neutral theory of molecular evolution

https://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution#The_.22neutralist.E2.80.93selectionist.22_debate

Neutral theory of molecular evolution

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For the monograph by Kimura, see The Neutral Theory of Molecular Evolution.

The neutral theory of molecular evolution holds that at the molecular level most evolutionary changes and most of the variation within and between species is 

not caused by natural selection but by genetic drift of mutant alleles that are neutral. 

A neutral mutation is one that does not affect an organism's ability to survive and reproduce. 

The neutral theory allows for the possibility that most mutations are deleterious, 

but holds that because these are rapidly purged by natural selection, 

they do not make significant contributions to variation within and between species at the molecular level. 

Mutations that are not deleterious are assumed to be mostly neutral rather than beneficial. 

In addition to assuming the primacy of neutral mutations, the theory also assumes that the fate of neutral mutations is 

determined by the sampling processes described by specific models of random genetic drift.^[1]

The theory was introduced by a Japanese biologist Motoo Kimura in 1968, 

and independently by two American biologists Jack Lester King and Thomas Hughes Jukes in 1969. 

According to Kimura, the theory applies only for evolution at the molecular level, 

and phenotypic evolution is controlled by natural selection, as postulated by Charles Darwin. 

The proposal of the neutral theory was followed by an extensive "neutralist-selectionist" controversy over the interpretation of patterns of molecular divergence and polymorphism, peaking in the 1970s and 1980s. 

The controversy is still unsettled among evolutionary biologists.

Contents

  [hide] 

• 1Overview
• 2The "neutralist–selectionist" debate
• 3See also
• 4References
• 5External links

Overview[edit]

While some scientists, such as Freese (1962)^[2] and Freese and Yoshida (1965),^[3] had suggested that neutral mutations were probably widespread, 

a coherent theory of neutral evolution was proposed by Motoo Kimura in 1968,^[4] and by King and Jukes independently in 1969.^[5]

Kimura, King, and Jukes suggested that 

when one compares the genomes of existing species, the vast majority of molecular differences are selectively "neutral", 

i.e. the molecular changes represented by these differences do not influence the fitness of organisms. 

As a result, the theory regards these genomic features as neither subject to, nor explicable by, natural selection. 

This view is based in part on the degenerate genetic code, in which sequences of three nucleotides (codons) may 

differ and yet encode the same amino acid (GCC and GCA both encode alanine, for example). 

Consequently, many potential single-nucleotide changes are in effect "silent" or "unexpressed" (see synonymous or silent substitution). 

Such changes are presumed to have little or no biological effect.

A second hypothesis of the neutral theory is that most evolutionary change is the result of genetic drift acting on neutral alleles, 

rather than for example genetic hitchhiking of a neutral allele due to genetic linkage with non-neutral alleles. 

After appearing by mutation, a neutral allele may become more common within the population via genetic drift. 

Usually, it will be lost, or in rare cases it may become fixed, meaning that the new allele becomes standard in the population. 

This stochastic process is assumed to obey equations describing random genetic drift by means of accidents of sampling.

According to the neutral theory, mutations appear at rate μ in each of the 2N copies of a gene, and fix with probability 1/(2N). 

This means that if all mutations were neutral, 

the rate at which fixed differences accumulate between divergent populations is predicted to be equal to the per-individual mutation rate, 

e.g. during errors in DNA replication; both are equal to μ. 

When the proportion of mutations that are neutral is constant, so is the divergence rate between populations. 

This provides a rationale for the molecular clock, although the discovery of a molecular clock predated neutral theory.^[6]

Many molecular biologists and population geneticists also contributed to the development of the neutral theory, 

which is different from the neo-Darwinian theory.^[1][7][8]

Neutral theory does not deny the occurrence of natural selection. 

Hughes writes: "Evolutionary biologists typically distinguish two main types of natural selection: 

purifying selection, which acts to eliminate deleterious mutations; and 

positive (Darwinian) selection, which favors advantageous mutations. 

Positive selection can, in turn, be further subdivided into directional selection, which tends toward fixation of an advantageous allele, 

and balancing selection, which maintains a polymorphism. 

The neutral theory of molecular evolution predicts that purifying selection is ubiquitous, but that both forms of positive selection are rare, 

whereas not denying the importance of positive selection in the origin of adaptations."^[9] 

In another essay, Hughes writes: "Purifying selection is the norm in the evolution of protein coding genes. Positive selection is a relative rarity — but of great interest, precisely because it represents a departure from the norm."^[10] 

A more general and more recent view of molecular evolution is presented by Nei.^[8]

The "neutralist–selectionist" debate[edit]

See also: History of evolutionary thought and History of molecular evolution

A heated debate arose when Kimura's theory was published, 

largely revolving around the relative percentages of alleles that are "neutral" versus "non-neutral" in any given genome. 

Contrary to the perception of many onlookers, the debate was not about whether natural selection does occur. 

Kimura argued that molecular evolution is dominated by selectively neutral evolution 

but at the phenotypic level, changes in characters were probably dominated by natural selection rather than genetic drift.^[11]

According to the neutral theory of molecular evolution, 

the amount of genetic variation within a species should be proportional to the effective population size. 

Levels of genetic diversity vary much less than census population sizes, giving rise to the "paradox of variation" .^[12] 

While high levels of genetic diversity were one of the original arguments in favor of neutral theory, 

the paradox of variation has been one of the strongest arguments against neutral theory.

Tomoko Ohta emphasized the importance of nearly neutral mutations, in particularly slightly deleterious mutations.^[13] 

The population dynamics of nearly neutral mutations is essentially the same as that of neutral mutations unless the absolute magnitude of the selection coefficient is greater than 1/N, where N is the effective population size with respect to selection.^[1][7][8]

 The value of N may therefore affect how many mutations can be treated as neutral and how many as deleterious.

There are a large number of statistical methods for testing whether neutral theory is a good description of evolution (e.g., McDonald-Kreitman test^[14]), 

and many authors claimed detection of selection (Fay et al. 2002,^[15] Begun et al. 2007,^[16] Shapiro et al. 2007,^[17] Hahn 2008,^[18] Akey 2009.^[19]). 

However, Nei et al. (2010).^[20] have argued that their methods for claiming so depend on many assumptions which are not biologically justified.

See also[edit]

• Adaptive evolution in the human genome
• Coalescent theory
• Evolution
• Masatoshi Nei
• Motoo Kimura
• Molecular evolution
• Nearly neutral theory of molecular evolution
• Tomoko Ohta
• Unified neutral theory of biodiversity

References[edit]

1. ^ Jump up to:^a b c Kimura, Motoo. (1983). The neutral theory of molecular evolution. Cambridge
2. Jump up^ Freese, E. (1962). On the evolution of base composition of DNA. J THeor Biol, 3:82-101.
3. Jump up^ Freese, E. and Yoshida, A. (1965). The role of mutations in evolution. In V Bryson, and H J Vogel, eds. Evolving Genes and Proteins, pp. 341-55. Academic, New York.
4. Jump up^ Kimura M. (1968). Evolutionary Rate at the Molecular Level. Nature 217:624-6.
5. Jump up^ King JL, Jukes TH. (1969). Non-Darwinian Evolution. Science 164:788-97.
6. Jump up^ Zuckerkandl, E. and Pauling, L.B. (1962). "Molecular disease, evolution, and genetic heterogeneity". In Kasha, M. and Pullman, B (editors). Horizons in Biochemistry. Academic Press, New York. pp. 189–225.
7. ^ Jump up to:^a b Nei, M. (2005). Selectionism and neutralism in molecular evolution. Mol Biol Evol, 22: 2318-42
8. ^ Jump up to:^a b c Nei, M. (2013). Mutation-driven evolution. Oxford University Press, Oxford
9. Jump up^ Hughes, Austin L. (2007). "Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level". Heredity. 99 (4): 364–373. doi:10.1038/sj.hdy.6801031. PMID 17622265.
10. Jump up^ Hughes, Austin L. (2000). Adaptive Evolution of Genes and Genomes. Oxford University Press. p. 53. ISBN 0-19-511626-7.
11. Jump up^ Provine (1991)
12. Jump up^ Lewontin, [by] R. C. (1973). The genetic basis of evolutionary change ([4th printing.] ed.). New York: Columbia University Press. ISBN 978-0231033923.