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Originally published as Genetics Published Articles Ahead of Print on June 14, 2005.
Genetics, Vol. 171, 2051-2062, December 2005, Copyright © 2005
doi:10.1534/genetics.104.036293
A Comparison of Three Estimators of the Population-Scaled Recombination Rate: Accuracy and Robustness
Nick G. C. Smith and Paul Fearnhead1
Department of Mathematics and Statistics, Lancaster University, Lancaster LA1 4YF, United Kingdom
1 Corresponding author: Department of Mathematics and Statistics, Lancaster University, Lancaster LA1 4YF, United Kingdom.
E-mail: p.fearnhead{at}lancs.ac.uk
We have performed simulations to assess the performance of three population genetics approximate-likelihood methods in estimating the population-scaled recombination rate from sequence data. We measured performance in two ways: accuracy when the sequence data were simulated according to the (simplistic) standard model underlying the methods and robustness to violations of many different aspects of the standard model. Although we found some differences between the methods, performance tended to be similar for all three methods. Despite the fact that the methods are not robust to violations of the underlying model, our simulations indicate that patterns of relative recombination rates should be inferred reasonably well even if the standard model does not hold. In addition, we assess various techniques for improving the performance of approximate-likelihood methods. In particular we find that the composite-likelihood method of HUDSON (2001) can be improved by including log-likelihood contributions only for pairs of sites that are separated by some prespecified distance.
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