soft sweep

Schrider DR, Mendes FK, Hahn MW & Kern AD 2015 Soft shoulders ahead: spurious signatures of soft and partial selective sweeps result from linked hard sweeps. Genetics, in press.
doi:10.1534/genetics.115.174912

  • we know little about the sources of adaptive substitution or about the number of adaptive variants currently segregating in nature
  • recombination in regions linked to, but distant from, sites of hard sweeps can create patterns of polymorphism that closely mirror what is expected to be found near soft sweeps
  • a very similar situation arises when using haplotype-based statistics that are aimed at detecting partial or ongoing selective sweeps
  • it is difficult to distinguish the shoulder of a hard sweep from the center of a partial sweep
  • knowing the location of the selected site mitigates this problem slightly
  • stochasticity in signatures of natural selection will frequently cause the signal to reach its zenith far from this site
  • this effect is more severe for soft sweeps
  • both the time since a sweep ends and biologically realistic levels of allelic gene conversion lead to errors in the classification and identification of selective sweeps
  • the more common hard sweeps have been in recent evolutionary history, the more prevalent spurious signatures of soft or partial sweeps may appear in some genome-wide scans
  • if a population's selective environment changes frequently enough, soft sweeps may be the primary mode of adaptation
  • an alternative phenomenon resulting in a somewhat similar type of soft sweeps is that of recurrent mutation to the adaptive allele, each of which could occur on distinct haplotypes during the sweep
  • a third scenario of positive selection that has garnered a great deal of attention over the last two decades is that of "partial" or "incomplete" sweeps, where a sweeping allele has not reached fixation
  • a new mutation is initially beneficial and rapidly increases in frequency, but does not reach fixation
  • perhaps because the sweep is still ongoing at the time the population is sampled
  • searching for signals of partial sweeps may thus reveal adaptive evolution in action
  • the signal of partial sweeps has been the focus of a popular class of haplotype-based tests for selection
  • partial sweeps may be observed under a scenario that is essentially the opposite of the soft sweep scenario
  • whenever a putative soft or partial sweep is found, one can attempt to rule out the possibility that it is simply the shoulder of another event by searching for evidence of a nearby hard sweep
  • one could miss many true sweeps, especially when positive selection repeatedly acts on the same locus or cluster of neighboring loci or if the region examined is large
  • gene conversion could be the biggest obstacle to accurate sweep detection and classification