Selective sweep

In

1. The "classic selective sweep" or "hard selective sweep" is expected to occur when beneficial mutations are rare, but once a beneficial mutation has occurred it increases in frequency rapidly, thereby drastically reducing genetic variation in the population.[1]
2. Another type of sweep, a "soft sweep from standing genetic variation," occurs when a previously neutral mutation that was present in a population becomes 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 doesn't erase all genetic variation in the population.^[2]
3. Finally, a "multiple origin soft sweep" occurs when mutations are common (for example in a large population) so that the same or similar beneficial mutations occurs on different genomic backgrounds such that no single genomic background can hitchhike to high frequency.^[3]

Sweeps do not occur when selection simultaneously causes very small shifts in allele frequencies at many loci each with standing variation (polygenic adaptation).

Detection

Whether or not a selective sweep has occurred can be investigated in various ways. One method is to measure linkage disequilibrium, i.e., whether a given haplotype is overrepresented in the population. Under neutral evolution, genetic recombination will result in the reshuffling of the different alleles within a haplotype, and no single haplotype will dominate the population. However, during a selective sweep, selection for a positively selected gene variant will also result in selection of neighbouring alleles and less opportunity for recombination. Therefore, the presence of strong linkage disequilibrium might indicate that there has been a recent 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.^[4]

In maize, a recent comparison of yellow and white corn genotypes surrounding Y1—the phytoene synthetase gene responsible for the yellow endosperm color, shows strong evidence for a selective sweep in yellow germplasm reducing diversity at this locus and linkage disequilibrium in surrounding regions. White maize lines had increased diversity and no evidence of linkage disequilibrium associated with a selective sweep.^[5]

Relevance to disease

Because selective sweeps allow for rapid adaptation, they have been cited as a key factor in the ability of

One example comes from the human influenza virus, which has been involved in an adaptive contest with humans for hundreds of years. While antigenic drift (the gradual change of surface antigens) is considered the traditional model for changes in the viral genotype, recent evidence^[7] suggests that selective sweeps play an important role as well. In several flu populations, the time to the most recent common ancestor (TMRCA) of "sister" strains, an indication of relatedness, suggested that they had all evolved from a common progenitor within just a few years. Periods of low genetic diversity, presumably resultant from genetic sweeps, gave way to increasing diversity as different strains adapted to their own locales.

A similar case can be found in Toxoplasma gondii, a remarkably potent protozoan parasite capable of infecting warm-blooded animals. T. gondii was recently discovered to exist in only three clonal lineages in all of Europe and North America.^[8] In other words, there are only three genetically distinct strains of this parasite in all of the Old World and much of the New World. These three strains are characterized by a single monomorphic version of the gene Chr1a, which emerged at approximately the same time as the three modern clones. It appears then, that a novel genotype emerged containing this form of Chr1a and swept the entire European and North American population of Toxoplasma gondii, bringing with it the rest of its genome via genetic hitchhiking. The South American strains of T. gondii, of which there are far more than exist elsewhere, also carry this allele of Chr1a.

Involvement in agriculture and domestication

Rarely are genetic variability and its opposing forces, including adaptation, more relevant than in the generation of domestic and agricultural species. Cultivated crops, for example, have essentially been genetically modified for more than ten thousand years,^[9] subjected to artificial selective pressures, and forced to adapt rapidly to new environments. Selective sweeps provide a baseline from which different varietals could have emerged.^[10]

For example, recent study of the corn (