The distribution of fitness effects of new deleterious amino acid mutations in humans

Genetics

Volumn 173, Issue 2, 2006, Pages 891-900

  Eyre Walker, Adam ^a,b   Woolfit, Megan ^a,c   Phelps, Ted ^a  

^a UNIVERSITY OF SUSSEX   (United Kingdom)

^b NATIONAL EVOLUTIONARY SYNTHESIS CENTER   (United States)

^c TRINITY COLLEGE DUBLIN   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

ARTICLE; DEMOGRAPHY; FITNESS; GENE FREQUENCY; GENE MUTATION; NONHUMAN; POPULATION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; AMINO ACID SUBSTITUTION; AMINO ACIDS; BIOMETRY; GENE FREQUENCY; GENETICS, POPULATION; HUMANS; MODELS, GENETIC; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT, HERITABLE; SELECTION (GENETICS); TIME FACTORS;

EID: 33745347447     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.057570     Document Type: Article

References (53)

1. ADAMS, A. M., and R. R. HUDSON, 2004 Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single nucleotide polymorphisms. Genetics 168: 1699-1712.
2. ANDOLFATTO, P., 2005 Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.
3. BERGMAN, C. M., and M. KREITMAN, 2001 Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome Res 11: 1335-1345.
4. CARDON, L. R., and J. I. BELL, 2001 Association study designs for complex diseases. Nat. Rev. Genet. 2: 91-99.
5. CARGILL, M., D. ALTSHULER, J. IRELAND, P. SKLAR, K. ARDLIE et al., 1999 Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nature Genetics 22: 231-238.
6. CHAMARY, J. V., and L. D. HURST, 2004 Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: evidence for selectively driven codon usage. Mol. Biol. Evol. 21: 1014-1023.
7. CHAO, L., and D. E. CARR, 1993 The molecular clock and the relationship between population size and generation time. Evolution 47: 688-690.
8. CHARLESWORTH, B.,M. T. MORGAN and D. CHARLESWORTH, 1993 The effect of deleterious mutationson neutral molecular variation. Genetics 134: 1289-1303.
9. CHARLESWORTH, B., H. BORTHWICK, C. BARTOLOME and P. PIGNATELLI, 2004 Estimates of the genomic rate of detrimental alleles in Drosophila melanogaster. Genetics 167: 815-826.
10. CHIMPANZEE SEQUENCING AND ANALYSIS CONSORTIUM, 2005 Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
11. COHEN, J. C., R. S. KISS, A. PERTSEMLIDIS, Y. L. MARCEL, R. MCPHERSON et al., 2004 Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 305: 869-872.
12. CROW, J. F., 1997 The high spontaneous mutation rate: Is it health risk? Proc. Natl. Acad. Sci. USA 94: 8380-8386.
13. DAVIES, E. K., A. D. PETERS and P. D. KEIGHTLEY, 1999 High frequency of cryptic deleterious mutations in Caenorhabditis elegans. Science 285: 1748-1751.
14. DERMITZAKIS, E. T., and A. G. CLARK, 2001 Differential selection after duplication in mammalian developmental genes. Mol. Biol. Evol. 18: 557-562.
15. DERMITZAKIS, E. T., A. REYMOND, N. SCAMUFFA, C. UCLA, E. KIRKNESS et al., 2003 Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science 302: 1033-1035.
16. ESTES, S., P. C. PHILLIPS, D. R. DENVER, W. K. THOMAS and M. LYNCH, 2004 Mutation accumulation in populations of varying size: the distribution of mutational effects for fitness correlates in Caenorhabditis elegans. Genetics 166: 1269-1279.
17. EYRE-WALKER, A., and P. D. KEIGHTLEY, 1999 High genomic deleterious mutation rates in hominids. Nature 397: 344-347.
18. EYRE-WALKER, A., P. D. KEIGHTLEY, N. G. C. SMITH and D. GAFFNEY, 2002 Quantifying the slightly deleterious model of molecular evolution. Mol. Biol. Evol. 19: 2142-2149.
19. FAY, J., G. J. WYCOFF and C.-I WU, 2001 Positive and negative selection on the human genome. Genetics 158: 1227-1234.
20. 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.
21. HADDRILL, P. R., B. CHARLESWORTH, D. L. HALLIGAN AND P. ANDOLFATTO, 2005 Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biol. 6: R67.
22. JORDE, L. B., M. BAMSHAD and A. R. ROGERS, 1997 Using mitochondrial and nuclear DNA markers to reconstruct human evolution. BioEssays 20: 126-136.
23. KEIGHTLEY, P. D., 1994 The distribution of mutation effects on viability in Drosophila melanogaster. Genetics 138: 1315-1322.
24. KEIGHTLEY, P. D., 1996 Nature of deleterious mutation load in Drosophila. Genetics 144: 1993-1999.
25. KEIGHTLEY, P. D., and D. J. GAFFNEY, 2003 Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proc. Natl. Acad. Sci. USA 100: 13402-13406.
26. KEIGHTLEY, P. D., M. J. LERCHER and A. EYRE-WALKER, 2005 Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol. 3: e42.
27. KIM, Y., and W. STEPHAN, 2002 Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
28. KIMURA, M., 1979 Model of effectively neutral mutations in which selective constraint is incorporated. Proc. Natl. Acad. Sci. USA 76: 3440-3444.
29. KIRKPATRICK, S., C. D. GELATT and M. P. VECCHI, 1983 Optimization by simulated annealing. Science 220: 671-680.
30. LANDE, R., 1994 The risk of population extinction from new deleterious mutations. Evolution 48: 1460-1469.
31. LIVINGSTON, R. J., A. VON NIEDERHAUSERN, A. G. JEGGA, D. C. CRAWFORD, C. S. CARLSON et al., 2004 Pattern of sequence variation across 213 environmental response genes. Genome Res. 14: 1821-1831.
32. LOEWE, L., B. CHARLESWORTH, C. BARTOLOME and V. NOEL, 2006 Estimating selection on nonsynonymous mutations. Genetics 172: 1079-1092.
33. LOHMUELLER, K. E., C. L. PEARCE, M. PIKE, E. S. LANDER and J. N. HIRSCHHORN, 2003 Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat. Genet. 33: 177-182.
34. LYNCH, M., J. BLANCHARD, D. HOULE, T. KIBOTA, S. SCHULTZ et al., 1999 Spontaneous deleterious mutation. Evolution 53: 645-663.
35. LYNCH, M., J. CONERY and R. BURGER, 1995 Mutation accumulation and the extinction of small populations. Am. Nat. 146: 489-518.
36. MCVEAN, G. A., and B. CHARLESWORTH, 2000 The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics 155: 929-944.
37. MULLER, H. J., 1950 Our load of mutations. Am. J. Hum. Genet. 2: 111-176.
38. NIELSEN, R., and Z. YANG, 2003 Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol. Biol. Evol. 20: 1231-1239.
39. OHTA, T., 1977 Extension of the neutral mutation drift hypothesis, pp. 148-167 in Molecular Evolution and Polymorphism, edited by M. KIMURA. National Institute of Genetics, Mishima, Japan.
40. OPHIR, R., and D. GRAUR, 1997 Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene 31: 191-202.
41. OTTO, S. P., and M. C. WHITLOCK, 1997 The probability of fixation in populations of changing size. Genetics 146: 723-733.
42. PIGANEAU, G., and A. EYRE-WALKER, 2003 Estimating the distribution of fitness effects from DNA sequence data: implications for the molecular clock. Proc. Natl. Acad. Sci. USA 100: 10335-10340.
43. SAWYER, S., R. J. KULATHINAL, C. D. BUSTAMANTE and D. L. HARTL, 2003 Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection. J. Mol. Evol. 57: 5154-5164.
44. SHABALINA, S. A., and A. S. KONDRASHOV, 1999 Pattern of selective constraint in C. elegans and C. briggsae genomes. Genet. Res. 74: 23-30.
45. SMITH, N. G. C., and A. EYRE-WALKER, 2002 Adaptive protein evolution in Drosophila. Nature 415: 1022-1024.
46. SVED, J., and A. P. BIRD, 1990 The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc. Natl. Acad. Sci. USA 87: 4692-4696.
47. URRUTIA, A. O., and L. D. HURST, 2003 The signature of selection mediated by expression on human genes. Genome Res. 13: 2260-2264.
48. VASSILIEVA, L., A. M. HOOK and M. LYNCH, 2000 The fitness effects of spontaneous mutations in Caenorhabditis elegans. Evolution 54: 1234-1246.
49. WEBSTER, M. T., N. G. C. SMITH, M. J. LERCHER and H. ELLEGREN, 2004 Gene expression, synteny and local similarity in human noncoding mutation rates. Mol. Biol. Evol. 21: 1820-1830.
50. WILLIAMSON, S. H., R. HERNANDEZ, A. FLEDEL-ALON, L. ZHU, R. NIELSEN et al., 2005 Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc. Natl. Acad. Sci. USA 102: 7882-7887.
51. WRIGHT, A., B. CHARLESWORTH, I. RUDAN, A. CAROTHERS AND H. CAMPBELL, 2003 A polygenic basis for late-onset disease. Trends Genet. 19: 97-106.
52. WRIGHT, S., 1938 The distribution of gene frequencies under irreversible mutation. Proc. Natl. Acad. Sci. USA 24: 253-259.
53. YAMPOLSKY, L. Y., F. A. KONDRASHOV and A. S. KONDRASHOV, 2005 Distribution of the strength of selection against amino acid replacements in human proteins. Hum. Mol. Genet. 14: 3191-3201.