Estimation of contemporary effective size of large continuously distributed populations

Abstract Estimation of the effective size ( N e ) of large populations with a continuous distribution across wide geographic areas and limited dispersal of individuals has been elusive so far. Estimates of the contemporary N e from genetic markers for such large, structured populations, typically of plant and marine species, tend to be strongly biased downwards, which has led to question their relevance. Here we show that a recently proposed estimation method of N e from linkage disequilibrium between markers, which accounts for population structure, yields estimates of metapopulation N e when the sampling area is sufficiently large. The method is applied to empirical data of maritime pine ( Pinus pinaster Aiton). While previous estimates of N e in pine populations were of the order of a few hundred individuals, we show that estimates of the metapopulation N e can reach values of the order of tens of thousands of individuals. This result is especially relevant from a conservation point of view, as populations with N e lower than 500 individuals are considered to be under the risk of extinction.