Soft Sweeps

Abstract

A population can adapt to a rapid environmental change or habitat expansion in two ways. It may adapt either through new beneficial mutations that subsequently sweep through the population or by using alleles from the standing genetic variation. We use diffusion theory to calculate the probabilities for selective adaptations and find a large increase in the fixation probability for weak substitutions, if alleles originate from the standing genetic variation. We then determine the parameter regions where each scenario-standing variation vs. new mutations-is more likely. Adaptations from the standing genetic variation are favored if either the selective advantage is weak or the selection coefficient and the mutation rate are both high. Finally, we analyze the probability of "soft sweeps," where multiple copies of the selected allele contribute to a substitution, and discuss the consequences for the footprint of selection on linked neutral variation. We find that soft sweeps with weaker selective footprints are likely under both scenarios if the mutation rate and/or the selection coefficient is high.

Signatures of selection in mammalian clock genes with coding trinucleotide repeats: Implications for studying the genomics of high‐pace adaptation

“…Such approaches generally have lower power than approaches based on environmental associations (De Mita et al., 2013) as they mainly aim to detect hard selective sweeps where only one or few beneficial alleles are selected to high frequency, producing more significant patterns of differentiation between populations (Hohenlohe, Philips, & Cresko, 2010; Raquin et al., 2008). Most genes, on the other hand, act in pleiotropy (Harrisson et al., 2014), which produces more modest increases in allele frequencies over multiple loci (Hermisson & Pennings, 2005) and is less likely to affect the patterns of divergence between populations. Indeed, LOSITAN does not address the issue of non‐linearity of F ST estimates that approach zero and, thus, is unlikely to detect low‐ F ST outliers when selection is not strong (Antao et al., 2008).…”

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

“…Throughout we have assumed that positive selection occurs only through completed hard selective sweeps. Indeed soft sweeps (Innan and Kim 2004;Hermisson and Pennings 2005;Pennings and Hermisson 2006;Garud et al 2015) and partial sweeps Sabeti et al 2002;Voight et al 2006), may be widespread, and differ in their effects on linked polymorphism (Orr and Betancourt 2001;Meiklejohn et al 2004;Przeworski et al 2005;Teshima et al 2006;Schrider et al 2015;Vy and Kim 2015). Polygenic selection, in which alleles at several different loci underlying a trait under selection will experience a change in frequency, is also thought to be widespread (Pritchard et al 2010;Berg and Coop 2014).…”

How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination

“…For example, reduced diversity occurs around the tb1 locus involved in maize domestication (Clark et al, 2004); for loci surrounding the waxy locus involved in domestication of japonica rice (Olsen et al, 2006) and for loci flanking the lactase locus in human populations that adopted dairying and evolved adult lactose persistence (Burger et al, 2007). Sweeps originating from new favourable mutations are referred to as hard sweeps, whereas those due to pre-existing polymorphisms are referred to as soft sweeps and typically have lesser impacts (Hermisson and Pennings, 2005). Natural selection against new deleterious mutations also reduces genetic diversity at linked loci (Charlesworth et al, 1993;Charlesworth, 1996).…”