Genetic hitchhiking

Genetic hitchhiking, also called genetic draft or the hitchhiking effect, refers to changes in the frequency of an allele because of linkage with a positively selected allele at another locus. It is a stochastic evolutionary force, meaning that it has relatively random probability.

There are two different kinds of genetic hitchhiking: Additionally, genetic hitchhiking can be complete, which means that it will reach fixation or incomplete, which means variation isn’t totally eliminated. The direct effect of incomplete hitchhiking is unknown and still being researched.
 * 1) Hitchhiking to fixation. This is when the mutations that are linked to a selectively advantageous mutation goes to fixation, where it replaces the ancestral allele that had existed before completely. An example that illustrates this kind of change is in Drosophila Melanogaster. Thanks to genetic hitchhiking, fixation aka a selective sweep of Y-linked mutations can take place.
 * 2) Hitchhiking to extinction. This is, in turn, the opposite. It is when the mutations on the same chromosome as the one with hitchhiking effect will be eliminated from the population. In this situation, this is background selection which is purifying/negative selection of linked deleterious alleles.

This process is closely related to natural selection. Traits often evolve by genetic drift or draft, not natural selection. It is important to keep in mind that population size is unimportant when thinking of genetic hitchhiking in a sense because population operates independent of the course of action will be for any allele. However, the number of allele copies correlates with the effects of genetic hitchhiking. With fewer allele copies, the effect is larger and with many allele copies, the effect is smaller. This is because allele quantities can be more linked when there are less of them.

Hitchhiking has different effects whether it is in the absence or the presence of recombination. Without recombination, hitchhiking gets rid of all linked variation. When recombination does exist, incomplete hitchhiking takes place. Unless the hitchhiking effect is very strong, it is unlikely that the genetic variation will experience an incomplete hitchhiking effect. Under positive selection, genetic hitchhiking will help spread the mutation. Nucleotide variability is also decreased by hitchhiking because when hitchhiking is acting, rare polymorphisms are likely to occur. Additionally, there is a correlation between distance between the locus under selection & the locus not under selection, and hitchhiking's impact.

History
Population geneticists working after the time of Mendel noticed the effect of hitchhiking, but did not quantify it at the time. In 1948, Fisher discovered that genetic hitchhiking was not related to the population size, but the name for this force still was not known/created. It was not until 1974 when Smith and Haigh quantified this idea that a name was actually created. Despite this development, the concept was not studied or covered by the field of genetics for about 20 years. Research was eventually then published on this subject in 1992 and contributions to the idea have been added to on by many authors since then.

Draft and drift
Genetic drift and genetic draft are both concepts that can involve linkage, but are somewhat opposites. They are both evolutionary forces as well. Drift is the change in the frequency of an allele in a population due to random sampling. It can also refer to the linkage of two neutral alleles, with one that does not help the fitness of an individual, but it does not have to involve linkage. However, draft is when a neutral allele is linked to beneficial allele, consequently meaning that it has a selective advantage. Depending on which of these two mechanisms of evolution are occurring, they can have totally different effects on organisms. Genetic drift is heavily dependent on population size, where genetic draft is not as much.

Applications
Genetic hitchhiking can creates fixation of Y-linked mutations. This has taken place in Drosophila Melanogaster and other studies are currently being conducted. Hitchhiking complements Muller's Ratchet by increasing the rate the ratchet turns, leads to fixation of Y-linked mutations, and accounts for some of the disintegration of the Y chromosomes into smaller portions. However, hitchhiking has the greatest effect when working in conjunction with Muller’s Ratchet, but still can work properly under conditions where Muller’s Ratchet cannot function. Genetic hitchhiking complements Muller's ratchet in three ways:
 * 1) Increases the rate of Muller's Ratchet, especially if it occurs directly after recombination
 * 2) Leads to fixation of Y-linked mutations
 * 3) Partially breaks down segments of the Y-chromosome

Some findings have determined that genetic hitchhiking is correlated with gene flow. This is only if the flow of alleles occurs over a long time period. It also increases the amount of local sweeps of gene flow. Hitchhiking does leave a distinct signature, which can be detected with some experiments, even if it is incomplete hitchhiking. However, the Founder Effect may harm the usability of this data and more research must be done to confirm this data.