FST (Fixation Index) Calculators

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FST — the fixation index — is the most widely used measure of genetic differentiation between populations. It quantifies how much of the total genetic variation in a species is explained by differences between populations, rather than variation within them. An FST of 0 means populations are genetically identical; an FST of 1 means they share no genetic variation at all. FST is a cornerstone of population genetics, applied in conservation biology, evolutionary studies, forensic genetics, and the detection of natural selection across the genome.

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What Is FST?

FST (Wright's fixation index) measures the degree of genetic differentiation among subpopulations relative to the total population. It was developed by Sewall Wright in 1951 and has since become the standard statistic for quantifying population structure in genetics.

FST is defined as:

FST = (HT − HS) / HT

Where:

  • HT — expected heterozygosity in the total (combined) population
  • HS — average expected heterozygosity within subpopulations

FST ranges from 0 to 1. The closer it is to 1, the more genetically distinct the populations are from one another.

Interpreting FST Values

Wright (1978) proposed qualitative guidelines for interpreting FST:

  • FST = 0–0.05: Little genetic differentiation
  • FST = 0.05–0.15: Moderate differentiation
  • FST = 0.15–0.25: Great differentiation
  • FST > 0.25: Very great differentiation

These are rough guidelines — the biological meaning of a given FST value depends heavily on the organism, the markers used, and the evolutionary history of the populations. Many closely related bird populations show FST > 0.3, while some morphologically distinct fish populations may have FST < 0.05 due to ongoing gene flow.

What Drives FST?

FST is shaped by the balance between factors that increase and decrease genetic differentiation:

  • Increases FST: Genetic drift (especially in small populations), geographic isolation, local adaptation, natural selection
  • Decreases FST: Gene flow (migration between populations), large effective population sizes

Wright's island model predicts: FST ≈ 1 / (1 + 4Nem), where Ne is effective population size and m is migration rate. This shows that even low levels of migration (Nem ≈ 1 migrant per generation) keep FST relatively low.

FST Variants and Alternatives

Several variants address limitations of the original FST:

  • GST: Nei's generalization for multiple alleles and populations
  • G'ST: Normalized version that corrects for within-population heterozygosity, allowing comparison across loci with different allelic diversity
  • Jost's D: An alternative differentiation statistic that is independent of within-population diversity
  • QST: Analogous to FST but applied to quantitative traits — used to test whether trait differentiation exceeds neutral genetic differentiation (evidence of local adaptation)

FST in Genome Scans for Selection

Genome-wide FST scans identify outlier loci — genomic regions with unusually high FST values compared to the genome-wide average. These outliers are candidate loci under divergent selection, where different alleles are favored in different environments. This approach has identified genes underlying local adaptation in numerous species, from stickleback fish to human populations.

Glossary

FST (Fixation Index)
A measure of genetic differentiation between subpopulations, calculated as the proportion of total genetic variation explained by between-population differences. Ranges from 0 (no differentiation) to 1 (complete differentiation).
Gene Flow
The transfer of alleles between populations through migration and interbreeding. Gene flow homogenizes allele frequencies across populations, reducing FST and preventing genetic divergence.
Genetic Drift
Random changes in allele frequencies due to chance sampling effects in finite populations. Genetic drift is stronger in small populations and leads to increased FST over time as populations diverge by chance.

Frequently Asked Questions

An FST of 0.1 means that 10% of the total genetic variation in the system is explained by differences between populations, while 90% is due to variation within populations. By Wright's guidelines, this falls in the 'moderate differentiation' range (0.05–0.15), suggesting some genetic structure but ongoing gene flow between populations.

FST measures the proportion of genetic variation distributed between vs. within populations and reflects the degree of differentiation. Genetic distance (e.g., Nei's D) estimates the number of allele frequency differences between two populations, increasing with divergence time and decreasing gene flow. FST is bounded between 0 and 1; genetic distance is unbounded. Both are used in population structure analysis but provide slightly different information.

Gene flow (migration of individuals between populations) reduces FST by homogenizing allele frequencies across populations. Even very low levels of gene flow — as few as one migrant per generation (Nem = 1) — can substantially reduce FST. Wright's island model predicts FST ≈ 1/(1 + 4Nem), so increasing migration rapidly drives FST toward zero.

Yes. Genome-wide FST scans compare FST values across many loci. Most loci evolve neutrally and show FST values near the genome-wide average. Loci under divergent selection — where different alleles are favored in different populations — show unusually high FST values, appearing as outliers. These are candidate regions for local adaptation.