Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes
Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes
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DOI：
10.1093/bioinformatics/btt153
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发表时间：
2013-06-01
期刊：
影响因子：
5.8
通讯作者：
Hohna, Sebastian
中科院分区：
文献类型：
--
作者：
Hohna, Sebastian
动机：多样化率和模式可以从重建的遗传学中推断出来。时间依赖和多样性依赖的生灭过程都可以产生相同的多样性随时间变化的观察模式。为了开发和测试描述多样化宏观演化过程的新模型，在这些模型下进行模拟的通用和快速算法是必要的。模拟不仅是重要的测试和开发模型，但在评估模型fit.Results：在这篇文章中，我认为作为一个全球性的时间依赖性的出生死亡过程中，每个物种有相同的利率，但利率可能会随着时间的推移而变化的模型发挥着重要的作用。对于这个模型，我从重建的系统发育树中推导出物种形成时间的可能性，并表明每个物种形成事件是独立和同分布的。这一事实可以用来模拟有效地重建系统发育树时，条件的物种数量，时间的过程或两者兼而有之。我显示的可用性的模拟近似的出生-死亡过程的后验预测分布与降低多样化率应用于已发表的鸟类的生殖（家庭鲸）。
Motivation: Diversification rates and patterns may be inferred from reconstructed phylogenies. Both the time-dependent and the diversity-dependent birth-death process can produce the same observed patterns of diversity over time. To develop and test new models describing the macro-evolutionary process of diversification, generic and fast algorithms to simulate under these models are necessary. Simulations are not only important for testing and developing models but play an influential role in the assessment of model fit.Results: In the present article, I consider as the model a global time-dependent birth-death process where each species has the same rates but rates may vary over time. For this model, I derive the likelihood of the speciation times from a reconstructed phylogenetic tree and show that each speciation event is independent and identically distributed. This fact can be used to simulate efficiently reconstructed phylogenetic trees when conditioning on the number of species, the time of the process or both. I show the usability of the simulation by approximating the posterior predictive distribution of a birth-death process with decreasing diversification rates applied on a published bird phylogeny (family Cettiidae).