Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods

Annals of Applied Statistics

Volumn 9, Issue 1, 2015, Pages 200-224

  Fearnhead, Paul ^a   Yu, Shoukai ^b   Biggs, Patrick ^b   Holland, Barbara ^c   French, Nigel ^b  

^a LANCASTER UNIVERSITY   (United Kingdom)

^b MASSEY UNIVERSITY   (New Zealand)

^c UNIVERSITY OF TASMANIA   (Australia)

Author keywords

Composite likelihood; Recombination; Single locus variants; Testing for rate variation

Indexed keywords

EID: 84929676451     PISSN: 19326157     EISSN: 19417330     Source Type: Journal    
DOI: 10.1214/14-AOAS795     Document Type: Article

References (29)

1. DIDELOT, X. and FALUSH, D. (2007). Inference of bacterial microevolution using multilocus sequence data. Genetics 175 1251–1266.
2. DIDELOT, X., LAWSON, D. and FALUSH, D. (2009). SimMLST: Simulation of multi-locus sequence typing data under a neutral model. Bioinformatics 25 1442–1444.
3. DIDELOT, X. and MAIDEN, M. C. J. (2010). Impact of recombination on bacterial evolution. Trends in Microbiology 18 315–322.
4. DIDELOT, X., LAWSON, D., DARLING, A. and FALUSH, D. (2010). Inference of homologous recombination in bacteria using whole-genome sequences. Genetics 186 1435–1449.
5. DONNELLY, P. and TAVARÉ, S. (1995). Coalescents and genealogical structure under neutrality. Annu. Rev. Genet. 29 401–421.
6. FEIL, E. J., MAIDEN, M. C. J., ACHTMAN, M. and SPRATT, B. G. (1999). The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis. Molecular Biology and Evolution 16 1496–1502.
7. FEIL, E. J., SMITH, J.M., ENRIGHT, M. C. and SPRATT, B. G. (2000). Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154 1439–1450.
8. FRASER, C., HANAGE, W. P. and SPRATT, B. G. (2007). Recombination and the nature of bacterial speciation. Science 315 476–480.
9. GRIFFITHS, R. C. and MARJORAM, P. (1997). An ancestral recombination graph. In Progress in Population Genetics and Human Evolution (Minneapolis, MN, 1994). IMA Vol. Math. Appl. 87 257–270 Springer, New York. MR1493031.
10. GUY, L., NYSTEDT, B., SUN, Y., NASLUND, K., BERGLUND, E. and ANDERSSON, S. G. (2012). A genome-wide study of recombination rate variation in Bartonella henselae. BMC Evolutionary Biology 12 65.
11. HUDSON, R. R. (2001). Two-locus sampling distributions and their application. Genetics 159 1805–1817.
12. JOLLEY, K. A. and MAIDEN, M. C. J. (2010). Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11 595.
13. KENT, J. T. (1982). Robust properties of likelihood ratio tests. Biometrika 69 19–27 MR0655667.
14. LARRIBE, F. and FEARNHEAD, P. (2011). On composite likelihoods in statistical genetics. Statist. Sinica 21 43–69 MR2796853.
15. LOW, K. B. and PORTER, D. D. (1978). Modes of gene transfer and recombination in bacteria. Annu. Rev. Genet. 12 249–287.
16. MAIDEN, M. C. J., 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.
17. MCVEAN, G. A. T., AWADALLA, P. and FEARNHEAD, P. (2002). A coalescent method for detecting recombination from gene sequences. Genetics 160 1231–1241.
18. MILKMAN, R. and BRIDGES, M. M. (1990). Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics 126 505–517.
19. MOLENBERGHS, G. and VERBEKE, G. (2005). Models for Discrete Longitudinal Data. Springer, New York. MR2171048.
20. PÉREZ-LOSADA, M., BROWNE, E. B., MADSEN, A., WIRTH, T., VISCIDI, R. P. and CRANDALL, K. A. (2006). Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data. Infection, Genetics and Evolution 6 97–112.
21. ROTNITZKY, A. and JEWELL, N. P. (1990). Hypothesis testing of regression parameters in semiparametric generalized linear models for cluster correlated data. Biometrika 77 485–497 MR1087838.
22. SHEPPARD, S. K., MCCARTHY, N. D., FALUSH, D. and MAIDEN, M. C. J. (2008). Convergence of Campylobacter species: Implications for bacterial evolution. Science 320 237–239.
23. SPRATT, B. G., HANAGE, W. P. and FEIL, E. J. (2001). The relative contributions of recombination and point mutation to the diversification of bacterial clones. Current Opinion in Microbiology 4 602–606.
24. VARIN, C. (2008). On composite marginal likelihoods. AStA Adv. Stat. Anal. 92 1–28 MR2414624.
25. VARIN, C., REID, N. and FIRTH, D. (2011). An overview of composite likelihood methods. Statist. Sinica 21 5–42 MR2796852.
26. VOS, M. (2009). Why do bacteria engage in homologous recombination? Trends Microbiol. 17 226–232.
27. VOS, M. and DIDELOT, X. (2009). A comparison of homologous recombination rates in bacteria and archaea. ISME J. 3 199–208.
28. WAKELEY, J. (2007). Coalescent Theory: An Introduction. Roberts and Company, Denver, CO.
29. YU, S., FEARNHEAD, P., HOLLAND, B. R., BIGGS, P., MAIDEN, M. and FRENCH, N. (2012). Estimating the relative roles of recombination and point mutation in the generation of single locus variants in Campylobacter jejuni and Campylobacter coli. J. Mol. Evol. 74 273–280.