Systematics and Comparative Biology


Biol 615 (Fall) - MWF 9:15-10:15, Museum Classroom

Instructor: Derek S. Sikes
Associate Professor of Entomology
University of Alaska Museum
907 Yukon Drive
Fairbanks, AK 99775-6960

email: dssikes@alaska.edu


 

Some Key Systematics Resources on the Web

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. These packages are to be installed and maintained on one's own computers - as such they differ from Arctos which exists online only (akin to gmail) and therefore all security and maintenance issues are handled by Arctos developers.

Specify:

http://specifysoftware.org/

Specify (and Arctos) is aimed at museum specimen management, a different target audience than Biota and Mantis listed below.

For a comparison of features with Arctos see this page.

Biota:

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

Macintosh and Windows, designed by Dr. Rob Colwell, University of CT for Project ALAS, ca. 7MB, formerly Published by Sinauer Press, version 3 now available free of charge.

Biota helps 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://140.247.119.138/mantis/

Macintosh and Windows, designed by Piotr Naskrecki, Museum of Comparative Zoology. ca. 2-5MB, free.

Mantis is a relational database manager designed primarily for systematic 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

A few examples of searchable taxonomic catalogs you might find useful. Simply Google the names which is a more reliable method of finding websites than relying on URLs (which often go bad.)

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.

Zoological Record:

http://thomsonreuters.com/products_services/science/science_products/a-z/zoological_record/

Zoological Record is the world's oldest continuing database of animal biology. It is considered the world's leading taxonomic reference, and with coverage back to 1864, has long acted as the world's unofficial register of animal names. The broad scope of coverage ranges from biodiversity and the environment to taxonomy and veterinary sciences. 75,000 records added every year; available with up to 3.5 million records to 1864.

See the Index to Organism Names within this site: (http://www.organismnames.com/), 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.

ZooBank:

http://zoobank.org/About

ZooBank is the official registry of Zoological Nomenclature, according to the International Commission on Zoological Nomenclature (ICZN).

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 10,000 pages have been written so far.

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

TreeBase: A database of phylogenetic knowledge:

http://www.treebase.org/treebase-web/home.html

"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 10,063 taxa. As of December 2011, TreeBASE contains 2,946 publications written by 6,106 different authors. These studies analyzed 5,717 matrices and resulted in 8,462 trees with 465,762 taxon labels that mapped to 82,043 distinct 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 was 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 392 software packages designed for phylogenetic analyses. Some are free to download. This is the largest listing of phylogeny programs on the web.


Biological Nomenclature: Codes

International Code of Botanical Nomenclature: (Vienna Code):

http://ibot.sav.sk/icbn/main.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 (Vienna Code). Regnum Vegetabile 146. A.R.G. Gantner Verlag KG. ISBN 3-906166-48-1

International Code of Zoological Nomenclature 4th ed.

http://www.nhm.ac.uk/hosted-sites/iczn/code/

A complete on-line version of the Zoological Code.

Phylocode

http://www.ohio.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://www.curioustaxonomy.net/

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