Browsing by Subject "selection"
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Item Bayes And Empirical-Bayes Multiplicity Adjustment In The Variable-Selection Problem(2010-10) Scott, James G.; Berger, James O.; Scott, James G.; Berger, James O.This paper studies the multiplicity-correction effect of standard Bayesian variable-selection priors in linear regression. Our first goal is to clarify when, and how, multiplicity correction happens automatically in Bayesian analysis, and to distinguish this correction from the Bayesian Ockham's-razor effect. Our second goal is to contrast empirical-Bayes and fully Bayesian approaches to variable selection through examples, theoretical results and simulations. Considerable differences between the two approaches are found. In particular, we prove a theorem that characterizes a surprising aymptotic discrepancy between fully Bayes and empirical Bayes. This discrepancy arises from a different source than the failure to account for hyperparameter uncertainty in the empirical-Bayes estimate. Indeed, even at the extreme, when the empirical-Bayes estimate converges asymptotically to the true variable-inclusion probability, the potential for a serious difference remains.Item Ecological Opportunity In Adaptive Radiation Of Galapagos Endemic Land Snails(2009-12) Parent, Christine E.; Crespi, Bernard J.; Parent, Christine E.The classic evolutionary hypothesis of ecological opportunity proposes that both heterogeneity of resources and freedom from enemies promote phenotypic divergence as a response to increased niche availability. Although phenotypic divergence and speciation have often been inferred to be the primary consequences of the release from competition or predation that accompanies a shift to a new adaptive zone, increased phenotypic variation within species is expected to represent the first stage resulting from such a shift. Using measures of intraspecific morphological variation of 30 species of Galapagos endemic land snails in a phylogenetically controlled framework, we show that the number of local congeners and the number of local plant species are associated with lower and higher intraspecific phenotypic variation, respectively. In this clade, ecological opportunity thus explicitly links the role of competition from congeners and the heterogeneity of resources to the extent of intraspecific phenotypic divergence as adaptive radiation proceeds.Item Evolution of Rhizaria: New insights From Phylogenomic Analysis of Uncultivated Protists(2010-12) Burki, Fabien; Kudryavtsev, Alexander; Matz, Mikhail V.; Aglyamova, Galina V.; Bulman, Simon; Fiers, Mark; Keeling, Patrick J.; Pawlowski, Jan; Matz, Mikhail V.; Aglyamova, Galina V.Recent phylogenomic analyses have revolutionized our view of eukaryote evolution by revealing unexpected relationships between and within the eukaryotic supergroups. However, for several groups of uncultivable protists, only the ribosomal RNA genes and a handful of proteins are available, often leading to unresolved evolutionary relationships. A striking example concerns the supergroup Rhizaria, which comprises several groups of uncultivable free-living protists such as radiolarians, foraminiferans and gromiids, as well as the parasitic plasmodiophorids and haplosporids. Thus far, the relationships within this supergroup have been inferred almost exclusively from rRNA, actin, and polyubiquitin genes, and remain poorly resolved. To address this, we have generated large Expressed Sequence Tag (EST) datasets for 5 species of Rhizaria belonging to 3 important groups: Acantharea (Astrolonche sp., Phyllostaurus sp.), Phytomyxea (Spongospora subterranea, Plasmodiophora brassicae) and Gromiida (Gromia sphaerica). Results: 167 genes were selected for phylogenetic analyses based on the representation of at least one rhizarian species for each gene. Concatenation of these genes produced a supermatrix composed of 36,735 amino acid positions, including 10 rhizarians, 9 stramenopiles, and 9 alveolates. Phylogenomic analyses of this large dataset revealed a strongly supported clade grouping Foraminifera and Acantharea. The position of this clade within Rhizaria was sensitive to the method employed and the taxon sampling: Maximum Likelihood (ML) and Bayesian analyses using empirical model of evolution favoured an early divergence, whereas the CAT model and ML analyses with fast-evolving sites or the foraminiferan species Reticulomyxa filosa removed suggested a derived position, closely related to Gromia and Phytomyxea. In contrast to what has been previously reported, our analyses also uncovered the presence of the rhizarian-specific polyubiquitin insertion in Acantharea. Finally, this work reveals another possible rhizarian signature in the 60S ribosomal protein L10a. Conclusions: Our study provides new insights into the evolution of Rhizaria based on phylogenomic analyses of ESTs from three groups of previously under-sampled protists. It was enabled through the application of a recently developed method of transcriptome analysis, requiring very small amount of starting material. Our study illustrates the potential of this method to elucidate the early evolution of eukaryotes by providing large amount of data for uncultivable free-living and parasitic protists.Item A Large-Scale Galaxy Structure At Z=2.02 Associated With The Radio Galaxy MRC 0156-252(2013-11) Galametz, Audrey; Stern, Daniel; Pentericcil, Laura; De Breuck, Carlos; Vernet, Joël; Wylezalek, Dominika; Fassbender, Rene; Hatch, Nina; Kurk, Jaron; Overzier, Roderik; Rettura, Alessandro; Seymour, Nick; Overzier, RoderikWe present the spectroscopic confirmation of a structure of galaxies surrounding the radio galaxy MRC 0156-252 at z = 2.02. The structure was initially discovered as an overdensity of both near-infrared selected z > 1.6 and mid-infrared selected z > 1.2 galaxy candidates. We used the VLT/FORS2 multi-object spectrograph to target similar to 80 high-redshift galaxy candidates, and obtain robust spectroscopic redshifts for more than half the targets. The majority of the confirmed sources are star-forming galaxies at z > 1.5. In addition to the radio galaxy, two of its close-by companions (<6 '') also show AGN signatures. Ten sources, including the radio galaxy, lie within vertical bar z - 2.020 vertical bar < 0.015 (i.e., velocity offsets < 1500 km s(-1)) and within projected 2 Mpc comoving of the radio galaxy. Additional evidence suggests not only that the galaxy structure associated with MRC 0156-252 is a forming galaxy cluster but also that this structure is most probably embedded in a larger-scale structure.Item Local Correlations in Codon Preferences do not Support a Model of tRNA Recycling(2014-09) Hussmann, Jeffrey A.; Press, William H.; Hussmann, Jeffrey A.; Press, William H.It has been proposed that patterns in the usage of synonymous codons provide evidence that individual tRNA molecules are recycled through the ribosome, translating several occurrences of the same amino acid before diffusing away. The claimed evidence is based on counting the frequency with which pairs of synonymous codons are used at nearby occurrences of the same amino acid, as compared to the frequency expected if each codon were chosen independently from a single genome-wide distribution. We show that such statistics simply measure variation in codon preferences across a genome. As a negative control on the potential contribution of pressure to exploit tRNA recycling on these signals, we examine correlations in the usage of codons that encode different amino acids. We find that these controls are statistically as strong as the claimed evidence and conclude that there is no informatic evidence that tRNA recycling is a force shaping codon usage.Item The Munich Near-Infrared Cluster Survey. II. The K-Band Luminosity Function Of Field Galaxies To Z Similar To 1.2(2003-10) Drory, Niv; Bender, Ralf; Feulner, G.; Hopp, Ulrich; Maraston, C.; Snigula, J.; Hill, Gary J.; Drory, Niv; Hill, Gary J.We present a measurement of the evolution of the rest-frame K-band luminosity function to z similar to 1.2 using a sample of more than 5000 K-selected galaxies drawn from the Munich Near- Infrared Cluster Survey (MUNICS) data set. Distances and absolute K-band magnitudes are derived using photometric redshifts from spectral energy distribution fits to BVRIJK photometry. These are calibrated using more than 500 spectroscopic redshifts. We obtain redshift estimates having an rms scatter of 0.055 and no mean bias. We use Monte Carlo simulations to investigate the influence of the errors in distance associated with photometric redshifts on our ability to reconstruct the shape of the luminosity function. Finally, we construct the rest-frame K-band LF in four redshift bins spanning 0.4 < z < 1.2 and compare our results to the local luminosity function. We discuss and apply two different estimators to derive likely values for the evolution of the number density, Phi*, and characteristic luminosity, M*, with redshift. While the first estimator relies on the value of the luminosity function binned in magnitude and redshift, the second estimator uses the individually measured {M, z} pairs alone. In both cases we obtain a mild decrease in number density by similar to25% to z = 1, accompanied by brightening of the galaxy population by 0.5 - 0.7 mag. These results are fully consistent with an analogous analysis using only the spectroscopic MUNICS sample. The total K-band luminosity density is found to scale as d log rhoL/dz = 0.24. We discuss possible sources of systematic errors and their influence on our parameter estimates. By comparing the luminosity density and the cumulative redshift distributions of galaxies in single survey fields to the sample averages, we show that cosmic variance is likely to significantly influence infrared selected samples on scales of similar to 100 arcmin(2).Item Optimal Foraging By Bacteriophages Through Host Avoidance(2008-04) Heineman, Richard H.; Springman, Rachael; Bull, James J.; Heineman, Richard H.; Springman, Rachael; Bull, James J.Optimal foraging theory explains diet restriction as an adaptation to best utilize an array of foods differing in quality, the poorest items not worth the lost opportunity of finding better ones. Although optimal foraging has traditionally been applied to animal behavior, the model is easily applied to viral host range, which is genetically determined. The usual perspective for bacteriophages ( bacterial viruses) is that expanding host range is always advantageous if fitness on former hosts is not compromised. However, foraging theory identifies conditions favoring avoidance of poor hosts even if larger host ranges have no intrinsic costs. Bacteriophage T7 rapidly evolved to discriminate among different Escherichia coli strains when one host strain was engineered to kill infecting phages but the other remained productive. After modifying bacteria to yield more subtle fitness effects on T7, we tested qualitative predictions of optimal foraging theory by competing broad and narrow host range phages against each other. Consistent with the foraging model, diet restriction was favored when good hosts were common or there was a large difference in host quality. Contrary to the model, the direction of selection was affected by the density of poor hosts because being able to discriminate was costly.Item Reduced Stability of mRNA Secondary Structure Near the Translation-Initiation Site in dsDNA Viruses(2011-03) Zhou, Tong; Wilke, Claus O.; Wilke, Claus O.Recent studies have demonstrated a selection pressure for reduced mRNA secondary-structure stability near the start codon of coding sequences. This selection pressure can be observed in bacteria, archaea, and eukaryotes, and is likely caused by the requirement of efficient translation initiation in cellular organism. Results: Here, we surveyed the complete genomes of 650 dsDNA virus strains for signals of reduced stability of mRNA secondary structure near the start codon. Our analysis included viruses infecting eukaryotic, prokaryotic, and archaeic hosts. We found that many viruses showed evidence for reduced mRNA secondary-structure stability near the start codon. The effect was most pronounced in viruses infecting prokaryotes, but was also observed in viruses infecting eukaryotes and archaea. The reduction in stability generally increased with increasing genomic GC content. For bacteriophage, the reduction was correlated with a corresponding reduction of stability in the phage hosts. Conclusions: We conclude that reduced stability of the mRNA secondary structure near the start codon is a common feature for dsDNA viruses, likely driven by the same selective pressures that cause it in cellular organisms.Item Rehabilitation In Bilingual Aphasia: Evidence For Within- And Between-Language Generalization(2013-05) Kiran, Swathi; Sandberg, Chaleece; Gray, Teresa; Ascenso, Elsa; Kester, Ellen; Kester, EllenPurpose: The goal of this study was to examine if there was a principled way to understand the nature of rehabilitation in bilingual aphasia such that patterns of acquisition and generalization are predictable and logical. Method: Seventeen Spanish-English bilingual individuals with aphasia participated in the experiment. For each participant, three sets of stimuli were developed for each language: (a) English Set 1, (b) English Set 2 (semantically related to each item in English Set 1), (c) English Set 3 (unrelated control items), (d) Spanish Set 1 (translations of English Set 1), (e) Spanish Set 2 (translations of English Set 2; semantically related to each item in Spanish Set 1), and (f) Spanish Set 3 (translations of English Set 3; unrelated control items). A single-subject experimental multiple baseline design across participants was implemented. Treatment was conducted in 1 language, but generalization to within- and between-language untrained items was examined. Results: Treatment for naming on Set 1 items resulted in significant improvement (i.e., effect size >4.0) on the trained items in 14/17 participants. Of the 14 participants who showed improvement, within-language generalization to semantically related items was observed in 10 participants. Between-language generalization to the translations of trained items was observed in 5 participants, and between-language generalization to the translations of the untrained semantically related items was observed in 6 participants. Conclusion: The results of this study demonstrated within- and between-language patterns that were variable across participants. These differences are indicative of the interplay between facilitation (generalization) and inhibition.Item Second-order selection for evolvability in a large Escherichia coli population(Science, 2011-03-18) Woods, Robert J.; Barrick, Jeffrey E.; Cooper, Tim F.; Shrestha, Utpala; Kauth, Mark R.; Lenski, Richard E.In theory, competition between asexual lineages can lead to second-order selection for greater evolutionary potential. To test this hypothesis, we revived a frozen population of Escherichia coli from a long-term evolution experiment and compared the fitness and ultimate fates of four genetically distinct clones. Surprisingly, two clones with beneficial mutations that would eventually take over the population had significantly lower competitive fitness than two clones with mutations that later went extinct. By replaying evolution many times from these clones, we showed that the eventual winners likely prevailed because they had greater potential for further adaptation. Genetic interactions that reduce the benefit of certain regulatory mutations in the eventual losers appear to explain, at least in part, why they were outcompeted.Item The Stabilizing Effect Of Intraspecific Genetic Variation On Population Dynamics In Novel And Ancestral Habitats(2009-08) Agashe, Deepa; Agashe, DeepaRecent studies show that intraspecific genetic variation in asexual species may have large effects on community and ecosystem functions, increasing their stability, productivity, and species richness. However, major questions regarding its population-level impact remain empirically unanswered: (a) How does intraspecific genetic diversity affect the ecological characteristics of sexual species, in which recombination can alter the outcome of causal mechanisms such as selection and niche diversification? (b) Does genetic diversity increase population dynamic stability? (c) Is the impact of genetic diversity dependent on the selective environment? To answer these questions, I founded replicate flour beetle (Tribolium castaneum) populations with different degrees of ecologically relevant, heritable trait variation and monitored their dynamics for approximately eight generations. I show that population stability and persistence increased with greater genetic variation but that the stabilizing effect was independent of the selective habitat (different proportions of ancestral and novel resources). Alleles from a single founding strain underwent a selective sweep in the homogeneous ancestral habitat but not in a novel heterogeneous habitat. These results expand current understanding of the ecological impacts of genetic diversity by showing that genetically more diverse sexual populations persist longer and are more stable but that the selective environment determines the mechanistic basis of increased stability.Item A Technique To Derive Improved Proper Motions For Kepler Objects Of Interest(2014-12) Benedict, G. Fritz; Tanner, Angelle M.; Cargile, Phillip A.; Ciardi, David R.; Benedict, G. FritzWe outline an approach yielding proper motions with higher precision than exists in present catalogs for a sample of stars in the Kepler field. To increase proper-motion precision, we combine first-moment centroids of Kepler pixel data from a single season with existing catalog positions and proper motions. We use this astrometry to produce improved reduced-proper-motion diagrams, analogous to a Hertzsprung-Russell (H-R) diagram, for stars identified as Kepler objects of interest. The more precise the relative proper motions, the better the discrimination between stellar luminosity classes. Using UCAC4 and PPMXL epoch 2000 positions (and proper motions from those catalogs as quasi-Bayesian priors), astrometry for a single test Channel (21) and Season (0) spanning 2 yr yields proper motions with an average per-coordinate proper-motion error of 1.0 mas yr(-1), which is over a factor of three better than existing catalogs. We apply a mapping between a reduced-proper-motion diagram and an H-R diagram, both constructed using Hubble Space Telescope parallaxes and proper motions, to estimate Kepler object of interest K-band absolute magnitudes. The techniques discussed apply to any future small-field astrometry as well as to the rest of the Kepler field.