Introduction to Biosystematics


Zoology 575 (Winter) - MWF 11-11:50, Sci B 142

Instructor: Derek S. Sikes
Department of Biological Sciences
2500 University Drive NW
University of Calgary
Calgary, AB, Canada, T2N 1N4

email: dsikes@ucalgary.ca


 

Key Systematics Resources on the Web


Webpage to join Taxacom Listserv

Go to this webpage to subscribe to Taxacom. This will result in you getting an additional 5-10 emails a day. You needn't read them all - but some will be educational and pertinant to the course. Additionally, you will get a sense of a portion of the world's taxonomic community - how they relate, what their concerns are, etc.


Specimen Data Management

These are software packages that lack data (they are empty - you put data into them) that one might use to manage specimen data

Specify:

http://www.specifysoftware.org/Specify

Windows only, designed by University of Kansas team with NSF funding.

Specify 4.6 is a complete biological collections database management package with all of the features needed to enter, edit, query and report on collections catalog data and to manage biological collections transactions. Specify has a highly customizable interface. Screen forms can be redesigned to reflect local usage and work protocols without changes to the underlying data model. The benefits of a single data model across collections are significant for promoting consistent cataloging and provide interoperability among databases. A single data model also permits us to support diverse collections with a single software package.

 

 

Biota:

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

Macintosh and Windows, designed by Dr. Rob Colwell, University of CT for Project ALAS, ca. 7MB, Published by Sinauer Press, version 2 available.

Biota helps you manage specimen-based biodiversity and collections data by providing an easy-to-use graphical interface to a fully relational database structure. For ecologists, conservation biologists, reserve managers, and biogeographers, Biota offers efficient and flexible tools for recording and analyzing locality- or sample-based survey data, including full geographic and taxonomic information and images. For taxonomists, systematists, and collections managers, Biota offers rigorous tools for recording data and images for specimen determinations as well as for revisions and evolutionary studies. You can export species-by-character matrices in NEXUS format and virtually journal-ready Specimens Examined lists.

 

Mantis:

http://140.247.119.145/Mantis/

Macintosh and Windows, designed by Piotr Naskrecki, University of CT. ca. 2-5MB, free.

Mantis is a relational database manager designed primarily for entomologists. Other biologists may find it useful, however, especially those dealing with sound-producing animals. Among others, the program allows you to: keep track of the synonymy of species, manage specimen and collection records, print specimen and locality labels, create a library of digitized images of insects, create a library of recorded sounds, and their spectrograms and oscillograms, maintain host-guest relationships between specimens and/or species (useful for those dealing with parasites or plant associated species)


General

Including searchable online databases

Biodiversity and Biological Collections Web Server:

http://www.biocollections.org/

"Devoted to information of interest to systematists and other biologists of the organismic kind. Within these pages you will find information about specimens in biological collections, taxonomic authority files, directories of biologists, the Delta system and links for hundreds of biodiversity and collection resources."

Includes links to on-line taxonomic catalogs, some searchable. It would take you weeks to explore all the resources linked from this site- VERY worthwhile.

A few examples of searchable taxonomic catalogs you might find useful (some are linked within the Muse site):

Global Biodiversity Information Facility:

http://www.gbif.org/

An organization that is devoted to the task of standardization of taxonomic databases and their interoperability across the globe. One goal is to create portals that allow users to search numerous biological databases, each residing in different institutions, simultaneously. Results are presented in a uniform format. Provides support for a variety of taxonomic digitization efforts.

Nomenclator Zoologicus:

http://uio.mbl.edu/NomenclatorZoologicus/

Search to determine if a genus name is preoccupied or obtain bibliographic data for a name. Nomenclator Zoologicus is a continuous record of the bibliographical origins of the names of every genus and subgenus in zoology published since the 10th ed. of Linnaeus' Systema Naturae in 1758 up to 1994 in nine volumes.  Names are listed alphabetically, with a bibliographic reference to the original description of each one and an indication of the animal group to which it belongs.  There are an estimated 340,000 genera represented in the text as well as approximately 3000 supplemental corrections.

Biosis Taxonomy and Nomenclature:

http://www.biosis.org/products/zr/

Nice collection of resources from Biosis and Zoological record (e.g. Statistics on new & changed animal names reported in the Zoological Record at http://www.biosis.org/support/zr-changes/), and valuable external links

See the Index to Organism Names within this site: (http://www.biosis.org.uk/ion/search.htm), covering animals, fungi & mosses; bacteria added Jan '98; algal species added Nov '98. No vascular plants, but this is one of few (only?) on-line search engines for all Animalia. Includes all names indexed by ZR since 1978.

 

Tree of Life:

http://tolweb.org/tree/phylogeny.html

By David Maddison. Information pages on higher taxa (genus and above) written by specialists, organized into a phylogeny based on current knowledge. Many taxa lack pages, but over 3000 pages have been written so far.

Biological Survey of Canada: Terrestrial Arthropods

http://www.biology.ualberta.ca/bsc/bschome.htm

The Biological Survey of Canada (Terrestrial Arthropods) helps to coordinate scientific research among specialists on the Canadian fauna of insects, mites, and their relatives

Biologia Centrali Americana

http://www.sil.si.edu/digitalcollections/bca/

Electronic version of the out-of-print 58 volume series. Includes descriptions of over 50,000 species from Central America. Absolutely required for any taxonomic work in this region. Incredible detail and very well illustrated.


Molecular Data

National Center for Biotechnology Information (NCBI):

http://www.ncbi.nlm.nih.gov/

"Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease."

This site contains the most well-funded biological databases on the web- over 3 billion base pairs of data, all quickly searchable by many fields, including DNA sequences (BLAST searches). Most journals require authors to deposit their DNA data into GenBank. A must-know website for all systematists who work with molecules.

 


Phylogenetics

PHYCOM

http://www.yphy.org/phycom/

"A phylogenetic community" - a website with current postings on new papers, software, ideas, blogs, etc. all related to phylogenetic analyses / phyloinformatics.

TreeBase: A database of phylogenetic knowledge:

http://www.treebase.org/treebase/

"TreeBASE is a relational database of phylogenetic information sponsored by 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. We encourage biologists to submit phylogenetic data that are either published or in press, especially if these data were not fully presented in the publication due to space limitations."

A unique site- there is no other website that has a database not only of the DATA, including morphological, but the trees published from them. As of 1999 the database included 574 authors, 350 studies, 959 trees, and 10063 taxa.

CIPRES: Cyberinfrastructure for Phylogenetic Research

http://www.phylo.org/

Building the Tree of Life: A National Resource for Phyloinformatics and Computational Phylogenetics. An open collaboration funded by the National Science Foundation involving researchers (biologists, computer scientists, statisticians, and mathematicians) at thirteen institutions.

The goal of the CIPRes project is to enable large-scale phylogenetic reconstructions on a scale that will enable analyses of huge datasets containing hundreds of thousands of biomolecular sequences.

 

Phylogeny Programs:

http://evolution.genetics.washington.edu/phylip/software.html

Joe Felstenstein's compendium of over 150 software packages designed for phylogenetic analyses. Some are free to download. This is the largest listing of phylogeny programs on the web.

UC Berkely has a nice list of weblinks to phylogenetic databases and information that is quite good.


Biological Nomenclature: Codes

International Code of Botanical Nomenclature: (St. Louis Code):

http://www.bgbm.fu-berlin.de/iapt/nomenclature/code/SaintLouis/0000St.Luistitle.htm

A complete on-line version of the Code. The printed and only official version of the Code has been published as International Code of Botanical Nomenclature (St Louis Code). Regnum Vegetabile 138. Koeltz Scientific Books, Königstein. ISBN 3-904144-22

International Code of Zoological Nomenclature 4th ed.

http://www.iczn.org/iczn/index.jsp

A complete on-line version of the Zoological Code.

Phylocode

http://www.ohiou.edu/phylocode/

The Phylocode - designed to name the parts of the tree of life by explicit reference to phylogeny. The PhyloCode will go into operation in a few years, but the exact date has not yet been determined. It is designed so that it may be used concurrently with the existing codes based on rank-based nomenclature (ICBN, ICZN, etc.).

Table of nomenclatural equivalences

http://darwin.eeb.uconn.edu/systsem/table.html

This table equates terms between the botanical and zoological codes which might be worth your time to print out.

Curiosities of Biological Nomenclature

http://home.earthlink.net/~misaak/taxonomy.html

Be sure to read the Curiosities of Biological Nomenclature, which includes many of the most interesting Latin names yet published.


Miscellaneous

Translations: AltaVista Babelfish:

http://babelfish.altavista.digital.com/cgi-bin/translate?

Will translate (sometimes a little oddly) webpages or text you paste in from/to- French, Italian, Portuguese, English, German, Spanish.

Latin Word for Mac OS X

http://homepage.mac.com/spr/words.html

A program / dictionary / translator with 30,000 latin words that can be downloaded and run under the Mac OS X operating system

 

Sikes lab links (Georeferencing):

http://homepages.ucalgary.ca/~dsikes/links.htm

Various links, some duplicated above that I find valuable. In particular check out the links on Georeferencing in the lower left corner.

Glossary of Phylogenetic Terms sensu Hennig et al:

http://www.bechly.de/glossary.htm

Although the author of this glossary is critical of the current methods in phylogenetics, this list of terms is well done.