pebgroup / global-plant-diversity

Code and data description to reproduce Tietje et al. (2022) Global variation in diversification rate and species richness are unlinked in plants (https://doi.org/10.1073/pnas.2120662119)

Drivers of global plant diversity

About

Code and data description to reproduce Tietje et al. (in prep) Drivers of global plant diversity

Reproducibility and data

We provide here a final dataset (processed_data/shp_object_fin_analysis.RDS) which contains measures on the botanical country level for species richness, diversification rates and environmental variables, as well as scripts to process figures, the SEM and to build this data set.

All files used and produced throughout each step are described here, however due to the large size and data ownership requirements, the source data needs to be downloaded (e.g. CRU TS, wordclim, soil data, WCVP) from the respective sources. Version number and information how to obtain data is listed in the description part below.

Scripts

Scripts are described in master_analysis.R, and also source some scripts. More information about system requirements and descriptions of each script can be found there.

Data

Primary data includes files obtained online / from collaborators. Processed data is the final datafile used for analysis.

Primary data

File	Description
checklist_names.txt	Text file containing World Checklist of Vascular Plants taxonomy, taxon status, unique ID and synonyms
checklist_distribution.txt	Text file containing World Checklist of Vascular Plants taxon presence data in botanical countries, provided by collaborators (publication in prep)
ALLMB.tre	Phylogeny with GenBank and Open Tree of Life taxa with a backbone provided by Magallón et al. (2015). From Smith & Brown 2018
GBMB.tre	Phylogeny with GenBank taxa with a backbone provided by Magallón et al. (2015). From Smith & Brown 2018. Used to identify taxa with molecular information
ott.rds	Open Tree of Life taxonomy file (.rds version of taxonomy.tsv, Version: 3.0. Available on https://tree.opentreeoflife.org/about/taxonomy-version/ott3.0). Used to identify source for tip label name (NCBI or GBIF)
fin_species_match_NCBI.rds	List with taxonomy matching results for NCBI phylogeny tip labels with WCVP IDs
gbif_all.rds	Download of taxonomic information from GBIF for GBIF phylogeny tip labels
fern_list.txt	List of fern and fern allies families (Pteridophytes), available on theplantlist.org/browse
soil_raster_layer_000832.tif	Soil raster layer with most probable soil types, available on https://files.isric.org/soilgrids/latest/data/wrb/MostProbable.vrt and saved as geotiff with lower resolution for reasonable computation time
shapefile_biomes/wwf_terr_ecos.*	Shapefile with terrestrial ecoregions of the world (biomes). Available on https://www.worldwildlife.org/publications/terrestrial-ecoregions-of-the-world
shapefile_bot_countries/level3.*	Shapefile with polygons for all 369 TDWG level 3 units
wc2.1_30s_elev.tif	WorldClim elevation data, available on https://biogeo.ucdavis.edu/data/worldclim/v2.1/base/wc2.1_30s_elev.zip
cru_ts4.04.1901.2019.pet.dat.nc	CRU TS v. 4.04, available on https://catalogue.ceda.ac.uk/uuid/89e1e34ec3554dc98594a5732622bce9. Free account required for download.
cru_ts4.04.1901.2019.tmp.dat.nc	See above
cru_ts4.04.1901.2019.pre.dat.nc	See above
tczti_mat_ann_fsy1.nc	Miocene mean annual temperature from https://www.paleo.bristol.ac.uk/ummodel/users/Bradshaw_et_al_2012/new2/
tczti_precip_ann_fsy1.nc	Miocene annual precipitation, source as above
tcztk-tczti_mat_ann_fsy1.nc	Miocene mean annual temperature anomaly
tcztk-tczti_precip_ann_fsy1.nc	Miocene annual precipitation anomaly
CHELSA_cur_V1_2B_r10m/10min/bio_1.tif	CHELSA Last Glacial Maxiumum Bioclims, Version 1.2, 5/29/2018, obrtained via paleoclim.org
CHELSA_cur_V1_2B_r10m/10min/bio_12.tif	see above
chelsa_LGM_v1_2B_r10m/10min/bio_1.tif	see above
chelsa_LGM_v1_2B_r10m/10min/bio_12.tif	see above
Islands_TDWG_AllData.txt	Island classifications from http://dx.doi.org/10.1111/j.1466-8238.2011.00728.x

Final data

Files to make figures and inspect final SEM (scripts 17-19).

File	Description
sem_input_data.RDS	Data.frame to feed to the Structural Equation Model selection process, including full names for each geographic unit (botanical country)
shp_object_fin_analysis.RDS	Spatial object including all data in sem_input_data.rds
best_model.RDATA	Best SEM lavaan model object

Analysis workflow