Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution

Genetic methods are routinely used to estimate contemporary effective population size (Ne) in natural populations, but the vast majority of applications have used only the temporal (two‐sample) method. We use simulated data to evaluate how highly polymorphic molecular markers affect precision and bias in the single‐sample method based on linkage disequilibrium (LD). Results of this study are as follows: (1) Low‐frequency alleles upwardly bias , but a simple rule can reduce bias to