Statistical and molecular analyses of evolutionary significance of red-green color vision and color blindness in vertebrates

Molecular Biology and Evolution

Volumn 22, Issue 4, 2005, Pages 968-975

  Yokoyama, Shozo ^a   Takenaka, Naomi ^a  

^a EMORY UNIVERSITY   (United States)

Author keywords

Adaptive evolution; M LWS pigments; Parallel evolution; Positive selection; Vertebrates

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; COLOR; COLOR BLINDNESS; COLOR VISION; EVOLUTIONARY ADAPTATION; MOLECULAR EVOLUTION; NATURAL SCIENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PIGMENT EPITHELIUM; SPECTRAL SENSITIVITY; SURVIVAL; VERTEBRATE;

ANIMALS; COLOR PERCEPTION; COLOR VISION DEFECTS; EVOLUTION, MOLECULAR; HUMANS; RETINAL PIGMENTS; VERTEBRATES;

EID: 16344369546     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi080     Document Type: Article

References (60)

1. Asenjo, A. B., J. Rim, and D. D. Oprian. 1994. Molecular determinants of human red/green color discrimination. Neuron 12:1131-1138.
2. Bowmaker, J. K. 1991. Evolution of photoreceptors and visual pigments. Pp. 63-81 in J. R. Cronly-Dillon and R. L. Gregory, eds. Evolution of the eye and visual pigments. CRC Press, Boca Raton, Fla.
3. Bowmaker, J. K., and A. Knowles. 1977. The visual pigments and oil droplets of the chicken retina. Vision Res. 17:755-764.
4. Caine, N. G., A. K. Surridge, and N. I. Mundy. 2003. Dichromatic and trichromatic Callithrix geoffroyi differ in relative foraging ability for red-green color-camouflaged and non-camouflaged food. Int. J. Primatol. 24:1163-1175.
5. Carroll, R. L. 1988. Vertebrate paleontology and evolution. W. H. Freeman & Co., New York.
6. Chinen, A., T. Hamaoka, Y. Yamada, and S. Kawamura. 2003. Gene duplication and spectral diversification of cone visual pigments of zebrafish. Genetics 163:663-675.
7. Deeb, S., M. J. Wakefield, T. Tada, L. Marotte, S. Yokoyama, and J. A. Marshall Graves. 2003. The cone visual pigments of an Australian marsupial, the Tammar wallaby (Macropus eugenii): sequence, spectral tuning, and evolution. Mol. Biol. Evol. 20:1642-1649.
8. Dominy, N. J. 2003. Color as an indicator of food quality to anthropoid primates: ecological evidence and an evolutionary scenario. Pp. 599-628 in C. F. Ross and R. F. Kay, eds. Anthropoid origins: new visions. Kluwer Academic, New York.
9. Dominy, N. J., P. A. Garber, J. C. Bicca-Marques, and M. A. D. O. Azevedo-Lopes. 2003. Do female tamarins use visual cues to detect fruit rewards more successfully than do males? Anim. Behav. 66:829-837.
10. Dominy, N. J., J.-C. Svenning, and W.-H. Li. 2003. Historical contingency in the evolution of primate color vision. J. Hum. Evol. 44:25-45.
11. Dulai, K. S., J. K. Bowmaker, J. D. Mollon, and D. M. Hunt. 1994. Sequence divergence, polymorphism and evolution of the middle-wave and long-wave visual pigment genes of great apes and old world monkeys. Vision Res. 34:2483-2491.
12. Ebrey, T., and Y. Koutalos. 2001. Vertebrate photoreceptors. Prog. Retin. Eye Res. 20:49-94.
13. st century. Valdenmar, Overland Park, Va.
14. Endler, J. A. 1991. Variation in the appearance of guppy color patterns to guppies and their predators under different visual conditions. Vision Res. 31:587-608.
15. Fasick, J. I., T. W. Cronin, D. M. Hunt, and P. R. Robinson. 1998. The visual pigments of the bottlenose dolphin (Tursiops truncates). Vis. Neurosci. 15:643-651.
16. Fodgen, M., and P. Fodgen. 1974. Animals and their colors. Crown Press, New York.
17. Harosi, F. I. 1994. Analysis of two spectral properties of vertebrate visual pigments. Vision Res. 34:1359-1367.
18. Hiramatsu, C., F. B. Radlwimmer, S. Yokoyama, and S. Kawamura. 2004. Mutagenesis and reconstitution of middle-to-long-wave-sensitive visual pigments of New World monkeys for testing the tuning effect of residues at sites 229 and 233. Vision Res. 44:2225-2231.
19. Jacobs, G. H. 1993. The distribution and nature of color vision among the mammals. Biol. Rev. 68:413-471.
20. Kawamura, S., N. S. Blow, and S. Yokoyama. 1999. Genetic analyses of visual pigments of the pigeon (Columba livia). Genetics 153:1839-1850.
21. Kawamura, S., and S. Yokoyama. 1998. Functional characterization of visual and nonvisual pigments of American chameleon (Anolis carolinensis). Vision Res. 38:37-44.
22. Lythgoe, J. N. 1979. The ecology of vision. Clarendon, Oxford.
23. Madsen, O., M. Scally, C. J. Douady, D. J. Kao, R. W. DeBry, R. Adkins, H. M. Amrine, M. J. Stanhope, W. W. de Jong, and M. S. Springer. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409:610-614.
24. Makino, C. L., T. W. Raft, R. A. Mathies, J. Lugtenburg, M. E. Miley, R. van der Steen, and D. A. Baylor. 1990. Effects of modified chromophores on the spectral sensitivity of salamander, squirrel and macaque cones. J. Physiol. 424:545-560.
25. McLaughlin, P. J., and M. O. Dayhoff. 1972. Evolution of species and proteins: a time scale. Pp. 47-66 in M. O. Dayhoff, ed. Atlas of protein sequence and structure. National Biomedical Research Foundation, Washington, D.C.
26. Merbs, S. L., and J. Nathans. 1992. Absorption spectrum of human cone pigments. Nature 356:433-435.
27. Mollon, J. 1991. The uses and evolutionary origins of primate color vision. Pp. 306-319 in J. R. Cronly-Dillon and R. L. Gregory, eds. Evolution of the eye and visual system. CRC Press, Boca Raton, Fla.
28. Morgan, M. J., A. Adam, and J. D. Mollon. 1992. Dichromats detect colour-camouflaged objects that are not detected by trichromats. Proc. R. Soc. Lond. B Biol. Sci. 248:291-295.
29. Murphy, W. J., E. Eizirik, W. E. Johnson, Y. P. Zhang, O. A. Ryder, and S. J. O'Brien. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
30. Nielsen, R., and Z. Yang. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936.
31. Oprian, D. D., A. B. Asenjo, N. Lee, and S. L. Pelletier. 1991. Design, chemical synthesis, and expression of genes for the three human color vision pigments. Biochemistry 30:11367-11372.
32. Palczewski, K., T. Kumasaka, and T. Hori. (12 co-authors). 2000. Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289:739-745.
33. Radlwimmer, F. B., and S. Yokoyama. 1997. Cloning and expression of the red visual pigment gene of goat (Capra hircus). Gene 198:211-215.
34. -. 1998. Genetic analyses of the green visual pigments of rabbit (Oryctolagus cuniculus) and rat (Rattus norvegicus). Gene 218:103-109.
35. Regan, B. C., C. Julliot, B. Simmen, F. Vienot, P. Charles-Dominique, and J. D. Mollon. 2001. Fruits, foliage and the evolution of primate colour vision. Philos. Trans. R. Soc. Lond. B Biol. Sci. 356:229-283.
36. Saitou, A., A. Mikami, Y. Ueno, S. Kawamura, K. A. Wiidayati, B. Suryobroto, Y. Mori, M. Teramoto, and T. Hasegawa. 2004. Advantage of dichromats over trichromats in discrimination of colour-camouflaged stimuli. Folia Primatol. 75:S186.
37. Shi, Y., and S. Yokoyama. 2003. Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates. Proc. Natl. Acad. Sci. USA 100:8308-8313.
38. Simunovic, M. P., B. C. Regan, and J. D. Mollon. 2001. Is color vision deficiency an advantage under scotopic conditions? Investig. Ophthalmol. Vis. Sci. 42:3357-3364.
39. Sun, H., J. P. Macke, and J. Nathans. 1997. Mechanisms of spectral tuning in the mouse green cone pigment. Proc. Natl. Acad. Sci. USA 94:8860-8865.
40. Surridge, A. K., D. Osorio, and N. I. Mundy. 2003. Evolution and selection of trichromatic vision in primates. Trends Ecol. Evol. 18:198-205.
41. Suzuki, Y., and T. Gojobori. 1999. A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16:1315-1328.
42. Suzuki, Y., T. Gojobori, and M. Nei. 2001. ADAPTSITE: detecting natural selection at single amino acid sites. Bioinformatics 17:660-661.
43. Suzuki, Y., and Nei. 2001. Reliabilities of parsimony-based and likelihood methods for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 18:2179-2185.
44. Suzuki, Y., and M. Nei. 2004. False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotrophic virus. Mol. Biol. Evol. 21:914-921.
45. Verhulst, S., and F. W. Maes. 1998. Scotopic vision in colour-blinds. Vision Res. 38:3387-3390.
46. Walls, G. L. 1942. The vertebrate eye and its adaptive dadiation. Hafher, New York.
47. Whitmore, A. V., and J. K. Bowmaker. 1989. Seasonal variation in cone sensitivity and short-wave absorbing visual pigments in the rudd Scadinius erythrophthalmus. J. Comp. Physiol. A Sens. Neural. Behav. Physiol. 166:103-115.
48. Winderickx, J., D. T. Lindsey, E. Sanocki, D. Y. Teller, A. G. Motulsky, and S. S. Deeb. 1992. Polymorphism in red photopigment underlies variation in color matching. Nature 356:431-433.
49. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
50. Yang, Z., and R. Nielsen. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:908-917.
51. Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acids. Genetics 155:431-449.
52. Yokoyama, S. 2000a. Molecular evolution of vertebrate visual pigments. Prog. Retin. Eye Res. 19:385-419.
53. -. 2000b. Phylogenetic analysis and experimental approaches to study color vision in vertebrates. Methods Enzymol. 315:312-325.
54. Yokoyama, S., and F. B. Radlwimmer. 1999. The molecular genetics of red and green color vision in mammals. Genetics 153:919-932.
55. -. 2001. The molecular genetics and evolution of red and green color vision in vertebrates. Genetics 158:1697-1710.
56. Yokoyama, S., F. B. Radlwimmer, and N. S. Blow. 2000. Molecular evolution of color vision of zebra finch. Gene 259:17-24.
57. Yokoyama, S., and N. Takenaka. 2004. The molecular basis of adaptive evolution of squirrelfish rhodopsins. Mol. Biol. Evol. 21:1-8.
58. Yokoyama, S., and R. Yokoyama. 1996. Adaptive evolution of photoreceptors and visual pigments in vertebrates. Annu. Rev. Ecol. Syst. 27:543-567.
59. Zhang, J. 2004. Frequent false detection of positive selection by the likelihood method with branch-site models. Mol. Biol. Evol. 21:1332-1339.
60. Zhang, J., and S. Kumar. 1997. Detection of convergent and parallel evolution at the amino acid sequence level. Mol. Biol. Evol. 14:527-536.