Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes

Molecular Biology and Evolution

Volumn 25, Issue 10, 2008, Pages 2199-2209

  Hughes, Austin L ^a   Friedman, Robert ^a   Rivailler, Pierre ^a   French, Jeffrey O ^a  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

Bacterial evolution; Homologous recombination; McDonald Kreitman test; Neutrality index; Nucleotide substitution

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIAL STRAIN; CONTROLLED STUDY; GENE LOCUS; GENETIC POLYMORPHISM; GENETIC VARIABILITY; NONHUMAN; PREDICTOR VARIABLE; STATISTICS;

BACTERIA (MICROORGANISMS);

EID: 51649122447     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn166     Document Type: Article

References (50)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Bazin E, Glémin S, Galtier N. 2006. Population size does not influence mitochondrial genetic diversity in animals. Science. 312:570-572.
3. Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, Hartl DL. 2002. The cost of inbreeding in Arabidopsis. Nature. 416:531-534.
4. Charlesworth J, Eyre-Walker A. 2006. The rate of adaptive evolution in enteric bacteria. Mol Biol Evol. 23:1348-1356.
5. Charlesworth J, Eyre-Walker A. 2007. The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations. Proc Natl Acad Sci USA. 104:16992-16997.
6. Cohan FM. 2002. What are bacterial species? Annu Rev Microbiol. 56:457-487.
7. Eyre-Walker A. 2002. Changing effective population size and the McDonald-Kreitman test. Genetics. 162:2017-2024.
8. Feil EJ, Holmes EC, Bessen DE, et al. (12 co-authors). 2001. Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences. Proc Natl Acad Sci USA. 98:182-187.
9. Fraser C, Hanage WP, Spratt BG. 2007. Recombination and the nature of bacterial speciation. Science. 315:476-480.
10. Hollander M, Wolfe DA. 1973. Nonparametric statistical methods. New York: Wiley.
11. Hughes AL. 2005. Evidence for abundant slightly deleterious polymorphisms in bacterial populations. Genetics. 169:533-538.
12. Hughes AL. 2007. Looking for Darwin in all the wrong places: The misguided quest for positive selection at the nucleotide sequence level. Heredity. 99:364-373.
13. Hughes AL, French JO. 2007. Homologous recombination and the pattern of nucleotide substitution in Ehrlichia ruminantium. Gene. 387:31-37.
14. Hughes AL, Friedman R. 2004. Patterns of sequence divergence in 5′ intergenic spacers and linked coding regions in 10 species of pathogenic Bacteria reveal distinct recombinational histories. Genetics. 168:1795-1803.
15. Hughes AL, Friedman R. 2005. Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus. J Bacteriol. 187:2698-2704.
16. Hughes AL, Friedman R, Glenn NL. 2006. The future of data analysis in evolutionary genomics. Curr Genomics. 7:227-234.
17. Hughes AL, Hughes MA. 2007a. More effective purifying selection on RNA viruses than in DNA viruses. Gene. 404:117-125.
18. Hughes AL, Hughes MA. 2007b. Coding sequence polymorphism in avian mitochondrial genomes reflects population histories. Mol Ecol. 16:1369-1376.
19. Hughes AL, Langley KL. 2007. Nucleotide usage, synonymous substitution pattern, and past recombination in genomes of Streptococcus pyogenes. Infect Genet Evol. 7:188-196.
20. Hughes AL, Piontkivska H. 2008. Nucleotide sequence polymorphism in circoviruses. Infect Genet Evol. 8:130-138.
21. Hughes AL, Packer B, Welsch R, Bergen AW, Chanock SJ, Yeager M. 2003. Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc Natl Acad Sci USA. 100:15754-15757.
22. Irausquin SJ, Hughes AL. 2008. Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures. J Gen Virol. 89:1921-1929.
23. Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8:275-282.
24. Kumar S, Tamura K, Nei M. 2004. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5:150-163.
25. Lynch M. 2007. The origins of genome architecture. Sunderland (MA): Sinauer.
26. Lynch M, Conery S. 2003. The origins of genome complexity. Science. 302:1401-1404.
27. Lynch M, Bürger R, Butcher D, Gabriel W. 1993. The mutational meltdown in asexual populations. J Hered. 84:339-344.
28. Majewski J. 2001. Sexual isolation in bacteria. FEMS Microbiol Lett. 199:161-169.
29. McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 351:114-116.
30. Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
31. Nei M, Jin L. 1989. Variances of the average numbers of nucleotide substitutions within and between populations. Mol Biol Evol. 6:290-300.
32. Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. New York: Oxford University Press.
33. Ohta T. 1973. Slightly deleterious mutant substitutions in evolution. Nature. 246:96-98.
34. Ohta T. 1993. Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size. Proc Natl Acad Sci USA. 90:4548-4551.
35. Rand DM, Kann LM. 1996. Excess amino acid polymorphism in mitochondrial DNA: Contrasts among genes from Drosophila, mice, and humans. Mol Biol Evol. 13:735-748.
36. Rocha EP, Maynard Smith J, Hurst LD, Holden MT, Cooper JE, Smith NH, Feil EJ. 2006. Comparisons of dN/dS are time dependent for closely related bacterial genomes. J Theor Biol. 239:226-235.
37. Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
38. Sawyer SA, Parsch J, Zhang Z, Hart DL. 2007. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. Proc Natl Acad Sci USA. 104:6504-6510.
39. Schaeffer SW. 2002. Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura. Genet Res. 80:163-175.
40. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 18:502-504.
41. Shapiro J, Huang W, Zhang C, et al. (12 co-authors). 2007. Adaptive genic evolution in Drosophila genomes. Proc Natl Acad Sci USA. 104:2271-2276.
42. Sharp PM. 1991. Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. J Mol Evol. 33:23-33.
43. Smith NG, Eyre-Walker A. 2002. Adaptive evolution in Drosophila. Nature. 415:1022-1024.
44. Sokal RR, Rohlf FJ. 1981. Biometry, 2nd ed. New York: W.H. Freeman.
45. Swofford DL. 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods). Sunderland (MA): Sinauer.
46. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:585-595.
47. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: Improvement of the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
48. Vulić M, Dionisio F, Taddei F, Radman M. 1997. Molecular keys to speciation: dNA polymorphism and the control of genetic exchange in enterobacteria. Proc Natl Acad Sci USA. 94:9763-9767.
49. Whittam TS, Nei M. 1991. Neutral mutation hypothesis test. Nature. 354:115-116.
50. Yang Z, Nielsen R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol. 17:32-43.