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Originally published as Genetics Published Articles Ahead of Print on March 4, 2007.

Genetics, Vol. 176, 421-440, May 2007, Copyright © 2007
doi:10.1534/genetics.106.063149

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A Maximum-Likelihood Method for the Estimation of Pairwise Relatedness in Structured Populations

Amy D. Anderson1 and Bruce S. Weir

Department of Biostatistics, University of Washington, Seattle, Washington 98195

1 Corresponding author: Department of Biostatistics, University of Washington, F-600 Health Sciences Bldg., Campus Mail Stop 357232, Seattle, WA 98195-7232.
E-mail: ada891{at}u.washington.edu

A maximum-likelihood estimator for pairwise relatedness is presented for the situation in which the individuals under consideration come from a large outbred subpopulation of the population for which allele frequencies are known. We demonstrate via simulations that a variety of commonly used estimators that do not take this kind of misspecification of allele frequencies into account will systematically overestimate the degree of relatedness between two individuals from a subpopulation. A maximum-likelihood estimator that includes FST as a parameter is introduced with the goal of producing the relatedness estimates that would have been obtained if the subpopulation allele frequencies had been known. This estimator is shown to work quite well, even when the value of FST is misspecified. Bootstrap confidence intervals are also examined and shown to exhibit close to nominal coverage when FST is correctly specified.


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