Abstract
Due to its central importance to many aspects of evolutionary biology and population genetics, the long-term effective population size (N-e) has been estimated for numerous species and populations. However, estimating contemporary N-e is difficult and in practice this parameter is often unknown. In principle, contemporary N-e can be estimated using either analyses of temporal changes in allele frequencies, or the extent of linkage disequilibrium (LD) between unlinked markers. We applied these approaches to estimate contemporary N-e of a relatively recently founded island population of collared flycatchers (Ficedula albicollis). We sequenced the genomes of 85 birds sampled in 1993 and 2015, and applied several temporal methods to estimate N-e at a few thousand (4000-7000). The approach based on LD provided higher estimates of N-e (20,000-32,000) and was associated with high variance, often resulting in infinite N-e. We conclude that whole-genome sequencing data offers new possibilities to estimate high (>1000) contemporary N-e, but also note that such estimates remain challenging, in particular for LD-based methods for contemporary N-e estimation.