Molecular Basis of Spectral Tuning in the Red- and Green-Sensitive (M/LWS) Pigments in Vertebrates

Yokoyama, Shozo; Yang, Hui; Starmer, William T.

doi:10.1534/genetics.108.090449

Cited by 103 publications

(126 citation statements)

References 35 publications

(49 reference statements)

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“…With reference to M/LWS, in which five sites are major determinants of optimum light sensitivity (λ max ) (12), tuna has the same amino acids as medaka and stickleback (S, H, Y, T, and A) ( Fig. S2C).…”

Section: Resultsmentioning

confidence: 99%

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Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

Nakamura

Mori

Saitoh

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

109

112

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Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing technology. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS), UV-sensitive (short-wavelength sensitive 1; SWS1), blue-sensitive (SWS2), rhodopsin (RH1), and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e., blue shift). Pacific bluefin tuna has at least five RH2 paralogs, the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover, phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus, Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1, RH2, and SWS2), which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and, thereby, could help to improve the technology to culture such fish in captivity for resource management.tuna genome | visual system | animal opsin

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Section: Resultsmentioning

confidence: 99%

“…In addition, many fish species have two copies of SWS2 genes, consistent with the concept that an ancient duplication occurred and each copy has been retained for a long time. Previous studies have accumulated molecular information on opsins, focusing on the residues surrounding the retinal-binding pocket (10)(11)(12).…”

mentioning

confidence: 99%

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

Nakamura

Mori

Saitoh

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

109

112

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“…Given that commonality, what cone pigments may have been present in the retinas of the early eutherians? Sequence comparisons of cone opsin genes have suggested that the ancestral mammalian pigments drawn from these two gene families peaked in the UV, at about 360 nm (Hunt et al 2001), and in the long wavelengths at 560 nm (Yokoyama et al 2008). Assuming the visual pigment chromophore of early mammals was 11-cis-retinal, the same as that of contemporary mammals, the cone pigments of early eutherian mammals would have had absorption properties similar to those sketched at the bottom of figure 1.…”

Section: (A) Monotremes and Marsupialsmentioning

confidence: 94%

Evolution of colour vision in mammals

Jacobs

2009

Phil. Trans. R. Soc. B

288

228

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Colour vision allows animals to reliably distinguish differences in the distributions of spectral energies reaching the eye. Although not universal, a capacity for colour vision is sufficiently widespread across the animal kingdom to provide prima facie evidence of its importance as a tool for analysing and interpreting the visual environment. The basic biological mechanisms on which vertebrate colour vision ultimately rests, the cone opsin genes and the photopigments they specify, are highly conserved. Within that constraint, however, the utilization of these basic elements varies in striking ways in that they appear, disappear and emerge in altered form during the course of evolution. These changes, along with other alterations in the visual system, have led to profound variations in the nature and salience of colour vision among the vertebrates. This article concerns the evolution of colour vision among the mammals, viewing that process in the context of relevant biological mechanisms, of variations in mammalian colour vision, and of the utility of colour vision.

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“…In some cases models have been shown to successfully predict a visual pigment's λ max . Some examples include experimental verifications of the "five-sites rule" (Yokoyama and Radlwimmer, 1998;Yokoyama et al , 2008b) and the effect of SWS1 substitutions of large effect that cause this pigment to shift from the violet to the UV region in birds (Ödeen et al, 2009;Hauser et al, 2014). However, predicting λ max from opsin sequence can be far from simple and highly dependent on genetic background.…”

Section: From Opsin Genes To Spectral Tuningmentioning

confidence: 99%

The evolution of opsins and color vision: connecting genotype to a complex phenotype

Bloch¹

2016

Acta biol. Colomb.

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Este artículo fue presentado por invitación de la Red Colombiana de Biología Evolutiva (COLEVOL) y Acta Biológica Colombiana con el fin de incentivar la investigación en el área de biología evolutiva. ABSTRACTDissecting the genetic basis of adaptive traits is key to our understanding of evolutionary processes. A major and essential step in the study of evolutionary genetics is drawing link between genotype and phenotype, which depends on the difficult process of defining the phenotype at different levels, from functional to organismal. Visual pigments are a key component of the visual system and their evolution could also provide important clues on the evolution of visual sensory system in response to sexual and natural selection. As a system in which genotype can be linked to phenotype, I will use visual pigments and color vision, particularly in birds, as a case of a complex phenotype. I aim to emphasize the difficulties in drawing the genotype-phenotype relationship for complex phenotypes and to highlight the challenges of doing so for color vision. The use of vision-based receiver models to quantify animal colors and patterns is increasingly important in many fields of evolutionary research, spanning studies of mate choice, predation, camouflage and sensory ecology. Given these models impact on evolution and ecology, it is important to provide other researchers with the opportunity to better understand animal vision and the corresponding advantages and limitations of these models.Keywords: avian visual pigments, color vision, complex phenotypes, genotype-phenotype, opsins. RESUMENEntender la base genética de los rasgos adaptativos es un paso crítico en el estudio de los procesos evolutivos. Para estudiar la conexión entre genotipo y fenotipo es importante definir el fenotipo a diferentes niveles: desde las proteínas que se construyen con base en un gen, hasta las características finales presentes en un organismo. Las opsinas y los fotopigmentos son elementos primordiales de la visión y entender cómo han evolucionado es fundamental en el estudio de la visión en los animales como un caracter derivado de selección natural o sexual. Este artículo se enfoca en este sistema, en el que se pueden conectar genotipo y fenotipo, como ejemplo de fenotipo complejo para ilustrar las dificultades de establecer una relación clara entre genotipo y fenotipo. Adicionalmente, este artículo tiene como objetivo discutir el funcionamiento del sistema de fotorrecepción, con énfasis particular en las aves, con el fin de enumerar varios factores que deben ser tenidos en cuenta para predecir cambios en la visión a partir del estudio de los fotopigmentos. Dado que los modelos basados en la visión de aves son cada vez más usados en diversas áreas de la biología evolutiva tales como: selección de pareja, depredación y camuflaje; se hace relevante entender los fundamentos y limitaciones de estos modelos. Por esta razón, en este artículo discuto los detalles y aspectos prácticos del uso de los modelos de visión existentes para aves, con el...

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Molecular Basis of Spectral Tuning in the Red- and Green-Sensitive (M/LWS) Pigments in Vertebrates

Cited by 103 publications

References 35 publications

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

Evolution of colour vision in mammals

The evolution of opsins and color vision: connecting genotype to a complex phenotype

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