Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments

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

mentary Table S3 , Supplementary Material online). In contrast, a free-ratio model for all mammals did fit the data significantly better than the corresponding one-ratio model, suggesting that heterogeneous selective pressures might occur along one or more specific evolutionary lineages. This was confirmed by a series of two-ratio branch models, in which each foreground branch of interest was in turn allowed to have a different ratio from the rest of the tree (background). These models were applied to test several species or ancestral branches that are associated with poor photopic environments, as described below.