Visual Pigment Genes: Evolution


More than 100 visual pigment genes have been cloned from a diverse range of vertebrates. Comparative sequence analyses of these genes and in vitro assays of engineered visual pigments have been used to elucidate not only the molecular bases of color vision but also the processes of adaptive evolution at the molecular level.

Keywords: opsins; visual pigments; absorption spectra; mutagenesis; adaptive evolution

Figure 1.

Structures of visual pigment genes, where exons and introns are represented by black boxes and horizontal lines respectively. The numbers after P refer to λmax. For Malawi fish pigments, Dc and Mz denote Dimidiochromis compressiceps and Metriaclima zebra respectively. Malawi fish‐Dc (P536), Malawi fish‐Mz (P533), Malawi fish‐2A‐Dc (P447), Malawi fish‐2B‐Dc (P488), Malawi fish‐Dc (P368), Malawi fish‐Dc (P569), marmoset (P561), marmoset (P553) and marmoset (P539) pigment genes are from GenBank (accession nos. AF247121, AF247122, AF247113, AF247118, AF191220, AF247125, AB046549s1–s6, AB046555s1–s6 and AB046561s1–s6 respectively). For other genes, see Yokoyama . The gene duplication of the human P530 and P560 genes occurred some 30 million years (MY) ago (Nathans et al., ). Two human (P560) genes have intron 1 length polymorphism, one of them being 2 kb longer than the other. Af: African; LWS/MWS: long wavelength‐ and middle wavelength‐sensitive; RH1: rhodopsins; RH2: RH1‐like; SWS1: short wavelength‐sensitive type 1; SWS2: SWS type 2.

Figure 2.

Phylogenetic tree for the vertebrate visual pigments by applying the neighbor‐joining method (Saitou and Nei, ) to their amino acid sequences. Ind. coelacanth (P485) and Ind. coelacanth (P478) are from Indonesian coelacanth (Latimeria menadoensis). Salamander (P431), bull frog (P432) and mole rat (P534) pigments are from GenBank (accession nos. AF038946, AB010085 and AF139726 respectively). Blackbird (P360) is from red‐winged blackbird (Agelaius pheniceus). For other sequences, see Yokoyama . The arrow indicates the root of the phylogenetic tree. The bar at the bottom indicates evolutionary distance measured as the number of amino acid replacements per site.

Figure 3.

Secondary structure of bovine RH1 opsin, showing naturally occurring amino acid mutations that cause more than 5 nm of λmax shift. The model is based on Palczewski et al.. Open square, filled square and filled circles indicate the amino acid sites that are involved mainly in the spectral tuning of SWS1, LWS/MWS and RH1/RH2 pigments respectively (see Yokoyama et al., ; Shi et al., ).



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Further Reading

Ebrey T and Koutalos Y (2001) Vertebrate photoreceptors. Progress in Retinal and Eye Research 20: 49–94.

Fernald RD (2006) Casting a genetic light on the evolution of eyes. Science 313: 194–1918.

Kochendoerfer GG, Lin SW, Sakmar TP and Mathies RA (1999) How color visual pigments are tuned. Trends in Biochemical Sciences 24: 300–305.

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Sharpe LT, Stockman A, Jagle H et al. (1998) Red, green and red–green hybrid pigments in the human retina: correlations between deduced protein sequences and psychophysically measured spectral sensitivities. Journal of Neuroscience 18: 10053–10069.

Yokoyama S (2002) Molecular evolution of color vision in vertebartes. Gene 300: 69–78.

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How to Cite close
Yokoyama, Shozo(Apr 2008) Visual Pigment Genes: Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0006148.pub2]