Estimation of the contemporary effective population size from SNP data while accounting for mating structure

A new method is developed to estimate the contemporary effective population size (N_e ) from linkage disequilibrium (LD) between SNPs without information on their location, which is the usual scenario in non-model species. The general theory of linkage disequilibrium is extended to include the contribution of full-sibs to the measure of LD, leading naturally to the estimation of N_e in monogamous and polygamous mating systems, as well as in multiparous species, and with non-random distributions of full-sib family size due to selection or other causes. Prediction of confidence intervals for N_e estimates was solved using a small artificial neural network trained on a dataset of over 10⁵ simulation results. The method, implemented in a user-friendly and fast software (currentNe), is able to estimate N_e even in problematic scenarios with large population sizes or small sample sizes and provides confidence intervals that are more consistent than resampling methods.