Chapter 2 : Studying Evolution Using Genome Sequence Data

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Studying Evolution Using Genome Sequence Data, Page 1 of 2

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The accumulation of well-annotated, complete genome sequences now offers an unprecedented view into the biology of microorganisms, including powerful and practical applications such as the inference of metabolic pathways and lifestyle choices without any experimental evidence. The chapter discusses how genome sequences can be used to examine microbial evolution. It reviews the many ways genomes can change over time, how these processes are inferred by analysis of extant sequences, and how these data sets can be employed to address broad-scale evolutionary questions. Genes certainly change by point mutation, and it is primarily this sort of variation among genomes that has been under scrutiny since the dawn of microbial population biology in the 1970s. As bacteria reproduce by binary fission, homologous recombination between genes found among closely related strains was once thought to be rare, with periodic selection of rare advantageous mutations being a popular and fairly well-supported view. In addition to the alteration of existing DNA, genomes may change by the gain of novel genetic information from outside sources. The bacterial origin of genes responsible for fungal invasion of ruminant intestinal tracts was also evident without genome sequences. Deletions can be a major driving force during genome reduction, whereby large portions--perhaps even the majority--of the genetic material of an organism are lost over time, with little gain of new genes. The chapter focuses on inference of phylogeny and organismal evolution, and new biological approaches enabled by complete genome sequences.

Citation: Lawrence J. 2006. Studying Evolution Using Genome Sequence Data, p 11-33. In Seifert H, DiRita V (ed), Evolution of Microbial Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815622.ch2

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Restriction Fragment Length Polymorphism
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Image of FIGURE 1

Replication slippage events. (A) Slippage at polynucleotide repeats can affect promoter regions, thereby altering expression at downstream loci. Here, replication slippage in the polyguanosine region can alter the separation and relative orientation of sites required for σ-factor recognition of the gene’s promoter. (B) Slippage within open reading frames can stochastically move downstream regions in and out of frame. Here, addition of a pentameric repeat to a region found in-frame will cause the downstream region of the gene to be translated out-of-frame, resulting in a useless protein or premature translation termination.

Citation: Lawrence J. 2006. Studying Evolution Using Genome Sequence Data, p 11-33. In Seifert H, DiRita V (ed), Evolution of Microbial Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815622.ch2
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Image of FIGURE 2

Occurrences of a skewed, asymmetrically distributed sequence in the genome of the α-proteobacterium . The lower panel depicts each sequence on either the Watson (top) or Crick (bottom) strand as a hash mark. The abundance of this sequence on each strand is tabulated in the graph above; the origin and terminus of replication can be inferred from analyses of G+C skew ( ) as well as the distribution of the octomer depicted here. Data are from H. Hendrickson and J. G. Lawrence ( ). The origin was distinguished from the terminus by (i) the position of the gene (typically origin-proximal), and (ii) the orientation of operons encoding rRNAs (typically transcribed away from the origin of replication).

Citation: Lawrence J. 2006. Studying Evolution Using Genome Sequence Data, p 11-33. In Seifert H, DiRita V (ed), Evolution of Microbial Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815622.ch2
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Image of FIGURE 3

A portion of the Z2491 genome ( ) containing the operon (encoding an NADH dehydrogenase). The genes depicted in gray have been inserted into this genome, likely by horizontal gene transfer, dispersing the genes. The plot above shows the overall G+C content over a 200-bp sliding window; non- genes show atypical G+C content, as well as other unusual properties. The average G+C content for each gene is shown as a horizontal bar on the plot.

Citation: Lawrence J. 2006. Studying Evolution Using Genome Sequence Data, p 11-33. In Seifert H, DiRita V (ed), Evolution of Microbial Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815622.ch2
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1. Abe, T.,, S. Kanaya,, M. Kinouchi,, Y. Ichiba,, T. Kozuki, and, T. Ikemura. 2003. Informatics for unveiling hidden genome signatures. Genome Res. 13:693702.
2. Ahmad, S.,, W. G. Weisburg, and, R. A. Jensen. 1990. Evolution of aromatic amino acid biosynthesis and application to the fine-tuned phylogenetic positioning of enteric bacteria. J. Bacteriol. 172:10511061.
3. Andersson, J. O. 2000. Evolutionary genomics: is Buchnera a bacterium or an organelle? Curr. Biol. 10:R866R868.
4. Andersson, J. O., and, S. G. Andersson. 1999. Genome degradation is an ongoing process in Rickettsia. Mol. Biol. Evol. 16:11781191.
5. Andersson, J. O., and, S. G. Andersson. 1999. Insights into the evolutionary process of genome degradation. Curr. Opin. Genet. Dev. 9:664671.
6. Andersson, S. G.,, A. Zomorodipour,, J. O. Andersson,, T. Sicheritz-Ponten,, U. C. Alsmark,, R. M. Podowski,, A. K. Naslund,, A. S. Eriksson,, H. H. Winkler, and, C. G. Kurland. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133140.
7. Arigoni, F.,, F. Talabot,, M. Peitsch,, M. D. Edgerton,, E. Meldrum,, E. Allet,, R. Fish,, T. Jamotte,, M. L. Curchod, and, H. Loferer. 1998. A genome-based approach for the identification of essential bacterial genes. Nat. Biotechnol. 16:851856.
8. Backofen, R.,, N. S. Narayanaswamy, and, F. Swidan. 2002. Protein similarity search under mRNA structural constraints: application to targeted selenocysteine insertion. In Silico Biol. 2:275290.
9. Barinaga, M. 1996. A shared strategy for virulencey. Science 272:12611263.
10. Battersby, A. R. 1994. How nature builds the pigments of life: the conquest of vitamin B12. Science 264:15511557.
11. Baumann, L.,, P. Baumann, and, N. A. Moran. 1998. The endosymbiont (Buchnera) of the aphid Diuraphis noxia contains all the genes of the tryptophan biosynthetic pathway. Curr. Microbiol. 37:5859.
12. Baumann, L.,, P. Baumann,, N. A. Moran,, J. Sandstrom, and, M. L. Thao. 1999. Genetic characterization of plasmids containing genes encoding enzymes of leucine biosynthesis in endosymbionts (Buchnera) of aphids. J. Mol. Evol. 48:7785.
13. Bekaert, M.,, L. Bidou,, A. Denise,, G. Duchateau-Nguyen,, J. P. Forest,, C. Froidevaux,, I. Hatin,, J. P. Rousset, and, M. Termier. 2003. Towards a computational model for –1 eukaryotic frameshifting sites. Bioinformatics 19:327335.
14. Bennett, A. F.,, K. M. Dao, and, R. E. Lenski. 1990. Rapid evolution in response to high-temperature selection. Nature 346:7981.
15. Berlyn, M. K. 1998. Linkage map of Escherichia coli K-12, edition 10: the traditional map. Microbiol. Mol. Biol. Rev. 62:814984.
16. Blattner, F. R.,, G. R. Plunkett,, C. A. Bloch,, N. T. Perna,, V. Burland,, M. Riley,, J. Collado-Vides,, J. D. Glasner,, C. K. Rode,, G. F. Mayhew,, J. Gregor,, N. W. Davis,, H. A. Kirkpatrick,, M. A. Goeden,, D. J. Rose,, B. Mau, and, Y. Shao. 1997. The complete genome sequence of Escherichia coliK-12. Science 277:14531474.
17. Brown, J. R.,, C. J. Douady,, M. J. Italia,, W. E. Marshall, and, M. J. Stanhope. 2001. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28:281285.
18. Brussow, H.,, C. Canchaya, and, W. D. Hardt. 2004. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 68:560602.
19. Capiaux, H.,, F. Cornet,, J. Corre,, M. Guijo,, K. Perals,, J. E. Rebollo, and, J. Louarn. 2001. Polarization of the Escherichia coli chromosome. A view from the terminus. Biochimie 83:161170.
20. Casjens, S., and, W. M. Huang. 1993. Linear chromosomal physical and genetic map of Borrelia burgdorferi, the Lyme disease agent. Mol. Microbiol. 8:967980.
21. Casjens, S.,, N. Palmer,, R. van Vugt,, W. M. Huang,, B. Stevenson,, P. Rosa,, R. Lathigra,, G. Sutton,, J. Peterson,, R. J. Dodson,, D. Haft,, E. Hickey,, M. Gwinn,, O. White, and, C. M. Fraser. 2000. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. Mol. Microbiol. 35:490516.
22. Caugant, D. A.,, L. F. Mocca,, C. E. Frasch,, O. Froholm,, W. D. Zollinger, and, R. K. Selander. 1987. Genetic structure of Neisseria meningitidis populations in relation to serogroup, serotype, and outer membrane protein pattern. J. Bacteriol. 169:27812792.
23. Chambaud, I.,, R. Heilig,, S. Ferris,, V. Barbe,, D. Samson,, F. Galisson,, I. Moszer,, K. Dybvig,, H. Wroblewski,, A. Viari,, E. P. Rocha, and, A. Blanchard. 2001. The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res. 29:21452153.
24. Chistoserdova, L.,, J. A. Vorholt,, R. K. Thauer, and, M. E. Lidstrom. 1998. C1 transfer enzymes and coenzymes linking methylotrophic bacteria and methanogenic Archaea. Science 281:99102.
25. Coghlan, A., and, K. H. Wolfe. 2002. Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res. 12:857867.
26. Cohan, F. M. 1994. Genetic exchange and evolutionary divergence in prokaryotes. Trends Ecol. Evol. 9:175180.
27. Cohan, F. M. 2001. Bacterial species and speciation. Syst. Biol. 50:513524.
28. Cohan, F. M. 2002. What are bacterial species? Annu. Rev. Microbiol. 56:457487.
29. Cole, S. T.,, K. Eiglmeier,, J. Parkhill,, K. D. James,, N. R. Thomson,, P. R. Wheeler,, N. Honore,, T. Garnier,, C. Churcher,, D. Harris,, K. Mungall,, D. Basham,, D. Brown,, T. Chillingworth,, R. Connor,, R. M. Davies,, K. Devlin,, S. Duthoy,, T. Feltwell,, A. Fraser,, N. Hamlin,, S. Holroyd,, T. Hornsby,, K. Jagels,, C. Lacroix,, J. Maclean,, S. Moule,, L. Murphy,, K. Oliver,, M. A. Quail,, M. A. Rajandream,, K. M. Rutherford,, S. Rutter,, K. Seeger,, S. Simon,, M. Simmonds,, J. Skelton,, R. Squares,, S. Squares,, K. Stevens,, K. Taylor,, S. Whitehead,, J. R. Woodward, and, B. G. Barrell. 2001. Massive gene decay in the leprosy bacillus. Nature 409:10071011.
30. Cooper, T. F.,, D. E. Rozen, and, R. E. Lenski. 2003. Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proc. Natl. Acad. Sci. USA 100:10721077.
31. Cooper, V. S.,, A. F. Bennett, and, R. E. Lenski. 2001. Evolution of thermal dependence of growth rate of Escherichia coli populations during 20,000 generations in a constant environment. Int. J. Org. Evol. 55:889896.
32. Cooper, V. S.,, D. Schneider,, M. Blot, and, R. E. Lenski. 2001. Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B. J. Bacteriol. 183:28342841.
33. Crawford, I. P., and, R. Milkman. 1991. Orthologous and paralogous divergence, reticulate evolution, and lateral gene transfer in bacterial trp genes, p. 77–95. In R. K. Selander,, A. G. Clark, and, T. S. Whittam (ed.), Evolution at the Molecular Level. Sinauer Associates, Sunderland, Mass.
34. Crook, D. W., and, B. G. Spratt. 1998. Multiple antibiotic resistance in Streptococcus pneumoniae. Br. Med. Bull. 54:595610.
35. Dandekar, T.,, S. Schuster,, B. Snel,, M. Huynen, and, P. Bork. 1999. Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem. J. 343:115124.
36. Dandekar, T.,, B. Snel,, M. Huynen, and, P. Bork. 1998. Conservation of gene order: a finger-print of proteins that physically interact. Trends Biochem. Sci. 23:324328.
37. Day, W. A., Jr.,, R. E. Fernandez, and, A. T. Maurelli. 2001. Pathoadaptive mutations that enhance virulence: genetic organization of the cadA regions of Shigella spp. Infect. Immun. 69:74717480.
38. Dean, A. M.,, D. E. Dykhuizen, and, D. L. Hartl. 1986. Fitness as a function of beta-galactosidase activity in Escherichia coli. Genet. Res. 48:18.
39. Dean, A. M.,, D. E. Dykhuizen, and, D. L. Hartl. 1988. Fitness effects of amino acid replacements in the beta-galactosidase of Escherichia coli. Mol. Biol. Evol. 5:469485.
40. Deng, W.,, S. R. Liou,, G. Plunkett III,, G. F. Mayhew,, D. J. Rose,, V. Burland,, V. Kodoyianni,, D. C. Schwartz, and, F. R. Blattner. 2003. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J. Bacteriol. 185:23302337.
41. Doolittle, W. F. 1999. Lateral genomics. Trends Cell Biol. 9:M5M8.
42. Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:21242129.
43. Doolittle, W. F. 2000. The nature of the universal ancestor and the evolution of the proteome. Curr. Opin. Struct. Biol. 10:355358.
44. Doolittle, W. F. 2000. Uprooting the tree of life. Sci. Am. 282:9095.
45. DuBose, R. F.,, D. E. Dykhuizen, and, D. L. Hartl. 1988. Genetic exchange among natural isolates of bacteria: recombination within the phoA gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 85:70367040.
46. Dykhuizen, D. E.,, A. M. Dean, and, D. L. Hartl. 1987. Metabolic flux and fitness. Genetics 115:2531.
47. Dykhuizen, D. E., and, L. Green. 1991. Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173:72577268.
48. Dykhuizen, D. E.,, S. A. Sawyer,, L. Green,, R. D. Miller, and, D. L. Hartl. 1985. Joint distribution of insertion elements IS4 and IS5 in natural isolates of Escherichia coli. Genetics 111:219231.
49. Edwards, R. A.,, G. J. Olsen, and, S. R. Maloy. 2002. Comparative genomics of closely related Salmonellae. Trends Microbiol. 10:9499.
50. Eisen, J. A.,, J. F. Heidelberg,, O. White, and, S. L. Salzberg. 2000. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol. 1:111.
51. Enright, M. C.,, N. P. Day,, C. E. Davies,, S. J. Peacock, and, B. G. Spratt. 2000. Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J. Clin. Microbiol. 38:10081015.
52. Feil, E. J.,, E. C. Holmes,, D. E. Bessen,, M. S. Chan,, N. P. Day,, M. C. Enright,, R. Goldstein,, D. W. Hood,, A. Kalia,, C. E. Moore,, J. Zhou, and, B. G. Spratt. 2001. Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc. Natl. Acad. Sci. USA 98:182187.
53. Feil, E. J.,, J. M. Smith,, M. C. Enright, and, B. G. Spratt. 2000. Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154:14391450.
54. Ferea, T. L.,, D. Botstein,, P. O. Brown, and, R. F. Rosenzweig. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. U.S.A. 96:97219726.
55. Ferrier, D. E., and, P. W. Holland. 2001. Ancient origin of the Hox gene cluster. Nat. Rev. Genet. 2:3338.
56. Fitzgerald, J. R., and, J. M. Musser. 2001. Evolutionary genomics of pathogenic bacteria. Trends Microbiol. 9:547553.
57. Fitz-Gibbon, S. T., and C. H. House. 1999. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27:42184222.
58. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J.-F. Tomb,, B. A. Dougherty,, J. M. Merrick,, K. McKenney,, G. G. Sutton,, W. FitzHugh,, C. A. Fields,, J. D. Gocayne,, J. D. Scott,, R. Shirley,, L. I. Liu,, A. Glodek,, J. M. Kelley,, J. F. Weidman,, C. A. Phillips,, T. Spriggs,, E. Hedblom,, M. D. Cotton,, T. Utterback,, M. C. Hanna,, D. T. Nguyen,, D. M. Saudek,, R. C. Brandon,, L. D. Fine,, J. L. Fritchman,, J. L. Fuhrmann,, N. S. Geoghagen,, C. L. Gnehm,, L. A. McDonald,, K. V. Small,, C. M. Fraser,, H. O. Smith, and, J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496512.
59. Fraser, C. M.,, S. Casjens,, W. M. Huang,, G. G. Sutton,, R. Clayton,, R. Lathigra,, O. White,, K. A. Ketchum,, R. Dodson,, E. K. Hickey,, M. Gwinn,, B. Dougherty,, J. F. Tomb,, R. D. Fleischmann,, D. Richardson,, J. Peterson,, A. R. Kerlavage,, J. Quackenbush,, S. Salzberg,, M. Hanson,, R. van Vugt,, N. Palmer,, M. D. Adams,, J. Gocayne,, J. C. Venter, et al. 1997. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390:580586.
60. Fraser, C. M.,, J. D. Gocayne,, O. White,, M. D. Adams,, R. A. Clayton,, R. D. Fleischmann,, C. J. Bult,, A. R. Kerlavage,, G. Sutton,, J. M. Kelley,, J. L. Fritchman,, J. F. Weidman,, K. V. Small,, M. Sandusky,, J. L. Fuhrmann,, D. T. Nguyen,, T. R. Utterback,, D. M. Saudek,, C. A. Phillips,, J. M. Merrick,, J.-F. Tomb,, B. A. Dougherty,, K. F. Bott,, P.-C. Hu,, T. S. Lucier,, S. N. Peterson,, H. O. Smith,, C. A. I. Hutchison, and, J. C. Venter. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270:397403.
61. Garcia-Vallve, S.,, A. Romeu, and, J. Palau. 2000. Horizontal gene transfer of glycosyl hydro-lases of the rumen fungi. Mol. Biol. Evol. 17:352361.
62. Giaever, G.,, A. M. Chu,, L. Ni,, C. Connelly,, L. Riles,, S. Veronneau,, S. Dow,, A. Lucau-Danila,, K. Anderson,, B. Andre,, A. P. Arkin,, A. Astromoff,, M. El-Bakkoury,, R. Bangham,, R. Benito,, S. Brachat,, S. Campanaro,, M. Curtiss,, K. Davis,, A. Deutschbauer,, K. D. Entian,, P. Flaherty,, F. Foury,, D. J. Garfinkel,, M. Gerstein,, D. Gotte,, U. Guldener,, J. H. Hegemann,, S. Hempel,, Z. Herman,, D. F. Jaramillo,, D. E. Kelly,, S. L. Kelly,, P. Kotter,, D. LaBonte,, D. C. Lamb,, N. Lan,, H. Liang,, H. Liao,, L. Liu,, C. Luo,, M. Lussier,, R. Mao,, P. Menard,, S. L. Ooi,, J. L. Revuelta,, C. J. Roberts,, M. Rose,, P. Ross-Macdonald,, B. Scherens,, G. Schimmack,, B. Shafer,, D. D. Shoemaker,, S. Sookhai-Mahadeo,, R. K. Storms,, J. N. Strathern,, G. Valle,, M. Voet,, G. Volckaert,, C. Y. Wang,, T. R. Ward,, J. Wilhelmy,, E. A. Winzeler,, Y. Yang,, G. Yen,, E. Youngman,, K. Yu,, H. Bussey,, J. D. Boeke,, M. Snyder,, P. Philippsen,, R. W. Davis, and, M. Johnston. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387391.
63. Gogarten, J. P.,, W. F. Doolittle, and, J. G. Lawrence. 2002. Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19:22262238.
64. Graham, D. E.,, R. Overbeek,, G. J. Olsen, and, C. R. Woese. 2000. An Archaeal genomic signature. Proc. Natl. Acad. Sci. USA 97:33043308.
65. Grantham, R.,, C. Gautier, and, M. Gouy. 1980. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 8:18931912.
66. Grantham, R.,, C. Gautier,, M. Gouy,, M. Jacobzone, and, R. Mercier. 1981. Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res. 9:4374.
67. Grantham, R.,, C. Gautier,, M. Gouy,, R. Mercier, and, A. Pave. 1980. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 8:r49r62.
68. Griffiths, E., and, R. S. Gupta. 2002. Protein signatures distinctive of chlamydial species: horizontal transfers of cell wall biosynthesis genes glmU from Archaea to chlamydiae and murA between chlamydiae and Streptomyces. Microbiology 148:25412549.
69. Groisman, E. A., and, H. Ochman. 1993. Cognate gene clusters govern invasion of host epithelial cells by Salmonella typhimurium and Shigella flexneri. EMBO J. 12:37793787.
70. Groisman, E. A., and, H. Ochman. 1994. How to become a pathogen. Trends Microbiol. 2:289294.
71. Groisman, E. A., and, H. Ochman. 1996. Pathogenicity islands: bacterial evolution in quantum leaps. Cell 87:791794.
72. Groisman, E. A., and, H. Ochman. 1997. How Salmonella became a pathogen. Trends Microbiol. 5:343349.
73. Guerdoux-Jamet, P.,, A. Hénaut,, P. Nitschké,, J. L. Risler, and, A. Danchin. 1997. Using codon usage to predict genes origin: is the Escherichia coli outer membrane a patchwork of products from different genomes? DNA Res. 4:257265.
74. Gupta, R. S. 2001. The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. Int. Microbiol. 4:187202.
75. Gupta, R. S., and, E. Griffiths. 2002. Critical issues in bacterial phylogeny. Theor. Popul. Biol. 61:423434.
76. Guttman, D. S., and, D. E. Dykhuizen. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science 266:13801383.
77. Guttman, D. S., and, D. E. Dykhuizen. 1994. Detecting selective sweeps in naturally occurring Escherichia coli. Genetics 138:9931003.
78. Hall, B. G. 1998. Activation of the bgl operon by adaptive mutation. Mol. Biol. Evol. 15:15.
79. Hartl, D. L., and, D. E. Dykhuizen. 1984. The population genetics of Escherichia coli. Annu. Rev. Genet. 18:3168.
80. Hartl, D. L.,, M. Medhora,, L. Green, and, D. E. Dykhuizen. 1986. The evolution of DNA sequences in Escherichia coli. Philos. Trans. R. Soc. Lond. B 312:191204.
81. Hayes, W. S., and, M. Borodovsky. 1998. How to interpret an anonymous bacterial genome: machine learning approach to gene identification. Genome Res. 8:11541171.
82. Hendrickson, H., and, J. G. Lawrence. 2006. Selection for chromosome architecture in bacteria. J. Mol. Evol., in press.
83. Hendrix, R. W.,, M. C. M. Smith,, R. N. Burns,, M. E. Ford, and, G. F. Hatfull. 1999. Evolutionary relationships among diverse bacteriophages and prophages: all the world’s a phage. Proc. Natl. Acad. Sci. USA 96:21922197.
84. Himmelreich, R.,, H. Plagens,, H. Hilbert,, B. Reiner, and, R. Herrmann. 1996. Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium. Nucleic Acids Res. 25:701712.
85. Hood, D. W.,, M. E. Deadman,, T. Allen,, H. Masoud,, A. Martin,, J. R. Brisson,, R. D. Fleischmann,, J. C. Venter,, J. C. Richards, and, E. R. Moxon. 1996. Use of the complete genome sequence information of Haemophilus influenzae strain Rd to investigate lipopolysaccha-ride biosynthesis. Mol. Microbiol. 22:951965.
86. Hood, D. W.,, M. E. Deadman,, M. P. Jennings,, M. Bisercic,, R. D. Fleischmann,, J. C. Venter, and, E. R. Moxon. 1996. DNA repeats identify novel virulence genes in Haemophilus influenzae. Proc. Natl. Acad. Sci. USA 93:1112111125.
87. Hutchison, C. A.,, S. N. Peterson,, S. R. Gill,, R. T. Cline,, O. White,, C. M. Fraser,, H. O. Smith, and, J. C. Venter. 1999. Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286:21652169.
88. Huynen, M. A.,, T. Dandekar, and, P. Bork. 1999. Variation and evolution of the citric-acid cycle: a genomic perspective. Trends Microbiol. 7:281291.
89. Huynen, M. A.,, B. Snel, and, P. Bork. 2001. Inversions and the dynamics of eukaryotic gene order. Trends Genet. 17:304306.
90. Iino, T., and, K. Kutsukake. 1981. Trans-acting genes of bacteriophages P1 and Mu mediate inversion of a specific DNA segment involved in flagellar phase variation of Salmonella. Cold Spring Harbor Symp. Quant. Biol. 45:1116.
91. Israel, D. A.,, N. Salama,, C. N. Arnold,, S. F. Moss,, T. Ando,, H. P. Wirth,, K. T. Tham,, M. Camorlinga,, M. J. Blaser,, S. Falkow, and, R. M. Peek, Jr. 2001. Helicobacter pylori strain-specific differences in genetic content, identified by microarray, influence host inflammatory responses. J. Clin. Investig. 107:611620.
92. Itoh, T.,, K. Takemoto,, H. Mori, and, T. Gojobori. 1999. Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol. Biol. Evol. 16:332346.
93. Jennings, M. P.,, D. W. Hood,, I. R. A. Peak,, M. Virji, and, E. R. Moxon. 1995. Molecular analysis of a locus for the biosynthesis and phase-variable expression of the lacto-N-neotetraose terminal lipopolysaccharide structure in Neisseria meningitidis. Mol. Microbiol. 18:729740.
94. Jin, Q.,, Z. Yuan,, J. Xu,, Y. Wang,, Y. Shen,, W. Lu,, J. Wang,, H. Liu,, J. Yang,, F. Yang,, X. Zhang,, J. Zhang,, G. Yang,, H. Wu,, D. Qu,, J. Dong,, L. Sun,, Y. Xue,, A. Zhao,, Y. Gao,, J. Zhu,, B. Kan,, K. Ding,, S. Chen,, H. Cheng,, Z. Yao,, B. He,, R. Chen,, D. Ma,, B. Qiang,, Y. Wen,, Y. Hou, and, J. Yu. 2002. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30:44324441.
95. Juhala, R. J.,, M. E. Ford,, R. L. Duda,, A. Youlton,, G. F. Hatfull, and, R. W. Hendrix. 2000. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J. Mol. Biol. 299:2751.
96. Kamp, D., and, R. Kahmann. 1981. The relationship of two invertible segments in bacteriophage Mu and Salmonella typhimurium DNA. Mol. Gen. Genet. 184:564566.
97. Kaneko, T.,, Y. Nakamura,, S. Sato,, E. Asamizu,, T. Kato,, S. Sasamoto,, A. Watanabe,, K. Idesawa,, A. Ishikawa,, K. Kawashima,, T. Kimura,, Y. Kishida,, C. Kiyokawa,, M. Kohara,, M. Matsumoto,, A. Matsuno,, Y. Mochizuki,, S. Nakayama,, N. Nakazaki,, S. Shimpo,, M. Sugimoto,, C. Takeuchi,, M. Yamada, and, S. Tabata. 2000. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res. 7:331338.
98. Karlin, S., and, C. Burge. 1995. Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 11:283290.
99. Karlin, S.,, J. Mrazek, and, A. M. Campbell. 1998. Codon usages in different gene classes of the Escherichia coli genome. Mol. Microbiol. 29:13411355.
100. Kato-Maeda, M.,, J. T. Rhee,, T. R. Gingeras,, H. Salamon,, J. Drenkow,, N. Smittipat, and, P. M. Small. 2001. Comparing genomes within the species Mycobacterium tuberculosis. Genome Res. 11:547554.
101. Koonin, E. V. 2000. How many genes can make a cell: the minimal-gene-set concept. Annu. Rev. Genomics Hum. Genet. 1:99116.
102. Krinos, C. M.,, M. J. Coyne,, K. G. Weinacht,, A. O. Tzianabos,, D. L. Kasper, and, L. E. Comstock. 2001. Extensive surface diversity of a commensal microorganism by multiple DNA inversions. Nature 414:555558.
103. Kroll, J. S.,, K. E. Wilks,, J. L. Farrant, and, P. R. Langford. 1998. Natural genetic exchange between Haemophilus and Neisseria: intergeneric transfer of chromosomal genes between major human pathogens. Proc. Natl. Acad. Sci. USA 95:1238112385.
104. Kurland, C. G. 2000. Something for everyone. EMBO Rep. 1:9295.
105. Lawrence, J. G. 1997. Selfish operons and speciation by gene transfer. Trends Microbiol. 5:355359.
106. Lawrence, J. G. 1999. Gene transfer and minimal genome size, p. 32–38. In A. Knoll,, M. J. Osborn,, J. Baross,, H. Berg,, N. R. Pace, and, M. Sogin (ed.), Size Limits of Very Small Organisms. National Research Council, Washington, D. C.
107. Lawrence, J. G. 1999. Gene transfer, speciation, and the evolution of bacterial genomes. Curr. Opin. Microbiol. 2:519523.
108. Lawrence, J. G. 2001. Catalyzing bacterial speciation: correlating lateral transfer with genetic headroom. Syst. Biol. 50:479496.
109. Lawrence, J. G. 2002. Gene transfer in bacteria: speciation without species? Theor. Popul. Biol. 61:449460.
110. Lawrence, J. G. 2002. Shared strategies in gene organization among prokaryotes and eukaryotes. Cell 110:407413.
111. Lawrence, J. G. 2003. When ELFs are ORFs, but don’t act like them. Trends Genet. 19:131132.
112. Lawrence, J. G.,, D. E. Dykhuizen,, R. F. DuBose, and, D. L. Hartl. 1989. Phylogenetic analysis using insertion sequence fingerprinting in Escherichia coli. Mol. Biol. Evol. 6:114.
113. Lawrence, J. G.,, G. F. Hatfull, and, R. W. Hendrix. 2002. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J. Bacteriol. 184:48914905.
114. Lawrence, J. G., and, H. Hendrickson. 2003. Lateral gene transfer: when will adolescence end? Mol. Microbiol. 50:739749.
115. Lawrence, J. G., and, H. Hendrickson. 2004. Chromosome structure and constraints on lateral gene transfer. Dynam. Genet. 50:319336.
116. Lawrence, J. G.,, R. W. Hendrix, and, S. Casjens. 2001. Where are the pseudogenes in bacterial genomes? Trends Microbiol. 9:535540.
117. Lawrence, J. G., and, H. Ochman. 1997. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44:383397.
118. Lawrence, J. G., and, H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95:94139417.
119. Lawrence, J. G., and, H. Ochman. 2002. Reconciling the many faces of gene transfer. Trends Microbiol. 10:14.
120. Lawrence, J. G., and, J. R. Roth. 1996. Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics 143:18431860.
121. Lawrence, J. G., and, J. R. Roth. 1998. Roles of horizontal transfer in bacterial evolution, p. 208–225. In M. Syvanen and, C. I. Kado (ed.), Horizontal Transfer. Chapman and Hall, London, United Kingdom.
122. Lawrence, J. G., and, J. R. Roth. 1999. Genomic flux: genome evolution by gene loss and acquisition, p. 263–289. In R. L. Charlebois (ed.), Organization of the Prokaryotic Genome. ASM Press, Washington, D. C.
123. Lenski, R. E.,, M. Slatkin, and, F. J. Ayala. 1989. Mutation and selection in bacterial populations: alternatives to the hypothesis of directed mutation. Proc. Natl. Acad. Sci. USA 86:27752778.
124. Levin, B. 1981. Periodic selection, infectious gene exchange, and the genetic structure of E. coli populations. Genetics 99:123.
125. Levin, B. R. 1988. Frequency-dependent selection in bacterial populations. Philos. Trans. R. Soc. Lond. B 319:459472.
126. Levings, P. P., and, J. Bungert. 2002. The human β-globin locus control region: a center of attraction. Eur. J. Biochem. 269:15891599.
127. Liu, G. R.,, A. Rahn,, W. Q. Liu,, K. E. Sanderson,, R. N. Johnston, and, S. L. Liu. 2002. The evolving genome of Salmonella enterica serovar Pullorum. J. Bacteriol. 184:26262633.
128. Liu, M.,, R. Deora,, S. R. Doulatov,, M. Gingery,, F. A. Eiserling,, A. Preston,, D. J. Maskell,, R. W. Simons,, P. A. Cotter,, J. Parkhill, and, J. F. Miller. 2002. Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Science 295:20912094.
129. Liu, S. L., and, K. E. Sanderson. 1995. The chromosome of Salmonella paratyphi A is inverted by recombination between rrnH and rrnG. J. Bacteriol. 177:65856592.
130. Liu, S. L., and, K. E. Sanderson. 1995. Rearrangements in the genome of the bacterium Salmonella typhi. Proc. Natl. Acad. Sci. USA 92:10181022.
131. Liu, S. L., and, K. E. Sanderson. 1996. Highly plastic chromosomal organization in Salmonella typhi. Proc. Natl. Acad. Sci. USA 93:1030310308.
132. Mahan, M. J., and, J. R. Roth. 1991. Ability of a bacterial chromosome segment to invert is dictated by included material rather than flanking sequence. Genetics 129:10211032.
133. Majewski, J., and, F. M. Cohan. 1999. DNA sequence similarity requirements for interspecific recombination in Bacillus. Genetics 153:15251533.
134. Majewski, J.,, P. Zawadzki,, P. Pickerill,, F. M. Cohan, and, C. G. Dowson. 2000. Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation. J. Bacteriol. 182:10161023.
135. Maniloff, J. 1996. The minimal cell genome: “On being the right size”. Proc. Natl. Acad. Sci. USA 93:1000410006.
136. Maurelli, A. T.,, R. E. Fernández,, C. A. Bloch,, C. K. Rode, and, A. Fasano. 1998. “Black holes” and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc. Natl. Acad. Sci. USA 95:39433948.
137. Maynard Smith, J.,, N. H. Smith,, M. O’Rourke, and, B. G. Spratt. 1993. How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90:43844388.
138. Mayr, E. 1942. Systematics and the Origin of Species. Columbia University Press, New York, N. Y.
139. Mayr, E. 1954. Change of genetic environment and evolution, p. 156–180. In J. S. Huxley,, A. C. Hardy, and, E. B. Ford (ed.), Evolution as a Process. Allen and Unwin, London, United Kingdom.
140. Mayr, E. 1963. Animal Species and Evolution. Harvard University Press, Cambridge, Mass.
141. McClelland, M.,, L. Florea,, K. Sanderson,, S. W. Clifton,, J. Parkhill,, C. Churcher,, G. Dougan,, R. K. Wilson, and, W. Miller. 2000. Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three Salmonella enterica serovars, Typhimurium, Typhi and Paratyphi. Nucleic Acids Res. 28:49744986.
142. McClelland, M.,, K. E. Sanderson,, J. Spieth,, S. W. Clifton,, P. Latreille,, L. Courtney,, S. Porwollik,, J. Ali,, M. Dante,, F. Du,, S. Hou,, D. Layman,, S. Leonard,, C. Nguyen,, K. Scott,, A. Holmes,, N. Grewal,, E. Mulvaney,, E. Ryan,, H. Sun,, L. Florea,, W. Miller,, T. Stoneking,, M. Nhan,, R. Waterston, and, R. K. Wilson. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413:852856.
143. McKane, M., and, R. Milkman. 1995. Transduction, restriction and recombination patterns in Escherichia coli. Genetics 139:3543.
144. McLysaght, A.,, K. Hokamp, and, K. H. Wolfe. 2002. Extensive genomic duplication during early chordate evolution. Nat. Genet. 31:200204.
145. Médigue, C.,, T. Rouxel,, P. Vigier,, A. Hénaut, and, A. Danchin. 1991. Evidence of horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol. 222:851856.
146. Miesel, L.,, A. Segall, and, J. R. Roth. 1994. Construction of chromosomal rearrangements in Salmonella by transduction: inversions of nonpermissive segments are not lethal. Genetics 137:919932.
147. Milkman, R. 1973. Electrophoretic variation in Escherichia coli from natural sources. Science 182:10241026.
148. Milkman, R., and, I. P. Crawford. 1983. Clustered third-base substitutions among wild strains of Escherichia coli. Science 221:378379.
149. Moszer, I.,, E. P. Rocha, and, A. Danchin. 1999. Codon usage and lateral gene transfer in Bacillus subtilis. Curr. Opin. Microbiol. 2:524528.
150. Mushegian, A. R., and, E. V. Koonin. 1996. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. USA 93:1026810273.
151. Musser, J. M.,, A. Amin, and, S. Ramaswamy. 2000. Negligible genetic diversity of Mycobacterium tuberculosis host immune system protein targets: evidence of limited selective pressure. Genetics 155:716.
152. Musser, J. M.,, D. A. Bemis,, H. Ishikawa, and, R. K. Selander. 1987. Clonal diversity and host distribution in Bordetella bronchiseptica. J. Bacteriol. 169:27932803.
153. Nakata, N.,, T. Tobe,, I. Fukuda,, T. Suzuki,, K. Komatsu,, M. Yoshikawa, and, C. Sasakawa. 1993. The absence of a surface protease, OmpT, determines the intercellular spreading ability of Shigella: the relationship between the ompT and kcpA loci. Mol. Microbiol. 9:459468.
154. Ng, I.,, S.-L. Liu, and, K. Sanderson. 1999. Role of genomic rearrangements in producing new ribotypes of Salmonella typhi. J. Bacteriol. 181:35363541.
155. Niedenthal, R.,, L. Riles,, U. Guldener,, S. Klein,, M. Johnston, and, J. H. Hegemann. 1999. Systematic analysis of S. cerevisiae chromosome VIII genes. Yeast 15:17751796.
156. Ochman, H. 2002. Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes. Trends Genet. 18:335337.
157. Ochman, H., and, E. A. Groisman. 1995. The evolution of invasion in enteric bacteria. Can. J. Microbiol. 41:555561.
158. Ochman, H., and, I. B. Jones. 2000. Evolutionary dynamics of full genome content in Escherichia coli. EMBO J. 19:66376643.
159. Ochman, H., and, J. G. Lawrence. 1996. Phylogenetics and the amelioration of bacterial genomes, p. 2627–2637. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter, and, H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: Cellular and molecular biology, 2nd ed. American Society for Microbiology, Washington, D. C.
160. Ochman, H.,, J. G. Lawrence, and, E. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299304.
161. Papadopoulos, D.,, D. Schneider,, J. Meier-Eiss,, W. Arber,, R. E. Lenski, and, M. Blot. 1999. Genomic evolution during a 10,000-generation experiment with bacteria. Proc. Natl. Acad. Sci. USA 96:38073812.
162. Parkhill, J. 2002. The importance of complete genome sequences. Trends Microbiol. 10:219220.
163. Parkhill, J.,, M. Achtman,, K. D. James,, S. D. Bentley,, C. Churcher,, S. R. Klee,, G. Morelli,, D. Basham,, D. Brown,, T. Chillingworth,, R. M. Davies,, P. Davis,, K. Devlin,, T. Feltwell,, N. Hamlin,, S. Holroyd,, K. Jagels,, S. Leather,, S. Moule,, K. Mungall,, M. A. Quail,, M. A. Rajandream,, K. M. Rutherford,, M. Simmonds,, J. Skelton,, S. Whitehead,, B. G. Spratt, and, B. G. Barrell. 2000. Complete DNA sequence of a serogroup A strain of Neisseria menigitidis Z2491. Nature 404:502506.
164. Parkhill, J.,, G. Dougan,, K. D. James,, N. R. Thomson,, D. Pickard,, J. Wain,, C. Churcher,, K. L. Mungall,, S. D. Bentley,, M. T. Holden,, M. Sebaihia,, S. Baker,, D. Basham,, K. Brooks,, T. Chillingworth,, P. Connerton,, A. Cronin,, P. Davis,, R. M. Davies,, L. Dowd,, N. White,, J. Farrar,, T. Feltwell,, N. Hamlin,, A. Haque,, T. T. Hien,, S. Holroyd,, K. Jagels,, A. Krogh,, T. S. Larsen,, S. Leather,, S. Moule,, P. O’Gaora,, C. Parry,, M. Quail,, K. Rutherford,, M. Simmonds,, J. Skelton,, K. Stevens,, S. Whitehead, and, B. G. Barrell. 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413:848852.
165. Patrick, S.,, J. Parkhill,, L. J. McCoy,, N. Lennard,, M. J. Larkin,, M. Collins,, M. Sczaniecka, and, G. Blakely. 2003. Multiple inverted DNA repeats of Bacteroides fragilis that control polysaccharide antigenic variation are similar to the hin region inverted repeats of Salmonella typhimurium. Microbiology 149:915924.
166. Pedulla, M. L.,, M. E. Ford,, J. M. Houtz,, T. Karthikeyan,, C. Wadsworth,, J. A. Lewis,, D. Jacobs-Sera,, J. Falbo,, J. Gross,, N. R. Pannunzio,, W. Brucker,, V. Kumar,, J. Kandasamy,, L. Keenan,, S. Bardarov,, J. Kriakov,, J. G. Lawrence,, W. R. Jacobs,, R. W. Hendrix, and, G. F. Hatfull. 2003. Origins of highly mosaic mycobacteriophage genomes. Cell 113:171182.
167. Perals, K.,, F. Cornet,, Y. Merlet,, I. Delon, and, J. M. Louarn. 2000. Functional polarization of the Escherichia coli chromosome terminus: the dif site acts in chromosome dimer resolution only when located between long stretches of opposite polarity. Mol. Microbiol. 36:3343.
168. Perna, N. T.,, G. Plunkett,, V. Burland,, B. Mau,, J. D. Glasner,, D. J. Rose,, G. F. Mayhew,, P. S. Evans,, J. Gregor,, H. A. Kirkpatrick,, G. Posfai,, J. Hackett,, S. Klink,, A. Boutin,, Y. Shao,, L. Miller,, E. J. Grotbeck,, N. W. Davis,, A. Lim,, E. T. Dimalanta,, K. D. Potamousis,, J. Apodaca,, T. S. Anantharaman,, J. Lin,, G. Yen,, D. C. Schwartz,, R. A. Welch, and, F. R. Blattner. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529533.
169. Pirie, N. W. 1973. “On being the right size”. Annu. Rev. Microbiol. 27:119132.
170. Plague, G. R.,, C. Dale, and, N. A. Moran. 2003. Low and homogeneous copy number of plasmid-borne symbiont genes affecting host nutrition in Buchnera aphidicola of the aphid Uroleucon ambrosiae. Mol. Ecol. 12:10951100.
171. Ragan, M. A. 2001. Detection of lateral gene transfer among microbial genomes. Curr. Opin. Genet. Dev. 11:620626.
172. Ragan, M. A. 2001. On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201:187191.
173. Rainey, P. B., and, M. Travisano. 1998. Adaptive radiation in a heterogeneous environment. Nature 394:6972.
174. Raymond, J.,, O. Zhaxybayeva,, J. P. Gogarten, and, R. E. Blankenship. 2003. Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach. Philos. Trans. R. Soc. Lond. B 358:223230.
175. Raymond, J.,, O. Zhaxybayeva,, J. P. Gogarten,, S. Y. Gerdes, and, R. E. Blankenship. 2002. Whole-genome analysis of photosynthetic prokaryotes. Science 298:16161620.
176. Razin, S. 1997. The minimal cellular genome of Mycoplasma. Indian J. Biochem. Biophys. 34:124130.
177. Reid, S. D.,, N. M. Green,, J. K. Buss,, B. Lei, and, J. M. Musser. 2001. Multilocus analysis of extracellular putative virulence proteins made by group A Streptococcus: population genetics, human serologic response, and gene transcription. Proc. Natl. Acad. Sci. USA 98:75527557.
178. Riley, M. S.,, V. S. Cooper,, R. E. Lenski,, L. J. Forney, and, T. L. Marsh. 2001. Rapid phenotypic change and diversification of a soil bacterium during 1000 generations of experimental evolution. Microbiology 147:9951006.
179. Rohwer, F., and, R. Edwards. 2002. The Phage Proteomic Tree: a genome-based taxonomy for phage. J. Bacteriol. 184:45294535.
180. Rosenzweig, R. F.,, R. R. Sharp,, D. S. Treves, and, J. Adams. 1994. Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli. Genetics 137:903917.
181. Roth, J. R.,, J. G. Lawrence,, M. Rubenfield,, S. Kieffer-Higgins, and, G. M. Church. 1993. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. J. Bacteriol. 175:33033316.
182. Rouhbakhsh, D.,, C. Y. Lai,, C. D. von Dohlen,, M. A. Clark,, L. Baumann,, P. Baumann,, N. A. Moran, and, D. J. Voegtlin. 1996. The tryptophan biosynthetic pathway of aphid endosymbionts (Buchnera): genetics and evolution of plasmid-associated anthranilate synthase (trpEG) within the aphididae. J. Mol. Evol. 42:414421.
183. Salama, N.,, K. Guillemin,, T. K. McDaniel,, G. Sherlock,, L. Tompkins, and, S. Falkow. 2000. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc. Natl. Acad. Sci. USA 97:1466814673.
184. Salzberg, S. L.,, A. J. Salzberg,, A. R. Kerlavage, and, J. F. Tomb. 1998. Skewed oligomers and origins of replication. Gene 217:5767.
185. Sanderson, K. E., and, C. A. Hall. 1970. F-prime factors of Salmonella typhimurium and an inversion between S. typhimurium and Escherichia coli. Genetics 64:215228.
186. Sanderson, K. E., and, S. L. Liu. 1998. Chromosomal rearrangements in enteric bacteria. Electrophoresis 19:569572.
187. Sanderson, K. E., and, J. R. Roth. 1988. Linkage map of Salmonella typhimurium, edition 7. Microbiol. Rev. 52:485532.
188. Sarkari, J.,, N. Pandit,, E. R. Moxon, and, M. Achtman. 1994. Variable expression of the Opc outer membrane protein in Neisseria meningitidis is caused by size variation of a promoter containing poly-cytidine. Mol. Microbiol. 13:207217.
189. Segall, A.,, M. J. Mahan, and, J. R. Roth. 1988. Rearrangement of the bacterial chromosome: forbidden inversions. Science 241:13141318.
190. Segall, A. M., and, J. R. Roth. 1989. Recombination between homologies in direct and inverse orientation in the chromosome of Salmonella: intervals which are nonpermissive for inversion formation. Genetics 122:737747.
191. Selander, R. K., and, B. R. Levin. 1980. Genetic diversity and structure in Escherichia coli populations. Science 210:545547.
192. Selander, R. K.,, R. M. McKinney,, T. S. Whittam,, W. F. Bibb,, D. J. Brenner,, F. S. Nolte, and, P. E. Pattison. 1985. Genetic structure of populations of Legionella pneumophila. J. Bacteriol. 163:10211037.
193. Semple, C., and, K. H. Wolfe. 1999. Gene duplication and gene conversion in the Caenorhabditis elegans genome. J. Mol. Evol. 48:555564.
194. Seoighe, C.,, N. Federspiel,, T. Jones,, N. Hansen,, V. Bivolarovic,, R. Surzycki,, R. Tamse,, C. Komp,, L. Huizar,, R. W. Davis,, S. Scherer,, E. Tait,, D. J. Shaw,, D. Harris,, L. Murphy,, K. Oliver,, K. Taylor,, M. A. Rajandream,, B. G. Barrell, and, K. H. Wolfe. 2000. Prevalence of small inversions in yeast gene order evolution. Proc. Natl. Acad. Sci. USA 97:1443314437.
195. Seoighe, C., and, K. H. Wolfe. 1998. Extent of genomic rearrangement after genome duplication in yeast. Proc. Natl. Acad. Sci. USA 95:44474452.
196. Shah, A. A.,, M. C. Giddings,, J. B. Parvaz,, R. F. Gesteland,, J. F. Atkins, and, I. P. Ivanov. 2002. Computational identification of putative programmed translational frameshift sites. Bioinformatics 18:10461053.
197. Shigenobu, S.,, H. Watanabe,, M. Hattori,, Y. Sakaki, and, H. Ishikawa. 2000. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407:8186.
198. Silverman, M.,, J. Zieg,, M. Hilmen, and, M. Simon. 1979. Phase variation in Salmonella: genetic analysis of a recombinational switch. Proc. Natl. Acad. Sci. USA 76:391395.
199. Slesarev, A. I.,, K. V. Mezhevaya,, K. S. Makarova,, N. N. Polushin,, O. V. Shcherbinina,, V. V. Shakhova,, G. I. Belova,, L. Aravind,, D. A. Natale,, I. B. Rogozin,, R. L. Tatusov,, Y. I. Wolf,, K. O. Stetter,, A. G. Malykh,, E. V. Koonin, and, S. A. Kozyavkin. 2002. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of Archaeal methanogens. Proc. Natl. Acad. Sci. USA 99:46444649.
200. Smith, J. M.,, C. G. Dowson, and, B. G. Spratt. 1991. Localized sex in bacteria. Nature 349:2931.
201. Smith, N. H.,, E. C. Holmes,, G. M. Donovan,, G. A. Carpenter, and, B. G. Spratt. 1999. Networks and groups within the genus Neisseria: Analysis of argF, recA, rho, and 16S rRNA sequences from human Neisseria species. Mol. Biol. Evol. 16:773783.
202. Snel, B.,, P. Bork, and, M. Huynen. 1999. Genome phylogeny based on gene content. Nat. Genet. 21:108110.
203. Stoltzfus, A.,, J. F. Leslie, and, R. Milkman. 1988. Molecular evolution of the Escherichia coli chromosome. I. Analysis of structure and natural variation in a previously uncharacterized region between trp and tonB. Genetics 120:345358.
204. Tamas, I.,, L. Klasson,, B. Canbäck,, A. K. Näslund,, A. S. Eriksson,, J. J. Wernegreen,, J. P. Sandström,, N. A. Moran, and, S. G. Andersson. 2002. 50 million years of genomic stasis in endosymbiotic bacteria. Science 296:23762379.
205. Tanimoto, K.,, Q. Liu,, J. Bungert, and, J. D. Engert. 1999. Effects of altered gene order or orientation of the locus control region on human β-globin gene expression in mice. Nature 398:344348.
206. Tekaia, F.,, A. Lazcano, and, B. Dujon. 1999. The genomic tree as revealed from whole proteome comparisons. Genome Res. 9:550557.
207. Treves, D. S.,, S. Manning, and, J. Adams. 1998. Repeated evolution of an acetate-cross-feeding polymorphism in long-term populations of Escherichia coli. Mol. Biol. Evol. 15:789797.
208. Vrba, E. S. (ed.). 1985. Species and Speciation. Transvaal Museum, Pretoria, South Africa.
209. Ward, D. M. 1998. A natural species concept for prokaryotes. Curr. Opin. Microbiol. 1:271277.
210. Wei, J.,, M. B. Goldberg,, V. Burland,, M. M. Venkatesan,, W. Deng,, G. Fournier,, G. F. Mayhew,, G. Plunkett III,, D. J. Rose,, A. Darling,, B. Mau,, N. T. Perna,, S. M. Payne,, L. J. Runyen-Janecky,, S. Zhou,, D. C. Schwartz, and, F., R. Blattner. 2003. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect. Immun. 71:27752786.
211. Welch, R. A.,, V. Burland,, G. Plunkett III,, P. Redford,, P. Roesch,, D. Rasko,, E. L. Buckles,, S. R. Liou,, A. Boutin,, J. Hackett,, D. Stroud,, G. F. Mayhew,, D. J. Rose,, S. Zhou,, D. C. Schwartz,, N. T. Perna,, H. L. Mobley,, M. S. Donnenberg, and, F. R. Blattner. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99:1702017024.
212. Wernegreen, J. J., and, N. A. Moran. 2000. Decay of mutualistic potential in aphid endosymbionts through silencing of biosynthetic loci: Buchnera of Diuraphis. Proc. R. Soc. Lond. B 267:14231431.
213. Wernegreen, J. J.,, A. O. Richardson, and, N. A. Moran. 2001. Parallel acceleration of evolutionary rates in symbiont genes underlying host nutrition. Mol. Phylogenet. Evol. 19:479485.
214. Whittam, T. S.,, H. Ochman, and, R. K. Selander. 1983. Multilocus genetic structure in natural populations of Escherichia coli. Proc. Natl. Acad. Sci. USA 80:17511755.
215. Woese, C. R., and, G. E. Fox. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA 74:50885090.
216. Woese, C. R.,, G. J. Olsen,, M. Ibba, and, D. Soll. 2000. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64:202236.
217. Woese, C. R.,, E. Stackebrandt,, T. J. Macke, and, G. E. Fox. 1985. A phylogenetic definition of the major eubacterial taxa. Syst. Appl. Microbiol. 6:143151.
218. Wolfe, K. H., and, D. C. Shields. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708713.
219. Wong, S.,, G. Butler, and, K. H. Wolfe. 2002. Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proc. Natl. Acad. Sci. USA 99:92729277.
220. Xiang, S. H.,, A. M. Haase, and, P. R. Reeves. 1993. Variation of the rfb gene clusters in Salmonella enterica. J. Bacteriol. 175:48774884.
221. Zieg, J.,, M. Silverman,, M. Hilmen, and, M. Simon. 1977. Recombinational switch for gene expression. Science 196:170172.
222. Zuckerkandl, E. 1965. The evolution of hemoglobin. Sci. Am. 212:110118.
223. Zuckerkandl, E., and, L. Pauling. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8:357366.

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