The probability of duplicate gene preservation by subfunctionalization

Genetics

Volumn 154, Issue 1, 2000, Pages 459-473

  Lynch, Michael ^a   Force, Allan ^a  

^a UNIVERSITY OF OREGON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE DUPLICATION; GENE EXPRESSION; GENE LOCUS; GENE MUTATION; GENOME; HYPOTHESIS; PRIORITY JOURNAL; PROBABILITY; TISSUE SPECIFICITY; ZEBRA FISH;

EVOLUTION; GENE DUPLICATION; MODELS, GENETIC; PROBABILITY;

DANIO RERIO;

EID: 0033972072     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (51)

1. ALLENDORF, F. W., F. M. UTTER and B. P. MAY, 1975 Gene duplication within the family Salmonidae: II. Detection and determination of the genetic control of duplicate loci through inheritance studies and the examination of populations, pp. 415-432 in Isozymes, Vol. IV: Genetics and Evolution, edited by C. L. MARKERI, Academic Press, New York.
2. AMORES, A., A. FORCE, Y.-L. YAN, L. JOLY, C. AMEMIYA et al., 1998 Zebrafish hox clusters and vertebrate genome evolution. Science 282: 1711-1714.
3. ARNONE, M. I., and E. H. DAVIDSON, 1997 The hardwiring of development: organization and function of genomic regulatory sequences. Development 124: 1851-1864.
4. BAILEY, G. S., R. T. M. POULTER and P. A. STOCKWELL, 1978 Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci. Proc. Natl. Acad. Sci. USA 75: 5575-5579.
5. BIRKY, C. W., JR., and J. B. WALSH, 1988 Effects of linkage on rates of molecular evolution. Proc. Natl. Acad. Sci. USA 85: 6414-6418.
6. BROOKFIELD, J. F. Y., 1997 Genetic redundancy. Adv. Genet. 36: 137-155.
7. CHRISTIANSEN, F. B., and O. FRYDENBERG, 1977 Selection-mutation balance for two nonallelic recessives producing an inferior double homozygote. Am. J. Hum. Genet. 29: 195-207.
8. CLARK, A. G., 1994 Invasion and maintenance of a gene duplication. Proc. Natl. Acad. Sci. USA 91: 2950-2954.
9. CLARK, A. G., L. WANG and T. HULLEBERB, 1995 Spontaneous mutation rate of modifiers of metabolism in Drosophila. Genetics 139: 767-779.
10. DILEONE, R. J., L. B. RUSSELL and D. M. KINGSLEY, 1998 An extensive 3′ regulatory region controls expression of Bmp5 in specific anatomical structures of the mouse embryo. Genetics 148: 401-408.
11. DONNELLY, P., and S. TAVARE, 1995 Coalescents and genealogical structure under neutrality. Annu. Rev. Genet. 29: 401-421.
12. FERRIS, S. D., and G. S. WHITE, 1979 Evolution of the differential regulation of duplicate genes after polyploidization. J. Mol. Evol. 12: 267-317.
13. FISHER, R. A., 1935 The sheltering of lethals. Am. Nat. 69: 446-455.
14. FORCE, A., M. LYNCH, F. B. PICKETT, A. AMORES, Y.-L. YAN et al., 1999 Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
15. GERHART, J., and M. KIRSCHNER, 1997 Cells, Embryos, and Evolution. Blackwell Science, Malden, MA.
16. GRAF, J.-D., and H. R. KOBEL, 1991 Genetics, pp. 19-34, in Methods in Cell Biology, Vol. 36, Xenopus laevis: Practical Uses in Cell and Molecular Biology, edited by B. K. KAY and H. B. PENG. Academic Press, New York.
17. HALDANE, J. B. S., 1933 The part played by recurrent mutation in evolution. Am. Nat. 67: 5-9.
18. HENIKOFF, S., E. A. GREENE S. PIETROKOVSKI, P. BORK, T. K. ATTWOOD et al., 1997 Gene families: the taxonomy of protein paralogs and chimeras. Science 278: 609-614.
19. HILL, W. G., and A. ROBERTSON, 1966 The effect of linkage on limits to artificial selection. Genet. Res. 8: 269-294.
20. HUANG, J. D., D. H. SCHWYIER, J. M. SHIROKAWA and A. J. COUREY, 1993 The interplay between multiple enhancer and silencer elements defines the pattern of decapentaplegic expression. Genes Dev. 7: 694-704.
21. HUDSON, R. R., 1991 Gene genealogies and the coalescent process. Oxford Surv. Evol. Biol. 7: 1-44.
22. HUGHES, M. K., and A. L. HUGHES, 1993 Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol. Biol. Evol. 10: 1360-1369.
23. JACK, J., and Y. DELOTTO, 1995 Structure and regulation of a complex locus: the cut gene of Drosophila. Genetics 139: 1689-1700.
24. KAMMANDEL, B., K. CHOWDHURY, A. STOYKOVA, S. APARICIO, S. BRENNER et al., 1999 Distinct cis-essential modules direct the time-space pattern of the Pax6 gene activity. Dev. Biol. 205: 79-97.
25. KIMURA, M., 1983 The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, United Kingdom.
26. KIMURA, M., and J. L. KING, 1979 Fixation of a deleterious allele at one of two "duplicate" loci by mutation pressure and random drift. Proc. Natl. Acad. Sci. USA 76: 2858-2861.
27. KIMURA, M., and T. OHTA, 1969 The average number of generations until fixation of a mutant gene in a finite population. Genetics 61: 763-771.
28. KINGMAN, J. F. C., 1982 The coalescent. Stoch. Proc. Appl. 13: 235-248.
29. KIRCHHAMER, C. V., C.-H. YUH and E. H. DAVIDSON. 1996 Modular cis-regulatory organization of developmentally expressed genes: two genes transcribed territorially in the sea urchin embryo, and additional examples. Proc. Natl. Acad. Sci. USA 93: 9322-9328.
30. LI, W.-H., 1980 Rate of gene silencing at duplicate loci: a theoretical study and interpretation of data from tetraploid fishes. Genetics 95: 237-258.
31. LI, W.-H., 1985 Accelerated evolution following gene duplication and its implication for the neutralist-selectionist controversy, pp. 333-352, in Population Genetics and Molecular Evolution, edited by T. OHTA and K. AOKI. Springer-Verlag, Berlin.
32. LUNDIN, L., 1993 Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16: 1-9.
33. NADEAU, J. H., and D. SANKOFF, 1997 Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution. Genetics 147: 1259-1266.
34. NEI, M., and A. K. ROYCHOUDHURY, 1973 Probability of fixation of nonfunctional genes at duplicate loci. Am. Nat. 107: 362-372.
35. NORMES, S., M. CLARKSON, I. MIKKOLA, M. PEDERSEN, A. BARDSLEY et al., 1998 Zebrafish contains two Pax6 genes involved in eye development. Mech. Dev. 77: 185-196.
36. NOWAK, M. A., M. C. BOERLIJST, J. COOKE and J. M. SMITH, 1997 Evolution of genetic redundancy. Nature 388: 167-170.
37. OHNO, S., 1970 Evolution by Gene Duplication. Springer-Verlag, Berlin.
38. OHTA, T., 1987 Simulating evolution by gene duplication. Genetics 115: 207-213.
39. OHTA, T., 1988 Time for acquiring a new gene by duplication. Proc. Natl. Acad. Sci. USA 85: 3509-3512.
40. POSTLETHWATI, J. H., Y.-L. YAN, M. GATES, S. HORNE, A. AMORES et al., 1998 Vertebrate genome evolution and the zebrafish gene map. Nat. Genet. 18: 345-349.
41. RAMOS-ONSINS, S., and M. AGUADE, 1998 Molecular evolution of the Cecropin multigene family in Drosophila: functional genes vs. pseudogenes. Genetics 150: 157-171.
42. SIDOW, A., 1996 Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6: 715-722.
43. SLUSARSKI, D. C., C. K. MOTSNY and R. HOLMGREN, 1995 Mutations that alter the timing and pattern of cubitus interruptus gene expression in Drosophila melanogaster. Genetics 139: 229-240.
44. STOLTZFUS, A., 1999 On the possibility of constructive neutral evolution. J. Mol. Biol. 49: 169-181.
45. TAKAHATA, N., and T. MARUYAMA, 1979 Polymorphism and loss of duplicate gene expression: a theoretical study with application to tetraploid fish. Proc. Natl. Acad. Sci. USA 76: 4521-4525.
46. WAGNER, A., 1999 Redundant gene functions and natural selection. J. Evol. Biol. 12: 1-16.
47. WALSH, J. B., 1995 How often do duplicated genes evolve new functions? Genetics 110: 345-364.
48. WATTERSON, G. A., 1983 On the time for gene silencing at duplicate loci. Genetics 105: 745-766.
49. WENDEL, J. F., 1999 Genome evolution in polyploids. Plant Mol. Biol. (in press).
50. WESTIN, J., and M. LARDELLI, 1997 Three novel notch genes in zebrafish: implications for vertebrate Notch gene evolution and function. Dev. Genes Evol. 207: 51-63.
51. XU, P.-X., X. ZHANG, S. HEANEY, A. YOON, A. M. MICHELSON et al., 1999 Regulation of Pax6 expression is conserved between mice and flies. Development 126: 383-395.