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A study of the substitution processes for different models of harmful alleles through mathematical analyses and computer simulations reveals that the rate of substitution has a concave relation to the selection strength. The models studied include the house-of-cards model, the Hartl-Dykhuizen-Dean (HDD) model, the exponential and gamma shift models and the optimum model. While the HDD and optimum models represent silent evolution adequately, no model represents protein evolution satisfactorily due to the variability in substitutions exhibited by them.

A completed simulation of the mechanism of nucleotide replacements in a finite haploid population, relying in selection in a randomly varying setting, yields surprising findings. A small mutation rate estimate explains why replacements are more consistent than random for quickly varying settings and several symmetrical constructs of molecular development with quickly altering indication may show replacements that are more uniform than random because this explanation does not wholly rely on specifics of the haploid model.

Selected substitutions at one locus can induce stochastic dynamics that resemble genetic drift at a closely linked neutral locus. The pseudohitchhiking model is a one-locus model that approximates these effects and can be used to describe the major consequences of linked selection. As the changes in neutral allele frequencies when hitchhiking are rapid, diffusion theory is not appropriate for studying neutral dynamics. A stationary distribution and some results on substitution processes are presented that use the theory of continuous-time Markov processes with discontinuous sample paths. The coalescent of the pseudohitchhiking model is shown to have a random number of branches at each node, which leads to a frequency spectrum that is different from that of the equilibrium neutral model. If genetic draft, the name given to these induced stochastic effects, is a more important stochastic force than genetic drift, then a number of paradoxes that have plagued population genetics disappear.