Demography-adjusted tests of neutrality based on genome-wide SNP data

Tests of the neutral evolution hypothesis are usually built on the standard null model which assumes that mutations are neutral and population size remains constant over time. However, it is unclear how such tests are affected if the last assumption is dropped. Here, we extend the unifying framework for tests based on the site frequency spectrum, introduced by Achaz and Ferretti, to populations of varying size. A key ingredient is to specify the first two moments of the frequency spectrum. We show that these moments can be determined analytically if a population has experienced two instantaneous size changes in the past. We apply our method to data from ten human populations gathered in the 1000 genomes project, estimate their demographies and define demography-adjust

A new perspective on the dynamics of fragmented populations

Understanding the time evolution of fragmented animal populations and their habitats, connected by migration, is a problem of both theoretical and practical interest. This paper presents a method for calculating the time evolution of the habitats population size distribution from a general stochastic dynamic within each habitat, using a deterministic approximation which becomes exact for an infinite number of habitats. Fragmented populations are usually thought to be characterized by a separation of time scale between, on the one hand, colonization and extinction of habitats and, on the other hand, the local population dynamics within each habitat. The analysis in this paper suggests an alternative view: the effective population dynamic stems from a law of large numbers, where stochastic fluctuations in population size of single habitats are buffered through the dispersal pool so that the global population dynamic remains approximately smooth. For illustration, the deterministic approximation is compared to simulations of a stochastic model with density dependent local recruitment and mortality. The article is concluded with a discussion of the general implications of the results, and possible extensions of the method.

Using force covariance to derive effective stochastic interactions in dissipative particle dynamics

There exist methods for determining effective conservative interactions in coarse grained particle based mesoscopic simulations. The resulting models can be used to capture thermal equilibrium behavior, but in the model system we study do not correctly represent transport properties. In this article we suggest the use of force covariance to determine the full functional form of dissipative and stochastic interactions. We show that a combination of the radial distribution function and a force covariance function can be used to determine all interactions in dissipative particle dynamics. Furthermore we use the method to test if the effective interactions in dissipative particle dynamics (DPD) can be adjusted to produce a force covariance consistent with a projection of a microscopic Lennard-Jones simulation. The results indicate that the DPD ansatz may not be consistent with the underlying microscopic dynamics. We discuss how this result relates to theoretical studies reported in the literature.