Data from: Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences

Phylogenetic estimation of evolutionary timescales has become routine in biology, forming the basis of a wide range of evolutionary and ecological studies. However, there are various sources of bias that can affect these estimates. We investigated whether tree imbalance, a property that is commonly observed in phylogenetic trees, can lead to reduced accuracy or precision of phylogenetic timescale estimates. We analysed simulated data sets with calibrations at internal nodes and at the tips, taking into consideration different calibration schemes and levels of tree imbalance. We also investigated the effect of tree imbalance on two empirical data sets: mitogenomes from primates and serial samples of the African swine fever virus. In analyses calibrated using dated, heterochronous tips, we found that tree imbalance had a detrimental impact on precision and produced a bias in which the overall timescale was underestimated. A pronounced effect was observed in analyses with shallow calibrations. The greatest decreases in accuracy usually occurred in the age estimates for medium and deep nodes of the tree. In contrast, analyses calibrated at internal nodes did not display a reduction in estimation accuracy or precision due to tree imbalance. Our results suggest that molecular-clock analyses can be improved by increasing taxon sampling, with the specific aims of including deeper calibrations, breaking up long branches and reducing tree imbalance.演化时间尺度的系统发育估计现已成为生物学研究中的常规手段，为诸多演化与生态学研究奠定了基础。然而，诸多偏倚来源均可能对这类估计结果产生影响。本研究旨在探究系统发育树中普遍存在的树不平衡（tree imbalance）是否会导致演化时间尺度估计的准确度与精度下降。我们针对不同校准方案与树不平衡程度的模拟数据集展开分析，这些数据集分别在内部分支节点与末端节点设置了校准点。此外，我们还探究了树不平衡对两组实证数据集的影响：一组为灵长类动物的线粒体基因组（mitogenomes），另一组为非洲猪瘟病毒的系列样本。在基于带年代信息的异时末端节点进行校准的分析中，我们发现树不平衡会对估计精度产生不利影响，并引发偏倚，导致整体演化时间尺度被低估。在采用浅层校准的分析中，该效应尤为显著。估计准确度降幅最大的通常为系统发育树中中层与深层节点的分化时间估计结果。与之相反，以内部节点作为校准点的分析并未因树不平衡出现估计准确度与精度的下降。本研究结果表明，可通过增加类群采样量来优化分子钟分析，具体目标为纳入深层校准点、拆分长分支并降低树不平衡程度。