Silent mutations, also called synonymous or samesense mutations, are mutations in DNA that do not have an observable effect on the organism's phenotype. The phrase silent mutation is often used interchangeably with the phrase synonymous mutation; however, synonymous mutations are not always silent, nor vice versa. Synonymous mutations can affect transcription, splicing, mRNA transport, and translation, any of which could alter phenotype, rendering the synonymous mutation non-silent. The substrate specificity of the tRNA to the rare codon can affect the timing of translation, and in turn the co-translational folding of the protein. This is reflected in the codon usage bias that is observed in many species. Mutations that cause the altered codon to produce an amino acid with similar functionality (e.g. a mutation producing leucine instead of isoleucine) are often classified as silent; if the properties of the amino acid are conserved, this mutation does not usually significantly affect protein function.
Silent mutations in the context of Genetic divergence
Genetic divergence is the process in which two or more populations of an ancestral species accumulate independent genetic changes (mutations) through time, often leading to reproductive isolation and continued mutation even after the populations have become reproductively isolated for some period of time, as there is not any genetic exchange anymore. In some cases, subpopulations cover living in ecologically distinct peripheral environments can exhibit genetic divergence from the remainder of a population, especially where the range of a population is very large (see parapatric speciation). The genetic differences among divergent populations can involve silent mutations (that have no effect on the phenotype) or give rise to significant morphological and/or physiological changes. Genetic divergence will always accompany reproductive isolation, either due to novel adaptations via selection and/or due to genetic drift, and is the principal mechanism underlying speciation.
On a molecular genetics level, genetic divergence is due to changes in a small number of genes in a species, resulting in speciation. However, researchers argue that it is unlikely that divergence is a result of a significant, single, dominant mutation in a genetic locus because if that were so, the individual with that mutation would have zero fitness. Consequently, they could not reproduce and pass the mutation on to further generations. Hence, it is more likely that divergence, and subsequently reproductive isolation, are the outcomes of multiple small mutations over evolutionary time accumulating in a population isolated from gene flow.
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