Comparative evaluation of a new effective population size estimator based on approximate bayesian computation

Genetics
David A TallmonMark A Beaumont

Abstract

We describe and evaluate a new estimator of the effective population size (N(e)), a critical parameter in evolutionary and conservation biology. This new "SummStat" N(e) estimator is based upon the use of summary statistics in an approximate Bayesian computation framework to infer N(e). Simulations of a Wright-Fisher population with known N(e) show that the SummStat estimator is useful across a realistic range of individuals and loci sampled, generations between samples, and N(e) values. We also address the paucity of information about the relative performance of N(e) estimators by comparing the SummStat estimator to two recently developed likelihood-based estimators and a traditional moment-based estimator. The SummStat estimator is the least biased of the four estimators compared. In 32 of 36 parameter combinations investigated using initial allele frequencies drawn from a Dirichlet distribution, it has the lowest bias. The relative mean square error (RMSE) of the SummStat estimator was generally intermediate to the others. All of the estimators had RMSE > 1 when small samples (n = 20, five loci) were collected a generation apart. In contrast, when samples were separated by three or more generations and N(e) < or = 50, the Su...Continue Reading

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Citations

Aug 15, 2009·Bioinformatics·Joao S LopesMark A Beaumont
Jul 29, 2005·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Jinliang Wang
Sep 7, 2005·Genetics·Scotland C LemanMarcy K Uyenoyama
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