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 an 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 datasets 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 datasets: 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.

进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，为众多进化与生态学研究奠定了基础。然而，此类估计过程中存在多种偏倚来源，可能对估计结果造成负面影响。我们探究了系统发育树中普遍存在的树不平衡（tree imbalance）特性是否会降低系统发育时间尺度估计的准确性与精确性。我们针对内部节点与末端节点校准场景下的模拟数据集展开分析，同时考量了不同校准方案与树不平衡程度的影响。此外，我们还研究了树不平衡对两类实证数据集的作用：灵长类线粒体基因组与非洲猪瘟病毒的连续采样样本。在采用带年代信息的异时末端校准的分析中，我们发现树不平衡会对估计精确性产生不利影响，并导致整体时间尺度被低估的偏倚。在浅层校准的分析中，这种效应尤为显著。准确性降幅最大的情况通常出现在树的中等深度与深层节点的年龄估计中。与之相反，采用内部节点校准的分析并未因树不平衡出现估计准确性或精确性的下降。我们的研究结果表明，可通过优化类群采样来改进分子钟分析，具体目标包括纳入深层校准节点、拆分长分支以及降低树不平衡程度。