Biodiversity

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

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

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

spoccutils: Light cleaning and visualization of biodiversity data.

Meta-repositories

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)

Vertebrates

eBird
Taxon: Birds
Where: Worldwide
Notes: Citizen science

FeederWatch
Taxon: Birds
Where: North America
Notes: Citizen science

FishBase
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).

VertNet
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

Invertebrates

AntWeb
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

Plants

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

Calflora
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

Frullania
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

TROPICOS
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

SIENET
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

VegBank
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

Canadensys
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

CONABIO
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

Fossilworks
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

ReefBase

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

Other

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

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