DOI: 10.5061/dryad.bp26v20
title: Data from: PHYLACINE 1.2: The Phylogenetic Atlas of Mammal Macroecology

description: Data needed for macroecological analyses are difficult to compile and
 often hidden away in supplementary material under non-standardized
 formats. Phylogenies, range data, and trait data often use conflicting
 taxonomies and require ad hoc decisions to synonymize species or fill in
 large amounts of missing data. Furthermore, most available data sets
 ignore the large impact that humans have had on species ranges and
 diversity. Ignoring these impacts can lead to drastic differences in
 diversity patterns and estimates of the strength of biological rules. To
 help overcome these issues, we assembled PHYLACINE, The Phylogenetic Atlas
 of Mammal Macroecology. This taxonomically integrated platform contains
 phylogenies, range maps, trait data, and threat status for all 5,831 known
 mammal species that lived since the last interglacial (~130,000 years ago
 until present). PHYLACINE is ready to use directly, as all taxonomy and
 metadata are consistent across the different types of data, and files are
 provided in easy-to-use formats. The atlas includes both maps of current
 species ranges and present natural ranges, which represent estimates of
 where species would live without anthropogenic pressures. Trait data
 include body mass and coarse measures of life habit and diet. Data gaps
 have been minimized through extensive literature searches and clearly
 labelled imputation of missing values. The PHYLACINE database will be
 archived here as well as hosted online so that users may easily contribute
 updates and corrections to continually improve the data. This database
 will be useful to any researcher who wishes to investigate large scale
 ecological patterns. Previous versions of the database has already
 provided valuable information and have for instance shown that megafauna
 extinctions caused substantial changes in vegetation structure and
 nutrient transfer patterns across the globe. All data and metadata
 provided here represent PHYLACINE Version 1.2.0.
description: PHYLACINE_1.2_MetadataThis text contains the metadata describing the purpose, construction, and data of PHYLACINE Version 1.2.0. Definitions for all the variables and values found in the constituent data of PHYLACINE are located here. Please read this metadata file carefully and in its entirety before attempting any analyses.Trait_dataThis spreadsheet contains trait data for all 5831 species of mammals that lived during the last ~130,000 years including both extant and extinct species. This data includes body mass, island endemicity, threat status, and rough measures of life habit and diet.Synonymy_table_valid_species_onlyThis spreadsheet contains synonymies between the species used in PHYLACINE Version 1.2.0, previous versions of this database, and other popular databases like EltonTraits and IUCN. It also contains information on the phylogenetic placement of species in PHYLACINE. Only the 5831 species considered valid in PHYLACINE Version 1.2.0 are included.Synonymy_table_with_unaccepted_speciesThis spreadsheet contains synonymies between the species used in PHYLACINE Version 1.2.0, previous versions of this database, and other popular databases like EltonTraits and IUCN. It also contains information on the phylogenetic placement of species in PHYLACINE. Unlike Synonymy_table_valid_species_only, this spreadsheet also contains species that were not accepted in PHYLACINE Version 1.2.0 but are accepted in other databases like EltonTraits and IUCN.Complete_phylogenyThis nexus file contains the dated phylogeny of all 5831 mammal species that lived during the last ~130,000 years including both extant and extinct species. 1000 individual trees are included in the phylogeny to capture uncertainties in branching times and topology.Small_phylogenyThis nexus file contains the dated phylogeny of 4253 mammal species that lived during the last ~130,000 years including both extant and extinct species. Unlike the Complete_phylogeny, this phylogeny only includes the 4253 mammal species that could be placed phylogenetically through genetic data or unambiguous taxonomic constraints. 1000 individual trees are included in the phylogeny to capture uncertainties in branching times and topology.CurrentThis file contains rasters of the current geographic ranges for all 5831 mammal species that lived during the last ~130,000 years including both extant and extinct species.Present_naturalThis file contains rasters of the present natural geographic ranges for all 5831 mammal species that lived during the last ~130,000 years including both extant and extinct species. Present natural ranges represent counterfactual scenarios showing where species would live today without strong anthropogenic impacts on their ranges. We stress that the present natural ranges for extinct species are not the fossil ranges where species occurred in the Pleistocene but rather where the species would be expected to occur now given today's climate.Spatial_metadataThis spreadsheet contains metadata describing the creation of range maps for all 5831 mammal species that lived during the last ~130,000 years including both extant and extinct species.PHYLACINE_logo_largeThis is a color logo of the PHYLACINE database for use in presentations.PHYLACINE_logo_large_bwThis is a black and white logo of the PHYLACINE database for use in presentations.