BAMM gives misleading rate estimates in simulated and empirical datasets
BAMM gives misleading rate estimates in simulated and empirical datasets
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DOI：
10.1111/evo.13574
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发表时间：
2018-10-01
期刊：
影响因子：
3.3
通讯作者：
Wiens, John J.
中科院分区：
文献类型：
--
作者：
Meyer, Andreas L. S.;Roman-Palacios, Cristian;Wiens, John J.
在之前的一篇论文中，我们使用模拟和经验数据来证明BAMM（宏观进化混合的贝叶斯分析）可能会对利率和利率变化做出误导性的估计。在模拟中，BAMM低估了分析的每棵树的速率变化，并将错误的速率分配给大多数树中的大多数分支。在实证分析中，BAMM表现得与模拟所预期的一样，并且当单独分析进化枝与跨树分析进化枝时（即，率的异质性）。Rabosky最近批评了我们的论文，主要集中在我们将BAMM与另一种方法（Magallon和Sanderson的矩估计方法或MS估计方法）进行比较对BAMM不公平的想法上。在这里，我们提供了进一步的证据，BAMM在实证研究中给出了误导性的利率估计。然后，我们描述如何Rabosky的rown方法比较被认为是有问题的或被描述不准确（有利于BAMM）。最后，我们表明，MS估计可以很好地执行时，利率随时间变化，尽管未经测试的断言，他们需要恒定的利率是准确的。许多其他方法可用于分析多样化率：我们认为，BAMM应避免估计多样化率和利率变动。
In a previous paper, we used simulations and empirical data to show that BAMM (Bayesian Analysis of Macroevolutionary Mixtures) can give misleading estimates of rates and rate shifts. In simulations, BAMM underestimated rate shifts across every tree analyzed, and assigned incorrect rates to most clades in most trees. In empirical analyses, BAMM behaved as expected from simulations, and assigned different rates to clades when clades were analyzed alone versus across the tree (i.e., with rate heterogeneity). Rabosky recently criticized our paper, focusing primarily on the idea that our comparison of BAMM to another approach (method-of-moments estimators of Magallon and Sanderson, or MS estimators) was unfair to BAMM. Here, we provide further evidence that BAMM gives misleading rate estimates in empirical studies. We then describe how Rabosky's rown method comparisons were either acknowledged as being problematic or were described inaccurately (to favor BAMM). Finally, we show that the MS estimators can perform well when rates vary over time, despite untested assertions that they require constant rates to be accurate. Many other methods are available for analyzing diversification rates: we argue that BAMM should be avoided for estimating both diversification rates and rate shifts.