Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets

<p>Abstract</p> <p>Background</p> <p>Explicit evolutionary models are required in maximum-likelihood and Bayesian inference, the two methods that are overwhelmingly used in phylogenetic studies of DNA sequence data. Appropriate selection of nucleotide substitution models is important because the use of incorrect models can mislead phylogenetic inference. To better understand the performance of different model-selection criteria, we used 33,600 simulated data sets to analyse the accuracy, precision, dissimilarity, and biases of the hierarchical likelihood-ratio test, Akaike information criterion, Bayesian information criterion, and decision theory.</p> <p>Results</p> <p>We demonstrate that the Bayesian information criterion and decision theory are the most appropriate model-selection criteria because of their high accuracy and precision. Our results also indicate that in some situations different models are selected by different criteria for the same dataset. Such dissimilarity was the highest between the hierarchical likelihood-ratio test and Akaike information criterion, and lowest between the Bayesian information criterion and decision theory. The hierarchical likelihood-ratio test performed poorly when the true model included a proportion of invariable sites, while the Bayesian information criterion and decision theory generally exhibited similar performance to each other.</p> <p>Conclusions</p> <p>Our results indicate that the Bayesian information criterion and decision theory should be preferred for model selection. Together with model-adequacy tests, accurate model selection will serve to improve the reliability of phylogenetic inference and related analyses.</p

Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals

<p>Abstract</p> <p>Background</p> <p>A well-informed choice of genetic locus is central to the efficacy of DNA barcoding. Current DNA barcoding in animals involves the use of the 5' half of the mitochondrial cytochrome oxidase 1 gene (<it>CO1</it>) to diagnose and delimit species. However, there is no compelling <it>a priori </it>reason for the exclusive focus on this region, and it has been shown that it performs poorly for certain animal groups. To explore alternative mitochondrial barcoding regions, we compared the efficacy of the universal <it>CO1 </it>barcoding region with the other mitochondrial protein-coding genes in eutherian mammals. Four criteria were used for this comparison: the number of recovered species, sequence variability within and between species, resolution to taxonomic levels above that of species, and the degree of mutational saturation.</p> <p>Results</p> <p>Based on 1,179 mitochondrial genomes of eutherians, we found that the universal <it>CO1 </it>barcoding region is a good representative of mitochondrial genes as a whole because the high species-recovery rate (> 90%) was similar to that of other mitochondrial genes, and there were no significant differences in intra- or interspecific variability among genes. However, an overlap between intra- and interspecific variability was still problematic for all mitochondrial genes. Our results also demonstrated that any choice of mitochondrial gene for DNA barcoding failed to offer significant resolution at higher taxonomic levels.</p> <p>Conclusions</p> <p>We suggest that the <it>CO1 </it>barcoding region, the universal DNA barcode, is preferred among the mitochondrial protein-coding genes as a molecular diagnostic at least for eutherian species identification. Nevertheless, DNA barcoding with this marker may still be problematic for certain eutherian taxa and our approach can be used to test potential barcoding loci for such groups.</p

Numerical investigation of the angle of repose of monosized spheres

This paper presents a numerical study of the angle of repose, a most important macroscopic parameter in characterizing granular materials, by means of a modified distinct element method. Emphasis is given to the effect of variables related to factors such as particle characteristics, material properties, and geometrical constraints. The results show that sliding and rolling frictions are the primary reasons for the formation of a sandpile; particle size and container thickness significantly influence the angle of repose; and the angle of repose is not so sensitive to density, Poisson\u27s ratio, damping coefficient, and Young\u27s modulus. Increasing rolling friction coefficient or sliding friction coefficient increases the angle of repose. Conversely, increasing particle size or container thickness decreases the angle of repose. The underlying mechanisms for these effects are discussed in terms of particle-particle and particle-wall interactions

Prediction of Young’s modulus : from effective clay clusters to polymer nanocomposites

This work aims to predict the properties of clay-polymer nanocomposites by a combination of molecular modelling and micromechanical model. The interface between clay and polymer matrix is considered when determining the effective size of clay clusters. The effective size of different clusters in nylon 6 and their Young's moduli are determined from molecular dynamics simulation. Then the clay-nylon 6 nanocomposite is considered as a multiphase composite and its Young's modulus is predicted by the rule-of-mixture method. Finally, it is demonstrated that the Young's moduli of nanocomposites with different fractions of effective clay clusters can be predicted

Prediction of the overall Young’s moduli of clay-based polymer nanocomposites

In our previous work, molecular dynamics simulation was used to calculate Young’s modulus of both fully and partially exfoliated effective clay (montmorillonite, MMT) clusters. In this work, we expand that work to predict the overall Young’s moduli of nylon 6/MMT nanocomposites. First, a micromechanics method (i.e. the rule-of-mixtures) is shown to be effective in calculating the overall Young’s moduli of clay-based polymer nanocomposites. Then, the overall Young’s moduli of clay-based polymer nanocomposites with either well-aligned or randomly dispersed effective clay clusters of various clay volume fractions are calculated based on the individual Young’s moduli of effective clay clusters and polymer matrix by the rule-of-mixtures method. By comparing the simulated results with measured data in the literature, it is shown that the present approach provides an effective way to predict the overall Young’s moduli of nylon 6/MMT nanocomposites

Effect of surface and interface energies on the nonlinear bending behaviour of nanoscale laminated thin plates

Using an improved multilayered plate model, the influence of surface and interface energies on the bending behaviour of laminated nanoplates is incorporated into the Kirchhoff plate theory. Governing equations taking into account the geometrical nonlinearity are obtained to study the influences of surface/interface energies. Based on the Navier and Ritz methods, closed-form solutions for both simply supported and clamped nanoplates are obtained. Numerical results for single- and multilayered nanoplates indicate that the interface effect can noticeably change the elastic behaviour of laminated plates on the nanometer scale. In addition, the flakiness ratio, external load, and number of layers also affect the surface/interface effects at large deformations. This study will be useful for the design and examination of nanoplates and nanoscale devices, especially multilayered plates at large deformations

Effects of surface energy on the nonlinear behaviors of laminated nanobeams

Using an improved multilayer-beams model, the surface effect caused by surface stress and surface elasticity on mechanical properties of laminated nanobeams in bending, bucking and vibration is incorporated into the nonlinear beam theory. Analytical solutions are obtained to study the influence of surface and interface effects for simply supported boundary conditions. Unlike the deduction of previous beam theory, the theoretical derivation in present work includes the effect of both surface and interface. Numerical cases of double layer and multilayer Nickel-silver laminated beams indicate that the interface effect observably change the elastic behaviour of laminated beams on the nanometer scale, especially for multilayer cases

Young's modulus of effective clay clusters in polymer nanocomposites

In polymer nanocomposites, the interfacial region plays a key role in the reinforcement of materials properties. Traditional two-phase micromechanical models usually ignore the contribution of such interfacial region to the overall materials properties. In this study, we use molecular dynamics simulation to determine the effective size and the Young's modulus of effective clay clusters which are regarded as basic building blocks in clay-based polymer nanocomposites. Two types of clay clusters are considered: one is fully exfoliated clay and another is partially exfoliated clay. The calculated Young's modulus of effective clay clusters can be used to predict the overall mechanical properties of clay-based polymer nanocomposites