PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data
PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data
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PyRate：一个根据不完整化石数据估计物种形成和灭绝率的新程序
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发表时间：
2014
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通讯作者：
J. Schnitzler
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作者：
D. Silvestro;N. Salamin;J. Schnitzler
尽管系统发育的方法来估计物种形成和灭绝率的进步，他们的权力可能是有限的可变率下，特别是高灭绝率和现存物种的数量少的分支。化石数据可以为研究多样化过程提供一个强有力的替代信息来源。在这里，我们提出了PyRate，一个计算机程序来估计物种形成和灭绝率及其时间动态的化石发生数据。率推断贝叶斯框架，并从系统发育树的估计。我们描述了如何使用PyRate来探索不同的多样化模式。除了多样化率外，它还提供了保存过程参数（物种化和取样）的估计数以及数据集中每一物种的形成和灭绝时间。此外，我们开发了一个新的生灭模型，将物种形成/灭绝速率的变化与连续性状的变化相关联。最后，我们演示了贝叶斯因子在模型选择中的使用，并展示了如何使用PyRate分析的后验估计来生成贝叶斯分子钟分析的校准密度。PyRate是一个开源的命令行Python程序，可在http://sourceforge.net/projects/pyrate/上获得。
Despite the advancement of phylogenetic methods to estimate speciation and extinction rates, their power can be limited under variable rates, in particular for clades with high extinction rates and small number of extant species. Fossil data can provide a powerful alternative source of information to investigate diversification processes. Here, we present PyRate, a computer program to estimate speciation and extinction rates and their temporal dynamics from fossil occurrence data. The rates are inferred in a Bayesian framework and are comparable to those estimated from phylogenetic trees. We describe how PyRate can be used to explore different models of diversification. In addition to the diversification rates, it provides estimates of the parameters of the preservation process (fossilization and sampling) and the times of speciation and extinction of each species in the data set. Moreover, we develop a new birth–death model to correlate the variation of speciation/extinction rates with changes of a continuous trait. Finally, we demonstrate the use of Bayes factors for model selection and show how the posterior estimates of a PyRate analysis can be used to generate calibration densities for Bayesian molecular clock analysis. PyRate is an open‐source command‐line Python program available at http://sourceforge.net/projects/pyrate/.