Silent base changes are mutations which do not alter the amino acid. (Those which do are called replacement mutations.)

Since they are less constrained than replacement sites, the geneticist Kimura had predicted, before DNA sequences were available, that silent changes would evolve more rapidly. It has now been well confirmed that they do; the table shows that evolution in silent sites runs at about five times the rate in replacement sites.

If silent codon positions were selectively unconstrained, they should show pan-neutral evolution. They should then evolve in a different manner from proteins and evolve at the rate of a 'universal' molecular clock, i.e. at their total mutation rate.

Recent evidence has not supported this claim:

• The evolutionary rates of different silent genes is not constant.

• It was discovered that there is a consistent non-random variation in the frequency of codons in a species. This suggests that silent alternative codons are not all functionally equivalent.