Table 2.
Number of Sites with Amino Acid (AA) Differences within the Transmembrane and Retinal Binding Pocket Regions for the Opsin Classes and Number of Positively Selected Sites Identified Using PAML.
| Sites with Amino Acid Differencesa |
Sites under Selection: P > 0.95a |
Significant PAML Result (P > 0.95) at Known Tuning Sites for Specific Opsina |
||||||
|---|---|---|---|---|---|---|---|---|
| Total | Transmembrane Regions | Retinal Binding Pockets | Known Tuning Sites for Specific Opsin | PAML Model 1/2a | PAML Model 8/8a | PAML Model 1/2a | PAML Model 8/8a | |
| RH1 | 34 | 22 | 3 | 2 (292 and 299) | 3 | 6 | 1 (292) | 1 (292) |
| RH2A | 65 | 36 | 3 | 0 | 3 | 13 | 0 | 0 |
| LWS | 97 | 48 | 13 | 1 (177) | 7 | 17 | 0 | 0 |
| SWS2B | 106 | 55 | 15 | 4 (52, 115, 122, and 275) | 9 | 19 | 0 | 1 (122) |
Note.—These results show that SWS2B has the highest number of sites with amino acid differences between the labrid species, followed by LWS, then the RH2A and RH1 opsins. The PAML models find similar results (Sites under selection: P > 0.95) although there were only two known tuning sites that were under positive selection as determined by the PAML models (where P > 0.95).
aAA sites based on labrid sequence numbers. Please refer to amino acid alignments (supplementary figs. S5–S8, Supplementary Material online) for corresponding bovine rhodopsin (RH1) amino acid site numbers.