Data from: Evaluating methods for estimating local effective population size with and without migration

Effective population size is a fundamental parameter in population genetics, evolutionary biology and conservation biology, yet its estimation can be fraught with difficulties. Several methods to estimate Ne from genetic data have been developed which take advantage of various approaches for inferring Ne. The ability of these methods to accurately estimate Ne, however, has not been comprehensively examined. In this study, we employ seven of the most cited methods for estimating Ne from genetic data (Colony2, CoNe, Estim, MLNe, ONeSAMP, TMVP, and NeEstimator including LDNe) across simulated datasets with populations experiencing migration or no migration. The simulated population demographies are an isolated population with no immigration, an island model metapopulation with a sink population receiving immigrants, and an isolation by distance stepping stone model of populations. We find considerable variance in performance of these methods, both within and across demographic scenarios, with some methods performing very poorly. The most accurate estimates of Ne can be obtained by using LDNe, MLNe, or TMVP; however each of these approaches is outperformed by another in a differing demographic scenario. Knowledge of the approximate demography of population as well as the availability of temporal data largely improves Ne estimates.

有效种群大小（Effective Population Size, Ne）是种群遗传学、进化生物学与保护生物学领域的核心参数，但其估算工作往往面临诸多挑战。目前学界已开发出多种利用不同推断手段，从遗传数据中估算Ne的方法。然而，目前尚未有研究对这些方法精准估算Ne的能力开展全面评估。在本研究中，我们针对涵盖存在迁移与无迁移种群的模拟数据集，选用了7种被引频次最高的Ne遗传估算方法，分别为Colony2、CoNe、Estim、MLNe、ONeSAMP、TMVP以及包含LDNe模块的NeEstimator。本次模拟设置了三类种群情景：无外来迁入的孤立种群、存在接收迁入汇种群的岛屿模型集合种群，以及遵循距离隔离法则的踏脚石种群模型。研究结果表明，这些方法在各类种群情景内部及不同情景间的表现均存在显著差异，部分方法的性能表现极差。采用LDNe、MLNe或TMVP可获得最为精准的Ne估算结果，但在不同的种群情景中，上述每种方法的表现均会被其他某一方法超越。了解种群的大致结构特征，同时具备时序遗传数据，可大幅提升Ne估算的准确性。