Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments

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

To determine whether the rhodopsin gene has undergone accelerated evolution in mammal species that are adapted to low light conditions, we derived maximum-likelihood estimates of the rate of non-synonymous substitutions (d N ) and the rate of synonymous substitutions (d S ) using the CODEML program in PAML version 4 [64] . The ratio d N /d S , termed omega (v), is ,1 where purifying selection dominates, approximates to 1 where neutral evolution dominates and is .1 when positive selection dominates. We used an unrooted tree based on the results of our phylogenetic reconstruction (Figure 1 ) following the removal of the non-mammalian outgroups. Where the gene tree differed from the species tree, we repeated the analyses with the species tree topology. Since differences in estimates of substitution rates will be influenced by species coverage, we also repeated our analyses with a reduced dataset comprising just bats.