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Genetics, Vol. 167, 1461-1473, July 2004, Copyright © 2004
doi:10.1534/genetics.103.025742

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Estimating Recombination Rates Using Three-Site Likelihoods

Jeffrey D. Wall1

Program in Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089

1 Address for correspondence: Program in Molecular and Computational Biology, University of Southern California, 1042 W. 36th Pl., Los Angeles, CA 90089.
E-mail: jeffwall{at}usc.edu

We introduce a new method for jointly estimating crossing-over and gene conversion rates using sequence polymorphism data. The method calculates probabilities for subsets of the data consisting of three segregating sites and then forms a composite likelihood by multiplying together the probabilities of many subsets. Simulations show that this new method performs better than previously proposed methods for estimating gene conversion rates, but that all methods require large amounts of data to provide reliable estimates. While existing methods can easily estimate an "average" gene conversion rate over many loci, they cannot reliably estimate gene conversion rates for a single region of the genome.




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