Data from: Environment and traits drive the mismatch between richness and diversification rates of Chinese Clematis

Description of the data and file structure This repository contains the datasets, scripts and phylogenies used in "Environment and traits drive the mismatch between richness and diversification rates of Chinese Clematis". Files and variables File: Scripts.zip Description: This compressed file contains all custom scripts used in the analyses presented in the study. It includes code for phylogenetic tree construction, diversification analysis, reconstruction of ancestral states, spatial analysis, and structural equation modeling (SEM). File: Tree.zip Description: This file includes all phylogenetic trees used in the study. In particular, the "TACT/" subfolder contains 100 phylogenetic trees generated from TACT (Taxonomic Addition for Complete Trees) simulations. These trees were used to account for uncertainties in tree topology and branch lengths in diversification analyses. File: Datasets.zip Description: This file contains the primary datasets used in the study, including sequence alignments, environmental data, and species distribution records. "Distribution_with_bio.csv" provides geographic distribution records for Clematis species across China, including coordinates and environmental variables used to assess spatial and ecological influences on diversification. Additional datasets, such as trait data, are available in the article's supplementary materials. Code/software All analyses were conducted using open-source software. The code is implemented in R and Python. Detailed information about specific packages and modules used is provided within each script file. For R scripts, required packages (e.g., ape, phytools, geiger, etc.) are listed at the beginning of each script and can be installed via install.packages() . For Python scripts, dependencies are specified within the code and can be installed using pip or conda.数据与文件结构说明 本仓库包含论文《环境与性状驱动中国铁线莲属物种丰富度与分化速率的错配》所使用的数据集、分析脚本及系统发育树。 ## 文件与变量说明 文件：Scripts.zip 说明：该压缩包包含本研究分析所用的全部自定义脚本，涵盖系统发育树构建、分化速率分析、祖先状态重建、空间分析以及结构方程模型（Structural Equation Modeling，SEM）的代码。 文件：Tree.zip 说明：该文件包含本研究使用的全部系统发育树。其中，"TACT/"子文件夹包含通过TACT（Taxonomic Addition for Complete Trees）模拟生成的100棵系统发育树，这些树被用于评估分化速率分析中树拓扑结构与分支长度的不确定性。 文件：Datasets.zip 说明：该压缩包包含本研究使用的核心数据集，涵盖序列比对结果、环境数据以及物种分布记录。其中"Distribution_with_bio.csv"提供了中国境内铁线莲属（Clematis）物种的地理分布记录，包含用于评估分化速率的空间与生态影响的坐标及环境变量。其余数据集（如性状数据）可在论文的补充材料中获取。 ## 代码与软件说明 所有分析均采用开源软件完成，代码基于R与Python语言实现。各脚本文件中已列明所使用的具体程序包与模块的详细信息。 针对R脚本，所需程序包（如ape、phytools、geiger等）已在各脚本开头列出，可通过install.packages()命令完成安装。 针对Python脚本，其依赖项已在代码中注明，可通过pip或conda进行安装。