We have seen how to infer that genes have various effects on a trait, but how does the spectrum of genetic effects arise, and how is the variation distributed over space and time? This chapter provides a brief travelog of some of the relevant concepts of population genetics, the theoretical basis of evolutionary biology {Crow, 1986; Hartl and Clark, 1989; Hedrick, 1985; Li and Graur, 1990; Nei, 1987}. These concepts are used in subsequent chapters.

Life is fundamentally stochastic: the fate of a new mutation

(Nearly) each new mutation is unique

For most of this century it was thought that only a few alleles could exist at a locus, of which new copies arose via recurrent mutation at some rate, generally estimated to be about 10-5 per locus per generation, providing a continual supply of a given allele. This view was based on phenotype data, but at the sequence level the probability that the same mutation will recur is very small. Think of a cistron (coding stretch) of, say, a thousand nucleotides. Three thousand different non-synonymous (nucleotidechanging) point mutations are possible.