Population structure and breed composition prediction in a multi-breed sheep population using genome-wide single nucleotide polymorphism genotypes

peer-reviewedKnowledge of population structure and breed composition of a population can be advantageous for a number of reasons; these include designing optimal (cross)breeding strategies in order to maximise non-additive genetic effects, maintaining flockbook integrity by authenticating animals being registered and as a quality control measure in the genotyping process. The objectives of the present study were to 1) describe the population structure of 24 sheep breeds, 2) quantify the breed composition of both flockbook-recorded and crossbred animals using single nucleotide polymorphism BLUP (SNP-BLUP), and 3) quantify the accuracy of breed composition prediction from low-density genotype panels containing between 2000 and 6000 SNPs. In total, 9334 autosomal SNPs on 11 144 flockbook-recorded animals and 1172 crossbred animals were used. The population structure of all breeds was characterised by principal component analysis (PCA) as well as the pairwise breed fixation index (Fst). The total number of animals, all of which were purebred, included in the calibration population for SNP-BLUP was 2579 with the number of animals per breed ranging from 9 to 500. The remaining 9559 flockbook-recorded animals, composite breeds and crossbred animals represented the test population; three breeds were excluded from breed composition prediction. The breed composition predicted using SNP-BLUP with 9334 SNPs was considered the gold standard prediction. The pairwise breed Fst ranged from 0.040 (between the Irish Blackface and Scottish Blackface) to 0.282 (between the Border Leicester and Suffolk). Principal component analysis revealed that the Suffolk from Ireland and the Suffolk from New Zealand formed distinct, non-overlapping clusters. In contrast, the Texel from Ireland and that from New Zealand formed integrated, overlapping clusters. Composite animals such as the Belclare clustered close to its founder breeds (i.e., Finn, Galway, Lleyn and Texel). When all 9334 SNPs were used to predict breed composition, an animal that had a majority breed proportion predicted to be ≥0.90 was defined as purebred for the present study. As the panel density decreased, the predicted breed proportion threshold, used to identify animals as purebred, also decreased (≥0.85 with 6000 SNPs to ≥0.60 with 2000 SNPs). In all, results from the study suggest that breed composition for purebred and crossbred animals can be determined with SNP-BLUP using ≥5000 SNPs

On the magnetism of Ln{2/3}Cu{3}Ti{4}O{12} (Ln = lanthanide)

The magnetic and thermodynamic properties of the complete Ln$_{2/3}$Cu$_3$Ti$_4$O$_{12}$ series were investigated. Here $Ln$ stands for the lanthanides La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, and Yb. %Most of the compounds were prepared as single phase polycrystalline powder %without any traces of impurities. Marginal amounts of %impurities $(< 2$ were detected $Ln=$ Gd, Er, and Tm. %Significant amounts of impurity phases were found for $Ln=$ Ce and Yb. All the samples investigated crystallize in the space group $Im\bar{3}$ with lattice constants that follow the lanthanide contraction. The lattice constant of the Ce compound reveals the presence of Ce$^{4+}$ leading to the composition Ce$_{1/2}$Cu$_3$Ti$_4$O$_{12}$. From magnetic susceptibility and electron-spin resonance experiments it can be concluded that the copper ions always carry a spin $S=1/2$ and order antiferromagnetically close to 25\,K. The Curie-Weiss temperatures can approximately be calculated assuming a two-sublattice model corresponding to the copper and lanthanide ions, respectively. It seems that the magnetic moments of the heavy rare earths are weakly coupled to the copper spins, while for the light lanthanides no such coupling was found. The $4f$ moments remain paramagnetic down to the lowest temperatures, with the exception of the Tm compound, which indicates enhanced Van-Vleck magnetism due to a non-magnetic singlet ground state of the crystal-field split $4f$ manifold. From specific-heat measurements we accurately determined the antiferromagnetic ordering temperature and obtained information on the crystal-field states of the rare-earth ions. The heat-capacity results also revealed the presence of a small fraction of Ce$^{3+}$ in a magnetic $4f^1$ state.Comment: 10 pages, 10 figure

On the spherical-axial transition in supernova remnants

A new law of motion for supernova remnant (SNR) which introduces the quantity of swept matter in the thin layer approximation is introduced. This new law of motion is tested on 10 years observations of SN1993J. The introduction of an exponential gradient in the surrounding medium allows to model an aspherical expansion. A weakly asymmetric SNR, SN1006, and a strongly asymmetric SNR, SN1987a, are modeled. In the case of SN1987a the three observed rings are simulated.Comment: 19 figures and 14 pages Accepted for publication in Astrophysics & Space Science in the year 201

Energy Level Statistics of the U(5) and O(6) Symmetries in the Interacting Boson Model

We study the energy level statistics of the states in U(5) and O(6) dynamical symmetries of the interacting boson model and the high spin states with backbending in U(5) symmetry. In the calculations, the degeneracy resulting from the additional quantum number is eliminated manually. The calculated results indicate that the finite boson number $N$ effect is prominent. When $N$ has a value close to a realistic one, increasing the interaction strength of subgroup O(5) makes the statistics vary from Poisson-type to GOE-type and further recover to Poisson-type. However, in the case of $N \to \infty$, they all tend to be Poisson-type. The fluctuation property of the energy levels with backbending in high spin states in U(5) symmetry involves a signal of shape phase transition between spherical vibration and axial rotation.Comment: 38 pages, 13 figure

Electrostatic Potentials in Supernova Remnant Shocks

Recent advances in the understanding of the properties of supernova remnant shocks have been precipitated by the Chandra and XMM X-ray Observatories, and the HESS Atmospheric Cerenkov Telescope in the TeV band. A critical problem for this field is the understanding of the relative degree of dissipative heating/energization of electrons and ions in the shock layer. This impacts the interpretation of X-ray observations, and moreover influences the efficiency of injection into the acceleration process, which in turn feeds back into the thermal shock layer energetics and dynamics. This paper outlines the first stages of our exploration of the role of charge separation potentials in non-relativistic electron-ion shocks where the inertial gyro-scales are widely disparate, using results from a Monte Carlo simulation. Charge density spatial profiles were obtained in the linear regime, sampling the inertial scales for both ions and electrons, for different magnetic field obliquities. These were readily integrated to acquire electric field profiles in the absence of self-consistent, spatial readjustments between the electrons and the ions. It was found that while diffusion plays little role in modulating the linear field structure in highly oblique and perpendicular shocks, in quasi-parallel shocks, where charge separations induced by gyrations are small, and shock-layer electric fields are predominantly generated on diffusive scales.Comment: 7 pages, 2 embedded figures, Accepted for publication in Astrophysics and Space Science, as part of the HEDLA 2006 conference proceeding

Topical Issues for Particle Acceleration Mechanisms in Astrophysical Shocks

Particle acceleration at plasma shocks appears to be ubiquitous in the universe, spanning systems in the heliosphere, supernova remnants, and relativistic jets in distant active galaxies and gamma-ray bursts. This review addresses some of the key issues for shock acceleration theory that require resolution in order to propel our understanding of particle energization in astrophysical environments. These include magnetic field amplification in shock ramps, the non-linear hydrodynamic interplay between thermal ions and their extremely energetic counterparts possessing ultrarelativistic energies, and the ability to inject and accelerate electrons in both non-relativistic and relativistic shocks. Recent observational developments that impact these issues are summarized. While these topics are currently being probed by astrophysicists using numerical simulations, they are also ripe for investigation in laboratory experiments, which potentially can provide valuable insights into the physics of cosmic shocks.Comment: 13 pages, no figures. Invited review, accepted for publication in Astrophysics and Space Science, as part of the HEDLA 2006 conference proceeding

Guiding the Way to Gamma-Ray Sources: X-ray Studies of Supernova Remnants

Supernova remnants have long been suggested as a class of potential counterparts to unidentified gamma-ray sources. The mechanisms by which such gamma-rays can arise may include emission from a pulsar associated with a remnant, or a variety of processes associated with energetic particles accelerated by the SNR shock. Imaging and spectral observations in the X-ray band can be used to identify properties of the remnants that lead to gamma-ray emission, including the presence of pulsar-driven nebulae, nonthermal X-ray emission from the SNR shells, and the interaction of SNRs with dense surrounding material.Comment: 16 pages, 11 figures, To appear in the proceedings of the workshop: "The Nature of the Unidentified Galactic Gamma-Ray Sources" held at INAOE, Mexico, October 2000, (A.Carraminana, O. Reiner and D. Thompson, eds.

Understanding hadronic gamma-ray emission from supernova remnants

We aim to test the plausibility of a theoretical framework in which the gamma-ray emission detected from supernova remnants may be of hadronic origin, i.e., due to the decay of neutral pions produced in nuclear collisions involving relativistic nuclei. In particular, we investigate the effects induced by magnetic field amplification on the expected particle spectra, outlining a phenomenological scenario consistent with both the underlying Physics and the larger and larger amount of observational data provided by the present generation of gamma experiments, which seem to indicate rather steep spectra for the accelerated particles. In addition, in order to study to study how pre-supernova winds might affect the expected emission in this class of sources, the time-dependent gamma-ray luminosity of a remnant with a massive progenitor is worked out. Solid points and limitations of the proposed scenario are finally discussed in a critical way.Comment: 30 pages, 5 figures; Several comments, references and a figure added. Some typos correcte

Magnetic fields in supernova remnants and pulsar-wind nebulae

We review the observations of supernova remnants (SNRs) and pulsar-wind nebulae (PWNe) that give information on the strength and orientation of magnetic fields. Radio polarimetry gives the degree of order of magnetic fields, and the orientation of the ordered component. Many young shell supernova remnants show evidence for synchrotron X-ray emission. The spatial analysis of this emission suggests that magnetic fields are amplified by one to two orders of magnitude in strong shocks. Detection of several remnants in TeV gamma rays implies a lower limit on the magnetic-field strength (or a measurement, if the emission process is inverse-Compton upscattering of cosmic microwave background photons). Upper limits to GeV emission similarly provide lower limits on magnetic-field strengths. In the historical shell remnants, lower limits on B range from 25 to 1000 microGauss. Two remnants show variability of synchrotron X-ray emission with a timescale of years. If this timescale is the electron-acceleration or radiative loss timescale, magnetic fields of order 1 mG are also implied. In pulsar-wind nebulae, equipartition arguments and dynamical modeling can be used to infer magnetic-field strengths anywhere from about 5 microGauss to 1 mG. Polarized fractions are considerably higher than in SNRs, ranging to 50 or 60% in some cases; magnetic-field geometries often suggest a toroidal structure around the pulsar, but this is not universal. Viewing-angle effects undoubtedly play a role. MHD models of radio emission in shell SNRs show that different orientations of upstream magnetic field, and different assumptions about electron acceleration, predict different radio morphology. In the remnant of SN 1006, such comparisons imply a magnetic-field orientation connecting the bright limbs, with a non-negligible gradient of its strength across the remnant.Comment: 20 pages, 24 figures; to be published in SpSciRev. Minor wording change in Abstrac