Estimating Effective Number of Breeders Under the Heterozygote‐Excess Equilibrium

ABSTRACT Estimating the effective number of breeders per reproductive cycle or cohort () can contribute to understanding the viability of wild populations. However, previous estimators based on heterozygote‐excess assume that parental genotypes are in accordance with Hardy–Weinberg equilibrium (HWE), and can only be applied to diploids. When these criteria are not fulfilled, estimates of expected heterozygosity may thus be biased. We extended a previous estimator to autopolyploids and account for parental genotypes either in HWE or heterozygote‐excess equilibrium (HEE). Results include the following: the distributions of genotypes converge to HEE within nine generations (with a relative error of ), the corrected estimators can asymptotically estimate without bias, and estimations for autopolyploids are slightly better than those for diploids. The relationships between and and the influence of variable effective breeding numbers across generations on were clarified. We find mainly reflects in the previous generation in diploids but is a weighted harmonic mean of in previous generations in polyploids. Our methods are implemented in a software package, polygene v 1.7 , which is freely available at https://github.com/huangkang1987/polygene .