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Taxonomy information

Taxonomy resources
General;
Algae;
Fungi;
Plants;
Vertebrates;
Insects;
Other arthropods;
Molluscs;
Other invertebrates; Other eukaryotes;
Archaea and Bacteria;
Viruses;
Culture collections


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Extinct organisms

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TAXONOMY RESOURCES

The following list is a compilation of some of the references and on-line resources used by the Taxonomy group at GenBank, ordered by the following categories:

General
Algae
Fungi
Plants
Vertebrates
Insects
Other arthropods
Molluscs
Other invertebrates
Other eukaryotes
Archaea and Bacteria
Viruses
Culture Collections

General

Biodiversity and Biological Collections Web Server (links to variety of databases, museums and other taxonomy resources):
http://biodiversity.uno.edu/

MarineSpecies.org:
http://marinespecies.org/

Hawaian flora and fauna checklists:
http://hbs.bishopmuseum.org/browsedata.html

Index of Organism Names:
http://www.biosis.org.uk/triton/indexfm.htm

Integrated Taxonomic Information System database of biological names:
http://www.itis.usda.gov/plantproj/itis/index.htm

Internet Resource Guide for Zoology. A directory to biological sites of all kinds, including systematics and nomenclature (not restricted to zoology links):
http://www.biosis.org/free_resources/resource_guide.html

List of phylogenetic databases and information:
http://www.UCMP.Berkeley.EDU/subway/phylo/phylodat.html

Tree of Life:
http://tolweb.org/tree/phylogeny.html

University of California Museum of Paleontology Phylogeny of Life:
http://www.ucmp.berkeley.edu/exhibit/phylogeny.html

World Species Lists for Animals/Plants/Microbes - the complete list of lists:
http://species.enviroweb.org/

Algae

Chretiennot-Dinet, M.-J., Sournia, A., Ricard, M. & Billard, C. 1993. A classification of the marine phytoplankton of the world from class to genus. Phycologia 32, 159-179.

AlgaeBase:
http://www.algaebase.org/

Index Nominum Algarum:
http://ucjeps.herb.berkeley.edu/INA.html

World Data Centre for Microorganisms:
http://wdcm.nig.ac.jp/cgi-bin/search.cgi

Other phycological collections (links to a number of specialized algal databases):
http://www.ucmp.berkeley.edu/collections/otherphy.html

Fungi

Farr, D.G. et al. 1989. Fungi on Plants and Plant Products in the United States. American Phytopathological Society Press.

Kirk, P.M., Cannon, P.F. and David, J.C. 2001 Ainsworth and Bisby's Dictionary of the Fungi (9th edition). CAB International.

Kurtzman, C.P. and J.W. Fell (Eds.). 1998. The Yeasts: A Taxonomic Study (4th edition). Elsevier.

Rossman, A.Y., M.E. Palm, and L.J. Spielman. 1987. A Literature Guide for the Identification of Plant Pathogenic Fungi. American Phytopathological Society Press.

Anamorph/Teleomorph Query:
http://www2.biology.ualberta.ca/jbrzusto/anatel.php

The CABI Bioscience Database of Fungal Names:
http://www.indexfungorum.org/

Centraalbureau voor Schimmelcultures (CBS) fungal database:
http://www.cbs.knaw.nl/DATABASE.HTML

Mycotaxon on-line:
http://www.mycotaxon.com/

Mycologia on-line:
http://www.erin.utoronto.ca/~w3msa/myc/myctab.htm

Myconet:
http://www.umu.se/myconet/Myconet.html

Mycology Resources:
http://mycology.cornell.edu/

North American Lichen Checklist:
http://www.ndsu.nodak.edu/instruct/esslinge/chcklst/chcklst7.htm

Systematic Biology and Mycology Fungal Databases:
http://NT.ars-grin.gov/fungaldatabases/databaseframe.cfm

Plants (embryophytes)

Bremer, K. Asteraceae: Cladistics and Classification.

Dressler, R.L. 1993. Phylogeny and Classificaton of the Orchid Family. Dioscorides Press.

Greuter, W. et al. 2000. International Code of Botanical Nomenclature (St Louis Code). Koenigstein, Koeltz Scientific.

Griffiths, M. 1994. Index of Garden Plants. Timber Press.

Kartesz, J.T. And C.A.Meacham. 2001. Synthesis of the North American Flora (version 1.0). CD for PC.

Mabberly, D.J. The Plant-Book. 1987. Cambridge University Press.

Staff of the Liberty Hyde Bailey Hortorium. 1976. Hortus Third. MacMillan Publ.

Stearn, W.T. 1992. Botanical Latin (4th Edition). Portland, Orgeon: Timber Press.

Trehane, P. 1989. Index Hortensis. Vol. 1: Perennials.

Watson, L, and Dallwitz, M.J. 1992. The Grass Genera of the World. CABI International.

On-line plant databases:

Plant Names (General)

The International Plant Names Index (source databases are the Index Kewensis, Gray Card Index and Australian Plant Names Index):
http://193.128.240.158/ipni/query_ipni.html

W3TROPICOS - The Missouri Botanical Garden vascular plant database:
http://mobot.mobot.org/W3T/Search/vast.html

IOPI Global Plant Checklist Prototype:
http://www.bgbm.fu-berlin.de/IOPI/GPC/query.htm

USDA PLANTS:
http://plants.usda.gov/

Names in Current Use for Extant Plant -- Genera:
http://www.bgbm.fu-berlin.de/iapt/ncu/genera/NCUGQuery.htm

Index Nominum Genericorum:
http://rathbun.si.edu/botany/ing/ingform.cfm

Cultivated Plants

USDA/Agricultural Research Service taxonomy:
http://www.ars-grin.gov/npgs/tax/taxgenform.html

Institute for Plant Genetics and Crop Plant Research (IPK):
http://mansfeld.ipk-gatersleben.de/

Regional Floras and Individual Plant Groups

Checklist of World Ferns:
http://homepages.caverock.net.nz/~bj/fern/

The Cycad Pages:
http://plantnet.rbgsyd.gov.au/PlantNet/cycad/index.html

The Gymnosperm Database:
http://www.botanik.uni-bonn.de/conifers/taxa.htm

Catalogue of New World Grasses:
http://mobot.mobot.org/Pick/Search/nwgc.html

Flora Europaea:
http://rbg-web2.rbge.org.uk/FE/fe.html

Flora of China Checklist:
http://mobot.mobot.org/W3T/Search/foc.html

LegumeWeb (pea family):
http://www.ildis.org/LegumeWeb

General Botany Resources

Internet Directory for Botany:
http://www.botany.net/IDB/

Index Herbariorum:
http://websun.nybg.org/bsci/ih/searchih.html

APG II Classification (Angiosperm Phylogeny Group):
http://www.flmnh.ufl.edu/deeptime/apgII2002.html

Angiosperm Phylogeny Website (PF Stevens, 2003):
http://www.mobot.org/MOBOT/Research/APweb/welcome.html

Bryophytes

TROPICOS Missouri Botanical Garden bryophyte database:
http://mobot.mobot.org/Pick/Search/most.html

New York Botanical Garden bryophyte catalog:
http://www.nybg.org/bsci/hcol/bryo/bry3.html

Vertebrates

Nelson, J.S. Fishes of the world. 3rd ed., J. Wiley & Sons, 1994.

Catalog of Fishes on-line:
http://www.calacademy.org/research/ichthyology/catalog/index.html

FishBase99:
http://www.fishbase.org/search.cfm

Guide to South American Cichlids:
http://www.nrm.se/ve/pisces/acara/cichwais.shtml

Neodat Project:
http://www.neodat.org/

Amphibians of the World on-line version (1999):
http://research.amnh.org/cgi-bin/herpetology/amphibia

University of California AmphibiaWeb:
http://elib.cs.berkeley.edu/aw/

The EMBL Reptile Database:
http://www.embl-heidelberg.de/~uetz/LivingReptiles.html

Edwards E.P. 1982. A coded workbook of birds of the world Volume1: Non-Passeriformes. 2nd ed., Sweet Briar (Virginia) (Common names).

Edwards, E.P. 1986. A coded workbook of birds of the world Volume 2: Passeriformes. 2nd ed., Sweet Briar (Virginia) (Common names).

Sibley, C.G. and Monroe, B.L. 1990. Distribution and Taxonomy of Birds of the World. Yale Univ. Press.

BirdNet: The Ornithological Information Source:
http://www.nmnh.si.edu/BIRDNET/ORDERS/BIRDACCOUNTS.html

Wilson and Reeder's Mammal species of the world on-line:
http://www.nmnh.si.edu/msw/

Insects

Arnett, R.H.,Jr. 1993. American Insects. A Handbook of the Insects of America North of Mexico. The Sandhill Crane Press, Gainesville, Fl.

Common Names of Insects and Related Organisms. Committee on Common Names of Insects (Chairman: F.G. Werner). 1982. Entomological Society of America.

Miller, J. Y. 1992. The Common Names of North American Butterflies. Smithsonian Institution Press.

Patterson J.T. & W.S. Stone. 1952. Evolution in the Genus Drosophila. Macmillan, New York.

Nomina Insecta Nearctica:
http://www.nearctica.com/nomina/nomina.htm

Coleoptera:
HTTP://www.sel.barc.usda.gov/coleoptera/col-home.htm
http://www.nearctica.com/nathist/insects/coleop.htm

Collembola:
http://www.geocities.com/~fransjanssens/

Diptera (Australasian and Oceanian):
http://www.bishop.hawaii.org/bishop/ento/aocat/aocathome.html

Drosophilidae:
http://taxodros.unizh.ch/

Formicidae (AMNH ants):
http://research.amnh.org/entomology/social_insects/ants/amnhants.html

Fulgoromorpha Lists On the WEB:
http://flow.snv.jussieu.fr/

Hymenoptera:
http://iris.biosci.ohio-state.edu/hymenoptera/hym_db.html
http://atbi.biosci.ohio-state.edu:8880/hymenoptera/nomenclator.home_page

Ichneumonidae:
http://iris.biosci.ohio-state.edu/catalogs/ichneumonids/master_list2.html

Isoptera:
http://www.utoronto.ca/forest/termite/taxon.htm
http://www.utoronto.ca/forest/termite/speclist.htm

Lepidoptera:
http://www.funet.fi/pub/sci/bio/life/warp/lepidoptera-index-e.html
http://www.troplep.org/famlist.htm

Mecoptera:
http://www.calacademy.org/research/entomology/mecoptera/index.htm

Odonata:
http://members.aol.com/odoweb/species.htm
http://www.ups.edu/biology/museum/NWOLAug2000.html

Orthoptera:
http://viceroy.eeb.uconn.edu/Orthoptera

Trichoptera:
http://entweb.clemson.edu/database/trichopt/hierarch.htm

Social insect page:
http://research.amnh.org/entomology/social_insects/siframe.html

Other arthropods

Crustacean classification to family level:
Martin, J. W. and G. E. Davis. IN PRESS. An Updated Classification of the Recent Crustacea. Science Series, Natural History Museum of Los Angeles County.

Common and Scientific Names of Aquatic Invertebrates from the United States and Canada: Decapod Crustaceans. 1989. American Fisheries Society Special Publication 17, Bethesda, Maryland.

Holthuis, L.B.: Shrimps and Prawns of the World. An Annotated Catalogue of Species of Interest to Fisheries. 1980. FAO Fisheries Synopsis (FAO Species Catalogue) # 125, vol. 1.

The Amphipod Homepage:
http://web.odu.edu/sci/biology/amphome

Cladocera:
http://www.cladocera.uoguelph.ca/

Copepoda:
http://www.nmnh.si.edu/iz/copepod/

Heterometrus (Asian forest scorpions):
http://web.singnet.com.sg/~caijw/hetero/hetero.htm

Smithsonian world list of aquatic and terrestrial Isopoda:
http://www.nmnh.si.edu/iz/isopod/

Scorpiones:
http://wrbu.si.edu/www/stockwell/classification/classification.html
http://wrbu.si.edu/www/stockwell/phylogeny/phylogeny.html

The World Spider Catalog:
http://research.amnh.org/entomology/spiders/catalog81-87/

Molluscs

Common and Scientific Names of Aquatic Invertebrates from the United States and Canada: Mollusks. 1998. American Fisheries Society Special Publication 26, Bethesda, Maryland. 2nd edition.

Roper, C.F.E., Sweeney, M.J., and Nauen, C.E.: Cephalopods of the World. FAO Fisheries Synopsis (FAO Species Catalogue) #125, vol. 3.

Gastropods, scaphopods, and cephalopods.
http://parallel.park.org/Guests/Shells/Shell_Catalogue/Shell_Pages/Shell_Catalogue_Home_Page.html

Opisthobranchs from around the World.
http://www.medslugs.de/Opi/Opisthobranchia.htm

Shells database (Mollusca classification).
http://shell.kwansei.ac.jp/~shell/pic_book/index.html

Other Invertebrates

Common and Scientific Names of Aquatic Invertebrates from the United States and Canada: Mollusks. 1998. American Fisheries Society Special Publication 26, Bethesda, Maryland. 2nd edition.

Cairns, S.D. et al. 1991. Common and Scientific names of Aquatic Invertebrates from the United States and Canada: Cnidaria and Ctenophora. American Fisheries Society Special Publication 22. Bethesda, Maryland.

Khalil, L.F., A. Jones and R.A. Bray, (Eds.). 1994. Keys to the Cestode Parasites of Vertebrates. CAB International.

Pennak R.W. 1989. Fresh-water Invertebrates of the United States. Protozoa to Mollusca. 3rd Edition. Jonh Wiley and Sons, New York.

Roper, C.F.E., Sweeney, M.J., and Nauen, C.E.: Cephalopods of the World. FAO Fisheries Synopsis (FAO Species Catalogue) #125, vol. 3.

Annelida:
http://www.itis.usda.gov/advanced_search.html

Brachiopoda: Classification to family level:
http://www.com.univ-mrs.fr/EuroBrachNet/CLASS/Class.htm

Indexes to Bryozoan Taxa:
http://www.civgeo.rmit.edu.au/bryozoa/indexes.html

Current Classification of Recent Cephalopoda:
http://www.mnh.si.edu/cephs/newclass.pdf

Cnidaria: Hexacorallians of the World:
http://www.kgs.ku.edu/Hexacoral/Biodata/

Corals: List of Extant Stony Corals:
http://www.nodc.noaa.gov/col/projects/coral/hardcoral/Hardcoralmain.html

Ctenophora classification:
http://faculty.washington.edu/cemills/Ctenophores.html

Echinoderm classification:
http://www.calacademy.org/research/izg/echinoderm/classify.htm

Echinoidea:
http://www.nhm.ac.uk/palaeontology/echinoids/

Gastropods, scaphopods, cephalopods:
http://parallel.park.org/Guests/Shells/Shell_Catalogue/Shell_Pages/Shell_Catalogue_Home_Page.html

Links to papers on Platyhelminthes, Nematoda, other invertebrates:
http://www.mnhn.fr/mnhn/bpph/
http://www.mnhn.fr/publication/zoosyst/azoosyst.html

Monogenea species:
http://erms.biol.soton.ac.uk/lists/full/Monogenea.shtml

Monogenea (flatworm) classification:
http://www.mnhn.fr/mnhn/bpph/Data/Mollaret2000/mollaret2000.html

Opisthobranchs from around the World:
http://www.medslugs.de/Opi/Opisthobranchia.htm

Porifera:
Boropjevic, R., Boury-Esnault, N. and Vacelet, J. (1990). A revision of the supraspecific classification of the subclass Calcinea (Porifera, class Calcarea). Bull. Mus. natn. Hist. nat. Paris. 4 ser. 12, sect. A (2): 243-276.

Sipuncula:
http://www.mcz.harvard.edu/Departments/InvertZoo/as.fldr/cutler/siptaxa.htm

Stauromedusae:
http://faculty.washington.edu/cemills/Stauromedusae.html

Turbellaria classification:
http://linius.umesci.maine.edu/turbellaria/

Neogene marine biota - bivalves, gastropods, bryozoans, corals, forams, ostracodes (fossil and living):
http://porites.geology.uiowa.edu/index.htm

Shells Database:
http://shell.kwansei.ac.jp/~shell/pic_book/index.html

Other Eukaryotes

The Astrobiology Institute's Microscope page has a classification of eukaryotes to the genus level:
http://microscope.mbl.edu/reflections/baypaul/microscope/general/page_01.htm

Aescht, E. 2001. Catalogue of the generic names of ciliates (Protozoa, Ciliophora). Denisia 01. Oberoesterreichisches Landesmuseum, Linz, Austria.

Canning, E.U., Lom, J. & Dykova, I. 1986. The microsporidia of vertebrates. p. 289. Academic Press, London, Orlando.

Cavalier-Smith, T. 1993. Kingdom Protozoa and its 18 phyla. Microbiological Reviews 57, 953-994.

Corliss, J. O. 1979. The ciliated protozoa: characterization, classification, and guide to the literature, 2nd ed. Pergamon Press, New York, New York.

Lee, J.J., Hutner, S.H. & Bovee, E.C. 1985. Illustrated guide to the Protozoa. Society of Protozoologists.

Levine et al. 1980. A newly revised classification of the protozoa. Journal of Protozoology 27, 37-58.

Patterson, DJ. 1994. Protozoa: Evolution and Systematics. Proceedings of the IX International Congress of Protozoology, Berlin 1993. Gustav Fischer Verlag, Stuttgart, Jena, New York.

Page, F. C. & Siemensma, F. J. 1991. Nackte Rhizopoda und Heliozoa. Fischer-Verlag, Stuttgart.

Small, E. B. & Lynn, D. H. 1985. Phylum Ciliophora. In An illustrated guide to the Protozoa (ed. J. J. Lee, Hutner, S.H. & Bovee, E.C.). Society of Protozoolo gists, Lawrence.

Sprague, V. 1977. Classification and phylogeny of the Microsporidia. In: Systematics of the Microsporidia, Comparative Pathobiology, Vol. 2 (Bulla, L.A., Cheng, T.C., eds.). New York-London: Plenum Press,

Sprague, V. 1977. Annotated list of species of microsporidia. In: Systematics of the Microsporidia, Comparative Pathobiology, Vol.2 (Bulla, L.A., Cheng, T.C., eds). New York-London: Plenum Press.

Archaea and Bacteria

The Prokaryotes: A Handbook on the Biology of Bacteria, Second Edition, Vol. 1-4, 1991. Springer-Verlag, New York NY. A. Balows, H. Truper, M. Dworkin, W. Harder & K.-H. Schleifer.

Bergey's Manual Trust: contains taxonomic outline for the second edition of Bergey's Manual of Systematic Bacteriology:
http://www.cme.msu.edu/bergeys/

DSMZ Bacterial Nomenclature up-to-date:
http://www.dsmz.de/bactnom/bactname.htm

Greengenes. 16S rRNA gene database and workbench:
http://greengenes.lbl.gov

International Journal of Systematic and Evolutionary Microbiology (IJSEM):
http://ijs.sgmjournals.org/

List of Bacterial Names with Standing in Nomenclature:
http://www.bacterio.cict.fr/

Ribosomal Database Project. Bacterial classification:
http://rdp.cme.msu.edu

The Taxonomic Outline of Bacteria and Archaea (TOBA):
http://www.taxonomicoutline.org/

Viruses

Granoff A & Webster RG. 1999. Encyclopedia of Virology. Academic Press, San Diego.

Index of Viruses on-line (ICTV-7):
http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/fr-index.htm

Culture Collections

American Type Culture Collection (ATCC):
http://www.atcc.org/

Centraalbureau voor Schimmelcultures (CBS):
http://www.cbs.knaw.nl/DATABASE.HTML

Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ):
http://www.dsmz.de/index.html

Oregon Collection of Methanogens (OCM):
http://methanogens.pdx.edu/

Pasteur Collection of Cyanobacteria (PCC):
http://www.pasteur.fr/Bio/PCC/

Provasoli-Guillard National Center for Culture of Marine Phytoplankton (CCMP):
http://ccmp.bigelow.org/

The Culture Collection of Algae at University of Texas (UTEX) :
http://www.bio.utexas.edu/research/utex/

World Data Centre for Microorganisms. Includes fungal, bacterial, algal and viral strain collections:
http://wdcm.nig.ac.jp/cgi-bin/search.cgi

Home Pages of Culture Collections of the World:
http://wdcm.nig.ac.jp/hpcc.html