soft sweep

Peter BM, Huerta-Sanchez E & Nielsen R 2012 Distinguishing between selective sweeps from standing variation and from a de novo mutation. PLoS Genet 8:e1003011.

• selection acts only to change the allele frequency in the selected site
• the effects of the selection on linkage disequilibrium, haplotype patterns, allele frequencies in linked sites, etc., are only through the effects caused by the change in allele frequency of the selected allele
• hitch-hiking effects
• this observation is the foundation for standard population genetic theory on selective sweeps (e.g., [27]–[28]) and forms the basis for several simulation methods
• the path of the selected mutation is first simulated and then neutral simulations are performed conditional on the allele frequency path

• the genetic signature of sweeps from standing variation differs in three important aspects from the signature of sweeps from new mutations
• the signal of selection from standing variation is 1) weaker and 2) affecting a narrower region
• as a third difference, we expect an increased variance in both allele age and trajectory