Molecular evolution of vertebrate visual pigments

Ali, 1974, Visual pigments: phylogeny and ecology, 481 Applebury, 1990, Insight into blindness, Nature, 343, 316, 10.1038/343316a0 Archer, 1996, Absorbance spectra and molecular structure of the blue-sensitive rod visual pigment in the conger eel (Conger conger), Proc. R. Soc. Lond. B., 263, 761, 10.1098/rspb.1996.0114 Archer, 1997, Opsin sequences of the rod visual pigments in two species of Poeciliid fish, J. Fish Biol., 51, 215, 10.1111/j.1095-8649.1997.tb02528.x Archer, 1996, The molecular basis for the blue-green sensitivity in the rod visual pigments of the European eel, Proc. R. Soc. Lond. B., 262, 289, 10.1098/rspb.1995.0208 Archer, 1992, Rod opsin cDNA sequence from the sand goby (Pomato schistus minutus) compared with those of other vertebrates, Proc. R. Soc. Lond. B., 248, 19, 10.1098/rspb.1992.0037 Arnold, 1987, Wavelength discrimination in the turtle, Pseudemys scripta elegans, Vision Res., 27, 1501, 10.1016/0042-6989(87)90159-3 Asenjo, 1994, Molecular determination of human red/green color discrimination, Neuron, 12, 1131, 10.1016/0896-6273(94)90320-4 Aschoff, 1981, Biological rhythms, Vol. 4 Avery, 1983, Ultraviolet sensitive receptors in a freshwater fish, J. Physiol., 334, 23 Batni, 1996, Characterization of the Xenopus rhodopsin gene, J. Biol. Chem., 271, 3179, 10.1074/jbc.271.6.3179 Beatty, 1966, A study of the succession of visual pigments in Pacific salmon (Oncorhyncus), Can J. Zool., 44, 429, 10.1139/z66-045 Beatty, 1975, Visual pigments of the American eel, Anguilla rostrata, Vision Res., 15, 771, 10.1016/0042-6989(75)90254-0 Beatty, 1984, Visual pigments and the labile scotopic visual system of fish, Vision Res., 24, 1563, 10.1016/0042-6989(84)90314-6 Bennett, 1996, Ultraviolet vision and mate choice in zebra finches, Nature, 380, 433, 10.1038/380433a0 Besharse, 1992, Light-evoked contraction of red absorbing cones in the Xenopus retina is maximally sensitive to green light, Vis. Neurosci., 8, 243, 10.1017/S0952523800002893 Besharse, 1988, Regulation of rhythmic photoreceptor metabolism: a role for post-receptoral neurons, Prog. Retinal Res., 7, 21, 10.1016/0278-4327(88)90004-1 Blackshaw, 1997, Parapinopsin, a novel catfish opsin localized to the parapineal organ, defines a new gene family, J. Neurosci., 17, 8083, 10.1523/JNEUROSCI.17-21-08083.1997 Bowmaker, 1977, The visual pigments, oil droplets and spectral sensitivity of the pigeon, Vision Res., 17, 1129, 10.1016/0042-6989(77)90147-X Bowmaker, 1991, Evolution of photoreceptors and visual pigments, 63 Bowmaker, 1988, Longwave-sensitive visual pigments in some deep sea fishes: segregation of paired rhodopsins and porphyropsins, J. Comp. Physiol. A, 163, 685, 10.1007/BF00603853 Bowmaker, 1980, Microspectrophotometric demonstration of four classes of photoreceptor in an old world primate, Macaca fascicularis, J. Physiol., 298, 131, 10.1113/jphysiol.1980.sp013071 Bowmaker, 1997, Visual pigments and oil droplets from six classes of photoreceptor in the retinas of birds, Vision Res., 37, 2183, 10.1016/S0042-6989(97)00026-6 Bowmaker, 1987, Polymorphism of photopigments in the squirrel monkey: a sixth phenotype, Proc. Roy. Soc. Lond. B., 231, 382, 10.1098/rspb.1987.0051 Bowmaker, 1977, The visual pigments and oil droplets of the chicken retina, Vision Res., 17, 755, 10.1016/0042-6989(77)90117-1 Bowmaker, 1987, Ultraviolet receptors, tetrachromatic colour vision and retinal mosaics in the brown trout (Salmo trutta): age-dependent changes, Vision Res., 27, 2102, 10.1016/0042-6989(87)90124-6 Bowmaker, 1991, Ultraviolet-sensitive cones in the goldfish, Vision Res., 31, 349, 10.1016/0042-6989(91)90087-L Bridges, 1959, The visual pigments of some common laboratory mammals, Nature, 184, 1727, 10.1038/1841727a0 Burkhardt, 1982, Birds, berries and UV. A note on some consequences of UV vision in birds, Naturwissenschaften, 69, 153, 10.1007/BF00364887 Burkhardt, 1989, UV vision: abird’s eye view of feathers, J. Comp. Physiol. A, 164, 787, 10.1007/BF00616750 Cahill, 1991, Rhythmic regulation of retinal melatonin: metabolic pathways, neurochemical mechanisms and the ocular circadian clock, Cell Mol. Neurobiol., 11, 529, 10.1007/BF00734814 Carulli, 1994, Phylogeny and physiology of Drosophila opsins, J. Mol. Evol., 38, 250, 10.1007/BF00176087 Chan, 1992, Introduction of hydroxyl-bearing amino acids causes bathochromic spectral shifts in rhodopsin: amino acid substitutions responsible for red-green color pigment spectral tuning, J. Biol. Chem., 267, 9478, 10.1016/S0021-9258(19)50115-6 Chen, 1996, Molecular cloning of a rhodopsin gene from salamander rods, Invest. Ophthalmol. Vis. Sci., 37, 1907 Chiu, 1994, Murine and bovine blue cone pigment genes: coning and characterization of two new members of the S family of visual pigments, Genomics, 21, 440, 10.1006/geno.1994.1292 Cloutier, 1996, Morphology, characters, and the interrelationships of basal Sacropterygians, 445 Cornwall, 1989, Membrane current responses of skate photoreceptors, J. Gen. Physiol., 94, 633, 10.1085/jgp.94.4.633 Cott, 1940 Cowman, 1986, An opsin gene expressed in only one photoreceptor cell type of the Drosophila eye, Cell, 44, 705, 10.1016/0092-8674(86)90836-6 Crescitelli, 1956, The nature of the gecko visual pigment, J. Gen. Physiol., 40, 217, 10.1085/jgp.40.2.217 Crescitelli, 1972, The visual cells and visual pigments of the vertebrate eye, Vol. VII/1, 245 Crescitelli, 1953, Human visual purple, Nature, 172, 195, 10.1038/172195a0 Crescitelli, 1954, A photosensitive pigment of the carp retina, J. Physiol., 125, 607, 10.1113/jphysiol.1954.sp005184 Cronin, 1982, Quantum efficiency and photosensitivity of the rhodopsin equilibrium metarhodopsin conversion in crayfish photoreceptors, Photochem. Photobiol., 36, 447, 10.1111/j.1751-1097.1982.tb04401.x Dartnall, 1972, Visual pigment of the coelacanth, Nature, 239, 341, 10.1038/239341a0 Dartnall, 1965, The spectral clustering of visual pigments, Vision Res., 5, 81, 10.1016/0042-6989(65)90057-X Das, 1999, Visual pigments and oil droplets in the retina of a passerine bird, the canary, Serinus canaria: microspectrophotometry and opsin sequences, Vision Res., 39, 2801, 10.1016/S0042-6989(99)00023-1 Doi, 1990, Role of the intradiscal domain in rhodopsin assembly and function, Proc. Natl. Acad. Sci. USA, 87, 4991, 10.1073/pnas.87.13.4991 Douglas, 1989, The spectral transmission of freshwater teleost ocular media—an interspecific comparison and a guide to potential ultraviolet sensitivity, Vision Res., 29, 871, 10.1016/0042-6989(89)90098-9 Douglas, 1999, Enhanced retinal longwave sensitivity using a chlorophyll-derived photosensitiser in Malacosteus niger, a deep-sea dragon fish with far red bioluminescence, Vision Res., 39, 2817, 10.1016/S0042-6989(98)00332-0 Douglas, 1998, The visual systems of deep-sea fish I-optics, tapeta, visual and lenticular pigmentation, Prog. Ret. Eye Res., 17, 597, 10.1016/S1350-9462(98)00002-0 Drummond-Borg, 1989, Molecular patterns of X chromosome-linked color vision genes among 134 men of European ancestry, Proc. Natl. Acad. Sci. USA, 86, 983, 10.1073/pnas.86.3.983 Dunlap, 1999, Molecular basis for circadian clocks, Cell, 96, 271, 10.1016/S0092-8674(00)80566-8 Emmerton, 1980, Wavelength discrimination in the “visible” and ultraviolet spectrum by pigeons, J. Comp. Physiol., 141, 47, 10.1007/BF00611877 Fasick, 1998, The visual pigments of the bottlenose dolphin (Tursiops truncatus), Vis. Neurosci., 15, 643, 10.1017/S0952523898154056 Fasick, 1999, Spectral tuning in the human blue cone pigment, Biochemistry, 38, 11593, 10.1021/bi991600h Fasick, 1998, Mechanism of spectral tuning in the dolphin visual pigments, Biochemistry, 37, 432, 10.1021/bi972500j Feiler, 1992, Ectopic expression of ultraviolet-rhodopsins in the blue photoreceptor cells of Drosophila: visual physiology and photochemistry of transgenic animals, J. Neurosci., 12, 3862, 10.1523/JNEUROSCI.12-10-03862.1992 Ferrari, 1993 Fitzgibbon, 1995, The rhodopsin-encoding gene of bony fish lacks introns, Gene, 164, 273, 10.1016/0378-1119(95)00458-I Fleishman, 1993, Ultraviolet vision in lizard, Nature, 365, 397, 10.1038/365397a0 Fricke, 1995, Yet more danger for coelacanths, Nature, 374, 314, 10.1038/374314a0 Fryxell, 1987, An opsin gene that is expressed only in the R7 photoreceptor cell of Drosophila, EMBO J., 6, 443, 10.1002/j.1460-2075.1987.tb04774.x Golding, 1998, The structural basis of molecular adaptation, Mol. Biol. Evol., 15, 355, 10.1093/oxfordjournals.molbev.a025932 Goldsmith, 1980, Hummingbirds see near UV light, Science, 207, 786, 10.1126/science.7352290 Goldsmith, 1984, The cone oil droplets of avian retinas, Vision Res., 24, 1661, 10.1016/0042-6989(84)90324-9 Hara, 1972, Cephalopod retinochrome, Vol. VII/1, 720 Hargrave, 1983, The structure of bovine rhodopsin, Biophys. Struct. Mech., 9, 235, 10.1007/BF00535659 Harosi, 1985, Ultraviolet- and violet-absorbing vertebrate visual pigments: dichromatic and bleaching properties, 41 Harosi, 1994, An analysis of two spectral properties of vertebrate visual pigments, Vision Res., 34, 1359, 10.1016/0042-6989(94)90134-1 Harosi, 1983, Ultraviolet visual pigment in a vertebrate: a tetrachromatic cone system in the dace, Science, 222, 1021, 10.1126/science.6648514 Harosi, 1993, Visual pigments in the sea lamprey, Petromyzon marinus, Vis. NeuroSci., 10, 711, 10.1017/S0952523800005411 Hart, 1998, Visual pigments, oil droplets and photoreceptor distribution in the European starling (Sturnus vulgaris), J. Exp. Biol., 201, 1433, 10.1242/jeb.201.9.1433 Hinton, 1973, Natural deception, 6 Hisatomi, 1991, Isolation and characterization of lamprey rhodopsin cDNA, Biochem. Biophys. Res. Commu., 174, 1125, 10.1016/0006-291X(91)91537-M Hisatomi, 1996, Molecular cloning and characterization of the putative ultraviolet-sensitive visual pigment of goldfish, Vision Res., 36, 933, 10.1016/0042-6989(95)00189-1 Ishida, 1999, Biological clocks, Proc. Natl. Acad. Sci. USA, 96, 8819, 10.1073/pnas.96.16.8819 Jacobs, 1981 Jacobs, 1992, Ultraviolet vision in vertebrates, Am. Zool., 342, 544, 10.1093/icb/32.4.544 Jacobs, 1993, The distribution and nature of colour vision among the mammals, Biol. Rev., 68, 413, 10.1111/j.1469-185X.1993.tb00738.x Jacobs, 1987, Polymorphism of the middle wavelength cone in two species of South American monkey: Cebus appela and Callicebus moloch, Vision Res., 27, 1263, 10.1016/0042-6989(87)90202-1 Jacobs, 1987, Inheritance of color vision in a New World monkey (Saimiri sciureus), Proc. Natl. Acad. Sci. USA, 84, 2545, 10.1073/pnas.84.8.2545 Jacobs, 1987, Color vision polymorphism and its photopigment basis in a callitrichid monkey (Saguinus fuscicollis), Vision Res., 27, 2089, 10.1016/0042-6989(87)90123-4 Jacobs, 1991, Retinal receptors in rodents maximally sensitive to ultraviolet light, Nature, 353, 655, 10.1038/353655a0 Jacobs, 1996, Trichromatic color vision in New World monkeys, Nature, 382, 156, 10.1038/382156a0 Jacobs, 1993, Genetic basis of polymorphism in the color vision of platyrrhine monkeys, Vision Res, 33, 269, 10.1016/0042-6989(93)90083-9 Jerlov, 1976 Johnson, 1993, Cloning and expression of goldfish opsin sequences, Biochemistry, 32, 208, 10.1021/bi00052a027 Jorgensen, 1990, Molecular genetics of X chromosome-linked color vision among populations of African and Japanese ancestry: high frequency of a shortened red pigment gene among Afro-Americans, Proc. Natl. Acad. Sci. USA, 87, 6512, 10.1073/pnas.87.17.6512 Kawamura, 1999, Genetic analyses of visual pigments of the pigeon (Columba livia), Genetics, 153, 1839, 10.1093/genetics/153.4.1839 Kawamura, 1994, Cloning of the rhodopsin-encoding gene from the rod-less lizard Anolis carolinensis, Gene, 149, 267, 10.1016/0378-1119(94)90159-7 Kawamura, 1996, Molecular characterization of the pigeon P-opsin gene, Gene, 182, 1213, 10.1016/S0378-1119(96)00476-3 Kawamura, 1996, Phylogenetic relationships among short wavelength-sensitive opsins of American chameleon (Anolis carolinensis) and other vertebrates, Vision Res., 36, 2797, 10.1016/0042-6989(96)00034-X Kawamura, 1997, Expression of visual and nonvisual opsins in American chameleon, Vision Res., 37, 1867, 10.1016/S0042-6989(96)00309-4 Kawamura, 1998, Functional characterization of visual and nonvisual pigments of American chameleon (Anolis carolinensis), Vision Res., 38, 37, 10.1016/S0042-6989(97)00160-0 Kayada, 1995, Cloning and expression of frog rhodopsin cDNA, Comp. Biochem. Physiol., 110B, 599, 10.1016/0305-0491(94)00179-X Kitamoto, 1998, Two visual pigments in a single photoreceptor cell: identification and histological localization of three mRNAs encoding visual pigment opsins in the retina of the butterfly Papilio xuthus, J. Exp. Biol., 201, 1255, 10.1242/jeb.201.9.1255 Kleinschmidt, 1992, Anion sensitivity and spectral tuning of cone visual pigments in situ, Proc. Natl. Acad. Sci. USA, 89, 9181, 10.1073/pnas.89.19.9181 Knowles, 1977, Habitat, habit and visual pigments, Vol. 2B, 103 Kojima, 1992, Cone visual pigments are present in gecko rod cells, Proc. Natl. Acad. Sci. USA, 89, 6841, 10.1073/pnas.89.15.6841 Kojima, 1996, Molecular properties of chimerical mutants of gecko blue and bovine rhodopsin, Biochemistry, 35, 2625, 10.1021/bi9511548 Koller, 1965 Levine, 1982, Color vision in fishes, Sci. Amer., 246, 108, 10.1038/scientificamerican0282-140 Lin, 1998, Mechanisms of spectral tuning in blue cone visual pigments: visible and raman spectroscopy of blue-shifted rhodopsin mutants, J. Biol. Chem., 273, 24583, 10.1074/jbc.273.38.24583 Locket, 1973, Retinal structure in Latimeria chalumnae, Phil. Trans. R. Soc. Lond. B., 266, 493, 10.1098/rstb.1973.0054 Locket, 1977, Adaptations to the deep-sea environment, Vol. VII/5, 67 Locket, 1980, Some advances in coelacanth biology, Proc. R. Soc. Lond. B., 208, 265, 10.1098/rspb.1980.0052 Loew, 1978, The ecology of cone pigments in teleost fishes, Vision Res., 18, 715, 10.1016/0042-6989(78)90150-5 Lythgoe, 1972, The adaptation of visual pigments to their photic environment, Vol. VII/1, 566 Lythgoe, 1979 Lythgoe, 1984, Visual pigments and environmental light, Vision Res., 24, 1539, 10.1016/S0042-6989(84)80003-6 Maisey, 1996 Marshall, 1954 Marshall, 1971 Max, 1995, Pineal opsin: a nonvisual opsin expressed in chick pineal, Science, 267, 1502, 10.1126/science.7878470 Mcfarland, 1971, Cetacean visual pigments, Vision Res., 11, 1065, 10.1016/0042-6989(71)90113-1 Meijer, 1989, Neurophysiology of the suprachiasmatic circadian pacemaker in rodents, Physiol. Rev., 69, 671, 10.1152/physrev.1989.69.3.671 Menzel, 1991, Colour vision in insects, 262 Merbs, 1992, Absorption spectra of human cone pigments, Nature, 356, 433, 10.1038/356433a0 Merbs, 1992, Absorption spectra of the hybrid pigments responsible for anomalous color vision, Science, 258, 464, 10.1126/science.1411542 Mollon, 1991, The uses and evolutionary origins of primate color vision, 306 Mollon, 1984, Variations of color vision in a New World primate can be explained by a polymorphism of retinal photopigments, Proc. R. Soc. Lond. B., 222, 373, 10.1098/rspb.1984.0071 Montell, 1987, A second opsin gene expressed in the ultraviolet-sensitive R7 photoreceptor cells of Drosophila melanogaster, J. Neurosci., 7, 1558, 10.1523/JNEUROSCI.07-05-01558.1987 Naito, 1981, Photoreactions of cephalopod rhodopsin, Vision Res., 21, 935, 10.1016/0042-6989(81)90195-4 Nakayama, 1991, Mapping of the amino acids in membrane-embedded helices that interact with the retinal chromophore in bovine rhodopsin, J. Biol. Chem., 266, 4269, 10.1016/S0021-9258(20)64317-4 Nathans, 1990, Determinations of visual pigment absorbance: role of charged amino acids in the putative transmembrane segments, Biochemistry, 29, 937, 10.1021/bi00456a013 Nathans, 1990, Determinants of visual pigment absorbance: identification of the retinylidene Schiff’s base counterion in bovine rhodopsin, Biochemistry, 29, 9746, 10.1021/bi00493a034 Nathans, 1999, The evolution and physiology of human color vision: Insights from molecular genetic studies of visual pigments, Neuron, 24, 299, 10.1016/S0896-6273(00)80845-4 Nathans, 1983, Isolation, sequence analysis, and intron-exon arrangement of the gene encoding bovine rhodopsin, Cell, 34, 807, 10.1016/0092-8674(83)90537-8 Nathans, 1984, Isolation and nucleotide sequence of the gene encoding human rhodopsin, Proc. Natl. Acad. Sci. USA, 81, 4851, 10.1073/pnas.81.15.4851 Nathans, 1986, Molecular genetics of human color vision: The genes encoding blue, green, and red pigments, Science, 232, 193, 10.1126/science.2937147 Nathans, 1986, Molecular genetics of inherited variation in human color vision, Science, 232, 203, 10.1126/science.3485310 Nei, 1997, Color vision of ancestral organisms of higher primates, Mol. Biol. Evol., 14, 611, 10.1093/oxfordjournals.molbev.a025800 Neitz, 1984, Electroretinogram measurements of cone spectral sensitivity in dichromatic monkeys, J. Opt. Soc. Am. A, 1, 1175, 10.1364/JOSAA.1.001175 Neitz, 1989, Analysis of fusion gene and encoded photopigment of colour-blind human, Nature, 342, 679, 10.1038/342679a0 Neitz, 1996, Visual pigment gene structure and the severity of color vision defects, Science, 274, 801, 10.1126/science.274.5288.801 Neitz, 1995, Numbers and ratios of visual pigment genes for normal red-green color vision, Science, 267, 1013, 10.1126/science.7863325 Neitz, 1995, Polymorphism in the numbers of genes encoding long-wavelength-sensitive cone pigments among males with normal color vision, Vision Res., 35, 2395, 10.1016/0042-6989(95)00008-9 Neitz, 1991, Spectral tuning of pigments underlying red-green color vision, Science, 252, 971, 10.1126/science.1903559 Ohno, 1970 Okano, 1992, Primary structures of chicken cone visual pigments; Vertebrate rhodopsins have evolved out of cone visual pigments, Proc. Natl. Acad. Sci. USA, 89, 5932, 10.1073/pnas.89.13.5932 Okano, 1994, Pinopsin is a chicken pineal photoreceptive molecule, Nature, 372, 94, 10.1038/372094a0 Oprian, 1991, Design, chemical synthesis, and expression of genes for the three human color vision pigments, Biochemistry, 30, 11367, 10.1021/bi00112a002 Oprian, 1987, Expression of a synthetic bovine rhodopsin gene in monkey kidney cells, Proc. Natl. Acad. Sci. USA, 84, 8874, 10.1073/pnas.84.24.8874 O’Tousa, 1995, The Drosophila melanogaster nina E gene encodes an opsin, Cell, 40, 839, 10.1016/0092-8674(85)90343-5 Palacios, 1998, Spectral sensitivity of cones in the goldfish, Carassius auratus, Vision Res., 38, 2135, 10.1016/S0042-6989(97)00411-2 Partridge, 1988, Visual pigments in the individual rods of deep-sea fish, J. Comp. Physiol. A, 162, 543, 10.1007/BF00612519 Partridge, 1995, Far-red sensitivity of dragon fish, Nature, 375, 21, 10.1038/375021a0 Partridge, 1989, Interspecific variation in the visual pigments of deep-sea fishes, J. Comp. Physiol. A, 164, 513, 10.1007/BF00610445 Perry, 1991, Response properties of cones from the retina of the tiger salamander, J. Physiol., 433, 561, 10.1113/jphysiol.1991.sp018444 Phillips, 1992, Rhodopsin/transducin interactions. I: characterization of the binding of the transducin-βγ subunit complex to rhodopsin using fluorescence spectrophotoscopy, J. Biol. Chem., 267, 17032, 10.1016/S0021-9258(18)41888-1 Pittler, 1992, Primary structure of frog rhodopsin (Rana pipiens), FEBS Lett., 313, 103, 10.1016/0014-5793(92)81422-I Pollock, 1988, Transcript localization of four opsin genes in the three visual organs of Drosophila; RH2 is ocellus specific, Nature, 333, 779, 10.1038/333779a0 Provencio, 1993, Vitamin A2-based photopigments within the pineal gland of a fully terrestrial vertebrate, Neurosci. Lett., 155, 223, 10.1016/0304-3940(93)90713-U Provencio, 1992, Vitamin A2-based visual pigments in fully terrestrial vertebrates, Vision Res., 32, 2201, 10.1016/0042-6989(92)90084-V Pu, 1981, Anatomical and physiological characteristics of pineal photoreceptor cell in the larval lamprey, Petomyzon marinus, J. Neurophysiol., 46, 1018, 10.1152/jn.1981.46.5.1018 Radlwimmer, 1997, Cloning and expression of the red visual pigment gene of goat (Capra hircus), Gene, 198, 211, 10.1016/S0378-1119(97)00316-8 Radlwimmer, 1998, Genetic analyses of the green visual pigments of rabbit (Oryctolagus cuniculus) and rat (Rattus norvegicus), Gene, 218, 103, 10.1016/S0378-1119(98)00359-X Register, 1994, Multiple origins of the green-sensitive opsin genes in fish, J. Mol. Evol., 39, 268, 10.1007/BF00160150 Robinson, 1993, Zebrafish ultraviolet visual pigment: absorption spectrum, sequence, and localization, Proc. Natl. Acad. Sci. USA, 90, 6009, 10.1073/pnas.90.13.6009 Saitou, 1987, The neighbor-joining method: a new method for estimating phylogenetic trees, Mol. Biol. Evol., 4, 406 Sakamoto, 1996, Two opsins from the compound eye of the crab Hemigrapsus sanguineus, J. Exp. Biol., 199, 441, 10.1242/jeb.199.2.441 Sakmar, 1996, Properties and photoactivity of rhodopsin mutants, Israel J. Chem., 35, 325, 10.1002/ijch.199500034 Sakmar, 1989, Glutamic acid-113 serves as the retinylidene Schiff base counterion in bovine rhodopsin, Proc. Natl. Acad. Sci. USA, 86, 8013, 10.1073/pnas.86.21.8309 Schliewen, 1993, Which home for the coelacanth?, Nature, 363, 405, 10.1038/363405a0 Schwanzara, 1967, The visual pigments of freshwater fishes, Vision Res., 7, 121, 10.1016/0042-6989(67)90079-X Smith, 1993, Opsin from the lateral eyes and ocelli of the horseshoe crab, Limulus polyphemus, Proc. Natl. Acad. Sci. USA, 90, 6150, 10.1073/pnas.90.13.6150 Solessio, 1993, Antagonistic chromatic mechanisms in photoreceptors of the parietal eye of lizards, Nature, 364, 442, 10.1038/364442a0 Somiya, 1982, Yellow lens eyes of a stomiatoid deep-sea fish, Malacosteus niger, Proc. Roy. Soc. Lond. B., 215, 4812, 10.1098/rspb.1982.0055 Soni, 1997, A novel and ancient vertebrate opsin, FEBS Lett., 406, 279, 10.1016/S0014-5793(97)00287-1 Starace, 1998, Cloning and expression of a Xenopus short wavelength cone pigment, Exp. Eye Res., 67, 209, 10.1006/exer.1998.0507 Stavenga, 1973, Rhodopsin processes and the function of the pupil mechanism in flies., 175 Strader, 1994, Structure and function of G protein-coupled receptors, Ann. Rev. Biochem., 63, 101, 10.1146/annurev.bi.63.070194.000533 Sun, 1997, Mechanisms of spectral tuning in the mouse green cone pigment, Proc. Natl. Acad. Sci. USA, 94, 8860, 10.1073/pnas.94.16.8860 Takahashi, 1989, The avian pineal, a vertebrate model system of the circadian oscillator: cellular regulation of circadian rhythms by light, second messengers and macromolecular synthesis, Rec. Prog. Horm. Res., 45, 279 Tan, 1999, Trichromatic vision in prosimians, Nature, 402, 36, 10.1038/46947 Thresher, 1998, Role of mouse cryptochrome blue-light photoreceptor in circadian photoresponses, Science, 282, 1490, 10.1126/science.282.5393.1490 Thompson, 1991 Tosini, 1996, Circadian rhythms in cultured mammalian retina, Science, 272, 419, 10.1126/science.272.5260.419 Townson, 1998, Honeybee blue- and ultraviolet-sensitive opsins: cloning, heterologous expression in Drosophila, and physiological characterization, J. Neurosci., 18, 2412, 10.1523/JNEUROSCI.18-07-02412.1998 Travis, 1988, Polymorphism of visual pigments in a callitrichid monkey, Vision Res., 28, 481, 10.1016/0042-6989(88)90170-8 Underwood, 1970, The eye, 1 Van Der Horst, 1999, Mammalian Cry1 and Cry2 are essential for maintenance of circadian rhythms, Nature, 398, 627, 10.1038/19323 Viitala, 1995, Attraction of kestrels to vole scent marks visible in ultraviolet light, Nature, 373, 425, 10.1038/373425a0 Wald, 1935, Carotenoids and the visual cycle, J. Gen. Physiol., 19, 351, 10.1085/jgp.19.2.351 Wald, 1955, The photoreceptor process in vision, Am. J. Ophthalmol., 40, 18, 10.1016/0002-9394(55)91835-3 Walls, 1934, The reptilian retina, Amer. J. Ophthalmol, 17, 892, 10.1016/S0002-9394(34)93309-2 Walls, 1942 Weitz, 1993, Rhodopsin activation: effect of the metarhodopsin I-metarhodopsin II equilibrium of neutralization or introduction of charged amino acids within putative transmembrane segments, Biochemistry, 32, 14176, 10.1021/bi00214a016 Whitmore, 1989, Seasonal variation in cone sensitivity and short-wave absorbing visual pigments in the rudd Scadinius erythrophythalmus., J. Comp. Physiol. A, 166, 103, 10.1007/BF00190215 Wickler, 1968 Wilkie, 1998, The molecular basis for UV vision in birds: spectral characteristics, cDNA sequence and retinal localization of the UV-sensitive visual pigment of the budgerigar (Melopsittacus undulatus), Biochem. J., 15, 541, 10.1042/bj3300541 Yokoyama, 1995, Rhodopsin from the fish, Astyanax: Role of tyrosine 261 in the red shift, Invest. Ophthalmol. Visual Sci., 36, 939 Yokoyama, 1990, Convergent evolution of the red- and green-like visual pigment genes in fish, Astyanax, and human, Proc. Natl. Acad. Sci. USA, 87, 9315, 10.1073/pnas.87.23.9315 Yokoyama, 1994, Gene duplications and evolution of the short wavelength-sensitive visual pigments in vertebrates, Mol. Biol. Evol., 11, 32 Yokoyama, 1995, Amino acid replacements and wavelength absorption of visual pigments in vertebrates, Mol. Biol. Evol., 12, 53, 10.1093/oxfordjournals.molbev.a040190 Yokoyama, 1997, Molecular genetic basis of adaptive selection: examples from color vision invertebrates, Ann. Rev. Genet., 31, 315, 10.1146/annurev.genet.31.1.315 Yokoyama, S. (2000a) Color vision of the coelacanth (Latimeria chalumnae) and adaptive evolution of rhodopsin (RH1 and rhodopsin-like (RH2) pigments. J. Heredity (in press) Yokoyama, S. (2000b) Molecular bases of color vision in vertebrates. Genes Genet. Syst. (in press) Yokoyama, 2000, Phylogenetic analysis and experimental approaches to study color vision in vertebrates, 315, 312 Yokoyama, 1999, The molecular genetics of red and green color vision in mammals, Genetics, 153, 919, 10.1093/genetics/153.2.919 Yokoyama, S., Radlwimmer, F. B. and Blow, N. S. (2000) Ultraviolet pigments of birds evolved from violet pigments by a single amino acid change. Proc. Natl. Acad. Sci. USA (submitted) Yokoyama, 1998, Regeneration of ultraviolet pigments of vertebrates, FEBS Lett., 423, 155, 10.1016/S0014-5793(98)00086-6 Yokoyama, 1996, Evolution of the G-protein-coupled receptor superfamily, 93 Yokoyama, 1993, Paralogous origin of the red- and green-sensitive visual pigment genes in vertebrates, Mol. Biol. Evol., 10, 527 Yokoyama, 1989, Molecular evolution of human visual pigment genes, Mol. Biol. Evol., 6, 186 Yokoyama, 1996, Adaptive evolution of photoreceptors and visual pigments in vertebrates, Annu. Rev. Ecol. Syst., 27, 543, 10.1146/annurev.ecolsys.27.1.543 Yokoyama, 2000, Comparative molecular biology of visual pigments, 10.1016/S1383-8121(00)80009-3 Yokoyama, 1997, Cloning and characterization of the pineal gland-specific opsin gene of marine lamprey (Petromyzon marinus), Gene, 202, 89, 10.1016/S0378-1119(97)00458-7 Yokoyama, 1999, Adaptive evolution of color vision of the Comoran coelacanth (Latimeria chalumnae), Proc. Natl. Acad. Sci. USA, 96, 6279, 10.1073/pnas.96.11.6279 Zhang, 1997, Molecular evolution of the rhodopsin gene of marine lamprey, Petromyzon marinus, Gene, 191, 1, 10.1016/S0378-1119(96)00864-5 Zhao, 1997, Molecular cloning and localization of rhodopsin kinase in the mammalian pineal, Vis. Neurosci., 14, 225, 10.1017/S0952523800011366 Zhukovsky, 1989, Effect of carboxylic acid side chains on the absorption maximum of visual pigments, Science, 246, 928, 10.1126/science.2573154 Zuker, 1985, Isolation and structure of a rhodopsin gene from D. melanogaster, Cell, 40, 851, 10.1016/0092-8674(85)90344-7 Zuker, 1987, A rhodopsin gene expressed in photoreceptor cell R7 of the Drosophila eye: homologies with other signal-transducing molecules, J. Neurosci., 7, 1550, 10.1523/JNEUROSCI.07-05-01550.1987