Fixation index

Fixation index (FST) is a measure of population differentiation based on genetic polymorphism data (such as SNPs or microsatellites). It is a special case of F-statistics, concept developed in the 1920s by Sewall Wright.

This statistic compares the genetic variability within and between population and is frequently used in the field of population genetics.

Several definitions of Fst have been used, all measuring different but related quantities. A common definition has been proposed by Hudson, Slatkin and Maddison (1992):

$$ F_{ST} = \frac{ \Pi_{Between} - \Pi_{Within} } { \Pi_{Between} } $$

where $$ \Pi_{Between} $$ and $$ \Pi_{Within} $$ represent the average number of pairwise differences between two individuals sampled from different  ($$ \Pi_{Between} $$) or the same ($$ \Pi_{Within} $$) population. Note that when using this definition $$ \Pi_{Within} $$ should be computed for each population and then averaged. Otherwise, random sampling of pairs within populations put all the weight on the population with the largest sample size.