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Originally published as Genetics Published Articles Ahead of Print on November 15, 2004.
Genetics, Vol. 169, 1589-1599, March 2005, Copyright © 2005
doi:10.1534/genetics.104.029553
Estimation of Long-Term Effective Population Sizes Through the History of Durum Wheat Using Microsatellite Data
A.-C. Thuillet, T. Bataillon, S. Poirier, S. Santoni and J. L. David1
Institut National de la Recherche Agronomique-UMR 1097 Diversité et Génomes des Plantes Cultivées, 34130 Mauguio, France
1 Corresponding author: INRA-UMR Diversité et Génomes des Plantes Cultivées, Domaine de Melgueil, 34130 Mauguio, France.
E-mail: david{at}ensam.inra.fr
Estimation of long-term effective population size (Ne) from polymorphism data alone requires an independent knowledge of mutation rate. Microsatellites provide the opportunity to estimate Ne because their high mutation rate can be estimated from observed mutations. We used this property to estimate Ne in allotetraploid wheat Triticum turgidum at four stages of its history since its domestication. We estimated the mutation rate of 30 microsatellite loci. Allele-specific mutation rates µ were predicted from the number of repeats of the alleles. Effective population sizes were calculated from the diversity parameter 
= 4Neµ. We demonstrated from simulations that the unbiased estimator of based on Nei's heterozygosity is the most appropriate for estimating Ne because of a small variance and a relative robustness to variations in the mutation model compared to other estimators. We found a Ne of 32,500 individuals with a 95% confidence interval of [20,739; 45,991] in the wild ancestor of wheat, 12,000 ([5790; 19,300]) in the domesticated form, 6000 ([2831; 9556]) in landraces, and 1300 ([689; 2031]) in recent improved varieties. This decrease illustrates the successive bottlenecks in durum wheat. No selective effect was detected on our loci, despite a complete loss of polymorphism for two of them.
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