While some scientists, such as Freese (1962) and Freese and Yoshida (1965), had suggested that neutral mutations were probably widespread, the original mathematical derivation of the theory had been published by R.A. Fisher in 1930. Fisher, however, gave a reasoned argument for believing that, in practice, neutral gene substitutions would be very rare. 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 focused on differences within species.
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.
According to ISM, selectively neutral mutations appear at rate
μ
{\displaystyle \mu }
in each of the
2
N
{\displaystyle 2N}
copies of a gene, and fix with probability
1
/
(
2
N
)
{\displaystyle 1/(2N)}
. Because any of the
2
N
{\displaystyle 2N}
genes have the ability to become fixed in a population,
1
/
2
N
{\displaystyle 1/2N}
is equal to
μ
{\displaystyle \mu }
, resulting in the rate of evolutionary rate equation:
k
=
v
{\displaystyle k=v}
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.
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".
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. 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.
CNE has also been put forwards as the null hypothesis for explaining complex structures, and thus adaptationist explanations for the emergence of complexity must be rigorously tested on a case-by-case basis against this null hypothesis prior to acceptance. Grounds for invoking CNE as a null include that it does not presume that changes offered an adaptive benefit to the host or that they were directionally selected for, while maintaining the importance of more rigorous demonstrations of adaptation when invoked so as to avoid the excessive flaws of adaptationism criticized by Gould and Lewontin.
Predictions derived from the neutral theory are generally supported in studies of molecular evolution. One of corollaries of the neutral theory is that the efficiency of positive selection is higher in populations or species with higher effective population sizes. This relationship between the effective population size and selection efficiency was evidenced by genomic studies of species including chimpanzee and human and domesticated species. In small populations (e.g., a population bottleneck during a speciation event), slightly deleterious mutations should accumulate. Data from various species supports this prediction in that the ratio of nonsynonymous to synonymous nucleotide substitutions between species generally exceeds that within species. In addition, nucleotide and amino acid substitutions generally accumulate over time in a linear fashion, which is consistent with neutral theory. Arguments against the neutral theory cite evidence of widespread positive selection and selective sweeps in genomic data. Empirical support for the neutral theory may vary depending on the type of genomic data studied and the statistical tools used to detect positive selection. For example, Bayesian methods for the detection of selected codon sites and McDonald-Kreitman tests have been criticized for their rate of erroneous identification of positive selection.
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