Centre National de la Recherche Scientifique, Laboratoire Evolution et Diversité Biologique, Unité Mixte de Recherche, CNRS/Université Paul Sabatier 5174, F-31062 Toulouse, France.
Genetics. 2010 Nov;186(3):983-95. doi: 10.1534/genetics.110.118661. Epub 2010 Aug 25.
The idea that molecular data should contain information on the recent evolutionary history of populations is rather old. However, much of the work carried out today owes to the work of the statisticians and theoreticians who demonstrated that it was possible to detect departures from equilibrium conditions (e.g., panmictic population/mutation-drift equilibrium) and interpret them in terms of deviations from neutrality or stationarity. During the last 20 years the detection of population size changes has usually been carried out under the assumption that samples were obtained from populations that can be approximated by a Wright-Fisher model (i.e., assuming panmixia, demographic stationarity, etc.). However, natural populations are usually part of spatial networks and are interconnected through gene flow. Here we simulated genetic data at mutation and migration-drift equilibrium under an n-island and a stepping-stone model. The simulated populations were thus stationary and not subject to any population size change. We varied the level of gene flow between populations and the scaled mutation rate. We also used several sampling schemes. We then analyzed the simulated samples using the Bayesian method implemented in MSVAR, the Markov Chain Monte Carlo simulation program, to detect and quantify putative population size changes using microsatellite data. Our results show that all three factors (genetic differentiation/gene flow, genetic diversity, and the sampling scheme) play a role in generating false bottleneck signals. We also suggest an ad hoc method to counter this effect. The confounding effect of population structure and of the sampling scheme has practical implications for many conservation studies. Indeed, if population structure is creating "spurious" bottleneck signals, the interpretation of bottleneck signals from genetic data might be less straightforward than it would seem, and several studies may have overestimated or incorrectly detected bottlenecks in endangered species.
认为分子数据应该包含有关种群近期进化历史的信息的观点由来已久。然而，今天所进行的大部分工作都归功于统计学家和理论家的工作，他们证明了有可能检测到偏离平衡条件（例如，混合种群/突变-漂变平衡），并根据偏离中性或稳定性来解释它们。在过去的 20 年中，通常在假定从可以近似为 Wright-Fisher 模型的种群中获得样本的假设下进行种群大小变化的检测（即，假设混合，人口稳定性等）。然而，自然种群通常是空间网络的一部分，并通过基因流相互连接。在这里，我们在 n-岛和踏脚石模型下模拟了突变和迁移-漂变平衡下的遗传数据。模拟种群因此是静止的，不受任何种群大小变化的影响。我们改变了种群之间的基因流动水平和缩放突变率。我们还使用了几种采样方案。然后，我们使用贝叶斯方法在 MSVAR 中分析了模拟样本，该方法是 Markov Chain Monte Carlo 模拟程序，用于使用微卫星数据检测和量化潜在的种群大小变化。我们的结果表明，所有三个因素（遗传分化/基因流动，遗传多样性和采样方案）都在产生假瓶颈信号方面发挥了作用。我们还提出了一种专门的方法来对抗这种影响。种群结构和采样方案的混杂效应对许多保护研究具有实际意义。实际上，如果种群结构产生了“虚假”瓶颈信号，那么从遗传数据推断瓶颈信号的解释可能并不像看起来那样简单，并且一些研究可能高估或错误地检测到了濒危物种的瓶颈。
