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.

中文翻译：

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大岛有领鹟（Ficedula albicollis）的当代有效种群规模的基因组推断

由于其对进化生物学和种群遗传学的许多方面的核心重要性，已经估计了许多物种和种群的长期有效种群大小 ( N _e )。然而，估计当代N _e是困难的，而且在实践中这个参数通常是未知的。原则上，可以使用等位基因频率的时间变化分析或未连锁标记之间的连锁不平衡 (LD) 程度来估计当代N _e。我们应用这些方法来估计一个相对新近建立的有领鹟 ( Ficedula albicollis) 的岛屿种群的当代N _e）。我们对 1993 年和 2015 年采样的 85 只鸟类的基因组进行了测序，并应用了几种时间方法来估计N _e为几千（4000-7000）。基于 LD 的方法提供了更高的N _e (20,000–32,000)估计值，并且与高方差相关，通常会导致N _e无穷大。我们得出结论，全基因组测序数据为估计高 (>1000) 当代N _e提供了新的可能性，但也注意到这种估计仍然具有挑战性，特别是对于基于 LD 的当代N _e估计方法。