The diversity of a distributed genome in bacterial populations

Annals of Applied Probability

Volumn 20, Issue 5, 2010, Pages 1567-1606

  Baumdicker, F ^a   Hess, W R ^a   Pfaffelhuber, P ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

Gene content; Infinitely many genes model; Infinitely many sites model; Kingman's coalescent

Indexed keywords

EID: 77957711376     PISSN: 10505164     EISSN: 10505164     Source Type: Journal    
DOI: 10.1214/09-AAP657     Document Type: Article

References (31)

1. BENTLEY, S. (2009). Sequencing the species pan-genome. Nature Rev. Microbiol. 7 258-259.
2. DUFRESNE, A., OSTROWSKI, M., SCANLAN, D. J., GARCZAREK, L., MAZARD, S., PALENIK, B. P., PAULSEN, I. T., DE MARSAC, N. T., WINCKER, P., DOSSAT, C., FERRIERA, S., JOHNSON, J., POST, A. F., HESS, W. R. and PARTENSKY, F. (2008). Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biol. 9 R90.
3. DURRETT, R. (2008). Probability Models for DNA Sequence Evolution, 2nd ed. Springer, New York. MR2439767
4. DURRETT, R. and POPOVIC, L. (2009). Degenerate diffusions arising from gene duplication models. Ann. Appl. Probab. 19 15-48. MR2498670
5. DYKHUIZEN, D. E. and GREEN, L. (1991). Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173 7257-7268.
6. EHRLICH, G. D., HU, F. Z., SHEN, K., STOODLEY, P. and POST, J. C. (2005). Bacterial plurality as a general mechanism driving persistence in chronic infections. Clin. Orthop. Relat. Res. 437 20-24.
7. EVANS, S., SHVETS, S. and SLATKIN, M. (2007). Non-equlibrium theory of the allele frequency spectrum. Theo. Pop. Biol. 71 109-119.
8. EWENS, W. J. (2004). Mathematical Population Genetics. I. Theoretical Introduction, 2nd ed. Interdisciplinary Applied Mathematics 27. Springer, New York. MR2026891
9. FRASER, C., HANAGE, W. P. and SPRATT, B. G. (2007). Recombination and the nature of bacterial speciation. Science 315 476-480.
10. FU, Y. X. (1995). Statistical properties of segregating sites. Theo. Pop. Biol. 48 172-197.
11. GRIFFITHS, R. C. (2003). The frequency spectrum of a mutation and its age, in a general diffusion model. Theo. Pop. Biol. 64 241-251.
12. HILLER, N. L., JANTO, B., HOGG, J. S., BOISSY, R., YU, S., POWELL, E., KEEFE, R., EHRLICH, N. E., SHEN, K., HAYES, J., BARBADORA, K., KLIMKE, W., DERNOVOY, D., TATUSOVA, T., PARKHILL, J., BENTLEY, S. D., POST, J. C., EHRLICH, G. D. and HU, F. Z. (2007). Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: Insights into the pneumococcal supragenome. J. Bacteriol. 189 8186-8195.
13. HOGG, J. S., HU, F. Z., JANTO, B., BOISSY, R., HAYES, J., KEEFE, R., POST, J. C. and EHRLICH, G. D. (2007). Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biol. 8 R103.
14. HUSON, D. H. and STEEL, M. (2004). Phylogenetic trees based on gene content. Bioinformatics 20 2044-2049.
15. KETTLER, G. C., MARTINY, A. C., HUANG, K., ZUCKER, J., COLEMAN, M. L., RODRIGUE, S., CHEN, F., LAPIDUS, A., FERRIERA, S., JOHNSON, J., STEGLICH, C., CHURCH, G. M., RICHARDSON, P. and CHISHOLM, S. W. (2007). Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet. 3 e231.
16. KIMURA, M. (1964). Diffusion models in population genetics. J. Appl. Probab. 1 177-232. MR0172727
17. KINGMAN, J. F. C. (1982). The coalescent. Stochastic Process. Appl. 13 235-248. MR671034
18. KUNIN, V. and OUZOUNIS, C. A. (2003). GeneTRACE-reconstruction of gene content of ancestral species. Bioinformatics 19 1412-1416.
19. LAPIERRE, P. and GOGARTEN, J. P. (2009). Estimating the size of the bacterial pan-genome. Trends in Genetics 25 107-110.
20. LEFÉBURE, T. and STANHOPE, M. J. (2007). Evolution of the core and pan-genome of Streptococcus: Positive selection, recombination, and genome composition. Genome Biol. 8 R71.
21. MAIDEN, M. C., BYGRAVES, J. A., FEIL, E., MORELLI, G., RUSSELL, J. E., URWIN, R., ZHANG, Q., ZHOU, J., ZURTH, K., CAUGANT, D. A., FEAVERS, I. M., ACHTMAN, M. and SPRATT, B. G. (1998). Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95 3140-3145.
22. MAYNARD-SMITH, J. (1995). Do bacteria have population genetics? In Population Genetics of Bacteria 1-12. Cambridge Univ. Press, Cambridge.
23. MEDINI, D., DONATI, C., TETTELIN, H., MASIGNANI, V. and RAPPUOLI, R. (2005). The microbial pan-genome. Curr. Opin. Genet. Dev. 15 589-594.
24. MÖHLE, M. and SAGITOV, S. (2001). A classification of coalescent processes for haploid exchangeable population models. Ann. Probab. 29 1547-1562. MR1880231 (Pubitemid 33406000)
25. PERNA, N. T., PLUNKETT, G., BURLAND, V., MAU, B., GLASNER, J. D., ROSE, D. J., MAYHEW, G. F., EVANS, P. S., GREGOR, J., KIRKPATRICK, H. A., PÉSFAI, G., HACKETT, J., KLINK, S., BOUTIN, A., SHAO, Y., MILLER, L., GROTBECK, E. J., DAVIS, N. W., LIM, A., DIMALANTA, E. T., POTAMOUSIS, K. D., APODACA, J., ANANTHARAMAN, T. S., LIN, J., YEN, G., SCHWARTZ, D. C., WELCH, R. A. and BLATTNER, F. R. (2001). Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409 529-533. (Pubitemid 32144360)
26. RILEY, M. A. and LIZOTTE-WANIEWSKI, M. (2009). Population genomics and the bacterial species concept. Methods Mol. Biol. 532 367-377.
27. TETTELIN, H., MASIGNANI, V., CIESLEWICZ, M. J., DONATI, C., MEDINI, D., WARD, N. L., ANGIUOLI, S. V., CRABTREE, J., JONES, A. L., DURKIN, A. S., DEBOY, R. T., DAVID-SEN, T. M., MORA, M., SCARSELLI, M., MARGARIT Y ROS, I., PETERSON, J. D., HAUSER, C. R., SUNDARAM, J. P., NELSON, W. C., MADUPU, R., BRINKAC, L. M., DODSON, R. J., ROSOVITZ, M. J., SULLIVAN, S. A., DAUGHERTY, S. C., HAFT, D. H., SELENGUT, J., GWINN, M. L., ZHOU, L., ZAFAR, N., KHOURI, H., RADUNE, D., DIMITROV, G., WATKINS, K., O'CONNOR, K. J., SMITH, S., UTTERBACK, T. R., WHITE, O., RUBENS, C. E., GRANDI, G., MADOFF, L. C., KASPER, D. L., TELFORD, J. L., WESSELS, M. R., RAPPUOLI, R. and FRASER, C. M. (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome." Proc. Natl. Acad. Sci. USA 102 13950-13955.
28. TETTELIN, H., RILEY, D., CATTUTO, C. and MEDINI, D. (2008). Comparative genomics: The bacterial pan-genome. Curr. Opin. Microbiol. 11 472-477.
29. VULIC, M., DIONISIO, F., TADDEI, F. and 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.
30. WAKELEY, J. (2008). Coalescent Theory: An Introduction. Roberts and Company, Colorado.
31. WRIGHT, S. (1938). The distribution of gene frequencies under irreversible mutation. Proc. Natl. Acad. Sci. USA 24 253-259.