Map of nucleotide substitution patterns at Toll-like receptor loci in birds.

<p>The analysed region of each gene is positioned on an <i>x</i>-axis aligned with chicken TLRs. Within each panel of the figure, vertical black lines indicate the degree of positive (<i>d_N</i>-<i>d_S</i>>0) or negative (<i>d_N</i>-<i>d_S</i><0) selection at each codon site. Note that the <i>y</i>-axes vary in scale. Panel backgrounds are shaded to illustrate locations of conserved domains within the alignment region (based on LRRfinder <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089632#pone.0089632-Offord1" target="_blank">[43]</a>) (pink = signal domain; light green = extracellular LRR regions; dark green = C-terminal LRR regions; cyan = transmembrane domain; orange = TIR). Within each panel, three rows of symbols indicate codons for which statistically significant evidence of selection was detected: the top row of symbols (circles) indicates codons under positive selection in the current study, using either the SLAC or REL methods, larger symbols are used where the two methods correspond. The second row of symbols (triangles) indicates codons detected in the current study as being under episodic diversifying selection, using the MEME analysis. The third row of symbols (asterisks) indicates sites previously observed to be under positive selection in a smaller avian alignment of the same regions <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089632#pone.0089632-Alcaide1" target="_blank">[17]</a> using either the SLAC or REL methods, larger symbols indicate codons in which the two methods correspond.