The Opisthokonta and the Ecdysozoa May Not Be Clades: Stronger Support for the Grouping of Plant and Animal than for Animal and Fungi and Stronger Support for the Coelomata than Ecdysozoa

In considering the best possible solutions for answering phylogenetic questions from genomic sequences, we have chosen a strategy that we suggest is superior to others that have gone previously. We have ignored multigene families and instead have used single-gene families. This minimizes the inadvertent analysis of paralogs. We have employed strict data controls and have reasoned that if a protein is not capable of recovering the uncontroversial parts of a phylogenetic tree, then why should we use it for the more controversial parts? We have sliced and diced the data in as many ways as possible in order to uncover the signals in that data. Using this strategy, we have tested two controversial hypotheses concerning eukaryotic phylogenetic relationships: the placement of arthropoda and nematodes and the relationships of animals, plants, and fungi. We have constructed phylogenetic trees from 780 single-gene families from 10 completed genomes and amalgamated these into a single supertree. We have also carried out a total evidence analysis on the only universally distributed protein families that can accurately reconstruct the uncontroversial parts of the phylogenetic tree: a total of five families. In doing so, we ignore the majority of single-gene families that are universally distributed as they do not have the appropriate signals to recover the uncontroversial parts of the tree. We have also ignored every protein that has ever been used previously to address this issue, simply because none of them meet our strict criteria. Using these data controls, site stripping, and multiple analyses, 24 out of 26 analyses strongly support the grouping of vertebrates with arthropods (Coelomata hypothesis) and plants with animals. In the other two analyses, the data were ambivalent. The latter finding overturns an 11-year theory of Eukaryotic evolution; the first confirms what has already been said by others. In the light of this new tree, we reanalyze the evolution of intron gain and loss in the rpL14 gene and find that it is much more compatible with the hypothesis presented here than with the Opisthokonta hypothesis

The integration of 'omic' disciplines and systems biology in cattle breeding

Enormous progress has been made in the selection of animals, including cattle, for specific traits using traditional quantitative genetics approaches. Nevertheless, considerable variation in phenotypes remains unexplained, and therefore represents potential additional gain for animal production. In addition, the paradigm shift in new disciplines now being applied to animal breeding represents a powerful opportunity to prise open the 'black box' underlying the response to selection and fully understand the genetic architecture controlling the traits of interest. A move away from traditional approaches of animal breeding toward systems approaches using integrative analysis of data from the 'omic' disciplines represents a multitude of exciting opportunities for animal breeding going forward as well as providing alternatives for overcoming some of the limitations of traditional approaches such as the expressed phenotype being an imperfect predictor of the individual's true genetic merit, or the phenotype being only expressed in one gender or late in the lifetime of an animal. This review aims to discuss these opportunities from the perspective of their potential application and contribution to cattle breeding. Harnessing the potential of this paradigm shift also poses some new challenges for animal scientists - and they will also be discussed

Preparing the COROT space mission: new variable stars in the galactic Anticenter direction

The activities related to the preparation of the asteroseismic, photometric space mission COROT are described. Photoelectric observations, wide--field CCD photometry, uvbyB calibrations and further time--series have been obtained at different observatories and telescopes. They have been planned to complete the COROT programme in the direction of the galactic Anticenter. In addition to suitable asteroseismic targets covering the different evolutionary stages between ZAMS and TAMS, we discovered several other variable stars, both pulsating and geometrical. We compared results on the incidence of variability in the galactic Center and Anticenter directions. Physical parameters have been obtained and evolutionary tracks fitting them have been calculated. The peculiarities of some individual stars alre pointed out. Paper based on observations collected at the San Pedro Martir, Sierra Nevada, Teide, La Silla, Haute-Provence and Roque de Los Muchachos (Telescopio Nazionale Galileo and Mercator telescopes) observatories.Comment: 13 pages, 9 figures. Accepted for The Astronomical Journal (2005 May volume

Characterizing two solar-type Kepler subgiants with asteroseismology: KIC10920273 and KIC11395018

Determining fundamental properties of stars through stellar modeling has improved substantially due to recent advances in asteroseismology. Thanks to the unprecedented data quality obtained by space missions, particularly CoRoT and Kepler, invaluable information is extracted from the high-precision stellar oscillation frequencies, which provide very strong constraints on possible stellar models for a given set of classical observations. In this work, we have characterized two relatively faint stars, KIC10920273 and KIC11395018, using oscillation data from Kepler photometry and atmospheric constraints from ground-based spectroscopy. Both stars have very similar atmospheric properties; however, using the individual frequencies extracted from the Kepler data, we have determined quite distinct global properties, with increased precision compared to that of earlier results. We found that both stars have left the main sequence and characterized them as follows: KIC10920273 is a one-solar-mass star (M=1.00 +/- 0.04 M_sun), but much older than our Sun (t=7.12 +/- 0.47 Gyr), while KIC11395018 is significantly more massive than the Sun (M=1.27 +/- 0.04 M_sun) with an age close to that of the Sun (t=4.57 +/- 0.23 Gyr). We confirm that the high lithium abundance reported for these stars should not be considered to represent young ages, as we precisely determined them to be evolved subgiants. We discuss the use of surface lithium abundance, rotation and activity relations as potential age diagnostics.Comment: 12 pages, 3 figures, 5 tables. Accepted by Ap

Properties of 42 Solar-type Kepler Targets from the Asteroseismic Modeling Portal

Recently the number of main-sequence and subgiant stars exhibiting solar-like oscillations that are resolved into individual mode frequencies has increased dramatically. While only a few such data sets were available for detailed modeling just a decade ago, the Kepler mission has produced suitable observations for hundreds of new targets. This rapid expansion in observational capacity has been accompanied by a shift in analysis and modeling strategies to yield uniform sets of derived stellar properties more quickly and easily. We use previously published asteroseismic and spectroscopic data sets to provide a uniform analysis of 42 solar-type Kepler targets from the Asteroseismic Modeling Portal (AMP). We find that fitting the individual frequencies typically doubles the precision of the asteroseismic radius, mass and age compared to grid-based modeling of the global oscillation properties, and improves the precision of the radius and mass by about a factor of three over empirical scaling relations. We demonstrate the utility of the derived properties with several applications.Comment: 12 emulateapj pages, 9 figures, 1 online-only extended figure, 1 table, ApJS accepted (typo corrected in Eq.8

A precise asteroseismic age and radius for the evolved Sun-like star KIC 11026764

The primary science goal of the Kepler Mission is to provide a census of exoplanets in the solar neighborhood, including the identification and characterization of habitable Earth-like planets. The asteroseismic capabilities of the mission are being used to determine precise radii and ages for the target stars from their solar-like oscillations. Chaplin et al. (2010) published observations of three bright G-type stars, which were monitored during the first 33.5 days of science operations. One of these stars, the subgiant KIC 11026764, exhibits a characteristic pattern of oscillation frequencies suggesting that it has evolved significantly. We have derived asteroseismic estimates of the properties of KIC 11026764 from Kepler photometry combined with ground-based spectroscopic data. We present the results of detailed modeling for this star, employing a variety of independent codes and analyses that attempt to match the asteroseismic and spectroscopic constraints simultaneously. We determine both the radius and the age of KIC 11026764 with a precision near 1%, and an accuracy near 2% for the radius and 15% for the age. Continued observations of this star promise to reveal additional oscillation frequencies that will further improve the determination of its fundamental properties.Comment: 16 pages, 6 figures, 4 tables, ApJ in pres

Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome

Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated individual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform diversity for each microbial gene identified. The animal replicates were used to calculate confidence intervals to test for differences in diversity of functional isoforms between microbes that may drive niche specialisation. We identified 153 genes with significant differences in functional isoform diversity between the two most abundant bacterial genera in the rumen (Prevotella and Clostridium). We found Prevotella possesses a more diverse range of isoforms capable of degrading hemicellulose, whereas Clostridium for cellulose. Furthermore, significant differences were observed in key metabolic processes indicating that isoform diversity plays an important role in maintaining their niche specialisation. The methods presented represent a novel approach for untangling complex interactions between microorganisms in natural environments and have resulted in an expanded catalogue of gene targets central to rumen cellulosic biomass degradation

Asteroseismology of the solar analogs 16 Cyg A & B from Kepler observations

The evolved solar-type stars 16 Cyg A & B have long been studied as solar analogs, yielding a glimpse into the future of our own Sun. The orbital period of the binary system is too long to provide meaningful dynamical constraints on the stellar properties, but asteroseismology can help because the stars are among the brightest in the Kepler field. We present an analysis of three months of nearly uninterrupted photometry of 16 Cyg A & B from the Kepler space telescope. We extract a total of 46 and 41 oscillation frequencies for the two components respectively, including a clear detection of octupole (l=3) modes in both stars. We derive the properties of each star independently using the Asteroseismic Modeling Portal, fitting the individual oscillation frequencies and other observational constraints simultaneously. We evaluate the systematic uncertainties from an ensemble of results generated by a variety of stellar evolution codes and fitting methods. The optimal models derived by fitting each component individually yield a common age (t=6.8+/-0.4 Gyr) and initial composition (Z_i=0.024+/-0.002, Y_i=0.25+/-0.01) within the uncertainties, as expected for the components of a binary system, bolstering our confidence in the reliability of asteroseismic techniques. The longer data sets that will ultimately become available will allow future studies of differential rotation, convection zone depths, and long-term changes due to stellar activity cycles.Comment: 6 pages, 2 figures, 2 tables, ApJ Letters (accepted

Verifying asteroseismically determined parameters of Kepler stars using hipparcos parallaxes: self-consistent stellar properties and distances

Accurately determining the properties of stars is of prime importance for characterizing stellar populations in our Galaxy. The field of asteroseismology has been thought to be particularly successful in such an endeavor for stars in different evolutionary stages. However, to fully exploit its potential, robust methods for estimating stellar parameters are required and independent verification of the results is mandatory. With this purpose, we present a new technique to obtain stellar properties by coupling asteroseismic analysis with the InfraRed Flux Method. By using two global seismic observables and multi-band photometry, the technique allows us to obtain masses, radii, effective temperatures, bolometric fluxes, and hence distances for field stars in a self-consistent manner. We apply our method to 22 solar-like oscillators in the Kepler short-cadence sample, that have accurate Hipparcos parallaxes. Our distance determinations agree to better than 5%, while measurements of spectroscopic effective temperatures and interferometric radii also validate our results. We briefly discuss the potential of our technique for stellar population analysis and models of Galactic Chemical Evolution.Comment: 28 pages, 5 figures, ApJ, accepte