BioNames: linking taxonomy, texts, and trees

BioNames is a web database of taxonomic names for animals, linked to the primary literature and, wherever possible, to phylogenetic trees. It aims to provide a taxonomic “dashboard” where at a glance we can see a summary of the taxonomic and phylogenetic information we have for a given taxon and hence provide a quick answer to the basic question “what is this taxon?” BioNames combines classifications from the Global Biodiversity Information Facility (GBIF) and GenBank, images from the Encyclopedia of Life (EOL), animal names from the Index of Organism Names (ION), and bibliographic data from multiple sources including the Biodiversity Heritage Library (BHL) and CrossRef. The user interface includes display of full text articles, interactive timelines of taxonomic publications, and zoomable phylogenies. It is available at http://bionames.org

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem

<p>Abstract</p> <p>Background</p> <p>Evolutionary methods are increasingly challenged by the wealth of fast growing resources of genomic sequence information. Evolutionary events, like gene duplication, loss, and deep coalescence, account more then ever for incongruence between gene trees and the actual species tree. Gene tree reconciliation is addressing this fundamental problem by invoking the minimum number of gene duplication and losses that reconcile a rooted gene tree with a rooted species tree. However, the reconciliation process is highly sensitive to topological error or wrong rooting of the gene tree, a condition that is not met by most gene trees in practice. Thus, despite the promises of gene tree reconciliation, its applicability in practice is severely limited.</p> <p>Results</p> <p>We introduce the problem of reconciling unrooted and erroneous gene trees by simultaneously rooting and error-correcting them, and describe an efficient algorithm for this problem. Moreover, we introduce an error-corrected version of the gene duplication problem, a standard application of gene tree reconciliation. We introduce an effective heuristic for our error-corrected version of the gene duplication problem, given that the original version of this problem is NP-hard. Our experimental results suggest that our error-correcting approaches for unrooted input trees can significantly improve on the accuracy of gene tree reconciliation, and the species tree inference under the gene duplication problem. Furthermore, the efficiency of our algorithm for error-correcting reconciliation is capable of handling truly large-scale phylogenetic studies.</p> <p>Conclusions</p> <p>Our presented error-correction approach is a crucial step towards making gene tree reconciliation more robust, and thus to improve on the accuracy of applications that fundamentally rely on gene tree reconciliation, like the inference of gene-duplication supertrees.</p

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

Supplementary tables S1, sections 2.1–2.3, and figures S1–S11 are available at Molecular Biology and Evolution online (http://www.mbe.oxfordjournals.org/).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 context. Here, we present SPIMAP, an efficient Bayesian method for reconstructing gene trees in the presence of a known species tree. We observe many improvements in reconstruction accuracy, achieved by modeling multiple aspects of evolution, including gene duplication and loss (DL) rates, speciation times, and correlated substitution rate variation across both species and loci. We have implemented and applied this method on two clades of fully sequenced species, 12 Drosophila and 16 fungal genomes as well as simulated phylogenies and find dramatic improvements in reconstruction accuracy as compared with the most popular existing methods, including those that take the species tree into account. We find that reconstruction inaccuracies of traditional phylogenetic methods overestimate the number of DL events by as much as 2–3-fold, whereas our method achieves significantly higher accuracy. We feel that the results and methods presented here will have many important implications for future investigations of gene evolution.National Science Foundation (U.S.) (CAREER award NSF 0644282

The prospects for constraining dark energy with future X-ray cluster gas mass fraction measurements

We examine the ability of a future X-ray observatory to constrain dark energy via measurements of the cluster X-ray gas mass fraction, fgas. We find that fgas measurements for a sample of ~500 hot, X-ray bright, dynamically relaxed clusters, to a precision of ~5 per cent, can be used to constrain dark energy with a Dark Energy Task Force (DETF) figure of merit of 15-40, with the possibility of boosting these values by 40 per cent or more by optimizing the redshift distribution of target clusters. Such constraints are comparable to those predicted by the DETF for other leading, planned dark energy experiments. A future fgas experiment will be preceded by a large X-ray or SZ survey that will find hot, X-ray luminous clusters out to high redshifts. Short `snapshot' observations with the new X-ray observatory should then be able to identify a sample of ~500 suitably relaxed systems. The redshift, temperature and X-ray luminosity range of interest has already been partially probed by existing X-ray cluster surveys which allow reasonable estimates of the fraction of clusters that will be suitably relaxed for fgas work. Our analysis uses a Markov Chain Monte Carlo method which fully captures the relevant degeneracies between parameters and facilitates the incorporation of priors and systematic uncertainties in the analysis. We explore the effects of such uncertainties for scenarios ranging from optimistic to pessimistic. We conclude that the fgas experiment will provide tight constraints on the mean matter and dark energy densities, with a peak sensitivity for dark energy work at redshifts midway between those of supernovae and baryon acoustic oscillation/weak lensing/cluster number counts experiments. In combination, these experiments should enable a precise measurement of the evolution of dark energy. (Abridged)Comment: Accepted for publication in MNRAS. 16 pages, 6 figures, 4 tables. Predicted cluster redshift distribution consistent with the observed evolution of massive clusters reported by Mantz et al 2008 (arXiv:0709.4294). Additional discussion included. Conclusions unchange

The attitudes of owners and veterinary professionals in the United Kingdom to the risk of adverse events associated with using non- steroidal anti-inflammatory drugs (NSAIDs) to treat dogs with osteoarthritis

Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly prescribed by veterinary surgeons for the treatment of canine osteoarthritis, and affected dogs may receive these drugs for long periods of time. Whilst short term administration of NSAIDs to dogs is linked to adverse events such as gastrointestinal haemorrhage and renal injury, reports of adverse events associated with their long-term administration are limited in the veterinary literature. This study aimed to investigate the attitudes towards the long term use of NSAIDs for canine osteoarthritis held by three groups who manage osteoarthritic dogs in the United Kingdom: dog owners, veterinary surgeons and veterinary nurses. A qualitative methodology was adopted, using semi-structured interviews and focus groups. Thematic analysis of these data identified three themes: awareness of potential risks; recognition of adverse events; and influence of risk perception on the use of NSAIDs. Awareness of, and concern about, the risk of adverse events associated with NSAID administration to dogs with osteoarthritis was high in all groups, with veterinary surgeons being one of a variety of information sources used by owners to acquire this knowledge. Veterinary surgeons described difficulty in recognising, managing and avoiding adverse events associated with NSAIDs. When adverse events occurred, a wide range of management approaches were adopted ranging from a brief drug respite to permanent cessation of administration of any NSAIDs to that dog. Commonly employed approaches to minimise risk included dose reduction and screening blood tests. This study describes a high level of concern about the risks associated with long term NSAID administration to dogs with osteoarthritis and highlights a diverse range of strategies employed to minimise these risks. The evidence base for these strategies is poor, and this may present a risk to animal welfare if the affected dogs are not receiving adequate analgesia. In order to address this, more accurate and comprehensive data must be supplied to both veterinary professionals and owners on the true frequency of adverse events associated with long term administration of veterinary NSAIDs and how best to avoid them

Genetic relationships within and among Iberian fescues (Festuca L.) based on PCR-amplified markers

The genus Festuca comprises approximately 450 species and is widely distributed around the world. The Iberian Penninsula, with more than 100 taxa colonizing very diverse habitats, is one of its main centers of diversification. This study was conducted to assess molecular genetic variation and genetic relatedness among 91 populations of 31 taxa of Iberian fescues, based on several molecular markers (random amplified polymorphic DNA, amplified fragment length polymorphisms, and trnL sequences). The analyses showed the paraphyletic origin of the broad-leaved (subgenus Festuca, sections Scariosae and Subbulbosae, and subgenus Schedonorus) and the fine-leaved fescues (subgenus Festuca, sections Aulaxyper, Eskia, and Festuca). Schedonorus showed a weak relationship with Lolium rigidum and appeared to be the most recent of the broad-leaved clade. Section Eskia was the most ancient and Festuca the most recent of the fine-leaved clade. Festuca and Aulaxyper were the most related sections, in concordance with their taxonomic affinities. All taxa grouped into their sections, except F. ampla and F. capillifolia (section Festuca), which appeared to be more closely related to Aulaxyper and to a new independent section, respectively. Most populations clustered at the species level, but some subspecies and varieties mixed their populations. This study demonstrated the value in combining different molecular markers to uncover hidden genetic relationships between populations of Festuca

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses

<p>Abstract</p> <p>Background</p> <p>The abundance of new genomic data provides the opportunity to map the location of gene duplication and loss events on a species phylogeny. The first methods for mapping gene duplications and losses were based on a parsimony criterion, finding the mapping that minimizes the number of duplication and loss events. Probabilistic modeling of gene duplication and loss is relatively new and has largely focused on birth-death processes.</p> <p>Results</p> <p>We introduce a new maximum likelihood model that estimates the speciation and gene duplication and loss events in a gene tree within a species tree with branch lengths. We also provide an, in practice, efficient algorithm that computes optimal evolutionary scenarios for this model. We implemented the algorithm in the program DrML and verified its performance with empirical and simulated data.</p> <p>Conclusions</p> <p>In test data sets, DrML finds optimal gene duplication and loss scenarios within minutes, even when the gene trees contain sequences from several hundred species. In many cases, these optimal scenarios differ from the lca-mapping that results from a parsimony gene tree reconciliation. Thus, DrML provides a new, practical statistical framework on which to study gene duplication.</p

Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization

<p>Abstract</p> <p>Background</p> <p>Construction and interpretation of phylogenetic trees has been a major research topic for understanding the evolution of genes. Increases in sequence data and complexity are creating a need for more powerful and insightful tree visualization tools.</p> <p>Results</p> <p>We have developed 3D Phylogeny Explorer (3DPE), a novel phylogeny tree viewer that maps trees onto three spatial axes (species on the X-axis; paralogs on Z; evolutionary distance on Y), enabling one to distinguish at a glance evolutionary features such as speciation; gene duplication and paralog evolution; lateral gene transfer; and violation of the "molecular clock" assumption. Users can input any tree on the online 3DPE, then rotate, scroll, rescale, and explore it interactively as "live" 3D views. All objects in 3DPE are clickable to display subtrees, connectivity path highlighting, sequence alignments, and gene summary views, and etc. To illustrate the value of this visualization approach for microbial genomes, we also generated 3D phylogeny analyses for all clusters from the public COG database. We constructed tree views using well-established methods and graph algorithms. We used Scientific Python to generate VRML2 3D views viewable in any web browser.</p> <p>Conclusion</p> <p>3DPE provides a novel phylogenetic tree projection method into 3D space and its web-based implementation with live 3D features for reconstruction of phylogenetic trees of COG database.</p

Inhibitory effect of cadmium on estrogen signaling in zebrafish brain and protection by zinc

International audienceThe present study was conducted to assess the effects of Cd exposure on estrogen signaling in the zebrafish brain, as well as the potential protective role of Zn against Cd-induced toxicity. For this purpose, the effects on transcriptional activation of the estrogen receptors (ERs), aromatase B (Aro-B) protein expression and molecular expression of related genes were examined in vivo using wild-type and transgenic zebrafish embryos. For in vitro studies, an ER-negative glial cell line (U251MG) transfected with different zebrafish ER subtypes (ERα, ERβ1 and ERβ2) was also used. Embryos were exposed either to estradiol (E2), Cd, E2+Cd or E2+Cd+Zn for 72 h and cells were exposed to the same treatments for 30 h. Our results show that E2 treatment promoted the transcriptional activation of ERs and increased Aro-B expression, at both the protein and mRNA levels. Although exposure to Cd, does not affect the studied parameters when administered alone, it significantly abolished the E2-stimulated transcriptional response of the reporter gene for the three ER subtypes in U251-MG cells, and clearly inhibited the E2 induction of Aro-B in radial glial cells of zebrafish embryos. These inhibitory effects were accompanied by a significant downregulation of the expression of esr1, esr2a, esr2b and cyp19a1b genes compared to the E2-treated group used as a positive control. Zn administration during simultaneous exposure to E2 and Cd strongly stimulated zebrafish ERs transactivation and increased Aro-B protein expression, whereas mRNA levels of the three ERs as well as the cyp19a1b remained unchanged in comparison with Cd-treated embryos. In conclusion, our results clearly demonstrate that Cd acts as a potent anti-estrogen in vivo and in vitro, and that Cd-induced E2 antagonism can be reversed, at the protein level, by Zn supplement

Improved constraints on dark energy from Chandra X-ray observations of the largest relaxed galaxy clusters

We present constraints on the mean matter density, Omega_m, dark energy density, Omega_de, and the dark energy equation of state parameter, w, using Chandra measurements of the X-ray gas mass fraction (fgas) in 42 hot (kT>5keV), X-ray luminous, dynamically relaxed galaxy clusters spanning the redshift range 0.05<z<1.1. Using only the fgas data for the 6 lowest redshift clusters at z<0.15, for which dark energy has a negligible effect on the measurements, we measure Omega_m=0.28+-0.06 (68% confidence, using standard priors on the Hubble Constant, H_0, and mean baryon density, Omega_bh^2). Analyzing the data for all 42 clusters, employing only weak priors on H_0 and Omega_bh^2, we obtain a similar result on Omega_m and detect the effects of dark energy on the distances to the clusters at ~99.99% confidence, with Omega_de=0.86+-0.21 for a non-flat LCDM model. The detection of dark energy is comparable in significance to recent SNIa studies and represents strong, independent evidence for cosmic acceleration. Systematic scatter remains undetected in the fgas data, despite a weighted mean statistical scatter in the distance measurements of only ~5%. For a flat cosmology with constant w, we measure Omega_m=0.28+-0.06 and w=-1.14+-0.31. Combining the fgas data with independent constraints from CMB and SNIa studies removes the need for priors on Omega_bh^2 and H_0 and leads to tighter constraints: Omega_m=0.253+-0.021 and w=-0.98+-0.07 for the same constant-w model. More general analyses in which we relax the assumption of flatness and/or allow evolution in w remain consistent with the cosmological constant paradigm. Our analysis includes conservative allowances for systematic uncertainties. The small systematic scatter and tight constraints bode well for future dark energy studies using the fgas method. (Abridged)Comment: Published in MNRAS. 20 pages, 11 figures. The data and analysis code (in the form of a patch to CosmoMC) are now available at http://www.stanford.edu/~drapetti/fgas_module