Estimation of the contemporary effective population size from <scp>SNP</scp> data while accounting for mating structure

Abstract 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 10 5 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.