Table 2 Amino acid sites in photophore-bearing species identified by (1) PAML, with a probability higher than 95% (or >99% in bold) to be under positive selection (ω > 1) according to the BEB analysis under the Branch-site Model A, (2) BUSTED-MH with an evidence ratio threshold >10 for ω > 1 and by (3) MEME that have significant LRT values (adj. p < 0.05) for ω > 1, but are not foreground (photophore-bearing) specific
Opsin | Hypothesis tested | PAML | BUSTED | MEME |
|---|---|---|---|---|
MWS1 | Photophore-bearing | – | – | 83, 92, 134, 161, 165, 187, 252, 310, 368 |
Oplophoridae | – | – | ||
Shallow migrators (<200 m) | – | – | ||
MWS2 | Photophore-bearing | 178, 199, 283 | 160, 199 | 124, 155, 160, 199, 350 |
Oplophoridae | 178 | 160, 199 | ||
Shallow migrators (<200 m) | 283 | – | ||
LWS2 | Photophore-bearing | – | 70, 225, 229, 237, 279 | 12, 60, 70, 106, 139, 150, 161, 168, 185, 224, 225, 229, 233, 279, 283, 309, 364 |
Oplophoridae | – | 70, 225, 229, 237, 279 | ||
Shallow migrators (<200 m) | 125, 243 | 70, 225, 229, 237 |
