Data from: Clade composition of a plant community indicates its phylogenetic diversity

Data from: Bitomský M., Mládková P., Pakeman RJ, & Duchoslav M. (2020). Clade composition of a plant community indicates its phylogenetic diversity. Ecology and Evolution. doi: 10.1002/ece3.6170

Data summarises results from the case studies and simulations presented in our paper. In addition, we provide an R script for calculation of proposed phylogenetic diversity metrics (the clade indices).

Brief description of each file:
1. Grasslands_DNA_markers_info.xls - Accession numbers of all DNA markers used for phylogeny inference in grasslands
2. Grasslands_DNA_alignment_BEFORE_GBlocks.fasta - DNA alignment matrix before utilisation of the GBlocks tool
3. Grasslands_DNA_alignment_AFTER_GBlocks.fasta - DNA alignment matrix after utilisation of the GBlocks tool
4. Grasslands_BEAST_file.xml - BEAST .xml file submitted to the CIPRES portal (www.phylo.org)
5. Grasslands_tree.txt - Dated MCC tree, grasslands (newick format)
6. Grasslands_tree.nex - Dated MCC tree, grasslands (nexus format)
7. Phyto-database_pruned_tree.txt - Pruned dated tree from the super tree of European flora (Durka & Michalski 2012, Ecology), phytosociological database (newick format)
8. Plot_data.slx - plot data of all case studies + species lists
9. Simulation_results.txt - Summary of R2 values (phylogeny-based metric ~ the clade index) for simulated phylogenies and community matrices (manipulated: phylogenetic scale, species pool size and species richness range)
10. Bitomsky2020EE_R_script_indices.R - An R script for computation of the clade indices (with notes and examples)

数据来源：Bitomský M.，Mládková P.，Pakeman RJ，及Duchoslav M.（2020年）. 植物群落谱系组成的分析揭示了其系统发育多样性. 生态学与进化（Ecology and Evolution），DOI：10.1002/ece3.6170。

数据集概述了本文中提出的案例研究和模拟实验的结果。此外，我们还提供了一款R脚本，用于计算所提出的谱系多样性指标（谱系指数）。

各文件简要描述如下：
1. Grasslands_DNA_markers_info.xls - 用于草原谱系推断的DNA标记的登录号。
2. Grasslands_DNA_alignment_BEFORE_GBlocks.fasta - 使用GBlocks工具前的DNA对齐矩阵。
3. Grasslands_DNA_alignment_AFTER_GBlocks.fasta - 使用GBlocks工具后的DNA对齐矩阵。
4. Grasslands_BEAST_file.xml - 提交至CIPRES门户（www.phylo.org）的BEAST .xml文件。
5. Grasslands_tree.txt - 草原的带时间标记的最大共同祖先树（newick格式）。
6. Grasslands_tree.nex - 草原的带时间标记的最大共同祖先树（nexus格式）。
7. Phyto-database_pruned_tree.txt - 欧洲植物超树（Durka & Michalski 2012，生态学）的修剪版带时间标记树，植物群落学数据库（newick格式）。
8. Plot_data.slx - 所有案例研究的地块数据及物种列表。
9. Simulation_results.txt - 模拟谱系和群落矩阵（操作：谱系尺度、物种库大小及物种丰富度范围）的R²值（基于谱系的指标 ~ 谱系指数）的总结。
10. Bitomsky2020EE_R_script_indices.R - 计算谱系指数的R脚本（附注释及示例）。