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 ind...

瓶颈检测是分子生态学中的常见研究任务。尽管已开发出多种瓶颈检测方法，但现有研究对其检测效能的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组成部分，Peery等人（）分析了两种方法——M比值法（M-ratio）与杂合子过剩检验（heterozygote excess tests）——在检测中等程度瓶颈事件（例如有效种群大小Ne降至约100的场景）时的效能，这类情景在诸多保护生物学场景中具备现实代表性。在本评论中，我们针对Peery等人的研究未涉及的三个关键议题展开探讨：在中等瓶颈情景下，我们分别测试了(i) 增加标记位点与增加采样个体数二者的相对优势；(ii) 利用数十个微卫星（microsatellites）标记开展检测时的潜在效能（这在当代研究中具备现实可行性）；以及(iii) 瓶颈事件后种群出现恢复时检测效能的降幅。针对所考察的现实场景，我们的研究结果表明：(i) 加倍基因座数量所获得的检测效能，优于甚至等同于三倍采样个体数的效果……