Signatures of selective constraint within species as a function of core-genome divergence.

Ratio of divergence at nondegenerate nonsynonymous sites (d_N) and 4-fold degenerate synonymous sites (d_S) as a function of d_S (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 d_N and d_S 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 d_N and d_S values for all quasi-phaseable host pairs with core-genome-wide synonymous divergence less than d_S. The narrow shaded region denotes 95% confidence intervals estimated by Poisson resampling (S1D Text), which shows that d_N/d_S≲1, even for low d_S.