Signatures of selective constraint within species as a function of core-genome divergence.
Ratio of divergence at nondegenerate nonsynonymous sites (dN) and 4-fold degenerate synonymous sites (dS) as a function of dS (S1D Text) for all species × host1 × host2 combinations in Fig 2 (gray circles). Crosses (x) denote species-wide estimates obtained from the ratio of the median dN and dS within each species. The red line denotes the theoretical prediction from the purifying selection null model in S1D Text. Inset shows the ratio between the cumulative private dN and dS values for all quasi-phaseable host pairs with core-genome-wide synonymous divergence less than dS. The narrow shaded region denotes 95% confidence intervals estimated by Poisson resampling (S1D Text), which shows that dN/dS≲1, even for low dS.