Amount of Information Needed for Model Choice in Approximate Bayesian Computation

Approximate Bayesian Computation (ABC) has become a popular technique in evolutionary genetics for elucidating population structure and history due to its flexibility. The statistical inference framework has benefited from significant progress in recent years. In population genetics, however, its outcome depends heavily on the amount of information in the dataset, whether that be the level of genetic variation or the number of samples and loci. Here we look at the power to reject a simple constant population size coalescent model in favor of a bottleneck model in datasets of varying quality. Not only is this power dependent on the number of samples and loci, but it also depends strongly on the level of nucleotide diversity in the observed dataset. Whilst overall model choice in an ABC setting is fairly powerful and quite conservative with regard to false positives, detecting weaker bottlenecks is problematic in smaller or less genetically diverse datasets and limits the inferences possible in non-model organism where the amount of information regarding the two models is often limited. Our results show it is important to consider these limitations when performing an ABC analysis and that studies should perform simulations based on the size and nature of the dataset in order to fully assess the power of the study

Melting as a String-Mediated Phase Transition

We present a theory of the melting of elemental solids as a dislocation-mediated phase transition. We model dislocations near melt as non-interacting closed strings on a lattice. In this framework we derive simple expressions for the melting temperature and latent heat of fusion that depend on the dislocation density at melt. We use experimental data for more than half the elements in the Periodic Table to determine the dislocation density from both relations. Melting temperatures yield a dislocation density of (0.61\pm 0.20) b^{-2}, in good agreement with the density obtained from latent heats, (0.66\pm 0.11) b^{-2}, where b is the length of the smallest perfect-dislocation Burgers vector. Melting corresponds to the situation where, on average, half of the atoms are within a dislocation core.Comment: 18 pages, LaTeX, 3 eps figures, to appear in Phys. Rev.

The Dictyostelium discoideum acaA Gene Is Transcribed from Alternative Promoters during Aggregation and Multicellular Development

Background: Extracellular cAMP is a key extracellular signaling molecule that regulates aggregation, cell differentiation and morphogenesis during multi-cellular development of the social amoeba Dictyostelium discoideum. This molecule is produced by three different adenylyl cyclases, encoded by the genes acaA, acrA and acgA, expressed at different stages of development and in different structures. Methodology/Principal Findings: This article describes the characterization of the promoter region of the acaA gene, showing that it is transcribed from three different alternative promoters. The distal promoter, promoter 1, is active during the aggregation process while the more proximal promoters are active in tip-organiser and posterior regions of the structures. A DNA fragment containing the three promoters drove expression to these same regions and similar results were obtained by in situ hybridization. Analyses of mRNA expression by quantitative RT-PCR with specific primers for each of the three transcripts also demonstrated their different temporal patterns of expression. Conclusions/Significance: The existence of an aggregation-specific promoter can be associated with the use of cAMP as chemo-attractant molecule, which is specific for some Dictyostelium species. Expression at late developmental stages indicates that adenylyl cyclase A might play a more important role in post-aggregative development than previously considered

Perovskite-Inspired Photovoltaic Materials: Toward Best Practices in Materials Characterization and Calculations

Recently, there has been an explosive growth in research based on hybrid lead–halide perovskites for photovoltaics owing to rapid improvements in efficiency. The advent of these materials for solar applications has led to widespread interest in understanding the key enabling properties of these materials. This has resulted in renewed interest in related compounds and a search for materials that may replicate the defect-tolerant properties and long lifetimes of the hybrid lead-halide perovskites. Given the rapid pace of development of the field, the rises in efficiencies of these systems have outpaced the more basic understanding of these materials. Measuring or calculating the basic properties, such as crystal/electronic structure and composition, can be challenging because some of these materials have anisotropic structures, and/or are composed of both heavy metal cations and volatile, mobile, light elements. Some consequences are beam damage during characterization, composition change under vacuum, or compound effects, such as the alteration of the electronic structure through the influence of the substrate. These effects make it challenging to understand the basic properties integral to optoelectronic operation. Compounding these difficulties is the rapid pace with which the field progresses. This has created an ongoing need to continually evaluate best practices with respect to characterization and calculations, as well as to identify inconsistencies in reported values to determine if those inconsistencies are rooted in characterization methodology or materials synthesis. This article describes the difficulties in characterizing hybrid lead–halide perovskites and new materials and how these challenges may be overcome. The topic was discussed at a seminar at the 2015 Materials Research Society Fall Meeting & Exhibit. This article highlights the lessons learned from the seminar and the insights of some of the attendees, with reference to both recent literature and controlled experiments to illustrate the challenges discussed. The focus in this article is on crystallography, composition measurements, photoemission spectroscopy, and calculations on perovskites and new, related absorbers. We suggest how the reporting of the important artifacts could be streamlined between groups to ensure reproducibility as the field progresses

Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica

Genome duplication is widespread in wild and crop plants. However, little is known about genome-wide selection in polyploids due to the complexity of duplicated genomes. In polyploids, the patterns of purifying selection and adaptive substitutions may be affected by masking owing to duplicated genes or homeologs as well as effective population size. Here, we resequence 25 accessions of the allotetraploid Arabidopsis kamchatica, which is derived from the diploid species A. halleri and A. lyrata. We observe a reduction in purifying selection compared with the parental species. Interestingly, proportions of adaptive non-synonymous substitutions are significantly positive in contrast to most plant species. A recurrent pattern observed in both frequency and divergence–diversity neutrality tests is that the genome-wide distributions of both subgenomes are similar, but the correlation between homeologous pairs is low. This may increase the opportunity of different evolutionary trajectories such as in the HMA4 gene involved in heavy metal hyperaccumulation

Novel phase diagram behavior and materials design in heterostructural semiconductor alloys

Structure and composition control the behavior of materials. Isostructural alloying is historically an extremely successful approach for tuning materials properties, but it is often limited by binodal and spinodal decomposition, which correspond to the thermodynamic solubility limit and the stability against composition fluctuations, respectively. We show that heterostructural alloys can exhibit a markedly increased range of metastable alloy compositions between the binodal and spinodal lines, thereby opening up a vast phase space for novel homogeneous single-phase alloys. We distinguish two types of heterostructural alloys, that is, those between commensurate and incommensurate phases. Because of the structural transition around the critical composition, the properties change in a highly nonlinear or even discontinuous fashion, providing a mechanism for materials design that does not exist in conventional isostructural alloys. The novel phase diagram behavior follows from standard alloy models using mixing enthalpies from first-principles calculations. Thin-film deposition demonstrates the viability of the synthesis of these metastable single-phase domains and validates the computationally predicted phase separation mechanism above the upper temperature bound of the nonequilibrium single-phase region

High Performance Flexible All Perovskite Tandem Solar Cells with Reduced Voc Deficit in Wide Bandgap Subcell

Among various types of perovskite based tandem solar cells TSCs , all perovskite TSCs are of particular attractiveness for building and vehicle integrated photovoltaics, or space energy areas as they can be fabricated on flexible and lightweight substrates with a very high power to weight ratio. However, the efficiency of flexible all perovskite tandems is lagging far behind their rigid counterparts primarily due to the challenges in developing efficient wide bandgap WBG perovskite solar cells on the flexible substrates as well as their low open circuit voltage VOC . Here, it is reported that the use of self assembled monolayers as hole selective contact effectively suppresses the interfacial recombination and allows the subsequent uniform growth of a 1.77 eV WBG perovskite with superior optoelectronic quality. In addition, a postdeposition treatment with 2 thiopheneethylammonium chloride is employed to further suppress the bulk and interfacial recombination, boosting the VOC of the WBG top cell to 1.29 V. Based on this, the first proof of concept four terminal all perovskite flexible TSC with a power conversion efficiency of 22.6 is presented. When integrating into two terminal flexible tandems, 23.8 flexible all perovskite TSCs with a superior VOC of 2.1 V is achieved, which is on par with the VOC reported on the 28 all perovskite tandems grown on the rigid substrat

Genetic Diversity and Ecological Niche Modelling of Wild Barley:Refugia, Large-Scale Post-LGM Range Expansion and Limited Mid-Future Climate Threats?

Describing genetic diversity in wild barley (Hordeum vulgare ssp. spontaneum) in geographic and environmental space in the context of current, past and potential future climates is important for conservation and for breeding the domesticated crop (Hordeum vulgare ssp. vulgare). Spatial genetic diversity in wild barley was revealed by both nuclear- (2,505 SNP, 24 nSSR) and chloroplast-derived (5 cpSSR) markers in 256 widely-sampled geo-referenced accessions. Results were compared with MaxEnt-modelled geographic distributions under current, past (Last Glacial Maximum, LGM) and mid-term future (anthropogenic scenario A2, the 2080s) climates. Comparisons suggest large-scale post-LGM range expansion in Central Asia and relatively small, but statistically significant, reductions in range-wide genetic diversity under future climate. Our analyses support the utility of ecological niche modelling for locating genetic diversity hotspots and determine priority geographic areas for wild barley conservation under anthropogenic climate change. Similar research on other cereal crop progenitors could play an important role in tailoring conservation and crop improvement strategies to support future human food security