MovingOptimum_IndBased

C++ code used for individual-based simulations of the multidimensional moving-optimum model. These simulations implement all model assumptions (i.e., they represent the "full" model). In particular, they keep track of the action of selection, recombination and mutation on multilocus genotypes in a finite population. Individual-based simulations are, thus, realistic (but also more time-consuming) than "adaptive-walk simulations" (see SimulateMovingOptimum.cpp)

SimulateMovingOptimum

C++ code used for "adaptive-walk" simulations of the multidimensional moving-optimum model. In these simulations, the population is assumed to be monomorphic at all times, and new mutations are immediately lost or fixed. As a result, adaptation proceeds as a series of discrete "steps". Adaptive-walk simulations are much faster than individual-based simulations, and are more closely related to the analytical results in the paper. Similar assumptions have been used in other models of the genetics of adaptation (Gillespie, Orr...), and have been justified by the so-called strong-selection-weak-mutation assumption

MonteCarlo_SimulationData

Simulation data from the Monte-Carlo simulation procedure described in the 'Model and Methods' section (paragraph 'The adaptive-walk approximation'). Corresponding simulation program: SimulateMovingOptimum.cpp. ReadMe files are contained within the .zip archive

Interpreting the pervasive observation of U-shaped Site Frequency Spectra.

The standard neutral model of molecular evolution has traditionally been used as the null model for population genomics. We gathered a collection of 45 genome-wide site frequency spectra from a diverse set of species, most of which display an excess of low and high frequency variants compared to the expectation of the standard neutral model, resulting in U-shaped spectra. We show that multiple merger coalescent models often provide a better fit to these observations than the standard Kingman coalescent. Hence, in many circumstances these under-utilized models may serve as the more appropriate reference for genomic analyses. We further discuss the underlying evolutionary processes that may result in the widespread U-shape of frequency spectra.</p