Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments

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

For each dataset, we modeled selection using a combination of branch models, site models and clade models. For branch models, we first estimated an independent v value for each branch under the free-ratio model. Second, we estimated v under a one-ratio model in which the same ratio occurs across the tree, and third, we used the two-ratio 'branch model' to compare the estimated v ratio on specific foreground branches (v 1 ) in the phylogeny to the background ratio (v 0 ) ( Figure 1 and Table S3 , Supplementary Material online). Branch models were applied to branches leading to taxa or clades of taxa that are adapted for living in low light environments, several of which also show loss of their SWS1 opsin gene.