10.1371/journal.pbio.3000102.g003
Nandita R. Garud
Nandita
R. Garud
Benjamin H. Good
Benjamin
H. Good
Oskar Hallatschek
Oskar
Hallatschek
Katherine S. Pollard
Katherine
S. Pollard
Signatures of selective constraint within species as a function of core-genome divergence.
Public Library of Science
2019
between-host
dynamic
strain
hosts Gut microbiota
species
6- month timescales
sweep
mutation
evolution
gut bacteria
replacement
2019-01-23 18:52:44
Figure
https://plos.figshare.com/articles/figure/Signatures_of_selective_constraint_within_species_as_a_function_of_core-genome_divergence_/7621625
<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>