The calculation of a genetic distance between two populations gives a relative estimate of the time that has passed since the populations have existed as single cohesive units. Small estimations of distance may indicate population substructure (i.e. subpopulations in which there is random mating, but between which there is a reduced amount of gene flow). However, small estimations of distance may also be present because the populations are completely isolated but have only been separated for a short period of time. When two populations are genetically isolated, the two processes of mutation and genetic drift lead to differentiation in the allele frequencies at selectively neutral loci. As the amount of time that two populations are separated increases, the difference in allele frequencies should also increase until each population is completely fixed for separate alleles. A number of methods have been developed which estimate genetic distance from these allele frequency differences. Estimations of genetic distance determined from differences in microsatellite allele frequencies can be summarised into the two categories, IAM and SMM/TPM based estimators.

Some of the more useful measures of population subdivision are the F-statistics developed by Wright (1965). F-statistics can be thought of as a measure of the correlation of alleles within individuals and are related to inbreeding coefficients. An inbreeding coefficient is really a measure of the nonrandom association of alleles within an individual. As such, F- statistics describe the amount inbreeding-like effects within subpopulations , among subpopulations , and within the entire population . These can also be classified as IAM and SMM/TPM based estimators of F-statistics.

If there is no migration occurring between two subpopulations,
eventually alternate alleles will become fixed and will reach
1. Alternatively, it has long been known that if the migration rate,
measured in terms of **Nm**, is **>** 1 (where **N** is the effective
population size and **m** is the fraction of migrants per generation),
the allele frequencies in the subpopulations will remain homogenised
(Wright 1931). If, however, migration is present but **Nm** **<** 1, an
equilibrium based on the rate of mutation, migration, and genetic drift
will be established.
Estimating **Nm** from microsatellite data.