Population Differentiation Calculators

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Population differentiation describes the degree to which allele frequencies or genotypes differ between populations as a result of genetic drift, natural selection, reduced gene flow, or founder effects. The most widely used measure is Wright's fixation index FST = (HT − HS) / HT, where HT is the expected heterozygosity in the total population and HS is the average expected heterozygosity within subpopulations. FST ranges from 0 (no differentiation) to 1 (complete differentiation — fixed for different alleles). FST values of 0.05–0.15 indicate moderate differentiation; > 0.25 indicates great differentiation. Outlier FST loci (unusually high FST compared to the genome average) may indicate local adaptation through natural selection.

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FST Formula

FST = (HT − HS) / HT

HT = total expected heterozygosity = 2p̄(1−p̄) where p̄ = overall allele frequency. HS = mean within-subpopulation expected heterozygosity. FST = 0: populations have same allele frequencies. FST = 1: populations fixed for different alleles. Wright's interpretation: 0–0.05 = little; 0.05–0.15 = moderate; 0.15–0.25 = great; > 0.25 = very great differentiation.

Causes of Population Differentiation

  • Genetic drift: random allele frequency change; stronger in small populations; leads to fixation of different alleles by chance
  • Reduced gene flow: physical or behavioral barriers → populations diverge independently
  • Natural selection: different environments favor different alleles → local adaptation
  • Founder effects / bottlenecks: small founding populations → high drift

Population Structure Analysis

STRUCTURE / ADMIXTURE: Bayesian/likelihood model assigns individuals to K populations; ancestry proportions estimated. PCA (principal component analysis): visual separation of populations by allele frequency variation. AMOVA (analysis of molecular variance): partitions variance among vs. within groups.

Glossary

FST (Fixation Index)
FST = (HT − HS)/HT; measures genetic differentiation; 0 = identical allele frequencies; 1 = complete fixation of different alleles; 0–0.05 = little; > 0.25 = very great differentiation.
FST Outlier
Loci with unusually high FST vs. genome-wide average; may indicate local adaptation through divergent natural selection; detected by BayeScan, OutFLANK, or percentile-based approaches.
Genetic Drift
Random changes in allele frequency due to sampling variation in finite populations; causes divergence between isolated populations over time; stronger in small populations; leads to fixation by chance.

Frequently Asked Questions

FST (fixation index) measures genetic differentiation between populations: FST = (HT − HS) / HT. HT = total heterozygosity = expected Het if all populations were one: 2p̄(1−p̄) where p̄ = overall allele frequency. HS = mean within-population heterozygosity = mean of 2pᵢ(1−pᵢ) across subpopulations. Example: 2 populations; population 1: p₁ = 0.8; population 2: p₂ = 0.2. HS = (2×0.8×0.2 + 2×0.2×0.8)/2 = (0.32+0.32)/2 = 0.32. p̄ = (0.8+0.2)/2 = 0.5. HT = 2×0.5×0.5 = 0.50. FST = (0.50−0.32)/0.50 = 0.36 → very great differentiation.

Genetic drift: random sampling of alleles each generation causes allele frequency changes; in small populations, drift is strong → alleles randomly fix at different frequencies in isolated populations. Reduced gene flow: geographic, behavioral, or ecological barriers prevent migration → populations evolve independently → diverge. Natural selection: different environments favor different alleles → directional selection increases specific allele frequencies in each local environment → adaptive divergence (local adaptation). Founder effects and bottlenecks: when a small number of individuals colonize a new area or survive a population crash, the founders carry a random subset of alleles → new population may be very different from the source.

Genome-wide FST distribution: most loci have FST reflecting the overall population history (drift, gene flow). FST outlier loci: loci with unusually high FST compared to the genome-wide average — may indicate local adaptation through divergent natural selection. Logic: drift causes random FST values across all loci; selection increases FST at a specific locus because one allele is favored in one population and a different allele in another (local adaptation). Detection: compare observed FST distribution to a neutral model; loci in the upper 5% of the FST distribution are 'outliers.' Tools: Arlequin, BayeScan, OutFLANK, pcadapt. Caution: outlier FST can also result from background selection or demographic artifacts — interpretation requires caution.

STRUCTURE / ADMIXTURE: model-based Bayesian or ML method; assumes K source populations; assigns each individual fractional ancestry from each of K populations; identifies admixed individuals. PCA (principal component analysis): plots individuals in a space where PC1 and PC2 capture the most allele frequency variation; natural clustering corresponds to population structure. AMOVA (analysis of molecular variance): partitions total genetic variance into: among groups, among populations within groups, within populations; related to FST but applicable to haplotype data. Isolation-by-distance: correlation between genetic and geographic distance; plotted as FST vs. geographic distance. Discriminant analysis of principal components (DAPC): R package adegenet; useful when group membership is partially known.