Population Genetics & Allele Frequency Solver

Understanding Allele Frequency and Population Genetics

Population genetics is the study of genetic variation within populations, and involves the examination and modelling of changes in the frequencies of genes and alleles in populations over space and time. A fundamental metric in this field is the allele frequency, which represents the incidence of a gene variant in a population.

The Hardy-Weinberg Principle

The Hardy-Weinberg principle provides a mathematical baseline for examining whether evolution is occurring in a population. It states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences. These influences include genetic drift, mate choice, assortative mating, natural selection, sexual selection, mutation, gene flow, meiotic drive, genetic hitchhiking, population bottleneck, founder effect and inbreeding.

For a gene with two alleles, the dominant allele is usually denoted as p and the recessive allele as q. The frequencies must sum to one:

\(p + q = 1\)

The Hardy-Weinberg equation allows us to calculate the expected frequencies of genotypes (AA, Aa, and aa) if the population is in equilibrium:

\(p^2 + 2pq + q^2 = 1\)

Where:

• \(p^2\) represents the frequency of the homozygous dominant genotype (AA).
• \(2pq\) represents the frequency of the heterozygous genotype (Aa).
• \(q^2\) represents the frequency of the homozygous recessive genotype (aa).

Calculating Allele Frequencies from Genotype Counts

To determine the actual frequencies of alleles in a population based on observed data, we look at the total number of alleles. Since organisms (in this context) are diploid, each individual carries two alleles for a given locus.

The total number of alleles is calculated as:

\(Total\ Alleles = 2 \times Total\ Individuals\)

The frequency of the dominant allele (p) is calculated by summing two times the number of homozygous dominant individuals plus the number of heterozygous individuals, divided by the total number of alleles:

\(p = \frac{(2 \times N_{AA}) + N_{Aa}}{2 \times N_{Total}}\)

Similarly, the frequency of the recessive allele (q) is:

\(q = \frac{(2 \times N_{aa}) + N_{Aa}}{2 \times N_{Total}}\)

Comparing Observed vs. Expected Values

One of the primary uses of this calculator is to compare the observed genotype counts from your sample against the expected counts derived from the Hardy-Weinberg equation. If there is a significant difference between the observed and expected values, it suggests that the population may not be in equilibrium, indicating that evolutionary forces such as selection, migration, or mutation may be at play.