A global analysis of phylogenetic diversity focused on seed plants (Spermatophyta). The analyses capitalises on the recently completed World Checklist of Vascular Plants [1], a publicly accessible, comprehensive taxonomic checklist of vascular plants and their geographic distributions, in conjunction with a complete phylogeny of seed plants.
This work is currently in review with New Phytologist.
This repo contains all code necessary to repeat the study. Since some steps include computation-intense steps (e.g. supplementing the phylogeny with TACT), we also provide some processed data files to enable skipping the data preparation steps.
All analysis were done in R version 4.2.1 (R Core Team, 2022).
Upon publication, this repo will be archived on Zenodo.
Adding missing taxa to the phylogenetic tree with TACT [2] takes about 80 hours and requires 150GB RAM for each run. Due to the stochastic nature of the procedure, we ran TACT 100 times, and calculated the phylogeny-derived estimates as average values from all 100 trees.
[1] Govaerts, R., Nic Lughadha, E., Black, N. et al. The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity. Sci Data 8, 215 (2021). https://doi.org/10.1038/s41597-021-00997-6
[2] Jonathan Chang, Daniel L Rabosky, Michael E Alfaro, Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions, Systematic Biology, Volume 69, Issue 3, May 2020, Pages 602–611, https://doi.org/10.1093/sysbio/syz081