Optimum Sample Size for SSR-based Estimation of Representative Allele Frequencies and Genetic Diversity in Scots Pine Populations

Abstract

We used the random subsampling approach based on the empirical data to identify the representative sample size for accurate estimates of allele frequencies within a population. The empirical data consisted of 12 nuclear microsatellite marker scores for 400 individuals sampled within 1 ha area in a representative natural stand of Scots pine. For each sample size, 100 resampled subsets were randomly drawn (without replacement). The sample size, at which 95 % of the resampled subsets contained all the alleles at a given frequency present in the empirical data set, was considered as a 95 % probability of sampling these alleles. The resampled subsets were also used to calculate main genetic diversity parameters and their variances to be used as a measure of accuracy of sampling. The results showed that at the 95 % probability level, the sample sizes of 20-25 and 65-80 individuals were large enough to capture all the alleles at frequency above 0.05 and 0.01-0.05, respectively. 300-350 individuals were required to sample the alleles at frequencies below 0.01 at the 95 % probability. The upper bound of the sample sizes was required for the loci exhibiting high He values (>0.80).