The power of allele frequency comparisons to detect the footprint of selection in natural and experimental situations

Recently, inter-population comparisons of allele frequencies to detect past selection haven gained popularity. Data from genome-wide scans are used to detect the number and position of genes that have responded to unknown selection pressures in natural populations, or known selection pressures in experimental lines. Yet, the limitations and possibilities of these methods have not been well studied. In this paper, the objectives were (1) to investigate the distance over which a signal of directional selection is detectable under various scenarios, and (2) to study the power of the method depending on the properties of the used markers, for both natural populations and experimental set-ups. A combination of recurrence equations and simulations was used. The results show that intermediate strength selection on new mutations can be detected with a marker spacing of about 0.5 cM in large natural populations, 200 to 400 generations after the divergence of subpopulations. In experimental situations, only strong selection will be detectable, while markers can be spaced a few cM apart. Adaptation from standing variation in the base population will be hard to detect, though some solutions are presented for experimental designs.