Figure 4.

Simple example of quantifying mutational spectra. Intraspecific analyses of directional base changes allow estimations of underlying mutational processes. Schematic shows a simple analysis of a 100-bp sequence. (A) Testing for mutational equilibrium addresses the question: Is current base composition explained by mutation alone? Comparing the absolute numbers of GC→AT versus AT→GC changes within species sheds light on underlying mutational pressure. If the number of AT→GC changes does not equal the number of GC→AT changes along a given sequence, then under mutation alone, the base composition of the sequence is expected to shift. By contrast, if GC→AT and AT→GC changes are equal, this implies the sequence is at mutational equilibrium. Lack of equilibrium may result from a recent change in mutational pressure or the action of natural selection favoring either GC→AT or AT→GC changes. In this example, GC→AT changes far outnumber AT→GC changes, so the sequence is not at mutational equilibrium. Rather, under mutation alone, it would become more AT-rich. (B) Quantifying directional mutation biases addresses the question: Is mutation AT or GC biased? Per-site rates of AT→GC and GC→AT changes (v and u, respectively) are obtained by dividing the absolute number of inferred changes by the frequency of the original nucleotides. In this example, v = 3/35, and u = 7/65. From these per-site rates, one can then calculate the relative AT→GC per-site mutational bias as v/(v + u). In this example, this relative per-site bias is 44.3%. Since it is less than 50%, this implies a slight GC→AT mutational bias (any given GC pair is more likely to mutate to AT, than vice versa). This value equals the base composition that would be expected under mutation alone (GC_pred). In this example, the sequence is expected to be slightly AT-rich (44.3% GC) under mutation alone. The fact that the sequence is actually 65% GC suggests that selection favors AT→GC mutations.