soft sweep - senecio7の日記

Cutter AD & Payseur BA 2013 Genomic signatures of selection at linked sites: unifying the disparity among species. Nat Rev Genet 14:262-274.

mutation-limited adaptation
when mutational input into a population is sufficiently low, the rate of adaptation will be limited by the input of new beneficial mutations
this common theoretical assumption will be violated in real species with populations that are large, subdivided or subject to frequent changes in selective regime

this notion of mutation-limited adaptation at the molecular level might not be the norm in nature

in Drosophila simulans, one approach that can quantify only hard sweeps suggests that ~13% of replacement-site substitutions were fixed in such a manner versus ~90% of such sites inferred to have fixed through either hard or soft sweeps
soft sweeps could represent upwards of 85% of positively selected substitutions
formal analyses are desperately needed to disentangle the relative contributions of hard and soft sweeps to divergence
the relative incidence of hard and soft sweeps is a major unsolved problem
relaxing the classic hard sweep assumption that selected alleles are rapidly driven to fixation generates a new suite of predictions
a challenge is to determine why the incidence of hard versus soft sweeps in adaptation might differ among organisms and whether it varies in predictable ways
species-wide soft sweeps could dominate when populations are subdivided

the few theoretical studies to date on polygenic selective sweep effects suggest weaker signatures of selection at linked sites

when a beneficial mutation is linked to deleterious mutations, those mildly deleterious mutations can hitch-hike to fixation
the fixed region will be susceptible to repeated bouts of positive selection as compensatory alleles arise and replace the detrimental alleles that had hitch-hiked with the original beneficial mutation
the linkage to deleterious mutations slows the fixation process and increases the incidence of recombinant genetic backgrounds, obscuring the signatures of a selective sweep

even without positive selection, purifying selection against multiple linked targets similarly reduces the efficacy of selection
this mitigation of classic background selection effects, owing to Hill–Robertson interference, has largely been explored through simulation
a complete mathematical association with recombination rate has not yet been established
fitness-class coalescent modelling appears to be promising

much effort has been devoted to distinguishing background selection from hitch-hiking effects of recurrent selective sweeps
this is difficult and is perhaps a false dichotomy
background selection should be taken into account as a part of a null model of molecular evolution
deleterious mutations arise inexorably and in turn are subjected to purifying selection