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

Published: 13 Jan 2020 | Version 1 | DOI: 10.17632/gbv472pxsb.1
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Description of this data

Data from: Bitomský M., Mládková P., Pakeman RJ, & Duchoslav M. (accepted pending minor revision 12.11.2020). Clade composition of a plant community indicates its phylogenetic diversity. Ecology and Evolution

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. Phyto-database_pruned_tree.txt - Pruned dated tree from the super tree of European flora (Durka & Michalski 2012, Ecology), phytosociological database (newick format)
  7. Plot_data.slx - plot data of all case studies + species lists
  8. 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)
  9. Bitomsky2020EE_R_script_indices.R - An R script for computation of the clade indices (with notes and examples)

Experiment data files

Latest version

  • Version 1

    2020-01-13

    Published: 2020-01-13

    DOI: 10.17632/gbv472pxsb.1

    Cite this dataset

    Bitomský, Martin; Mládková, Pavla; Pakeman, Robin; Duchoslav, Martin (2020), “Data from: Clade composition of a plant community indicates its phylogenetic diversity”, Mendeley Data, v1 http://dx.doi.org/10.17632/gbv472pxsb.1

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Categories

Ecology, Phylogenetics, Biodiversity, Vegetation

Licence

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The files associated with this dataset are licensed under a Creative Commons Attribution 4.0 International licence.

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