Madagascar's extraordinary biodiversity: a data repository

Data repository for the two sister reviews of Madagascar's biodiversity:

Antonelli et al.: "Madagascar's extraordinary biodiversity: Evolution, distribution, and use", Science 378 (6623): eabf0869 – https://doi.org/10.1126/science.abf0869

Ralimanana et al.: "Madagascar's extraordinary biodiversity: Threats and opportunities",  Science 378 (6623): eadf1466 – https://doi.org/10.1126/science.adf1466

Please note the author order of this data repository is different from the author order and contributions in the review papers.

REVIEW I: EVOLUTION, DISTRIBUTION AND USE

catalogue_of_vascular_plants_of_madagascar.csv -- Comma-separated table with comprehensive taxonomic database of vascular plants of Madagascar, from the Catalogue of the Vascular Plants of Madagascar project. Contact: Peter Phillipson - [e-mail] and Marina Rabarimanarivo - [e-mail]

fungi_supplementary_material.zip -- Zipped archive containing: R script to get fungal endemism estimates from GBIF/UNITE and process data; comma-separated tables from GBIF, PlutoF, Goodman lichen checklist and Index Fungorum (as of 02/12/20): comma-separated table listing Madagascan taxa with endemism status. Contact: Rowena Hill - [e-mail]

lineages_madagascar.csv -- Comma-separated table with crown and stem ages, number of species, and geographic origin or distribution of sister clade of Malagasy endemic lineages, extracted from the literature. Contact: Jan Hackel - [e-mail] and Angelica Crottini - [e-mail]

madagascar_fossil_genera_occurrences.csv -- Comma-separated table with worldwide fossil records for Malagasy species, downloaded from the PaleoBiology Database. -- Contact: Juan Carillo - [e-mail]

species_richness_modeling_occurrences.csv -- Comma-separated table with specimen-based occurrence data for Malagasy amphibians, grasses, lemurs, palms, reptiles, and Sarcolaenaceae. Contact: Weston Testo - [e-mail]

taxon_description_by_year.csv -- Comma-separated table with years of basionym publication for Malagasy amphibians, reptiles, vascular plants, and ants. Contact: Weston Testo - [e-mail]

vegetation_moatsmith_1km_extended.zip -- Raster geotiff with new expanded vegetation types based on Moat & Smith (2007). Contact: Justin Moat - [e-mail]

vertebrate_species_list.csv -- Comma-separated table with native species list and associated endemism of freshwater fishes, amphibians, reptiles, birds, and mammals of Madagascar (author-curated list based on data from The New Natural History of Madagascar and the IUCN Red List). Contact: Weston Testo - [e-mail], Angelica Crottini - [e-mail], Ferran Sayol - [e-mail]

REVIEW II: THREATS AND OPPORTUNITIES

catalogue_of_vascular_plants_of_madagascar.csv -- Comma-separated table with comprehensive taxonomic database of vascular plants of Madagascar, from the Catalogue of the Vascular Plants of Madagascar project. Contact: Peter Phillipson - [e-mail] and Marina Rabarimanarivo - [e-mail]

ex_situ_plants.csv -- Comma-separated table with numbers of ex situ conserved plant species, per family, from BGCI’s PlantSearch database and collections of Jardin Botanique Educatif and Parc Ivoloina. Contact: Malin Rivers - [e-mail]

ex_situ_vertebrates.csv -- Excel spreadsheet with the list of extant native Malagasy vertebrates with information on their presence in at least one international zoo holding and whether they have been bred successfully over the last 12 months. Data from the Zoological Information Management (ZIM) Software performed in February 2021. Contact: Angelica Crottini - [e-mail]

extinct_animals_madagascar.csv -- Comma-separated table of all known anthropogenic extinctions before 1500 CE in Madagascar. Contact: Ferran Sayol - [e-mail]

madagascar_protected_areas_sources.csv -- Comma-separated table with comments and sources for columns in the protected area data in the csv and shapefile. Contact: Maria S. Vorontsova - [e-mail]

madagascar_terrestrial_protected_areas.csv -- Comma-separated values with description of the pretected areas, matching the Protected Area Shapefile. This file contains French accents; correct display may depend on the software used. Contact: Daniel Edler - [e-mail] and Henintsoa Razanajatovo - [e-mail]

madagascar_terrestrial_protected_areas.zip -- ESRI Shapefile for the synthesized protected areas of Madagascar, including Key Biodiversity Areas and attributes. Contact: Daniel Edler - [e-mail] and Rasolohery Andriambolantsoa - [e-mail]

observed_and_predicted_threats.csv -- Comma-separated table with the number of species with each listed threat, as defined by the IUCN or predicted by our model, across taxonomic groups. Contact: Rob Cooke - [e-mail]

phylogenetic_diversity_methods.zip -- Zipped archive containing community matrices, species range shapefiles, and R script used to estimate phylogenetic diversity for amphibians, mammals, and reptiles. Contact: Weston Testo - [e-mail]

predicting_species_IUCN_status.zip -- Zipped archive containing data, scripts and an Rstudio project to: (1) prepare features for using IUCNN v1.0 to predict the conservation status for Not Evaluated species (01_feature_preparation); (2) predict species IUCN status assessment using neural networks (02_predicting_species_IUCN_status); (3) predict species’ threat status using neural networks (03_predicting_species_threats). Contact: Alexander Zizka - [e-mail] and Daniele Silvestro - [e-mail]

threat_predictions_iucnn.txt -- Tab-separated table with results of the conservation status prediction from a Bayesian Neural Network for 5,887 species of vascular plants from Madagascar. Values are the mean posterior probabilities for each IUCN Red List category. Contact: Daniele Silvestro - [e-mail]