A method to estimate effective population size from linkage disequilibrium when generations overlap

Effective population size (Ne) is a key parameter in evolutionary and conservation studies. It represents the number of individuals of an ideal panmictic population that would have the same genetic drift as the observed population and can be used to establish management programmes. Several methods have been developed to estimate this parameter. Currently, for studies with one sample in time, the simplest methods are based on linkage disequilibrium. These methods rely on simple models, and biases have been shown when populations deviate from the assumptions made in those models. This occurs in particular when populations are age-structured or have overlapping generations. Recently, several methods have been developed to correct such biases. Here, we develop analytical equations to predict linkage disequilibrium within age groups, and use such results to infer cohort size from samples of newborn individuals. We can in turn use these equations to estimate Ne accurately for a variety of species. Furthermore, using publicly available data, we apply our method to the white-crowned sparrow (Zonotrichia leucophrys).