An allele is any specific version of a gene. Some genes have only one allele in a population, while others have two or more. There is no fixed maximum number of alleles that a gene can have in a population, but the actual number depends on the mutation rate, natural selection pressure, genetic drift and the population size.
Nearly all animals and later-evolved plants are diploid, meaning they have two alleles at each gene location on a chromosome, one inherited from each parent. All alleles for a particular gene are located at the same position on a chromosome under normal conditions. The two can be identical (homozygous), or they can be different (heterozygous). This combination of similarities and differences can have important effects on the appearance, behavior and other characteristics of the organism (i.e., its phenotype).
Alleles can differ slightly in their DNA sequences without affecting phenotype. Some alleles are dominant and some are recessive. When an organism carries one of each, the dominant allele usually determines its phenotype. However, alleles can sometimes exhibit codominance or incomplete dominance, where neither fully dominates, resulting in mixed or intermediate traits.
New alleles arise primarily through mutations, which are changes in their DNA sequences. The rate at which a beneficial new allele spreads through a population depends on whether it is dominant or recessive, the strength of natural selection, the population size, and the population structure (including subdivision, mating patterns, and migration).
If a beneficial trait is caused by a dominant allele, it tends to spread quickly because having just one copy of that allele allows the trait to appear and helps the organism survive or reproduce better. However, if the beneficial trait is from a recessive allele, it initially spreads more slowly because the organism needs two copies for the trait to appear and provide a survival or reproductive benefit.
The spread of a new allele can occur over a few or many generations, influenced largely by whether the population is growing or declining. In a growing population, beneficial alleles are more likely to increase and eventually become fixed because individuals carrying them tend to have more offspring. In declining populations, even beneficial alleles may be lost due to random genetic drift.