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Genetics, Vol. 174, 1995-2008, December 2006, Copyright © 2006
doi:10.1534/genetics.106.061887
Approximate Genealogies Under Genetic Hitchhiking
P. Pfaffelhuber*,1,
B. Haubold
and
A. Wakolbinger
* Biocenter, Ludwig-Maximilian University, 82152 Planegg, Germany, Department of Biotechnology and Bioinformatics, University of Applied Sciences, 85350 Freising, Germany and Department of Computer Science and Mathematics, Goethe University, 60054 Frankfurt, Germany
1 Corresponding author: Biocenter, Ludwig-Maximilian University, Grosshaderner Strasse 2, D-82152 Planegg, Germany.
E-mail: p.p{at}lmu.de
The rapid fixation of an advantageous allele leads to a reduction in linked neutral variation around the target of selection. The genealogy at a neutral locus in such a selective sweep can be simulated by first generating a random path of the advantageous allele's frequency and then a structured coalescent in this background. Usually the frequency path is approximated by a logistic growth curve. We discuss an alternative method that approximates the genealogy by a random binary splitting tree, a so-called Yule tree that does not require first constructing a frequency path. Compared to the coalescent in a logistic background, this method gives a slightly better approximation for identity by descent during the selective phase and a much better approximation for the number of lineages that stem from the founder of the selective sweep. In applications such as the approximation of the distribution of Tajima's D, the two approximation methods perform equally well. For relevant parameter ranges, the Yule approximation is faster.
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