Fast Bayesian inference of phylogenies from multiple continuous characters

Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remains challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counterparts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods' properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous character..., 1. The data for well-calibrated validation and simulation studies can be simulated by running R scripts inside corresponding folders (i.e., 01validation, 02simulation and 03carnivora).
2. The XML files are used for Carnivoran analyses. The molecular and continuous traits data can be obtained from Sandra Álvarez-Carretero et al., 2019. The discrete trait data can be obtained from Paul Z. Barrett et al., 2021.
3. Data processing details can be found on the Github repository https://github.com/Rong419/MorphologyDocument.git., , # Supplementary materials for \"Fast Bayesian inference of phylogenies from multiple continuous characters\"

This file will guide you to reproduce the simulations and analyses in the main manuscript.

---

# 1 Simulation study I

This section performs well-calibrated simulation study to validate the implementation of our Brownian motion (BM) model, which produces Figure 1 in the main manuscript.

Make sure your working directory is at `zhang_etal_2023/01validation`. Please make sure that the BEAST2 XML template `BMPruneLikelihood_CalValSimMorph_template.xml` is inside the folder.

## 1.1 Simulate Fossilised Birth-death (FBD) trees

Execute the R script by

```
Rscript 01SimulateFBDTree.R
```

The parameters of FBD model prior distributions are detailed as follows:

* `div.meanlog`: mean value of the LogNormal distribution for diversification rate
* `div.sdlog`: standard deviation of the LogNormal distribution for diversification rate
* `turn.alpha`: alpha value of the Beta distri...

时间校准系统发育树（time-scaled phylogenetic trees）是进化生物学的终极研究目标，也是比较研究的必要组成部分。尽管基因组数据的积累已在很大程度上厘清了生命之树的框架，但若无化石年代、形态性状等外部信息，确定进化事件发生的时间仍极具挑战，甚至几乎不可能实现。将形态数据纳入树结构推断的方法，其发展进度一直落后于分子类方法，针对连续形态性状的相关方法更是如此。尽管近年来已有相关进展，但随着我们对分子数据所能揭示的进化信息的挖掘逐渐触及瓶颈，这类工具依然有着迫切的需求。本研究开发了一套适用于系统发育学分析的前沿连续形态性状分析方法，并通过大规模模拟研究对该方法的性能进行了全面验证与特性探索。在保留模型通用性与可扩展性的同时，我们实现了基于多组连续形态性状的绝对与相对分化时间估算...

1. 用于精准验证与模拟研究的数据集可通过运行对应文件夹（即01validation、02simulation与03carnivora）内的R脚本生成。
2. XML文件用于食肉目类群的分析。分子数据与连续性状数据可从Sandra Álvarez-Carretero等人2019年的研究中获取，离散性状数据可从Paul Z. Barrett等人2021年的研究中获取。
3. 数据处理的详细步骤可在GitHub仓库https://github.com/Rong419/MorphologyDocument.git中查阅。

# 题为"基于多组连续形态性状的系统发育树快速贝叶斯推断"的论文补充材料
本文档将指导您复现主论文中的模拟研究与分析流程。

---

# 1 模拟研究一
本章节通过精准校准的模拟研究，对我们的布朗运动（Brownian Motion, BM）模型的实现效果进行验证，对应主论文中的图1。

请确保您的工作目录位于`zhang_etal_2023/01validation`下，且该文件夹内包含BEAST2的XML模板文件`BMPruneLikelihood_CalValSimMorph_template.xml`。

## 1.1 模拟化石出生死亡（Fossilised Birth-Death, FBD）树

通过以下命令运行R脚本：

Rscript 01SimulateFBDTree.R

FBD模型的先验分布参数详情如下：
* `div.meanlog`：多样化速率的对数正态分布均值
* `div.sdlog`：多样化速率的对数正态分布标准差
* `turn.alpha`：Beta分布的α参数...