Estimating 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 ) from linkage disequilibrium 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 Ne in monogamous and polygamous mating systems, as well as in multiparous species, and non-random distributions of full-sib family size due to selection or other causes. The prediction of confidence intervals for N estimates was solved using a small artificial neural network trained on a dataset of over 10 simulation results. The method, implemented in a user-friendly and fast software ( currentNe ) is able to estimate N even in problematic scenarios with large population sizes or small sample sizes, and provides confidence intervals that are more consistent than parametric methods or resampling.