Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

BACKGROUND: A number of different statistics are used for detecting natural selection using DNA sequencing data, including statistics that are summaries of the frequency spectrum, such as Tajima’s D. These statistics are now often being applied in the analysis of Next Generation Sequencing (NGS) data. However, estimates of frequency spectra from NGS data are strongly affected by low sequencing coverage; the inherent technology dependent variation in sequencing depth causes systematic differences in the value of the statistic among genomic regions. RESULTS: We have developed an approach that accommodates the uncertainty of the data when calculating site frequency based neutrality test statistics. A salient feature of this approach is that it implicitly solves the problems of varying sequencing depth, missing data and avoids the need to infer variable sites for the analysis and thereby avoids ascertainment problems introduced by a SNP discovery process. CONCLUSION: Using an empirical Bayes approach for fast computations, we show that this method produces results for low-coverage NGS data comparable to those achieved when the genotypes are known without uncertainty. We also validate the method in an analysis of data from the 1000 genomes project. The method is implemented in a fast framework which enables researchers to perform these neutrality tests on a genome-wide scale

Piston-driven numerical wave tank based on WENO solver of well-balanced shallow water equations

A numerical wave tank equipped with a piston type wave-maker is presented for long-duration simulations of long waves in shallow water. Both wave maker and tank are modelled using the nonlinear shallow water equations, with motions of the numerical piston paddle accomplished via a linear mapping technique. Three approaches are used to increase computational efficiency and accuracy. First, the model satisfies the exact conservation property (C-property), a stepping stone towards properly balancing each term in the governing equation. Second, a high-order weighted essentially non-oscillatory (WENO) method is used to reduce accumulation of truncation error. Third, a cut-off algorithm is implemented to handle contaminated digits arising from round-off error. If not treated, such errors could prevent a numerical scheme from satisfying the exact C-property in long-duration simulations. Extensive numerical tests are performed to examine the well-balanced property, high order accuracy, and shock-capturing ability of the present scheme. Correct implementation of the wave paddle generator is verified by comparing numerical predictions against analytical solutions of sinusoidal, solitary, and cnoidal waves. In all cases, the model gives satisfactory results for small-amplitude, low frequency waves. Error analysis is used to investigate model limitations and derive a user criterion for long wave generation by the model

Numerical study on impacts of a concurrent storm-tide-tsunami event in Macau and Hong Kong

202209 bcfcNot applicableOthersNational Research Foundation to the National University of SingaporePublished24 month

Deep learning of interfacial curvature: A symmetry-preserving approach for the volume of fluid method

10.1016/j.jcp.2023.112110Journal of Computational Physics485112110-11211

RUNUP OF SOLITARY WAVES ON A CIRCULAR ISLAND

This is a study of the interactions of solitary waves climbing up a circular island. A series of large-scale laboratory experiments with waves of different incident height-to-depth ratios and different crest lengths is described. Detailed two-dimensional run-up height measurements and time histories of surface elevations around the island are presented. A numerical model based on the two-dimensional shallow-water wave equations including runup calculations was developed. Numerical model predictions agreed very well with the laboratory data and the model was used to study wave trapping and the effect of slope. Under certain conditions, enhanced runup and wave trapping on the lee side of the island were observed, suggesting a possible explanation for the devastation reported by field surveys in Babi Island off Flores, Indonesia, and in Okushiri Island, Japan

Physical and numerical modelling of tsunami generation by a moving obstacle at the bottom boundary

This paper presents a study of the waves generated by a solid block landslide moving along a horizontal boundary. The landslide was controlled using a mechanical system in a series of physical experiments, and laser-induced fluorescence measurements resolved both spatial and temporal variations in the free surface elevation. During its constant-velocity motion, the landslide transferred energy into ‘trapped’ offshore-propagating waves within a narrow frequency band. The wave trapping is demonstrated by investigating the wave dispersion characteristics using a two-dimensional Fourier Transform. The first of the trailing waves broke at Froude numbers greater than or equal to 0.625. The parametric dependence of the largest-amplitude waves and the potential energy within the wave field are discussed. The experimental results were compared to the predictions of an incompressible Navier–Stokes solver with and without turbulence models. The numerical model under-predicted the measured wave amplitudes, although it accurately predicted the measured wave phasing. The turbulent model more accurately predicted the shapes of the trailing waves. Both experimental and numerical results confirmed that investigations into wave generation by submerged objects moving at constant velocity should also consider the initial acceleration of the object, as this affects the overall evolution of the wave field. The applicability of the horizontal-boundary results to more realistic field scenarios is discussed