How can the almost unimaginable amount of genetic variation, arising in an almost unimaginably variable environmental context, be related to specific phenotypes? This chapter extends the concepts of frequency and association developed in the previous chapter, to provide the basic concepts needed for a genetic model of how genes may affect a trait and how they act. Such models take advantage of the special constraints that billions of years of evolution have placed on traits controlled by genes.

Frequency concepts for genetic traits

The prevalence of a genetically related trait in a population depends on the amount of genetic variation that affects it.

Allele and genotype frequencies

The most fundamental quantitative variable in population genetics is the allele frequency (often carelessly called the ‘gene’ frequency), a prevalence measure. If, among the 2N copies of a given gene in a population of N diploid individuals, ni are allele i, then the frequency of that allele is defined as pi = ni/2N. There is no theoretical restriction on the number of alleles that can exist at a locus, but their frequencies must sum to 1. Thus, if one allele is very common, others must be correspondingly rare.