All of the rules of population genetics apply to molecular alleles. Practically speaking, there are an infinite number of possible molecular alleles. A given phenotypic allele observed in the population could, in principle, consist of a set of different molecularly-defined alleles. B. RFLP's are molecular alleles 1. Restriction sites can be assayed for polymorphism within a population by Southern hybridization.
Restriction sites can reveal polymorphism between genotypes.
DNA sequences are mutating all the time. As two populations diverge over time, they each accumulate different mutations at different sites. When restriction sites in the vicinity of a given gene are compared from one genotype to another, one genotype may have the site, and the other will not. This is referred to as a polymorphism . High polymorphism between two genotypes is evidence of genetic divergence.