Interval estimation of the effective population size from heterozygote-excess in SNP markers

The effective population size N(e) is an important parameter in population genetics and conservation biology. In recent years, there has been great interest in the use of molecular markers to estimate N(e). Although the point estimates from molecular markers in general suffer from a low reliability, the use of single nucleotide polymorphism (SNP) markers over a wide range of genome is expected to remarkably improve the reliability. In this study, expressions were derived for interval estimates of N(e) from one published method, the heterozygote-excess method, when it is applied to SNP markers. The conditional variance theory is applied to the derivation of a confidence interval for N(e) under random union of gametes, monogamy and polygyny. Stochastic simulation shows that the obtained confidence interval is slightly conservative, but fairly useful for practical applications. The result is illustrated with real data on SNP markers in a pig strain.