FST and Genetic Distance Calculator

Calculate FST, genetic distance, and population differentiation from allele frequencies.

Allele frequency in pop 1 (p₁)

Allele frequency in pop 2 (p₂)

Sample size pop 1 (n₁)

Sample size pop 2 (n₂)

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What F_ST Actually Compares

F_ST asks how much of the total genetic variation lies between populations rather than within them. It is a proportion, bounded by 0 and 1.

F_ST = (H_T − H_S) / H_T

F_ST	Differentiation	Example
0–0.05	Little	Populations connected by gene flow
0.05–0.15	Moderate	Human continental groups ≈ 0.10–0.15
0.15–0.25	Great	Long-isolated populations
> 0.25	Very great	Approaching separate species

The human figure is worth stating carefully: roughly 85–90% of human genetic variation exists within populations, and only 10–15% between them. This is Lewontin's classic finding and it is why F_ST is often cited in discussions of human genetic diversity.

Migration and the One-Migrant Rule

F_ST ≈ 1 / (4N_em + 1)

Rearranging gives a striking result: about one migrant per generation is enough to prevent substantial differentiation, regardless of population size. One effective migrant gives F_ST near 0.20; ten give about 0.024.

The reason it is independent of population size is that drift is stronger in small populations but a single migrant also represents a larger fraction of them. The two effects cancel. This underpins conservation guidance on connectivity between fragmented habitats.

Limitations

Issue	Consequence
Depends on within-population diversity	Highly variable markers give lower F_ST ceilings
Single number for complex structure	Cannot show direction or timing of gene flow
Assumes equilibrium	Recent divergence is not at migration-drift balance

Because F_ST is bounded by within-population heterozygosity, highly polymorphic markers such as microsatellites cannot reach high values even between completely isolated populations. Standardised measures such as G″_ST and Jost's D address this, which is why modern studies often report several alongside each other.

Worked Examples

Example 1: Human populations: p1=0.7, p2=0.3

FST=(Ht-Hs)/Ht

Result: FST≈0.15 for divergent human populations

African vs European: FST~0.15 for typical SNPs

Example 2: Local fish pops: p1=0.8, p2=0.2

Large frequency difference

Result: High FST indicates limited gene flow

Isolated lake populations

Example 3: The one-migrant rule

N_em = 1 versus N_em = 10

Result: F_ST 0.20 versus 0.024

One effective migrant per generation keeps differentiation moderate regardless of population size, because drift strength and migrant proportion scale together.

Example 4: Why human F_ST is low

Continental groups, F_ST ≈ 0.12

Result: Most variation is within populations

Roughly 88% of human genetic variation exists within any single population. Between-group differentiation accounts for the remainder.

Common Mistakes

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Comparing F_ST across different marker types

Highly variable markers have a lower maximum F_ST. Microsatellite and SNP values from the same populations are not directly comparable.

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Interpreting F_ST as a measure of similarity between individuals

It partitions variance between populations. Individuals from different populations are frequently more similar than two from the same one.

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Assuming migration–drift equilibrium

Recently diverged populations have not reached balance, so the one-migrant relationship does not apply and F_ST underestimates isolation.

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Reading a single F_ST value as a complete description

It gives no information about direction of gene flow, timing of divergence, or which loci drive the differentiation.

Frequently Asked Questions

FST interpretation?

FST=0: identical allele frequencies, panmixia. FST=1: complete fixation (different alleles fixed in each pop). Human global FST ~0.12-0.15 (low compared to other species). Outlier loci with high FST: candidates for local adaptation.

Beyond FST?

GST (multiallelic extension of FST). G'ST (standardized for high diversity loci). Jost's D (actual allele differentiation). QST (quantitative trait FST analog). All measure population differentiation, but differ in assumptions and sensitivity.

What does F_ST measure?

The proportion of total genetic variation that lies between populations rather than within them. It ranges from 0 to 1.

What is a typical F_ST for human populations?

Around 0.10–0.15 between continental groups, meaning roughly 85–90% of human genetic variation exists within populations rather than between them.

What is the one-migrant-per-generation rule?

Approximately one effective migrant per generation prevents substantial differentiation, regardless of population size, because drift strength and migrant proportion scale together.

Why can't F_ST be compared across marker types?

Because its maximum is limited by within-population heterozygosity. Highly variable markers cannot reach high values even between fully isolated populations.