Allele Frequency Calculators

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Allele frequency is the relative proportion of a specific allele at a genetic locus in a population — expressed as a value between 0 and 1, or as a percentage. For a biallelic locus with alleles A and a in a diploid population of N individuals: p = frequency of A = (2 × number of AA + number of Aa) / (2N); q = frequency of a = 1 − p. Allele frequencies are the fundamental currency of population genetics — they change over generations through natural selection, genetic drift, mutation, gene flow, and non-random mating. The Hardy-Weinberg principle provides the null model: allele frequencies remain constant in the absence of these forces.

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Allele Frequency Calculation

For a diploid population of N individuals with genotype counts: n_AA, n_Aa, n_aa. Total alleles = 2N. p(A) = (2n_AA + n_Aa) / 2N. q(a) = (2n_aa + n_Aa) / 2N. p + q = 1 (for biallelic locus). Example: 200 individuals; 80 AA, 100 Aa, 20 aa. Total alleles = 400. p = (160+100)/400 = 0.65; q = (40+100)/400 = 0.35.

Hardy-Weinberg Expected Genotypes

Expected frequencies under HWE: AA = p²; Aa = 2pq; aa = q². Expected counts: E_AA = 200 × 0.65² = 84.5; E_Aa = 200 × 2×0.65×0.35 = 91; E_aa = 200 × 0.35² = 24.5. Chi-square test: H₀ = HWE; df = 1.

Factors Changing Allele Frequency

  • Natural selection: alleles with higher fitness increase in frequency
  • Genetic drift: random sampling → allele loss or fixation (stronger in small populations)
  • Mutation: new alleles created; μ per generation is very slow
  • Gene flow: migrant alleles enter or leave population → homogenize frequencies
  • Non-random mating: changes genotype frequencies but not necessarily allele frequencies

Glossary

Allele Frequency
p = (2n_AA + n_Aa)/2N; proportion of a specific allele in a population; p + q = 1 for biallelic; changed by selection, drift, mutation, and gene flow.
Hardy-Weinberg Equilibrium (HWE)
Allele and genotype frequencies remain constant when: large population; random mating; no selection; no mutation; no gene flow; genotype frequencies: AA = p²; Aa = 2pq; aa = q².
Selection Coefficient (s)
A measure of the fitness disadvantage of a genotype relative to the most fit genotype; s = 0 = neutral; s = 1 = lethal; determines the rate at which allele frequencies change under selection.

Frequently Asked Questions

Allele frequency = proportion of a specific allele among all alleles at that locus in a population. For diploid organisms: each individual carries 2 alleles per locus; a population of N individuals has 2N alleles. p(A) = (2×n_AA + n_Aa) / 2N; q(a) = (2×n_aa + n_Aa) / 2N; p + q = 1. Example: 100 individuals; 36 AA, 48 Aa, 16 aa: p = (72+48)/200 = 0.60; q = (32+48)/200 = 0.40. Allele frequencies can also be estimated from Hardy-Weinberg: if disease frequency (aa) = q² is known, q = √(disease frequency); p = 1 − q.

Hardy-Weinberg equilibrium (HWE): in a large, randomly mating population with no selection, mutation, migration, or drift, allele frequencies remain constant across generations. Expected genotype frequencies: AA = p²; Aa = 2pq; aa = q². These frequencies are reached after just one generation of random mating. HWE test: compare observed vs. expected genotype frequencies by chi-square (df=1 for biallelic). Deviation from HWE indicates: selection; population structure (Wahlund effect — mixing populations → excess homozygotes); inbreeding; recent bottleneck; genotyping error in GWAS studies.

Natural selection changes allele frequencies when genotypes differ in fitness (reproductive success relative to others). Positive selection: beneficial allele increases in frequency over generations. Rate of change: Δp = p × q × s × p / (1 − q²s) approximately, where s = selection coefficient (0 = neutral; 1 = lethal). Selective sweep: strongly beneficial allele rapidly replaces the ancestral allele → leaves a signature of reduced variation in nearby DNA (hitchhiking). Balancing selection: maintains multiple alleles (heterozygote advantage): sickle cell HbAS carriers have higher fitness in malaria-endemic regions → both HbA and HbS maintained. Purifying (negative) selection: removes deleterious alleles → most common form of selection.

Allele frequency data guides conservation decisions: Genetic diversity assessment: average expected heterozygosity He = 1 − Σpᵢ² across loci; populations with low He have reduced adaptive potential. Inbreeding detection: FIS = 1 − Ho/He; high FIS = inbreeding from small population or non-random mating. Population structure: FST = (HT − HS)/HT; measures differentiation between populations; high FST = populations are genetically distinct (may warrant separate management units). Genetic rescue: introducing individuals from other populations (adding new alleles) can increase He and fitness in inbred populations. Minimum viable population: Ne ≥ 50 to prevent rapid inbreeding (ΔF < 1%/generation); Ne ≥ 500 to maintain evolutionary potential.