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

Citation

Fearnhead, P and Yu, S and Biggs, P and Holland, B and French, N, Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods, The Annals of Applied Statistics, 9, (1) pp. 200-224. ISSN 1932-6157 (2015) [Refereed Article]


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Copyright Statement

Copyright 2015 Institute of Mathematical Statistics

DOI: doi:10.1214/14-AOAS795

Abstract

A number of studies have suggested using comparisons between DNA sequences of closely related bacterial isolates to estimate the relative rate of recombination to mutation for that bacterial species. We consider such an approach which uses single-locus variants: pairs of isolates whose DNA differ at a single gene locus. One way of deriving point estimates for the relative rate of recombination to mutation from such data is to use composite likelihood methods. We extend recent work in this area so as to be able to construct confidence intervals for our estimates, without needing to resort to computationally-intensive bootstrap procedures, and to develop a test for whether the relative rate varies across loci. Both our test and method for constructing confidence intervals are obtained by modeling the dependence structure in the data, and then applying asymptotic theory regarding the distribution of estimators obtained using a composite likelihood. We applied these methods to multi-locus sequence typing (MLST) data from eight bacteria, finding strong evidence for considerable rate variation in three of these: Bacillus cereus, Enterococcus faecium and Klebsiella pneumoniae.

Item Details

Item Type:Refereed Article
Keywords:composite likelihood, recombination, single-locus variants, testing for rate variation
Research Division:Mathematical Sciences
Research Group:Applied Mathematics
Research Field:Biological Mathematics
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Biological Sciences
UTAS Author:Holland, B (Associate Professor Barbara Holland)
ID Code:100326
Year Published:2015
Funding Support:Australian Research Council (FT100100031)
Web of Science® Times Cited:2
Deposited By:Mathematics and Physics
Deposited On:2015-05-12
Last Modified:2017-10-30
Downloads:764 View Download Statistics

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