Table 4. Analyses used to elucidate sites coevolving with site 122 in Vertebrate rhodopsins (rh1).
In bold are the results of interest described in the main text, including: elevated dN/dS, long-term shifts in selection between teleosts and tetrapods, amino acid statistical covariation with site 122 in the teleost dataset, and phylogenetically correlated amino acid variation with site 122.
| Site | Distance to site 122 (Å)* | Tetrapod M8 dN/dS† | Teleost M8 dN/dS† | Characiphysi M8 dN/dS† | Posterior probability of long-term shift in selection (tetrapod/characiphysi)‡ |
Z-score covariation§ | Significant correlated evolution? |
|---|---|---|---|---|---|---|---|
| 118 | 5 | 0.05 | 0.05 | 0.05 | 0.00/0.00 | −1.54 | No |
| 119 | 3.5 | 0.14 | 0.168 | 0.05 | 0.57/0.19 | 30.2 | Yes |
| 120 | 3.1 | 0.05 | 0.05 | 0.05 | 0.00/0.00 | −1.91 | No |
| 121 | N/A | 0.05 | 0.05 | 0.05 | 0.00/0.00 | −0.94 | No |
| 122 | N/A | 0.05 | 0.322 | 0.05 | 1.00/1.00 | N/A | N/A |
| 123 | N/A | 0.19 | 0.094 | 0.05 | 0.00/0.00 | 20.4 | No |
| 124 | 3.2 | 0.05 | 0.411 | 0.05 | 1.00/1.00 | 5.53 | No |
| 125 | 3.4 | 0.05 | 0.05 | 0.05 | 0.00/0.00 | 1.19 | No |
| 126 | 3.7 | 0.05 | 0.05 | 0.05 | 0.00/0.00 | −1.60 | No |
| 127 | 4.9 | 0.05 | 0.065 | 0.05 | 0.00/0.00 | 27.1 | Yes |
| 160 | 5.1 | 0.05 | 0.05 | 0.05 | 0.00/0.00 | 3.90 | No |
| 164 | 4.2 | 0.05 | 0.05 | 0.05 | 0.00/0.00 | 7.88 | No |
| 167 | 3.8 | 0.05 | 0.05 | 0.05 | 0.00/0.00 | −1.38 | No |
| 168 | 5.9 | 0.05 | 0.308 | 0.192 | 1.00/1.00 | 34.2 | No |
| 207 | 4.9 | 0.05 | 0.05 | 0.05 | 0.00/0.00 | −1.21 | No |
| 211 | 2.7 | 0.05 | 0.05 | 0.05 | 0.00/0.00 | −1.38 | No |
| 265 | 5.1 | 0.05 | 0.05 | 0.05 | 0.00/0.00 | −1.44 | No |
∗From structural analysis of distances between amino acids and site 122 within the MII crystal structure 3PQR (Choe et al., 2011).
‡Bayes empirical Bayes posterior probability of long-term shift in selection calculated in Clade model C (CmC) (Yang, 2007) analyses (CmC_Teleost vs Tetrapod/CmC_Characi clade) described in Tables 3 and 5, respectively.
§Phylogenetically corrected MI z-scores (MISTIC; [Simonetti et al., 2013]) of covariation with site 122 from analyses on Teleost RH1 dataset. Values were considered significant if greater than the top absolute z-score (21.6) from all site-wise comparisons from all analyses of 150 randomized datasets, as described (Ashenberg and Laub, 2013).
¶Tests of correlated evolution in amino acid variation (Pagel, 1994) between a given site and site 122. p-values were calculated by performing Monte Carlo tests using data from simulations (n > 1000) in MESQUITE (Maddison and Maddison, 2017). p-Values were subjected to a Bonferroni-correction to determine significance (p<0.002).