Accuracy of generalized gradient approximation functionals for density functional perturbation theory calculations

We assess the validity of various exchange-correlation functionals for computing the structural, vibrational, dielectric, and thermodynamical properties of materials in the framework of density-functional perturbation theory (DFPT). We consider five generalized-gradient approximation (GGA) functionals (PBE, PBEsol, WC, AM05, and HTBS) as well as the local density approximation (LDA) functional. We investigate a wide variety of materials including a semiconductor (silicon), a metal (copper), and various insulators (SiO$_2$ $\alpha$-quartz and stishovite, ZrSiO$_4$ zircon, and MgO periclase). For the structural properties, we find that PBEsol and WC are the closest to the experiments and AM05 performs only slightly worse. All three functionals actually improve over LDA and PBE in contrast with HTBS, which is shown to fail dramatically for $\alpha$-quartz. For the vibrational and thermodynamical properties, LDA performs surprisingly very good. In the majority of the test cases, it outperforms PBE significantly and also the WC, PBEsol and AM05 functionals though by a smaller margin (and to the detriment of structural parameters). On the other hand, HTBS performs also poorly for vibrational quantities. For the dielectric properties, none of the functionals can be put forward. They all (i) fail to reproduce the electronic dielectric constant due to the well-known band gap problem and (ii) tend to overestimate the oscillator strengths (and hence the static dielectric constant)

First-principles study of iron oxyfluorides and lithiation of FeOF

First-principles studies of iron oxyfluorides in the FeF[subscript 2] rutile framework (FeO[subscript x]F[subscript 2−x], 0≤x≤1) are performed using density functional theory (DFT) in the general gradient approximation (GGA) with a Hubbard U correction. Studies of O/F orderings reveal FeOF to be particularly stable compared to other FeO[subscript x]F[subscript 2−x] (x≠1) structures, where FeF[subscript 2]-FeOF mixing is not energetically favored. The band gap of FeF[subscript 2] is found to decrease as oxygen is substituted into its structure. The GGA + U electronic structure evolves from that of a Mott-Hubbard insulator (x=0) to a charge transfer semiconductor (x=1). Lithiation studies reveal that lithiation sites offering mixed O/F environments are the most stable. An insertion voltage plateau up to Li[subscript 0.5]FeOF on lithiation is found, in agreement with recent Li-ion battery experiments. The energetics of further lithiation with respect to conversion scenarios are discussed.United States. Dept. of Energy. Office of Basic Energy Sciences (Northeastern Center for Chemical Energy Storage Award DE-SC0001294

Hystricognathy vs Sciurognathy in the Rodent Jaw: A New Morphometric Assessment of Hystricognathy Applied to the Living Fossil Laonastes (Diatomyidae)

While exceptional for an intense diversification of lineages, the evolutionary history of the order Rodentia comprises only a limited number of morphological morphotypes for the mandible. This situation could partly explain the intense debates about the taxonomic position of the latest described member of this clade, the Laotian rock rat Laonastes aenigmamus (Diatomyidae). This discovery has re-launched the debate on the definition of the Hystricognathi suborder identified using the angle of the jaw relative to the plane of the incisors. Our study aims to end this ambiguity. For clarity, it became necessary to revisit the entire morphological diversity of the mandible in extant and extinct rodents. However, current and past rodent diversity brings out the limitations of the qualitative descriptive approach and highlights the need for a quantitative approach. Here, we present the first descriptive comparison of the masticatory apparatus within the Ctenohystrica clade, in combining classic comparative anatomy with morphometrical methods. First, we quantified the shape of the mandible in rodents using 3D landmarks. Then, the analysis of osteological features was compared to myological features in order to understand the biomechanical origin of this morphological diversity. Among the morphological variation observed, the mandible of Laonastes aenigmamus displays an intermediate association of features that could be considered neither as sciurognathous nor as hystricognathous

Good Vibrations : The evolution of whisking in small mammals

Special Issue: Extreme Anatomy: Living Beyond the Edge. January 2020Abstract While most mammals have whiskers, some tactile specialists - mainly small, nocturnal and arboreal species - can actively move their whiskers in a symmetrical, cyclic movement called whisking. Whisking enables mammals to rapidly, tactually scan their environment in order to efficiently guide locomotion and foraging in complex habitats. The muscle architecture that enables whisking is preserved from marsupials to primates, prompting researchers to suggest that a common ancestor might have had moveable whiskers. Studying the evolution of whisker touch sensing is difficult, and we suggest that measuring an aspect of skull morphology that correlates with whisking would enable comparisons between extinct and extant mammals. We find that whisking mammals have larger infraorbital foramen (IOF) areas, which indicates larger infraorbital nerves and an increase in sensory acuity. While this relationship is quite variable and IOF area cannot be used to solely predict the presence of whisking, whisking mammals all have large IOF areas. Generally, this pattern holds true regardless of an animal's substrate preferences or activity patterns. Data from fossil mammals and ancestral character state reconstruction and tracing techniques for extant mammals suggest that whisking is not the ancestral state for therian mammals. Instead, whisking appears to have evolved independently as many as seven times across the clades Marsupialia, Afrosoricida, Eulipotyphla and Rodentia, with Xenarthra the only placental superordinal clade lacking whisking species. However, the term whisking only captures symmetrical and rhythmic movements of the whiskers, rather than all possible whisker movements, and early mammals may still have had moveable whiskers. This article is protected by copyright. All rights reserved.Peer reviewe

Dental eruption and growth in Hyracoidea (Mammalia, Afrotheria)

We investigated dental homologies, development, and growth in living and fossil hyracoids, and tested if hyracoids and other mammals show correlations between eruption patterns, gestation time, and age at maturity. Unlike living species, fossil hyracoids simultaneously possess replaced P1 and canine teeth. Fossil species also have shorter crowns, an upper and lower I3 locus, an upper I2, and a hypoconulid on m3. Prenatal specimens of the living $\textit{Procavia capensis}$ and $\textit{Heterohyrax brucei}$ show up to three tooth buds posterior to upper dI1 and anterior to the seven upper cheek teeth that consistently erupt; these include an anterior premolar but not a canine. Most lower cheek teeth finish eruption during growth in hyracoids, not after growth as in most other afrotherians. All hyracoids show the m1 at (lower) or near (upper) the beginning of eruption of permanent teeth; M3/m3 is the last permanent tooth to erupt. The living P. capensis erupts most lower antemolar loci before m2. In contrast, fossil hyraxes erupt lower antemolars after m2. While the early eruption of antemolars correlates with increased gestation time and age at maturity in primates and $\textit{Tupaia}$ (i.e., "Schultz's Rule"), and while modern hyraxes resemble some anthropoid primates in exhibiting long gestation and eruption of antemolars at or before molars, eruption patterns do not significantly co-vary with either life history parameter among afrotherians sampled so far. However, we do observe a shift in eruption timing and crown height in $\textit{Procavia}$ relative to fossil hyracoids, mirroring observations recently made for other ungulate-grade mammals.Collection of Fayum hyracoids has been funded by U.S. National Science Foundation grants to E. L. Simons (BCS-0114856), to ELS and E. R. Seiffert (BCS- 0416164), to ERS (BCS-0819186), and to ERS, J. G. Fleagle, G. F. Gunnell, and D. M. Boyer (BCS-1231288). Fieldwork was undertaken in collaboration with the Egyptian Mineral Resources Authority and the Egyptian Geological Museum, and was managed by P. Chatrath. RJA, LH, and DP acknowledge support from the Leverhulme Trust and the Department of Zoology, University of Cambridge. We thank C. Riddle and V. Yarborough for access to fossils and fossil preparation, and C. Soubiran for help with segmentation of extant hyrax CT scans. Some CTscan data presented in this work were produced thanks to the imaging facilities of the MRI Platform and of the LabEx CeMEB (Montpellier)

Biodiversity promotes ecosystem functioning despite environmental change

Three decades of research have demonstrated that biodiversity can promote the functioning of ecosystems. Yet, it is unclear whether the positive effects of biodiversity on ecosystem functioning will persist under various types of global environmental change drivers. We conducted a meta-analysis of 46 factorial experiments manipulating both species richness and the environment to test how global change drivers (i.e. warming, drought, nutrient addition or CO2 enrichment) modulated the effect of biodiversity on multiple ecosystem functions across three taxonomic groups (microbes, phytoplankton and plants). We found that biodiversity increased ecosystem functioning in both ambient and manipulated environments, but often not to the same degree. In particular, biodiversity effects on ecosystem functioning were larger in stressful environments induced by global change drivers, indicating that high-diversity communities were more resistant to environmental change. Using a subset of studies, we also found that the positive effects of biodiversity were mainly driven by interspecific complementarity and that these effects increased over time in both ambient and manipulated environments. Our findings support biodiversity conservation as a key strategy for sustainable ecosystem management in the face of global environmental change

Effects of intra-annual precipitation patterns on grassland productivity moderated by the dominant species phenology

Phenology and productivity are important functional indicators of grassland ecosystems. However, our understanding of how intra-annual precipitation patterns affect plant phenology and productivity in grasslands is still limited. Here, we conducted a two-year precipitation manipulation experiment to explore the responses of plant phenology and productivity to intra-annual precipitation patterns at the community and dominant species levels in a temperate grassland. We found that increased early growing season precipitation enhanced the above-ground biomass of the dominant rhizome grass, Leymus chinensis, by advancing its flowering date, while increased late growing season precipitation increased the above-ground biomass of the dominant bunchgrass, Stipa grandis, by delaying senescence. The complementary effects in phenology and biomass of the dominant species, L. chinensis and S. grandis, maintained stable dynamics of the community above-ground biomass under intra-annual precipitation pattern variations. Our results highlight the critical role that intra-annual precipitation and soil moisture patterns play in the phenology of temperate grasslands. By understanding the response of phenology to intra-annual precipitation patterns, we can more accurately predict the productivity of temperate grasslands under future climate change

Grand challenges in biodiversity-ecosystem functioning research in the era of science-policy platforms require explicit consideration of feedbacks

Feedbacks are an essential feature of resilient socio-economic systems, yet the feedbacks between biodiversity, ecosystem services and human wellbeing are not fully accounted for in global policy efforts that consider future scenarios for human activities and their consequences for nature. Failure to integrate feedbacks in our knowledge frameworks exacerbates uncertainty in future projections and potentially prevents us from realizing the full benefits of actions we can take to enhance sustainability. We identify six scientific research challenges that, if addressed, could allow future policy, conservation and monitoring efforts to quantitatively account for ecosystem and societal consequences of biodiversity change. Placing feedbacks prominently in our frameworks would lead to (i) coordinated observation of biodiversity change, ecosystem functions and human actions, (ii) joint experiment and observation programmes, (iii) more effective use of emerging technologies in biodiversity science and policy, and (iv) a more inclusive and integrated global community of biodiversity observers. To meet these challenges, we outline a five-point action plan for collaboration and connection among scientists and policymakers that emphasizes diversity, inclusion and open access. Efforts to protect biodiversity require the best possible scientific understanding of human activities, biodiversity trends, ecosystem functions and—critically—the feedbacks among them