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中的核心参数，但其估算工作往往颇具挑战。学界已开发出多种基于遗传数据估算Ne的方法，这些方法依托多样化的Ne推断技术路径。然而，目前尚未有研究对这些方法准确估算Ne的能力进行全面评估。本研究针对存在基因流与无基因流的种群构建模拟数据集，并选用7种被引频次最高的遗传数据Ne估算方法：Colony2、CoNe、Estim、MLNe、ONeSAMP、TMVP以及包含LDNe的NeEstimator。本次模拟的种群动态场景涵盖三类：无外源迁入的孤立种群、由接收外来个体的汇种群构成的岛屿模型复合种群，以及遵循距离隔离法则的踏脚石种群模型。研究发现，这些方法的性能在同一动态场景内与不同场景间均存在显著差异，部分方法的表现极差。LDNe、MLNe与TMVP可生成最为精准的Ne估算结果，但在不同的种群动态场景下，这三种方法的表现互有胜负，即某一场景中表现最佳的方法，在另一场景中会被其他方法超越。若能知晓种群的大致动态历史，且可获取时序遗传数据，则可大幅提升Ne估算的准确性。