The ClaDS rate-heterogeneous birth-death prior for full phylogenetic inference in BEAST2

Bayesian phylogenetic inference requires a tree prior, which models the underlying diversification process which gives rise to the phylogeny. Existing birth-death diversification models include a wide range of features, for instance lineage-specific variations in speciation and extinction rates. While across-lineage variation in speciation and extinction rates is widespread in empirical datasets, few heterogeneous rate models have been implemented as tree priors for Bayesian phylogenetic inference. As a consequence, rate heterogeneity is typically ignored when reconstructing phylogenies, and rate heterogeneity is usually investigated on fixed trees. In this paper, we present a new BEAST2 package implementing the cladogenetic diversification rate shift (ClaDS) model as a tree prior. ClaDS is a birth-death diversification model designed to capture small progressive variations in birth and death rates along a phylogeny. Unlike previous implementations of ClaDS, which were designed to be us..., The data contained in this dataset was created and analyzed using the code in the Software section., Software required:
BEAST2 (https://www.beast2.org/) version 2.6.6
R (https://cran.r-project.org/)

贝叶斯系统发育推断（Bayesian phylogenetic inference）需要树先验（tree prior），其可对催生系统发育树的潜在多样化过程进行建模。现有出生-死亡多样化模型（birth-death diversification model）涵盖诸多特征，例如物种形成与灭绝速率的支系特异性变异（lineage-specific variations）。尽管物种形成与灭绝速率的跨支系变异在经验数据集（empirical datasets）中广泛存在，但目前可作为贝叶斯系统发育推断树先验的异质速率模型仍寥寥无几。因此，在重建系统发育树时，速率异质性（rate heterogeneity）通常被忽略；而速率异质性的相关研究也通常基于固定树开展。本文提出一款全新的BEAST2软件包，将支系分化速率漂移（cladogenetic diversification rate shift, ClaDS）模型实现为树先验。ClaDS属于出生-死亡多样化模型，旨在捕捉系统发育树沿枝的渐进式微小速率变异。与此前专为……设计的ClaDS实现方案不同，本数据集的相关数据均通过"软件"章节中的代码生成与分析。所需软件包括：BEAST2（https://www.beast2.org/）2.6.6版本，以及R语言（https://cran.r-project.org/）。