Fixation Index - Definition

Definition

Two of the most commonly used definitions for FST are based on the variance of allele frequencies between populations, and on the probability of Identity by descent.

If is the average frequency of an allele in the total population, is the variance in the frequency of alleles in different subpopulations, and is the variance of allele frequencies in the total population, FST is defined as

This definition, which is due to Wright, illustrates that FST measures the amount of genetic variance that can be explained by population structure.

Alternatively,

where is the probability of identity by descent of two individuals from the same subpopulation, and is the probability that two individuals from the total population are identical by descent. Using this definition, FST can be interpreted as measuring how much more closely two individuals from the same subpopulation are, compared to the total population. If the mutation rate is small, this interpretation can be made more explicit by linking the probability of identity by descent to coalescent times: Let T0 and T denote the average time to coalescence for individuals from the same subpopulation and the total population, respectively. Then,

This formulation has the advantage that the expected time to coalescence can easily be estimated from genetic data, which led to the development of various estimators for FST.

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