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Comparative Study
. 2005 Dec;171(4):2051-62.
doi: 10.1534/genetics.104.036293. Epub 2005 Jun 14.

A comparison of three estimators of the population-scaled recombination rate: accuracy and robustness

Nick G C Smith  1 , Paul Fearnhead
Affiliations
Comparative Study

A comparison of three estimators of the population-scaled recombination rate: accuracy and robustness

Nick G C Smith et al. Genetics. 2005 Dec.

Abstract

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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Figures

Figure 1.
Figure 1.
QQ plots of the likelihood-ratio (LR) statistics of the three methods with a formula image-distribution. The LR statistic from maxhap was divided by the number of segregating sites. Approximate 99% confidence intervals for the QQ plots are shown by dashed lines.
See this image and copyright information in PMC

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