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Originally published as Genetics Published Articles Ahead of Print on September 15, 2004.

Genetics, Vol. 168, 2363-2372, December 2004, Copyright © 2004
doi:10.1534/genetics.104.029488

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The Probability and Chromosomal Extent of trans-specific Polymorphism

Carsten Wiuf*,1, Keyan Zhao{dagger}, Hideki Innan{dagger},2 and Magnus Nordborg{dagger},3

* Department of Statistics, University of Oxford, Oxford, OX1 3TG, United Kingdom
{dagger} Program in Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-1340

3 Corresponding author: Molecular and Computational Biology, University of Southern California, SHS 172, 835 W. 37th St., Los Angeles, CA 90089-1340.
E-mail: magnus{at}usc.edu

Balancing selection may result in trans-specific polymorphism: the maintenance of allelic classes that transcend species boundaries by virtue of being more ancient than the species themselves. At the selected site, gene genealogies are expected not to reflect the species tree. Because of linkage, the same will be true for part of the surrounding chromosomal region. Here we obtain various approximations for the distribution of the length of this region and discuss the practical implications of our results. Our main finding is that the trans-specific region surrounding a single-locus balanced polymorphism is expected to be quite short, probably too short to be readily detectable. Thus lack of obvious trans-specific polymorphism should not be taken as evidence against balancing selection. When trans-specific polymorphism is obvious, on the other hand, it may be reasonable to argue that selection must be acting on multiple sites or that recombination is suppressed in the surrounding region.




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