Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments

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

We reconstructed the ancestral states of the critical sites (wavelength specific sites) that control spectral tuning of rhodopsin using two methods. First, after removing the incomplete sequences of the horse and Hottentot golden mole, we used the maximum likelihood method [62] implemented in the PAML package. This approach calculates both the joint and marginal ancestral reconstructions. The former seeks to find the most likely character for all internal nodes, which maximizes the joint likelihood of the tree, whereas the latter compares the likelihood of all possible amino acids at a particular interior node and selects the one that yields the maximum likelihood tree. Second, we also used the parsimony approach in Mesquite version 2.6 [63] , which generates the ancestral states that minimize the number of evolutionary steps. Since the parsimony method allows missing data, horse and Hottentot golden mole were included. We modeled each nucleotide as one character, and reconstructed the ancestral states at each node for each character, then checked the positions where the critical sites are located.