Estimation of long-term effective population sizes through the history of durum wheat using microsatellite data

Abstract

Estimation of long-term effective population size (N(e)) from polymorphism data alone requires an independent knowledge of mutation rate. Microsatellites provide the opportunity to estimate N(e) because their high mutation rate can be estimated from observed mutations. We used this property to estimate N(e) 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 mu were predicted from the number of repeats of the alleles. Effective population sizes were calculated from the diversity parameter theta = 4N(e)mu. We demonstrated from simulations that the unbiased estimator of theta based on Nei's heterozygosity is the most appropriate for estimating N(e) because of a small variance and a relative robustness to variations in the mutation model compared to other estimators. We found a N(e) 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.

Figure 1.—

Magnitude of the bias on θ̂_F (solid circles) and on θ̂_He (open circles) for different values of θ. The x-axis represents the parametric value of θ used for the simulations. Each point represents the average bias estimated on the basis of 1000 simulated data sets. Simulations were realized assuming either a constant population size and (a) a SMM or (b) a TPM or a bottlenecked population and (c) a SMM or (d) a TPM.

Figure 2.—

Correlation between θ̂_F and the predicted mutation rate in the wild group of wheat (R² = 0.56, P < 0.003).

Figure 3.—

Reductions of heterozygosity (H_e) and effective population size (N_e) from the wild form, T. t. dicoccoides, to the elite varieties of durum wheat. Values are shown relative to the value in the wild form that is retained in the subsequent population.