Genetic variation in populations can be analyzed and quantified by the frequency of alleles. Two fundamental calculations are central to population genetics: allele frequencies and genotype frequencies. Genotype frequency in a population is the number of individuals with a given genotype divided by the total number of individuals in the population. In population genetics, the genotype frequency is the frequency or proportion (i.e., 0 < f < 1) of genotypes in a population. Although allele and genotype frequencies are related, it is important to clearly distinguish them. Genotype frequency may also be used in the future (for "genomic profiling") to predict someone's having a disease or even a birth defect. It can also be used to determine ethnic diversity. Genotype frequencies may be represented by a De Finetti diagram.
Numerical example As an example, consider a population of 100 four-o-'clock plants (Mirabilis jalapa) with the following genotypes:
49 red-flowered plants with the genotype AA 42 pink-flowered plants with genotype Aa 9 white-flowered plants with genotype aa When calculating an allele frequency for a diploid species, remember that homozygous individuals have two copies of an allele, whereas heterozygotes have only one. In our example, each of the 42 pink-flowered heterozygotes has one copy of the a allele, and each of the 9 white-flowered homozygotes has two copies. Therefore, the allele frequency for a (the white color allele) equals
f ( a ) = ( A a ) + 2 × ( a a ) 2 × ( A A ) + 2 × ( A a ) + 2 × ( a a ) = 42 + 2 × 9 2 × 49 + 2 × 42 + 2 × 9 = 60 200 = 0.3 {\displaystyle {\begin{aligned}f({a})&={(Aa)+2\times (aa) \over 2\times (AA)+2\times (Aa)+2\times (aa)}={42+2\times 9 \over 2\times 49+2\times 42+2\times 9}={60 \over 200}=0.3\\\end{aligned}}}
This result tells us that the allele frequency of a is 0.3. In other words, 30% of the alleles for this gene in the population are the a allele. Compare genotype frequency: let's now calculate the genotype frequency of aa homozygotes (white-flowered plants).
f ( a a ) = 9 49 + 42 + 9 = 9 100 = 0.09 = ( 9 % ) {\displaystyle {\begin{aligned}f({aa})&={9 \over 49+42+9}={9 \over 100}=0.09=(9\%)\\\end{aligned}}}
Allele and genotype frequencies always sum to one (100%).
Equilibrium The Hardy–Weinberg law describes the relationship between allele and genotype frequencies when a population is not evolving. Let's examine the Hardy–Weinberg equation using the population of four-o'clock plants that we considered above:
if the allele A frequency is denoted by the symbol p and the allele a frequency denoted by q, then p+q=1. For example, if p=0.7, then q must be 0.3. In other words, if the allele frequency of A equals 70%, the remaining 30% of the alleles must be a, because together they equal 100%. For a gene that exists in two alleles, the Hardy–Weinberg equation states that (p2) + (2pq) + (q2) = 1. If we apply this equation to our flower color gene, then
f ( A A ) = p 2 {\displaystyle f(\mathbf {AA} )=p^{2}} (genotype frequency of homozygotes)
f ( A a ) = 2 p q {\displaystyle f(\mathbf {Aa} )=2pq} (genotype frequency of heterozygotes)
f ( a a ) = q 2 {\displaystyle f(\mathbf {aa} )=q^{2}} (genotype frequency of homozygotes) If p=0.7 and q=0.3, then
f ( A A ) = p 2 {\displaystyle f(\mathbf {AA} )=p^{2}} = (0.7)2 = 0.49
f ( A a ) = 2 p q {\displaystyle f(\mathbf {Aa} )=2pq} = 2×(0.7)×(0.3) = 0.42
f ( a a ) = q 2 {\displaystyle f(\mathbf {aa} )=q^{2}} = (0.3)2 = 0.09 This result tells us that, if the allele frequency of A is 70% and the allele frequency of a is 30%, the expected genotype frequency of AA is 49%, Aa is 42%, and aa is 9%.
References
Notes Brooker R, Widmaier E, Graham L, Stiling P (2011). Biology (2nd ed.). New York: McGraw-Hill. ISBN 978-0-07-353221-9.