Data mining resources for species distribution modeling and macroecology

Research projects in ecology, evolution, and conservation biology increasingly rely upon ecological modeling and GIS data and tools for manipulating and analyzing spatially linked data from across a variety of spatial scales. Of particular importance are species distribution modeling (SDM; also known as Ecological Niche Models, or ENMs, or Environmental Niche Models) and niche divergence tools, geospatial data layers representing Earth environments from a variety of perspectives and scales, and GIS and mapping software.

This post provides a list of links to resources (mainly databases and websites) from which researchers can mine data for conducting SDM and macroecology analyses. I intend to curate this list and update it as I learn about or use new data or data mining resources. This is the first draft of the list, and so it will necessarily contain some gaps; however, I have tried to link to the most popular databases and software programs. Websites in the References section provide additional lists, but most of the software they list has been incorporated herein. Species distribution modeling software and GIS methods will not be reviewed here (see manuscripts and online lists of these elsewhere).

Along with my collaborators, I am currently using these data sources and software programs to conduct species distribution modeling analyses of North American conifers and Neotropical freshwater fishes.

Jump to…

• Species Occurrences & Range Map Data
• Climate Data Layers
• Other GIS Data Layers & Maps
• GIS Software

Species Occurrence & Range Map Data

• GBIF - Global Biodiversity Information Facility
  • GBIF 0ccurrences search - http://www.gbif.org/occurrence
  • GBIF species search - http://www.gbif.org/species
• IUCN - International Union for Conservation of Nature and Natural Resources
  • Red List Spatial Data Download portal - http://www.iucnredlist.org/technical-documents/spatial-data
• speciesLink (searchable CRIA server for Brazilian species occurrences and taxonomy)
  • Main page in English - http://splink.cria.org.br/index?criaLANG=en

Climate Data Layers

• Worldclim.org - Worldclim datasets, including bioclimatic data layers and altitude (DEM)
  • http://www.worldclim.org/
  • Worldclim v2, new version, updated monthly climate data - http://worldclim.org/version2
  • Worldclim v1, old version - http://worldclim.org/version1

NOTE: I don’t have time now but I plan to add links to download pages for several global circulation models, as well as future climate models, here in the near future. ~J

Other GIS Data Layers & Maps

• ArcGIS Resources online
  • http://resources.arcgis.com
• EEA Global Landcover
  • http://www.eea.europa.eu
• ESDI - Earth Science Data Interface
  
  • http://glcfapp.glcf.umd.edu
• European Environmental Agency
  
  • www.eea.europa.eu/data-and-maps
• ICES - International Council for Exploration of the Sea
  
  • http://www.ices.dk
• LPDAAC - Land Processes Distributed Active Archive Center
  
  • http://edcdaac.usgs.gov/dataproducts.asp
• NASA Reverb, next-generation metadata and service server (replaced WIST)
  • https://reverb.echo.nasa.gov/
  • About Reverb - https://www.echo.nasa.gov/reverb/about_reverb.htm
• NOAA (U.S. National Oceanic and Atmospheric Administration) 1-km DEM data
  
  • http://www.ngdc.noaa.gov
• Oak Ridge National Laboratory, Geographic Information Science and Technology
  
  • http://www.ornl.gov/sci/gist
• United Nations Environment Programme GEO data portal
  
  • http://geodata.grid.unep.ch
• USGS - United States Geological Survey
  
  • http://gisdata.usgs.net
• WWF HydroSHEDS dataset
  • WWF main site - http://www.hydrosheds.org/
  • USGS main site - https://hydrosheds.cr.usgs.gov/ o Data download page - https://hydrosheds.cr.usgs.gov/dataavail.php

GIS Software

• ArcGIS software ($$$)
  
  • About - http://www.esri.com/arcgis/about-arcgis
• DIVA-GIS (free)
  
  • http://www.diva-gis.org/
• QGIS (free)
  
  • http://www.qgis.org/en/site/
• GRASS (free)
  
  • https://grass.osgeo.org/
• R Environment (free)
  • Comprehensive R Archive Network - https://cran.r-project.org/

Note: Check back… more links coming soon! ~J

References

CMEC (2017) Software and GIS data. Center for Macroecology, Evolution and Climate. Natural History Museum of Denmark, available at: http://macroecology.ku.dk/resources/software/.

WWF (2017) Conservation Science Data and Tools. World Wildlife Fund, available at: https://www.worldwildlife.org/pages/conservation-science-data-and-tools.

Other Resources

MVZ (Museum of Vertebrate Zoology) GIS Portal, University of California, Berkeley - https://mvzgis.wordpress.com/