Editing Natural selection (section)

===Selection, genetic variation, and drift===
{{Main|Genetic variation|Genetic drift}}

A portion of all genetic variation is functionally neutral, producing no phenotypic effect or significant difference in fitness. [[Motoo Kimura]]'s [[neutral theory of molecular evolution]] by [[genetic drift]] proposes that this variation accounts for a large fraction of observed genetic diversity.<ref name=Kimura>{{cite book |author=Kimura, Motoo |author-link=Motoo Kimura |date=1983 |title=The neutral theory of molecular evolution |publisher=Cambridge University Press |isbn=978-0-521-23109-1 |oclc=8776549}}</ref> Neutral events can radically reduce genetic variation through [[population bottleneck]]s.<ref>{{cite encyclopedia |editor-last=Robinson |editor-first=Richard |encyclopedia=Genetics |title=Population Bottleneck |url=https://archive.org/details/genetics0000unse |year=2003 |publisher=Macmillan Reference US |volume=3 |isbn=978-0-02-865609-0 |oclc=3373856121 |url-access=registration }}</ref> which among other things can cause the [[founder effect]] in initially small new populations.<ref name=Campbell1996>{{cite book |last=Campbell |first=Neil A. |author-link=Neil Campbell (scientist) |year=1996 |title=Biology |url=https://archive.org/details/biologycamp00camp |url-access=registration |edition=4th |publisher=[[Benjamin Cummings]] |isbn=978-0-8053-1940-8 |oclc=3138680061 |page=[https://archive.org/details/biologycamp00camp/page/423 423]}}</ref> When genetic variation does not result in differences in fitness, selection cannot directly affect the frequency of such variation. As a result, the genetic variation at those sites is higher than at sites where variation does influence fitness.<ref name=Rice/> However, after a period with no new mutations, the genetic variation at these sites is eliminated due to genetic drift. Natural selection reduces genetic variation by eliminating maladapted individuals, and consequently the mutations that caused the maladaptation. At the same time, new mutations occur, resulting in a [[mutation–selection balance]]. The exact outcome of the two processes depends both on the rate at which new mutations occur and on the strength of the natural selection, which is a function of how unfavourable the mutation proves to be.<ref name=Lynch>{{cite journal |last1=Lynch |first1=Michael |title=Evolution of the mutation rate |journal=Trends in Genetics |date=August 2010 |volume=26 |issue=8 |pages=345–352 |doi=10.1016/j.tig.2010.05.003 |pmid=20594608 |pmc=2910838}}</ref>

[[Genetic linkage]] occurs when the [[locus (genetics)|loci]] of two alleles are close on a chromosome. During the formation of gametes, recombination reshuffles the alleles. The chance that such a reshuffle occurs between two alleles is inversely related to the distance between them. [[Selective sweep]]s occur when an allele becomes more common in a population as a result of positive selection. As the prevalence of one allele increases, closely linked alleles can also become more common by "[[genetic hitchhiking]]", whether they are neutral or even slightly deleterious. A strong selective sweep results in a region of the genome where the positively selected [[haplotype]] (the allele and its neighbours) are in essence the only ones that exist in the population. Selective sweeps can be detected by measuring [[linkage disequilibrium]], or whether a given haplotype is overrepresented in the population. Since a selective sweep also results in selection of neighbouring alleles, the presence of a block of strong linkage disequilibrium might indicate a 'recent' selective sweep near the centre of the block.<ref name=MaynardSmithHaigh>{{Cite journal |last1=Smith |first1=John Maynard |author-link1=John Maynard Smith |last2=Haigh|first2=John |date=1974 |title=The hitch-hiking effect of a favourable gene |journal=Genetics Research |volume=23 |issue=1 |pages=23–35 |doi=10.1017/S0016672300014634 |pmid=4407212|doi-access=free }}</ref>

[[Background selection]] is the opposite of a selective sweep. If a specific site experiences strong and persistent purifying selection, linked variation tends to be weeded out along with it, producing a region in the genome of low overall variability. Because background selection is a result of deleterious new mutations, which can occur randomly in any haplotype, it does not produce clear blocks of linkage disequilibrium, although with low recombination it can still lead to slightly negative linkage disequilibrium overall.<ref name="Keightley & Otto 2006">{{cite journal |last1=Keightley |first1=Peter D. |author-link1=Peter Keightley |last2=Otto |first2=Sarah P. |author-link2=Sarah Otto |date=7 September 2006 |title=Interference among deleterious mutations favours sex and recombination in finite populations |journal=[[Nature (journal)|Nature]] |volume=443 |issue=7107 |pages=89–92 |doi=10.1038/nature05049  |pmid=16957730|bibcode=2006Natur.443...89K |s2cid=4422532 }}</ref>