Data from: Posterior predictive checks of coalescent models: P2C2M, an R package

Bayesian inference operates under the assumption that the empirical data are a good statistical fit to the analytical model, but this assumption can be challenging to evaluate. Here, we introduce a novel R package that utilizes posterior predictive simulation to evaluate the fit of the multispecies coalescent model used to estimate species trees. We conduct a simulation study to evaluate the consistency of different summary statistics in comparing posterior and posterior predictive distributions, the use of simulation replication in reducing error rates, and the utility of parallel process invocation towards improving computation times. We also test P2C2M on two empirical data sets in which hybridization and gene flow are suspected of contributing to shared polymorphism, which is in violation with the coalescent model: Tamias chipmunks and Myotis bats. Our results indicate that (a) probability-based summary statistics display the lowest error rates, (b) the implementation of simulation replication decreases the rate of type II errors, and (c) our R package displays improved statistical power compared to previous implementations of this approach. We also test P2C2M on two empirical data sets in which hybridization and gene flow are suspected of contributing to shared polymorphism, which is in violation with the coalescent model: Tamias chipmunks and Myotis bats. When probabilistic summary statistics are used, P2C2M corroborates the assumption that genealogies collected from Tamias and Myotis are not a good fit to the multispecies coalescent model. Taken as a whole, our findings argue that an assessment of the fit of the multispecies coalescent model should accompany any phylogenetic analysis that estimates a species tree.贝叶斯推断（Bayesian inference）基于如下假设：实测数据与分析模型具备良好的统计拟合性，但该假设的评估往往颇具挑战。本研究推出一款全新的R软件包，其借助后验预测模拟（posterior predictive simulation）来评估用于物种树估计的多物种溯祖模型（multispecies coalescent model）的拟合优度。我们开展了一项模拟研究，用以评估不同汇总统计量（summary statistics）在后验分布与后验预测分布对比中的一致性、模拟重复在降低错误率方面的应用效果，以及并行进程调用对缩短计算时长的效用。我们还将P2C2M应用于两组疑似存在杂交与基因流导致共享多态性、违背溯祖模型假设的实测数据集：花鼠属（Tamias）松鼠与鼠耳蝠属（Myotis）蝙蝠。研究结果显示：(a) 基于概率的汇总统计量具备最低的错误率；(b) 采用模拟重复可降低第二类错误（type II error）的发生概率；(c) 相较于此前的同类实现方案，本研究的R软件包具备更优的统计功效。我们再次将P2C2M应用于上述两组疑似存在杂交与基因流导致共享多态性、违背溯祖模型假设的实测数据集：花鼠属松鼠与鼠耳蝠属蝙蝠。当使用基于概率的汇总统计量时，P2C2M证实：花鼠属与鼠耳蝠属的基因谱系并不符合多物种溯祖模型的拟合要求。综合来看，本研究结论表明：在任何用于估计物种树的系统发育分析中，都应当配套开展多物种溯祖模型的拟合优度评估。