In genetics, when multiple copies of a beneficial mutation become established and fix together it is called soft sweep. Depending on the origin of these copies, linked variants might then be retained and emerge as haplotype structures in the population. There are two major forms of soft sweeps:
1) A beneficial mutation previously separated in the population neutrally and therefore existed as multiple haplotypes at the time of the selective shift in which the mutation became beneficial. In this way, a single beneficial mutation may carry multiple haplotypes to an intermediate frequency, while itself becomes fixed.
2) Another model happening when multiple beneficial mutations independently occur in short succession of one another — consequently, a second copy occur through mutation before the selective fixation of the first copy.
Soft sweeps can occur from both standing variation and rapidly repeating beneficial mutations.
Overview
A selective sweep occurs when, due to strong positive natural selection, beneficial alleles quickly go to fixation in a population and results in the reduction or elimination of variation among the nucleotides near that allele. A selective sweep can occur when a rare or a formerly absent allele that improves the fitness of the carrier relative to other members of the population increases in frequency quickly due to natural selection. As the frequency of such a beneficial allele increases, genetic variants that happen to be present in the DNA neighborhood of the beneficial allele will also become more prevalent; this phenomenon called genetic hitchhiking. A Selective sweep arise if rapid changes within the frequency of a beneficial allele, driven by positive selection, distort the genealogical history of samples from the region around the selected locus. It is now recognized that not all sweeps reduce genetic variation in the same way, but rather selective sweeps can be categorized into three main categories: First, the classic selective sweep or hard sweep is expected to occur when beneficial mutations are rare but when a beneficial mutation that has occurred increases in frequency rapidly, drastically reducing genetic variation in the population. Second, soft sweep from standing genetic variation (SGV) occurs when previously neutral mutations that were present in a population become beneficial because of an environmental change. Such a mutation may be present on several genomic backgrounds so that when it rapidly increases in frequency it does not erase all genetic variation in the population. Finally, a multiple origin soft sweep happens when mutations are common, for example in a large population, so that the same or similar beneficial mutations occur on a different genomic background such that no single genomic background can hitchhike the high frequency. Whether the selective sweep has occurred can be explored in various ways. One method is to measure linkage disequilibrium, that is whether a given haplotype is overrepresented in the population. Under neutral evolution, genetic recombination will result in the reshuffling of the different alleles within the haplotypes, and no single haplotype will dominate the population. However, during a selective sweep, selection for a positively selected gene variant will also result in hitchhiking of neighboring alleles and less opportunity for recombination. Therefore, the presence of strong linkage disequilibrium might indicate that there has been a selective sweep and can be used to identify sites recently under selection. There have been many scans for selective sweeps in humans and other species using a variety of statistical approaches and assumptions.