But the clock, tick-tock: The preeminence of relaxed clock models in total-evidence dated phylogenetics

Phylogenetic clock models translate inferred amounts of evolutionary change (calculated from either genotypes or phenotypes) into estimates of elapsed time, providing a mechanism for time scaling phylogenetic trees. Relaxed clock models, which accommodate variation in evolutionary rates across branches, are one of the main components of Bayesian dating, yet their consequences for total-evidence phylogenetics have not been thoroughly explored. Here, we combine morphological, molecular (both transcriptomic and Sanger-sequenced), and stratigraphic datasets for all major lineages of echinoids (sea urchins, heart urchins, sand dollars). We then perform total-evidence dated inference under the fossilized birth-death prior, varying two analytical conditions: the choice between autocorrelated and uncorrelated relaxed clocks, which enforce (or not) evolutionary rate inheritance; and the ability to recover ancestor-descendant relationships. Our results show that the latter has no impact on either..., , , # Data from: But the clock, tick-tock: The preeminence of relaxed clock models in total-evidence dated phylogenetics

[https://doi.org/10.5061/dryad.xgxd254s5](https://doi.org/10.5061/dryad.xgxd254s5)

## Description of the data and file structure

The data contained in this repository supports the results presented in Mongiardino Koch et al. (2025), presenting the latest total-evidence dated phylogeny of all major living and extinct clades of echinoids (sea urchins, sand dollars, heart urchins, and allies). Inference in built upon state-of-the-art morphological, molecular (both transcriptomic and Sanger-sequenced, and stratigraphic datasets, and provides new approaches for automatically extracting and combining this different sources of phylogenetic information. It furthermore explores the phylogenetic and macroevolutionary consequences of two methodological decisions generally determined arbitrarily by researchers: 1) the choice of clock model, and 2) the implementation of direct ance...,

系统发育钟模型（phylogenetic clock models）可将由基因型或表型计算得到的推断演化改变量转换为经历时间的估计值，为系统发育树的时间校准提供了实现机制。宽松钟模型（relaxed clock models）可容纳不同分支间的演化速率差异，是贝叶斯定年（Bayesian dating）的核心组成部分之一，但其对总证据系统发育学（total-evidence phylogenetics）的影响尚未得到充分探究。本研究整合了海胆类（echinoids，包括海胆、心形海胆、沙钱）所有主要演化支的形态学、分子学（涵盖转录组与Sanger测序数据）以及地层学数据集。随后基于化石化生灭先验（fossilized birth-death prior）开展总证据定年推断，设置了两项可变分析条件：一是选择强制演化速率遗传的自相关宽松钟与无强制遗传的无相关宽松钟；二是能否恢复祖先-后裔关系。本研究结果显示，后者对……均无显著影响。
# 数据来源：《时钟滴答作响：宽松钟模型在总证据定年系统发育学中的主导地位》
[https://doi.org/10.5061/dryad.xgxd254s5]

## 数据与文件结构说明
本仓库收录的数据支撑了Mongiardino Koch等人2025年的研究成果，呈现了海胆类（海胆、沙钱、心形海胆及其近缘类群）所有现存与灭绝主要演化支的最新总证据定年系统发育树。本研究基于当前前沿的形态学、分子学（转录组与Sanger测序）以及地层学数据集开展推断分析，并提出了自动提取与整合多源系统发育信息的新方法。此外，本研究还探讨了研究者通常任意设定的两项方法学决策对系统发育与宏观演化的影响：1）钟模型的选择；2）直接祖先……（原文未完整）