Interpreting the pervasive observation of U-shaped Site Frequency Spectra

by Fabian Freund, Elise Kerdoncuff, Sebastian Matuszewski, Marguerite Lapierre, Marcel Hildebrandt, Jeffrey D. Jensen, Luca Ferretti, Amaury Lambert, Timothy B. Sackton, Guillaume Achaz

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.