User:Cba021/Neutral theory of molecular evolution

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Nearly neutral theory
Tomoko Ohta also emphasized the importance of nearly neutral mutations, in particularly slightly deleterious mutations. The Nearly neutral theory stems from the prediction of neutral theory that the balance between selection and genetic drift depends on effective population size. Nearly neutral mutations are those that carry selection coefficients less than the inverse of twice the effective population size. The population dynamics of nearly neutral mutations differ from those of neutral mutations in that their behavior depends on the relative strength of selection and effective population size. The effective population size affects whether slightly deleterious mutations can be treated as neutral or as deleterious. In large populations, selection can decrease the frequency of slightly deleterious mutations, therefore acting as if they are deleterious. However, in small populations, genetic drift can more easily overcome selection, causing slightly deleterious mutations to act as if they are neutral and drift to fixation or loss.

Empirical evidence for the neutral theory
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 population 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.