DOI: 10.16904/envidat.246
title: Data from: Earth history events shaped the evolution of uneven biodiversity across tropical moist forests

description: Datasets and R scripts 
~~~~~Datasets
Dataset_S1.csv: Distribution of species diversity in plant and vertebrate clades. Total clade level diversity and species diversity in tropical moist forests (TMF) across the Neotropics, Indomalaya and Afrotropics. Pantropical clades are found in all three TMF regions with at least one-third of the clades’ total diversity spread throughout these regions. Pantropical diversity disparity (PDD) clades show lower diversity in TMF in the Afrotropics than in the Neotropics and Indomalaya.
Dataset_S2.csv: Environmental and species richness data across 110 km x 110 km grid cells in Neotropical, Indomalayan and Afrotropical moist forest sites. Variables include x and y coordinates in the Behrmann equal area coordinate reference system, potential evapotranspiration (PET), mean annual temperature (MAT), mean annual precipitation (MAP), amphibian, mammal, bird and squamate reptile species richness and biogeographic region, as well as the first two principal components of a principal component analysis on PET, MAT and MAP (PC1, PC2).
Dataset_S3.csv: Global reconstructed paleo-temperature estimates and spatial coordinates across 200 million years at 170,000 year intervals at 2 degree spatial resolution.
Dataset_S4.csv: Gen3sis model parameters and biodiversity summary statistics. Summary statistics include the number of extant species, the number of extinct species, the total number of species, the number of species within the tropical moist forest biome boundaries in the Neotropics, the Afrotropics and Indomalaya, the pantropical index, and the pantropical disparity index, as well as the running time-step and diversity of unfinished simulations.
Dataset_S5.csv: Net relatedness index (NRI) values for vertebrate clades showing an observed disparity in pantropical diversity in the Neotropical, Indomalayan and Afrotropical moist forest regions and associated P-values. Positive values indicate phylogenetic clustering, whereas negative values indicate phylogenetic overdispersion.
~~~~~Scripts
Script_1 - GLS.R. R script to replicate the linear modelling analyses.
Script_2 - Gen3sis_config_template.R. R script to generate the configurations files to run the simulation experiment.
Script_3 - Gen3sis_config_creator.R. R script to generate the configurations files to run the simulation experiment.
description: Resource Title: Dataset_S1
 Size: 8409 bytes
 Format: application/vnd.ms-excel
 URL: https://www.envidat.ch/dataset/b7783edd-a5bc-4854-8e7d-1698afc875b9/resource/dfbd6861-c745-4bf2-8988-3ddd790bcaad/download/dataset_s1.csv
 Description: Dataset_S1.csv includes species diversity counts for 237 clades in tropical moist forests (TMF) in the Neotropics (NeotropicalTMF), Indomalaya (IndomalayanTMF), Afrotropics (AfrotropicalTMF), All three TMF regions together (AllTMF), all non-TMF regions (NonTMF), and in total (Total). As well as whether the clade is pantropical (Pantropical_clade) and shows the pantropical diversity disparity (PDD_clade). Pantropical clades are found in all three TMF regions with at least one-third of the clades’ total diversity spread throughout these regions. Pantropical diversity disparity (PDD) clades show lower diversity in TMF in the Afrotropics than in the Neotropics and Indomalaya.
description: Resource Title: Dataset_S2
 Size: 207900 bytes
 Format: application/vnd.ms-excel
 URL: https://www.envidat.ch/dataset/b7783edd-a5bc-4854-8e7d-1698afc875b9/resource/ec608c8b-edbc-40f8-8e11-bfa9d6462923/download/dataset_s2.csv
 Description: Dataset_S2.csv: Environmental and species richness data across 110 km x 110 km grid cells in Neotropical, Indomalayan and Afrotropical moist forest sites. Variables include x and y coordinates in the Behrmann equal area coordinate reference system, potential evapotranspiration (PET), mean annual temperature (MAT), mean annual precipitation (MAP), amphibian, mammal, bird and squamate reptile species richness and biogeographic region, as well as the first two principal components of a principal component analysis on PET, MAT and MAP (PC1, PC2). Environmental data is from CHELSA and ENVIREM and species richness summarised from published data (vertLife, MOL, IUCN, GARD).
description: Resource Title: Dataset_S3
 Size: 147810332 bytes
 Format: application/vnd.ms-excel
 URL: https://www.envidat.ch/dataset/b7783edd-a5bc-4854-8e7d-1698afc875b9/resource/140b8a2f-120f-4975-afe6-e40927f50442/download/dataset_s3.csv
 Description: Dataset_S3.csv: - Paleoenvironmental reconstructions (details in the associated SI appendix) including latitude (y), longitude (x), and temperature data across 200 myrs at 170 kyr intervals.
description: Resource Title: Dataset_S4
 Size: 46904 bytes
 Format: application/vnd.ms-excel
 URL: https://www.envidat.ch/dataset/b7783edd-a5bc-4854-8e7d-1698afc875b9/resource/993d0dae-ce0d-4b0f-bc22-427d2673cd13/download/dataset_s4.csv
 Description: Dataset_S4.csv: simulation model parameters and diversity summary statistics. Including rate of temperature niche evolution (Tev), temperature niche width (TW), divergence threshold (S), Dispersal probability distribution shape (WeibullShape), model identifier (model), and random seed (seed). Also includes information on number of extinct species (n_extinct), number of extant species (n_extant), total species (total_diversity), Spearman correlation coefficient between absolute latitude and species richness (latitude_richness_cor), and diversity in the Neotropics (neotropical_diversity), Indomalaya (indomalayan_diversity), Afrotropics (afrotropical_diversity). Also, whether the simulation generated pantropical distribution of species (pantropicality_index), or the pantropical diversity disparity (PDD_index). Finally what time step the simulation exited at (0 for complete simulations) and the number of species in the ending timestep (running_diversity).
description: Resource Title: Dataset_S5
 Size: 1652 bytes
 Format: application/vnd.ms-excel
 URL: https://www.envidat.ch/dataset/b7783edd-a5bc-4854-8e7d-1698afc875b9/resource/eb72dfb6-ddcd-4363-8ce5-b605ea8bd1f3/download/dataset_s5.csv
 Description: Dataset_S5.csv: Net relatedness index (NRI) values for vertebrate clades showing an observed disparity in pantropical diversity in the Neotropical, Indomalayan and Afrotropical moist forest regions and associated P-values. Positive values indicate phylogenetic clustering, whereas negative values indicate phylogenetic overdispersion.
description: Resource Title: Script_1
 Size: 8705 bytes
 Format: .r
 URL: https://www.envidat.ch/dataset/b7783edd-a5bc-4854-8e7d-1698afc875b9/resource/f7e89750-58cc-4d19-a5d0-32cf41e7deef/download/gls.r
 Description: R script to replicate the linear modelling analyses.
description: Resource Title: Script_2
 Size: 6345 bytes
 Format: .r
 URL: https://www.envidat.ch/dataset/b7783edd-a5bc-4854-8e7d-1698afc875b9/resource/e02e013f-3977-4387-89ce-e0ede683e7e1/download/gen3sis_config_template.r
 Description: Script used to generate the configurations files to run the simulation experiment.
description: Resource Title: Script_3
 Size: 3070 bytes
 Format: .r
 URL: https://www.envidat.ch/dataset/b7783edd-a5bc-4854-8e7d-1698afc875b9/resource/128aaa9b-008c-40a9-91c2-661848a9d9d8/download/gen3sis_config_creator.r
 Description: Script used to generate the configurations files to run the simulation experiment.