among plant species. Polycultures of phylogenetically dissimilar plant species supported more phylogenetically dissimilar consumer communities than did phylogenetically similar polycultures. Finally, we separated the effects of plant species richness and relatedness in predicting the phylogenetic distribution of the arthropod assemblages in this experiment. The phylogenetic diversity of plant communities predicted the phylogenetic diversity of herbivore communities even after accounting for plant species richness. The phylogenetic diversity of secondary consumers differed by guild, with predator phylogenetic diversity responding to herbivore relatedness, while parasitoid phylogenetic diversity was driven by plant relatedness. Evolutionary associations between plants and their consumers are apparent in plots only meters apart in a single field, indicating a strong role for host-plant phylogenetic diversity in sustaining landscape consumer biodiversity. PMID:26230020

  19. Molecular phylogenetics and species delimitation of leaf-toed geckos (Phyllodactylidae: Phyllodactylus) throughout the Mexican tropical dry forest.

    PubMed

    Blair, Christopher; Méndez de la Cruz, Fausto R; Law, Christopher; Murphy, Robert W

    2015-03-01

    Methods and approaches for accurate species delimitation continue to be a highly controversial subject in the systematics community. Inaccurate assessment of species' limits precludes accurate inference of historical evolutionary processes. Recent evidence suggests that multilocus coalescent methods show promise in delimiting species in cryptic clades. We combine multilocus sequence data with coalescence-based phylogenetics in a hypothesis-testing framework to assess species limits and elucidate the timing of diversification in leaf-toed geckos (Phyllodactylus) of Mexico's dry forests. Tropical deciduous forests (TDF) of the Neotropics are among the planet's most diverse ecosystems. However, in comparison to moist tropical forests, little is known about the mode and tempo of biotic evolution throughout this threatened biome. We find increased speciation and substantial, cryptic molecular diversity originating following the formation of Mexican TDF 30-20million years ago due to orogenesis of the Sierra Madre Occidental and Mexican Volcanic Belt. Phylogenetic results suggest that the Mexican Volcanic Belt, the Rio Fuerte, and Isthmus of Tehuantepec may be important biogeographic barriers. Single- and multilocus coalescent analyses suggest that nearly every sampling locality may be a distinct species. These results suggest unprecedented levels of diversity, a complex evolutionary history, and that the formation and expansion of TDF vegetation in the Miocene may have influenced subsequent cladogenesis of leaf-toed geckos throughout western Mexico. PMID:25620603

  20. The Classification Conundrum.

    ERIC Educational Resources Information Center

    Granger, Charles R.

    1983-01-01

    Argues against the five-kingdom scheme of classification as using inconsistent criteria, ending up with divisions that are forced, not natural. Advocates an approach using cell type/complexity and modification of the metabolic machinery, recommending the five-kingdom scheme as starting point for class discussion on taxonomy and its conceptual…

  1. Equivalent Diagnostic Classification Models

    ERIC Educational Resources Information Center

    Maris, Gunter; Bechger, Timo

    2009-01-01

    Rupp and Templin (2008) do a good job at describing the ever expanding landscape of Diagnostic Classification Models (DCM). In many ways, their review article clearly points to some of the questions that need to be answered before DCMs can become part of the psychometric practitioners toolkit. Apart from the issues mentioned in this article that…

  2. Improving Student Question Classification

    ERIC Educational Resources Information Center

    Heiner, Cecily; Zachary, Joseph L.

    2009-01-01

    Students in introductory programming classes often articulate their questions and information needs incompletely. Consequently, the automatic classification of student questions to provide automated tutorial responses is a challenging problem. This paper analyzes 411 questions from an introductory Java programming course by reducing the natural…

  3. Shark Teeth Classification

    ERIC Educational Resources Information Center

    Brown, Tom; Creel, Sally; Lee, Velda

    2009-01-01

    On a recent autumn afternoon at Harmony Leland Elementary in Mableton, Georgia, students in a fifth-grade science class investigated the essential process of classification--the act of putting things into groups according to some common characteristics or attributes. While they may have honed these skills earlier in the week by grouping their own…

  4. The Biglan Classification Revisited.

    ERIC Educational Resources Information Center

    Stoecker, Judith L.

    This study replicated previous research that tested the validity of A. Biglan's classification scheme, a theoretical framework for empirically examining the differences among academic disciplines and classifying them according to three dimensions (hard-soft, pure-applied, life-nonlife). In addition, new data were used to attempt continued…

  5. Normal Cell-Type Epigenetics and Breast Cancer Classification: A Case Study of Cell Mixture–Adjusted Analysis of DNA Methylation Data from Tumors

    PubMed Central

    Houseman, Eugene Andrés; Ince, Tan A

    2014-01-01

    Historically, breast cancer classification has relied on prognostic subtypes. Thus, unlike hematopoietic cancers, breast tumor classification lacks phylogenetic rationale. The feasibility of phylogenetic classification of breast tumors has recently been demonstrated based on estrogen receptor (ER), androgen receptor (AR), vitamin D receptor (VDR) and Keratin 5 expression. Four hormonal states (HR0–3) comprising 11 cellular subtypes of breast cells have been proposed. This classification scheme has been shown to have relevance to clinical prognosis. We examine the implications of such phylogenetic classification on DNA methylation of both breast tumors and normal breast tissues by applying recently developed deconvolution algorithms to three DNA methylation data sets archived on Gene Expression Omnibus. We propose that breast tumors arising from a particular cell-of-origin essentially magnify the epigenetic state of their original cell type. We demonstrate that DNA methylation of tumors manifests patterns consistent with cell-specific epigenetic states, that these states correspond roughly to previously posited normal breast cell types, and that estimates of proportions of the underlying cell types are predictive of tumor phenotypes. Taken together, these findings suggest that the epigenetics of breast tumors is ultimately based on the underlying phylogeny of normal breast tissue. PMID:25574126

  6. Classification of Surgical Complications

    PubMed Central

    Dindo, Daniel; Demartines, Nicolas; Clavien, Pierre-Alain

    2004-01-01

    Objective: Although quality assessment is gaining increasing attention, there is still no consensus on how to define and grade postoperative complications. This shortcoming hampers comparison of outcome data among different centers and therapies and over time. Patients and Methods: A classification of complications published by one of the authors in 1992 was critically re-evaluated and modified to increase its accuracy and its acceptability in the surgical community. Modifications mainly focused on the manner of reporting life-threatening and permanently disabling complications. The new grading system still mostly relies on the therapy used to treat the complication. The classification was tested in a cohort of 6336 patients who underwent elective general surgery at our institution. The reproducibility and personal judgment of the classification were evaluated through an international survey with 2 questionnaires sent to 10 surgical centers worldwide. Results: The new ranking system significantly correlated with complexity of surgery (P < 0.0001) as well as with the length of the hospital stay (P < 0.0001). A total of 144 surgeons from 10 different centers around the world and at different levels of training returned the survey. Ninety percent of the case presentations were correctly graded. The classification was considered to be simple (92% of the respondents), reproducible (91%), logical (92%), useful (90%), and comprehensive (89%). The answers of both questionnaires were not dependent on the origin of the reply and the level of training of the surgeons. Conclusions: The new complication classification appears reliable and may represent a compelling tool for quality assessment in surgery in all parts of the world. PMID:15273542

  7. Efficient Fingercode Classification

    NASA Astrophysics Data System (ADS)

    Sun, Hong-Wei; Law, Kwok-Yan; Gollmann, Dieter; Chung, Siu-Leung; Li, Jian-Bin; Sun, Jia-Guang

    In this paper, we present an efficient fingerprint classification algorithm which is an essential component in many critical security application systems e. g. systems in the e-government and e-finance domains. Fingerprint identification is one of the most important security requirements in homeland security systems such as personnel screening and anti-money laundering. The problem of fingerprint identification involves searching (matching) the fingerprint of a person against each of the fingerprints of all registered persons. To enhance performance and reliability, a common approach is to reduce the search space by firstly classifying the fingerprints and then performing the search in the respective class. Jain et al. proposed a fingerprint classification algorithm based on a two-stage classifier, which uses a K-nearest neighbor classifier in its first stage. The fingerprint classification algorithm is based on the fingercode representation which is an encoding of fingerprints that has been demonstrated to be an effective fingerprint biometric scheme because of its ability to capture both local and global details in a fingerprint image. We enhance this approach by improving the efficiency of the K-nearest neighbor classifier for fingercode-based fingerprint classification. Our research firstly investigates the various fast search algorithms in vector quantization (VQ) and the potential application in fingerprint classification, and then proposes two efficient algorithms based on the pyramid-based search algorithms in VQ. Experimental results on DB1 of FVC 2004 demonstrate that our algorithms can outperform the full search algorithm and the original pyramid-based search algorithms in terms of computational efficiency without sacrificing accuracy.

  8. Converting Endangered Species Categories to Probabilities of Extinction for Phylogenetic Conservation

    E-print Network

    Mooers, Arne

    Converting Endangered Species Categories to Probabilities of Extinction for Phylogenetic) Converting Endangered Species Categories to Probabilities of Extinction for Phylogenetic Conservation Wildlife in Canada when ranking species under the Canadian Species at Risk Act (see www

  9. Analyses of 32 Loci Clarify Phylogenetic Relationships among Trypanosoma cruzi Lineages and Support a

    E-print Network

    Machado, Carlos A.

    Analyses of 32 Loci Clarify Phylogenetic Relationships among Trypanosoma cruzi Lineages and Support: The genetic diversity of Trypanosoma cruzi, the etiological agent of Chagas disease, has been traditionally Clarify Phylogenetic Relationships among Trypanosoma cruzi Lineages and Support a Single Hybridization

  10. Markov chain Monte Carlo and its applications to phylogenetic tree construction

    E-print Network

    Luczynska, Marta Magdalena

    2007-01-01

    This thesis addresses the application of Bayesian methods to problems in phylogenetics. Specifically, we focus on using genetic data to estimate phylogenetic trees representing the evolutionary history of genes and species. ...

  11. Phylogenetic analysis of tribe habrolepidini and revision of Homalopoda and Ceraptroceroideus (Hymenoptera: Encyrtidae) 

    E-print Network

    Rodriguez Velez, Beatriz

    2006-04-12

    A taxonomic and phylogenetic study of the tribe Habrolepidini is described. A cladistic analysis was carried out in order to establish the phylogenetic relationships of the supraspecific taxa of the tribe. An illustrated ...

  12. Phylogenetic methodology for detecting protein interactions.

    PubMed

    Waddell, Peter J; Kishino, Hirohisa; Ota, Rissa

    2007-03-01

    Detecting protein-protein interactions and assigning proteins to functional complexes are key challenges of modern biology. The rise of genomics has lead to evidence that correlated patterns of presence/absence and/or fusing of proteins in any organism suggest these proteins interact. Unfortunately, methods based on such data work best with divergent genomes, whereas major sequencing efforts in vertebrates, for example, are yielding alignments of the same set of proteins sampled from the same set of taxa (species). Using vertebrate mitochondrial genomes to illustrate a novel method, we associate proteins based on vectors of their evolutionary tree edge (branch or internode) lengths. This approach is based on the expectation that molecular coevolution is greatest between proteins that interact in some way. Mitochondrial DNA-encoded proteins are associated into groups largely consistent with the complexes they come from. This association is apparently not due to the tree structure or mutation processes, leaving coevolution as the best explanation. We show that it is important that the tree used to derive the edge-length vector is estimated accurately in terms of both topology and edge lengths. Although more complex substitution models reduce systematic error, they also inflate stochastic error. This makes the use of less complex substitution models preferable in some circumstances. We describe a method to estimate correlations of pairwise evolutionary distances, which adjusts for non-independent correlations due to shared evolutionary history. Associations of proteins based on their edge-length vectors are visualized and assessed using a variety of hierarchical clustering and multidimensional scaling methods. New formula for estimating the fit of data to model, including the average percent standard deviation of distances on least squares trees, are presented. Use of edge-length vectors is compared and contrasted with correlated distance methods, correlated rates methods, and site-specific evidence of coevolution. PMID:17158779

  13. BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

    PubMed Central

    Satija, Rahul; Novák, Ádám; Miklós, István; Lyngsø, Rune; Hein, Jotun

    2009-01-01

    Background We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. Results We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the ?-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. Conclusion BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from PMID:19715598

  14. Bioproducts from diverse phylogenetic clades of Aureobasidium pullulans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    More than 90 isolates of the fungus A. pullulans from tropical and temperate climates were classified into 13 phylogenetic clades using multilocus sequence analyses (ITS, IGS, BT2, RPB2, and EF-1a). Tropical isolates appeared to exhibit the greatest genetic diversity. Representatives of each clade...

  15. A Structural EM Algorithm for Phylogenetic Inference Nir Friedman

    E-print Network

    Batzoglou, Serafim

    Science & Engineering Hebrew University Jerusalem, 91904, Israel ninio@cs.huji.ac.il Itsik Pe'er School and real sequence data, and show that for protein sequences even our basic algorithm finds more plausible are dramatically faster than such methods, enabling, for the first time, phylogenetic analysis of large protein

  16. A Structural EM Algorithm for Phylogenetic Inference # Nir Friedman +

    E-print Network

    Friedman, Nir

    Science & Engineering Hebrew University Jerusalem, 91904, Israel ninio@cs.huji.ac.il Itsik Pe'er School and real sequence data, and show that for protein sequences even our basic algorithm finds more plausible are dramatically faster than such methods, enabling, for the first time, phylogenetic analysis of large protein

  17. Mitochondrial DNA phylogenetic analysis of Myrmecolacidae (Insecta: Strepsiptera) va 

    E-print Network

    Halbert, Natalie Rose

    2013-02-22

    Popondetta (POP). Elenchus japonicus (Strepsiptera: Elenchidae) was used as an outgroup to generate a phylogenetic tree of the COI region. Analysis of the 12S region showed 37% variation between the C. fenyesi male and putative female, 0.3% variation between...

  18. Preliminary phylogenetic analysis of the fern genus Lomariopsis (Lomariopsidaceae)

    E-print Network

    Preliminary phylogenetic analysis of the fern genus Lomariopsis (Lomariopsidaceae) Germinal Rouhan1 the first phylogeny for the genus. Key words: Ferns, biogeography, phylogeny, taxonomy, leaf development, Bronx, NY 10458-5126 U.S.A. #12;Lomariopsis Fée is a pantropical fern genus with a few extensions

  19. Phylogenetic Relationships of the Enigmatic Malesian Fern Thylacopteris (Polypodiaceae, Polypodiidae)

    E-print Network

    Schneider, Harald; Janssen, Thomas; Hovenkamp, Peter; Smith, Alan R.; Cranfill, Raymond; Haufler, Christopher H.; Ranker, Tom A.

    2004-11-01

    Thylacopteris is the sister to a diverse clade of polygrammoid ferns that occurs mainly in Southeast Asia and Malesia. The phylogenetic relationships are inferred from DNA sequences of three chloroplast genome regions (rbcL, rps4, rps4?trnS IGS...

  20. PHENOLOGY MILWAUKEE 2012 A phylogenetic comparative study of flowering phenology

    E-print Network

    Dhindsa, Rajinder

    PHENOLOGY ­ MILWAUKEE 2012 A phylogenetic comparative study of flowering phenology along environmental conditions. We explored the time of the first appearance of flowers (first flowering day, FFD) and flowering duration across subarctic species composing different commu- nities, from boreal forest to tundra

  1. MOLECULAR PHYLOGENETIC EXPLORATIONS OF NATURAL MICROBIAL COMMUNITY COMPOSITION AND DIVERSITY

    EPA Science Inventory

    Comparative sequence analysis of ribosomal RNA molecules has let to a phylogenetic-based approach to characterize natural microbial communities. he approach has been applied to study natural communities of sulfate-reducing bacteria, hybridization probes were used to measure relat...

  2. Phylogenetic analysis and alignment of behavioral sequences by direct optimization

    E-print Network

    Phylogenetic analysis and alignment of behavioral sequences by direct optimization Tony Robillard1 Paris cedex 05, France; 2 University of Missouri, Division of Biological Sciences, 215 Tucker Hall, Columbia, MO 65211, USA Accepted 28 June 2006 Abstract We propose a new approach to consider behavioral

  3. Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily

    PubMed Central

    Lakshmi, Balasubramanian; Mishra, Madhulika; Srinivasan, Narayanaswamy; Archunan, Govindaraju

    2015-01-01

    Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity. PMID:26263546

  4. Phylogenetic Relationships within Cation Transporter Families of Arabidopsis1

    E-print Network

    Sze, Heven

    and alkali cations across plant plasma and organellar membranes is essential for plant growth, developmentPhylogenetic Relationships within Cation Transporter Families of Arabidopsis1 Pascal Ma¨ser2 , Se, and development. Approximately 5% of the Arabidopsis genome appears to encode mem- brane transport proteins

  5. Evolution & Phylogenetic Analysis: Classroom Activities for Investigating Molecular & Morphological Concepts

    ERIC Educational Resources Information Center

    Franklin, Wilfred A.

    2010-01-01

    In a flexible multisession laboratory, students investigate concepts of phylogenetic analysis at both the molecular and the morphological level. Students finish by conducting their own analysis on a collection of skeletons representing the major phyla of vertebrates, a collection of primate skulls, or a collection of hominid skulls.

  6. Phylogenetic Divergence Time, Algorithms for Improved Accuracy and Performance 

    E-print Network

    Crosby, Ralph

    2015-07-28

    in the specification of model parameters that is not completely understood. These parameters include both the topology of the phylogenetic tree and, more importantly for our purposes, the set of fossils used to calibrate the tree. In this work, we present new...

  7. Cancer Phylogenetics from Single-Cell Assays Gregory Pennington

    E-print Network

    Cancer Phylogenetics from Single-Cell Assays Gregory Pennington Stanley Shackney Russell Schwartz of possible ways different genetic lesions might uncouple cell growth from normal controls. Two cancers the Carnegie Mellon University Berkman Faculty Development Fund. #12;Keywords: computational biology, cancer

  8. Phylogenetics of modern birds in the era of genomics

    E-print Network

    Edwards, Scott

    Review Phylogenetics of modern birds in the era of genomics Scott V. Edwards*, W. Bryan Jennings and maturation of the genomics era, the completion of the chicken genome and a suite of technologies that promise genomics strategies, including adoption of objective quality scores for sequence data, analysis

  9. Origin, evolution, and biogeography of Juglans: a phylogenetic perspective

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phylogenetic analyses of extant Juglans (Juglandaceae) using five cpDNA intergenic spacer (IGS) sequences (trnT-trnF, psbA-trnH, atpB-rbcL, trnV-16S rRNA, and trnS-trnfM) were performed to elucidate the origin, diversification, historical biogeography, and evolutionary relationships within the genus...

  10. Phylogenetic constraint on male parental care in the dabbling ducks

    E-print Network

    Johnson, Kevin P.

    Phylogenetic constraint on male parental care in the dabbling ducks Kevin P. Johnson1 {, Frank Mc changes in male parental care behaviour in the dabbling ducks (family: Anatidae; tribe: Anatini) using and Southern hemisphere dabbling ducks but is lacking in all Northern hemisphere species. Southern hemisphere

  11. Systematic Conservation Planning for Groundwater Ecosystems Using Phylogenetic Diversity

    PubMed Central

    Asmyhr, Maria G.; Linke, Simon; Hose, Grant; Nipperess, David A.

    2014-01-01

    Aquifer ecosystems provide a range of important services including clean drinking water. These ecosystems, which are largely inaccessible to humans, comprise a distinct invertebrate fauna (stygofauna), which is characterized by narrow distributions, high levels of endemism and cryptic species. Although being under enormous anthropogenic pressure, aquifers have rarely been included in conservation planning because of the general lack of knowledge of species diversity and distribution. Here we use molecular sequence data and phylogenetic diversity as surrogates for stygofauna diversity in aquifers of New South Wales, Australia. We demonstrate how to incorporate these data as conservation features in the systematic conservation planning software Marxan. We designated each branch of the phylogenetic tree as a conservation feature, with the branch length as a surrogate for the number of distinct characters represented by each branch. Two molecular markers (nuclear 18S ribosomal DNA and mitochondrial cytochrome oxidase subunit I) were used to evaluate how marker variability and the resulting tree topology affected the site-selection process. We found that the sites containing the deepest phylogenetic branches were deemed the most irreplaceable by Marxan. By integrating phylogenetic data, we provide a method for including taxonomically undescribed groundwater fauna in systematic conservation planning. PMID:25514422

  12. A PHYLOGENETIC ANALYSIS OF SEXUAL SIZE DIMORPHISM J. STEPHEN GOSNELL

    E-print Network

    Blob, Richard W.

    evident in turtles, as predicted by life-history theory. Key words: Egg size; Evolution; FecundityA PHYLOGENETIC ANALYSIS OF SEXUAL SIZE DIMORPHISM IN TURTLES J. STEPHEN GOSNELL 1,2,3 , GABRIEL presence has been associated with a range of evolutionary and ecological factors. Turtles, as a lineage

  13. Molecular evidence on the origin of and the phylogenetic relationships

    E-print Network

    Zardoya, Rafael

    for comparative studies in this group. The first major landmark in vertebrate evolution was the origin of jaws, turtles, squamates, crocodiles, and birds) (Fig. 18.1). The origin of amniotes dates back evolution of each lineage. In the particular case of vertebrates, the relative phylogenetic positions

  14. A Deliberate Practice Approach to Teaching Phylogenetic Analysis

    ERIC Educational Resources Information Center

    Hobbs, F. Collin; Johnson, Daniel J.; Kearns, Katherine D.

    2013-01-01

    One goal of postsecondary education is to assist students in developing expert-level understanding. Previous attempts to encourage expert-level understanding of phylogenetic analysis in college science classrooms have largely focused on isolated, or "one-shot," in-class activities. Using a deliberate practice instructional approach, we…

  15. Identifying optimal incomplete phylogenetic data sets from sequence databases

    E-print Network

    Sanderson, Michael J.

    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 on the graph the- oretic concept of a-quasi-bicliques. The quasi-biclique method searches large sequence

  16. Complete mitogenome of asiatic lion resolves phylogenetic status within Panthera

    PubMed Central

    2013-01-01

    Background The origin, evolution and speciation of the lion, has been subject of interest, debate and study. The present surviving lions of the genus Panthera comprise of eight sub-species inclusive of Asiatic lion Panthera leo persica of India's Gir forest. Except for the Asiatic lion, the other seven subspecies are found in different parts of Africa. There have been different opinions regarding the phylogenetic status of Panthera leo, as well as classifying lions of different geographic regions into subspecies and races. In the present study, mitogenome sequence of P. leo persica deduced, using Ion Torrent PGM to assess phylogeny and evolution which may play an increasingly important role in conservation biology. Results The mtDNA sequence of P. leo persica is 17,057 bp in length with 40.8% GC content. Annotation of mitogenome revealed total 37 genes, including 13 protein coding, 2 rRNA and 22 tRNA. Phylogenetic analysis based on whole mitogenome, suggests Panthera pardus as a neighbouring species to P. leo with species divergence at ~2.96 mya. Conclusion This work presents first report on complete mitogenome of Panthera leo persica. It sheds light on the phylogenetic and evolutionary status within and across Felidae members. The result compared and evaluated with earlier reports of Felidae shows alteration of phylogenetic status and species evolution. This study may provide information on genetic diversity and population stability. PMID:23968279

  17. Ceftolozane-Tazobactam Activity against Phylogenetically Diverse Clostridium difficile Strains.

    PubMed

    Gonzalez, Mark D; Wallace, Meghan A; Hink, Tiffany; Dubberke, Erik R; Burnham, Carey-Ann D

    2015-11-01

    Ceftolozane-tazobactam (C/T) is approved for the treatment of complicated intra-abdominal and urinary tract infections and has varied activity against anaerobic bacteria. Here, we evaluate the activity of C/T against a phylogenetically diverse collection of Clostridium difficile isolates and report uniformly high MICs (?256 ?g/ml) to C/T. PMID:26282409

  18. A phylogenetic perspective on the distribution of plant diversity

    E-print Network

    Saleska, Scott

    of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, P. O. Box 208106 historical biogeography climate change The rise of phylogenetic biology has revolutionized the study of molecular data were partly a function of the belief that molecular characters were less subject to selection

  19. parison with other proposed phylogenetic placements of monotremes (Fig. 4).

    E-print Network

    parison with other proposed phylogenetic placements of monotremes (Fig. 4). As noted earlier of these taxa with respect to true mammals (monotremes and theriiforms), none provides unequivocal support crown pattern, similar to that of the Early Cretaceous (Albian) monotreme Steropodon and the Cenozoic

  20. A phylogenetic analysis of the megadiverse Chalcidoidea (Hymenoptera)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chalcidoidea (Hymenoptera) are extremely diverse with an estimated 500,000 species. We present the first phylogenetic analysis of the superfamily based on a cladistic analysis of both morphological and molecular data. A total of 233 morphological characters were scored for 300 taxa and 265 genera, a...

  1. Land-Sparing Agriculture Best Protects Avian Phylogenetic Diversity.

    PubMed

    Edwards, David P; Gilroy, James J; Thomas, Gavin H; Uribe, Claudia A Medina; Haugaasen, Torbjørn

    2015-09-21

    The conversion of natural habitats to farmland is a major driver of the global extinction crisis. Two strategies are promoted to mitigate the impacts of agricultural expansion on biodiversity: land sharing integrates wildlife-friendly habitats within farmland landscapes, and land sparing intensifies farming to allow the offset of natural reserves. A key question is which strategy would protect the most phylogenetic diversity--the total evolutionary history shared across all species within a community. Conserving phylogenetic diversity decreases the chance of losing unique phenotypic and ecological traits and provides benefits for ecosystem function and stability. Focusing on birds in the threatened Chocó-Andes hotspot of endemism, we tested the relative benefits of each strategy for retaining phylogenetic diversity in tropical cloud forest landscapes threatened by cattle pastures. Using landscape simulations, we find that land sharing would protect lower community-level phylogenetic diversity than land sparing and that with increasing distance from forest (from 500 to >1,500 m), land sharing is increasingly inferior to land sparing. Isolation from forest also leads to the loss of more evolutionarily distinct species from communities within land-sharing landscapes, which can be avoided with effective land sparing. Land-sharing policies that promote the integration of small-scale wildlife-friendly habitats might be of limited benefit without the simultaneous protection of larger blocks of natural habitat, which is most likely to be achieved via land-sparing measures. PMID:26344093

  2. PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic

    E-print Network

    Jensen, Shane T.

    PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes Dongsheng Che1, this popular strategy may not be directly applicable to prokaryotic genomes, where typically about half binding sites in prokaryotes. The prediction software package PFP is available at http

  3. Taxonomic, phylogenetic, and trait Beta diversity in South American hummingbirds.

    PubMed

    Weinstein, Ben G; Tinoco, Boris; Parra, Juan Luis; Brown, Leone M; McGuire, Jimmy A; Stiles, F Gary; Graham, Catherine H

    2014-08-01

    Comparison of the taxonomic, phylogenetic, and trait dimensions of beta diversity may uncover the mechanisms that generate and maintain biodiversity, such as geographic isolation, environmental filtering, and convergent adaptation. We developed an approach to predict the relationship between environmental and geographic distance and the dimensions of beta diversity. We tested these predictions using hummingbird assemblages in the northern Andes. We expected taxonomic beta diversity to result from recent geographic barriers limiting dispersal, and we found that cost distance, which includes barriers, was a better predictor than Euclidean distance. We expected phylogenetic beta diversity to result from historical connectivity and found that differences in elevation were the best predictors of phylogenetic beta diversity. We expected high trait beta diversity to result from local adaptation to differing environments and found that differences in elevation were correlated with trait beta diversity. When combining beta diversity dimensions, we observe that high beta diversity in all dimensions results from adaption to different environments between isolated assemblages. Comparisons with high taxonomic, low phylogenetic, and low trait beta diversity occurred among lowland assemblages separated by the Andes, suggesting that geographic barriers have recently isolated lineages in similar environments. We provide insight into mechanisms governing hummingbird biodiversity patterns and provide a framework that is broadly applicable to other taxonomic groups. PMID:25058281

  4. Serologic and hexon phylogenetic analysis of ruminant adenoviruses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objectives of this study were to determine the antigenic relationship among ruminant adenoviruses and determine their phylogenetic relationship based on the deduced hexon gene amino acid sequence. Results of reciprocal cross-neutralization tests demonstrated antigenic relationships in either on...

  5. Estimating phylogenetic trees from genome-scale data.

    PubMed

    Liu, Liang; Xi, Zhenxiang; Wu, Shaoyuan; Davis, Charles C; Edwards, Scott V

    2015-12-01

    The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as "species tree" methods have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Here we review theory and empirical examples that help clarify conflicts between species tree and concatenation methods, and misconceptions in the literature about the performance of species tree methods. Considering concatenation as a special case of the multispecies coalescent model helps explain differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences and long-branch attraction. We show that approaches, such as binning, designed to augment the signal in species tree analyses can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods incorporating biological realism are a key to phylogenetic analysis of whole-genome data. PMID:25873435

  6. Position: Postdoctoral Research Associate Position Available in Honey Bee Phylogenetics

    E-print Network

    Ishida, Yuko

    Position: Postdoctoral Research Associate Position Available in Honey Bee Phylogenetics Date, 32611-0629 http://entnemdept.ifas.ufl.edu/honeybee/index.shtml Appointment: The position is full. Position Description: We seek to appoint a highly motivated Postdoctoral Researcher to coordinate the HBREL

  7. 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. The implementation of new or modified algorithms for handling large sequence datasets is paramount to our that it rapidly becomes prohibitive to analyze all possible tree topologies for a modestly sized dataset. Since MP

  8. RESEARCH ARTICLE Open Access Phylogenetic patterns of emergence of new

    E-print Network

    Zhang, Jianzhi

    paralogous genes or gene families [4,5]. It has been proposed that orphan genes are likely to play a major this second possibility seemed initially rather un- likely, such genes have been found in Drosophila [8RESEARCH ARTICLE Open Access Phylogenetic patterns of emergence of new genes support a model

  9. A Deliberate Practice Approach to Teaching Phylogenetic Analysis

    PubMed Central

    Hobbs, F. Collin; Johnson, Daniel J.; Kearns, Katherine D.

    2013-01-01

    One goal of postsecondary education is to assist students in developing expert-level understanding. Previous attempts to encourage expert-level understanding of phylogenetic analysis in college science classrooms have largely focused on isolated, or “one-shot,” in-class activities. Using a deliberate practice instructional approach, we designed a set of five assignments for a 300-level plant systematics course that incrementally introduces the concepts and skills used in phylogenetic analysis. In our assignments, students learned the process of constructing phylogenetic trees through a series of increasingly difficult tasks; thus, skill development served as a framework for building content knowledge. We present results from 5 yr of final exam scores, pre- and postconcept assessments, and student surveys to assess the impact of our new pedagogical materials on student performance related to constructing and interpreting phylogenetic trees. Students improved in their ability to interpret relationships within trees and improved in several aspects related to between-tree comparisons and tree construction skills. Student feedback indicated that most students believed our approach prepared them to engage in tree construction and gave them confidence in their abilities. Overall, our data confirm that instructional approaches implementing deliberate practice address student misconceptions, improve student experiences, and foster deeper understanding of difficult scientific concepts. PMID:24297294

  10. Short Communication Phylogenetic relationships of leopard frogs (Rana pipiens complex)

    E-print Network

    Markow, Therese

    Short Communication Phylogenetic relationships of leopard frogs (Rana pipiens complex) from June 2008 Available online xxxx Keywords: Control region Cryptic species Mexican leopard frogs the control region and 12S rRNA in leopard frogs from the Sierra El Aguaje of southern Sonora, Mexico

  11. Phylogenetic sequence of metabolic pathways in Precambrian cellular life

    NASA Technical Reports Server (NTRS)

    Barnabas, J.; Schwartz, R. M.; Dayhoff, M. O.

    1981-01-01

    A sequence of major metabolic events is presented as they may have appeared during prokaryote evolution. This is based on (1) the phylogenetic schema derived from sequences of bacterial ferredoxin, 2Fe-2S ferredoxin, 5S ribosomal RNA, and c-type cytochromes; (2) metabolic settings in which these macromolecules are found; and (3) metabolic capabilities of the prokaryotes that carry these molecules.

  12. Gene tree discordance, phylogenetic inference and the multispecies

    E-print Network

    Rosenberg, Noah

    Gene tree discordance, phylogenetic inference and the multispecies coalescent James H. Degnan1 histories often exist in different genes throughout the genome. Recent advances in genealogi- cal modeling occur- ring genomic variability in evolutionary histories. The problem of gene tree discordance Until

  13. Multispectral rock-type separation and classification.

    SciTech Connect

    Moya, Mary M.; Fogler, Robert Joseph; Paskaleva, Biliana; Hayat, Majeed M.

    2004-06-01

    This paper explores the possibility of separating and classifying remotely-sensed multispectral data from rocks and minerals onto seven geological rock-type groups. These groups are extracted from the general categories of metamorphic, igneous and sedimentary rocks. The study is performed under ideal conditions for which the data is generated according to laboratory hyperspectral data for the members, which are, in turn, passed through the Multi-spectral Thermal Imager (MTI) filters yielding 15 bands. The main challenge in separability is the small size of the training data sets, which initially did not permit direct application of Bayesian decision theory. To enable Bayseian classification, the original training data is linearly perturbed with the addition minerals, vegetation, soil, water and other valid impurities. As a result, the size of the training data is significantly increased and accurate estimates of the covariance matrices are achieved. In addition, a set of reduced (five) linearly-extracted canonical features that are optimal in providing the most important information about the data is determined. An alternative nonlinear feature-selection method is also employed based on spectral indices comprising a small subset of all possible ratios between bands. By applying three optimization strategies, combinations of two and three ratios are found that provide reliable separability and classification between all seven groups according to the Bhattacharyya distance. To set a benchmark to which the MTI capability in rock classification can be compared, an optimization strategy is performed for the selection of optimal multispectral filters, other than the MTI filters, and an improvement in classification is predicted.

  14. A higher level classification of all living organisms.

    PubMed

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

    2015-01-01

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

  15. A Higher Level Classification of All Living Organisms

    PubMed Central

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

    2015-01-01

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

  16. Accurate time-frequency-wavenumber analysis to study coda waves

    NASA Astrophysics Data System (ADS)

    Schisselé, Estelle; Guilbert, Jocelyn; Gaffet, Stéphane; Cansi, Yves

    2004-08-01

    An accurate method is developed to characterize the seismic coda phases recorded by small-aperture arrays. The coda is modelled as a superposition of several interfering wavelets identified by their arrival time, frequency content, backazimuth and apparent velocity of propagation. The wavelets are caused by the diffraction and refraction of the direct wavefield by heterogeneities of the propagation medium. The deterministic modelling is different from the statistical one generally used to retrieve mean parameters of the medium. As the complexity of the medium increases, separation of interfering wavelets needs an accurate time-frequency-wavenumber decomposition method that consists of detection and characterization of the different coherent wavelets propagating through the array. Detection is realized by mean time-frequency decomposition, based on the ridges algorithm. The MUltiple SIgnal Classification (MUSIC) algorithm, allowing a higher separation of simultaneous wavelets in the wavenumber domain, is then used to characterize the propagation parameters of the detected components. An optimal use of the MUSIC algorithm assumes the knowledge of the number of sources that simultaneously propagate through the array. The new iterative technique presented here allows the automatic determination of this number of sources. This methodology is applied to synthetic signals simulated in a heterogeneous medium. Results obtained show that: (i) the diffracted wavefield may be more energetic than the primary direct one and (ii) the relative energy diffracted by each heterogeneity is strongly dependent on the location of the array within the medium. The well-controlled results obtained for the synthetic examples allow interpretations of the observations made during the Annot experiment in the southern French Alps in 1998, where four small-aperture arrays were deployed, with small distances between each array (~10 km). The time-azimuth-velocity evolutions determined for the earthquakes recorded during this experiment are used to characterize the heterogeneous structures of the medium.

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

    PubMed Central

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

    2011-01-01

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

  18. Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling

    PubMed Central

    2011-01-01

    Background With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and classification of Characidae is currently uncertain, despite significant efforts based on analysis of morphological and molecular data. No consensus about the monophyly of this group or its position within the order Characiformes has been reached, challenged by the fact that many key studies to date have non-overlapping taxonomic representation and focus only on subsets of this diversity. Results In the present study we propose a new definition of the family Characidae and a hypothesis of relationships for the Characiformes based on phylogenetic analysis of DNA sequences of two mitochondrial and three nuclear genes (4,680 base pairs). The sequences were obtained from 211 samples representing 166 genera distributed among all 18 recognized families in the order Characiformes, all 14 recognized subfamilies in the Characidae, plus 56 of the genera so far considered incertae sedis in the Characidae. The phylogeny obtained is robust, with most lineages significantly supported by posterior probabilities in Bayesian analysis, and high bootstrap values from maximum likelihood and parsimony analyses. Conclusion A monophyletic assemblage strongly supported in all our phylogenetic analysis is herein defined as the Characidae and includes the characiform species lacking a supraorbital bone and with a derived position of the emergence of the hyoid artery from the anterior ceratohyal. To recognize this and several other monophyletic groups within characiforms we propose changes in the limits of several families to facilitate future studies in the Characiformes and particularly the Characidae. This work presents a new phylogenetic framework for a speciose and morphologically diverse group of freshwater fishes of significant ecological and evolutionary importance across the Neotropics and portions of Africa. PMID:21943181

  19. Revisiting the phylogenetic relationships, biogeography, and taxonomy of spider monkeys (genus Ateles) in light of new molecular data.

    PubMed

    Morales-Jimenez, Alba Lucia; Disotell, Todd; Di Fiore, Anthony

    2015-01-01

    Spider monkeys (Ateles) are one of the most endangered groups of primates in the Neotropics. The genus is widely distributed from Mexico to the north of Bolivia and includes many morphologically distinct forms in terms of pelage color and patterning. The taxonomy, phylogenetic relationships, and biogeographic history of the genus have been subject to much debate, making scientific communication difficult and creating challenges for conservation actions. We extracted DNA from samples of all currently recognized species of spider monkeys collected from across the geographic range of the genus, sequenced ?3.5 kilobases of coding sequence from the mitochondrial genome, and used this large dataset to (a) infer the phylogenetic relationships among the different forms of spider monkeys, (b) evaluate whether currently recognized species of spider monkeys form reciprocally monophyletic groups that are concordant with contemporary classifications, and (c) estimate divergence dates among the different lineages of Ateles. We found that all proposed species of spider monkeys for which we have samples from multiple localities indeed appear to form monophyletic groups. However, in contrast to previous studies, several of our analyses robustly inferred Ateles marginatus from northeast Brazil as the sister taxon to all other spider monkeys. A Bayesian dating analysis suggests that the most recent common ancestor of extant Ateles dates to ?6.7 Ma, in the late Miocene, and most species-level splits within the genus took place in the late Pliocene, suggesting that the modern diversity in spider monkeys cannot be explained principally by isolation and divergence of populations in forest refugia during the Pleistocene. Based on our new phylogenetic inference and dating analysis, we propose a revised biogeographic scenario for the evolution of this genus. PMID:25451801

  20. Identification of medicinal Dendrobium species by phylogenetic analyses using matK and rbcL sequences.

    PubMed

    Asahina, Haruka; Shinozaki, Junichi; Masuda, Kazuo; Morimitsu, Yasujiro; Satake, Motoyoshi

    2010-04-01

    Species identification of five Dendrobium plants was conducted using phylogenetic analysis and the validity of the method was verified. Some Dendrobium plants (Orchidaceae) have been used as herbal medicines but the difficulty in identifying their botanical origin by traditional methods prevented their full modern utilization. Based on the emerging field of molecular systematics as a powerful classification tool, a phylogenetic analysis was conducted using sequences of two plastid genes, the maturase-coding gene (matK) and the large subunit of ribulose 1,5-bisphosphate carboxylase-coding gene (rbcL), as DNA barcodes for species identification of Dendrobium plants. We investigated five medicinal Dendrobium species, Dendrobium fimbriatum, D. moniliforme, D. nobile, D. pulchellum, and D. tosaense. The phylogenetic trees constructed from matK data successfully distinguished each species from each other. On the other hand, rbcL, as a single-locus barcode, offered less species discriminating power than matK, possibly due to its being present with little variation. When results using matK sequences of D. officinale that was deposited in the DNA database were combined, D. officinale and D. tosaense showed a close genetic relationship, which brought us closer to resolving the question of their taxonomic identity. Identification of the plant source as well as the uniformity of the chemical components is critical for the quality control of herbal medicines and it is important that the processed materials be validated. The methods presented here could be applied to the analysis of processed Dendrobium plants and be a promising tool for the identification of botanical origins of crude drugs. PMID:20140532

  1. Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies

    PubMed Central

    Hoyal Cuthill, Jennifer; Charleston, Michael

    2012-01-01

    The unpalatable and warning-patterned butterflies Heliconius erato and Heliconius melpomene provide the best studied example of mutualistic Müllerian mimicry, thought–but rarely demonstrated–to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of H. erato and H. melpomene, and this was initially hailed as one of the most striking known cases of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of H. erato and H. melpomene, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of H. erato and H. melpomene. Cophylogenetic historical reconstructions support repeated codivergence of mimetic populations, from the base of the sampled radiations. Pairwise distance correlation tests, based on our coalescent analyses plus recently published AFLP and wing colour pattern gene data, also suggest that the phylogenies of H. erato and H. melpomene show significant topological congruence. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of H. erato and H. melpomene occurred over the same time period, and are compatible with a series of temporally congruent codivergence events. Our results suggest that differences in within-species genetic divergence are the result of a greater overall effective population size for H. erato relative to H. melpomene and do not imply incongruence in the timing of their phylogenetic radiations. Repeated codivergence between Müllerian co-mimics, predicted to exert mutual selection pressures, strongly suggests coevolution. Our results therefore support a history of reciprocal coevolution between Müllerian co-mimics characterised by phylogenetic codivergence and parallel phenotypic change. PMID:22586474

  2. Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable

    PubMed Central

    Pardi, Fabio; Scornavacca, Celine

    2015-01-01

    Phylogenetic networks represent the evolution of organisms that have undergone reticulate events, such as recombination, hybrid speciation or lateral gene transfer. An important way to interpret a phylogenetic network is in terms of the trees it displays, which represent all the possible histories of the characters carried by the organisms in the network. Interestingly, however, different networks may display exactly the same set of trees, an observation that poses a problem for network reconstruction: from the perspective of many inference methods such networks are indistinguishable. This is true for all methods that evaluate a phylogenetic network solely on the basis of how well the displayed trees fit the available data, including all methods based on input data consisting of clades, triples, quartets, or trees with any number of taxa, and also sequence-based approaches such as popular formalisations of maximum parsimony and maximum likelihood for networks. This identifiability problem is partially solved by accounting for branch lengths, although this merely reduces the frequency of the problem. Here we propose that network inference methods should only attempt to reconstruct what they can uniquely identify. To this end, we introduce a novel definition of what constitutes a uniquely reconstructible network. For any given set of indistinguishable networks, we define a canonical network that, under mild assumptions, is unique and thus representative of the entire set. Given data that underwent reticulate evolution, only the canonical form of the underlying phylogenetic network can be uniquely reconstructed. While on the methodological side this will imply a drastic reduction of the solution space in network inference, for the study of reticulate evolution this is a fundamental limitation that will require an important change of perspective when interpreting phylogenetic networks. PMID:25849429

  3. Phylogenetic analysis of a new Cetacean morbillivirus from a short-finned pilot whale stranded in the Canary Islands.

    PubMed

    Bellière, E N; Esperón, F; Fernández, A; Arbelo, M; Muñoz, M J; Sánchez-Vizcaíno, J M

    2011-04-01

    Cetacean morbillivirus (CeMV) is considered the most pathogenic virus in cetaceans. Three strains have been already described: the dolphin morbillivirus (DMV), the porpoise morbillivirus (PMV) and the tentatively named pilot whale morbillivirus (PWMV). This study describes the molecular characterization of a strain of CeMV detected in the brain of a short-finned pilot whale that had stranded in the Eastern Atlantic Ocean around the Canary Islands and that showed lesions compatible with morbilliviral disease. Sequences for the nucleoprotein, phosphoprotein, fusion protein and haemagglutinin genes were obtained. The phylogenetic study showed high homology (97%) with the PWMV strain previously detected from a long-finned pilot whale stranded in the Western Atlantic Ocean. These results support the existing classification of CeMV into three principal genetic clusters. PMID:20576281

  4. Archaea in Organic-Lean and Organic-Rich Marine Subsurface Sediments: An Environmental Gradient Reflected in Distinct Phylogenetic Lineages

    PubMed Central

    Durbin, Alan M.; Teske, Andreas

    2012-01-01

    Examining the patterns of archaeal diversity in little-explored organic-lean marine subsurface sediments presents an opportunity to study the association of phylogenetic affiliation and habitat preference in uncultured marine Archaea. Here we have compiled and re-analyzed published archaeal 16S rRNA clone library datasets across a spectrum of sediment trophic states characterized by a wide range of terminal electron-accepting processes. Our results show that organic-lean marine sediments in deep marine basins and oligotrophic open ocean locations are inhabited by distinct lineages of archaea that are not found in the more frequently studied, organic-rich continental margin sediments. We hypothesize that different combinations of electron donor and acceptor concentrations along the organic-rich/organic-lean spectrum result in distinct archaeal communities, and propose an integrated classification of habitat characteristics and archaeal community structure. PMID:22666218

  5. Phylogenetic relationships of the Hamamelidaceae inferred from sequences of internal transcribed spacers (ITS) of nuclear ribosomal DNA.

    PubMed

    Li, J; Bogle, A L; Klein, A S

    1999-07-01

    Intergeneric relationships in the Hamamelidaceae have long been controversial. In this study, sequences of the internal transcribed spacers of nuclear ribosomal DNA were used to reconstruct the phylogeny for the Hamamelidaceae. Three major clades were recognized in the ITS-based phylogenetic tree: (1) Mytilaria-Exbucklandia-Rhodoleia, (2) Disanthus, and (3) the Hamamelidoideae. Within the Hamamelidoideae there were three well-supported lineages: (1) Corylopsis-Loropetalum-Tetrathyrium-Maingaya-Matudaea, (2) Eustigmateae sensu Endress, plus Molinadendron-Dicoryphinae, and (3) Hamamelis-Fothergilleae sensu Endress, excluding Matudaea and Molinadendron. The Exbucklandioideae sensu Endress were not monophyletic, nor were the tribes in the Hamamelidoideae in their current circumscriptions except for the Corylopsideae. Strap-shaped petals, apetaly, and wind pollination have evolved three times independently in the Hamamelidaceae s.s. (Hamamelidaceae minus Altingioideae), suggesting that homoplasy should be considered in future classifications of the family. PMID:10406726

  6. The serpin superfamily in channel catfish: identification, phylogenetic analysis and expression profiling in mucosal tissues after bacterial infections.

    PubMed

    Li, Yun; Liu, Shikai; Qin, Zhenkui; Yao, Jun; Jiang, Chen; Song, Lin; Dunham, Rex; Liu, Zhanjiang

    2015-04-01

    The superfamily of serine protease inhibitors (serpins) are broadly distributed in all kingdoms of life. Serpins play critical roles in an array of fundamental biological processes. In this study, we identified a complete set of 25 serpin genes from channel catfish genome by comprehensive data mining of existing genomic resources. Phylogenetic analysis verified their identities and supported the classification of serpins into six families as in mammals. Extensive comparative genomic analyses suggested that most serpins were conserved among vertebrates, while some were lineage-specific. Analysis of serpin gene expression in mucosal tissues after bacterial infections indicated that serpin genes were regulated in a tissue-specific and time-dependent manner. Distinct expression patterns between infections of the two pathogens were observed, indicating that much more rapid host responses of serpin expression were initiated after ESC infection than after columnaris infection. These studies set the foundation for future studies of host-pathogen interactions. PMID:25499033

  7. The Complete Mitochondrial Genome of the Beet Webworm, Spoladea recurvalis (Lepidoptera: Crambidae) and Its Phylogenetic Implications

    PubMed Central

    He, Shi-Lin; Zou, Yuan; Zhang, Li-Fang; Ma, Wen-Qi; Zhang, Xiu-Yue; Yue, Bi-Song

    2015-01-01

    The complete mitochondrial genome (mitogenome) of the beet webworm, Spoladea recurvalis has been sequenced. The circular genome is 15,273 bp in size, encoding 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes and containing a control region with gene order and orientation identical to that of other ditrysian lepidopteran mitogenomes. The nucleotide composition of the mitogenome shows a high A+T content of 80.9%, and the AT skewness is slightly negative (-0.023). All PCGs start with the typical ATN codons, except for COX1, which may start with the CGA codon. Nine of 13 PCGs have the common stop codon TAA; however, COX1, COX2 and ND5 utilize the T nucleotide and ND4 utilizes TA nucleotides as incomplete termination codons. All tRNAs genes are folded into the typical cloverleaf structure of mitochondrial tRNAs, except for the tRNASer(AGY) gene, in which the DHU arm fails to form a stable stem-loop structure. A total of 157 bp intergenic spacers are scattered in 17 regions. The overlapping sequences are 42 bp in total and found in eight different locations. The 329 bp AT-rich region is comprised of non-repetitive sequences, including the motif ATAG, which is followed by a 14 bp poly-T stretch, a (AT11 microsatellite-like repeat, which is adjacent to the motif ATTTA, and a 9 bp poly-A, which is immediately upstream from the tRNAMet gene. Phylogenetic analysis, based on 13 PCGs and 13 PCGs+2 rRNAs using Bayesian inference and Maximum likelihood methods, show that the classification position of Pyraloidea is inconsistent with the traditional classification. Hesperioidea is placed within the Papilionoidea rather than as a sister group to it. The Pyraloidea is placed within the Macrolepidoptera with other superfamilies instead of the Papilionoidea. PMID:26091291

  8. Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles

    E-print Network

    Shaffer, H. Bradley

    Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles of Evolution and Ecology, University of California, 2320 Storer Hall, Davis, CA 95616, USA b Center phylogenetics PCR primers Turtle a b s t r a c t We present a strategy for phylogenetic marker development

  9. Genome Biology 2007, 8:216 Topological variation in single-gene phylogenetic trees

    E-print Network

    Castresana, Jose

    Genome Biology 2007, 8:216 Minireview Topological variation in single-gene phylogenetic trees Jose phylogenetic trees constructed from single genes, highlighting the problems that can be associated with gene of evolution by comparing phylogenetic trees con- structed from different protein-coding genes from the same

  10. Classification of brain tumors using MRI and MRS data

    NASA Astrophysics Data System (ADS)

    Wang, Qiang; Liacouras, Eirini Karamani; Miranda, Erickson; Kanamalla, Uday S.; Megalooikonomou, Vasileios

    2007-03-01

    We study the problem of classifying brain tumors as benign or malignant using information from magnetic resonance (MR) imaging and magnetic resonance spectroscopy (MRS) to assist in clinical diagnosis. The proposed approach consists of several steps including segmentation, feature extraction, feature selection, and classification model construction. Using an automated segmentation technique based on fuzzy connectedness we accurately outline the tumor mass boundaries in the MR images so that further analysis concentrates on these regions of interest (ROIs). We then apply a concentric circle technique on the ROIs to extract features that are utilized by the classification algorithms. To remove redundant features, we perform feature selection where only those features with discriminatory information (among classes) are used in the model building process. The involvement of MRS features further improves the classification accuracy of the model. Experimental results demonstrate the effectiveness of the proposed approach in classifying brain tumors in MR images.

  11. Establishing a classification system and criteria for veneer preparations.

    PubMed

    LeSage, Brian

    2013-02-01

    The concept of no- or minimal-preparation veneers is more than 25 years old, yet there is no classification system categorizing the extent of preparation for different veneer treatments. The lack of veneer preparation classifications creates misunderstanding and miscommunication with patients and within the dental profession. Such a system could be indicated in various clinical scenarios and would benefit dentists and patients, providing a guide for conservatively preparing and placing veneers. A classification system is proposed to divide preparation and veneering into reduction--referred to as space requirement, working thickness, or material room--volume of enamel remaining, and percentage of dentin exposed. Using this type of metric provides an accurate measurement system to quantify tooth structure removal, with preferably no reduction, on a case-by-case basis, dissolve uncertainty, and aid with multiple aspects of treatment planning and communication. PMID:23556319

  12. Nuclear Ribosomal ITS Functional Paralogs Resolve the Phylogenetic Relationships of a Late-Miocene Radiation Cycad Cycas (Cycadaceae)

    PubMed Central

    Xiao, Long-Qian; Möller, Michael

    2015-01-01

    Cycas is the most widespread and diverse genus among the ancient cycads, but the extant species could be the product of late Miocene rapid radiations. Taxonomic treatments to date for this genus are quite controversial, which makes it difficult to elucidate its evolutionary history. We cloned 161 genomic ITS sequences from 31 species representing all sections of Cycas. The divergent ITS paralogs were examined within each species and identified as putative pseudogenes, recombinants and functional paralogs. Functional paralogs were used to reconstruct phylogenetic relationships with pseudogene sequences as molecular outgroups, since an unambiguous ITS sequence alignment with their closest relatives, the Zamiaceae, is unachievable. A fully resolved and highly supported tree topology was obtained at the section level, with two major clades including six minor clades. The results fully supported the classification scheme proposed by Hill (2004) at the section level, with the minor clades representing his six sections. The two major clades could be recognised as two subgenera. The obtained pattern of phylogenetic relationships, combined with the different seed dispersal capabilities and paleogeography, allowed us to propose a late Miocene rapid radiation of Cycas that might have been promoted by vicariant events associated with the complex topography and orogeny of South China and adjacent regions. In contrast, transoceanic dispersals might have played an important role in the rapid diversification of sect. Cycas, whose members have evolved a spongy layer in their seeds aiding water dispersals. PMID:25635842

  13. Evolutionary history of the Tricladida and the Platyhelminthes: an up-to-date phylogenetic and systematic account.

    PubMed

    Riutort, Marta; Álvarez-Presas, Marta; Lázaro, Eva; Solà, Eduard; Paps, Jordi

    2012-01-01

    Within the free-living platyhelminths, the triclads, or planarians, are the best-known group, largely as a result of long-standing and intensive research on regeneration, pattern formation and Hox gene expression. However, the group's evolutionary history has been long debated, with controversies ranging from their phyletic structure and position within the Metazoa to the relationships among species within the Tricladida. Over the the last decade, with the advent of molecular phylogenies, some of these issues have begun to be resolved. Here, we present an up-to-date summary of the main phylogenetic changes and novelties with some comments on their evolutionary implications. The phylum has been split into two groups, and the position of the main group (the Rhabdithophora and the Catenulida), close to the Annelida and the Mollusca within the Lophotrochozoa, is now clear. Their internal relationships, although not totally resolved, have been clarified. Tricladida systematics has also experienced a revolution since the implementation of molecular data. The terrestrial planarians have been demonstrated to have emerged from one of the freshwater families, giving a different view of their evolution and greatly altering their classification. The use of molecular data is also facilitating the identification of Tricladida species by DNA barcoding, allowing better knowledge of their distribution and genetic diversity. Finally, molecular phylogenetic and phylogeographical analyses, taking advantage of recent data, are beginning to give a clear picture of the recent history of the Dugesia and Schmidtea species in the Mediterranean. PMID:22450992

  14. Molecular phylogenetic analysis supports a Gondwanan origin of the Hyriidae (Mollusca: Bivalvia: Unionida) and the paraphyly of Australasian taxa.

    PubMed

    Graf, Daniel L; Jones, Hugh; Geneva, Anthony J; Pfeiffer, John M; Klunzinger, Michael W

    2015-04-01

    The freshwater mussel family Hyriidae (Mollusca: Bivalvia: Unionida) has a disjunct trans-Pacific distribution in Australasia and South America. Previous phylogenetic analyses have estimated the evolutionary relationships of the family and the major infra-familial taxa (Velesunioninae and Hyriinae: Hyridellini in Australia; Hyriinae: Hyriini, Castaliini, and Rhipidodontini in South America), but taxon and character sampling have been too incomplete to support a predictive classification or allow testing of biogeographical hypotheses. We sampled 30 freshwater mussel individuals representing the aforementioned hyriid taxa, as well as outgroup species representing the five other freshwater mussel families and their marine sister group (order Trigoniida). Our ingroup included representatives of all Australian genera. Phylogenetic relationships were estimated from three gene fragments (nuclear 28S, COI and 16S mtDNA) using maximum parsimony, maximum likelihood, and Bayesian inference, and we applied a Bayesian relaxed clock model calibrated with fossil dates to estimate node ages. Our analyses found good support for monophyly of the Hyriidae and the subfamilies and tribes, as well as the paraphyly of the Australasian taxa (Velesunioninae, (Hyridellini, (Rhipidodontini, (Castaliini, Hyriini)))). The Hyriidae was recovered as sister to a clade comprised of all other Recent freshwater mussel families. Our molecular date estimation supported Cretaceous origins of the major hyriid clades, pre-dating the Tertiary isolation of South America from Antarctica/Australia. We hypothesize that early diversification of the Hyriidae was driven by terrestrial barriers on Gondwana rather than marine barriers following disintegration of the super-continent. PMID:25659337

  15. Phylogenetic and functional diversity of metagenomic libraries of phenol degrading sludge from petroleum refinery wastewater treatment system

    PubMed Central

    2012-01-01

    In petrochemical refinery wastewater treatment plants (WWTP), different concentrations of pollutant compounds are received daily in the influent stream, including significant amounts of phenolic compounds, creating propitious conditions for the development of particular microorganisms that can rapidly adapt to such environment. In the present work, the microbial sludge from a refinery WWTP was enriched for phenol, cloned into fosmid vectors and pyrosequenced. The fosmid libraries yielded 13,200 clones and a comprehensive bioinformatic analysis of the sequence data set revealed a complex and diverse bacterial community in the phenol degrading sludge. The phylogenetic analyses using MEGAN in combination with RDP classifier showed a massive predominance of Proteobacteria, represented mostly by the genera Diaphorobacter, Pseudomonas, Thauera and Comamonas. The functional classification of phenol degrading sludge sequence data set generated by MG-RAST showed the wide metabolic diversity of the microbial sludge, with a high percentage of genes involved in the aerobic and anaerobic degradation of phenol and derivatives. In addition, genes related to the metabolism of many other organic and xenobiotic compounds, such as toluene, biphenyl, naphthalene and benzoate, were found. Results gathered herein demonstrated that the phenol degrading sludge has complex phylogenetic and functional diversities, showing the potential of such community to degrade several pollutant compounds. This microbiota is likely to represent a rich resource of versatile and unknown enzymes which may be exploited for biotechnological processes such as bioremediation. PMID:22452812

  16. Nuclear ribosomal ITS functional paralogs resolve the phylogenetic relationships of a late-miocene radiation cycad Cycas (Cycadaceae).

    PubMed

    Xiao, Long-Qian; Möller, Michael

    2015-01-01

    Cycas is the most widespread and diverse genus among the ancient cycads, but the extant species could be the product of late Miocene rapid radiations. Taxonomic treatments to date for this genus are quite controversial, which makes it difficult to elucidate its evolutionary history. We cloned 161 genomic ITS sequences from 31 species representing all sections of Cycas. The divergent ITS paralogs were examined within each species and identified as putative pseudogenes, recombinants and functional paralogs. Functional paralogs were used to reconstruct phylogenetic relationships with pseudogene sequences as molecular outgroups, since an unambiguous ITS sequence alignment with their closest relatives, the Zamiaceae, is unachievable. A fully resolved and highly supported tree topology was obtained at the section level, with two major clades including six minor clades. The results fully supported the classification scheme proposed by Hill (2004) at the section level, with the minor clades representing his six sections. The two major clades could be recognised as two subgenera. The obtained pattern of phylogenetic relationships, combined with the different seed dispersal capabilities and paleogeography, allowed us to propose a late Miocene rapid radiation of Cycas that might have been promoted by vicariant events associated with the complex topography and orogeny of South China and adjacent regions. In contrast, transoceanic dispersals might have played an important role in the rapid diversification of sect. Cycas, whose members have evolved a spongy layer in their seeds aiding water dispersals. PMID:25635842

  17. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support

    E-print Network

    Hillis, David

    Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures World genera of dwarf boas (Exiliboa, Trachyboa, Tropidophis, and Ungaliophis) have been placed by many lineages, including the placement of the dwarf boas, are poorly understood. We obtained mtDNA sequence data

  18. Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets

    PubMed Central

    2012-01-01

    Background While progress has been made to develop automatic segmentation techniques for mitochondria, there remains a need for more accurate and robust techniques to delineate mitochondria in serial blockface scanning electron microscopic data. Previously developed texture based methods are limited for solving this problem because texture alone is often not sufficient to identify mitochondria. This paper presents a new three-step method, the Cytoseg process, for automated segmentation of mitochondria contained in 3D electron microscopic volumes generated through serial block face scanning electron microscopic imaging. The method consists of three steps. The first is a random forest patch classification step operating directly on 2D image patches. The second step consists of contour-pair classification. At the final step, we introduce a method to automatically seed a level set operation with output from previous steps. Results We report accuracy of the Cytoseg process on three types of tissue and compare it to a previous method based on Radon-Like Features. At step 1, we show that the patch classifier identifies mitochondria texture but creates many false positive pixels. At step 2, our contour processing step produces contours and then filters them with a second classification step, helping to improve overall accuracy. We show that our final level set operation, which is automatically seeded with output from previous steps, helps to smooth the results. Overall, our results show that use of contour pair classification and level set operations improve segmentation accuracy beyond patch classification alone. We show that the Cytoseg process performs well compared to another modern technique based on Radon-Like Features. Conclusions We demonstrated that texture based methods for mitochondria segmentation can be enhanced with multiple steps that form an image processing pipeline. While we used a random-forest based patch classifier to recognize texture, it would be possible to replace this with other texture identifiers, and we plan to explore this in future work. PMID:22321695

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

    PubMed Central

    Zhang, Xianchun; Xiang, Qiaoping

    2015-01-01

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

  20. Automated Defect Classification (ADC)

    Energy Science and Technology Software Center (ESTSC)

    1998-01-01

    The ADC Software System is designed to provide semiconductor defect feature analysis and defect classification capabilities. Defect classification is an important software method used by semiconductor wafer manufacturers to automate the analysis of defect data collected by a wide range of microscopy techniques in semiconductor wafer manufacturing today. These microscopies (e.g., optical bright and dark field, scanning electron microscopy, atomic force microscopy, etc.) generate images of anomalies that are induced or otherwise appear on wafermore »surfaces as a result of errant manufacturing processes or simple atmospheric contamination (e.g., airborne particles). This software provides methods for analyzing these images, extracting statistical features from the anomalous regions, and applying supervised classifiers to label the anomalies into user-defined categories.« less