What is neutrality of the nucleotide sequence variations?
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When the idea of a constant molecular clock first emerged, it was thought that the predominant evolutionary force underlying amino acid or nucleotide substitutions was natural selection. Following this line of thinking, a constant molecular clock would indicate that adaptive substitutions in different species occur constantly over time. However, it is hard to explain how adaptive substitutions would occur in such a clock-like manner. Theoretically, the fates of adaptive mutations are determined by several evolutionary parameters, such as the strength of the selective advantage of that mutation, the size of the effective population, and adaptive mutation rates (Kimura 1983). These parameters are likely to differ between species, and even within a species, depending upon specific mutations and their interactions with environments.
Instead, Kimura (1968, 1969) proposed that most changes at the molecular level have little functional consequences, or are ‘neutral'. If a mutation has no fitness consequence, its fate in the population is determined completely by random chance. This means that we cannot predict whether a specific neutral mutation will eventually be fixed in the population. However, the rate at which neutral substitutions occur in the population can be predicted because it depends upon a single parameter, namely the mutation rate (Kimura 1968).
Let's imagine a population with N number of haploid individuals. If neutral mutations occur at rate u per individual per generation, the total number of mutations in one generation will be N times u. Since all these new mutations are neutral, their fates are completely determined by chance. In other words, all mutations have equal chance of reaching fixation (which leads to a ‘substitution'). The probability that each new neutral mutation will reach fixation, given that a substitution occurred, is simply 1/N. The rate of substitutions is calculated as the number of new mutations in each generation (Nu) multiplied by the probability each new mutation reaches fixation (1/N), which equals u. In other words, for neutral mutations, the rate of substitution is equal to the rate of mutation!
Therefore, if most mutations are neutral (as proposed in the neutral theory) and if mutation rates are constant over time, substitutions should occur constantly over time as well. We should then observe clock-like regular rates of substitutions at the molecular level. Kimura (1969) thus considered the observation of relatively constant molecular clock in protein sequences as strong support for the neutral theory of molecular evolution.
Instead, Kimura (1968, 1969) proposed that most changes at the molecular level have little functional consequences, or are ‘neutral'. If a mutation has no fitness consequence, its fate in the population is determined completely by random chance. This means that we cannot predict whether a specific neutral mutation will eventually be fixed in the population. However, the rate at which neutral substitutions occur in the population can be predicted because it depends upon a single parameter, namely the mutation rate (Kimura 1968).
Let's imagine a population with N number of haploid individuals. If neutral mutations occur at rate u per individual per generation, the total number of mutations in one generation will be N times u. Since all these new mutations are neutral, their fates are completely determined by chance. In other words, all mutations have equal chance of reaching fixation (which leads to a ‘substitution'). The probability that each new neutral mutation will reach fixation, given that a substitution occurred, is simply 1/N. The rate of substitutions is calculated as the number of new mutations in each generation (Nu) multiplied by the probability each new mutation reaches fixation (1/N), which equals u. In other words, for neutral mutations, the rate of substitution is equal to the rate of mutation!
Therefore, if most mutations are neutral (as proposed in the neutral theory) and if mutation rates are constant over time, substitutions should occur constantly over time as well. We should then observe clock-like regular rates of substitutions at the molecular level. Kimura (1969) thus considered the observation of relatively constant molecular clock in protein sequences as strong support for the neutral theory of molecular evolution.
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