Data from: The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation-based study

Detecting bottlenecks is a common task in molecular ecology. While several bottleneck detection methods exist, evaluations of their power have focused only on severe bottlenecks (e.g. to Ne ~10). As a component of a recent review, Peery et al. () analysed the power of two approaches, the M-ratio and heterozygote excess tests, to detect moderate bottlenecks (e.g. to Ne ~100), which is realistic for many conservation situations. In this Comment, we address three important points relevant to but not considered in Peery et al. Under moderate bottleneck scenarios, we test the (i) relative advantage of sampling more markers vs. more individuals, (ii) potential power to detect the bottleneck when utilizing dozens of microsatellites (a realistic possibility for contemporary studies) and (iii) reduction in power when postbottleneck recovery has occurred. For the realistic situations examined, we show that (i) doubling the number of loci shows equal or better power than tripling the number of individuals, (ii) increasing the number of markers (up to 100) results in continued additive gains in power, and (iii) recovery after a moderate amount of time or gradual change in size reduces power, by up to one-half. Our results provide a practical supplement to Peery et al. and encourage the continued use of bottleneck detection methods in the genomic age, but also emphasize that the power under different sampling schemes should be estimated, using simulation modelling, as a routine component of molecular ecology studies.

瓶颈检测是分子生态学（molecular ecology）领域的常见研究任务。尽管目前已开发出多种瓶颈检测方法，但相关方法的效能评估仅聚焦于极端瓶颈事件（例如有效种群大小Ne降至约10的场景）。作为近期一篇综述的研究内容，Peery等人分析了M值法（M-ratio）与杂合子过剩检验（heterozygote excess tests）两种方法在检测中等程度瓶颈事件（例如Ne降至约100的场景）时的效能，这类瓶颈情景在诸多保护生物学场景中具备现实代表性。在本评论文章中，我们针对Peery等人的研究未涉及的三项关键相关议题展开探讨：针对中等程度瓶颈情景，我们分别检验了(1) 增加分子标记（markers）样本量与增加个体样本量的相对优势；(2) 利用数十个微卫星标记（microsatellites）——这在当代相关研究中具备现实可行性——检测瓶颈事件的潜在效能；(3) 瓶颈事件后种群恢复对检测效能的削弱作用。针对本次研究所考察的现实场景，我们的分析结果显示：其一，加倍位点数量所带来的检测效能，等同于甚至优于将个体样本量增至三倍的效果；其二，将分子标记数量提升至最多100个时，检测效能会持续获得累加增益；其三，经过适度时长的恢复或种群规模的渐进式变化，检测效能会出现最高可达50%的衰减。本研究结果为Peery等人的工作提供了实用补充，既支持在组学时代（genomic age）继续推广瓶颈检测方法的应用，同时也强调：在分子生态学研究中，应将通过模拟建模（simulation modelling）估算不同采样方案下的检测效能作为常规研究环节。