Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments

Zhao, Huabin; Ru, Binghua; Teeling, Emma C.; Faulkes, Christopher G.; Zhang, Shuyi; Rossiter, Stephen J.

In the dataset of all mammals (I), models F1 (cetaceans versus background) and I1 (West Indian manatee versus background) were significantly better fits to the data than the one-ratio model (A1). However, while the v value estimated for branch CET (ancestral to cetaceans) was around five times higher than the background, that of the West Indian manatee branch was actually lower (0.009 versus 0.041). It is also noteworthy that the foreground v estimate (0.104) of the branch ancestral to African mole-rats (AFM) was found to be nearly three times higher than the background, and the associated likelihood ratio test was on the margin of statistical significance (P = 0.05) ( Table 2) . Finally, we also tested the lineage of the elephant seal, because it has been previously shown to have spectral tuning to blue wavelengths of light [37] , and this was also found to be significant (data not shown).