Supplement to Inferring the evolutionary history of the Sino-Himalayan biodiversity hotspot using a Bayesian birth-death skyline model

This repository contains the supplementary files for: Allen BJ, Vaughan TG, du Plessis L, Schouten TLA, Yuan Z, Willett SD, Stadler T. 2024. Inferring the evolutionary history of the Sino-Himalayan biodiversity hotspot using a Bayesian birth-death skyline model. Geological Society of London Special Publications, 549. Description of files This repository contains the cleaned tree file, raw log files, simulated trees, XML files for running the analyses in BEAST2, and R code to process the datasets. Liu_et_al_SinoHimalayan.nex - the phylogeny inferred by Liu et al. (2021), trimmed to only include the 8864 tips associated with genetic data Skyline_logs.zip - skyline logs produced by BEAST2 analyses (see below for naming convention) Regression_results.zip - results of the linear modelling between global palaeotemperature and diversification estimates Sim_trees.trees - the phylogenies simulated by ReMASTER Adequacy_logs.zip - skyline logs produced from the analyses using the simulated phylogenies Description of BEAST2 XMLs The XML files contain the BEAST2 configurations for: Liu_et_al_bd.xml, Liu_et_al_bd_high.xml, Liu_et_al_bd_mid.xml, Liu_et_al_bd_low.xml - skyline analyses using equal length time bins, with beta sampling prior, high fixed sampling, mid fixed sampling, and low fixed sampling respectively Liu_et_al_bd_geol.xml, Liu_et_al_bd_geol_high.xml, Liu_et_al_bd_geol_mid.xml, Liu_et_al_bd_geol_low.xml - skyline analyses using geological time bins, with beta sampling prior, high fixed sampling, mid fixed sampling, and low fixed sampling respectively Remaster_simulation.xml - simulating new phylogenies based on the inferred skylines using ReMASTER Sim_trees.xml - skyline analyses conducted on the simulated phylogenies Description of R code The R code is subdivided into the following files: BDSKY_skylines.R - code for processing and plotting skyline data from the BEAST2 log files BDSKY_adjacent_bins.R - code for the analyses examining the increase or decrease in evolutionary rates between adjacent skyline bins Plot_palaeotemp_comparison.R - code for plotting the diversification estimates against global palaeotemperature, as taken from Scotese et al. (2021) Palaeotemperature_regressions.R - code for linear modelling between global palaeotemperature and diversification estimates Remaster_processing.R - code for processing and plotting inferred skylines from the simulated datasets本仓库包含以下学术文献的补充材料： Allen BJ、Vaughan TG、du Plessis L、Schouten TLA、Yuan Z、Willett SD、Stadler T. 2024. 利用贝叶斯出生-死亡天际线模型（Bayesian birth-death skyline model）推断中国-喜马拉雅生物多样性热点区域的演化历史. 伦敦地质学会特刊, 549. ### 文件说明 本仓库包含清理后的系统发育树文件、原始日志文件、模拟谱系树、用于在BEAST2中运行分析的XML配置文件，以及用于处理数据集的R代码： 1. Liu_et_al_SinoHimalayan.nex：Liu等人（2021）推断的系统发育树，经修剪后仅保留与遗传数据相关的8864个类群末端节点 2. Skyline_logs.zip：BEAST2分析生成的天际线日志文件（命名规范详见下文） 3. Regression_results.zip：全球古温度与多样化速率估计值之间线性建模的结果 4. Sim_trees.trees：由ReMASTER模拟生成的系统发育树 5. Adequacy_logs.zip：基于模拟谱系树开展分析得到的天际线日志文件 ### BEAST2 XML配置文件说明 本仓库中的XML文件包含以下分析的BEAST2配置： 1. Liu_et_al_bd.xml、Liu_et_al_bd_high.xml、Liu_et_al_bd_mid.xml、Liu_et_al_bd_low.xml：分别对应采用等长时间窗（time bins）、且分别使用β抽样先验、高固定抽样比例、中固定抽样比例、低固定抽样比例的天际线分析 2. Liu_et_al_bd_geol.xml、Liu_et_al_bd_geol_high.xml、Liu_et_al_bd_geol_mid.xml、Liu_et_al_bd_geol_low.xml：分别对应采用地质时间窗、且分别使用β抽样先验、高固定抽样比例、中固定抽样比例、低固定抽样比例的天际线分析 3. Remaster_simulation.xml：基于已推断的天际线，使用ReMASTER模拟生成新的系统发育树的配置文件 4. Sim_trees.xml：基于模拟谱系树开展的天际线分析配置文件 ### R代码说明 本仓库的R代码分为以下文件： 1. BDSKY_skylines.R：用于处理并绘制BEAST2日志文件中的天际线数据的代码 2. BDSKY_adjacent_bins.R：用于分析相邻天际线时间窗之间演化速率增减情况的代码 3. Plot_palaeotemp_comparison.R：用于将多样化速率估计值与取自Scotese等人（2021）的全球古温度数据进行可视化对比的代码 4. Palaeotemperature_regressions.R：用于开展全球古温度与多样化速率估计值之间线性建模的代码 5. Remaster_processing.R：用于处理并绘制模拟数据集的推断天际线的代码