Data from: TipDatingBeast: an R package to assist the implementation of phylogenetic tip-dating tests using BEAST

Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. In this context, BEAST, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce TipDatingBeast, an R package built to assist the implementation of various phylogenetic tip-dating tests using BEAST. TipDatingBeast currently contains two main functions. The first one allows preparing date-randomization analyses, which assess the temporal signal of a dataset. The second function allows performing leave-one-out analyses, which test for the consistency between independent calibration sequences and allow pinpointing those leading to potential bias. We apply those functions to an empirical dataset and supply practical guidance for results interpretation.

系统发育树的分子末端定年（Molecular tip-dating）是一门蓬勃发展的交叉学科，其依托不同时间点采集的DNA序列，联合估算演化事件发生时间与分子进化速率。在此研究框架下，用于分子序列贝叶斯分析的软件BEAST是目前应用最为广泛的系统发育分析工具。本文介绍一款基于R语言开发的工具包TipDatingBeast，旨在辅助用户借助BEAST完成各类系统发育分子末端定年分析测试。TipDatingBeast目前包含两大核心功能：其一可开展日期随机化分析，用于评估数据集的时间信号强度；其二可执行留一法分析，用于检验独立校准序列间的一致性，并定位可能引入分析偏倚的序列。我们将上述功能应用于一个实测数据集，并为分析结果的解读提供实操指引。