Bayesian Analysis Suggests that Most Amino Acid Replacements in Drosophila Are Driven by Positive Selection

Journal of Molecular Evolution

Volumn 57, Issue SUPPL. 1, 2003, Pages

  Sawyer, Stanley A ^a   Kulathinal, Rob J ^b   Bustamante, Carlos D ^c   Hartl, Daniel L ^b  

^a WASHINGTON UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

^c Department of Obstetrics Gynecology   (United States)

Author keywords

Beneficial deleterious mutations; Markov chain Monte Carlo (MCMC); Poisson random field; Polymorphism divergence; Positive selection; Selective neutrality

Indexed keywords

AMINO ACID; DNA;

AMINO ACID SUBSTITUTION; BAYES THEOREM; CONFERENCE PAPER; DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; GENETIC POLYMORPHISM; MONTE CARLO METHOD; NATURAL SELECTION; NONHUMAN; POPULATION GENETICS; PROBABILITY; STATISTICAL MODEL;

AMINO ACID SUBSTITUTION; ANIMALS; BAYES THEOREM; DROSOPHILA; MODELS, GENETIC; MUTATION; POLYMORPHISM, GENETIC; SELECTION (GENETICS); X CHROMOSOME; Y CHROMOSOME;

DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; MELANOGASTER; NES;

EID: 0347380978     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-0022-3     Document Type: Conference Paper

References (42)

1. Adams MD, Celniker SE, Holt RA, et al. (2000) The genome sequence of Drosophila melanogaster. Science 287:2185-2195
2. Akashi H (1995) Inferring weak selection from patterns of poly-morphism and divergence at "silent" sites in Drosophila DNA. Genetics 139:1067-1076
3. Bustamante CD, Nielsen R, Hartl DL (2002a) A maximum likelihood method for analyzing pseudogene evolution: Implications for silent site evolution in humans and rodents. Mol Biol Evol 19:110-117
4. Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, Hartl DL (2002b) The cost of inbreeding in Arabidopsis. Nature 416:531-534
5. Carlin BP, Louis TA (2000) Bayes and empirical Bayes methods for data analysis. Chapman & Hall, London
6. Charlesworth B, Charlesworth D (1997) Rapid fixation of deleterious alleles can be caused by Muller's ratchet. Genet Res 70:63-73
7. Comeron JM, Kreitman M (2002) Population, evolutionary and genomic consequences of interference selection. Genetics 161:389-410
8. Ewens WJ (1972) The sampling theory of selectively neutral alleles. Theor Popul Biol 3:87-112
9. Fay JC, Wu C-I (2000) Hitchhiking under positive Darwinian selection. Genetics 155:1405-1413
10. Fay JC, Wyckoff GJ, Wu C-I (2002) Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415:1024-1026
11. Fu Y-X, Li W-H (1993) Statistical tests of neutrality of mutations. Genetics 133:693-709
12. Galtier N, Depaulis F, Barton NH (2000) Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics 155:981-987
13. Gelman A, Carlin JS, Stern HS, Rubin DB (1997) Bayesian data analysis. Chapman & Hall, London
14. Gilks R, Richardson S, Spiegelhalter DJ (1996) Markov chain Monte Carlo in practice. Chapman & Hall, London
15. Gillespie JH (2000) Genetic drift in an infinite population. The pseudohitchhiking model. Genetics 155:909-919
16. Gould SJ (1989) Tires to sandals: As we strive to understand nature, do we seek truth or solace? Nat Hist 98:8-15
17. Hartl DL, Clark AG (1997) Principles of population genetics. Sinauer Associates, Sunderland, MA
18. Hartl DL, Taubes CH (1996) Compensatory nearly neutral mutations: Selection without adaptation. J Theor Biol 182:303-309
19. Hartl DL, Moriyama EN, Sawyer SA (1994) Selection intensity for codon bias. Genetics 138:227-234
20. Hudson RR (1990) Gene geneologies and the coalescent process. In: Futuyma D, Antonovics J (eds) Oxford surveys in evolutionary biology, Oxford University Press, Oxford, pp 1-44
21. Hudson RR, Bailey K, Skarecky D, Kwiatowski J, Ayala FJ (1994) Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 136:1329-1340
22. Kim Y, Stephan W (2000) Joint effects of genetic hitchhiking and background selection on neutral variation. Genetics 155:1415-1427
23. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
24. Kirby DA, Stephan W (1996) Multi-locus selection and the structure of variation at the white gene of Drosophila melanogaster. Genetics 144:635-645
25. Lewontin RC (1974) The genetic basis of evolutionary change. Columbia University Press, New York
26. Liu JS (2001) Monte Carlo strategies in scientific computing. Springer, New York
27. Maynard Smith J, Haigh J (1974) The hitch-hiking effect of a favorable gene. Genet Res 23:23-35
28. McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654
29. Metropolis N, Rosenbluth A, Rosenbluth M, Teller A, Teller E (1953) Equations of state calculations by fast computing machines. J Chem Phys 21:1087-1091
30. Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-I envelope gene. Genetics 148:929-936
31. Nurminsky DI (2001) Genes in sweeping competition. Cell Mol Life Sci 58:125-134
32. Ohta T (1992) The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23:263-286
33. Sawyer SA, Hartl DL (1992) Population genetics of polymorphism and divergence. Genetics 132:1161-1176
34. Schmid KJ, Tautz D (1997) A screen for fast evolving genes from Drosophila. Proc Natl Acad Sci USA 94:9746-9750
35. Smith NGC, Eyre-Walker A (2002) Adaptive protein evolution in Drosophila. Nature 415:1022-1024
36. Stephan W (1996) The rate of compensatory evolution. Genetics 144:419-426
37. Swanson W.J, Clark AG, Waldrip-Dail HM, Wolfner MF, Aquadro CF (2001) Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proc Natl Acad Sci USA 98:7375-7379
38. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595
39. Templeton AR (1998) Nested clade analysis of phylogeographical data: Testing hypotheses about gene flow and population history. Mol Ecol 7:381-397
40. Templeton AR (2002) Out of Africa again and again. Nature 416:45-51
41. Wakeley J (2000) The effects of subdivision on the genetic divergence of populations and species. Evol Int J Org Evol 54:1092-1101
42. Yang Z (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 15:568-573