Data from: Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record

Phylogeny-based approaches can be used to infer diversification dynamics and the rate and pattern of trait change. Applying these analyses to fossil data often requires time-scaling a cladogram of morphotaxon relationships. Although several time-scaling methods have been developed for this purpose, the incomplete sampling of the fossil record can distort the apparent timing of branching. It is unclear how well different time-scaling methods reconstruct the true temporal relationships or how any such inaccuracy could affect tree-based evolutionary analyses. I developed process-based simulations of the fossil record that allow the comparison of approximated time-scaled trees to true time-scaled trees. I used this simulation framework to test the effect of time-scaling methods on the fidelity of several commonly applied tree-based analyses, across a range of simulation conditions. When the fidelity of time-scaling methods differed, the stochastic “cal3” time-scaling method with ancestral assignment produced preferable results. Estimating rates and models of continuous trait evolution was particularly sensitive to bias from scenarios that forced the insertion of many short branch lengths, a bias that is not solved by any of the considered time-scaling methods in all scenarios. The cal3 method of time-scaling can be recommended as the preferred time-scaling method among those tested, but caution must be exercised because tree-based analyses are prone to easily overlooked biases.

基于系统发育（Phylogeny）的方法可用于推断物种多样化动态以及性状变化的速率与模式。将此类分析应用于化石数据时，通常需要对包含形态类群（morphotaxon）亲缘关系的分支图（cladogram）开展时间标度（time-scaling）处理。尽管目前已为此开发了多种时间标度方法，但化石记录的不完全采样可能会扭曲分支事件的表观发生时间。目前尚不清楚不同时间标度方法对真实时间维度演化关系的重建效果，也不明确此类误差会如何影响基于树结构的演化分析。本研究开发了基于演化过程的化石记录模拟框架，可将近似时间标度树与真实时间标度树进行对比。借助该模拟框架，本研究在多种模拟条件下测试了时间标度方法对多种常用基于树结构的分析结果保真度（fidelity）的影响。当不同时间标度方法的保真度存在差异时，带有祖先赋值的随机"cal3"时间标度方法可获得更优的分析结果。连续性状演化的速率与模型估计对那些强制插入大量短分支的模拟场景所带来的偏差尤为敏感，而本次测试的所有时间标度方法均无法在所有场景下消除此类偏差。在本次测试的所有时间标度方法中，cal3时间标度法可被推荐为最优选择，但仍需谨慎使用，因为基于树结构的演化分析极易受到易被忽视的偏差影响。