Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species

Comparing inferences among datasets generated using short read sequencing may provide insight into the concerted impacts of divergence, gene flow and selection across organisms, but comparisons are complicated by biases introduced during dataset assembly. Sequence similarity thresholds allow the de novo assembly of short reads into clusters of alleles representing different loci, but the resulting datasets are sensitive to both the similarity threshold used and to the variation naturally present in the organism under study. Thresholds that require high sequence similarity among reads for assembly (stringent thresholds) as well as highly variable species may result in datasets in which divergent alleles are lost or divided into separate loci (‘over-splitting’), whereas liberal thresholds increase the risk of paralogous loci being combined into a single locus (‘under-splitting’). Comparisons among datasets or species are therefore potentially biased if different similarity thresholds are applied or if the species differ in levels of within-lineage genetic variation. We examine the impact of a range of similarity thresholds on assembly of empirical short read datasets from populations of four different non-model bird lineages (species or species pairs) with different levels of genetic divergence. We find that, in all species, stringent similarity thresholds result in fewer alleles per locus than more liberal thresholds, which appears to be the result of high levels of over-splitting. The frequency of putative under-splitting, conversely, is low at all thresholds. Inferred genetic distances between individuals, gene tree depths, and estimates of the ancestral mutation-scaled effective population size (θ) differ depending upon the similarity threshold applied. Relative differences in inferences across species differ even when the same threshold is applied, but may be dramatically different when datasets assembled under different thresholds are compared. These differences not only complicate comparisons across species, but also preclude the application of standard mutation rates for parameter calibration. We suggest some best practices for assembling short read data to maximize comparability, such as using more liberal thresholds and examining the impact of different thresholds on each dataset

Dynamic Structure Factor of Liquid and Amorphous Ge From Ab Initio Simulations

We calculate the dynamic structure factor S(k,omega) of liquid Ge (l-Ge) at temperature T = 1250 K, and of amorphous Ge (a-Ge) at T = 300 K, using ab initio molecular dynamics. The electronic energy is computed using density-functional theory, primarily in the generalized gradient approximation, together with a plane wave representation of the wave functions and ultra-soft pseudopotentials. We use a 64-atom cell with periodic boundary conditions, and calculate averages over runs of up to 16 ps. The calculated liquid S(k,omega) agrees qualitatively with that obtained by Hosokawa et al, using inelastic X-ray scattering. In a-Ge, we find that the calculated S(k,omega) is in qualitative agreement with that obtained experimentally by Maley et al. Our results suggest that the ab initio approach is sufficient to allow approximate calculations of S(k,omega) in both liquid and amorphous materials.Comment: 31 pages and 8 figures. Accepted for Phys. Rev.

Results of two multi-chord stellar occultations by dwarf planet (1) Ceres

We report the results of two multi-chord stellar occultations by the dwarf planet (1) Ceres that were observed from Brazil on 2010 August 17, and from the USA on 2013 October 25. Four positive detections were obtained for the 2010 occultation, and nine for the 2013 occultation. Elliptical models were adjusted to the observed chords to obtain Ceres' size and shape. Two limb fitting solutions were studied for each event. The first one is a nominal solution with an indeterminate polar aspect angle. The second one was constrained by the pole coordinates as given by Drummond et al. Assuming a Maclaurin spheroid, we determine an equatorial diameter of 972 $\pm$ 6 km and an apparent oblateness of 0.08 $\pm$ 0.03 as our best solution. These results are compared to all available size and shape determinations for Ceres made so far, and shall be confirmed by the NASA's Dawn space mission.Comment: 9 pages, 6 figures. Accepted for publication in MNRA

High-Field Quasiparticle Tunneling in Bi_2Sr_2CaCu_2O_8+delta: Negative Magnetoresistance in the Superconducting State

We report on the c-axis resistivity rho_c(H) in Bi_2Sr_2CaCu_2O_{8+\delta} that peaks in quasi-static magnetic fields up to 60 T. By suppressing the Josephson part of the two-channel (Cooper pair/quasiparticle) conductivity \sigma_c (H), we find that the negative slope of \rho_c(H) above the peak is due to quasiparticle tunneling conductivity \sigma_q(H) across the CuO_2 layers below H_{c2}. At high fields (a) \sigma_q(H) grows linearly with H, and (b) \rho_c(T) tends to saturate (sigma_c \neq 0) as T->0, consistent with the scattering at the nodes of the d-gap. A superlinear sigma_q(H) marks the normal state above T_c.Comment: 4p., 5 fig. (.eps), will be published in Phys. Rev. Let

Evidence for LineLike Vortex Liquid Phase in Tl2_2Ba2_2CaCu2_2O8_8 Probed by the Josephson Plasma Resonance

We measured the Josephson plasma resonance (JPR) in optimally doped Tl$_2$Ba$_2$CaCu$_2$O$_{8+\delta}$ thin films using terahertz time-domain spectroscopy in transmission. The temperature and magnetic field dependence of the JPR frequency shows that the c-axis correlations of pancake vortices remain intact at the transition from the vortex solid to the liquid phase. In this respect Tl$_2$Ba$_2$CaCu$_2$O$_{8+\delta}$ films, withanisotropy parameter $\gamma\approx 150$, are similar to the less anisotropic YBa$_2$Cu$_3$O$_{7-\delta}$ $(\gamma\approx 8)$ rather than to the most anisotropic Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ single crystals $\gamma\geq 500$).Comment: Submitted to Physical Review Letter

An investigation into CLIL-related sections of EFL coursebooks : issues of CLIL inclusion in the publishing market

The current ELT global coursebook market has embraced CLIL as a weak form of bilingual education and an innovative component to include in General English coursebooks for EFL contexts. In this paper I investigate how CLIL is included in ELT coursebooks aimed at teenaged learners, available to teachers in Argentina. My study is based on the content analysis of four series which include a section advertised as CLIL-oriented. Results suggest that such sections are characterised by (1) little correlation between featured subject specific content and school curricula in L1, (2) oversimplification of contents, and (3) dominance of reading skills development and lower-order thinking tasks. Through this study, I argue that CLIL components become superficial supplements rather than a meaningful attempt to promote weak forms of bilingual education

Interlayer Quasiparticle Transport in the Vortex State of Josephson Coupled Superconductors

We calculate the dependence of the interlayer quasiparticle conductivity, $\sigma_q$, in a Josephson coupled d-wave superconductor on the magnetic field B||c and the temperature T. We consider a clean superconductor with resonant impurity scattering and a dominant coherent interlayer tunneling. When pancake vortices in adjacent layers are weakly correlated at low T the conductivity increases sharply with B before reaching an extended region of slow linear growth, while at high T it initially decreases and then reaches the same linear regime. For correlated pancakes $\sigma_q$ increases much more strongly with the applied field.Comment: 4 pages, 3 figure