R Tools for Biodiversity | Vertebrates | Invertebrates | Plants | Diseases & Pathogens | Any Taxon | Other

Endangered Species Act

Federal Efforts to Ensure Biodiversity: The Endangered Species Act
An excellent written and video summary of the US EPA and its protection of endangered species (thanks, Anabel!).

Special note

The article by Bingham et al. provides a birds-eye-view of 74 biodiversity repositories–many more than listed here! For anyone wanting to maximize their biodiversity “gain” I recommend this article.

R Tools for Biodiversity

biogeo: For cleaning biodiversity data.

FedData: For downloading GIS data from several US government data sources (CRAN, GitHub)

spocc: For downloading data from GBIF, BISON, AntWeb, and others.

spoccutils: Light cleaning and visualization of biodiversity data.


GRBio (Global Registry of Biodiversity Repositories)
What: A database of natural history museums, herbaria, and the like
Where: Worldwide
See also: Schindel et al. 2016. The Global Registry of Biodiversity Repositories: A call for community Curation.  Biodiversity Data Journal 4:e10293.  (article)


Taxon: Birds
Where: Worldwide
Notes: Citizen science

Taxon: Birds
Where: North America
Notes: Citizen science

What: Specimen records of fish
Where: Worldwide
Notes: Also see VertNet

A global database on freshwater fish species occurrence in drainage basins 
What: Species lists of fish occurring in each drainage basin
Where: Worldwide 
Citation: Tedesco et al. 2016 A global database on freshwater fish species occurrence in drainage basins. Scientific Data 4:170141.

Life History Data of Lizards of the World
What: Life history data
Where: Worldwide
Citation: Mesquita et al. 2015. Life history data of lizards of the world.  Ecology 96:594.

Proyecto AVIS (Spanish | English)
What: Citizen science observations of birds
Where: Spain
Also see article by Verela et al. (2014).

What: Specimen records of vertebrates (fish, birds, mammals, reptiles, and amphibians)
Where: Worldwide
Notes: Aggregates MaNIS (mammals), ORNIS (birds), HerpNet (reptiles and amphibians), and FishBase
R: See package rvertnet for downloading records in R


What: Specimen records and images of ants
Where: Worldwide

Butterflies & Moths of North America
What: Citizen science point observations of Lepidoptera
Where: North America

Migratory Dragonfly Partnership
What: Citizen science point observations of Odonata
Where: North America


Butler University Friesner Herbarium Digital Collection
What: Specimen records of plants
Where: United States (especially Indiana)

What: Specimen records and images of plants
Where: United States, especially California

Consortium of American Bryophyte Herbaria
What: Specimen records of bryophytes and lichens
Where: Worldwide, especially North America

Consortium of North American Lichen Herbaria
What: Specimen records of lichens
Where: Worldwide, especially North America

Chinese Virtual Herbarium (Chinese | English)
What: Specimen records of plants
Where: Worldwide, especially China

D3 (Dispersal Diaspore Database)
What: A database of dispersal syndromes for plants
Where: Worldwide, but especially Europe

E-Flora BC (Electronic Atlas of the Flora of British Columbia, Canada)
What: Specimen records of plants, fungi, algae, and slime molds
Where: British Columbia, Canada

EuphORBia: A Global Inventory of the Spurges
What: Specimen records, taxonomic descriptions, images, and molecular data for Euphorbiaceae
Where: Worldwide
Note: Website in progress as of November, 2014

FIA (Forest Inventory and Analysis) Program
What: Plot data for plants: species, dbh, dead wood, etc.
Where: United States

National Museum of France Herbarium (HerbariumFrench Muséum national d’histoire naturelle vascular plant herbarium collection)
What: Specimen records of plants
Where: Worldwide, with special focus on France and its former colonies

What: Specimen records of the Marchantiophyta (liverwort) genus Frullania
Where: Worldwide

Harvard University Herbarium Index of Botanists
What: Database of botanists and their locations and years of activity
Where: Worldwide

Herbario Nacional de Costa Rica (CR)
What: Specimen records of plants
Where: Costa Rica

IPNI (The International Plant Names Index)
What: Taxonomic name resolution for plants
Where: Worldwide
Notes: See also The Plant List and World Flora Online (pending)

Kew SID (Seed Information Database)
What: Database on seed mass, storage behavior, dispersal syndrome, chemical content, salt tolerance, and morphology
Where: Worldwide

Les Herbonautes
What: Citizen science deciphering of plant specimen metadata
Where: Worldwide
Notes: In French, but English version coming soon!

Little’s Tree Maps from “Atlas of United States Trees”
What: Range maps of trees
Where: North and Central America, especially the United States

TR8 (article | CRAN)
What: R package for retreving plant function traits from online databases
Where: Worldwide but especially Europe

What: Specimen records of vascular and non-vascular plants
Where: Worldwide, with a concentration on Latin America

Seed Zone Mapper
What: Zones of local adaptation of plants useful for sourcing seeds for planting
Where: United States

What: Specimen records
Where: North America, especially Arizona

The Plant List
What: Taxonomic name resolution for plants
Where: Worldwide

The University and Jepson Herbarium
What: Specimen records of plants
Where: Worldwide, especially California

vPlants: A Virtual Herbarium of the Chicago Region
What: Specimens records and images of plants
Where: Vicinity of Chicago, USA

What: Plot data for plants
Where: North America

Diseases & Parasites

Natural History Museum Host-Parasite Database
What: Names of thousands of hosts and their parasites
Where: Worldwide
Notes: Can search by host and/or parasite and by place

Any Taxon or Mixed Taxa

BISON (Biodiversity Information Serving Our Nation)
What: Specimen records of any taxon
Where: United States
Notes: The United States’ GBIF portal

What: Specimen records of any taxon
Where: Worldwide, especially Canada
Notes: Canada’s GBIF portal

China Animal Scientific Database (in Chinese)
What: Specimen records of animals
Where: China and East Asia

What: Specimen records of any taxon
Where: Southwestern United States, Mexico, northern Mesoamerica

Encyclopedia of Life (EOL)
What: Attempts to catalog all information on all species, especially good for taxonomic authority
Where: Worldwide

What: Fossil records
Where: Worldwide

GBIF (Global Biodiversity Information Facility)
What: World’s largest repository of specimen records or any taxon
Where: Worldwide

Global Freshwater Biodiversity Atlas
What: Specimen records of any freshwater taxon, laws pertinent to freshwater biodiversity, user-contributed maps, and other information on conservation
Where: Worldwide

iDigBio (Integrated Digitized Biocollections)
What: Specimen records, vouchered images and recordings Where: Worldwide with a focus on institutions of the United States

ITIS (Integrated Taxonomic Information System)
What: Taxonomic name resolution service for any taxon
Where: North America

New Mexico Biodiversity Collections Consortium
What: Specimen records of any taxon
Where: United States with a focus on New Mexico

Ocean Biogeographic Information System
What: Specimen records of marine species
Where: Worldwide

Open Tree of Life
What: Compilation of published phylogenetic trees of any taxon
Where: Worldwide
Relevant R package(s): rotl

What:  Reef maps, specimen point records, bleaching events, monitoring networks, etc.
Where: Worldwide

World Register of Marine Species (WoRMS)
What: Taxonomic name resolution for marine species
Where: Worldwide
R package: worms


Global Biotic Interactions
What: Documented interactions between species
What: Worldwide
Relevant R package: rglobi

Mapping the World
What: Maps of biodiversity
Where: Worldwide with special focus on Brazil and North America

PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems)
What: Compilation hundreds of studies contrasting responses of biodiversity (presence/absence, abundance, or richness) to anthropogenic threats
Where: Worldwide
Introductory article: Hudson et al. 2014 Ecology & Evolution