PAML data from: Evolutionary ecology of the visual opsin gene sequence and its expression in turbot (Scophthalmus maximus)

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.

背景：作为比目鱼（flatfish），大菱鲆（turbot）的生命周期包含变态发育过程。幼虫阶段的大菱鲆栖息于海洋表层，待变态发育完成后，它们会迁移至深水水域并转为底栖生活方式。由此，不同生命阶段的光照环境差异极大。视觉系统在生物演化中占据重要地位，但目前针对视觉系统与底栖生活之间关联的研究报道仍较为稀缺。本研究对大菱鲆的视蛋白基因（opsin genes）开展了分子与演化分析，并揭示了发育进程中视蛋白表达的异时性移位（heterochronic shifts）。
结果：基因共线性（gene synteny）分析显示，大菱鲆的RH2C亚型并未与其余4种绿敏视蛋白基因（RH2）处于同一基因簇，而是从6号染色体易位至8号染色体。通过分支位点检验（branch-site test）与光谱调谐位点分析，我们发现RH2C中受正选择作用的E122Q与M207L氨基酸替换，与最优光敏感度的蓝移现象紧密相关。实时荧光定量PCR（real-time PCR）结果表明，大菱鲆发育过程中优势视蛋白基因从红敏视蛋白（LWS）转变为RH2B1，这可能促使光谱敏感度向短波长方向偏移。
结论：本研究首次报道，RH2C或是大菱鲆乃至其他比目鱼物种在演化过程中保留的一类重要绿视蛋白基因亚型。此外，RH2C中的E122Q与M207L氨基酸替换，或有助于大菱鲆在蓝色调海洋环境中存活。而视蛋白表达的异时性移位，可能是大菱鲆适应底栖生活的关键策略之一。