Synthesis of experimental molecular biology and evolutionary biology: An example from the world of vision

BioScience

Volumn 62, Issue 11, 2012, Pages 939-948

  Yokoyama, Shozo ^a  

^a EMORY UNIVERSITY   (United States)

Author keywords

Ancestral phenotypes; Molecular adaptation; Phenotypic adaptation; Quantum chemistry; Visual pigments

Indexed keywords

EID: 84871238113     PISSN: 00063568     EISSN: None     Source Type: Journal    
DOI: 10.1525/bio.2012.62.11.3     Document Type: Review

References (60)

1. Altun A, Morokuma K, Yokoyama S. 2011. H-bond network around retinal regulates the evolution of ultraviolet and violet vision. ACS Chemical Biology 6: 775-780.
2. Asenjo AB, Rim J, Oprian DD. 1994. Molecular determinants of human red/green color discrimination. Neuron 12: 1131-1138.
3. Bakewell MA, Shi P, Zhang J. 2007. More genes underwent positive selection in chimpanzee evolution than in human evolution. Proceedings of the National Academy of Sciences 104: 7489-7494.
4. Bridgham JT, Carroll SM, Thornton JW. 2006. Evolution of hormonereceptor complexity by molecular exploitation. Science 312: 97-101.
5. Buckling A, Craig Maclean R, Brockhurst MA, Colegrave N. 2009. The Beagle in a bottle. Nature 457: 824-829.
6. Carroll SB. 2006. The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution. Norton.
7. Dean AM, Thornton JW. 2007. Mechanistic approaches to the study of evolution: The functional synthesis. Nature Reviews Genetics 8: 675-688.
8. Dykhuizen D, Hartl DL. 1980. Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background. Genetics 96: 801-817.
9. Ebrey T, Koutalos Y. 2001. Vertebrate photoreceptors. Progress in Retinal and Eye Research 20: 49-94.
10. Elena SF, Lenski RE. 2003. Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation. Nature Reviews Genetics 4: 457-469.
11. Fasick JI, Applebury ML, Oprian DD. 2002. Spectral tuning in the mammalian short-wavelength sensitive cone pigments. Biochemistry 41: 6860-6865.
12. Golding GB, Dean AM. 1998. The structural basis of molecular adaptation. Molecular Biology and Evolution 15: 355-369.
13. Harms MJ, Thornton JW. 2010. Analyzing protein structure and function using ancestral gene reconstruction. Current Opinion in Structural Biology 20: 360-366.
14. Hughes AL. 2007. Looking for Darwin in all the wrong places: The misguided quest for positive selection at the nucleotide sequence level. Heredity 99: 364-373.
15. - 2008. The origin of adaptive phenotypes. Proceedings of the National Academy of Sciences 105: 13193-13194.
16. Hughes AL, Nei M. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167-170.
17. Kimura M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press.
18. Lythgoe JN. 1979. The Ecology of Vision. Clarendon.
19. Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B. 2011. How many species are there on Earth and in the ocean? PLOS Biology 9 (art. e1001127). doi:10.1371/journal.pbio.1001127
20. Munz FW, McFarland WN. 1973. The significance of spectral position in the rhodopsins of tropical marine fishes. Vision research 13: 1829-1874.
21. Nathans J, Hogness DS. 1983. Isolation, sequence analysis, and intron-exon arrangement of the gene encoding bovine rhodopsin. Cell 34: 807-814.
22. - 1984. Isolation and nucleotide sequence of the gene encoding human rhodopsin. Proceedings of the National Academy of Sciences 81: 4851-4855.
23. Nathans J, Thomas D, Hogness DS. 1986. Molecular genetics of human color vision: The genes encoding blue, green, and red pigments. Science 232: 193-202.
24. Nei M. 2005. Selectionism and neutralism in molecular evolution. Molecular Biology and Evolution 22: 2318-2342.
25. Nei M, Suzuki Y, Nozawa M. 2010. The neutral theory of molecular evolution in the genomic era. Annual Review of Genomics and Human Genetics 11: 265-289.
26. Nielsen R, Yang Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
27. Nozawa M, Suzuki Y, Nei M. 2009a. Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proceedings of the National Academy of Sciences 106: 6700-6705.
28. - 2009b. Response to Yang et al.: Problems with Bayesian methods of detecting positive selection at the DNA sequence level. Proceedings of the National Academy of Sciences 106: E96. doi:10.1073/pnas.0906089106
29. O'Day WT, Fernandez HR. 1974. Aristostomias scintillans (Malacosteidae): A deep-sea fish with visual pigments apparently adapted to its own bioluminescence. Vision Research 14: 545-550.
30. Okada T, Sugihara M, Bondar AN, Elstner M, Entel P, Buss V. 2004. The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. Journal of Molecular Biology 342: 571-583.
31. Oprian DD, Molday RS, Kaufman RJ, Khorana HG. 1987. Expression of a synthetic bovine rhodopsin gene in monkey kidney cells. Proceedings of the National Academy of Sciences 84: 8874-8878.
32. Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW. 2007. Crystal structure of an ancient protein: Evolution by conformational epistasis. Science 317: 1544-1548.
33. Palczewski K. 2006. G protein-coupled receptor rhodopsin. Annual Review of Biochemistry 75: 743-767.
34. Shi Y, Yokoyama S. 2003. Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates. Proceedings of the National Academy of Sciences 100: 8308-8313.
35. Shi Y, Radlwimmer FB, Yokoyama S. 2001. Molecular genetics and the evolution of ultraviolet vision in vertebrates. Proceedings of the National Academy of Sciences 98: 11731-11736.
36. Suzuki Y, Gojobori T. 1999. A method for detecting positive selection at single amino acid sites. Molecular Biology and Evolution 16: 1315-1328.
37. Suzuki Y, Gojobori T, Nei M. 2001. ADAPTSITE: Detecting natural selection at single amino acid sites. Bioinformatics 17: 660-661.
38. Tada T, Altun A, Yokoyama S. 2009. Evolutionary replacement of UV vision by violet vision in fish. Proceedings of the National Academy of Sciences 106: 17457-17462.
39. Takahashi Y, Yokoyama S. 2005. Genetic basis of spectral tuning in the violet-sensitive visual pigment of African clawed frog, Xenopus laevis. Genetics 171: 1153-1160.
40. Walls GL. 1942. The Vertebrate Eye and Its Adaptive Radiation. Cranbrook Institute of Science.
41. Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24: 1586-1591.
42. Yang Z, dos Reis M. 2011. Statistical properties of the branch-site test of positive selection. Molecular Biology and Evolution 28: 1217-1228.
43. Yang Z, Nielsen R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular Biology and Evolution 19: 908-917.
44. Yang Z, Kumar S, Nei M. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141: 1641-1650.
45. Yang Z, Nielsen R, Goldman N, Pedersen A-MK. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449.
46. Yang Z, Wong WSW, Nielsen R. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution 22: 1107-1118.
47. Yang Z, Nielsen R, Goldman N. 2009. In defense of statistical methods for detecting positive selection. Proceedings of the National Academy of Sciences 106: E395. doi:10.1073/pnas.0904550106
48. Yokoyama S. 1994. Gene duplications and evolution of the short wavelength-sensitive visual pigments in vertebrates. Molecular Biology and Evolution 11: 32-39.
49. - 1995. Amino acid replacements and wavelength absorption of visual pigments in vertebrates. Molecular Biology and Evolution 12: 53-61.
50. - 1997. Molecular genetic basis of adaptive selection: Examples from color vision in vertebrates. Annual Review of Genetics 31: 315-336.
51. - 2000. Molecular evolution of vertebrate visual pigments. Progress in Retinal and Eye Research 19: 385-419.
52. - 2008. Evolution of dim-light and color visual pigments. Annual Review of Genome and Human Genetics 9: 259-282.
53. Yokoyama S, Radlwimmer FB. 2001. The molecular genetics and evolution of red and green color vision in vertebrates. Genetics 158: 1697-1710.
54. Yokoyama S, Takenaka N. 2005. Statistical and molecular analyses of evolutionary significance of red-green color vision and color blindness in vertebrates. Molecular Biology and Evolution 22: 968-975.
55. Yokoyama S, Yokoyama R. 1996. Adaptive evolution of photoreceptors and visual pigments in vertebrates. Annual Review of Ecology and Systematics 27: 543-567.
56. Yokoyama S, Yang H, Starmer WT. 2008a. Molecular basis of spectral tuning in the red- and green-sensitive (M/LWS) pigments in vertebrates. Genetics 179: 2037-2043.
57. Yokoyama S, Tada T, Zhang H, Britt L. 2008b. Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates. Proceedings of the National Academy of Sciences 105: 13480-13485.
58. Zhang J, Nei M. 1997. Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods. Journal of Molecular Evolution 44 (suppl. 1): S139-S146.
59. Zhang J, Nielsen R, Yang Z. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution 22: 2472-2479.
60. Zhuang H, Chien M-S, Matsunami H. 2009. Dynamic functional evolution of an odorant receptor for sex-steroid-derived odors in primates. Proceedings of the National Academy of Sciences 106: 21247-21251.