Figure 1.

Between-species divergence and within-species polymorphism for detecting positive selection. (a and b) Phylogeny of Drosophila and Arabidopsis species. Both the MK and PAML tests are forced to detect positive selection along the branches marked in red. The MK test uses polymorphisms (indicated by the blue triangles) for reference. The reference for PAML is described in Supplementary Methods. (c and d) The Pa/Ps ratio as a function of the mutant frequency in D. melanogaster and A. thaliana. The dashed line, separating low- and high-frequency bins, is placed where the Pa/Ps ratio reaches a steady level.