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Journal of Molecular Evolution

, Volume 74, Issue 5–6, pp 273–280 | Cite as

Estimating the Relative Roles of Recombination and Point Mutation in the Generation of Single Locus Variants in Campylobacter jejuni and Campylobacter coli

  • Shoukai Yu
  • Paul Fearnhead
  • Barbara R. Holland
  • Patrick Biggs
  • Martin Maiden
  • Nigel FrenchEmail author
Article

Abstract

Single locus variants (SLVs) are bacterial sequence types that differ at only one of the seven canonical multilocus sequence typing (MLST) loci. Estimating the relative roles of recombination and point mutation in the generation of new alleles that lead to SLVs is helpful in understanding how organisms evolve. The relative rates of recombination and mutation for Campylobacter jejuni and Campylobacter coli were estimated at seven different housekeeping loci from publically available MLST data. The probability of recombination generating a new allele that leads to an SLV is estimated to be roughly seven times more than that of mutation for C. jejuni, but for C. coli recombination and mutation were estimated to have a similar contribution to the generation of SLVs. The majority of nucleotide differences (98 % for C. jejuni and 85 % for C. coli) between strains that make up an SLV are attributable to recombination. These estimates are much larger than estimates of the relative rate of recombination to mutation calculated from more distantly related isolates using MLST data. One explanation for this is that purifying selection plays an important role in the evolution of Campylobacter. A simulation study was performed to test the performance of our method under a range of biologically realistic parameters. We found that our method performed well when the recombination tract length was longer than 3 kb. For situations in which recombination may occur with shorter tract lengths, our estimates are likely to be an underestimate of the ratio of recombination to mutation, and of the importance of recombination for creating diversity in closely related isolates. A parametric bootstrap method was applied to calculate the uncertainty of these estimates.

Keywords

Single locus variant MLST Purifying selection Evolution of Campylobacter Mutation Recombination 

Notes

Acknowledgments

The authors acknowledge the Marsden Fund project 08-MAU-099 (Cows, starlings and Campylobacter in New Zealand: unifying phylogeny, genealogy, and epidemiology to gain insight into pathogen evolution) for funding this project. This publication made use of the Campylobacter Multi Locus Sequence Typing website (http://pubmlst.org/campylobacter/) developed by Keith Jolley and sited at the University of Oxford (Jolley and Maiden 2010, BMC Bioinformatics, 11:595). The development of this site has been funded by the Wellcome Trust. BRH acknowledges the Australian Research Council (Grant FT100100031).

Supplementary material

239_2012_9505_MOESM1_ESM.pdf (137 kb)
Supplementary material 1 (PDF 136 kb)
239_2012_9505_MOESM2_ESM.doc (40 kb)
Supplementary material 2 (DOC 39 kb)
239_2012_9505_MOESM3_ESM.pdf (83 kb)
Supplementary material 3 (PDF 82 kb)

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Shoukai Yu
    • 1
  • Paul Fearnhead
    • 2
  • Barbara R. Holland
    • 3
  • Patrick Biggs
    • 1
  • Martin Maiden
    • 4
  • Nigel French
    • 1
    • 5
    Email author
  1. 1.Infectious Disease Research Centre, Institute of Veterinary, Animal, and Biomedical SciencesMassey UniversityPalmerston NorthNew Zealand
  2. 2.Department of Mathematics and StatisticsLancaster UniversityLancasterUK
  3. 3.School of Mathematics and PhysicsUniversity of TasmaniaHobartAustralia
  4. 4.Department of ZoologyUniversity of OxfordOxfordUK
  5. 5.Allan Wilson Centre for Molecular Ecology and EvolutionMassey UniversityPalmerston NorthNew Zealand

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