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Genetics, Vol. 168, 563-568, September 2004, Copyright © 2004
doi:10.1534/genetics.103.025908
On the Distribution of Temporal Variations in Allele Frequency
Consequences for the Estimation of Effective Population Size and the Detection of Loci Undergoing Selection
Isabelle Goldringer*,1 and
Thomas Bataillon
* UMR de Génétique Végétale, INRA UPS INA-PG CNRS, Ferme du Moulon, 91190 Gif sur Yvette, France
UMR 1097 Diversité et Génomes des Plantes Cultivées, INRA Domaine de Melgueil, 34130 Mauguio, France
1 Corresponding author: UMR de Génétique Végétale, INRA UPS INA-PG CNRS, Ferme du Moulon, 91190 Gif sur Yvette, France.
E-mail: isa{at}moulon.inra.fr
The effective population size (Ne) is frequently estimated using temporal changes in allele frequencies at neutral markers. Such temporal changes in allele frequencies are usually estimated from the standardized variance in allele frequencies (Fc). We simulate Wright-Fisher populations to generate expected distributions of Fc and of 
c (Fc averaged over several loci). We explore the adjustment of these simulated c distributions to a chi-square distribution and evaluate the resulting precision on the estimation of Ne for various scenarios. Next, we outline a procedure to test for the homogeneity of the individual Fc across loci and identify markers exhibiting extreme Fc-values compared to the rest of the genome. Such loci are likely to be in genomic areas undergoing selection, driving Fc to values greater (or smaller) than expected under drift alone. Our procedure assigns a P-value to each locus under the null hypothesis (drift is homogeneous throughout the genome) and simultaneously controls the rate of false positive among loci declared as departing significantly from the null. The procedure is illustrated using two published data sets: (i) an experimental wheat population subject to natural selection and (ii) a maize population undergoing recurrent selection.
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