Estimating the fitness effect of an insertion sequence

Journal of Mathematical Biology

Volumn 66, Issue 1-2, 2013, Pages 95-114

  Bichsel, Manuel ^a   Barbour, A D ^a   Wagner, Andreas ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Fitness effect; Horizontal gene transfer; Insertion sequence; Maximum likelihood; Mobile DNA; Ordinary differential equation system

Indexed keywords

PROKARYOTA; PROTEOBACTERIA;

EID: 84871947032     PISSN: 03036812     EISSN: 14321416     Source Type: Journal    
DOI: 10.1007/s00285-012-0504-2     Document Type: Article

References (36)

1. Berg DE (1989) Transposon Tn5. In: Berg DE, Howe MM (eds) Mobile DNA. American Society for Microbiology, Washington, D. C., pp 185-210.
2. Bichsel M, Barbour AD, Wagner A (2010) The early phase of a bacterial insertion sequence infection. Theor Popul Biol 78: 278-288.
3. Blot M (1994) Transposable elements and adaptation of host bacteria. Genetica 93(1-3): 5-12.
4. Chandler M, Mahillon J (2002) Insertion sequences revisited. In: Craig NL, Craigie R, Gellert M, Lambowitz AM (eds) Mobile DNA II. American Society for Microbiology, Washington, D. C., pp 305-366.
5. Charlesworth B, Sniegowski P, Stephan W (1994) The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371: 215-219.
6. Dahlberg C, Bergström M, Hermansson M (1998) In situ detection of high levels of horizontal plasmid transfer in marine bacterial communities. Appl Environ Microbiol 64(7): 2670-2675.
7. Dawkins R (1976) The selfish gene. Oxford University Press, Oxford.
8. Doolittle WF, Sapienza C (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601-603.
9. Dröge M, Pühler A, Selbitschka W (1999) Horizontal gene transfer among bacteria in terrestrial and aquatic habitats as assessed by microcosm and field studies. Biol Fertil Soils 29(3): 221-245.
10. Efron B, Tibshirani RJ (1994) An introduction to the bootstrap. Chapman & Hall/CRC, New York.
11. Galas DJ, Chandler M (1989) Bacterial insertion sequences. In: Berg DE, Howe MM (eds) Mobile DNA. American Society for Microbiology, Washington, D. C., pp 109-162.
12. Gibbons RJ, Kapsimalis B (1967) Estimates of the overall rate of growth of the intestinal microflora of hamsters, guinea pigs, and mice. J Bacteriol 93(1): 510-512.
13. Hall BG (1999) Transposable elements as activators of cryptic genes in E. coli. Genetica 107: 181-187.
14. Jiang SC, Paul JH (1998) Gene transfer by transduction in the marine environment. Appl Environ Microbiol 64(8): 2780-2787.
15. Kleckner N (1989) Transposon Tn10. In: Berg DE, Howe MM (eds) Mobile DNA. American Society for Microbiology, Washington, D. C., pp 227-268.
16. Lan R, Reeves PR (2002) Escherichia coli in disguise: molecular origins of shigella. Microbes Infect 4(11): 1125-1132.
17. Lynch M (2007) The origins of genome architecture. Sinauer Associates, Inc, Sunderland.
18. Madigan MT, Martinko JM, Dunlap PV, Clark DP (2009) Brock biology of microorganisms, 12th edn. Pearson Benjamin Cummings, San Francisco.
19. Mahillon J, Siguier P, Chandler M (2009) IS Finder. http://www-is. biotoul. fr.
20. NCBI (2011) National Center for Biotechnology Information. http://www. ncbi. nlm. nih. gov.
21. Nelder JA, Mead R (1965) A simplex-method for function minimization. Comput J 7(4): 308-313.
22. Nuzhdin SV (1999) Sure facts, speculations, and open questions about the evolution of transposable element copy number. Genetica 107: 129-137.
23. Orgel LE, Crick FHC (1980) Selfish DNA: the ultimate parasite. Nature 284: 604-607.
24. Savageau MA (1983) Escherichia coli habitats, cell types, and molecular mechanisms of gene control. Am Naturalist 122(6): 732-744.
25. Sawyer SA, Dykhuizen DE, DuBose RF, Green L, Mutangadura-Mhlanga T, Wolczyk DF, Hartl DL (1987) Distribution and abundance of insertion sequences among natural isolates of Escherichia coli. Genetics 115: 51-63.
26. Schneider D, Lenski RE (2004) Dynamics of insertion sequence elements during experimental evolution of bacteria. Res Microbiol 155: 319-327.
27. Seneta E (1981) Non-negative matrices and Markov chains. Springer, New York.
28. Shapiro JA (1999) Transposable elements as the key to a 21st century view of evolution. Genetica 107: 171-179.
29. So M, McCarthy BJ (1980) Nucleotide sequence of the bacterial transposon TN1681 encoding a heat-stable (ST) toxin and its identification in enterotoxigenic Escherichia coli strains. Proc Natl Acad Sci USA 77(7): 4011-4015.
30. Tavakoli NP, Derbyshire KM (2001) Tipping the balance between replicative and simple transposition. EMBO J 20(11): 2923-2930.
31. Top EM, Springael D (2003) The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr Opin Biotechnol 14: 262-269.
32. Touchon M, Rocha EPC (2007) Causes of insertion sequences abundance in prokaryotic genomes. Mol Biol Evol 24(4): 969-981.
33. Wagner A (2006) Periodic extinctions of transposable elements in bacterial lineages: evidence from intragenomic variation in multiple genomes. Mol Biol Evol 23(4): 723-733.
34. Wagner A, Lewis C, Bichsel M (2007) A survey of bacterial insertion sequences using IScan. Nucleic Acids Res 35(16): 5284-5293.
35. Williams HG, Day MJ, Fry JC, Stewart GJ (1996) Natural transformation in river epilithon. Appl Environ Microbiol 62(8): 2994-2998.
36. Wolfram S (2003) The mathematica book, 5th edn. Wolfram Media, Champaign.