Detection of genetic incompatibilities in non-model systems using simple genetic markers: hybrid breakdown in the haplodiploid spider mite Tetranychus evansi

When two related species interbreed, their hybrid offspring frequently suffer from reduced fitness. The genetics of hybrid incompatibility are described by the Bateson–Dobzhansky–Muller (BDM) model, where fitness is reduced by epistatic interactions between alleles of heterospecific origin. Unfortunately, most empirical evidence for the BDM model comes from a few well-studied model organisms, restricting our genetic understanding of hybrid incompatibilities to limited taxa. These systems are predominantly diploid and incompatibility is often complete, which complicates the detection of recessive allelic interactions and excludes the possibility to study viable or intermediate stages. Here, we advocate research into non-model organisms with haploid or haplodiploid reproductive systems and incomplete hybrid incompatibility because (1) dominance is absent in haploids and (2) incomplete incompatibility allows comparing affected with unaffected individuals. We describe a novel two-locus statistic specifying the frequency of individuals for which two alleles co-occur. This approach to studying BDM incompatibilities requires genotypic characterization of hybrid individuals, but not genetic mapping or genome sequencing. To illustrate our approach, we investigated genetic causes for hybrid incompatibility between differentiated lineages of the haplodiploid spider mite Tetranychus evansi, and show that strong, but incomplete, hybrid breakdown occurs. In addition, by comparing the genotypes of viable hybrid males and inviable hybrid male eggs for eight microsatellite loci, we show that nuclear and cytonuclear BDM interactions constitute the basis of hybrid incompatibility in this species. Our approach opens up possibilities to study BDM interactions in non-model taxa, and may give further insight into the genetic mechanisms behind hybrid incompatibility

A structured overview of simultaneous component based data integration

<p>Abstract</p> <p>Background</p> <p>Data integration is currently one of the main challenges in the biomedical sciences. Often different pieces of information are gathered on the same set of entities (e.g., tissues, culture samples, biomolecules) with the different pieces stemming, for example, from different measurement techniques. This implies that more and more data appear that consist of two or more data arrays that have a shared mode. An integrative analysis of such coupled data should be based on a simultaneous analysis of all data arrays. In this respect, the family of simultaneous component methods (e.g., SUM-PCA, unrestricted PCovR, MFA, STATIS, and SCA-P) is a natural choice. Yet, different simultaneous component methods may lead to quite different results.</p> <p>Results</p> <p>We offer a structured overview of simultaneous component methods that frames them in a principal components setting such that both the common core of the methods and the specific elements with regard to which they differ are highlighted. An overview of principles is given that may guide the data analyst in choosing an appropriate simultaneous component method. Several theoretical and practical issues are illustrated with an empirical example on metabolomics data for <it>Escherichia coli </it>as obtained with different analytical chemical measurement methods.</p> <p>Conclusion</p> <p>Of the aspects in which the simultaneous component methods differ, pre-processing and weighting are consequential. Especially, the type of weighting of the different matrices is essential for simultaneous component analysis. These types are shown to be linked to different specifications of the idea of a fair integration of the different coupled arrays.</p

Direct CP violation in radiative b decays in and beyond the Standard Model

We consider the partial rate asymmetry in the inclusive decay modes b to s gamma and b to d gamma, concentrating on non-standard models with new charged Higgs interactions. We find that the charged Higgs contribution to the asymmetry for b to s gamma is small in such models due to a universal cancellation mechanism. The asymmetry is therefore difficult to distinguish experimentally from the Standard Model (SM) value, which is also small. The cancellation mechanism is found to be rendered inoperative in supersymmetry due to the presence of chargino loops. Unlike b to s gamma, the rate asymmetry for b to d gamma in Higgs models can be quite different from its SM value, generally ranging from -20% to +20%. Specific model calculations are performed for the Three-Higgs Doublet Model and the ``Top'' Two-Higgs Doublet Model to serve as illustrations. We also offer some suggestions that may be helpful to experimentalists in the detection of the inclusive mode b to d gamma.Comment: RevTex, 24 pages, 6 figures, minor changes, version to appear in PR

Strong CP and Mu Problems in Theories with Gauge Mediated Supersymmetry Breaking

We provide a simple solution to the $\mu$ and strong CP problems in the context of gauge mediated supersymmetry breaking. The generic appearance of R symmetry in dynamical supersymmetry breaking is used to implement Peccei-Quinn symmetry. Acceptable $\mu$ and $B$ terms as well as the large symmetry breaking scale are induced in the presence of nonrenormalizable interactions. Cosmological consequences of this scheme turn out to yield constraints on the PQ symmetry breaking scale and the number of the messenger/heavy quarks. Complexity in introducing non-R Peccei-Quinn symmetry is contrasted with the case of R symmetry.Comment: 10 pages, Revtex. Significantly modified version to apear in Phys. Rev.

Scattering From a Two Dimensional Array of Flux Tubes: A Study of The Validity of Mean Field Theory

Mean Field Theory has been extensively used in the study of systems of anyons in two spatial dimensions. In this paper we study the physical grounds for the validity of this approximation by considering the Quantum Mechanical scattering of a charged particle from a two dimensional array of magnetic flux tubes. The flux tubes are arranged on a regular lattice which is infinitely long in the ``$y$'' direction but which has a (small) finite number of columns in the ``$x$'' direction. Their physical size is assumed to be infinitesimally small. We develop a method for computing the scattering angle as well as the reflection and transmission coefficients to lowest order in the Aharonov--Bohm interaction. The results of our calculation are compared to the scattering of the same particle from a region of constant magnetic field whose magnitude is equal to the mean field of all the flux tubes. For an incident plane wave, the Mean Field approximation is shown to be valid provided the flux in each tube is much less than a single flux quantum. This is precisely the regime in which Mean Field Theory for anyons is expected to be valid. When the flux per tube becomes of order 1, Mean Field Theory is no longer valid.Comment: 23 pages, University of British Columbia Preprint UBCTP93-01

Ubiquitous CP violation in a top-inspired left-right model

We explore CP violation in a Left-Right Model that reproduces the quark mass and CKM rotation angle hierarchies in a relatively natural way by fixing the bidoublet Higgs VEVs to be in the ratio m_b:m_t. Our model is quite general and allows for CP to be broken by both the Higgs VEVs and the Yukawa couplings. Despite this generality, CP violation may be parameterized in terms of two basic phases. A very interesting feature of the model is that the mixing angles in the right-handed sector are found to be equal to their left-handed counterparts to a very good approximation. Furthermore, the right-handed analogue of the usual CKM phase delta_L is found to satisfy the relation delta_R \approx delta_L. The parameter space of the model is explored by using an adaptive Monte Carlo algorithm and the allowed regions in parameter space are determined by enforcing experimental constraints from the K and B systems. This method of solution allows us to evaluate the left- and right-handed CKM matrices numerically for various combinations of the two fundamental CP-odd phases in the model. We find that all experimental constraints may be satisfied with right-handed W and Flavour Changing Neutral Higgs masses as low as about 2 TeV and 7 TeV, respectively.Comment: 37 pages, 13 figure

Levinson's theorem and scattering phase shift contributions to the partition function of interacting gases in two dimensions

We consider scattering state contributions to the partition function of a two-dimensional (2D) plasma in addition to the bound-state sum. A partition function continuity requirement is used to provide a statistical mechanical heuristic proof of Levinson's theorem in two dimensions. We show that a proper account of scattering eliminates singularities in thermodynamic properties of the nonideal 2D gas caused by the emergence of additional bound states as the strength of an attractive potential is increased. The bound-state contribution to the partition function of the 2D gas, with a weak short-range attraction between its particles, is found to vanish logarithmically as the binding energy decreases. A consistent treatment of bound and scattering states in a screened Coulomb potential allowed us to calculate the quantum-mechanical second virial coefficient of the dilute 2D electron-hole plasma and to establish the difference between the nearly ideal electron-hole gas in GaAs and the strongly correlated exciton/free-carrier plasma in wide-gap semiconductors such as ZnSe or GaN.Comment: 10 pages, 3 figures; new version corrects some minor typo

Generalized messengers of supersymmetry breaking and the sparticle mass spectrum

We investigate the sparticle spectrum in models of gauge-mediated supersymmetry breaking. In these models, supersymmetry is spontaneously broken at an energy scale only a few orders of magnitude above the electroweak scale. The breakdown of supersymmetry is communicated to the standard model particles and their superpartners by "messenger" fields through their ordinary gauge interactions. We study the effects of a messenger sector in which the supersymmetry-violating F-term contributions to messenger scalar masses are comparable to the supersymmetry-preserving ones. We also argue that it is not particularly natural to restrict attention to models in which the messenger fields lie in complete SU(5) GUT multiplets, and we identify a much larger class of viable models. Remarkably, however, we find that the superpartner mass parameters in these models are still subject to many significant contraints.Comment: 24 pages, LaTeX, uses epsf.sty, 4 figures. Assumptions clarified, numerical bounds tweaked, typos correcte

Novel CP-violating Effects in B decays from Charged-Higgs in a Two-Higgs Doublet Model for the Top Quark

We explore charged-Higgs cp-violating effects in a specific type III two-Higgs doublet model which is theoretically attractive as it accommodates the large mass of the top quark in a natural fashion. Two new CP-violating phases arise from the right-handed up quark sector. We consider CP violation in both neutral and charged B decays. Some of the important findings are as follows. 1) Large direct-CP asymmetry is found to be possible for B+- to psi/J K+-. 2) Sizable D-anti-D mixing effect at the percent level is found to be admissible despite the stringent constraints from the data on K-anti-K mixing, b to s gamma and B to tau nu decays. 3) A simple but distinctive CP asymmetry pattern emerges in decays of B_d and B_s mesons, including B_d to psi/J K_S, D+ D-, and B_s to D_s+ D_s-, psi eta/eta^prime, psi/J K_S. 4) The effect of D-anti-D mixing on the CP asymmetry in B+- to D/anti-D K+- and on the extraction of the angle gamma of the unitarity triangle from such decays can be significant.Comment: 32 pages, 5 figures, section V.A revised, version to appear in PR