Allele Frequency Calculator
Calculate allele and genotype frequencies for population genetics analysis. Test for Hardy-Weinberg equilibrium and analyze genetic variation in populations.
Observed Genotype Counts
Enter the number of individuals with each genotype in your population sample
Allele Frequencies
Enter allele frequencies (must sum to 1.0)
Allele Frequencies
Hardy-Weinberg Equation
p² + 2pq + q² = 1
Genotype Frequencies
| Genotype | Observed | Observed % | Expected (HW) | Expected % |
|---|---|---|---|---|
| AA (p²) | ||||
| Aa (2pq) | ||||
| aa (q²) |
Hardy-Weinberg Equilibrium Test
Note: For HW equilibrium testing, we use 1 degree of freedom because we estimate 1 parameter (p) from the data, and we have 3 genotype categories (3 - 1 - 1 = 1 df).
Genotype Distribution
Interpretation
Understanding Allele Frequencies
Allele frequency (also called gene frequency) is the proportion of a particular allele among all allele copies in a population. It's a fundamental concept in population genetics that helps us understand genetic variation, evolution, and inheritance patterns at the population level.
Key Formulas
Allele Frequencies:
p = (2 × AA + Aa) / (2 × Total)
q = (2 × aa + Aa) / (2 × Total)
p + q = 1
Hardy-Weinberg Equation:
p² + 2pq + q² = 1
- • p² = frequency of AA genotype
- • 2pq = frequency of Aa genotype
- • q² = frequency of aa genotype
Chi-Square Test:
χ² = Σ [(Observed - Expected)² / Expected]
If χ² > 3.841 (critical value at α=0.05, df=1), reject HW equilibrium
Hardy-Weinberg Equilibrium Principle
The Hardy-Weinberg principle, independently formulated by G.H. Hardy and Wilhelm Weinberg in 1908, states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of evolutionary influences.
Five Assumptions for HW Equilibrium:
1. No Mutations
Allele frequencies remain constant because no new alleles are introduced through mutation. In reality, mutations occur but usually at such low rates that their immediate effect on allele frequencies is negligible.
2. Random Mating
All individuals in the population have an equal opportunity to mate with any other individual. No mating preferences based on genotype. Deviations include assortative mating, inbreeding, or sexual selection.
3. No Gene Flow (Migration)
No immigration or emigration of individuals that could introduce or remove alleles from the population. Migration can rapidly change allele frequencies, especially in small populations.
4. Large Population Size (No Genetic Drift)
Population must be infinitely large to prevent random sampling errors (genetic drift). In small populations, chance events can cause large changes in allele frequencies between generations.
5. No Natural Selection
All genotypes have equal fitness - they survive and reproduce at equal rates. Selection for or against certain genotypes will change allele frequencies over time.
Important Note:
No natural population perfectly meets all five assumptions. Hardy-Weinberg equilibrium serves as a null hypothesis - a baseline for comparison. Deviations from HW equilibrium indicate that evolutionary forces are acting on the population.
Applications of Allele Frequency Analysis
Evolutionary Biology
- • Detect natural selection in populations
- • Track evolutionary changes over time
- • Identify genetic bottlenecks or founder effects
- • Study adaptation to environmental changes
- • Compare different populations or species
Conservation Biology
- • Assess genetic diversity in endangered species
- • Monitor effects of habitat fragmentation
- • Plan breeding programs for conservation
- • Detect inbreeding depression
- • Evaluate reintroduction success
Medical Genetics
- • Estimate carrier frequencies for genetic diseases
- • Predict disease prevalence in populations
- • Study genetic risk factors
- • Understand pharmacogenetic variation
- • Design screening programs
Forensics & Anthropology
- • DNA profiling and paternity testing
- • Population structure analysis
- • Trace human migration patterns
- • Study ancient DNA samples
- • Identify individuals in mixed samples
Real-World Examples
Sickle Cell Anemia
In certain African populations, the sickle cell allele (HbS) has a frequency of about 0.1-0.2. Heterozygotes (HbA/HbS) have resistance to malaria, demonstrating balancing selection. The population is NOT in HW equilibrium because heterozygotes have a selective advantage.
Homozygous HbS/HbS: Severe anemia
Heterozygous HbA/HbS: Malaria resistance, mild symptoms
Homozygous HbA/HbA: Normal, but susceptible to malaria
ABO Blood Groups
ABO blood type frequencies vary by population. In European populations: O (45%), A (40%), B (11%), AB (4%). This is actually a three-allele system (I^A, I^B, i), but simplified two-allele calculations can be performed for educational purposes.
Cystic Fibrosis
In European populations, about 1 in 2,500 newborns has cystic fibrosis (genotype: ff). Using HW: q² = 1/2500 = 0.0004, so q ≈ 0.02 and p ≈ 0.98. The carrier frequency (2pq) ≈ 0.039 or about 1 in 25 people.
Industrial Melanism (Peppered Moths)
Classic example of rapid evolution. Before industrialization, light-colored moths were common (typica). With pollution darkening tree bark, dark moths (carbonaria) became advantageous. Allele frequencies shifted dramatically within decades, clearly violating HW equilibrium due to strong selection pressure.
Factors That Disrupt Hardy-Weinberg Equilibrium
| Factor | Effect on Allele Frequencies | Example |
|---|---|---|
| Natural Selection | Increases frequency of advantageous alleles | Antibiotic resistance in bacteria |
| Genetic Drift | Random changes, stronger in small populations | Founder effect, bottleneck effect |
| Gene Flow | Introduces new alleles or changes frequencies | Migration between populations |
| Mutation | Creates new alleles (slow process) | New disease resistance alleles |
| Non-random Mating | Changes genotype frequencies (not allele frequencies) | Inbreeding, assortative mating |
References
The Hardy-Weinberg principle and population genetics concepts are based on established scientific literature:
Related Calculators
Educational Disclaimer: This allele frequency calculator is designed for educational purposes in population genetics. Hardy-Weinberg equilibrium is a theoretical model that assumes ideal conditions rarely met in nature. Real populations are influenced by selection, mutation, migration, genetic drift, and non-random mating. Chi-square test results provide statistical evidence but should be interpreted in biological context. For research or medical applications, consult with population geneticists or genetic counselors.
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