Rhodopsin molecular evolution in mammals inhabiting low light environments

PLoS ONE

Volumn 4, Issue 12, 2009, Pages

  Zhao, Huabin ^a   Ru, Binghua ^a   Teeling, Emma C ^b   Faulkes, Christopher G ^c   Zhang, Shuyi ^a   Rossiter, Stephen J ^c  

^a EAST CHINA NORMAL UNIVERSITY   (China)

^b UNIVERSITY COLLEGE DUBLIN   (Ireland)

^c QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

RHODOPSIN;

ANIMAL TISSUE; ARTICLE; BAT; CONTROLLED STUDY; ECHOLOCATION; ENVIRONMENTAL FACTOR; GENE SEQUENCE; LIGHT; MOLECULAR EVOLUTION; MONOPHYLY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHOTOPIC VISION; PHYLOGENY; PROTEIN DOMAIN; PROTEIN FUNCTION; RAT; RETINA ROD; SPECIES DIVERSITY; SPECIES HABITAT; SPECTRAL SENSITIVITY; VISION;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; ECOSYSTEM; EVOLUTION, MOLECULAR; EXTINCTION, BIOLOGICAL; LIGHT; LIKELIHOOD FUNCTIONS; MAMMALS; PHYLOGENY; RHODOPSIN; SELECTION, GENETIC; SPECIES SPECIFICITY;

MAMMALIA; PINNIPEDIA; RATTUS; RODENTIA;

EID: 77949497133     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008326     Document Type: Article

References (66)

1. Cott HB (1940) Adaptive coloration in animals. London: Oxford University Press.
2. Walls GL (1942) The vertebrate eye and its adaptive radiation. New York: Hafner.
3. Wickler W (1968) Mimicry in plants and animals. New York: McGraw-Hill.
4. Hinton HE (1973) Natural deception. Gregory RL, Gombrich EH, eds. London: Duckworth.
5. Ferrari M (1993) Colors for survival: mimicry and camouflage in nature. Charlottesville: Thomasson-Grant.
6. Peichl L (2005) Diversity of mammalian photoreceptor properties: adaptations to habitat and lifestyle? Anat Rec 287: 1001-1012.
7. Mass AM, Supin AY (2007) Adaptive features of aquatic mammals' eye. Anat Rec 290: 701-715.
8. Yokoyama S, Yokoyama R (1996) Adaptive evolution of photoreceptors and visual pigments in vertebrates. Annu Rev Ecol Syst 27: 543-567.
9. Yokoyama S, Shi Y (2000) Genetics and evolution of ultraviolet vision in vertebrates. FEBS Lett 486: 167-172.
10. Wald G (1968) The molecular basis of visual excitation. Nature 219: 800-807.
11. Jacobs GH (1993) The distribution and nature of colour vision among the mammals. Biol Rev Camb Philos Soc 68: 413-471.
12. Yokoyama R, Yokoyama S (1990) Convergent evolution of the red- and greenlike visual pigment genes in fish, Astyanax fasciatus, and human. Proc Natl Acad Sci USA 87: 9315-9318.
13. Kochendoerfer GG, Lin SW, Sakmar TP, Mathies RA (1999) How color visual pigments are tuned. Trends Biochem Sci 24: 300-305.
14. Fasick JI, Robinson PR (2000) Spectral-tuning mechanisms of marine mammal rhodopsins and correlations with foraging depth. Vis Neurosci 17: 781-788.
15. 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.
16. Yokoyama S, Takenaka N (2004) The molecular basis of adaptive evolution of squirrelfish rhodopsins. Mol Biol Evol 21: 2071-2078.
17. Yokoyama S, Tada T, Zhang H, Britt L (2008) Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates. Proc Natl Acad Sci USA 105: 13480-13485.
18. Shi Y, Yokoyama S (2003) Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates. Proc Natl Acad Sci USA 100: 8308-8313.
19. David-Gray ZK, Bellingham J, Munoz M, Avivi A, Nevo E, et al. (2002) Adaptive loss of ultraviolet-sensitive/violet-sensitive (UVS/VS) cone opsin in the blind mole rat (Spalax ehrenbergi). Eur J Neurosci 16: 1186-1194.
20. Levenson DH, Dizon A (2003) Genetic evidence for the ancestral loss of shortwavelength-sensitive cone pigments in mysticete and odontocete cetaceans. Proc Biol Sci 270: 673-679.
21. Carvalho Ldos S, Cowing JA, Wilkie SE, Bowmaker JK, Hunt DM (2006) Shortwave visual sensitivity in tree and flying squirrels reflects changes in lifestyle. Curr Biol 16: R81-83.
22. Zhao H, Rossiter SJ, Teeling E, Li C, Cotton JA, et al. (2009) The evolution of color vision in nocturnal mammals. Proc Natl Acad Sci USA 106: 8980-8985.
23. Hunt DM, Dulai KS, Partridge JC, Cottrill P, Bowmaker JK (2001) The molecular basis for spectral tuning of rod visual pigments in deep-sea fish. J Exp Biol 204: 3333-3344.
24. Levenson DH, Ponganis PJ, Crognale MA, Deegan JF, Dizon A, et al. (2006) Visual pigments of marine carnivores: pinnipeds, polar bear, and sea otter. J Comp Physiol A 192: 833-843.
25. Muntz WR (1976) Visual pigments of cichlid fishes from Malawi. Vision Res 16: 897-903.
26. Partridge JC, Archer SN, Lythgoe JN (1988) Visual pigments in the individual rods of deep-sea fishes. J Comp Physiol A 162: 543-550.
27. Crescitelli F (1991) The scotopic photoreceptors and their visual pigments of fishes: functions and adaptations. Vision Res 31: 339-348.
28. Hunt DM, Fitzgibbon J, Slobodyanyuk SJ, Bowmaker JK (1996) Spectral tuning and molecular evolution of rod visual pigments in the species flock of cottoid fish in Lake Baikal. Vision Res 36: 1217-1224.
29. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, et al. (2000) Crystal structure of rhodopsin: A G protein-coupled receptor. Science 289: 739-745.
30. Wang JK, McDowell JH, Hargrave PA (1980) Site of attachment of 11-cisretinal in bovine rhodopsin. Biochemistry 19: 5111-5117.
31. Nathans J (1990) Determinants of visual pigment absorbance: identification of the retinylidene Schiff's base counterion in bovine rhodopsin. Biochemistry 29: 9746-9752.
32. Karnik SS, Sakmar TP, Chen HB, Khorana HG (1988) Cysteine residues 110 and 187 are essential for the formation of correct structure in bovine rhodopsin. Proc Natl Acad Sci USA 85: 8459-8463.
33. Karnik SS, Ridge KD, Bhattacharya S, Khorana HG (1993) Palmitoylation of bovine opsin and its cysteine mutants in COS cells. Proc Natl Acad Sci USA 90: 40-44.
34. Murphy WJ, Pringle TH, Crider TA, Springer MS, Miller W (2007) Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res 17: 413-421.
35. Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, et al. (2001) Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294: 2348-2351.
36. Yokoyama S, Takenaka N, Agnew DW, Shoshani J (2005) Elephants and human color-blind deuteranopes have identical sets of visual pigments. Genetics 170: 335-344.
37. Southall KD, Oliver GW, Lewis JW, Le Boeuf BJ, Levenson DH, et al. (2002) Visual pigment sensitivity in three deep diving marine mammals. Mar Mam Sci 18: 275-281.
38. Yang Z, Nielsen R (1998) Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol 46: 409-418.
39. Nemec P, Cvekova P, Benada O, Wielkopolska E, Olkowicz S, et al. (2008) The visual system in subterranean African mole-rats (Rodentia, Bathyergidae): retina, subcortical visual nuclei and primary visual cortex. Brain Res Bull 75: 356-364.
40. Bennett N, Faulkes C (2000) African Mole-rats: Ecology and Eusociality. Cambridge: Cambridge University Press.
41. Henry E, Remple M, O'Riain M, Catania K (2006) Organization of somatosensory cortical areas in the naked mole-rat (Heterocephalus glaber). J Comp Neurol 495: 434-452.
42. Kimchi T, Terkel J (2002) Seeing and not seeing. Curr Opin Neurobiol 12: 728-734.
43. Peichl L, Behrmann G, Kroger RH (2001) For whales and seals the ocean is not blue: a visual pigment loss in marine mammals. Eur J Neurosci 13: 1520-1528.
44. Madsen CJ, Herman ML (1980) Social and ecological correlates of cetacean vision and visual appearance. In: Herman ML, ed. Cetacean Behavior. New York: Wiley.
45. Griebel U, Schmid A (1992) Color vision in the California sea lion (Zalophus californianus). Vision Res 32: 477-482.
46. Griebel U, Konig G, Schmid A (2006) Spectral sensitivity in two species of pinnipeds (Phoca vitulina, Otaria byronia). Mar Mam Sci 22: 156-166.
47. Griebel U (2002) Color vision in marine mammals: a review. In: Bright M, Dworschak PC, Stachowitsch M, eds. The Vienna school of marine biology: a tribute to Jorg Ott. Facultas Universitätsverlag: Wien.
48. Griebel U, Peichl L (2003) Colour vision in aquatic mammals: facts and open questions. Aquatic Mammals 29: 18-30.
49. Li G, Wang J, Rossiter SJ, Jones G, Cotton JA, et al. (2008) The hearing gene Prestin reunites echolocating bats. Proc Natl Acad Sci USA 105: 13959-13964.
50. Ulloa-Aguirre A, Stanislaus D, Janovick JA, Conn PM (1999) Structure-activity relationships of G protein-coupled receptors. Arch Med Res 30: 420-435.
51. Ji T, Grossman M, Ji I (1998) G protein-coupled receptors I Diversity of receptor-ligand interactions J Biol Chem 273: 17299.
52. Trumpp-Kallmeyer, Chini B, Mouillac B, Barberis C, Hoflack J, et al (1995) Towards understanding the role of the first extracellular loop for the binding of peptide hormones to G-protein coupled receptors Pharm Acta Helv 70: 255.
53. Wadsworth HL, Chazenbalk GD, Nagayama Y, Russo D, Rapoport B (1990) An insertion in the human thyrotropin receptor critical for high affinity hormone binding Science 249: 1423.
54. DeMartino JA, Riper GV, Siciliano SJ, Molineaux CJ, Konteatis ZD, et al (1994) The amino terminus of the human C5a receptor is required for high affinity C5a binding and for receptor activation by C5a but not C5a analogs J Biol Chem 269: 14446.
55. Moss CF, Sinha SR (2003) Neurobiology of echolocation in bats Curr Opin Neurobiol 13: 751-758.
56. Jones G, Teeling EC (2006) The evolution of echolocation in bats Trends Ecol Evol 21: 149-156.
57. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 25: 4876-4882.
58. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution Bioinformatics 14: 817-818.
59. Swofford DL (2003) PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4 Sunderland, Massachusetts: Sinauer Associates.
60. Hulsenbeck JP, Ronquist F (2001) MrBayes 2.01, Bayesian Inference of Phylogeny New York: University of Rochester.
61. Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol Biol Evol 16: 1114-1116.
62. Yang Z, Kumar S, Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences Genetics 141: 1641-1650.
63. Maddison W, Maddison D (2009) Mesquite: a modular system for evolutionary analysis Version 2.6 http://mesquiteprojectorgVersion2.6.
64. Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood Mol Biol Evol 24: 1586-1591.
65. Nei M, Kumar S (2000) Molecular Evolution and Phylogenetics New York: Oxford University Press.
66. Pride DT (2004) SWAPP 1.0 2: a tool for analyzing substitutions and similarity in multiple alignments Available at: http://asiago stanford edu/SWAAP/SwaapPage htm.