Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr)

In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two Arabian leopards and assembled the most complete genomic dataset for leopards to date. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades: the African and the Asian. Conservation genomic analyses indicate a prolonged population decline, which has led to an increase in inbreeding and runs of homozygosity, with consequent purging of deleterious mutations in both Arabian individuals. Our study represents the first attempt to genetically inform captive breeding programmes for this Critically Endangered subspecies.

Giant room temperature compression and bending in ferroelectric oxide pillars

Plastic deformation in ceramic materials is normally only observed in nanometre-sized samples. However, we have observed high levels of plasticity (>50% plastic strain) and excellent elasticity (6% elastic strain) in perovskite oxide Pb(In1/2Nb1/2)O3-Pb(Mg1/3Nb2/3)O3-PbTiO3, under compression along <100>pc pillars up to 2.1 μm in diameter. The extent of this deformation is much higher than has previously been reported for ceramic materials, and the sample size at which plasticity is observed is almost an order of magnitude larger. Bending tests also revealed over 8% flexural strain. Plastic deformation occurred by slip along {110} <1[Formula: see text]0 > . Calculations indicate that the resulting strain gradients will give rise to giant flexoelectric polarization. First principles models predict that a high concentration of oxygen vacancies weaken the covalent/ionic bonds, giving rise to the unexpected plasticity. Mechanical testing on oxygen vacancies-rich Mn-doped Pb(In1/2Nb1/2)O3-Pb(Mg1/3Nb2/3)O3-PbTiO3 confirmed this prediction. These findings will facilitate the design of plastic ceramic materials and the development of flexoelectric-based nano-electromechanical systems.

Anisotropic diffusion creep in postperovskite provides a new model for deformation at the core-mantle boundary

The lowermost portion of Earth's mantle (D″) above the core-mantle boundary shows anomalous seismic features, such as strong seismic anisotropy, related to the properties of the main mineral MgSiO3 postperovskite. But, after over a decade of investigations, the seismic observations still cannot be explained simply by flow models which assume dislocation creep in postperovskite. We have investigated the chemical diffusivity of perovskite and postperovskite phases by experiment and ab initio simulation, and derive equations for the observed anisotropic diffusion creep. There is excellent agreement between experiments and simulations for both phases in all of the chemical systems studied. Single-crystal diffusivity in postperovskite displays at least 3 orders of magnitude of anisotropy by experiment and simulation (Da = 1,000 Db; Db ≈ Dc) in zinc fluoride, and an even more extreme anisotropy is predicted (Da = 10,000 Dc; Dc = 10,000 Db) in the natural MgSiO3 system. Anisotropic chemical diffusivity results in anisotropic diffusion creep, texture generation, and a strain-weakening rheology. The results for MgSiO3 postperovskite strongly imply that regions within the D″ region of Earth dominated by postperovskite will 1) be substantially weaker than regions dominated by perovskite and 2) develop a strain-induced crystallographic-preferred orientation with strain-weakening rheology. This leads to strain localization and the possibility to bring regions with significantly varying textures into close proximity by strain on narrow shear zones. Anisotropic diffusion creep therefore provides an attractive alternative explanation for the complexity in observed seismic anisotropy and the rapid lateral changes in seismic velocities in D″.

Competing Deformation Mechanisms in Periclase: Implications for Lower Mantle Anisotropy

Seismic anisotropy is observed above the core-mantle boundary in regions of slab subduction and near the margins of Large Low Shear Velocity Provinces (LLSVPs). Ferropericlase is believed to be the second most abundant phase in the lower mantle. As it is rheologically weak, it may be a dominant source for anisotropy in the lowermost mantle. Understanding deformation mechanisms in ferropericlase over a range of pressure and temperature conditions is crucial to interpret seismic anisotropy. The effect of temperature on deformation mechanisms of ferropericlase has been established, but the effects of pressure are still controversial. With the aim to clarify and quantify the effect of pressure on deformation mechanisms, we perform room temperature compression experiments on polycrystalline periclase to 50 GPa. Lattice strains and texture development are modeled using the Elasto-ViscoPlastic Self Consistent method (EVPSC). Based on modeling results, we find that { 110 } ⟨ 1 1 ¯ 0 ⟩ slip is increasingly activated with higher pressure and is fully activated at ~50 GPa. Pressure and temperature have a competing effect on activities of dominant slip systems. An increasing { 100 } ⟨ 011 ⟩ : { 110 } ⟨ 1 1 ¯ 0 ⟩ ratio of slip activity is expected as material moves from cold subduction regions towards hot upwelling region adjacent to LLSVPs. This could explain observed seismic anisotropy in the circum-Pacific region that appears to weaken near margins of LLVSPs.

A simple variant selection in stress-driven martensitic transformation

The study of orientation variant selection helps to reveal the mechanism and dynamic process of martensitic transformations driven by temperature or pressure/stress. This is challenging due to the multiple variants which may coexist. While effects of temperature and microstructure in many martensitic transformations have been studied in detail, effects of stress and pressure are much less understood. Here, an in situ variant selection study of Mn₂O₃ across the cubic-to-orthorhombic martensitic transformation explores orientation variants at pressures up to 51.5 GPa and stresses up to 5.5 GPa, using diamond anvil cells in radial geometry with synchrotron X-ray diffraction. The diamonds not only exert pressure but also impose stress and cause plastic deformation and texture development. The crystal orientation changes were followed in situ and a {110} _c 〈001〉 _c // (100) _o 〈010〉 _o relationship was observed. Only the {110} _c plane perpendicular to the stress direction was selected to become (100) _o , resulting in a very strong texture of the orthorhombic phase. Contrary to most other martensitic transformations, this study reveals a clear and simple variant selection that is attributed to structural distortions under pressure and stress.

Prediction of Mechanical Twinning in Magnesium Silicate Post-Perovskite

The plastic properties of MgSiO3 post-perovskite are considered to be one of the key issues necessary for understanding the seismic anisotropy at the bottom of the mantle in the so-called D" layer. Although plastic slip in MgSiO3 post-perovskite has attracted considerable attention, the twinning mechanism has not been addressed, despite some experimental evidence from low-pressure analogues. On the basis of a numerical mechanical model, we present a twin nucleation model for post-perovskite involving the emission of 1/6 <110> partial dislocations. Relying on first-principles calculations with no adjustable parameters, we show that {110} twin wall formation resulting from the interaction of multiple twin dislocations occurs at a twinning stress comparable in magnitude to the most readily occurring slip system in post-perovskite. Because dislocation activities and twinning are competitive strain-producing mechanisms, twinning should be considered in future models of crystallographic preferred orientations in post-perovskite to better interpret seismic anisotropy in the lowermost lower mantle.

Seismic anisotropy of the D″ layer induced by (001) deformation of post-perovskite

Crystallographic preferred orientation (CPO) of post-perovskite (Mg,Fe)SiO₃ (pPv) has been believed to be one potential source of the seismic anisotropic layer at the bottom of the lower mantle (D″ layer). However, the natural CPO of pPv remains ambiguous in the D″ layer. Here we have carried out the deformation experiments of pPv-(Mg_0.75,Fe_0.25)SiO₃ using synchrotron radial X-ray diffraction in a membrane-driven laser-heated diamond anvil cell from 135 GPa and 2,500 K to 154 GPa and 3,000 K. Our results show that the intrinsic texture of pPv-(Mg_0.75,Fe_0.25)SiO₃ should be (001) at realistic P–T conditions of the D″ layer, which can produce a shear wave splitting anisotropy of ∼3.7% with V_SH>V_SV. Considering the combined effect of both pPv and ferropericlase, we suggest that 50% or less of deformation is sufficient to explain the origin of the shear wave anisotropy observed seismically in the D″ layer beneath the circum-Pacific rim.

The source of the anisotropic layer (D'' layer) at the bottom of the lower mantle remains unclear. Here, using high pressure and temperature experiments, the authors find that seismic anisotropy observed at the D'' layer is caused by 50% deformation of the minerals post-perovskite and ferropericlase.

Modeling defects and plasticity in MgSiO3 post-perovskite: Part 3-Screw and edge [001] dislocations

In this study, we investigate the complex structure of [001] screw and edge dislocation cores in MgSiO₃ post-perovskite at the atomic scale. Both [001] screw and edge dislocations exhibit spontaneous dissociation in (010) into two symmetric partials characterized by the presence of <100> component. In case of edge dislocations, dissociation occurs into ½<101> partials, while for the screw dislocations the <100> component reaches only 15%. Under applied stress, both [001](010) screw and edge dislocations behave similarly. Above the Peierls stress, the two partials glide together while keeping their stacking-fault widths (~11 and ~42 Å for the screw and edge dislocations, respectively) constant. The Peierls stress opposed to the glide of [001](010) screw dislocations is 3 GPa, while that of edge dislocations is 33% lower. Relying on the observed characteristics of the dislocation cores, we estimate the efficiency of [001](010) dislocation glide under the P-T conditions relevant to the lowermost mantle and demonstrate that dislocation creep for this slip system would occur in the so-called athermal regime where lattice friction for the considered slip system vanishes when the temperature rises above the critical T _a value of ~2,000 K.

High-pressure studies with x-rays using diamond anvil cells

Pressure profoundly alters all states of matter. The symbiotic development of ultrahigh-pressure diamond anvil cells, to compress samples to sustainable multi-megabar pressures; and synchrotron x-ray techniques, to probe materials' properties in situ, has enabled the exploration of rich high-pressure (HP) science. In this article, we first introduce the essential concept of diamond anvil cell technology, together with recent developments and its integration with other extreme environments. We then provide an overview of the latest developments in HP synchrotron techniques, their applications, and current problems, followed by a discussion of HP scientific studies using x-rays in the key multidisciplinary fields. These HP studies include: HP x-ray emission spectroscopy, which provides information on the filled electronic states of HP samples; HP x-ray Raman spectroscopy, which probes the HP chemical bonding changes of light elements; HP electronic inelastic x-ray scattering spectroscopy, which accesses high energy electronic phenomena, including electronic band structure, Fermi surface, excitons, plasmons, and their dispersions; HP resonant inelastic x-ray scattering spectroscopy, which probes shallow core excitations, multiplet structures, and spin-resolved electronic structure; HP nuclear resonant x-ray spectroscopy, which provides phonon densities of state and time-resolved Mössbauer information; HP x-ray imaging, which provides information on hierarchical structures, dynamic processes, and internal strains; HP x-ray diffraction, which determines the fundamental structures and densities of single-crystal, polycrystalline, nanocrystalline, and non-crystalline materials; and HP radial x-ray diffraction, which yields deviatoric, elastic and rheological information. Integrating these tools with hydrostatic or uniaxial pressure media, laser and resistive heating, and cryogenic cooling, has enabled investigations of the structural, vibrational, electronic, and magnetic properties of materials over a wide range of pressure-temperature conditions.

Low viscosity and high attenuation in MgSiO3 post-perovskite inferred from atomic-scale calculations

This work represents a numerical study of the thermal activation for dislocation glide of the [100](010) slip system in MgSiO₃ post-perovskite (Mg-ppv) at 120 GPa. We propose an approach based on a one-dimensional line tension model in conjunction with atomic-scale calculations. In this model, the key parameters, namely, the line tension and the Peierls barrier, are obtained from density functional theory calculations. We find a Peierls stress σ_p = 2.1 GPa and a line tension Γ = 9.2 eV/Å, which lead to a kink-pair enthalpy (under zero stress) of 2.69 eV. These values confirm that this slip system bears a very low lattice friction because it vanishes for temperatures above approximately 500 K under mantle conditions. In the Earth’s mantle, high-pressure Mg-ppv silicate is thus expected to become as ductile as ferropericlase. These results confirm the hypothesis of a weak layer in the D″ layer where Mg-ppv is present. Easy glide along [100](010) suggests strong preferred orientations with (010) planes aligned. Highly mobile [100] dislocations are also likely to respond to stresses related to seismic waves, leading to energy dissipation and strong attenuation.

Deformation Behavior across the Zircon-Scheelite Phase Transition

The pressure effects on plastic deformation and phase transformation mechanisms of materials are of great importance to both Earth science and technological applications. Zircon-type materials are abundant in both nature and the industrial field; however, there is still no in situ study of their deformation behavior. Here, by employing radial x-ray diffraction in a diamond anvil cell, we investigate the dislocation-induced texture evolution of zircon-type gadolinium vanadate (GdVO_{4}) in situ under pressure and across its phase transitions to its high-pressure polymorphs. Zircon-type GdVO_{4} develops a (001) compression texture associated with dominant slip along ⟨100⟩{001} starting from 5 GPa. This (001) texture transforms into a (110) texture during the zircon-scheelite phase transition. Our observation demonstrates a martensitic mechanism for the zircon-scheelite transformation. This work will help us understand the local deformation history in the upper mantle and transition zone and provides fundamental guidance on material design and processing for zircon-type materials.

Modeling defects and plasticity in MgSiO3 post-perovskite: Part 1-generalized stacking faults

In this work, we examine the transferability of a pairwise potential model (derived for MgSiO₃ perovskite) to accurately compute the excess energies of the generalized stacking faults (GSF, also called γ-surfaces) in MgSiO₃ post-perovskite. All calculations have been performed at 120 GPa, a pressure relevant to the D″ layer. Taking into account an important aspect of crystal chemistry for complex materials, we consider in detail all possible locations of slip planes in the post-perovskite structure. The γ-surface calculations emphasize the easiness of glide of slip systems with the smallest shear vector [100] and of the [001](010) slip system. Our results are in agreement with previous ab initio calculations. This validates the use the chosen potential model for further full atomistic modeling of dislocations in MgSiO₃ post-perovskite.

Detecting grain rotation at the nanoscale

It is well-believed that below a certain particle size, grain boundary-mediated plastic deformation (e.g., grain rotation, grain boundary sliding and diffusion) substitutes for conventional dislocation nucleation and motion as the dominant deformation mechanism. However, in situ probing of grain boundary processes of ultrafine nanocrystals during plastic deformation has not been feasible, precluding the direct exploration of the nanomechanics. Here we present the in situ texturing observation of bulk-sized platinum in a nickel pressure medium of various particle sizes from 500 nm down to 3 nm. Surprisingly, the texture strength of the same-sized platinum drops rapidly with decreasing grain size of the nickel medium, indicating that more active grain rotation occurs in the smaller nickel nanocrystals. Insight into these processes provides a better understanding of the plastic deformation of nanomaterials in a few-nanometer length scale.

Orientation relations during the α-ω phase transition of zirconium: in situ texture observations at high pressure and temperature

Transition metals Ti, Zr, and Hf have a hexagonal close-packed structure (α) at ambient conditions, but undergo phase transformations with increasing temperature and pressure. Of particular significance is the high-pressure hexagonal ω phase which is brittle compared to the α phase. There has been a long debate about transformation mechanisms and orientation relations between the two crystal structures. Here we present the first high pressure experiments with in situ synchrotron x-ray diffraction texture studies on polycrystalline aggregates. We follow crystal orientation changes in Zr, confirming the original suggestion by Silcock for an α→ω martensitic transition for Ti, with (0001)(α)||(1120)(ω), and a remarkable orientation memory when ω reverts back to α.

Combined resistive and laser heating technique for in situ radial X-ray diffraction in the diamond anvil cell at high pressure and temperature

To extend the range of high-temperature, high-pressure studies within the diamond anvil cell, a Liermann-type diamond anvil cell with radial diffraction geometry (rDAC) was redesigned and developed for synchrotron X-ray diffraction experiments at beamline 12.2.2 of the Advanced Light Source. The rDAC, equipped with graphite heating arrays, allows simultaneous resistive and laser heating while the material is subjected to high pressure. The goals are both to extend the temperature range of external (resistive) heating and to produce environments with lower temperature gradients in a simultaneously resistive- and laser-heated rDAC. Three different geomaterials were used as pilot samples to calibrate and optimize conditions for combined resistive and laser heating. For example, in Run#1, FeO was loaded in a boron-mica gasket and compressed to 11 GPa then gradually resistively heated to 1007 K (1073 K at the diamond side). The laser heating was further applied to FeO to raise temperature to 2273 K. In Run#2, Fe-Ni alloy was compressed to 18 GPa and resistively heated to 1785 K (1973 K at the diamond side). The combined resistive and laser heating was successfully performed again on (Mg0.9Fe0.1)O in Run#3. In this instance, the sample was loaded in a boron-kapton gasket, compressed to 29 GPa, resistive-heated up to 1007 K (1073 K at the diamond side), and further simultaneously laser-heated to achieve a temperature in excess of 2273 K at the sample position. Diffraction patterns obtained from the experiments were deconvoluted using the Rietveld method and quantified for lattice preferred orientation of each material under extreme conditions and during phase transformation.

High-pressure experimental geosciences: state of the art and prospects

This paper aims at reviewing the current advancements of high pressure experimental geosciences. The angle chosen is that of in situ measurements at the high pressure (P) and high temperature (T) conditions relevant of the deep Earth and planets, measurements that are often carried out at large facilities (X-ray synchrotrons and neutron sources). Rather than giving an exhaustive catalogue, four main active areas of research are chosen: the latest advancements on deep Earth mineralogy, how to probe the properties of melts, how to probe Earth dynamics, and chemical reactivity induced by increased P-T conditions. For each area, techniques are briefly presented and selected examples illustrate their potentials, and what that tell us about the structure and dynamics of the planet.