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

<p>Ratio of divergence at nondegenerate nonsynonymous sites (<i>d</i><sub><i>N</i></sub>) and 4-fold degenerate synonymous sites (<i>d</i><sub><i>S</i></sub>) as a function of <i>d</i><sub><i>S</i></sub> (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3000102#pbio.3000102.s027" target="_blank">S1D Text</a>) for all species × host1 × host2 combinations in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3000102#pbio.3000102.g002" target="_blank">Fig 2</a> (gray circles). Crosses (<i>x</i>) denote species-wide estimates obtained from the ratio of the median <i>d</i><sub><i>N</i></sub> and <i>d</i><sub><i>S</i></sub> within each species. The red line denotes the theoretical prediction from the purifying selection null model in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3000102#pbio.3000102.s027" target="_blank">S1D Text</a>. Inset shows the ratio between the cumulative private <i>d</i><sub><i>N</i></sub> and <i>d</i><sub><i>S</i></sub> values for all quasi-phaseable host pairs with core-genome-wide synonymous divergence less than <i>d</i><sub><i>S</i></sub>. The narrow shaded region denotes 95% confidence intervals estimated by Poisson resampling (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3000102#pbio.3000102.s027" target="_blank">S1D Text</a>), which shows that <i>d</i><sub><i>N</i></sub>/<i>d</i><sub><i>S</i></sub>≲1, even for low <i>d</i><sub><i>S</i></sub>.</p>