The stepwise mutation model (SMM) is a mathematical theory, developed by Motoo Kimura and Tomoko Ohta, that allows for investigation of the equilibrium distribution of allelic frequencies in a finite population where neutral alleles are produced in step-wise fashion.
[1] The original model assumes that if an allele has a mutation that causes it to change in state, mutations that occur in repetitive regions of the genome will increase or decrease by a single repeat unit at a fixed rate (i.e. by the addition or subtraction of one repeat unit per generation) and these changes in allele states are expressed by an integer (.
[3] Given the underlying assumptions of the SMM, it has been widely adopted for use with microsatellite markers that contain repeat regions, are co-dominate, and have high rates of mutation.
Variance in allele sizes are used to make inferences about the genetic distance between individuals or populations.
By comparing summary statistics at different levels of organization it is possible to make inferences about population histories.