The contemporary effective population size is important in many disciplines including population genetics, conservation science and pest management. One of the most popular methods of estimating this quantity uses temporal changes in allele frequency due to genetic drift. A significant assumption of the existing methods is the independence among loci while constructing confidence intervals (CI), which restricts the types of species or genetic data applicable to the methods. Although genetic linkage does not bias point estimates, applying these methods to linked loci can yield unreliable CI that are far too narrow. We extend the current methods to enable the use of many linked loci to produce precise contemporary estimates, while preserving the targeted CI width and coverage. This is achieved by deriving the covariance of changes in allele frequency at linked loci in the face of recombination and sampling errors, such that the extra sampling variance due to between-locus correlation is properly handled. Extensive simulations are used to verify the new method. We apply the method to two temporally spaced genomic data sets of Anopheles mosquitoes collected from a cluster of villages in Burkina Faso between 2012 and 2014. With over 33,000 linked loci considered, the estimate for Anopheles coluzzii is 9,242 (95% CI 5,702–24,282), and for Anopheles gambiae it is 4,826 (95% CI 3,602–7,353).

中文翻译：

---

使用具有链接位点的时间间隔数据进行当代 Ne 估计

当代有效种群规模在许多学科中都很重要，包括种群遗传学、保护科学和害虫管理。估计这个数量的最流行的方法之一是使用由于遗传漂变引起的等位基因频率的时间变化。现有方法的一个重要假设是在构建置信区间 (CI) 时基因座之间的独立性，这限制了适用于这些方法的物种类型或遗传数据。尽管遗传连锁不会使点估计产生偏差，但将这些方法应用于连锁基因座可能会产生太窄的不可靠 CI。我们扩展了当前的方法，以便能够使用许多链接的位点来产生精确的当代估计，同时保留目标 CI 宽度和覆盖范围。这是通过在面对重组和采样错误时推导连锁基因座上等位基因频率变化的协方差来实现的，这样由于基因座间相关性导致的额外采样方差得到适当处理。大量的模拟被用来验证新方法。我们将该方法应用于2012 年至 2014 年间从布基纳法索的一组村庄收集的两个按时间间隔的按蚊基因组数据集。考虑到超过 33,000 个连锁位点，按蚊的估计值为 9,242（95% CI 5,702–24,282） ，而冈比亚按蚊为 4,826（95% CI 3,602–7,353）。