What is an allele?
Most animals (including humans) are diploid — they carry two copies of each chromosome, one inherited from each parent. For any given gene, an individual therefore carries two alleles — one on each homologous chromosome at the same position (the locus).
Alleles arise by mutation — changes in the DNA sequence of a gene. A single nucleotide substitution, insertion, deletion or duplication can create a new allele. Most new alleles are neutral or harmful, but occasionally one improves fitness and spreads by natural selection.
Key vocabulary:
- Locus — the specific position of a gene on a chromosome.
- Genotype — the combination of alleles an individual carries (e.g., AA, Aa, aa).
- Phenotype — the physical expression of the genotype, influenced by environment.
- Homozygous — both alleles at a locus are the same (AA or aa).
- Heterozygous — the two alleles differ (Aa).
For the molecular basis of how DNA sequences are inherited, see our DNA, genes and heredity guide and the DNA glossary entry. For how alleles are physically separated during cell division, see our mitosis and meiosis guide.
Dominant, recessive and codominant alleles
The relationship between alleles in a heterozygote determines the phenotype observed. Three patterns:
- Complete dominance — one allele (the dominant, symbol A) completely masks the effect of the other (recessive, a). Heterozygote Aa is phenotypically identical to homozygote AA. Cystic fibrosis is a classic example of a recessive disorder — carriers (Aa) have no disease symptoms.
- Codominance — both alleles are expressed equally. In ABO blood groups, I^A and I^B are codominant: genotype I^A I^B produces both A and B antigens on red blood cells (blood group AB).
- Incomplete dominance — the heterozygote shows an intermediate phenotype. In snapdragons, red (R) × white (r) gives pink (Rr) flowers. This is not blending — cross two pink plants and you get a 1:2:1 ratio of red : pink : white.
The heterozygote advantage is a special case where the heterozygous genotype has higher fitness than either homozygote. The HbA/HbS sickle cell heterozygote shows this: neither sickle cell disease (HbSHbS) nor complete susceptibility to malaria (HbAHbA) in malaria-endemic regions. This maintains both alleles in the population — a form of balancing selection. For the evolutionary consequences, see our natural selection guide.
Clinically relevant allele examples
Allele frequency and evolution
Evolution at the molecular level is the change in allele frequencies in a population over time. The Hardy-Weinberg principle states that, in a large, random-mating population with no mutation, selection, migration or genetic drift, allele frequencies remain constant from generation to generation.
Any departure from Hardy-Weinberg equilibrium indicates that one of these forces is acting. Natural selection, genetic drift (random change in small populations), mutation, and gene flow (migration) all change allele frequencies. For a full treatment see our evolution guide.
CRISPR-based therapies for allele-linked diseases (sickle cell, beta-thalassaemia) directly correct the pathogenic allele in a patient's cells. See our CRISPR gene editing article for how this is done clinically.