Episodic Positive Selection in the Evolution of Avian Toll-Like Receptor Innate Immunity Genes
Positively selected sites were determined by MEME analysis; trees are available in Figure S1. Points indicate observed proportions; error bars are Agresti-Coull binomial 95% confidence intervals  calculated using the R package “binom” . Crosses indicate the proportion expected under a null hypothesis of random distribution, based on the sum of internal/terminal branch lengths. Values along the x-axis are sample sizes of mapped MEME results; note that these values can be larger than those presented in Table 1, as some sites are selected on multiple branches, while not all sites under selection were mapped to specific branches (i.e. they showed pervasive selection) (see also Figure S5).