Editing Natural selection (section)

==Genetic basis==

===Genotype and phenotype===
{{Main|Genotype–phenotype distinction}}

Natural selection acts on an organism's phenotype, or physical characteristics. Phenotype is determined by an organism's genetic make-up (genotype) and the environment in which the organism lives. When different organisms in a population possess different versions of a gene for a certain trait, each of these versions is known as an [[allele]]. It is this genetic variation that underlies differences in phenotype. An example is the [[ABO]] blood type [[antigen]]s in humans, where three alleles govern the phenotype.<ref>{{cite web |url=http://omim.org/entry/110300 |title=ABO Glycosyltransferase; ABO |author1=McKusick, Victor A. |author2=Gross, Matthew B. |date=18 November 2014 |work=Online Mendelian Inheritance in Man |publisher=National Library of Medicine |access-date=7 November 2016}}</ref>

Some traits are governed by only a single gene, but most traits are influenced by the interactions of many genes. A variation in one of the many genes that contributes to a trait may have only a small effect on the phenotype; together, these genes can produce a continuum of possible phenotypic values.<ref>{{harvnb|Falconer|Mackay|1996}}</ref>

===Directionality of selection===<!-- This section is linked from [[Race and intelligence]] -->
{{Main|Directional selection}}

When some component of a trait is heritable, selection alters the frequencies of the different alleles, or variants of the gene that produces the variants of the trait. Selection can be divided into three classes, on the basis of its effect on allele frequencies: [[directional selection|directional]], [[stabilizing selection|stabilizing]], and [[disruptive selection]].<ref name="Rice">{{harvnb|Rice|2004|loc=See especially chapters 5 and 6 for a quantitative treatment}}</ref> Directional selection occurs when an allele has a greater fitness than others, so that it increases in frequency, gaining an increasing share in the population. This process can continue until the allele is [[fixation (population genetics)|fixed]] and the entire population shares the fitter phenotype.<ref>{{cite journal |author1=Rieseberg, L.H. |author2=Widmer, A. |author3=Arntz, A.M. |author4=Burke, J.M. |date=2002 |title=Directional selection is the primary cause of phenotypic diversification |journal=PNAS |volume=99 |issue=19 |pages=12242–12245 |doi=10.1073/pnas.192360899 |pmid=12221290 |pmc=129429|bibcode=2002PNAS...9912242R |doi-access=free }}</ref> Far more common is stabilizing selection, which lowers the frequency of alleles that have a deleterious effect on the phenotype—that is, produce organisms of lower fitness. This process can continue until the allele is eliminated from the population. Stabilizing selection [[Conserved sequence|conserves]] functional genetic features, such as [[protein biosynthesis|protein-coding genes]] or [[regulatory sequence]]s, over time by selective pressure against deleterious variants.<ref>{{cite journal |vauthors=Charlesworth B, Lande R, Slatkin M |date=1982 |title=A neo-Darwinian commentary on macroevolution |journal=Evolution |volume=36 |issue=3 |doi=10.1111/j.1558-5646.1982.tb05068.x |pmid=28568049 |pages=474–498|jstor=2408095 |s2cid=27361293 |doi-access=free }}</ref> Disruptive (or diversifying) selection is selection favouring extreme trait values over intermediate trait values. Disruptive selection may cause [[sympatric speciation]] through [[niche partitioning]].

Some forms of [[balancing selection]] do not result in fixation, but maintain an allele at intermediate frequencies in a population. This can occur in [[diploid]] species (with pairs of chromosomes) when [[Zygosity#Heterozygous|heterozygous]] individuals (with just one copy of the allele) have a higher fitness than homozygous individuals (with two copies). This is called heterozygote advantage or over-dominance, of which the best-known example is the resistance to malaria in humans heterozygous for [[sickle-cell anaemia]]. Maintenance of allelic variation can also occur through [[disruptive selection|disruptive or diversifying selection]], which favours genotypes that depart from the average in either direction (that is, the opposite of over-dominance), and can result in a [[Multimodal distribution|bimodal distribution]] of trait values. Finally, balancing selection can occur through frequency-dependent selection, where the fitness of one particular phenotype depends on the distribution of other phenotypes in the population. The principles of [[game theory]] have been applied to understand the fitness distributions in these situations, particularly in the study of kin selection and the evolution of [[reciprocal altruism]].<ref name="Hamilton"/><ref name="Trivers">{{cite journal |last=Trivers |first=Robert L. |author-link=Robert Trivers |date=March 1971 |title=The Evolution of Reciprocal Altruism |journal=The Quarterly Review of Biology |volume=46 |issue=1 |pages=35–57 |doi=10.1086/406755 |jstor=2822435|s2cid=19027999 }}</ref>

===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>