Figure 1
Phylogenetic tree of opsins. Phylogenetic reconstruction of c-opsins, group 4 opsins and r-opsins using Bayesian Inference as implemented in MrBayes 3.2.1 [24]. Every 100th tree of 5,000,000 generations of 2x4 Markov chains under a WAG distribution model of amino acid substitutions was sampled. The Bayesian tree represents the half compatibility consensus of this sample after discarding 200,000 generations as burn-in. Opsin sequences were aligned with clustalW and regions outside of the 7 transmembrane domains were excluded. Numbers at nodes represent Bayesian posterior probabilities (top), parsimony bootstrap values (middle; 5,000 replicates in PAUP* 4.10b [2002]) and Maximum Likelihood (ML) bootstrap values (lower; 100 replicates in PHYML. The scale bar shows substitutions per site. The C. salei and E. kanangrensis positions are marked with arrowheads. The colours of the different groups are: onychopsins dark green, melanopsins pink, arthropsins light blue, arthropod c-opsins dark blue, peropsins red. The accession numbers of included species are provided in Additional file 5. Abbreviations, bws o = blue wavelength sensitive, ence = encephalopsin, gws o = green wavelength sensitive opsin, lws o = long wavelength sensitive opsin, m4m = melanopsin (opn4) mammalian-like, m4x = melanopsin (opn4) non-mammalian-like, o = opsin, parapi = parapinopsin, pariet = parietopsin, pto = pteropsin, rh = rhodopsin, RPE = RPE-retinal G protein-coupled receptor, TMT o = teleost multiple tissue opsin, uvs o = ultraviolet sensitive opsin, VA o = vertebrate ancient opsin.