CURRICULUM VITAE

Shozo Yokoyama

Shozo Yokoyama, Ph. D. Asa Griggs Candler Professor of Biology Department of Biology O. Wayne Rollins Research Center 1510 Clifton Road Emory University Atlanta, GA 30322 Tel. 404-727-5379 Fax. 404-727-2880 E-mail: [email protected]

Education: B. S. (Biology), Miyazaki University, Miyazaki, Japan, 1968 M. S. (Biology), , Fukuoka, Japan, 1971 Ph. D. (Biomathematics), University of Washington, Seattle, WA, 1977 Advisor: Dr. Joseph Felsenstein

Professional Appointments: Asa G. Candler Professor of Biology, Department of Biology, Emory University, Atlanta, 2003 - present.

Distinguished Professor, Department of Biology, Syracuse University, Syracuse, 2002 - 2003.

Professor, Department of Biology, Syracuse University, Syracuse, 1991 - 2001

Associate Professor, Department of Ecology, Ethology and , University of Illinois, Urbana-Champaign, 1987 - 1991

Assistant Professor, Departments of Psychiatry, Genetics, & Biology, Washington University, St. Louis, 1980 - 1987

Instructor, Department of Psychiatry, Washington University, St. Louis, 1978 - 1979

Research Associate (with Dr. Masatoshi Nei), University of Texas at Houston, Houston, 1977 - 1978

Research Assistant (for Dr. Joseph Felsenstein), University of Washington, 1973 - 1977

Teaching Assistant, Division of Biological & Medical Sciences, Brown University, 1972

1 - 1973

Research Assistant (for Dr. Masatoshi Nei), Brown University, 1971 - 1972

Professional Organizations, Editorial Boards and Officers: American Association for the Advancement of Science Society for Molecular Biology and Evolution The Association for Research in Vision and Ophthalmology

Editorial Board: The Open Evolution Journal (2007 - present) Editorial Board: International Journal of Evolutionary Biology (2009 - present) Associate Editor: Marine Genomics (2007 - 2011) Associate Editor: Gene (1996 - 2011) Associate Editor: Journal of Heredity (2000 - 2008) Associate Editor: Molecular Biology and Evolution (1993 - 2000) Associate Editor: Genetics (1998 - 2008)

President-Elect, President, and Past President, American Genetic Association, (2003-2005)

Fellow of the American Association for the Advancement of Science, elected 2004

Service on Advisory Committees: 1. Panel Member: National Institutes of Health, Genetics Study Section (1988 - 1991) 2. Cofounder of the Eastern Great Lake Molecular Evolution group (with Dr. Barry G. Hall) (1994). 3. National Chairman for the Search for the President for the Society for the Molecular Biology and Evolution (1996) 4. International Organizing Committee: Symposium on "Evolutionary Genomics," Tokyo (2001). 5. Member: National Institutes of Health, Study Section Boundary team (2002). 6. Co-organizers of the Symposium on “Evolution of Color Vision,” 10th annual meeting of the Society of Molecular Biology and Evolution, 6/26-29, 2003. 7. Organizing Committee for the joint conference between the Society for Molecular Biology and Evolution and American Genetic Association “ and Evolution 2004”. 8. Co-organizers of the Symposium on “Nei Legacy Platinum Jubilee,” 13th annual meeting of the Society of Molecular Biology and Evolution, 5/24-28, 2006. 9. International Program Committee, 12th international Conference on Retinal Proteins, June 4-8, 2006. 10. Global organization Committee, SMBE 2011, Kyoto, Japan.

2

Service on Departmental Committees: Syracuse University 1. Graduate Student Recruiting Committee (1992 - 2003). 2. Graduate Student Education Committee (1992 - 1993). 3. Departmental Seminar Committee (1992 - 1994). 4. Chair, Under-represented Faculty Search Committee (1994). 5. Chair, Faculty Search for Cell & Molecular Biologists (1996). 6. Chair, Departmental Chairperson Search Committee (1998). 7. Faculty Search for Developmental Biologists (1999) 8. Faculty Search for Cell/Molecular Biologists (2001) 9. Faculty Search for Cell/Molecular Biologists (2002) Emory University 1. Faculty Search Committee for Molecular Evolutionists (2003-2004) 2. Faculty Search Committee for Molecular Evolutionists (2004-2005) 3. Executive Committee for Genetics & Molecular Biology Program (2003-2008)

Invited Talks at Conferences & Workshops: 1. The Conference on "Recent Trends in Medical Genetics," Madras, India, 12/15- 12/17, 1983. 2. Gordon Conference on "Population Biology and Evolution of Microorganisms," 8/17 - 8/21, 1987. 3. The Conference on "The Genetic Variation of Immunodeficiency Viruses", NIH: 7/19 - 7/20, 1988. 4. The Fourth International Symposium on "Population Biology of Genes and Molecules", Tokyo, Japan, 11/17 - 11/18, 1988. 5. The Conference on "Evolution at the Molecular Level", Pennsylvania State University: 6/15 - 6/18, 1989. 6. The Fifth International Workshop on "Enzymology and Molecular Biology of Carbonyl Metabolism", Purdue University, 6/12 - 6/15, 1990. 7. The third Annual Meeting on the "New England Molecular Evolution", Brown University, 11/8, 1992. 8. The International Conference on “Bioinformatics and Molecular Evolution,” Mishima, Japan, 4/16 - 4/17, 1993. 9. The Second Annual Meeting for the Society of Molecular Biology and Evolution, Univ. of Georgia, 6/15 - 6/19, 1994. 10. The Twenty-Third Annual Meeting for the American Society for Photobiology, Washington, DC, 6/17 - 6/22, 1995. 11. The Fourth International Congress of Comparative Physiology and Biochemistry, Birmingham, UK: 8/6 - 8/11, 1995. 12. The International Conference on "Diversity of Homeotic Genes and Evolution of the Eye," Kyoto University, Japan, 11/17 - 11/18, 1995. 13. Te International Conference on "Network and Evolution of Molecular Information," Tokyo, Japan, 4/20 - 4/22, 1996. 14. The Fourth annual meeting of the Society for Molecular Biology and Evolution,

3 Tucson, AZ, 6/8 - 6/11, 1996. 15. The annual meeting of the Australian Society for Biochemistry & Molecular Biology, Canberra, Australia, 9/29 - 10/2, 1996. 16. The Summer Conference on "Oscillation" at the Graduate University for Advanced Studies, Hayama, Japan, 9/24 - 9/27, 1997. 17. The International Symposium on “Population Genetics on Evolutionary Mechanism,” Fukuoka, Japan, 8/18 - 8/22, 1998. 18. The annual meeting on the "New England Molecular Evolution", New York University, 10/31, 1998. 19. The Symposium on “Genomic diversity and evolution,” American Genetics Association, Pennsylvania State University, 6/11-13, 1999. 20. The Gordon Conference on Molecular Evolution, Hayama, Japan, 11/24-29, 1999. 21. The symposium on "Evolution 2000", Tokyo, Japan, 3/3 - 5, 2000. 22. The symposium on "Neutralism and selectionism: The end of a debate," Ischia, Italy, 5/4 - 6, 2000. 23. The symposium on "Beyond the Identification of Transcribed Sequences: Functional d Expression Analysis," Heidelberg, Germany, 10/28 - 31, 2000. 24. Workshop Faculty on "Molecular Evolution," MBL, Woods Hole, MA, 7/31 - 8/11, 2000. 25. The symposium on "Chromosomes: structure, function and evolution", Guanacaste, Costa Rica, 1/8 - 12, 2001. 26. Workshop Faculty on "Molecular Evolution," MBL, Woods Hole, MA, 7/29 - 8/10, 2001. 27. The symposium on "Natural selection and Neutral Theory," at the 8th Annual Meeting for the Society of Molecular Biology and Evolution, Capri, Italy, 10/28 - 30, 2001. 28. The symposium on "Evolutionary Genomics", Atami, Japan, 11/3 - 7, 2001. 29. The symposium on "Adaptive evolution of proteins", Sorrento, Italy, 6/13-16, 2002. 30. The 10th International Retinal Protein Conference, Seattle, WA, 8/20-24, 2002. 31. Workshop Faculty on "Molecular Evolution," MBL, Woods Hole, MA, 7/28 - 8/9, 2002. 32. The symposium on “Evolution of Color Vision” at the 10th annual meeting of the Society of Molecular Biology and Evolution, Newport Beach, CA, 6/26-29, 2003. 32. The 17th Symposium of the International Color Vision Society, University of Washington, Seattle, WA, 7/11-15, 2003. 33. The 2nd European Conference on Avian Colour Vision, Paris, France, 10/20-22, 2003. 34. Workshop Faculty on "Workshop on Molecular Evolution," MBL, Woods Hole, MA, 7/28 - 8/9, 2004. 35. The Mishima Workshop on “Population genetics and molecular evolution: past, present, and future,” Hakone, Japan, 11/25-27, 2004. 36. The Symposium on Structural and Evolutionary Genomics “ and RNA: Expression and functions,” Puntarenas, Costa Rica, 2/26-3/2, 2005. 37. Plenary speaker at the South Carolina Bioinformatics Symposium, Columbia, SC, 3/19/2005.

4 38. Workshop Faculty on "Workshop on Molecular Evolution," MBL, Woods Hole, MA, 7/24 - 8/12, 2005. 39. The Symposium on “Omics informatics symposium,” Tokyo Medical and Dental University, Tokyo, Japan, 3/20-21, 2006. 40. The Symposium on “Evolution and adaptation,” 13th annual meeting of the Society of Molecular Biology and Evolution, Arizona State University, Tempe, AZ, 5/24-28, 2006. 41. The 12th International Retinal Protein Conference, Awajishima, Japan, 6/4-8, 2006. 42. The Optical Society of America Vision Meeting, University of Rochester, Rochester, NY, 10/6-8, 2006. 43. The International Conference on “Marine Genomics,” Sorrento, Italy, October 28- November 1, 2006. 44. The “Symposium on Evolutionary Genomics,” San Jose, Costa Rica, January 7- 12, 2007. 45. The keynote speaker in the “Workshop on the Evolution of Opsin Genes,” Taipei, Taiwan, May 26-June 1, 2007. 46. The “New Insight of into Fundamental Life Activities,” Tokyo, Japan, March 27-28, 2008. 47. The international satellite symposium on “Evolutionary Studies for High School Students,” Graduate University for Advanced Studies, Hayama, Japan, August 21, 2008 48. The symposium on “Neo-Mutationism and Phenotypic Evolution” in the 10th annual meeting of the Japanese Society of Evolutionary Studies, Tokyo University, Tokyo, Japan, August 22-24, 2008. 49. Invited Course Instructor on “Bioinformatics of the Gene,” Ochanomizu University, Tokyo, Japan, September 28-October 2, 2009. 50. Workshop Faculty on "Workshop on Molecular Evolution," MBL, Woods Hole, MA, 7/25 - 8/6, 2010. 51. Penn State SMBE Symposium on Molecular and Genomic Evolution, University Park, PA, 3/19-3/20, 2011. 52. Symposium on “Origin and diversification of sensory organs” at SMBE 2011, Kyoto, Japan, 7/26-30, 2011. 53. Workshop Faculty on "Workshop on Molecular Evolution," MBL, Woods Hole, MA, 7/24 - 8/3, 2011. 54. NSF IGERT symposium on “Evolution, Development and Genomics Symposium: The Future of Evo-Devo,” Portland OR, 2/10-2/12, 2012. 55. SMBE Satellite Symposium on Phylomedicine, Arisona State University, Tempe, AZ, 3/23-3/24, 2012. 56. EMBO Workshop on “Evolution in the Time of Genomics,” Venice, Italy, 5/7- 5/9, 2012.

Research Grants:

Active 1. NIH, EY016400, Adaptive evolution of color vision, Shozo Yokoyama (PI), 25%

5 effort, 2/1/11-1/31/16, $1,937,500 (Total Amount).

Past 1. NIH, GM28672, Population genetics of deleterious genes, Shozo Yokoyama (PI), 50% effort, 1981-1983, $83,177 (DC) 2. NIMH, MH31302, Epidemiological Genetics and Family Study, Theodore Reich (PI), 50% effort - Project #9: Social selection in Human Populations, 1978-1986, $400,000 (DC). 3. NIH, 2S07 RRD5389-21, BRSG, Genome Reorganization of Tetrahymena, Shozo Yokoyama (PI), 1982-1983, $7,000 4. NIAAA, AA0359, Neurobiology, genetics, Epidemiology and Alcoholism, Samuel B. Guze (PI), 50% effort - project #5: DNA polymorphism of Alcohol Dehydrogenase (ADH) and Aldehyde Dehydrogenase (ALDH) Genes and the Asssociation to Alcoholism, 1985-1987, $100,000 (DC). 5. NIH, GM28672, Population Genetics of Deleterious Genes, Shozo Yokoyama (PI), 25% effort, 1984-1990, $250,384 (DC). 6. NIH, GM42379, Molecular Evolution of Visual pigment genes in Astyanax, Shozo Yokoyama (PI), 25% effort, 4/1/90-6/31/94, $327,473 (DC). 7. NIAAA, AA08241, Genetics of Alcohol Sensitivity, Shozo Yokoyama (PI), 25% effort, 9/28/90-8/31/94, $324,167 (DC). 8. NIH, GM42379, Evolutionary Genetics of Vertebrate Vision, Shozo Yokoyama (PI), 30% effort, 7/1/94-6/31/99, $1,112,578 (Total). 9. NIH, GM42379, Evolutionary Genetics of Vertebrate Vision, Shozo Yokoyama (PI), 30% effort, 4/1/99-3/31/06, $1,303,630 (Total).

Current Collaborators: 1. On molecular genetics and evolution of color vision genes a) Dr. Takashi Tada, Postdoctoral fellow, Department of Biology, Emory University. b) Dr. Jyni Xing, Postdoctoral fellow, Department of Biology, Emory University c) Dr. Davide Faggionato, Postdoctoral fellow, Department of Biology, Emory University d) Dr. Shiva Sekharan, Postdoctoral fellow, Departments of Biology & Chemistry, Emory University e) Dr. Huan Zhang, Research Associate Professor, Department of Marine Sciences, University of Connecticut. f) Dr. Lyle Britt, NOAA/NMFS/Alaska Fisheries Science Center, Seattle. g) Professor William T. Starmer, Professor, Syracuse University, Syracuse, NY h) Professor Walter Gehring, University of Basel, Switzerland. i) Dr. Hiroshi Suga, Instituto de Biologia Evolutiva (UPF-CSIC), Barcelona, Spain. j) Dr. Akihisa Terakita, Osaka City University, Japan k) Professor Jeanne Serb, Department of Ecology, Evolution & Organismal

6 Biology, Iowa state University, Ames, IA l) Professor Atsushi Ogura, Department of Biology, Ochanomizu University, Tokyo, Japan. m) Dr. Andy Baxevanis, National Human Genome Research Institute, NIH. n) Dr. Christy Schnitzler, National Human Genome Research Institute, NIH. o) Dr. Kevin Pang, University of Hawaii, HI. 2. On quantum chemical analyses of visual pigments a) Professor Keiji Morokuma, Department of Chemistry, Emory University b) Professor Takahisa Yamato, Department of Physics, Nagoya University, Nagoya, Japan 3. On the genome analyses of jellyfish species: a) Professor Takashi Gojobori, National Institute of Genetics, Mishima, Japan. b) Professor Kazuho Ikeo, National Institute of Genetics, Mishima, Japan.

Teaching: 1. Theoretical Population Genetics, 2 semester course, Washington University, 1979-1980. 2. Molecular Evolution, University of Illinois at Urbana-Champaign, every Fall Semester, 1987 - 1990. 3. Introduction to Quantitative Population Biology, University of Illinois at Urbana- Champaign, Spring Semester, 1988. 4. Population Biology, University of Illinois at Urbana-Champaign, Spring Semester, 1989 - 1990. 5. Molecular Biology and Evolution, Syracuse University, every Spring Semester, 1992 - 1996; every Fall Semester, 1997 - 2003. 6. Molecular Evolutionary Genetics, Syracuse University, every Fall Semester, 1992 - 1996. 7. The Human Genome Project and Diseases (Senior Seminar), Emory University, Spring 2004, 2006, 2010. 8. Molecular Biology and Evolutionary Genetics (for upper undergraduate & graduate students), Emory University, every Fall semester, 2003-present.

Publications (Peer reviewed): 1. Felsenstein, J. and Yokoyama, S. (1976) The evolutionary advantage of recombination. II. Individual selection for recombination. Genetics 83: 845-859. 2. Nei, M and Yokoyama, S. (1976) Effects of random fluctuation of selection intensity on genetic variability in a finite population. Japan. J. Genetics. 51: 355- 369. 3. Yokoyama, S. and Felsenstein, J. (1978) A model of kin selection for an altruistic trait considered as a quantitative character. Proc. Natl. Acad. Sci. USA 75: 420-422. 4. Chakraborty, R. and Yokoyama, S. (1978) Heterozygosity and monomorphism reconsidered. Heredity 41: 327-333. 5. Yokoyama, S. (1979) The rate of allelism of lethal genes in a geographically structured population. Genetics 93: 245-262.

7 6. Yokoyama, S. (1979) Role of genetic drift in the high frequency of Tay-Sachs disease among Ashkenazic Jews. Ann. Hum. Genet. 43: 133-136. 7. Yokoyama, S. and Nei, M. (1979) Population dynamics of sex-determining alleles in honey-bees and self-incompatibility alleles in plants. Genetics 91: 609- 626. 8. Yokoyama, S. (1980) The effect of social selection on population dynamics of rare deleterious genes. Heredity 45: 271-280. 9. Yokoyama, S. (1980) The effect of variable progeny size and social selection on the population dynamics of rare lethal genes. Social Biol. 27: 70-78. 10. Yokoyama, S. and Templeton, A. (1980) The effect of social selection on the population dynamics of Huntington's disease. Ann. Hum. Genet. 43: 413-417. 11. Templeton, A. and Yokoyama, S. (1980) Effect of reproductive compensation and the desire to have male offspring on the incidence of a sex-linked lethal disease. Am. J. Hum. Genet. 32: 575-581. 12. Yokoyama, S., Rice, J. P. and Yokoyama, R. W. (1980) The effect of social selection due to familial mental retardation on the marriage frequency of normal individuals. Social Biol. 27: 194-198. 13. Yokoyama, S. (1981) Social selection in human populations: I. Modification of the fitness of offspring by an affected parent. Am. J. Hum. Genet. 33: 407-417. 14. Yokoyama, S. (1981) Family size and evolution of Rh polymorphism. J. Theor. Biol. 92: 119-125. 15. Yokoyama, S. (1981) Concept of genetic and evolutionary fitness and hereditary polyposis coli. Am. J. Hum. Genet. 33: 995-998. 16. Yokoyama, S. (1981) Cultural inheritance of the desire for having male offspring and the incidence of a sex-linked lethal disease. Social Biol. 28: 315-327. 17. Nei, M. and Yokoyama, S. (1981) Estimation of fitness reduction due to a chronic disease in man. Ann. Hum. Genet. 45 :261-265. 18. Yokoyama, S., Reich, T. and Morgan, K. (1981) Inbreeding and the genetic control of nondisjunction. Human Genet. 59: 125-128. 19. Yokoyama, S. and Hetherington, L. E. (1982) The expected number of self- incompatibility alleles in finite plant populations. Heredity 48: 299-303. 20. Yokoyama, S. and Templeton, R. (1982) Effect of cultural inheritance of reproductive compensation on the incidence of a sex-linked lethal disease. J. Theor. Biol. 99: 389-395. 21. Yokoyama, S. (1983) Equilibrium frequencies of -globin genes. J. Theor. Biol. 100: 173-180. 22. Yokoyama, S. (1983) Selection for the -thalassemia genes. Genetics 103: 143- 148. 23. Yokoyama, S. (1983) Polymorphism in the 5'-flanking region of the human insulin gene and the incidence of diabetes. Am. J. Hum. Genet. 35: 193-200. 24. Yokoyama, S. (1983) Social selection in human populations: Fitness modification of offspring by an affected parent at two loci. Am. J. Hum. Genet. 35: 675-686. 25. Yokoyama, S. (1983) Social selection and evolution of human diseases. Am. J. Phys. Anthrop. 62: 61-66. 26. Yokoyama, S. (1983) Theories of social selection in human populations. Am. J. Hum. Genet. 35: 362-375.

8 27. Yokoyama, S. (1983) Social selection in human populations: Fitness interaction among sibs. Am. Nat. 122: 433-443. 28. Yokoyama, S. and Rice, J. P. (1983) Social selection in human populations: Deterministic analyses on the modification of the fitness of offspring by affected parents. Social Biol. 30: 181-188. 29. Hall, B. G., Yokoyama, S. and Calhoun, D. H. (1983) Role of cryptic genes in microbial evolution. Mol. Biol. Evol. 1: 109-124. 30. Yokoyama, S. (1984) Social selection in human populations: Differential modification of the fitness by the sex of an affected parent. J. Theor. Biol. 109: 453-459. 31. Yao, M.-C., Choi, J., Yokoyama, S., Austerberry, C. F. and Yao, C.-H. (1984) DNA elimination in tetrahymena: A developmental process involving extensive breakage and rejoining of DNA at defined sites. Cell 36: 433-440. 32. Yokoyama, S. and Ward, R. H. (1984) Age structure and the distribution of rare genetic diseases. Am. J. Med. Genet. 19: 65-79. 33. Yokoyama, S. (1985) DNA polymorphism and the susceptability to diseases. Am. J. Med. Genet. 21: 649-654. 34. Yokoyama, S. (1985) Social selection in human populations: Sufficient conditions for protection of deleterious alleles in a subdivided population. J. Theor. Biol. 115: 455-465. 35. Yokoyama, S. and Schaal, B. (1985) A note on multiple-niche polymorphisms in plant populations. Am. Nat. 125: 158-163. 36. Gojobori, T. and Yokoyama, S. (1985) Rates of evolution of the retroviral oncogene of Moloney murine sarcoma virus and of its cellular homologues. Proc. Natl. Acad. Sci. USA 82: 4198-4201. 37. Yokoyama, S. (1986) Deterministic behavior of HLA haplotypes under symmetric overdominant selection. Jpn. J. Genet. 61: 61-70. 38. Yokoyama, S. and Schaal, B. (1986) Population dynamics of mutant alleles under maternal effect in plant populations. J. Hered. 77: 256-260. 39. Rotwein, P., Yokoyama, S., Didier, D. K. and Chirgwin J. M. (1986) Genetic analysis of the hypervariable region flanking the human insulin gene. Am. J. Hum. Genet. 39: 291-299. 40. Yokoyama, S. (1987) Social selection in human populations: Protected polymorphism of deleterious alleles with incomplete penetrance. Genetic Epidemiology 4: 223-231. 41. Yokoyama, S. and Gojobori, T. (1987) Molecular evolution and phylogeny of the human AIDS viruses LAV, HTLV-III, and ARV. J. Mol. Evol. 24: 330-336. 42. Yokoyama, S., Moriyama, E. N. and Gojobori, T. (1987) Molecular phylogeny of the human immunodeficiency and related viruses. Proc. Japan Acad. 63: 147- 150. 43. Yokoyama, S. and Yokoyama, R. (1987) Molecular evolution of mammalian class I alcohol dehydrogenase. Mol. Biol. Evol. 4: 504-513. 44. Yokoyama, S., Yokoyama, R. and Rotwein, P. (1987) Molecular characterization of cDNA clones encoding the human alcohol dehydrogenase 1 and the evolutionary relationship to the other class I subunits and . Jpn. J. Genet. 62: 241-256.

9 45. Gojobori, T. and Yokoyama, S. (1987) Molecular evolutionary rates of oncogenes. J. Mol. Evol. 26: 148-156. 46. Gojobori, T., Moriyama, E. N. and Yokoyama, S. (1987) Molecular evolution of oncogenes. Jpn. J. Genet. 62: 163-177. 47. Yokoyama, S. (1988) Molecular evolution of the human and simian immunodeficiency viruses. Mol. Biol. Evol. 5: 645-659. 48*. Yokoyama, S., Chung, L. and Gojobori, T. (1988) Molecular evolution of the human immunodeficiency and related viruses. Mol. Biol. Evol. 5: 237-251.

(* Cited as a hot paper in The Scientist)

49. Yokoyama, S. and Yokoyama, R. (1989) Molecular evolution of human visual pigment genes. Mol. Biol. Evol. 6: 186-197. 50. Matsuo, Y. and Yokoyama, S. (1989) Molecular structure of the human alcohol dehydrogenase 1 gene. FEBS Lett. 243: 57-60. 51. Yokoyama, S., Isenberg, K. E. and Wright, A. F. (1989) Adaptive evolution of G protein coupled receptor genes. Mol. Biol. Evol. 6: 342-353. 52. Matsuo, Y., Yokoyama, R. and Yokoyama, S. (1989) The genes for human alcohol dehydrogenases 2 differ by only one nucleotide. Eur. J. Biochem. 183: 317-320. 53. Matsuo, Y. and Yokoyama, S. (1990) Cloning and sequencing of a processed pseudogene derived from the human class III alcohol dehydrogenase gene. Am. J. Hum. Genet. 46: 85-91. 54. Yokoyama, S., Yokoyama, R., Kinlaw, C. S. and Harry, D. E. (1990) Molecular evolution of the zinc-containing long-chain alcohol dehydrogenase genes. Mol. Biol . Evol. 7: 143-154. 55. Yokoyama, R, and Yokoyama, S. (1990) Isolation, DNA sequence and evolution of a color visual pigment gene of the blind cave fish Astyanax fasciatus. Vision Res. 30: 807-816. 56. Gojobori, T., Moriyama, E. N., Shimizu, N., Ina, Y., Ikeo, K., Miura, T., Tsujimoto, H., Hayami, M. and Yokoyama, S. (1990) Evolutionary origin of human and simian immunodeficiency viruses. Proc. Natl. Acad. Sci. USA 87: 4108-4111. 57. Yokoyama, R. and Yokoyama, S. (1990) Convergent evolution of the red- and green-like visual pigment genes in fish, Astyanax fasciatus, and human. Proc. Natl. Acad. Sci. USA 87: 9315-9318. 58. Yokoyama, S. and Starmer, W. T. (1992) Phylogeny and evolutionary rates of G protein subunit genes. J. Mol. Evol. 35: 230-238. 59. Yokoyama, S., Matsuo, Y., Rajasekharan, S. and Yokoyama, R. (1992) Molecular structure of the human alcohol dehydrogenase 3 gene. Jpn. J. Genet. 67: 167-171. 60. Yokoyama, S., Starmer, W. T. and Yokoyama, R. (1993) Paralogous origin of the red- and green-sensitive visual pigment genes in vertebrates. Mol. Biol. Evol. 10:527-538. 61. Kawamura, S. and Yokoyama, S. (1993) Molecular characterization of the red visual pigment gene of the American chameleon (Anolis carolinensis). FEBS

10 Lett. 323: 247-251. 62. Yokoyama, S. and Harry, D. E. (1993) Molecular phylogeny and evolutionary rates of alcohol dehydrogenases in vertebrates and plants. Mol. Biol. Evol. 10: 1215-1226. 63. Yokoyama, R. and Yokoyama, S. (1993) Molecular characterization of the blue visual pigment gene in the fish Astyanax fasciatus. FEBS Lett. 334: 27-31. 64. Yokoyama, S. (1994) Gene duplications and evolution of the short wavelength- sensitive visual pigment genes in vertebrates. Mol. Biol. Evol. 11: 32-39. 65. Register, E. A., Yokoyama, R. and Yokoyama, S. (1994) Multiple origins of the green-sensitive opsin genes in fish. J. Mol. Evol. 39: 268-273. 66. Yokoyama, S., Matsuo, Y., Ramsbotham, R. and Yokoyama, R. (1994) Molecular characterization of a class IV human alcohol dehydrogenase gene (ADH7). FEBS Lett. 351: 411-415. 67. Kawamura, S. and Yokoyama, S. (1994) Cloning of the rhodopsin-encoding gene from the rod-less lizard Anolis carolinensis. Gene 149: 267-270. 68. Yokoyama, S. (1995) Amino acid replacements and wavelength absorption of visual pigments in vertebrates. Mol. Biol. Evol. 12: 53-61. 69. Kawamura, S. and Yokoyama, S. (1995) Paralogous origin of the rhodopsin-like opsin genes in lizards. J. Mol. Evol. 40:594-600. 70*. Yokoyama, R., Knox, B. E. and Yokoyama, S. (1995) Rhodopsin from the fish, Astyanax: Role of tyrosine 261 in the red shift. Invest. Ophthalmol. Vis. Sci. 36: 939-945.

(*selected as the Editor’s choice)

71. Yokoyama, S., Meany, A., Wilkens, H. and Yokoyama, R. (1995) Initial mutational steps towards loss of opsin gene function in cavefish. Mol. Biol. Evol. 12: 527-532. 72. Yokoyama, S. (1996) Molecular evolution of retinal and nonretinal opsins. Genes To Cells 1: 787-794. 73. Kawamura, S. and Yokoyama, S. (1996) Phylogenetic relationships among short wavelength-sensitive opsin genes of American chameleon (Anolis carolinensis) and other vertebrates. Vision Res. 36: 2797-2804. 74. Kawamura, S. and Yokoyama, S. (1996) Molecular characterization of the pigeon P-opsin gene. Gene 182: 213-214. 75. Kawamura, S. and Yokoyama, S. (1997) Expression of visual and nonvisual opsins in American chameleon. Vision Res. 37: 1867-1871. 76. Zhang, H. and Yokoyama, S. (1997) Molecular evolution of the rhodopsin gene of marine lamprey, Petromyzon marinus. Gene 191: 1-6. 77. Nei, M., Zhang, J. and Yokoyama, S. (1997) Color vision of ancestral organisms of higher primates. Mol. Biol. Evol. 14: 611-618. 78. Radlwimmer, F. B. and Yokoyama, S. (1997) Cloning and expression of the red visual pigment gene of goat (Capra hircus). Gene 198: 211-215. 79. Yokoyama, S. and Zhang, H. (1997) Cloning and characterization of the pineal gland-specific opsin gene of marine lamprey (Petromyzon marinus). Gene 202: 89-93.

11 80. Kawamura, S. and Yokoyama, S. (1998) Functional characterization of visual and nonvisual pigments of American chameleon (Anolis carolinensis). Vision Res. 38: 37-44. 81. Yokoyama, S. and Radlwimmer, F. B. (1998) The "five-sites" rule and the evolution of red and green color vision in mammals. Mol. Biol. Evol. 15: 560- 567. 82. Yokoyama, S., Radlwimmer, F. B. and Kawamura, S. (1998) Regeneration of ultraviolet pigments of vertebrates. FEBS Lett. 423: 155-158. 83. Radlwimmer, F. B. and Yokoyama, S. (1998) Genetic analyses of the green visual pigments of rabbit (Oryctolagus cuniculus) and rat (Rattus norvegicus). Gene 218: 103-109. 84. Yokoyama, S. (1999) Molecular bases of color vision in vertebrates. Genes Genet. Syst. 74: 189-199. 85*. Yokoyama, S., Zhang, H., Radlwimmer, F. B. and Blow, N. S. (1999) Adaptive evolution of color vision of the Comoran coelacanth (Latimeria chalumnae). Proc. Natl. Acad. Sci. USA 96: 6279-6284. 86*. Yokoyama, S. and Radlwimmer, F. B. (1999) The molecular genetics of red and green color vision in mammals. Genetics 153: 919-932.

(*Introduced in Science (1999) Gaining new insight into the molecular basis of evolution 285: 654-655 by Elizabeth Pennisi.)

87. Kawamura, S., Blow, N. S. and Yokoyama, S. (1999) Genetic analyses of visual pigments of the pigeon (Columba livia). Genetics 153: 1839-1850. 88. Yokoyama, S. (2000) Color vision of the coelacanth (Latimeria chalumnae) and adaptive evolution of rhodopsin (RH1) and rhodopsin-like (RH2) pigments. J. Heredity 91: 215-220. 89. Yokoyama, S, Radlwimmer, F. B. and Blow, N. S. (2000) Ultraviolet pigments in birds evolved from violet pigments by a single amino acid change. Proc. Natl. Acad. Sci. USA 97: 7366-7371. 90. Yokoyama, S. and Shi, Y. (2000) Genetics and evolution of ultraviolet vision in vertebrates. FEBS Lett. 486: 167-172. 91. Yokoyama, S., Blow, N. S. and Radlwimmer, F. B. (2000) Molecular evolution of color vision in zebra finch. Gene 259: 17-24. 92. Yokoyama, S. and Tada, T. (2000) Adaptive evolution of the African and Indonesian coelacanths to deep-sea environments. Gene 261: 35-42. 93. Yokoyama, S and Blow, N. S. (2001) Molecular evolution of the cone visual pigments in the pure rod-retina of the nocturnal gecko, Gekko gekko. Gene 276: 117-125. 94. Yokoyama, S. and Radlwimmer, F. B. (2001) The molecular genetics and evolution of red and green color vision in vertebrates. Genetics 158: 1697-1710. 95. Kawamura, S., Hirai, M., Takenaka, O., Radlwimmer, F. B. and Yokoyama, S. (2001) Genomic and spectral analyses of long to middle wavelength-sensitive visual pigments of common marmoset (Calithrix jacchus). Gene 269: 45-51. 96. Shi, Y., Radlwimmer, F. B. and Yokoyama, S. (2001) Molecular genetics and the evolution of ultraviolet vision in vertebrates. Proc. Natl. Acad. Sci. USA 98:

12 11731- 11736. 97. Yokoyama, S. (2002) Molecular evolution of color vision in vertebrates. Gene 300: 69-78. 98. Yokoyama, S. and Tada, T. (2003) The spectral tuning in the short wavelength- sensitive type 2 pigments. Gene 306: 91-98. 99. Deeb, S. S., Wakefield, M. J., Tada, T., Marotte, L., Yokoyama, S. and Graves, J. A. M. (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. 100*. Shi, Y. and Yokoyama, S. (2003) Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates. Proc. Natl. Acad. Sci. USA 100: 8308-8313.

(*Accompanied with a COMENTARY “Paleomolecular biology unravels the evolutionary mystery of vertebrate UV vision” by J. Zhang in Proc. Natl. Acad. Sci. USA 100: 8045-8047.)

101. Yokoyama, S. and Takenaka, N. (2004) The molecular basis of adaptive evolution of squirrelfish rhodopsins. Mol. Biol. Evol. 21: 2071-2078. 102. Hiramatsu, C., Radlwimmer, F. B., Yokoyama, S. and Kawamura, S. (2004) Mutagenesis and reconstitution of middle-to-long wavelength-sensitive visual pigments of New World monkeys for testing the tuning effect of residues at sites 229 and 233. Vision Res. 44: 2225-2231. 103. Yokoyama, S. and Takenaka, N. (2005) Statistical and molecular analyses of evolutionary significance of red-green color vision and color blindness in vertebrates. Mol. Biol. Evol. 22: 968-975. 104. Yokoyama, S., Takenaka, N., Agnew, D. W. and Shoshani, J. (2005) Elephants and human color-blind deuteranopes have identical sets of visual pigments. Genetics 170: 335-344. 105. Takahashi, Y. and Yokoyama, S. (2005) Genetic basis of spectral tuning in the violet-sensitive visual pigments of African clawed frog, Xenopus laevis. Genetics 171: 1153-1160. 106. Yokoyama, S., Starmer, W. T., Takahashi, Y. & Tada, T. (2006) Tertiary structure and spectral tuning of UV and violet pigments in vertebrates. Gene 365: 95-103. 107. Yokoyama, S., Tada, T. and Yamato, T. (2007) Modulation of the absorption maximum of rhodopsin by amino acids in the C-terminus. Photochem. Photobiol. 83: 236-241. 108. Yokoyama, S., Takenaka, N and Blow, N. S. (2007) A novel spectral tuning in the short wavelength-sensitive (SWS1 and SWS2) pigments of bluefin killifish (Lucania goodei). Gene 396: 196-202. 109. Takenaka, N. and Yokoyama, S. (2007) Mechanisms of spectral tuning in the RH2 pigments of Tokay gecko and American chameleon. Gene 399: 26-32. 110. Altun, A., Yokoyama, S. and Morokuma, K. (2008) Quantum

13 Mechanical/Molecular Mechanical studies on spectral tuning mechanisms of visual pigments and other photoactive proteins. Photochem. Photobiol. 84: 845- 854. 111. Altun, A., Yokoyama, S. and Morokuma, K. (2008) Spectral tuning in visual pigments: An ONIOM(QM:MM) study on bovine rhodopsin and its mutants. J. Phys. Chem. B 112: 6814-6827. 112.*†‡Yokoyama, S., Tada, T., Zhang, H. and Britt, L. (2008) Elucidation of phenotypic adaptations: molecular analyses of dim-light vision proteins in vertebrates. Proc. Natl. Acad. Sci. USA 105: 13480-13485.

(*Introduced in IN THIS ISSUE “The evolution of low-light vision” in Proc. Natl. Acad. Sci. USA 105: 13186.

(†Accompanied with a COMENTARY “The origin of adaptive phenotypes” by Austin L. Hughes in Proc. Natl. Acad. Sci. USA 105: 13193-13194.)

(‡ Introduced in SEARCH AND DISCOVERY “Study tracks the changes in a vision protein as fish evolved” by Charles Day in PHYSICS TODAY (October 2008) 61: 20-22.)

(Introduced in BioBriefs “Fish Vision” by Cathy Lundmark in BioScience (January 2010) 60 (1): 88.)

113. Yokoyama, S., Yang, H. and Starmer, W. T. (2008) Molecular basis of spectral tuning in the red- and green-sensitive (M/LWS) pigments in vertebrates. Genetics 179: 2037-2043. 114. Altun, A., Yokoyama, S. and Morokuma, K. (2008) Mechanism of spectral tuning going from retinal in vacuo to bovine rhodopsin and its mutants: Multireference ab initio Quantum Mechanics/Molecular Mechanics studies. J. Phys. Chem. B. 112: 16883-16890. 115. Altun, A., Yokoyama, S. and Morokuma, K. (2009) Color tuning in short wavelength-sensitive human and mouse visual pigments: Ab initio quantum mechanics/molecular mechanicks studies. J. Phys. Chem. A 113: 11685-11692. 116. Tada, T., Altun, A. and Yokoyama, S. (2009) Evolutionary replacement of UV vision by violet vision in fish. Proc. Natl. Acad. Sci. USA 106: 17457-17462.

(Introduced in BioBriefs “Fish Vision” by Cathy Lundmark in BioScience (January 2010) 60 (1): 88.)

117. Yokoyama, S. and Tada, T. (2010) Evolutionary dynamics of rhodopsin type 2 (RH2) opsins in vertebrates. Mol. Biol. Evol. 27 (1): 133-141. 118. Watanabe, H. C., Mori, Y., Tada, T., Yokoyama, S. and Yamato, T. (2010) Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin. Biophysics 6: 67-78. 119. Yokoyama , S., Altun, A. and DeNardo, D. F. (2011) Molecular convergence of infrared vision in snakes. Mol. Biol. Evol. 28 (1): 45-48.

14 120. Altun, A., Morokuma, S. and Morokuma, K. (2011) Hydrogen-bond network around retinal regulates the evolution of ultraviolet and violet vision. ACS Chemical Biology 6, 775-780. 121. Sekharan, S., Yokoyama, S. and Morokuma, K. (2012) QM/MM Structure, Enantioselectivity, Spectroscopy of A3- and A4-Retinals in Visual Pigments: Implications for Insect Vision. J. Phys. Chem. B (in press).

Reviews & Chapters: 1. Yokoyama, S. (1977) Theoretical studies of the distribution of rare deleterious alleles in natural and human populations. Ph. D. Dissertation, University of Washington. 2. Yokoyama, S. (1983) Social selection and evolution of human diseases. in Genetics, Evolution, and Diseases. D. H. O'Rouke, G. M. Peterson, and F. E. Johnson (eds), Alan R. Liss, Inc., New York. (Also appeared as American Journal of Physical Anthropology, Vol. 62, No. 1) 3. Cloninger, C. R., Reich, T. and Yokoyama, S. (1983) Genetic diversity, genome organization, and investigation of the etiology of psychiatric diseases. Psychiatric Development 3: 225-246. 4. Yokoyama, S. (1984) Comments on "The sociobiology of sex and sexes today" by M. Blute. Current Anthropology 25: 206-207. 5. Yokoyama, S. (1986) The effect of social selection on the frequencies of genetic diseases. in Recent Trends in Medical Genetics. K. M. Marimuthu and P. M. Gopinath (eds), Pp. 207-216, Pergamon Press, Oxford. 6. Yokoyama, S. (1988) Evolution by social selection. Evol. Biol. 23: 85-126. 7. Yokoyama, S. and Yokoyama, R. (1990) Molecular evolution of visual pigment genes and other G-protein-coupled receptor genes. in Population Biology of Genes and Molecules, N. Takahata and J. F. Crow (eds.), pp. 307-322, Baifukan, Tokyo. 8. Yokoyama, S. (1991) Molecular evolution of the HIV and related viruses. in Evolution at the Molecular Level, R. K. Selander, A. G. Clark and T. S. Whittam (eds.), pp. 96-111, Sinauer, Sunderland. 9. Wilkie, T. M. and Yokoyama, S. (1994) Evolution of the G protein alpha subunit gene family. in Molecular Evolution of Physiological Processes. D. M. Fambrough (ed), Pp. 249-270, The Rockefeller Univ. Press, New York. 10. Yokoyama, S. and Starmer, W. T. (1996) Evolution of G-protein-coupled receptor superfamily. in Human Genome Evolution. M. S. Jackson, T. Strachan, and G. Dover (eds), Pp. 93-119, BIOS Scientific, Oxford. 11. Yokoyama, S. and Yokoyama, R. (1996) Adaptive evolution of photoreceptors and visual pigments in vertebrates. Annu. Rev. Ecol. Syst. 27: 543-567. 12. Yokoyama, S. (1997) Molecular genetic basis of adaptive selection: Examples from color vision in vertebrates. Annu. Rev. Genet. 31: 315-336. 13. Yokoyama, S. (2000) Phylogenetic analysis and experimental approaches to study color vision in vertebrates. In:Vertebrate Phototransduction and the Visual Cycle. Methods in Enzymology 315: 312-325. 14. Yokoyama, S. (2000) Molecular evolution of vertebrate visual pigments. Prog. Ret. Eye Res. 19: 385-419.

15 15. Yokoyama, S. and Yokoyama, R. (2000) Comparative molecular biology of visual pigments. in Handbook of Biological Physics, D. G. Stavenga, W. J. de Grip & E. N. Pugh, Jr. (eds.), pp. 257-296. Elesevier, Amsterdam. 16. Yokoyama, S. (2002) Evaluating adaptive evolution (News & Views). Nature Genet. 30: 350-351. 17. Yokoyama, S. (2005) Molecules, biodiversity and adaptive evolution. J. Hered. 96: 169-170. (Editorial introduction for a symposium volume.) 18. Yokoyama, S. (September 2006) Visual pigment genes: Evolution. In: ENCYCLOPEDIA OF LIFE SCIENCES. John Wiley & Sons, Ltd: Chichester http://www.net/[doi: 10.1002/npg.els.0006148]. 19. Yokoyama, S. and Tada, T. (2007) The evolution of ultraviolet vision in vertebrates. In: Evolution of Nervous Systems. (T. H. Bulloch, ed.). Elsevier, Amsterdam. Pp. 349-353. 20. Yokoyama, S. (2008) Evolution of dim-light and color vision pigments. Annu. Rev. Genomics Hum. Genet. 9: 259-282. 21. Yokoyama, S. (2012) Synthesis of experimental molecular biology and evolutionary biology. BioScience (invited review).

Book Reviews: 1. Yokoyama, S. Review of The Genetics of Altruism by S. A. Boorman and P. R. Levitt (Academic Press, New York, 1980). Am. J. Hum. Genet. 34:362-363. 2. Cloninger, C. R. and Yokoyama, S. Review of Genes, Minds, and Culture: The Co-evolutionary Processes by C. J. Lumsden and E. O. Wilson (Harvard Univ. Press, Cambridge, Mass., 1981). Science 213:749-751. 3. Yokoyama, S. Review of The Neutral Theory of Molecular Evolution by Motoo Kimura (Cambridge Univ. Press, Cambridge, 1983). Am. J. Phys. Anthrop. 65:401-402. 4. Yokoyama, S. Review of Population Genetics and Molecular Evolution, (T. Ohta and K. Aoki (eds) (Japan Scientific Societies Press, Tokyo, 1985). Mol. Biol. Evol. 3:459-460. 5. Yokoyama, S. Review of Oxford Surveys on Eukaryotic Genes. Vol. 7 N. McLean (ed) (Oxford Univ. Press, Oxford, 1991). Quart. Rev. Biol. 68:99-100.

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