Neutral theory of molecular evolution
The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species, are due to random genetic drift of mutant alleles that are selectively neutral. The theory applies only for evolution at the molecular level, and is compatible with phenotypic evolution being shaped by natural selection as postulated by Charles Darwin. The neutral theory allows for the possibility that most mutations are deleterious, but holds that because these are rapidly removed by natural selection, they do not make significant contributions to variation within and between species at the molecular level. A neutral mutation is one that does not affect an organism's ability to survive and reproduce. The neutral theory assumes that most mutations that are not deleterious are neutral rather than beneficial. Because only a fraction of gametes are sampled in each generation of a species, the neutral theory suggests that a mutant allele can arise within a population and reach fixation by chance, rather than by selective advantage.
The theory was introduced by the Japanese biologist Motoo Kimura in 1968, and independently by two American biologists Jack Lester King and Thomas Hughes Jukes in 1969, and described in detail by Kimura in his 1983 monograph The Neutral Theory of Molecular Evolution. The proposal of the neutral theory was followed by an extensive "neutralist-selectionist" controversy over the interpretation of patterns of molecular divergence and gene polymorphism, peaking in the 1970s and 1980s.
While some scientists, such as Freese (1962) and Freese and Yoshida (1965), had suggested that neutral mutations were probably widespread, and an original mathematical derivation of the theory had been published by R.A. Fisher in 1930, a coherent theory of neutral evolution was first proposed by Motoo Kimura in 1968, and by King and Jukes independently in 1969. Kimura initially focused on differences among species, King and Jukes on differences within species.
Many molecular biologists and population geneticists also contributed to the development of the neutral theory. Principles of population genetics, established by J.B.S. Haldane, R.A. Fisher and Sewall Wright, created a mathematical approach to analyzing gene frequencies that contributed to the development of Kimura's theory.
Haldane's dilemma regarding the cost of selection was used as motivation by Kimura. Haldane estimated that it takes about 300 generations for a beneficial mutation to become fixed in a mammalian lineage, meaning that the number of substitutions (1.5 per year) in the evolution between humans and chimpanzees was too high to be explained by beneficial mutations.
The neutral theory holds that as functional constraint diminishes, the probability that a mutation is neutral rises, and so should the rate of sequence divergence.
When comparing various proteins, extremely high evolutionary rates were observed in proteins such as fibrinopeptides and the C chain of the proinsulin molecule, which both have little to no functionality compared to their active molecules. Kimura and Ohta also estimated that the alpha and beta chains on the surface of a hemoglobin protein evolve at a rate almost ten times faster than the inside pockets, which would imply that the overall molecular structure of hemoglobin is less significant than the inside where the iron-containing heme groups reside.
There is evidence that rates of nucleotide substitution are particularly high in the third position of a codon, where there is little functional constraint. 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.
Kimura also developed the infinite sites model (ISM) to provide insight into evolutionary rates of mutant alleles. If were to represent the rate of mutation of gametes per generation of individuals, each with two sets of chromosomes, the total number of new mutants in each generation is . Now let represent the evolution rate in terms of a mutant allele becoming fixed in a population.
According to ISM, selectively neutral mutations appear at rate in each of the copies of a gene, and fix with probability . Because any of the genes have the ability to become fixed in a population, is equal to , resulting in the rate of evolutionary rate equation:
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, independent of population size. 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 - which predated neutral theory. The ISM also demonstrates a constancy that is observed in molecular lineages.
This stochastic process is assumed to obey equations describing random genetic drift by means of accidents of sampling, 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.
The "neutralist–selectionist" debate
A heated debate arose when Kimura's theory was published, largely revolving around the relative percentages of polymorphic and fixed alleles that are "neutral" versus "non-neutral".
A genetic polymorphism means that different forms of particular genes, and hence of the proteins that they produce, are co-existing within a species. Selectionists claimed that such polymorphisms are maintained by balancing selection, while neutralists view the variation of a protein as a transient phase of molecular evolution. Studies by Richard K. Koehn and W. F. Eanes demonstrated a correlation between polymorphism and molecular weight of their molecular subunits. This is consistent with the neutral theory assumption that larger subunits should have higher rates of neutral mutation. Selectionists, on the other hand, contribute environmental conditions to be the major determinants of polymorphisms rather than structural and functional factors.
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" . 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.
There are a large number of statistical methods for testing whether neutral theory is a good description of evolution (e.g., McDonald-Kreitman test), and many authors claimed detection of selection (Fay et al. 2002, Begun et al. 2007, Shapiro et al. 2007, Hahn 2008, Akey 2009, Kern 2018). Some researchers have nevertheless argued that the neutral theory still stands, while expanding the definition of neutral theory to include background selection at linked sites.
Nearly neutral theory
Tomoko Ohta also emphasized the importance of nearly neutral mutations, in particularly slightly deleterious mutations. The population dynamics of nearly neutral mutations are only slightly different from those of neutral mutations unless the absolute magnitude of the selection coefficient is greater than 1/N, where N is the effective population size in respect of selection. The value of N may therefore affect how many mutations can be treated as neutral and how many as deleterious.
- Adaptive evolution in the human genome
- Coalescent theory
- Masatoshi Nei
- Molecular evolution
- Tomoko Ohta
- Unified neutral theory of biodiversity
- Constructive neutral evolution
- Kimura, Motoo (1983). The neutral theory of molecular evolution. Cambridge University Press. ISBN 978-0-521-31793-1.
- Freese, E. (July 1962). "On the evolution of the base composition of DNA". Journal of Theoretical Biology. 3 (1): 82–101. doi:10.1016/S0022-5193(62)80005-8.
- Freese, E.; Yoshida, A. (1965). "The role of mutations in evolution.". In Bryson, V.; Vogel, H. J. (eds.). Evolving Genes and Proteins. New York: Academic. pp. 341–355.
- Fisher RA 1930. The distribution of gene ratios for rare mutations. Proceedings of the Royal Society of Edinburgh volume 50, pages 205-230.
- Kimura, Motoo (February 1968). "Evolutionary rate at the molecular level". Nature. 217 (5129): 624–6. Bibcode:1968Natur.217..624K. doi:10.1038/217624a0. PMID 5637732. S2CID 4161261.
- King, J. L.; Jukes, T. H. (May 1969). "Non-Darwinian evolution". Science. 164 (3881): 788–98. Bibcode:1969Sci...164..788L. doi:10.1126/science.164.3881.788. PMID 5767777.
- Nei, Masatoshi (December 2005). "Selectionism and neutralism in molecular evolution". Molecular Biology and Evolution. 22 (12): 2318–2342. doi:10.1093/molbev/msi242. PMC 1513187. PMID 16120807.
- Nei, Masatoshi (2013). Mutation-driven evolution. Oxford University Press.
- Kimura, M. (1969-08-01). "The Rate of Molecular Evolution Considered from the Standpoint of Population Genetics". Proceedings of the National Academy of Sciences. 63 (4): 1181–1188. doi:10.1073/pnas.63.4.1181. ISSN 0027-8424. PMC 223447. PMID 5260917.
- Bofkin, L.; Goldman, N. (2006-11-13). "Variation in Evolutionary Processes at Different Codon Positions". Molecular Biology and Evolution. 24 (2): 513–521. doi:10.1093/molbev/msl178. ISSN 0737-4038. PMID 17119011.
- CRICK, F.H.C. (1989), "Codon—Anticodon Pairing: The Wobble Hypothesis", Molecular Biology, Elsevier, pp. 370–377, doi:10.1016/b978-0-12-131200-8.50026-5, ISBN 978-0-12-131200-8, retrieved 2021-04-03
- Kimura, Motoo (November 1979). "The neutral theory of molecular evolution". Scientific American. 241 (5): 98–100, 102, 108 passim. Bibcode:1979SciAm.241e..98K. doi:10.1038/scientificamerican1179-98. JSTOR 24965339. PMID 504979.
- Zuckerkandl, Emile; Pauling, Linus B. (1962). "Molecular disease, evolution, and genetic heterogeneity". In Kasha, M.; Pullman, B. (eds.). Horizons in Biochemistry. Academic Press. pp. 189–225.
- Eanes, Walter F. (November 1999). "Analysis of Selection on Enzyme Polymorphisms". Annual Review of Ecology and Systematics. 30 (1): 301–326. doi:10.1146/annurev.ecolsys.30.1.301.
- Lewontin, Richard C. (1973). The genetic basis of evolutionary change (4th printing ed.). Columbia University Press. ISBN 978-0231033923.
- Kreitman, M. (2000). "Methods to detect selection in populations with applications to the human". Annual Review of Genomics and Human Genetics. 1 (1): 539–59. doi:10.1146/annurev.genom.1.1.539. PMID 11701640.
- Fay, J. C.; Wyckoff, G. J.; Wu, C. I. (February 2002). "Testing the neutral theory of molecular evolution with genomic data from Drosophila". Nature. 415 (6875): 1024–6. Bibcode:2002Natur.415.1024F. doi:10.1038/4151024a. PMID 11875569. S2CID 4420010.
- Begun, D. J.; Holloway, A. K.; Stevens, K.; Hillier, L. W.; Poh, Y. P.; Hahn, M. W.; Nista, P. M.; Jones, C. D.; Kern, A. D.; Dewey, C. N.; Pachter, L.; Myers, E.; Langley, C. H. (November 2007). "Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans". PLOS Biology. 5 (11): e310. doi:10.1371/journal.pbio.0050310. PMC 2062478. PMID 17988176.
- Shapiro, J. A.; Huang, W.; Zhang, C.; Hubisz, M. J.; Lu, J.; Turissini, D. A.; Fang, S.; Wang, H. Y.; Hudson, RR; Nielsen, R.; Chen, Z.; Wu, C. I. (February 2007). "Adaptive genic evolution in the Drosophila genomes". PNAS. 104 (7): 2271–6. Bibcode:2007PNAS..104.2271S. doi:10.1073/pnas.0610385104. PMC 1892965. PMID 17284599.
- Hahn, M. W. (February 2008). "Toward a selection theory of molecular evolution". Evolution; International Journal of Organic Evolution. 62 (2): 255–65. doi:10.1111/j.1558-5646.2007.00308.x. PMID 18302709.
- Akey, J. M. (May 2009). "Constructing genomic maps of positive selection in humans: where do we go from here?". Genome Research. 19 (5): 711–22. doi:10.1101/gr.086652.108. PMC 3647533. PMID 19411596.
- Kern, A. D.; Hahn, M. W. (June 2018). "The Neutral Theory in Light of Natural Selection". Molecular Biology and Evolution. 35 (6): 1366–1371. doi:10.1093/molbev/msy092. PMC 5967545. PMID 29722831.
- Jensen, J.D.; Payseur, B. A.; Stephan, W.; Aquadro C. F.; Lynch, M. Charlesworth, D.; Charlesworth, B. (January 2019). "The importance of the Neutral Theory in 1968 and 50 years on: A response to Kern and Hahn 2018". Evolution; International Journal of Organic Evolution. 73 (1): 111–114. doi:10.1111/evo.13650. PMC 6496948. PMID 30460993.CS1 maint: multiple names: authors list (link)
- Ohta, T. (December 2002). "Near-neutrality in evolution of genes and gene regulation". Proceedings of the National Academy of Sciences of the United States of America. 99 (25): 16134–7. Bibcode:2002PNAS...9916134O. doi:10.1073/pnas.252626899. PMC 138577. PMID 12461171.