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)