Self-contained Beta-with-Spikes approximation for inference under a Wright–Fisher model

We construct a reliable estimation method for evolutionary parameters within the Wright–Fisher model, which describes changes in allele frequencies due to selection and genetic drift, from time-series data. Such data exist for biological populations, for example via artificial evolution experiments, and for the cultural evolution of behavior, such as linguistic corpora that document historical usage of different words with similar meanings. Our method of analysis builds on a Beta-with-Spikes approximation to the distribution of allele frequencies predicted by the Wright–Fisher model. We introduce a self-contained scheme for estimating parameters in the approximation, and demonstrate its robustness with synthetic data, especially in the strong-selection and near-extinction regimes where previous approaches fail. We further apply the method to allele frequency data for baker’s yeast (Saccharomyces cerevisiae), finding a significant signal of selection in cases where independent evidence supports such a conclusion. We further demonstrate the possibility of detecting time points at which evolutionary parameters change in the context of a historical spelling reform in the Spanish language.