A gene is a segment of DNA that codes for a protein (or a microRNA). Each gene has a particular physical location on a chromosome, called its "genetic locus." For living things that have more than one copy of each chromosome, the same location on all copies is still referred to as a single locus. The single locus simply has multiple copies of the gene, collectively called a "genotype." A full set of genes that can make and run a living being is called a "genome."
What is an Allele?
Alleles are different versions of the same gene. They code for different versions of the same protein, which can affect the body differently. When there is more than one copy in the genome, they might all be the same allele (a homozygous genotype), or there may be different ones (heterozygous genotype). New alleles arise due to mutation, or to chromosome recombination through the middle of the gene. The latter is a process that occurs during meiosis, when pairs of chromosomes align with each other and can trade pieces with each other.
Multiple Alleles with Neutral Fitness
When there are multiple alleles for a gene, different individuals in a population will have different ones. An example is human blood types. In the ABO blood group system (where a person can have blood type A, B, AB, or O), three alleles of the same gene are responsible for all the possible types – one that codes for A, one that codes for B, and a nonfunctional one that codes for neither (usually designated with an O). Humans have two sets of chromosomes per person, thus two alleles per locus; if the two are AA or AO, the person has type A blood, if they're BB or BO, then it's type B, if it's AB, the type is AB, and if it's OO, the type is O.
In the case of ABO blood types, none of the alleles are particularly advantageous or disadvantageous over the others – all individuals in the population are equally able to survive and reproduce successfully (have equal evolutionary fitness) regardless of which type they have.
In a small population where all alleles of a gene have equal fitness, how they are proportioned will drift randomly from one generation to the next. In the absence of new mutations and new alleles migrating into the population, the general trend is for variability to go down, and eventually one of the alleles will be the only one that the population has (or, in the terminology of population genetics, one allele will become "fixed"). In a large population, the proportion of each allele from one generation to the next will be in Hardy-Weinberg equilibrium.
Multiple Alleles and Natural Selection
More often, in a given environment, some alleles will be beneficial and others will be deleterious. Individuals in a population with advantageous alleles will survive and reproduce better than those with disadvantageous ones. Over time, through natural selection, alleles of low fitness will disappear from the population.
Evolutionary fitness is not an absolute measure, but depends on environmental conditions. An allele that is beneficial in one environment might be deleterious in another. A classic example is peppered moths (Biston beularia) in England. Briefly: two alleles that code for two coloration types – lightly peppered and dark. Two environments – light-colored lichen-covered tree trunks and dark-colored soot-covered tree trunks. Bird predators that eat moths if they can see them on the tree trunks. As a result, the allele for dark color has higher fitness than the allele for light color in areas with high pollution and soot, while the reverse is true for populations living in unpolluted areas.
Ridley, Mark. 1993. Evolution. Blackwell Scientific Publications, Inc.
Griffiths, Anthony J.F., Jeffrey H. Miller, David T. Suzuki, Richard C. Lewontin, and William M. Gelbart. 1993. An Introduction to Genetic Analysis 5th ed. W.H. Freeman and Company.