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MBE Advance Access published online on February 12, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh066
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted December 2, 2003
© 2004 Society for Molecular Biology and Evolution

Original Articles

A Test of Neutrality and Constant Population Size Based on the Mismatch Distribution

Sylvain Mousset 1*, Nicolas Derome 2, and Michel Veuille 3

1 Laboratoire d'Ecologie, Ecole Pratique des Hautes Etudes, Université Pierre et Marie Curie, F-75005 Paris, France; Section of Evolutionary Biology, Department of Biology II, University of Munich, D-80333 Munich, Germany
2 Laboratoire d'Ecologie, Ecole Pratique des Hautes Etudes, Université Pierre et Marie Curie, F-75005 Paris, France; Laboratoire Populations Génétique et Evolution, CNRS, F-91198 Gif-sur-Yvette cedex, France
3 Laboratoire d'Ecologie, Ecole Pratique des Hautes Etudes, Université Pierre et Marie Curie, F-75005 Paris, France

* To whom correspondence should be addressed. E-mail: mousset{at}zi.biologie.uni-muenchen.de.


  Abstract

Several factors including demographic changes, selection, and recombination are known to affect the distribution of the number of pairwise differences between DNA sequences. The effects of each of these forces were previously used to estimate population parameter values using various assumptions about other factors. In this paper, we use the predictions of the mismatch distribution under a standard neutral equilibrium model to design a coalescent simulation-based test and detect any deviation from this equilibrium. When reliable independent estimates are available for the intragenic recombination rate, this test can be used as a neutrality test or a population expansion test in actual studies, under reasonable assumptions.

Key Words: neutrality test, DNA polymorphism, mismatch distribution, selective sweep, demography


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