Jenkins, Paul (2012) Stopping-time resampling and population genetic inference under coalescent models. Statistical Applications in Genetics and Molecular Biology, Vol.11 (No.1). pp. 1-20. doi:10.2202/1544-6115.1770

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Abstract

To extract full information from samples of DNA sequence data, it is necessary to use sophisticated model-based techniques such as importance sampling under the coalescent. However, these are limited in the size of datasets they can handle efficiently. Chen and Liu (2000) introduced the idea of stopping-time resampling and showed that it can dramatically improve the efficiency of importance sampling methods under a finite-alleles coalescent model. In this paper, a new framework is developed for designing stopping-time resampling schemes under more general models. It is implemented on data both from infinite sites and stepwise models of mutation, and extended to incorporate crossover recombination. A simulation study shows that this new framework offers a substantial improvement in the accuracy of likelihood estimation over a range of parameters, while a direct application of the scheme of Chen and Liu (2000) can actually diminish the estimate. The method imposes no additional computational burden and is robust to the choice of parameters.

Item Type:	Journal Article
Divisions:	Faculty of Science > Statistics
Journal or Publication Title:	Statistical Applications in Genetics and Molecular Biology
Publisher:	Walter de Gruyter GmbH & Co. KG
ISSN:	2194-6302
Official Date:	2012
Dates:	Date Event 2012 Published
Volume:	Vol.11
Number:	No.1
Page Range:	pp. 1-20
DOI:	10.2202/1544-6115.1770
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Related URLs:	Publisher

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