Madagascar's extraordinary biodiversity: a data repository

Data repository for the double review on Madagascar's biodiversity [ADD FULL CITATIONS + DOI WHEN ACCEPTED] REVIEW I: EVOLUTION, DISTRIBUTION AND USE CatalogueOfVascularPlantsOfMadagascar.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 - [email protected] and Marina Rabarimanarivo - [email protected] Fossils_Madagascar.csv -- Comma-separated table with Malagasy fossil records, downloaded from the PaleoBiology Database. Contact: Juan Carillo - [email protected] [REMOVE - NOT USED] 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 - [email protected] Genera_records_world.csv -- Comma-separated table with worldwide fossil records for Malagasy species, downloaded from the PaleoBiology Database. -- Juan Carillo - [email protected] [ADD FILE AND RENAME AS Malagasy_fossil_genera_occurrences.csv] lineage_data_clean_v4.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 - [email protected] and Angelica Crottini - [email protected] moatsmith_1km_extended.zip -- Raster geotiff with new expanded vegetation types based on Moat & Smith (2007). Contact: Justin Moat - [email protected] SpeciesRichnessModelingOccurrences.csv -- Comma-separated table with specimen-based occurrence data for Malagasy amphibians, grasses, lemurs, palms, reptiles, and Sarcolaenaceae. Contact: Weston Testo - [email protected] TaxonDescriptionByYear.csv -- Comma-separated table with years of basionym publication for Malagasy amphibians, reptiles, vascular plants, and ants. Contact: Weston Testo - [email protected] VertebrateSpeciesList.csv -- Comma-separated table with species list of freshwater fish, amphibians, reptiles, birds and mammals of Madagascar (curated list based on IUCN data). Contact: Weston Testo - [email protected] [FILE TO UPDATE] REVIEW II: THREATS AND OPPORTUNITIES CatalogueOfVascularPlantsOfMadagascar.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 - [email protected] and Marina Rabarimanarivo - [email protected] Ex_situ_plants.xlsx -- Excel spreadsheet 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 - [email protected] Ex_situ_vertebrates.xlsx -- 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 - [email protected] [FILE TO UPDATE] Extinct_Animals_madagascar.csv -- Comma-separated table of all known anthropogenic extinctions before 1500 CE in Madagascar. Contact: Ferran Sayol - [email protected] features_predict210325_predictions.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 - [email protected] 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 - [email protected] Madagascar_terrestrial_protected_areas.csv -- Comma-separated values with description of the pretected areas, matching the Protected Area Shapefile. Contact: Daniel Edler - [email protected] and Henintsoa Razanajatovo - [email protected] Madagascar_terrestrial_protected_areas.zip -- ESRI Shapefile for the synthesized protected areas of Madagascar, including Key Biodiversity Areas and attributes. Contact: Daniel Edler - [email protected] and Rasolohery Andriambolantsoa - [email protected] 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 - [email protected] PhylogeneticDiversityMethods.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 - [email protected] 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 - [email protected] and Daniele Silvestro - [email protected]