DOI: 10.5281/zenodo.16415110
title: TetrapodTrees Database: Anthropocene Imperilment of Ancient Diversity and Evolutionary Potential in Terrestrial Vertebrates

description: Zenodo Readme – TetrapodTrees Database

 

The data products here are described in the preprint "Anthropocene Imperilment of Ancient Diversity and Evolutionary Potential in Terrestrial Vertebrates."

 

Figure tree - this is a single randomly chosen tree that was used for illustration purposes in the main MS and can be used for your own quick testing and analyses:

tetrapoda_1.0_33281_full.1.tre

 

Tetrapod trees – these files contain the full 10,000 trees with 33,281 species, broken up into 10 sets of 1,000 trees:

tetrapoda_1.0_33281_full.1000.trees.zip

tetrapoda_1.0_33281_full.2000.trees.zip

tetrapoda_1.0_33281_full.3000.trees.zip

tetrapoda_1.0_33281_full.4000.trees.zip

tetrapoda_1.0_33281_full.5000.trees.zip

tetrapoda_1.0_33281_full.6000.trees.zip

tetrapoda_1.0_33281_full.7000.trees.zip

tetrapoda_1.0_33281_full.8000.trees.zip

tetrapoda_1.0_33281_full.9000.trees.zip

tetrapoda_1.0_33281_full.10000.trees.zip

 

Mammal trees – these 10,000 mammal trees were re-estimated using the methods described by Upham et al. (2019) with extinctionpr = fixed(0) to equal a Yule (i.e., pure-birth) process. These trees were used to create TetrapodTrees.

MamPhy_fullPosterior_PureBirth_vr_Completed_5911sp_topoCons_NDexp_all10k_v2_nexus.trees.zip: The tip labels are processed in _tetrapod_1.0.R with the file mamm_tax.csv.

 

Summary metrics – these files provide the summary and various statistics for ED/DR across the 10,000 trees:

tipRate_SUMMARY-ED_all10ktrees_tetrapoda_1.0_33281_full.csv

tipRate_SUMMARY-DR_all10ktrees_tetrapoda_1.0_33281_full.csv

 

Code Files – these files contain the R code necessary to assemble the trees and estimate the tip metrics.

_tetrapod_1.0.R: This code assembles the trees from the source publications:

Amphibians

Birds (Hackett backbone)

Lepidosaurs

Mammals (Pure-birth estimates – see above)

Testudines & Crocodylia

Most of these trees (other than the newly created mammal trees and the turtle/crocodilian set) can be downloaded from birdtree.org and vertlife.org. They should then be split into 10,000 separate files labeled arch/bird/squam/mamm/amph.tree.$SUFFIX as indicated in the trees.sample.csv file. The mamm_tax.csv file is also needed to process tip labels.

 

_Tetrapoda_tipFP_forHPC_v2.R: This code generates the ES/FP (i.e., DR/ED) values for the 10,000 trees, relying on tetrapod_groups.csv (see below) for taxon ordering.

 

Support files – these files are needed to support various functions above.

trees.sample.csv: Contains the randomly chosen tree order and suffixes to paste the trees together from the 5 underlying distributions.

mamm_tax.csv: Processes the tip labels of the Upham et al. (2019) mammal trees.

tetrapod_groups.csv: Contains the species lables to harmonize the metric ordering.

 

 



Part of the VertLife initiative: An NSF-sponsored, multi-institutional project to study the biodiversity of all terrestrial vertebrates (Tetrapoda), making them the first major global group of animals with near-complete species-level data on key evolutionary and ecological attributes.

Contact: Alex Pyron (rpyron@gwu.edu), Mario Moura (mariormoura@gmail.com), and Walter Jetz (wjetz@yale.edu). 

We thank the Map of Life team at the Yale Center for Biodiversity and Global Change for their contribution to earlier versions of this dataset and the E.O. Wilson Biodiversity Foundation for support in furtherance of the Half-Earth Project to W.J. This work was supported by funding from US National Science Foundation (NSF) grants to R.A.P. (DBI-0905765, DEB-1441719), R.C.K.B. (DEB-1441652), T.J.C. (DBI-2334779, DEB-2406685), J.E. (DEB-1441634, DEB-2244754), R.P.G (DEB-1441628), and W.J. (DEB-1441737). Additional funding came from US National Institutes of Health (NIH) grants to N.S.U. (1R21AI164268 and 1R35GM156919); US National Aeronautics and Space Administration (NASA) grants to W.J. (80NSSC17K0282 and 80NSSC18K0435); BR São Paulo Research Foundation (FAPESP) grants to M.R.M. (#2021/11840-6 and #2022/12231-6), K.C. (#2020/12558-0), and M.T.M. (#2023/14506-5); BR Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) fellowships for J.J.M.G.; BR Fonseca Leadership Program (GEF/FUNBIO #108/2025) to J.P.O.X., BR Conselho Nacional de Desenvolvimento Científico (CNPq) grants to K.C. (#444240/2024-1); NSERC Canada grants to A.Ø.M.; and a UCLA Chancellor’s Fellowship to R.M.P.