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）是一门快速发展的交叉学科，该方法依托不同时间点获取的DNA序列，联合估算演化事件的发生时间与分子进化速率。在此领域中，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。本文介绍一款名为TipDatingBeast的R语言工具包，旨在辅助研究者基于BEAST开展各类系统发育分子末端定年分析测试。TipDatingBeast目前包含两项核心功能：其一可构建日期随机化分析（date-randomization analyses）流程，用于评估数据集的时间信号强度；其二可执行留一法分析（leave-one-out analyses），用以检验独立校准序列间的一致性，并精准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证数据集，并为研究结果的解读提供了实操指南。