The genetic makeup of a cell or organism constitutes its genotype. A population with a gene pool that has many variants in many different genes will consist of organisms with numerous different genotypes. For example, any two human genomes are likely to differ at about 3 million nucleotide sites, or about one difference per thousand nucleotides across the genome. In other words, we differ from one person to the next in a very large number but very small fraction of nucleotides.

Mutations, as we have seen, are the ultimate source of differences among genotypes. If we consider any present-day population of organisms, we find that some mutations are very common. Geneticists use the term polymorphism to refer to any genetic difference among individuals that is sufficiently common that it would almost certainly be present in a group of 50 randomly chosen individuals. For example, if many people have an A–T pair at a particular site in the genome, but many others have a G–C pair at the same site, this difference is a polymorphism. Of course, the polymorphism is the result of a mutation. All individuals once had the same genotype at this site, but a mutation occurred at this site sometime in the past, and is now commonly found in the population.

Phenotype is an individual’s observable characteristics or traits, such as height, weight, eye color, and so forth. The phenotype may be visible, as in these characteristics, or may be seen in the development, physiology, or behavior of a cell or organism. For example, color blindness and lactose intolerance are phenotypes. The phenotype results in part from the genotype: A genotype with a mutated gene for an enzyme that would normally metabolize lactose can lead to the phenotype of lactose intolerance. However, the environment also commonly plays an important role, so it is most accurate to say that a phenotype results from an interaction between the genotype and the environment. These genotype–environment interactions are discussed in Chapter 18.