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 phylogenetic reconstruction based on coding sequences, we estimated the best-fit model of sequence evolution to be HKY + I + G (base frequencies = 0.2130, 0.3327, 0.4543; proportion of invariable sites = 0.4169; gamma distribution shape parameter = 0.8145) based on the AIC in Modeltest 3.7 [58] . Maximum likelihood (ML) and Bayesian approaches were undertaken to recover the rhodopsin phylogeny using PAUP* 4.10b [59] and MrBayes 3.1.1 [60] , respectively. The ML tree was generated by using tree bisection and reconnection (TBR) branch swapping, and the ML bootstrap values were calculated from 100 ML replicate trees using nearest-neighbor interchange (NNI) method. Each bootstrap replicate was started with an initial tree via the neighbour-joining (NJ) method. For the Bayesian tree, we ran six simultaneous Markov chains for one million generations. We used a flat prior and discarded the first 300,000 generations as burn-in to ensure sampling at stationarity. We included seven outgroups: three birds (Anas platyrhynchos, AF021240; Gallus gallus, NM_001030606; Taeniopygia guttata, NM_001076695), two amphibians (Xenopus tropicalis, U59922; Bufo marinus, NM_001097334) and two reptiles (Alligator mississippiensis, U23802; Ambystoma tigrinum, U36574).