Figure 3

Estimates of ω ratios for individual codons in the LBDs of 7 NR genes and the AHR gene. The graphs in (A) through (H) plot the estimated ω ratios for individual codons of the LBDs of 7 NR genes and the AHR gene derived from the 'best minimum' PAML discrete model. The location of the α-helices in the LBDs of the NR genes that correspond to codons are indicated in the abscissas (e.g., 'H1' denotes α-helix-1; 'H1-H3 insert' denotes the insertion region in the NR1I subfamily proteins between helix-1 and helix-3); the location of the PAS-B domain is also shown for the AHR gene. CAR lacks the H1-H3 insert but this region is plotted in (E) to keep the alignment consistent between (A) VDR, (C) PXR, and (E) CAR. Due to difficulties in alignment and extreme sequence divergence for VDR and PXR in the H1-H3 insertion region, PAML analysis for this region could be performed for mammals only for the PXR genes. For NR1I1, NR2B2, and NR3C4, analysis restricted to mammals resulted in a best minimum PAML discrete model of only one ω ratio population (i.e., the M0 model); therefore, only data for all vertebrate species is plotted for those three genes (note also that the CAR gene is only found in mammals). The plots in (A), (C), and (E) show data for all three NR1I subfamily members and reveal that PXR has the widest variation of ω ratios across codons both within this subfamily (with CAR intermediate between PXR and VDR) and compared to the other NR genes.