Differences in selection across LRR and other domains of four TLR genes in birds.

<p>In A, filled circles indicate the mean <i>d_N</i>-<i>d_S</i> values (estimated using the SLAC method) of codons located in LRR domains, while open circles indicate the mean values of all other codons; error bars indicate the standard error; numbers of codons assayed in each region are shown along <i>x</i>-axis. Panel B shows the proportion of statistically significant results for codons under positive selection (as determined by the SLAC or REL methods, circles on left, hits at the same site from multiple methods were counted separately) or episodic diversifying selection (as determined by the MEME method, diamonds on right), that fell within LRR domains of each toll-like receptor gene. Crosses indicate the proportion of results expected to fall within LRR domains under the null hypothesis, given the number of genotyped codons in those regions. Total numbers of significant findings by each method are shown along the <i>x</i>-axis; error bars are 95% confidence intervals for binomial proportions (see Methods).