Genotyping of Capreolus pygargus Fossil DNA from Denisova Cave Reveals Phylogenetic Relationships between Ancient and Modern Populations

BACKGROUND: The extant roe deer (Capreolus Gray, 1821) includes two species: the European roe deer (C. capreolus) and the Siberian roe deer (C. pygargus) that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia), where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan), Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains) are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples. CONCLUSION/SIGNIFICANCE: Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian roe deer represent a complex and heterogeneous species with high migration rates and without evident subspecies structure. Low genetic diversity of the West Siberian Plain population indicates a recent bottleneck or founder effect

QCD and strongly coupled gauge theories : challenges and perspectives

We highlight the progress, current status, and open challenges of QCD-driven physics, in theory and in experiment. We discuss how the strong interaction is intimately connected to a broad sweep of physical problems, in settings ranging from astrophysics and cosmology to strongly coupled, complex systems in particle and condensed-matter physics, as well as to searches for physics beyond the Standard Model. We also discuss how success in describing the strong interaction impacts other fields, and, in turn, how such subjects can impact studies of the strong interaction. In the course of the work we offer a perspective on the many research streams which flow into and out of QCD, as well as a vision for future developments.Peer reviewe

An investigation of the structural dynamics in the fast ionic conductor Cu2-delta Se using neutron scattering.

Energy resolved neutron diffraction measurements were performed on Cu1.75Se and Cu1.98Se samples for both α- and β-phases. In-situ measurements of the Cu1.98Se compound during heating show that the β-α phase transition takes place at 420K and has noticeable temperature hysteresis. In addition to Bragg reflections, the diffraction patterns of the α-Cu1.75Se at RT and α-Cu1.98Se at 435 K samples taken in conventional two-axis geometry show a broad maximum related to diffuse scattering. This diffuse background is suppressed in the energy resolved experiment which indicates a strong contribution from inelastic scattering coming from correlated thermal displacements of the ions in the super-ionic phase. On the other hand, the diffraction pattern of the non super-ionic β-phase shows only minor differences between spectra measured with and without the analyser crystal. © 2007, Elsevier Ltd

Diffuse scattering and lattice dynamics of superionic copper chalcogenides.

The energy-resolved neutron diffraction and inelastic neutron scattering study of diffuse scattering in copper chalcogenides was performed in order to clarify the role of static disorder versus low-energy phonons. Neutron diffraction patterns taken from Cu1.75Se, Cu1.98Se and Ag0.25Cu1.75Se powders in superionic phase show a broad maximum related to diffuse scattering. This diffuse background is suppressed in the energy-resolved experiment which indicates a strong contribution from inelastic scattering coming from correlated thermal displacements of the ions in the superionic phase. Diffraction experiments on a single crystal of α-Cu1.8Se have revealed an ordered structure with superstructure reflections at the G +/- 1/2 and G +/- 1/3 positions of reciprocal space at room temperature. In addition to superstructure spots, diffuse scattering was observed along the direction which is considered as a possible diffusion path of mobile Cu ions. In inelastic neutron scattering measurements with this single crystal sample strong inelastic scattering was observed along . This shows that the diffuse scattering found in conventional diffraction experiment is mainly inelastic and most probably comes from low-energy phonons. © 2009, Elsevier Ltd

Phonon dispersion in superionic copper selenide - observation of soft phonon modes in superionic phase transition.

This paper reports lattice dynamical measurements of Cu1.8Se superionic conductor in the superionic α-phase at ambient temperature. Measurements of phonon dispersion curves were performed with the new triple-axis spectrometer, TAIPAN, at the OPAL reactor. We found that TA [100], TA [111] and TA1 [110] phonon branches demonstrate a decrease in frequency at wavevectors q > 0.5 rather than the flattening observed previously. Results are compared with calculated density functional theoretical calculations showing the presence of unstable soft mode related to ordering of Cu atoms observed in Cu1.8Se at room temperature followed by α–β phase transition at a lower temperature. Superstructure arising from the ordering causes effects similar to the folding of the Brillouin zone, although phonon intensities at new Brillouin zone centres are weak. The coupling of low-energy phonon modes with displacement of mobile ions can explain the strong damping of phonons at q > 0.5 observed in the experiment

Neutron diffraction study of diffuse scattering in Cu2-delta Se superionic compounds

Crystal structure and short-range order in Cu2-delta Se compounds were studied in superionic and non-superionic phases using high-resolution neutron diffractometer Echidna at ANSTO. In diffraction patterns of beta-Cu-1.98 Se (ordered phase at ambient T), both Bragg peaks and diffuse background change sharply through the beta -> alpha structural phase transition at T = 414K during heating. In case of alpha-Cu1.75Se (disordered superionic phase at ambient T) the changes are monotonic, showing gradual shifts of Bragg peaks and increased intensity of the diffuse background as a function of temperature. On cooling, both compounds undergo a beta -> beta ' transformation. Diffuse scattering in the alpha-phase shows an oscillating dependence on wavevector, with broad peaks centred at Q similar to 3, 5.5 and 8 angstrom(-1). The measurements taken in energy dispersive mode show that the oscillating diffuse background arises from correlated thermal displacements of the ions. Diffuse scattering is higher for compositions close to stoichiometry and increases with temperature. Theoretical calculations show that the increase in diffuse intensity both with temperature and Cu content is related to correlated thermal vibrations of Se and Cu atoms, with Se-Cu(8c, 32f) and Cu(8c)-Cu(8c) correlations being the most important. (C) 2011 Elsevier B.V. All rights reserved

Dynamical mechanism of phase transitions in A-site ferroelectric relaxor (Na1/2Bi1/2)TiO3

The dynamical phase transition mechanism of (Na1/2Bi1/2)TiO3 (NBT) was studied using inelastic neutron scattering. Softening was observed of multiple phonon modes in the phase transition sequence of NBT. As usual, the softening of the zone center transverse optical modes Δ5 and Σ3 was observed in the (200) and (220) zones, showing the Ti vibration instabilities in TiO6 octahedra for both cubic-tetragonal (C-T) and tetragonal-rhombohedral (T-R) phase transitions. In these two phase transitions, however, Ti4+ has different preferential displacement directions. Surprisingly, the longitudinal optic mode also softens significantly toward the zone center in the range of the transition temperature, indicating the Na+/Bi3+ vibration instability against TiO6 octahedra during the T-R phase transition. Strong inelastic diffuse scattering shows up near M(1.5, 0.5, 0) and R(1.5, 1.5, 0.5) in the tetragonal and rhombohedral phases, respectively, indicating the condensations of the M3 and R25 optic modes for the corresponding transitions. This reveals the different rotation instabilities of TiO6 in the corresponding transition temperature range. Bottleneck or waterfall features were observed in the dispersion curves at certain temperatures but did not show close correlations to the formation of polar nanoregions. Additional instabilities could be the origin of the complexity of phase transitions and crystallographic structures in NBT.© 2014, American Physical Society

Derivation of inter-atomic force constants of Cu2O from neutron scattering measurement

Neutron scattering intensity from Cu2O compound has been measured at 10 K and 295 K with High Resolution Powder Diffractometer at JRR-3 JAEA. The oscillatory diffuse scattering related to correlations among thermal displacements of atoms was observed at 295 K. The correlation parameters were determined from the observed diffuse scattering intensity at 10 and 295 K. The force constants between the neighboring atoms in Cu2O were estimated from the correlation parameters and compared to those of Ag2O.© 2013, Atoms Indonesia

Coexistence of long-range magnetic ordering and singlet ground state in the spin-ladder superconductor SrCa13Cu24O41

A long-range magnetic order was discovered in the quasi-one-dimensional spin-ladder compound SrCa13Cu24O41 by susceptibility, specific heat, and neutron diffraction experiments. The temperature dependence of the magnetic Bragg peak intensity could be well fitted to the power law with a transition temperature TN = 4.23 K and a critical exponent β = 0.28, indicating a three-dimensional phase transition for a low-dimensional magnet. A computer program was coded and found two possible magnetic structure models fitting best with all the observed magnetic peaks. These models suggest the spin-ladder sublattice is magnetically ordered with Cu moments aligning along the a axis. The spin interactions are primarily antiferromagnetic along rungs and legs, while there are ferromagnetic clusters along legs. Surprisingly, the singlet-triplet spin-gap excitation is observable above and below TN, indicating a coexistence of the spin-singlet ground state and long-range magnetic ordering state in this compound. © 2013, American Physical Society

Inter-atomic force constants of Ag2O from diffuse neutron scattering measurement

Diffuse neutron scattering measurements have been performed on powder Ag(2)O at 8 and 295 K with the use of High Resolution Powder Diffractometer installed at JRR-3 in Japan Atomic Energy Agency. Oscillatory diffuse scattering intensities are clearly observed at 8 and 295 K. The observed diffuse scattering intensities are explained by including the correlation effects among thermal displacements of atoms. The force constants among neighboring atoms in Ag(2)O are obtained from the values of correlation effects and Debye-Waller temperature parameters at 295 K. © 2012, Elsevier Ltd