Genomic inference of contemporary effective population size in a large island population of collared flycatchers (<i>Ficedula albicollis</i>)
Krystyna Nadachowska‐Brzyska, Ludovic Dutoit, Linnéa Smeds, Marty Kardos, Lars Gustafsson, Hans Ellegren
Abstract
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.