Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
Syst Biol. 2020 Sep 1;69(5):973-986. doi: 10.1093/sysbio/syaa016.
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.].
异质种群可能导致系统发育过程中出生率和死亡率的重要差异。为了获得对基础种群动态的准确估计，有必要考虑这种异质性。我们提出了一种新的多类型出生-死亡模型（MTBD），可以估计谱系特异性的出生率和死亡率。这相当于估计物种系统发育的谱系相关的物种形成和灭绝率，以及病原体传播树的谱系相关的传播和恢复率。与之前的模型不同，我们不假定知道驱动速率差异的特征，也不禁止相同的速率出现在系统发育树的不同部分。使用模拟数据集，我们表明 MTBD 模型可以可靠地推断出多个进化阶段的存在、它们在树中的位置以及与每个阶段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 和现有的 BAMM 软件获得的结果。我们比较了模型的两种实现，一种是精确的，一种是近似的（假设树中灭绝部分不会发生速率变化），结果表明，近似值仅略微影响结果。MTBD 模型作为贝叶斯推断软件 BEAST 2 中的一个包实现，允许对系统发育和模型参数进行联合推断。[出生-死亡；谱系特异性速率，多类型模型。]
