Improved confidence intervals for the linkage disequilibrium method for estimating effective population size

Jones, A. T., Ovenden, J. R. and Wang, Y. -G. (2016) Improved confidence intervals for the linkage disequilibrium method for estimating effective population size. Heredity, . doi:10.1038/hdy.2016.19


Author Jones, A. T.
Ovenden, J. R.
Wang, Y. -G.
Title Improved confidence intervals for the linkage disequilibrium method for estimating effective population size
Journal name Heredity   Check publisher's open access policy
ISSN 1365-2540
0018-067X
Publication date 2016-03-23
Year available 2016
Sub-type Article (original research)
DOI 10.1038/hdy.2016.19
Open Access Status Not Open Access
Total pages 7
Place of publication London, United Kingdom
Publisher Nature Publishing Group
Collection year 2017
Language eng
Abstract The linkage disequilibrium method is currently the most widely used single sample estimator of genetic effective population size. The commonly used software packages come with two options, referred to as the parametric and jackknife methods, for computing the associated confidence intervals. However, little is known on the coverage performance of these methods, and the published data suggest there may be some room for improvement. Here, we propose two new methods for generating confidence intervals and compare them with the two in current use through a simulation study. The new confidence interval methods tend to be conservative but outperform the existing methods for generating confidence intervals under certain circumstances, such as those that may be encountered when making estimates using large numbers of single-nucleotide polymorphisms
Keyword Linkage disequilibrium method
Population size
Effective population size (Ne)
Confidence intervals
Simulation study
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: School of Mathematics and Physics
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