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Originally published as Genetics Published Articles Ahead of Print on August 20, 2008.
Genetics, Vol. 180, 341-357, September 2008, Copyright © 2008
doi:10.1534/genetics.108.091231
Second-Order Moments of Segregating Sites Under Variable Population Size
Daniel 
ivkovi
and
Thomas Wiehe1
Institut für Genetik, Universität zu Köln, 50674 Köln, Germany
1 Corresponding author: Institut für Genetik, Universität zu Köln, Zülpicher Strasse 47, 50674 Köln, Germany.
E-mail: twiehe{at}uni-koeln.de
The identification of genomic regions that have been exposed to positive selection is a major challenge in population genetics. Since selective sweeps are expected to occur during environmental changes or when populations are colonizing a new habitat, statistical tests constructed on the assumption of constant population size are biased by the co-occurrence of population size changes and selection. To delimit this problem and gain better insights into demographic factors, theoretical results regarding the second-order moments of segregating sites, such as the variance of segregating sites, have been derived. Driven by emerging genomewide surveys, which allow the estimation of demographic parameters, a generalized version of Tajima's D has been derived that takes into account a previously estimated demographic scenario to test single loci for traces of selection against the null hypothesis of neutral evolution under variable population size.
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