Inferences about the distribution of dominance drawn from yeast gene knockout data

Genetics

Volumn 187, Issue 2, 2011, Pages 553-566

  Agrawal, Aneil F ^a   Whitlock, Michael C ^b  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; FUNGAL GENE; FUNGAL GENETICS; GENE MUTATION; GENETIC HETEROGENEITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; SACCHAROMYCES CEREVISIAE; YEAST;

GENE KNOCKOUT TECHNIQUES; GENES, DOMINANT; GENETICS, POPULATION; MODELS, GENETIC; MUTATION; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES CEREVISIAE;

EID: 79951526578     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.110.124560     Document Type: Article

References (62)

1. BELL, G., 2010 Experimental genomics of fitness in yeast. Proc. R. Soc. B 277:1459-1467.
2. BOURGUET, D., 1999 The evolution of dominance. Heredity 83: 1-4.
3. BOURGUET, D., T. LENORMAND, T GUILEMAUD, V. MARCEL, D. FOURNIER et al., 1997 Variation of dominance of newly arisen adaptive genes. Genetics 147: 1225-1234.
4. CABALLERO, A., and P. D. KEIGHTLEY, 1994 A pleiotropic nonadditive model of variation in quantitative traits. Genetics 138: 883-900.
5. CABALLERO, A., P. D. KEIGHTLEY and M. TURELLI, 1997 Average dominance for polygenes: drawbacks of regression estimates. Genetics 147: 1487-1490.
6. CHARLESWORTH, B., 1979 Evidence against Fisher's theory of dominance. Nature 278: 848-849.
7. CHARLESWORTH, B., and D. CHARLESWORTH, 1987 Inbreeding depression and its evolutionary consequences. Annu. Rev. Ecol. Syst. 18: 237-268.
8. CHARLESWORTH, B., and D. CHARLESWORTH, 1998 Some evolutionary consequences of deleterious mutations. Genetica 102/103: 3-19.
9. CHARLESWORTH, D., M. T. MORGAN and B. CHARLESWORTH, 1990 Inbreeding depression, genetic load, and the evolution of outcrossing rates in a multilocus system with no linkage. Evolution 44: 1469-1489.
10. CHAVARRÍAS, D., C. LÓPEZ-FANJUL and A. GARCÍA- DORADO, 2001 The rate of mutation and the homozygous and heterozygous mutational effects for competitive viability: a long-term experiment with Drosophila melanogaster. Genetics 158: 681-693.
11. CLARKE, C. A., 1964 Frequency-dependent selection for the dominance of rare polymorphic genes. Evolution 18: 364-369.
12. DENG, H.-W., and M. LYNCH, 1996 Estimation of deleterious-mutation parameters in natural populations. Genetics 144: 349-360.
13. FISHER, R. A., 1928 The possible modi+cation of the response of the wild type to recurrent mutations. Am. Nat. 62: 115-126.
14. FRY, J. D., 2004 On the rate and linearity of viability declines in Drosophila mutation-accumulation experiments: genomic mutation rates and synergistic epistasis revisited. Genetics 166: 797-806.
15. FRY, J. D., and S. V. NUZHDIN, 2003 Dominance of mutations affecting viability in Drosophila melanogaster. Genetics 163: 1357-1364.
16. GARCÍA-DORADO, A., and A. CABALLERO, 2000 On the average coefficient of dominance of deleterious spontaneous mutations. Genetics 155: 1991-2001.
17. GIAEVER, G., A. M. CHU, L. NI, C. CONNELLY, L. RILES et al., 2002 Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
18. HALDANE, J. B. S., 1927 A mathematical theory of natural and artificial selection, part V: selection and mutation. Proc. Camb. Philos. Soc. 23: 838-844.
19. HALDANE, J. B. S., 1937 The effect of variation in fitness. Am. Nat. 71: 337-349.
20. HALDANE, J. B. S., 1939 The theory of the evolution of dominance. J. Genet. 37: 365-374.
21. HEDRICK, P. W., 1994 Purging inbreeding depression and the probability of extinction: full-sib mating. Heredity 73: 363-372.
22. HILLENMEYER, M. E., E. FUNG, J. WILDENHAIN, S. E. PIERCE, S. HOON et al., 2008 The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science 320: 362-365.
23. HOULE, D., K. A. HUGHES, S. ASSIMACOPOULOS and B. CHARLESWORTH, 1997 The effects of spontaneous mutation on quantitative traits. II. Dominance of mutations with effects on life-history traits. Genet. Res. Camb. 90: 27-34.
24. HUGHES, T. R., C. J. ROBERTS, H. DAI, A. R. JONES, M. R. MEYER et al., 2000 Widespread aneuploidy revealed by DNA microarray expression profiling. Nature Genetics 25: 333-337.
25. HURST, L. D., and J. P. RANDERSON, 2000 Dosage, deletions and dominance: simple models of the evolution of gene expression. J. Theor. Biol. 205: 641-647.
26. KACSER, H., and J. A. BURNS, 1981 The molecular basis of dominance. Genetics 97: 639-666.
27. KEIGHTLEY, P. D., 1996 Metabolic models of selection response. J. Theor. Biol. 182: 311-316.
28. KEIGHTLEY, P. D., and H. KACSER, 1987 Dominance, pleiotropy and metabolic structure. Genetics 117: 319-329.
29. KONDRASHOV, F. A., and E. V. KOONIN, 2004 A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends Genet. 20: 287-291.
30. LANDE, R., and D. W. SCHEMSKE, 1985 The evolution of self-fertilization and inbreeding depression in plants. I. Genetic models. Evolution 39: 24-40.
31. MACKAY, T. F. C., R. F. LYMAN and M. S. JACKSON, 1992 Effects of P element insertions on quantitative traits in Drosophila melanogaster. Genetics 130: 315-332.
32. MCANALLY, A. A., and L. Y. YAMPOLSKY, 2010 Widespread transcriptional autosomal dosage compensation in Drosophila correlates with gene expression level. Genome Biol. Evol. 2: 44-52.
33. MORTON, N. E., 1971 Population genetics and disease control. Soc. Biol. 18: 243-251.
34. MUKAI, T., 1969 The genetic structure of natural populations of Drosophila melanogaster. VI. Further studies on the optimum heterozygosity hypothesis. Genetics 61: 479-495.
35. MUKAI, T., and T. YAMAZAKI, 1968 The genetic structure of natural populations of Drosophila melanogaster. V. Coupling-repulsion effect of spontaneous mutant polygenes controlling viability. Genetics 59: 513-535.
36. MUKAI, T., S. CHIGUSA and I. YOSHIKAWA, 1964 The genetic structure of natural populations of Drosophila melanogaster. II. Overdominance of spontaneous mutant polygenes controlling viability in homozygous genetic background. Genetics 50: 711-715.
37. MUKAI, T., S. CHIGUSA and I. YOSHIKAWA, 1965 The genetic structure of natural populations of Drosophila melanogaster. III. Dominance effect of spontaneous mutant polygenes controlling viability in heterozygous genetic backgrounds. Genetics 52: 493-501.
38. MULLER, H. J., 1950 Our load of mutations. Am. J. Hum. Gen. 2: 111-176.
39. OHNISHI, O., 1977a Spontaneous and ethyl methanesulfonate-induced mutations controlling viability in Drosophila melanogaster. II. Homozygous effect of polygenic mutations. Genetics 87: 529-545.
40. OHNISHI, O., 1977b Spontaneous and ethyl methanesulfonate-induced mutations controlling viability in Drosophila melanogaster. III. Heterozygous effect of polygenic mutations. Genetics 87: 547-556.
41. OMHOLT, S. W., E. PLAHTE, L. ØYEHAUG and K. XIANG, 2000 Gene regulatory networks generating the phenomena of additivity, dominance, and epistasis. Genetics 155: 969-980.
42. ORR, H. A., 2003 The distribution of fitness effects among beneficial mutations. Genetics 163: 1519-1526.
43. ORR, H. A., and A. J. BETANCOURT, 2001 Haldane's sieve and adaptation from the standing genetic variation. Genetics 157: 875-884.
44. OTTO, S. P., and D. BOURGUET, 1999 Balanced polymorphisms and the evolution of dominance. Am. Nat. 153: 561-574.
45. PETERS, A. D., D. L. HALLIGAN, M. C. WHITLOCK and P. D. KEIGHTLEY, 2003 Dominance and overdominance of mildly deleterious induced mutations for fitness traits in Caenorhabditis elegans. Genetics 165: 589-599.
46. PHADNIS, N., and J. D. FRY, 2005 Widespread correlations between dominance and homozygous effects of mutations: implications for theories of dominance. Genetics 171: 385-392.
47. PROVINE, W. R., 1986 Sewall Wright and Evolutionary Biology. University of Chicago Press, Chicago.
48. R DEVELOPMENT CORE TEAM, 2009 R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna. http://www.R-project.org.
49. SGD PROJECT, 2009 Saccharomyces Genome Database. Accessed July 7, 2009. http://www.yeastgenome.org/
50. SHOEMAKER, D. D., D. A. LASHKARI, D. MORRIS, M. MITTMAN and R. W. DAVIS, 1996 Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat. Genet. 14: 450-456.
51. SIMMONS, M. J., and J. F. CROW, 1977 Mutations affecting fitness in Drosophila populations. Annu. Rev. Genet. 11: 49-78.
52. SLIWA, P., and R. KORONA, 2005 Loss of dispensable genes is not adaptive in yeast. Proc. Natl. Acad. Sci. USA 102: 17670-17674.
53. STEINMETZ, L. M., C. SCHARFE, A. M. DEUTSCHBAUER, D. MOKRANJAC, Z. S. HERMAN et al., 2002 Systematic screening for human disease genes in yeast. Nat. Genet. 31: 400-404.
54. SZAFRANIEC, K., D. M. WLOCH, P. SLIWA, R. H. BORTS and R. KORONA, 2003 Small fitness effects and weak genetic interactions between deleterious mutations in heterozygous loci of the yeast Saccharomyces cerevisiae. Genet. Res. Camb. 82: 19-31.
55. VASSILIEVA, L., A. HOOK and M. LYNCH, 2000 The fitness effects of spontaneous mutations in Caenorhabditis elegans. Evolution 54: 1234-1246.
56. VEITIA, R. A., 2005 Gene dosage balance: deletions, duplications and dominance. Trends Genet. 21: 33-35.
57. WAGNER, G., and R. BÜRGER, 1985 On the evolution of dominance modifiers II: a non-equilibrium approach to the evolution of genetic systems. J. Theor. Biol. 113: 475-500.
58. WARTON, D. I., and N. C. WEBER, 2002 Common slope tests for bivariate errors-in-variables models. Biom. J. 44: 161-174.
59. WHITLOCK, M. C., 2002 Selection, load, and inbreeding depression in a large metapopulation. Genetics 160: 1191-1202.
60. WILKIE, A. O. M., 1994 The molecular basis of genetic dominance. J. Med. Genet. 31: 89-98.
61. WRIGHT, S., 1929 Fisher's theory of dominance. Am. Nat. 63: 274-279.
62. WRIGHT, S., 1934 Physiological and evolutionary theories of dominance. Am. Nat. 67: 24-53.