soft sweep

McCoy RC & Akey JM 2017 Selection plays the hand it was dealt: evidence that human adaptation commonly targets standing genetic variation. Genome Biol 18:139.

  • Schrider and Kern [1] ... argue that adaptation is pervasive, but commonly targets standing variation and leaves subtle genomic footprints that have not been detectable by previous methods
  • scans for positive selection have traditionally targeted long, high-frequency, derived haplotypes in regions of reduced genetic variation
  • such a scenario is expected when the supply of adaptive mutations is limited
  • soft sweeps may arise either by selection on standing variation or through the recurrence of adaptive mutations prior to sweep completion
  • several classic examples of selective sweeps appear to fall into the soft-sweep category
  • the sweep appears hard at the local level but is soft at the global level
  • most sweeps were either population-specific or shared among a subset of a few populations, potentially reflecting the importance of local adaptation
  • the central observation of Schrider and Kern was a dramatic excess of soft selective sweeps, which comprised 92.2% of all sweep signatures
  • hard sweeps were relatively more common in non-African than in African populations, consistent with greater Ne in Africa as a result of the population bottleneck during the out-of-Africa migration
  • the widespread impacts of soft sweeps provide a strong argument against a model of mutation limitation, instead suggesting that the raw material necessary for adaptive evolution often segregates as standing variation at the time of selection onset
  • while potentially unexpected, given the low effective population size and genetic diversity of humans, Schrider and Kern [1] argue that these factors could be reconciled if the mutational target size—the number of sites at a given locus that when mutated produce an adaptive change in phenotype—is larger than previously assumed
  • an alternative explanation, that is not mutually exclusive, is that values of Ne are often estimated on the basis of standing levels of variation, which are highly sensitive to population bottlenecks and reflect longer time scales than are typically relevant for adaptation
  • if short-term Ne exceeds long-term Ne, as would be expected in a recurrent bottleneck scenario, long-term Ne may greatly underestimate the availability of new mutations
  • approximately half of the genome is influenced, via linkage disequilibrium, by a nearby selective sweep
  • even sophisticated methods may be limited in their capacity to detect polygenic adaptation affecting complex traits, which in contrast to completed sweeps involves subtle changes in allele frequencies at many loci