DOI: 10.5061/dryad.djh9w0w0m
title: PAML data from: Evolutionary ecology of the visual opsin gene sequence and its expression in turbot (Scophthalmus maximus)

description: Background: As flatfish, turbot undergo metamorphosis as part of their
 life cycle. In the larval stage, turbot live at the ocean surface, but
 after metamorphosis they move to deeper water and turn to benthic life.
 Thus, the light environment differs greatly between life stages. The
 visual system plays a great role in organic evolution, but
 reports of the relationship between the visual system and benthic life are
 rare. In this study, we reported the molecular and evolutionary analysis
 of opsin genes in turbot, and the heterochronic shifts in opsin
 expression during development. Results: Our gene synteny analysis
 showed that subtype RH2C was not on the same gene
 cluster as the other four green-sensitive opsin genes (RH2) in turbot. It
 was translocated to chromosome 8 from chromosome 6. Based on
 branch-site test and spectral tuning sites analyses, E122Q and M207L
 substitutions in RH2C, which were found to be under positive selection,
 are closely related to the blue shift of optimum light sensitivities. And
 real-time PCR results indicated the dominant opsin gene shifted from
 red-sensitive (LWS) to RH2B1 during turbot development,
 which may lead to spectral sensitivity shifts to shorter wavelengths.
 Conclusions: This is the first report that
 RH2C may be an important subtype of green opsin gene that was
 retained by turbot and possibly other flatfish species during evolution.
 Moreover, E122Q and M207L substitutions in RH2C may contribute to
 the survival of turbot in the bluish colored ocean. And heterochronic
 shifts in opsin expression may be an important strategy for turbot to
 adapt to benthic life.
description: To estimate the differences in selection pressure between five
 benthic species and four
 shallow water
 pelagic species, branch-specific
 models and branch-site models of maximum likelihood were implemented in
 the CODEML program of PAML4.9i. Tree topologies of each gene
 obtained by neighbor-joining method. First, we compared the one-ratio model and free-ratios model in the branch test of selection, to test whether positive selection are present. It attempted to investigate if different spectral environments have an impact on the evolution of opsin genes. We then compared null Model A against the alternative Model A in the branch-site test to determine whether there are positively selected sites was present. This step was tried to explore the differences in selection pressure acted on not only branches but also sites of amino acids. The likelihood ratio test (LRT) was used to compare all alternative models and their corresponding null models. The Bayes Empirical Bayes method was used to obtain the posterior probability of sites under positive selection. The divergence time of turbot RH2 genes was estimated by MCMCTREE within PAML4.9i. The neighbor-joining tree of six species (turbot; Atlantic salmon, <i>Salmo salar</i>; fugu, <i>Takifugu rubripes</i>; common carp, <i>Cyprinus carpio</i>; lungfish, <i>Neoceratodus forsteri</i>, and rainbow trout) was acquired by MEGA 7 by neighbor-joining method. The fossil calibrations were adopted from TimeTree. The tree topology and fossil calibrations were set as (((((((S.maximus_RH2B1, S.maximus_RH2B2), S.maximus_RH2C), T.rubripes_RH2), (S.maximus_RH2A1, S.maximus_RH2A2)), (S.salar_RH2, O.mykiss_RH2)) '&gt;1.86&lt;2.27', (C.carpio_RH2-1, C.carpio_RH2-2)) '&gt;2.05&lt;2.55', N.forsteri_RH2). The RootAge was set as '&lt;6.0'.