soft sweep - senecio7の日記

Jensen JD 2014 On the unfounded enthusiasm for soft selective sweeps. Nat Commun 5:5281.

the rate of adaptation is not strongly limited by the rate at which newly arising beneficial mutations enter the population
empirical and experimental evidence to date challenges the recent enthusiasm for invoking these models to explain observed patterns of variation in humans and Drosophila

the notion of a soft selective sweep has grown in popularity in the recent literature
with this increasing usage the definition of the term itself has grown increasingly vague
a soft sweep does not reference a particular population genetic model per se, but rather a set of very different models that may result in similar genomic patterns of variation

selection on standing variation requires that the beneficial mutation segregate at appreciable frequency in the preselection environment
the multiple beneficial model requires a high mutation rate to the beneficial genotype

Orr and Betancourt made a notable observation that even if selection is acting on standing variation instead of a new mutation, a single copy is nonetheless surprisingly likely to sweep to fixation
96% of the time a single copy will fix in the population, despite 20 copies segregating at mutation-selection balance before the shift in selection pressure
the population size must be in excess of N = 1.5 × 10⁵ (thus more than 300 copies segregating at mutation–selection balance) before multiple copies are more likely on fixation than a single copy

we are unlikely to have statistical resolution when attempting to distinguish between a hard sweep on a new mutation versus a hard sweep on a rare previously standing variant

the low plate morph is likely deleterious in marine populations
migration from the marine environment may indeed serve as an important source of variation for local freshwater hard sweeps
it is difficult to separate this hypothesis from that of local freshwater adaptation on new mutations, followed by back migration of locally adapted alleles into the marine population

distinguishing rare standing ancestral variation from newly accumulating mutations has also been a topic of note

multiple competing beneficial mutations may indeed be a likely model
a soft sweep from multiple beneficials is unlikely owing to non-equivalent selective effects between the mutations

conditional on the unsubstantiated assumption that adaptive fixations are common, the absence of hard sweep patterns in many natural populations has led some to conclude that soft sweeps must be the primary mechanism of adaptation
this assumption is poorly supported
theoretical and experimental insights to date suggest that soft sweeps from standing variation or from multiple beneficial mutations for populations of this size are unlikely
a quite separate point has also been neglected in this literature
namely, the power of existing tests of hard selective sweeps to identify these patterns within demographically complex populations

the ability of alternate models to produce these patterns needs to be more carefully weighed in future studies
alternative models of positive selection have also been suggested to produce qualitatively similar patterns—including hard selective sweeps in subdivided populations exchanging migrants^81-83 and polygenic adaptation⁸⁴
examples in the literature are accumulating in support of the models themselves
there is very little evidence of soft sweep fixations, with the best empirical and experimental examples to date almost universally pointing to hard sweep fixations under these models
this appears to primarily be owing to the low preselection allele frequency of the standing variants (which are seemingly often deleterious before the shift in selective pressure), and to the selective differential between competing beneficial mutations (or between the haplotypes carrying the beneficial mutations) resulting in the ultimate fixation of only a single haplotype
the field ought to take greater caution when invoking soft sweep fixations
hard sweep fixations (be it from models of selection on new mutations, standing variation or competing beneficial mutations) seem to remain as the most likely outcome across a wide parameter space relevant for many current populations of interest