Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations

Abstract Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have farreaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genomewide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele frequency spectrum analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to firstgeneration hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP analysis is a promising tool to quantify recent hybridization in free-living populations

Penetration depth, multiband superconductivity, and absence of muon-induced perturbation in superconducting PrOs4_{4}Sb12_{12}

Transverse-field muon spin rotation ($\mu$SR) experiments in the heavy-fermion superconductor PrOs$_{4}$Sb$_{12}$ ($T_{c}=1.85$ K) suggest that the superconducting penetration depth $\lambda(T)$ is temperature-independent at low temperatures, consistent with a gapped quasiparticle excitation spectrum. In contrast, radiofrequency (rf) inductive measurements yield a stronger temperature dependence of $\lambda(T)$, indicative of point nodes in the gap. This discrepancy appears to be related to the multiband structure of PrOs$_{4}$Sb$_{12}$. Muon Knight shift measurements in PrOs$_{4}$Sb$_{12}$ suggest that the perturbing effect of the muon charge on the neighboring Pr$^{3+}$ crystalline electric field is negligibly small, and therefore is unlikely to cause the difference between the $\mu$SR and rf results.Comment: 10 pages, 7 figure

Ab-initio multimode linewidth theory for arbitrary inhomogeneous laser cavities

We present a multimode laser-linewidth theory for arbitrary cavity structures and geometries that contains nearly all previously known effects and also finds new nonlinear and multimode corrections, e.g. a bad-cavity correction to the Henry $\alpha$ factor and a multimode Schawlow--Townes relation (each linewidth is proportional to a sum of inverse powers of all lasing modes). Our theory produces a quantitatively accurate formula for the linewidth, with no free parameters, including the full spatial degrees of freedom of the system. Starting with the Maxwell--Bloch equations, we handle quantum and thermal noise by introducing random currents whose correlations are given by the fluctuation--dissipation theorem. We derive coupled-mode equations for the lasing-mode amplitudes and obtain a formula for the linewidths in terms of simple integrals over the steady-state lasing modes.Comment: 24 pages, 7 figure

The VLA Low-frequency Sky Survey

The Very Large Array (VLA) Low-frequency Sky Survey (VLSS) has imaged 95% of the 3*pi sr of sky north of declination = -30 degrees at a frequency of 74 MHz (4 meter wavelength). The resolution is 80" (FWHM) throughout, and the typical RMS noise level is ~0.1 Jy/beam. The typical point-source detection limit is 0.7 Jy/beam and so far nearly 70,000 sources have been catalogued. This survey used the 74 MHz system added to the VLA in 1998. It required new imaging algorithms to remove the large ionospheric distortions at this very low frequency throughout the entire ~11.9 degree field of view. This paper describes the observation and data reduction methods used for the VLSS and presents the survey images and source catalog. All of the calibrated images and the source catalog are available online (http://lwa.nrl.navy.mil/VLSS) for use by the astronomical community.Comment: 53 pages, including 3 tables and 15 figures. Has been accepted for publication in the Astronomical Journa

Random matrix theory, the exceptional Lie groups, and L-functions

There has recently been interest in relating properties of matrices drawn at random from the classical compact groups to statistical characteristics of number-theoretical L-functions. One example is the relationship conjectured to hold between the value distributions of the characteristic polynomials of such matrices and value distributions within families of L-functions. These connections are here extended to non-classical groups. We focus on an explicit example: the exceptional Lie group G_2. The value distributions for characteristic polynomials associated with the 7- and 14-dimensional representations of G_2, defined with respect to the uniform invariant (Haar) measure, are calculated using two of the Macdonald constant term identities. A one parameter family of L-functions over a finite field is described whose value distribution in the limit as the size of the finite field grows is related to that of the characteristic polynomials associated with the 7-dimensional representation of G_2. The random matrix calculations extend to all exceptional Lie groupsComment: 14 page

Ground state properties of a one-dimensional condensate of hard core bosons in a harmonic trap

The exact N-particle ground state wave function for a one-dimensional condensate of hard core bosons in a harmonic trap is employed to obtain accurate numerical results for the one-particle density matrix, occupation number distribution of the natural orbitals, and momentum distribution. Our results show that the occupation of the lowest orbital varies as N^{0.59}, in contrast to N^{0.5} for a spatially uniform system, and N for a true BEC.Comment: 10 pages, 6 figures, submitted to Phys. Rev.

Reproductive skew and relatedness in social groups of European badgers, Meles meles

Abstract Reproductive skew is a measure of the proportion of individuals of each sex that breed in a group and is a valuable measure for understanding the evolution and maintenance of sociality. Here, we provide the first quantification of reproductive skew within social groups of European badgers Meles meles, throughout an 18-year study in a high-density population. We used 22 microsatellite loci to analyse within-group relatedness and demonstrated that badger groups contained relatives. The average within-group relatedness was high (R = 0.20) and approximately one-third of within-group dyads were more likely to represent first-order kin than unrelated pairs. Adult females within groups had higher pairwise relatedness than adult males, due to the high frequency of extra-group paternities, rather than permanent physical dispersal. Spatial clustering of relatives occurred among neighbouring groups, which we suggest was due to the majority of extra-group paternities being attributable to neighbouring males. Reproductive skew was found among withingroup candidate fathers (B = 0.26) and candidate mothers (B = 0.07), but not among breeding individuals; our power to detect skew in the latter was low. We use these results to evaluate reproductive skew models. Although badger society best fits the assumptions of the incomplete-control models, our results were not consistent with their predictions. We suggest that this may be due to female control of paternity, female-female reproductive suppression occurring only in years with high food availability resulting in competition over access to breeding sites, extra-group paternity masking the benefits of natal philopatry, and/or the inconsistent occurrence of hierarchies that are linear when established

High Resolution Spectroscopy of the Pulsating White Dwarf G29-38

We present the analysis of time-resolved, high resolution spectra of the cool white dwarf pulsator, G29-38. From measuring the Doppler shifts of the H-alpha core, we detect velocity changes as large as 16.5 km/s and conclude that they are due to the horizontal motions associated with the g-mode pulsations on the star. We detect seven pulsation modes from the velocity time-series and identify the same modes in the flux variations. We discuss the properties of these modes and use the advantage of having both velocity and flux measurements of the pulsations to test the convective driving theory proposed for DAV stars. Our data show limited agreement with the expected relationships between the amplitude and phases of the velocity and flux modes. Unexpectedly, the velocity curve shows evidence for harmonic distortion, in the form of a peak in the Fourier transform whose frequency is the exact sum of the two largest frequencies. Combination frequencies are a characteristic feature of the Fourier transforms of light curves of G29-38, but before now have not been detected in the velocities, nor does published theory predict that they should exist. We compare our velocity combination frequency to combination frequencies found in the analysis of light curves of G29-38, and discuss what might account for the existence of velocity combinations with the properties we observe. We also use our high-resolution spectra to determine if either rotation or pulsation can explain the truncated shape observed for the DAV star's line core. We are able to eliminate both mechanisms: the average spectrum does not fit the rotationally broadened model and the time-series of spectra provides proof that the pulsations do not significantly truncate the line.Comment: 24 pages, 9 figures, Accepted for publication in ApJ (June