Quantum corrections to Schwarzschild black hole

Using effective field theory techniques, we compute quantum corrections to spherically symmetric solutions of Einstein’s gravity and focus in particular on the Schwarzschild black hole. Quantum modifications are covariantly encoded in a non-local effective action. We work to quadratic order in curvatures simultaneously taking local and non-local corrections into account. Looking for solutions perturbatively close to that of classical general relativity, we find that an eternal Schwarzschild black hole remains a solution and receives no quantum corrections up to this order in the curvature expansion. In contrast, the field of a massive star receives corrections which are fully determined by the effective field theory

In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure

Background: Synonymous codon usage bias has typically been correlated with, and attributed to translational efficiency. However, there are other pressures on genomic sequence composition that can affect codon usage patterns such as mutational biases. This study provides an analysis of the codon usage patterns in Arabidopsis thaliana in relation to gene expression levels, codon volatility, mutational biases and selective pressures. Results: We have performed synonymous codon usage and codon volatility analyses for all genes in the A. thaliana genome. In contrast to reports for species from other kingdoms, we find that neither codon usage nor volatility are correlated with selection pressure (as measured by dN/dS), nor with gene expression levels on a genome wide level. Our results show that codon volatility and usage are not synonymous, rather that they are correlated with the abundance of G and C at the third codon position (GC3). Conclusions: Our results indicate that while the A. thaliana genome shows evidence for synonymous codon usage bias, this is not related to the expression levels of its constituent genes. Neither codon volatility nor codon usage are correlated with expression levels or selective pressures but, because they are directly related to the composition of G and C at the third codon position, they are the result of mutational bias. Therefore, in A. thaliana codon volatility and usage do not result from selection for translation efficiency or protein functional shift as measured by positive selection

Molecular adaptation of telomere associated genes in mammals

Background: Placental mammals display a huge range of life history traits, including size, longevity, metabolic rate and germ line generation time. Although a number of general trends have been proposed between these traits, there are exceptions that warrant further investigation. Species such as naked mole rat, human and certain bat species all exhibit extreme longevity with respect to body size. It has long been established that telomeres and telomere maintenance have a clear role in ageing but it has not yet been established whether there is evidence for adaptation in telomere maintenance proteins that could account for increased longevity in these species. Results: Here we carry out a molecular investigation of selective pressure variation, specifically focusing on telomere associated genes across placental mammals. In general we observe a large number of instances of positive selection acting on telomere genes. Although these signatures of selection overall are not significantly correlated with either longevity or body size we do identify positive selection in the microbat species Myotis lucifugus in functionally important regions of the telomere maintenance genes DKC1 and TERT, and in naked mole rat in the DNA repair gene BRCA1. Conclusion: These results demonstrate the multifarious selective pressures acting across the mammal phylogeny driving lineage-specific adaptations of telomere associated genes. Our results show that regardless of the longevity of a species, these proteins have evolved under positive selection thereby removing increased longevity as the single selective force driving this rapid rate of evolution. However, evidence of molecular adaptations specific to naked mole rat and Myotis lucifugus highlight functionally significant regions in genes that may alter the way in which telomeres are regulated and maintained in these longer-lived species

The evolution of methods for establishing evolutionary timescales

The fossil record is well known to be incomplete. Read literally, it provides a distorted view of the history of species divergence and extinction, because different species have different propensities to fossilize, the amount of rock fluctuates over geological timescales, as does the nature of the environments that it preserves. Even so, patterns in the fossil evidence allow us to assess the incompleteness of the fossil record. While the molecular clock can be used to extend the time estimates from fossil species to lineages not represented in the fossil record, fossils are the only source of information concerning absolute (geological) times in molecular dating analysis. We review different ways of incorporating fossil evidence in modern clock dating analyses, including node-calibrations where lineage divergence times are constrained using probability densities and tip-calibrations where fossil species at the tips of the tree are assigned dates from dated rock strata. While node-calibrations are often constructed by a crude assessment of the fossil evidence and thus involves arbitrariness, tip-calibrations may be too sensitive to the prior on divergence times or the branching process and influenced unduly affected by well-known problems of morphological character evolution, such as environmental influence on morphological phenotypes, correlation among traits, and convergent evolution in disparate species. We discuss the utility of time information from fossils in phylogeny estimation and the search for ancestors in the fossil record. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’

The Dawn of Open Access to Phylogenetic Data

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation - extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for ~60% of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Although the situation appears dire, our analyses suggest that it is far from hopeless: recent initiatives by the scientific community -- including policy changes by journals and funding agencies -- are improving the state of affairs

Quantum Gravity in Everyday Life: General Relativity as an Effective Field Theory

This article is meant as a summary and introduction to the ideas of effective field theory as applied to gravitational systems. Contents: 1. Introduction 2. Effective Field Theories 3. Low-Energy Quantum Gravity 4. Explicit Quantum Calculations 5. ConclusionsComment: 56 pages, 2 figures, JHEP style, Invited review to appear in Living Reviews of Relativit

Pure-glue hidden valleys through the Higgs portal

We consider the possibility that the Higgs boson can act as a link to a hidden sector in the context of pure-glue hidden valley models. In these models the standard model is weakly coupled, through loops of heavy messengers fields, to a hidden sector whose low energy dynamics is described by a pure-Yang-Mills theory. Such a hidden sector contains several metastable hidden glueballs. In this work we shall extend earlier results on hidden valleys to include couplings of the messengers to the standard model Higgs sector. The effective interactions at one-loop couple the hidden gluons to the standard model particles through the Higgs sector. These couplings in turn induce hidden glueball decays to fermion pairs, or cascade decays with multiple Higgs emission. The presence of effective operators of different mass dimensions, often competing with each other, together with a great diversity of states, leads to a great variability in the lifetimes and decay modes of the hidden glueballs. We find that most of the operators considered in this paper are not heavily constrained by precision electroweak physics, therefore leaving plenty of room in the parameter space to be explored by the future experiments at the LHC.Comment: 44 pages, 16 figures. Major revision for JHEP, corrected an error in Eq. 5.1, comments adde

Paternally expressed imprinted genes under positive Darwinian selection in Arabidopsis thaliana

Genomic imprinting is an epigenetic phenomenon where autosomal genes display uniparental expression depending on whether they are maternally or paternally inherited. Genomic imprinting can arise from parental conflicts over resource allocation to the offspring, which could drive imprinted loci to evolve by positive selection. We investigate whether positive selection is associated with genomic imprinting in the inbreeding species Arabidopsis thaliana. Our analysis of 140 genes regulated by genomic imprinting in the A. thaliana seed endosperm demonstrates they are evolving more rapidly than expected. To investigate whether positive selection drives this evolutionary acceleration, we identified orthologs of each imprinted gene across 34 plant species and elucidated their evolutionary trajectories. Increased positive selection was sought by comparing its incidence among imprinted genes with non-imprinted controls. Strikingly, we find a statistically significant enrichment of imprinted paternally expressed genes (iPEGs) evolving under positive selection, 50.6% of the total, but no such enrichment for positive selection among imprinted maternally expressed genes (iMEGs). This suggests that maternally- and paternally-expressed imprinted genes are subject to different selective pressures. Almost all positively selected amino acids were fixed across 80 sequenced A. thaliana accessions, suggestive of selective sweeps in the A. thaliana lineage. The imprinted genes under positive selection are involved in processes important for seed development including auxin biosynthesis and epigenetic regulation. Our findings support a genomic imprinting model for plants where positive selection can affect paternally-expressed genes due to continued conflict with maternal sporophyte tissues, even when parental conflict is reduced in predominantly inbreeding species

Effective Theory of a Dynamically Broken Electroweak Standard Model at NLO

We consider the Standard Model as an effective theory at the weak scale $v$ of a generic new strong interaction that dynamically breaks electroweak symmetry at the energy scale $\Lambda\sim$ (few) TeV. Assuming only the minimal field content with the Standard Model fermions and gauge bosons, but without a light Higgs particle, we construct the complete Lagrangian through next-to-leading order, that is, including terms of order $v^2/\Lambda^2$. The systematics behind this expansion is clarified. Although similar to chiral perturbation theory, it is not governed by the dimension of operators alone, but depends in an essential way on the loop expansion. Power-counting formulas are derived that indicate the classes of operators required at the next-to-leading order. The complete set of operators at leading and next-to-leading order is then listed, based on the restrictions implied by the Standard-Model gauge symmetries. We recover the well-known operators discussed in the literature in connection with the electroweak chiral Lagrangian and in similar contexts, but we collect a complete and systematic list of all terms through order $v^2/\Lambda^2$. This includes some operators not discussed in explicit terms before. We also show that a few of the previously considered operators can be eliminated via the equations of motion. As another important result we confirm the known list of dimension-6 operators in the Standard Model with an elementary Higgs doublet, essentially as a special case of our scenario.Comment: 35 pages, 1 figure; references adde

Minimal Flavour Violation with hierarchical squark masses

In a supersymmetric model with hierarchical squark masses we analyze a pattern of flavour symmetry breaking centered on the special role of the top Yukawa coupling and, by extension, of the full Yukawa couplings for the up-type quarks. For sufficiently heavy squarks of the first and second generation this leads to effective Minimal Flavour Violation of the Flavour Changing Neutral Current amplitudes. For this to happen we determine the bounds on the masses of the heavy squarks with QCD corrections taken into account, properly including previously neglected effects. We believe that the view presented in this paper altogether strengthens the case for hierarchical sfermions.Comment: 13 pages, 1 figure. v2: an equation correcte