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Genetic and phenotypic variation

By Levi Clancy for Student Reader on

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A phenotype is the physical expression of genes. The genotype is the set of alleles conferring the phenotype

For example, red hair is the phenotype of the genotype (HairredHairred, one for each chromosome) encoding for red hair pigment. A population evolves when individuals with different genotypes survive or reproduce at different rates. Thus, evolution acts on heritable genetic variation. Genes have different forms called alleles. A single individual has only some of the alleles found in the greater population. The sum of all the alleles in a population is the gene pool.

Genetic variation (varying alleles) within the gene pool produce different phenotypes that are selected for or against by evolution. Natural populations possess genetic variation -- for example, selection for traits in a wild mustard has produced many important crop plants.

Penetrance is the likelihood that a specific genotype leads to its accompanying phenotype.

For example, there is 70% penetrance if only 700 individuals express red phenotype out of 1,000 HairredHairred individuals. If penetrance of a phenotype is not 100%, then it has reduced penetrance. Mechanisms of reduced penetrance are not always clear. Expressivity is another important concept in describing genotype-phenotype correlation. Expressivity describes the severity of a phenotype among individuals with the same genotype. For example, if a condition has variable expressivity then one individual might have mild symptoms while another might have severe symptoms (although they have the same genotype). If a trait has constant expressivity then individuals with the same genotype will have the same degree of symptoms.

Mechanisms of variable expressivity are not always clear. Although there is typically a clear genotype-phenotype correlation that associates a specific allele with a specific phenotype, this link is frequently muddled. Even individuals with identical genotypes can have different phenotypes due to genetic variation (the mechanisms of which are in the table below).

Allelic HeterogeneityAllelic heterogeneity is the presence of many different alleles for a certain gene within a population. These different alleles can confer remarkably different phenotypes, thus making the correlation between genotype and phenotype confusing. Different alleles can lead: to only certain traits or to reduced penetrance -- alleles at the cystic fibrosis gene sometimes confer only some symptoms of the disease ; to remarkably different phenotypes -- hemoglobin alleles can cause everything from harmless cyanosis (blue skin) to deadly hemolysis (red blood cell death); and to symptoms with seemingly no correlation to the function of encoded proteins.
Locus HeterogeneityMultiple loci can associate to confer a certain phenotype. For example, mutations in any of five different genes can confer phenylalanine sensitivity (hyperphenylalaninemia). However, an individual with mutation in more than one of these genes will have phenylketonuria.
Modifier GeneSometimes reduced penetrance has seemingly no explanation. This can be due to environmental factors, but sometimes two mutations will interact to neutralize or offset each disease phenotype. In such a a case, each gene is a modifier genes for the other. For example, have a nonfunctional β hemoglobin gene leads to a detrimental imbalance in the α:β ratio; however, an additional mutation reducing the quantity of α chains corrects that ratio.

Allele Frequency

A locally interbreeding group within a geographic population is called a Mendelian population. The relative proportions, or frequencies, of all alleles in a population are a measure of that population’s genetic variation. Biologists can estimate allele frequencies for a given locus by measuring numbers of alleles in a sample of individuals from a population. Measurements of allele frequencies range from 0 to 1, and the sum of all allele frequencies at a locus is 1. An allele’s frequency (p) is calculated by dividing the number of copies of the allele in a population by the sum of alleles in the population.

P = ( number of copies of the allele in a population ) / ( sum of alleles in the population )

If only two alleles (A and a) for a given locus are found among the members of a diploid population, they may combine to form three different genotypes: AA, Aa, and aa.

Allele frequencies can be calculated using mathematics with the following variables:

  1. NAA = the number of individuals that are homozygous for the A allele (AA)

  2. NAa = the number of individuals that are heterozygous (Aa)

  3. Naa = the number of individuals that are homozygous for the a allele (aa)

Note that NAA + NAa + Naa = N, the total number of individuals in a population.

The total number of alleles in a population is 2N because each individual is diploid (in this case, either AA, Aa, or aa).
p = the frequency of allele A.
q = the frequency of allele a.
For each population, p + q = 1.

P = 2 NAA + NAa / 2 N

p = 2 Naa + NAa / 2 N