Figure 1. Two theories are diagrammed, neutral evolution and adaptive evolution.

These theories describe how genetic mutations persist in the genome, leading to the development of new traits in a species. To differentiate between these two theories, the McDonald–Kreitman approach estimates the amount of adaptive evolution in diverging populations. This method involves comparing two ratios: d/d₀, which is the number of substitutions at functional sites in a protein’s DNA sequence (d; green squares) divided by the number of substitutions at neutral sites (d₀; light blue squares); and p/p₀, which is the number of polymorphisms at functional sites (p; green circles) divided by the number of polymorphisms at neutral sites (p₀; light blue circles). These two ratios can also be used to estimate the fraction (α) of substitutions driven by adaptation, via the formula α = 1 – (d₀/d)(p/p₀). (A) Under neutral evolution, we assume that all mutations at neutral sites have no effect on how the resulting protein works and that all mutations at functional sites either have no effect or are strongly deleterious. In this case, d/d₀ = p/p₀, and α = 0. (B) Under adaptive evolution, there is an excess of substitutions at functional sites relative to the number of polymorphisms seen at functional sites, i.e., d/d₀ > p/p₀. In this case, α > 0.