Abstract Heterogeneous populations can lead to important differences in birth and death rates across a phylogeny. Taking this heterogeneity into account is necessary to obtain accurate estimates of the underlying population dynamics. We present a new multitype birth–death model (MTBD) that can estimate lineage-specific birth and death rates. This corresponds to estimating lineage-dependent speciation and extinction rates for species phylogenies, and lineage-dependent transmission and recovery rates for pathogen transmission trees. In contrast with previous models, we do not presume to know the trait driving the rate differences, nor do we prohibit the same rates from appearing in different parts of the phylogeny. Using simulated data sets, we show that the MTBD model can reliably infer the presence of multiple evolutionary regimes, their positions in the tree, and the birth and death rates associated with each. We also present a reanalysis of two empirical data sets and compare the results obtained by MTBD and by the existing software BAMM. We compare two implementations of the model, one exact and one approximate (assuming that no rate changes occur in the extinct parts of the tree), and show that the approximation only slightly affects results. The MTBD model is implemented as a package in the Bayesian inference software BEAST 2 and allows joint inference of the phylogeny and the model parameters.[Birth–death; lineage specific rates, multi-type model.]

中文翻译：

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用于谱系特定出生率和死亡率的贝叶斯推断的多类型出生-死亡模型

摘要 异质种群会导致系统发育中出生率和死亡率的重要差异。考虑到这种异质性对于获得潜在人口动态的准确估计是必要的。我们提出了一种新的多类型出生-死亡模型 (MTBD)，可以估计特定谱系的出生率和死亡率。这对应于估计物种系统发育的谱系依赖性物种形成和灭绝率，以及病原体传播树的谱系依赖性传播和恢复率。与以前的模型相比，我们不假定知道导致速率差异的特征，也不禁止相同的速率出现在系统发育的不同部分。使用模拟数据集，我们表明 MTBD 模型可以可靠地推断多个进化机制的存在，它们在树中的位置，以及与每个相关的出生率和死亡率。我们还对两个经验数据集进行了重新分析，并比较了 MTBD 和现有软件 BAMM 获得的结果。我们比较了模型的两种实现，一种是精确的，一种是近似的（假设树的灭绝部分没有发生速率变化），并表明近似对结果的影响很小。MTBD 模型作为贝叶斯推理软件 BEAST 2 中的一个包实现，并允许系统发育和模型参数的联合推理。血统特定率，多类型模型。] 我们比较了模型的两种实现，一种是精确的，一种是近似的（假设树的灭绝部分没有发生速率变化），并表明近似对结果的影响很小。MTBD 模型作为贝叶斯推理软件 BEAST 2 中的一个包实现，并允许系统发育和模型参数的联合推理。血统特定率，多类型模型。] 我们比较了模型的两种实现，一种是精确的，一种是近似的（假设树的灭绝部分没有发生速率变化），并表明近似对结果的影响很小。MTBD 模型作为贝叶斯推理软件 BEAST 2 中的一个包实现，并允许系统发育和模型参数的联合推理。血统特定率，多类型模型。]