Salmonid opsin sequences undergo positive selection and indicate an alternate evolutionary relationship in Oncorhynchus

Journal of Molecular Evolution

Volumn 58, Issue 4, 2004, Pages 400-412

  Dann, Stephen G ^a   Allison, W Ted ^a   Levin, David B ^a   Taylor, John S ^a   Hawryshyn, Craig W ^a  

^a UNIVERSITY OF VICTORIA   (Canada)

Author keywords

Color vision; Opsin evolution; Salmon; Teleost; Trout; Visual pigments

Indexed keywords

OPSIN;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; GENE; GENE SEQUENCE; LWS GENE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; ONCORHYNCHUS; RH1 GENE; RH2 GENE; SALMON; SALMONID; SPECIES DIFFERENCE; STATISTICAL ANALYSIS; SWS1 GENE; SWS2 GENE;

ANIMALS; BASE SEQUENCE; CLONING, MOLECULAR; DNA PRIMERS; DNA, COMPLEMENTARY; EVOLUTION, MOLECULAR; ONCORHYNCHUS MYKISS; OPSIN; PHYLOGENY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SELECTION (GENETICS);

ANIMALIA; CICHLIDAE; ONCORHYNCHUS; SALMO SALAR; SALMONIDAE; TELEOSTEI;

EID: 14744287110     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-2562-y     Document Type: Article

References (79)

1. Alexander G, Sweeting R, McKeown B (1994) The shift in visual pigment dominance in the retinae of juvenile coho salmon (Oncorhynchus kisutch): An indicator of smolt status. J Exp Biol 195:185-197
2. Ali MA, Wagner HJ (1974) Visual pigments: Phylogeny and ecology. In: Ali MA (ed) Vision in fishes: New approaches. Plenum Press, New York
3. Allen DM, Macfarland W, Munz FW, Poston HA (1973) Changes in the visual pigments of trout. Can J Zool 51:901-914
4. Allison WT, Dann SG, Helvik JV, Bradley C, Moyer HD, Hawryshyn CW (2003) Ontogeny of ultraviolet-sensitive cones in the retina of rainbow trout (Oncorhynchus mykiss). J Comp Neurol 461:294-306
5. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
6. Beatty DD (1984) Visual pigments and the labile scotopic visual system of fish. Vision Res 24:1563-1573
7. Beaudet L, Novales Flamarique I, Hawryshyn CW (1997) Cone photoreceptor topography in the retina of sexually mature Pacific salmonid fishes. J Comp Neurol 383:49-59
8. Bowmaker JK (1998) Evolution of colour vision in vertebrates. Eye 12:541-547
9. Browman HI, Hawryshyn CW (1992) Thyroxine induces a precocial loss of ultraviolet photosensitivity in rainbow trout (Oncorhynchus mykiss, Teleostei). Vision Res 32:2303-2312
10. Carleton KL, Kocher TD (2001) Cone opsin genes of african cichlid fishes: Tuning spectral sensitivity by differential gene expression. Mol Biol Evol 18:1540-1550
11. Carleton KL, Harosi FI, Kocher TD (2000) Visual pigments of African cichlid fishes: Evidence for ultraviolet vision from microspectrophotometry and DNA sequences. Vision Res 40:879-890
12. Chang BS, Crandall KA, Carulli JP, Hartl DL (1995) Opsin phylogeny and evolution: A model for blue shifts in wavelength regulation. Mol Phylogenet Evol 4:31-43
13. Chinen A, Hamaoka T, Yamada Y, Kawamura S (2003) Gene duplication and spectral diversification of cone visual pigments of zebrafish. Genetics 163:663-675
14. Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162:156-159
15. Clarke WC, Groot C, Margolis L (1995) Physiological ecology of Pacific salmon. University of British Columbia Press, Vancouver, p 510
16. Cowing JA, Poopalasundaram S, Wilkie SE, Bowmaker JK, Hunt DM (2002a) Spectral tuning and evolution of short wave-sensitive cone pigments in cottoid fish from Lake Baikal. Biochemistry 41:6019-6025
17. Cowing JA, Poopalasundaram S, Wilkie SE, Robinson PR, Bowmaker JK, Hunt DM (2002b) The molecular mechanism for the spectral shifts between vertebrate ultraviolet- and violet-sensitive cone visual pigments. Biochem J 367:129-135
18. Creevey CJ, McInerney JO (2002) An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences. Gene 300:43-51
19. de Gaudemar B (1998) Sexual selection and breeding patterns: Insights from salmonids (salmonidae). Acta Biotheor 46:235-251
20. Deutschlander ME, Greaves DK, Haimberger TJ, Hawryshyn CW (2001) Functional mapping of ultraviolet photosensitivity during metamorphic transitions in a salmonid fish, Oncorhynchus mykiss. J Exp Biol 204:2401-2413
21. Dopazo J (1994) Estimating errors and confidence intervals for branch lengths in phylogenetic trees by a bootstrap approach. J Mol Evol 38:300-304
22. Fasick JI, Robsinson PR (1998) Mechanism of spectral tuning in the dolphin visual pigments. Biochemistry 37:433-438
23. Foote CJ, Brown GS, Hawryshyn CW (2004) Female colour and male choice in sockeye salmon: Can a pre-existing bias explain convergent evolution between anadromous and non-anadromous morphs. Anim Behav (in press)
24. Groot C, Margolis L (1991) Pacific salmon life histories. University of British Columbia Press, Vancouver, p 564
25. Hawryshyn CW (2000) Ultraviolet polarization vision in fishes: Possible mechanisms for coding e-vector. Philos Trans R Soc Lond B Biol Sci 355:1187-1190
26. Hawryshyn CW, Harosi FI (1994) Spectral characteristics of visual pigments in rainbow trout (Oncorhynchus mykiss). Vision Res 34:1385-1392
27. Hawryshyn CW, Haimberger TJ, Deutschlander ME (2001) Microspectrophotometric measurements of vertebrate photoreceptors using CCD-based detection technology. J Exp Biol 204:2431-2438
28. Hawryshyn CW, Martens G, Allison WT, Anholt BR (2003) Regeneration of ultraviolet-sensitive cones in the retinal cone mosaic of thyroxin-challenged post-juvenile rainbow trout (Oncorhynchus mykiss). J Exp Biol 206:2665-2673
29. Helvik JV, Drivenes O, Naess TH, Fjose A, Seo HC (2001) Molecular cloning and characterization of five opsin genes from the marine flatfish Atlantic halibut (Hippoglossus hippoglossus). Vis Neurosci 18:767-780
30. Hisatomi O, Kayada S, Aoki Y, Iwasa T, Tokunaga F (1994) Phylogenetic relationships among vertebrate visual pigments. Vision Res 34:3097-3102
31. Johnson RL, Grant KB, Zankel TC, Boehm MF, Merbs SL, Nathans J, Nakanishi K (1993) Cloning and expression of goldfish opsin sequences. Biochemistry 32:208-214
32. Kamermans M, van Dijk BW, Spekreijse H (1991) Color opponency in cone-driven horizontal cells in carp retina. A specific pathway between cones and horizontal cells. J Gen Physiol 97:819-843
33. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245
34. Levine JS, MacNichol EF (1979) Visual pigments in teleost fishes: effects of habitat, microhabitat and behaviour on visual system evolution. Sens Processes 3:95-130
35. Lipkin VM, Obukhov AN (2000) Structure and mechanisms of function of visual system proteins. Membr Cell Biol 13:165-193
36. Ma JX, Kono M, Xu L, Das J, Ryan JC, Hazard 3rd ES, Oprian DD, Crouch RK (2001) Salamander UV cone pigment: Sequence, expression, and spectral properties. Vis Neurosci 18:393-399
37. McDonald CG, Hawryshyn CW (1999) Latencies and discharge patterns of color-opponent neurons in the rainbow trout optic tectum. Vision Res 39:2195-2799
38. Merbs SL, Nathans J (1992) Absorption spectra of human cone pigments. Nature 356:433-435
39. Meyer A, Kocher TD, Basasibwaki P, Wilson AC (1990) Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences. Nature 347:550-553
40. Munz FW, Beatty DD (1965) A critical analysis of the visual pigments of salmon and trout. Vision Res 5:1-17
41. Murata S, Takasaki N, Saitoh M, Okada N (1993) Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proc Natl Acad Sci USA 90:6995-6999
42. Murata S, Takasaki N, Saitoh M, Tachida H, Okada N (1996) Details of retropositional genome dynamics that provide a rationale for a generic division: the distinct branching of all the pacific salmon and trout (Oncorhynchus) from the Atlantic salmon and trout (Salmo). Genetics 142:915-926
43. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418-426
44. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York
45. Novales Flamarique I, Hawryshyn CW (1993) Spectral characteristics of salmonid migratory routes from southern Vancouver-Island (British Columbia). Can J Fish Aqu Sci 50:1706-1716
46. Novales Flamarique I, Hawryshyn CW (1997) Is the use of underwater polarized light by fish restricted to crepuscular time periods? Vision Res 37:975-989
47. Novales Flamarique I, Hendry A, Hawryshyn CW (1992) The photic environment of a salmonid nursery lake. J Exp Biol 169:121-141
48. Oakley TH, Phillips RB (1999) Phylogeny of salmonine fishes based on growth hormone introns: Atlantic (Salmo) and Pacific (Oncorhynchus) salmon are not sister taxa. Mol Phylogenet Evol 11:381-393
49. Olsen RE, Mortensen A (1997) The influence of dietary astaxanthin and temperature on flesh colour in Arctic charr Salvelinus alpinus L. Aquat Res 28:51-58
50. Osinov AG, Lebedev VS (2000) Genetic divergence and phylogeny of the Salmoninae based on allozyme data. J Fish Biol 57:354-381
51. Palacios AG, Varela FJ, Srivastava R, Goldsmith TH (1998) Spectral sensitivity of cones in the goldfish, Carassius auratus. Vision Res 38:2135-2146
52. Parkyn DC, Hawryshyn CW (2000) Spectral and ultraviolet-polarisation sensitivity in juvenile salmonids: A comparative analysis using electrophysiology. J Exp Biol 203:1173-1191
53. Philp AR, Bellingham J, Garcia-Fernandez J, Foster RG (2000) A novel rod-like opsin isolated from the extra-retinal photoreceptors of teleost fish. FEBS Lett 468:181-188
54. Rzhetsky A, Nei M (1993) Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 10:1073-1095
55. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
56. Seehausen O, Mayhew PJ, Van Alphen JJM (1999a) Evolution of colour patterns in East African cichlid fish. J Evol Biol 12:514-534
57. Seehausen O, Van Alpen JJM, Witte F (1999b) Can ancient colour polymorphisms explain why some cichlid lineages speciate rapidly under disruptive sexual selection? Belgian J Zool 129:43-60
58. Seehausen O, van Alphen JJM (1998) The effect of male coloration on female mate choice in closely related Lake Victoria cichlids (Haplochromis nyererei complex). Behav Ecol Sociobiol 42:1-8
59. Seehausen O, van Alphen JJM, Lande R (1999c) Color polymorphism and sex ratio distortion in a cichlid fish as an incipient stage in sympatric speciation by sexual selection. Ecol Lett 2:367-378
60. Shedlock AM, Parker JD, Crispin DA, Pietsch TW, Burmer GC (1992) Evolution of the salmonid mitochondrial control region. Mol Phylogenet Evol 1:179-192
61. Staley KB, Ewing RD (1992) Purine levels in the skin of juvenile coho salmon (Oncorhynchus kisutch) during parr-smolt transformation and adaptation to seawater. Comp Biochem Physiol B 101:447-452
62. Stell WK, Lightfood DO, Wheeler TG, Leeper HF (1975) Goldfish retina: functional polarization of cone horizontal cell dendrites and synapses. Science 190:989-990
63. Steven DM (1947) Carotenoid pigmentation in trout. Nature 160:540-541
64. Sugawara T, Terai Y, Okada N (2002) Natural selection of the rhodopsin gene during the adaptive radiation of East African Great Lakes cichlid fishes. Mol Biol Evol 19:1807-1811
65. Terai Y, Mayer WE, Klein J, Tichy H, Okada N (2002) The effect of selection on a long wavelength-sensitive (LWS) opsin gene of Lake Victoria cichlid fishes. Proc Natl Acad Sci USA 99:15501-15506
66. Twig G, Levy H, Perlman I (2003) Color opponency in horizontal cells of the vertebrate retina. Prog Retin Eye Res 22:31-68
67. Vihtelic TS, Doro CJ, Hyde DR (1999) Cloning and characterization of six zebrafish photoreceptor opsin cDNAs and immunolocalization of their corresponding proteins. Vis Neurosci 16:571-555
68. Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17:32-43
69. Yokoyama S (1996) Molecular evolution of retinal and nonretinal opsins. Genes Cells 1:787-794
70. Yokoyama S (2000a) Color vision of the coelacanth (Latimeria chalumnae) and adaptive evolution of rhodopsin (RH1) and rhodopsin-like (RH2) pigments. J Hered 91:215-220
71. Yokoyama S (2000b) Molecular evolution of vertebrate visual pigments. Prog Retin Eye Res 19:385-419
72. Yokoyama S (2000c) Phylogenetic analysis and experimental approaches to study color vision in vertebrates. Methods Enzymol 315:312-325
73. Yokoyama S, Blow NS, Radlwimmer FB (2000) Molecular evolution of color vision of zebra finch. Gene 259:17-24
74. Yokoyama S, Radlwimmer FB (1999) The molecular genetics of red and green color vision in mammals. Genetics 153:919-932
75. Yokoyama S, Radlwimmer FB (2001) The molecular genetics and evolution of red and green color vision in vertebrates. Genetics 158:1697-1710
76. Yokoyama S, Shi Y (2000) Genetics and evolution of ultraviolet vision in vertebrates. FEBS Lett 486:167-172
77. Yokoyama S, Tada T (2000) Adaptive evolution of the African and Indonesian coelacanths to deep-sea environments. Gene 261:35-42
78. Yokoyama S, Tada T (2003) The spectral tuning in the short wavelength-sensitive type 2 pigments. Gene 306:91-98
79. Yokoyama S, Zhang H, Radlwimmer FB, Blow NS (1999) Adaptive evolution of color vision of the Comoran coelacanth (Latimeria chalumnae). Proc Natl Acad Sci 96:6279-6284