Links to Systematics and Evolutionary Biology Web Sites

The following is a brief listing of other sites on the WWWeb that are related to systematics and evolutionary biology. As always, this page will be continually updated as new sites appear and disappear. Let me know the URL of any other sites on the web that should be considered for inclusion as well as any broken links.

General: All Organisms

  1. Resources for Ecology, Evolutionary Biology, Systematics, and Conservation Biology. Maintained by Kent Holsinger (University of Connecticut). Lists taxonomic and phylogenetic information, phylogeny software, taxonomic information on specific groups, nomenclature, interactive identification software, collections mangagement software, bibliographies, resources for plant systematists, and floras and Atlases online. VERY USEFUL!
  2. The Tree of Life is used by those interested in locating information about a particular group of organisms, by biologists seeking identification keys, figures, phylogenetic trees, and other systematic information for a group of organisms, and by educators teaching about organismal diversity. The site was designed by David Maddison, Wayne Maddison, and Katja Schulz and is continually evolving as new data are entered.
  3. DiversityOfLife.org. Has a search engine that provides access to known illustrations and photographs of living organisms. Links to additional information also provided.
  4. TreeBASE. is a relational database of phylogenetic information sponsored by the NSF, Harvard University Herbaria, and the University of California, Davis. TreeBASE stores phylogenetic trees and the data matrices used to generate them from published research papers.
  5. NCBI Taxonomy Browser. Allows access to molecular data on all living organisms via a taxonomic hierarchy.
  6. ITIS. Integrated Taxonomic Information System. Allows one to: locate scientific name and other information for a taxon, generate reports, extract scientific name and other associated data from ITIS, download data, load data to your office/home site, compare taxonomy/nomenclature, match your list of taxa to the ITIS Database, submit data to the ITIS database, access the Taxonomic Workbench and download the Workbench software.
  7. The Expert Center for Taxonomic Identification sponsored by the Netherlands Organization for Scientific Research (NWO), the University of Amsterdam and UNESCO, publishes taxonomic information on interactive multimedia CD-ROMs and sponsor the online World Biodiversity Database.
  8. Species 2000. Has the objective of enumerating all known species of organisms on Earth (animals, plants, fungi and microbes) as the baseline dataset for studies of global biodiversity.
  9. Biodiversity on the Internet. See large collection of links on THIS page.
  10. INBio. The National Biodiversity Institute (INBio) of Costa Rica is a private research and biodiversity management center, established in 1989 to support efforts to gather knowledge on the country's biological diversity and promote its sustainable use. INBio is a non-governmental, non-profit, public interest organization of civil society that works in close collaboration with different government institutions, universities, the private sector and other public and private organizations, both within and outside Costa Rica. INBio's work focuses on the following areas of action:Inventory and Monitoring, Conservation, Communications and education, Biodiversity informatics, and Bio-prospecting.
  11. Natural History Museum of London Collection Navigator. Collections Navigator gives web access to the wide range of collections held at the Natural History Museum. It includes very general data about the science department collections. There are also lists of the manuscript collections found in the Entomology Library and the Library at Tring.
  12. Digital Taxonomy is an attempt to present a wide-ranging resource of information for biodiversity data management in the World Wide Web, and promote the effective use of computers for handling biological sofware development projects. Digital Taxonomy provides a range of links on software, hardware, methodologies, standards, data sources, and projects related to biodiversity data management, covering DELTA, taxonomic databases, ecology, morphometrics, and phylogenetic analysis software, with emphasis on the exchange of free scientific software tools (preferably those including source code), computer techniques, and Internet addresses of developers and distributors of free bioinformatics software.
  13. Universal Biological Indexer and Organizer. uBio is an initiative within the science library community to join international efforts to create and utilize a comprehensive and collaborative catalog of names of all living (and once-living) organisms. The Taxonomic Name Server (TNS) catalogs names and classifications to enable tools that can help users find information on living things using any of the names that may be related to an organism.
  14. Glasgow Taxonomic Name Server The Glasgow Name Server is an experimental tool for finding taxonomic names. Developed by Rod Page.
  15. Discover Life. Helps you to identify things, share ways to teach and study nature's wonders, use maps, report your findings, and contribute to and learn from the Web's growing encyclopedia of life. The Polistes Foundation and its partners link tools and databases to the site. Our plan is to make identification guides and valuable information on a million species freely available to everyone. We invite you to join us in a quest to reduce disease, increase food production, stop destructive species, protect endangered ones, and enjoy rather than struggle with nature.
  16. PEET (Partnerships for Enhancing Expertise in Taxonomy. This list is provided as a preliminary guide to some examples of the systematic data, databases and systematic tools currently available on the internet. It is not exhaustive, but instead is intended to provide access to some additional sites that conform to the spirit of the PEET program in making systematic/taxonomic data available in electronic format, and to the tools that make that possible.

Plants

General

  1. Systematics Servers. From the Department of Ecology and Evolutionary Biology, University of Connecticut. Very useful- lists taxonomic and phylogenetic information, phylogeny software, taxonomic information on specific groups, nomenclature, interactive identification software, collections mangagement software, bibliographies, resources for plant systematists, and floras and Atlases Online. Maintained by Kent Holsinger.
  2. Internet Directory for Botany. Maintained by R. Lampinen, Botanical Museum, Finnish Museum of Natural History. A well-organized site for a diverse assemblage of botanical information.
  3. International Organization for Plant Information.Managed by the IOPI is the Global Plant Checklist (GPC), a cooperative international project designed to help humanity manage the earth's biodiversity efficiently and sustainably. The Database has records from 6 major floristic datasets that have been imported, as well as 7 specialized family datasets. With a total of 248400 source records, the GPC now covers 201,397 different plant names belonging to 135,491 "potential taxa".
  4. Botanical Images. List compiled by D. Nickrent (Southern Illinois University).
  5. PlantSystematics.org. This site enables you to easily find images of all vascular plants and has electronic, interactive keys for certain groups. Managed by Kevin Nixon, Cornell University.
  6. The Virtual Library of Botany/Plant Biology by Scott Russell.

Taxonomic/Nomenclatural Databases

  1. International Plant Names Index. The data in the IPNI comes from three sources: the Index Kewensis (IK), the Gray Card Index (GCI) and the Australian Plant Names Index (APNI). Detailed information about these indices is available through the links above.
  2. ePIC. International Plant Information Centre. ePIC is a major project to bring together all of Kew's digitised information about plants and make it easier to search. You can use it to pinpoint information of interest in our varied collections, bibliographies, nomenclators and checklists, publications and taxonomic works, as well as links to information resources provided by external organisations.
  3. Vascular Plant Families and Genera. Organized by Kew Botanic Gardens, this is an extremely useful resource for those wishing complete lists of genera for ferns, fern allies, gymnosperms and angiosperms.
  4. Index Nominum Genericorum (Plantarum). This searchable database is a collaborative project of the International Association for Plant Taxonomy (IAPT) and the Smithsonian Institution, was initiated in 1954 as a compilation of generic names published for all organisms covered by the International Code of Botanical Nomenclature.
  5. Plants Database. The USDA PLANTS Database provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories. It includes names, plant symbols, checklists, distributional data, species abstracts, characteristics, images, plant links, references, crop information, and automated tools. PLANTS reduces costs by minimizing duplication and making information exchange possible across agencies and disciplines.
  6. Diagnostic Keys. This page is a component of PlantSystematics.Org that gives keys to angiosperms, ferns, and several other plant and animal groups (e.g. wasps).

On-Line (Digital) Herbaria

  1. SALVIAS. Synthesis and Analysis of Local Vegetation Inventories Across Scales. SALVIA is a web-based utility for compiling data on diverse aspects of plant organismal biology, including taxonomy, demography, phenology, and biogeography. It is global in scope, but coverage is currently strongly biased toward the Central and South American tropics. It is a source of the following types of data: local plant inventories, tree plots, vegetation cover plots, local species lists; compiled into a single, standardized database; herbarium specimens; samples of individual plants from herbarium databases worldwide; includes complete collection information and geocoordinates, when available; plant nomenclature.
  2. The Virtual Herbarium of the New York Botanical Garden. Only a tiny fraction of their specimens are currently online, but more are added all the time. The Vascular Plants Types Catalog, also at NY, provides specimen data and mages of all vascular plant type specimens at this institution.
  3. Australia's Virtual Herbarium. AVH provides immediate access to the wealth of data associated with the scientific plant collections held in each major Australian herbarium. Australian herbaria house over six million specimens that date from the earliest days of European exploration. They are the primary source of information of classification and distribution of plants, including algae, and fungi. In the future, the records of the AVH will be enhanced by images, descriptive text and identification tools.
  4. The Linnean Herbarium at the Swedish Museum of Natural History
  5. Type Specimens of the Dutch Herbaria
  6. The John Clayton Herbarium at the Natural History Museum in London
  7. Fairchild Tropical Garden Virtual Herbarium.
  8. TROPICOS Image Index (Missouri Botanical Garden). W3TROPICOS provides access to the Missouri Botanical Garden's VAST (VAScular Tropicos) nomenclatural database and associated authority files. .
  9. Field Museum of Natural History type photograph collection.
  10. The University of Texas at Austin Herbaria. Includes the Flora of Texas Database, the Mexican Vascular Plant Database, and the Type Database.
  11. Smithsonian Botanical Types. Department of Systematic Biology - Botany.
  12. SMASCH. Specimen Management System for California Herbaria. Jepson Herbarium.

Taxon-Specific databases

  1. Land Plants Online. This website, developed by Dan Nickrent and Karen Renzaglia (SIUC).
  2. Deep Green. The Green Plant Phylogeny Research Coordination Group.
  3. Angiosperm Phylogeny Website. Maintained by Peter Stevens at the Missouri Botanical Garden.
  4. Angiosperm Phylogeny Group. APGI (1998) and APGII (2003).
  5. The Families of Flowering Plants This site was constructed by L. Watson and M. M. Dallwitz. It contains description of families and links to illustrations.
  6. Flowering Plant Gateway at Texas A & M University Much useful information about plant families.

Bacterial and Viral Databases

  1. LBSN. List of Bacterial names with Standing in Nomenclature
  2. Bacterial Nomenclature Up-to-Date.
  3. Virus Database.
  4. American Type Culture Collection
  5. Encyclopedia of E. coli Genes and Metabolism

Animal and Protist Databases

General

  1. Animal Diversity Web Site. The University of Michigan Museum of Zoology.
  2. Zoology, Internet Resource Guide for. Zoological Record, BIOSIS, and the Zoological Society of London.
  3. TRITON Project. TRITON, the Taxonomy Resource & Index To Organism Names, is a system under development by BIOSIS UK as a mechanism for making data related to names of both fossil and recent organisms, and in particular animal nomenclatural data from the Zoological Record (ZR), available on the www. TRITON accesses a database of over a million animal names, at all taxonomic ranks, reported from the scientific literature of the last 18 years, plus some 400,000 names of other non-animal organisms provided by collaborating organizations.
  4. The Zoological Record. Published by BIOSIS (not free). Index to organism names is a free resource.
  5. Protist Databases. This index attempts to provide a sampling of "the best of the Web" on the diverse eukaryotes included within the protistan universe. Emphasis is on sites that provide direct access to scholarly information on the morphology, ultrastructure, molecular biology, taxonomy, ecology and physiology of these organisms.

Mammals

  1. Mammal Species of the World. contains the names of the 4,629 currently recognized species of mammals, in a taxonomic hierarchy that includes Order, Family, Subfamily, and Genus. Smithsonian National Museum of Natural History.

Fish

  1. American Fisheries Society.
  2. A Catalog of the Species of Fish.
  3. FishBase FishBase on the web contains practically all fish species known to science. FishBase 2004 is also available on DVD or CD-ROMs with full information on 28,500 species.
  4. DeepFin. Contains a searchable database of systematic ichthyologists with their contact information, research interests, and publications. Also contains phylogenetic trees for many groups of fishes. DeepFin is sponsored in part by the American Society of Ichthyologists and Herpetologists and is affiliated with the Tree of Life Web Project.
  5. All Catfish Species Inventory, a NSF funded project that aims to facilitate the discovery, description & dissemination of knowledge of all catfish species by a global consortium of taxonomists & systematists. Contains a listing of catfish families, identification keys, and phylogenies.
  6. Australian Museum Fish Collection. Contains interactive identification keys, as well as a searchable database of the museum's fish collections.
  7. California Academy of Sciences Ichthyology Search their collection, general catalog of fishes, or primary literature containing fishes of interest.
  8. Phylogeny of cypriniform fishes. Includes an interactive identification key, searchable database, as well as references.
  9. NISbase An International Nonindigenous Species Database Network. Allows the user to search up to 6 databases for information on invasive species. Results include information on the species' taxonomy, ecology, distribution, and collection records.

Birds

  1. BirdNet. The Ornithological Information Source.
  2. The Internet Bird Collection. The Internet Bird Collection (IBC) is a non-profit endeavour with the ultimate goal of disseminating knowledge about the world's avifauna. It is an on-line audiovisual library of footage of the world's birds that is available to the general public free of charge. While the initial aim is to post at least one video per species, the long-term objective is to eventually include several videos showing a variety of biological aspects (e.g. feeding, breeding, etc.) for every species.
  3. Birdlife International. BirdLife International is a global Partnership of conservation organisations that strives to conserve birds, their habitats and global biodiversity, working with people towards sustainability in the use of natural resources.
  4. Birdingonthe.Net.

Herps

  1. EMBL Reptile Database.
  2. Center for North American Herpetology
  3. AmphibiaWeb

Invertebrates

  1. Entomology Index of Internet Resources. A directory and search engine of insect-related resources on the Internet from Iowa State.
  2. Scarab Beetle Research.
  3. Bishop Museum Hawaiian Arthropod Checklist Database.
  4. Biogeoinformatics of Hexacorals. Biogeoinformatics of hexacorallia (corals, sea anemones, and their allies): interfacing geospatial, taxonomic, and environmental data for a group of marine invertebrates.
  5. CephBase. CephBase is a dynamic relational database-driven web site that has been online since 1998. The purpose of CephBase is to provide taxonomic data, life history, distribution, images, videos, references and scientific contact information on all living species of cephalopods (octopus, squid, cuttlefish and nautilus) in an easy to access, user-friendly manner.
  6. WWWeb Sites on Invertebrates. Provides a multitude of links to both database, and general information websites on invertebrates.
  7. PEET Bivales. Bivalves - Research, Training, Electronic Dissemination of Data
  8. Diagnostic Keys. This page is a component of PlantSystematics.Org that gives keys to angiosperms, ferns, and several other plant and animal groups (e.g. wasps).

Taxonomic Software

Key Generation/Identification Programs

  1. DELTA. DEscription Language for TAxonomy is a flexible format for encoding taxonomic descriptions for computer processing. It can be used to produce natural-language descriptions, keys, classifications, and systems for interactive identification and information retrieval.
  2. PANKEY is a package of programs that provide specialised tools for problems of diagnosis or identification in biology or medicine. The programs are designed to process descriptive data that are presented in DELTA format (above) and generate output suitable for use when preparing monographs, handbooks, floras or faunas. The same data can be used in the interactive identification system also included in the package. The programs were written by R. Pankhurst (r.pankhurst@rbge.org.uk).
  3. LucID. Lucid tools are powerful and highly flexible knowledge management software applications designed to help users with identification or diagnostic tasks. Lucid software is a special type of expert system, specifically designed for identification and diagnostic purposes, which enables expert knowledge to be "cloned" and distributed to a wide audience via CD or the Internet. The large number of functions incorporated in the software and the ability to include multi-media makes the creation and use of identification and diagnostic keys easy, effective and enjoyable. The Lucid toolkit currently includes matrix key development packages - Lucid Professional 2.1 and Lucid3 - and a dichotomous key conversion and development package - Lucid Phoenix - as well as a number of specific utilities designed to facilitate the development of identification or diagnostic keys.
  4. Biota2: The Biodiversity Database Manager. This commercial software, written by Robert K. Colwell at the Univ. Connecticut, is available through Sinauer Associates (their webpage HERE). Demonstration versions of the software can be downloaded HERE. Biota2 is a specimen-based biodiversity and collections database manager. It manages images linked to species, specimen, collection and locality records and integrates a reference manager for literatuare citations. With additional licensing, Biota2 files can be made web-accessible.
  5. Linnaeus II 2.5. Commercial software (Mac and Windows) from ETI. This interactive software facilitates biodiversity documentation and species identification. It supports the creation of taxonomic databases, optimizes the construction of easy-to-use identification keys, expedites the display and comparison of distribution patterns, and promotes the use of taxonomic data for biodiversity studies. A demonstration version can be downloaded.
  6. MEKA. Free software (Windows). From Christopher Meacham, Jepson Herbarium, Berkeley CA.
  7. PollyClave. Free. By Tim Dickinson, Royal Ontario Museum.
  8. XID. Commercial software (Mac & Windows) Richard Old, XID Services, Inc., Pullman, WA. Free demonstration version..
  9. Cladistics.com. Software for Systematics, including the tree-search parsimony-based programs NONA and TNT and the data management analysis and tree editing program WinClada.
  10. TDWG Subgroup on Biological Collection Data.  Software for Biological Collection Management - a compilation of sites.

Other

  1. TaxonScrubber. SALVIAS TaxonScrubber (version 1.2 Sept. 2004, a PC application for MS Access) is a stand-alone application for automated standardization of taxonomic names. In addition to removing spelling errors in species names, TaxonScrubber splits concatenated information into separate fields, and can be used to restructure flat-file specimen data prior to importing to a relational database. Although designed primarily for standardizing inventory data for the SALVIAS plots database, TaxonScrubber can be used whenever large numbers of taxonomic records need to be error-checked and reformated.
  2. Botanical Latin Homepage. Here you can download a program that translates your new-species descriptions into botanical Latin.
  3. Specify. Specify is a research software application, a database, and network interface for biological collections information. It manages specimen data such as descriptions of collecting locations, participants and determination histories as well as information about collections transactions such as loans, exchanges, acccessions and gifts.
  4. Tracy: a Herbarium Management System. Tracy is a system for the management of herbarium collections. It is not a huge, all inclusive database tool. Rather it was specifically designed to facilitate rapid entry of specimen data by relatively un-skilled operators and to provide mechanisms that allow complex queries of the data to be carried out with a minimum of training. 
  5. TDWG. Taxonomic Database Working Group. The International Working Group on Taxonomic Databases is a not for profit scientific and educational association, affiliated to the International Union of Biological Sciences, formed to establish international collaboration among biological database projects so as to promote the wider and more effective dissemination of information about the World's heritage of biological organisms for the benefit of the world at large.

Phylogeny

  1. Phylogenetics Resouces from UC Berkeley. A list of sites useful for scientists in phylogenetics.
  2. UCMP Phylogeny of Life. University of California Museum of Paleontology. Learn about the history and diversity of life—everything from whales to bacteria over 3.5 billion years of life's history—by browsing our extensive exhibit on the phylogeny of life on Earth. Wondering what in the world "phylogeny" means, and how it relates to paleontology? Read an introduction to phylogeny! Read tips on navigating the Phylogeny Wing. Use our Web Lift to Taxa to look for a particular group of organisms.
  3. Phylodiversity Network. A permanent home for biodiversity, systematics, phylogenetics, and bioinformatics research.
  4. Phylomatic. Automatically produces trees for lists of taxa. Other utilities compare phylogenies among communities. By Cam Webb.
  5. Phylogeny Programs. This site is maintained by Joe Felsenstein at the University of Washington, Seattle. Lists (and describes) over 100 phylogeny packages and 5 free servers. An extremely comprehensive and useful site for those who think PAUP and PHYLIP are the only packages out there!
  6. PhyloCode. A formal set of rules governing phylogenetic nomenclature. But not everyone agrees with this new idea. See The Systematics Association discussion.
 
SIUC / College of Science / Plants and Society
URL: http://www.science.siu.edu/Plant-Biology/PLB449/SystematicsLinks.html
Last updated: 07-Jul-07 / dln