Molecular Evolution and Polymorphism: SAS-CFF Meets the Mutational Landscape

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Abstract
A Markov model of molecular evolution resulting from natural selection in a fluctuating environment that appears to be in substantial agreement with many of the observations on genetic variation within and between species is described. Although the Markov model is based on a particular model of selection, the Stochastic Additive Scale-Concave Fitness Function model, the approach.sbd.which uses strong-selection, weak-mutation limits.sbd.suggests a general strategy for approximating the dynamics of a much broader class of models. The main dynamic features of the model are a rapid buildup phase that introduces new alleles into the population, an allelic-exchange phase that slowly replaces polymorphic alleles, and allelic constrictions, rare events that cause a complete turnover of alleles. The model exhibits many properties commonly observed in sequence data, among which are the variability of rates of evolution, the frequency spectrum of segregating sites, and the generation-time effect.