TreeSimGM: Simulating phylogenetic trees under general Bellman-Harris models with lineage-specific shifts of speciation and extinction in R.
TreeSimGM: Simulating phylogenetic trees under general Bellman-Harris models with lineage-specific shifts of speciation and extinction in R.
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DOI：
10.1111/2041-210x.12917
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发表时间：
2018-03
影响因子：
6.6
通讯作者：
Stadler T
中科院分区：
文献类型：
--
作者：
Hagen O;Stadler T
利用系统发生树来理解宏观进化过程是一个具有挑战性和复杂的过程，涉及数学、计算机科学和生物学。随着复杂数学模型的发展和计算处理能力的提高，仿真工具变得越来越流行。为了模拟系统发育树，大多数进化生物学家被迫建立自己的算法或使用建立在不同平台和/或作为独立程序的现有工具。缺乏模拟工具，以适应用户选择的模型规格限制，除其他外，模型测试和管道与近似贝叶斯计算方法或其他后续统计分析。我们介绍了“TreeSimGM”，这是一个通用Bellman和Harris模型下的系统发育树的r - package模拟工具。这个包允许用户指定任何期望的概率分布，直到物种形成和灭绝的等待时间（例如，年龄依赖的物种形成/灭绝）。在物种形成时，用户可以指定一个后代物种是否与继承其年龄的祖先物种相对应，或者两个后代物种是否都是年龄为0的新物种。此外，对于新形成的物种来说，等待时间可以按比例缩放到物种形成/灭绝。因此，“TreeSimGM”不仅允许用户模拟随机系统发育树，假设几种流行的现有模型，如Yule模型、恒速率出生-死亡模型和比例可区分排列模型，而且还允许用户制定新的模型进行探索。这里简要说明了支持的模型，并提供了一些如何使用我们的包的示例。作为一个软件包，“TreeSimGM”允许灵活和强大的随机系统发育树模拟。此外，它促进了r中的其他功能输出或输入的流水线。“TreeSimGM”为r社区在生态和进化领域提供了可用的工具，在GPL‐2许可下免费提供，可以从https://cran.r-project.org/web/packages/TreeSimGM下载。
Understanding macroevolutionary processes using phylogenetic trees is a challenging and complex process that draws on mathematics, computer science and biology. Given the development of complex mathematical models and the growing computational processing power, simulation tools are becoming increasingly popular. In order to simulate phylogenetic trees, most evolutionary biologists are forced to build their own algorithms or use existing tools built on different platforms and/or as standalone programmes. The absence of a simulation tool accommodating for user‐chosen model specifications limits, amongst others, model testing and pipelining with approximate Bayesian computation methods or other subsequent statistical analysis. We introduce “TreeSimGM,” an r‐package simulation tool for phylogenetic trees under a general Bellman and Harris model. This package allows the user to specify any desired probability distribution for the waiting times until speciation and extinction (e.g. age‐dependent speciation/extinction). Upon speciation, the user can specify whether one descendant species corresponds to the ancestor species inheriting its age or whether both descendant species are new species of age 0. Moreover, it is possible to scale the waiting time to speciation/extinction for newly formed species. Thus, “TreeSimGM” not only allows the user to simulate stochastic phylogenetic trees assuming several popular existing models, such as the Yule model, the constant‐rate birth–death model, and proportional to distinguishable arrangement models, but it also allows the user to formulate new models for exploration. A short explanation of the supported models and a few examples of how to use our package are presented here. As an r‐package, “TreeSimGM” allows flexible and powerful stochastic phylogenetic tree simulations. Moreover, it facilitates the pipelining of outputs or inputs with other functions in r. “TreeSimGM” contributes to the tools available to the r community in the fields of ecology and evolution, is freely available under the GPL‐2 licence and can be downloaded at https://cran.r-project.org/web/packages/TreeSimGM.