Functional DNA Positions Change as Frequently as Do Neutral Ones

Much work has been done in statistically describing how DNA changes through evolution. Relative to models for neutral DNA sequence positions, models for functional DNA sequence positions usually include a far-from-uniform equilibrium probability distribution and a significantly reduced rate of change. We examine the mathematical basis for these modifications to the functional-DNA model. We find that, although non-lethal selection pressures will skew the equilibrium probability distribution of alleles, thus making fitter alleles more common in the population, selection pressures do not significantly affect the rate of allele change. Even beyond consideration of DNA sequences, the word “conservation” would more appropriately be used to indicate the non-uniformity of an equilibrium probability distribution of alleles, rather than to denote a reduced rate of change. The design of statistical models of substitution for functional alleles should reflect this characterization.