Treelists, constraints and logfiles for: Relative time constraints improve molecular dating

Dating the tree of life is central to understanding the evolution of life on Earth. Molecular clocks calibrated with fossils represent the state of the art for inferring the ages of major groups. Yet, other information on the timing of species diversification can be used to date the tree of life. This is the case for instance for horizontal gene transfer events and ancient coevolutionary relationships such as (endo)symbioses, which can imply temporal relationships between two nodes in a phylogeny (Davin et al. 2018). This can be particularly helpful when the geological record is sparse, e.g. for microorganisms, which represent the vast majority of extant and extinct biodiversity. Here, we demonstrate that relative age constraints, when combined with fossil calibrations, can significantly improve both the accuracy and resolution of molecular clock estimates. We provide an implementation of relative age constraints in RevBayes (Hoehna et al. 2016) that can be combined in a modular manner with the wide range of molecular dating methods available in the software. To validate our method in a realistic data setting we apply it to two data sets of 40 Cyanobacteria and 62 Archaea respectively, and provide cross-validations of fossil calibrations and relative age constraints.

Methods
The data set contains, for both Archaea and Bacteria:

1. concatenated CAT GTR treelists used in approximating the phylogenetic likelihood, obtained using PhyloBayes

2. constraints used for the dating;

3. log files used in producing the plots in the paper

确定生命之树的年代，是理解地球生命演化历程的核心议题。以化石校准的分子钟，是推断主要生物类群分化时间的主流技术手段。然而，物种分化时间的其他相关信息，同样可用于生命之树的年代标定。例如水平基因转移（horizontal gene transfer）事件以及古老的共演化关系（如（内）共生作用）即可提供此类信息，这类关系能够暗示系统发育树中两个节点间的时间关联（Davin等，2018）。在地质记录匮乏的场景下，这类信息尤为实用——比如占现存与灭绝生物多样性绝大多数的微生物类群。本研究证明，将相对年龄约束与化石校准相结合，可显著提升分子钟估算的精度与分辨率。我们在RevBayes（Hoehna等，2016）中实现了相对年龄约束模块，该模块可与该软件中已有的各类分子定年方法以模块化方式灵活结合。为在真实数据场景下验证所提方法，我们分别将其应用于包含40个蓝细菌（Cyanobacteria）物种与62个古菌（Archaea）物种的两套数据集，并针对化石校准与相对年龄约束开展交叉验证。

方法
本数据集涵盖古菌与细菌两类群的以下数据：
1. 用于近似系统发育似然值的串联CAT GTR树列表，通过PhyloBayes软件生成；
2. 定年分析所用的约束条件；
3. 用于绘制本文中各类图表的日志文件。