Phylogenetic analysis of LWS1, LWS2, Rh2, and Rh1 elephant shark vertebrate retinal opsin sequences and coding sequences of other related vertebrate species. (A) A neighbor-joining tree was constructed (Saitou and Nei 1987) by applying a Kimura 2-parameter substitution matrix (Kimura 1980) with 1000 bootstrapping replications (degree of support for internal branching is shown as a percentage at the base of each node). (B) A maxiumum likelihood tree was generated with a Kimura 2-parameter substitution matrix (Kimura 1980), a gamma distribution parameter of 1 using PHYML (Guindon et al. 2005) and bootstrapping with 500 replicates (degree of support for internal branching is shown as a percentage at the base of each node). (C) A Bayesian probabilistic inference method was performed with a Metropolis Markov chain Monte Carlo algorithm (Huelsenbeck and Ronquist 2001; Ronquist and Huelsenbeck 2003). A general time-reversal model (Lanave et al. 1984) was used with posterior probability values (represented as a percentage) indicated at the base of each node. The scale bar indicates the number of nucleotide substitutions per site. The Drosophila melanogaster (fruit fly) Rh4 (accession no. NM057353) was used as an outgroup. The sequences used for generating the tree are as follows: (a) RhA/Rh1 opsin class: zebrafish (Danio rerio), NM131084; goldfish (Carassius auratus), L11863; guppy (Poecilia reticulata), Y11147; John Dory (Zeus faber), Y14484; smaller spotted catshark (Scyliorhinus canicula), Y17585; dogfish (Galeus melastomus), Y17586; little skate (Raja erinacea), U81514; elephant shark (Callorhinchus milii), EF565167; sea lamprey (Petromyzon marinus) (RhA), AH005459; Arctic lamprey (Lethenteron japonica) (RhA), M63632; pouched lamprey (Geotria australis) (RhA), AY366493; (b) RhB/Rh2 opsin class: zebrafish (Danio rerio), AB087805 (Rh2.1), AB087806 (Rh2.2), AB087807 (Rh2.3), AB087808 (Rh2.4); goldfish (Carassius auratus), L11865 (Rh2.1), L11866 (Rh2.2); bluefin killifish (Lucania goodei), AY296739; rainbow trout (Oncorhynchus mykiss), AF425072; elephant shark (Callorhinchus milii), EF565168; pouched lamprey (Geotria australis) (RhB), AY366494; (c) SWS2 opsin class: zebrafish (Danio rerio), NM131192; goldfish (Carassius auratus), L11864; bluefin killifish (Lucania goodei), AY296737; rainbow trout (Oncorhynchus mykiss), AF425075; pouched lamprey (Geotria australis), AY366492; (d) SWS1 opsin class: zebrafish (Danio rerio), NM131319; goldfish (Carassius auratus), D85863; pouched lamprey (Geotria australis), AY366495; (e) LWS opsin class: zebrafish (Danio rerio), NM131175; goldfish (Carassius auratus), L11867; pouched lamprey (Geotria australis), AY366491; elephant shark (Callorhinchus milii), EF565165 (LWS1), EF565166 (LWS2).
