Figure 4.

Sites under positive and negative selection in OR coding sequences. Nucleotide alignments were generated from the corresponding amino acid alignment [see 2] after removal of N- and C-terminal sequences and gap removal with respect to OR124-3, and subjected to two analyses of selective pressure. (a) Analysis of dN/dS ratios by sub-regions of OR coding sequences indicates that OR genes in general are under negative or purifying selection (dN/dS < 1). However, analysis of informative pairwise comparisons reveals that transmembrane domains (TMs) 3–6, and to a lesser degree TM1, have significantly higher average pairwise dN/dS ratios when compared with the average for non-transmembrane coding sequence (asterisks; p < 1 × 10^-3). Error bars show standard errors of the means. (b) A schematic representation of OR124-3 (an example OR) with transmembrane domains one through seven shown from left to right. SLAC analysis reveals sites under positive selection (dN/dS > 1) with p < 0.1 (red), p < 0.2 (orange), p < 0.5 (yellow), and sites under negative selection (dN/dS < 1) with p < 0.05 (dark blue), p < 0.1 (light blue), p < 0.2 (turquoise), p < 0.5 (green). The null hypothesis is that a site is neutrally evolving with dN/dS = 1. Yellow and green residues may be considered neutrally evolving. Sites on the representative OR124-3 sequence with dN/dS > 1 and p < 0.1 are: V108 (dN/dS = 1.39), F145 (dN/dS = 1.52), E261 (dN/dS = 1.48) and T262 (dN/dS = 1.42). Snake plot generated using the RbDe web service [48].