An allele is a specific version of a gene. You inherit two copies of every gene, one from each biological parent, and those copies don’t have to be identical. The small differences between them are what make you genetically unique. Every variation of a particular gene, whether common or rare, counts as an allele of that gene.
Genes vs. Alleles
A gene is a stretch of DNA on a chromosome that carries instructions for some biological function, like producing a protein that determines eye color. An allele is one particular version of that gene. Think of a gene as a recipe category (“cookie recipe”) and alleles as the specific recipes within it (“chocolate chip” vs. “oatmeal raisin”). The gene defines what the instructions are for; the allele determines exactly what those instructions say.
Every human carries two alleles for each gene because chromosomes come in pairs. Those two alleles sit at the same physical location, called a locus, on each paired chromosome. If both alleles carry identical DNA sequences, you’re homozygous for that gene. If they differ, you’re heterozygous.
How New Alleles Form
New alleles arise through mutation, which is any change in a DNA sequence. This can be as small as a single base swapping for another, a base getting deleted, or a break in the DNA strand. Most of these changes are subtle, and many have no noticeable effect at all. But over time, mutation is the engine that creates genetic variation within a species.
Once a new allele exists, sexual reproduction shuffles it into new combinations. During the process of making eggs and sperm, chromosomes exchange segments and sort independently, meaning the allele combinations a parent passes on are never quite the same twice. This is why siblings who share the same two parents can look and function so differently from each other.
Dominant and Recessive Alleles
When you carry two different alleles for the same gene, one often has a stronger influence on the trait you actually display. That allele is called dominant. The other, whose effect gets masked, is recessive. If you carry one allele for brown eyes (dominant) and one for blue eyes (recessive), your eyes will typically be brown. The blue-eye allele is still in your DNA, and you can still pass it to your children, but it doesn’t show up in your appearance.
For a recessive trait to appear, you need two copies of the recessive allele, one from each parent. This is why two brown-eyed parents can have a blue-eyed child: both parents carried a hidden recessive allele for blue eyes, and the child happened to inherit both copies. The same logic applies to traits like straight vs. curly hair or sensitivity to poison ivy.
At the molecular level, over 90% of mutations are recessive. In most cases, one working copy of a gene produces enough protein to keep things functioning normally, so the dominant allele effectively picks up the slack for a recessive one that codes for a less functional protein.
When Dominance Isn’t Simple
Not every gene follows a clean dominant-or-recessive pattern. Two other common patterns are incomplete dominance and codominance.
In incomplete dominance, the heterozygous result is a blend. Neither allele fully wins, so the trait lands somewhere in between. A classic example is flower color in snapdragons: crossing a red-flowered plant with a white-flowered plant produces pink offspring, not red or white.
In codominance, both alleles are fully expressed at the same time rather than blending. Human blood type is the most familiar example. The ABO blood group system has three alleles: A, B, and O. A and B are codominant with each other, meaning someone who inherits one A allele and one B allele will have type AB blood, with both A and B markers present on their red blood cells in equal numbers. Meanwhile, both A and B are dominant over O, so a person with one A allele and one O allele simply has type A blood.
Some Genes Have Many Alleles
While any single person can carry at most two alleles for a given gene (one per chromosome), the broader population can harbor dozens or even hundreds of alleles for the same gene. The ABO blood group is a straightforward example with three main alleles, but genes involved in immune function can have hundreds of variants circulating in the human population. This diversity is one reason organ transplant matching is so difficult: the immune-related genes that need to match between donor and recipient exist in a vast number of allele combinations.
Alleles and Your Health
Many genetic conditions trace back to specific allele combinations. If both copies of a gene carry a mutation that disrupts normal protein function, the result can be a genetic disease. Sickle cell anemia is one of the most studied examples. A single-base change in the gene for hemoglobin, the protein that carries oxygen in red blood cells, creates the sickle cell allele. People who inherit two copies of this allele (homozygous) develop sickle cell disease, where red blood cells deform into a crescent shape and cause serious health problems.
But people who carry just one sickle cell allele alongside one normal allele (heterozygous) generally don’t have symptoms of anemia. They do, however, gain a significant survival advantage in regions where malaria is common. Research published in Nature confirms that heterozygous carriers have lower densities of the malaria parasite in their blood compared to people with two normal alleles. This is the textbook example of heterozygote advantage: the allele is harmful in double dose but beneficial in single dose, which is why it persists at high frequencies in populations historically exposed to malaria. Malaria has been called the strongest evolutionary selective force in recent human history, and the sickle cell allele is direct evidence of how disease pressure shapes which alleles survive in a population.
Alleles in Evolution
Zooming out from individuals to whole populations, allele frequency is the measure scientists use to track evolution in action. Evolution, at its most precise definition, is a change in the genetic composition of a population over time. When the frequency of a particular allele rises or falls across generations, evolution is happening.
Three main forces drive these shifts. Natural selection favors alleles that improve survival or reproduction in a given environment, like the sickle cell allele in malaria zones. Genetic drift causes random fluctuations in allele frequency, especially in small populations where chance plays a bigger role. And gene flow introduces new alleles when individuals migrate between populations. The interplay of these forces across thousands of generations is what produces the genetic diversity we see in every species today.