Why is it that in biology we often say that a gene has two alleles? When we analyze allele frequencies (e.g. using Hardy-Weinberg Equilibrium), formulas are often generalized for two alleles of a gene.
Given mutations, isn't it quite likely that a population will have more than two alleles for a gene?
The two-allele scenario is often used in genetics teaching because of its simplicity. However, quite a few genes have more than two alleles. Some examples that readily come to mind are:
The ABO gene in humans: This determines ABO blood group, and has six common alleles. Many more rare alleles have been described [1].
The human leukocyte antigen (HLA) genes: These are well-known for their allelic diversity. One of them, HLA-A, alone has over 6,000 alleles [2].
Reference
Seltsam A, Hallensleben M, Kollmann A, Blasczyk R. The nature of diversity and diversification at the ABO locus. Blood 2003; 102(8):3035–3042. https://doi.org/10.1182/blood-2003-03-0955
Robinson J, Halliwell JA, Hayhurst JD, et al. The IPD and IMGT/HLA database: allele variant databases. Nucleic Acids Research 2015; 43:D423-431. http://hla.alleles.org/nomenclature/stats.html
Depending at which level you are defining an allele. As @Adhish described, at the molecular level there is no theoretical limit on the number of alleles of a given gene. The presence or not of more than 2 alleles depends on evolutionary factors such as population size, fitness change, genetic drift, etc. Hardy-Weinberg Equilibrium with two alleles is easier to understand but is possible to extend the genotype predictions for multiple alleles in the equilibrium. Also remember that the Hardy-Weinberg Equilibrium is theoretical and requires assumptions that are never really met in nature, so is extremely hard for multi allele systems to ever reach the equilibrium.
