WEEK 1 WEEKS 2 - 5 WEEK 6 WEEK 7

 

WEEK 1: Introduction to Plant Taxonomy

PLANT TAXONOMY

Several of the professional societies organized for plant taxonomists and systematists now have web pages.

The International Association of Plant Taxonomists publishes the journal Taxon and sponsors a number of research projects in plant taxonomy. The IAPT web-site provides on-line access to the International Code of Botanical Nomenclature which was adopted at the 18th International Botanical Congress held in 2011 in Melbourne, Australia.

The American Society of Plant Taxonomists publishes the journal Systematic Botany. Their web-site includes information about the society, its annual meeting, the journal Systematic Botany (and a membership directory that can be queried by member's Research Interests.

The International Plant Names Index is a database with bibliographic references for more than 1.3 million species of plants.

An on-line Glossary of Roots of Botanical Names is available that will provide the meanings of many of the Latin and Greek words that serve as the roots of botanical scientific names.

If singing helps you to learn, be sure to listen to "What Are The Parts Of A Flower" (download from the AFS server or find it on YouTube). You can try seaching on "Singing Science Records" to find more of the informative nature songs (the former site exists only at the Internet Archives "Way Back Machine").

HERBARIA

Plant herbaria provide researchers with access to important collections of preserved plant materials and serve as institutional centers for much of the research conducted in plant taxonomy and systematics. To read about some of the important functions provided by herbaria, consult the short FAQ available from the UC Berkeley Herbarium, entitled "What are all those dead plants for, anyway? ". Below are links to several important herbaria that have information available at their sites on the WWW. Many of these institutions now support on-line access to their databases. The first two (OSU. and UC Berkeley) are important west coast institutions, while the other three (Missouri Botanical Garden, NY Botanical Garden, and RBG at Kew) are internationally renowned centers for research in plant systematics and taxonomy.

The importance of herbarium research to Darwin's developmnet as a scientist is recounted in a recent article: "What Henslow taught Darwin: how a herbarium helped to lay the foundations of evolutionary thinking" (Kohn et al., 2005; Nature 436: 643-645).

A listing of the world's herbaria can be found in the New York Botanic Garden's Index Herbariorum. The Intermountain Herbarium at Utah State University has provided a map showing the locations of many of the western North America herbaria.

Consortium of
Pacific Northwest
Herbaria
The Consortium of Pacific Northwest Herbaria was created in 2007 to give digital access to 57 of our region's herbaria, providing an online portal to the wealth of existing and emerging information about the flora of Pacific Northwest North America. Over 3.6 million specimen records and numerous online electronic resources are managed by the region's herbaria. Reed's collection was digitized in 2011 and the records and images have been added to the Consortium's database.
Oregon State University
Herbarium
The O.S.U. herbarium in Corvallis now serves as the main herbarium for Oregon, with more than 405,00 specimens in their collections. The herbarium includes the collection from the University of Oregon's herbarium, which was moved to Corvallis in 1993. The collection of Morton Peck, former Professor of Biology at Willamette University and author of an Oregon Flora, is now also housed in Corvallis. A new Oregon Flora is one of the projects currently underway at the O.S.U. herbarium.
University and Jepson
Herbaria, UC Berkeley
The two herbaria housed at the University of California, Berkeley (the Jepson and University Herbaria) together contain 2.2 million specimens, providing the largest collection on the west coast. The herbarium web site provides digital access to the collections through the SMASCH database (300,000 records, with text and images, are available). This site also provides access to an on-line compilation of the species descriptions in the Jepson Manual, which provides the most recent treatment of nearly 8,000 species in California.
Missouri Botanical Garden
Herbarium
The Missouri Botanical Garden Herbarium houses a collection with more than 5.8 million mounted specimens of vascular plants. Ongoing construction will enlarge the research facility and give the herbarium the capacity to eventually hold 12-15 million specimens. The Garden is an important research center, and also serves as the host institution for important botanical programs including the Center for Plant Conservation and is one of the institutions participating in the Flora of North America project, which is in the process of publishing a new flora for the 20,000 species of plants found in North America (north of Mexico).
New York Botanical Garden
Herbarium
With more than 7 million specimens in its collection, the NYBG herbarium is the fourth largest in the world, and the largest in the Western Hemisphere.
Kew Royal Botanic Garden
Herbarium
With more than 7 million specimens in its collection, the Royal Botanic Garden at Kew, England, is one of the world's largest herbaria. With 350,000 type specimens in its collection, it is also an important center for taxonomic research. The web-site at Kew has links describing both the systematic research projects of its staff and their efforts at Biodiversity Assessment in many of the world's most botanically-rich regions.

 

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WEEKS 2 - 5: Phylogeny Estimation: Phenetic and Cladistic Methods

Mustard Diversity

The plants we are using for the Phylogeny Reconstruction lab are from genetic stocks which have undergone some artificial selection for an accelerated life-cycle. The seed stocks were acquired from the Crucifer Genetics Cooperative at the Univ. of Wisconsin-Madison.

The genus Brassica is a diverse group, with many important vegetable crops derived from species in this genus. A pictorial tour of Brassica diversity can be found at the Wisconsin Fastplant's "Around the World with Brassicas" site.

Phylogenies on the Web

The Tree of Life is a web-based examination of the phylogenetic history of life on Earth. The site includes a tree that can be navigated by moving up or down the branches, taking you out to the tip and current biodiversity or deep into evolutionary history.

TreeBASE is a project being created by the Harvard University Herbaria, and the University of California, Davis that will provide for web-based access to phylogenetic data. The site will serve as an on-line repository for phylogenies and the data matrices from which they were estimated.

DEEP GREEN - the Green Plant Phylogeny Research Coordination Group (hosted by the Jepson Herbarium at UC Berkeley) is coordinating the gathering and dessemination of data that address the phylogenetic relationships among members of the plant kingdom. Their site provides access to a number of datasets (NEXUS format) that provide for phylogenetic analysis of the plant kingdom.

Cladistics on the Web

The Willi Hennig Society , which publishes the journal Cladistics, has a homepage that describes the activities of the Society and includes information about their journal.

A Brief Introduction to Cladistics can be found at the Museum of Paleontology's site at the University of California, Berkekly.

Computer Packages

Many computer programs are available for estimating phylogenies. Several WWW sites are available with information about these packages. In some cases, the packages themselves can be downloaded from these sites.

MacClade
Homepage
MacClade is no longer licensed through Sinauer and can be freely downloaded from the website.  It will not run under Mac OS 10.7 or later.
PAUP* As of 2002, PAUP (4.0) is expected to be released "soon" and will be available commercially through Sinauer Associates.  The GUI for Mac OS requires Classic, so newer OS run the program from command line.
Phylogeny
packages
Dr. Joe Felsenstein of the Dept. of Zoology at the University of Washington maintains a list that includes information on more than 100 packages for phylogeny estimation. Dr. Felsenstein has his own package available for inferring phylogenies which is called PHYLIP and which can be down loaded from the PHYLIP homepage at the University of Washington

Chromosome Data

You will need to have chromosome counts for your mustard species to complete the final assignment for the phylogeny exercise. The link below will take you to a gopher site where you can retreive these data.

Index to Plant
Chromosome Numbers
The Missouri Botanical Garden has several databases available online, including this site which allows a search of the IPCN database. By choosing the appropriate family and then genus, you will see a listing of plant taxa for which chromosome counts are available in the database.

 

Genetic Data for Molecular Systematic

PCR-RFLP results for mustard taxa Image files for each chloroplast DNA digest (also posted in lab).
NCBI/GenBank The National Center for Biotechnology Information hosts a repository for genetic data called GenBank that can be searched by taxonomic identity, by gene name, or by sequence matching (you enter your sequence of interst and it matches with sequences depositied in the database).

 

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WEEK 6: Indian Plum and the evolution of dioecy

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image 3 image 4

Oemleria cerasiformis (Indian Plum) in flower and fruit. Clockwise from upper left: male inflorescence; female inflorescence; male inflorescence with insect visitor; fruiting female.


 

Indian Plum References

Reed Library stacks Allen, GA. 1986. Flowering pattern and fruit production in the dioecious shrub Oemleria cerasiformis (Rosaceae). Canadian Journal of Botany 64: 1216-1220.
JSTOR Allen, GA, and JA Antos. 1988. Relative reproductive effort in males and females of the dioecious shrub Oemleria cerasiformis. Oecologia 76: 111-118.
JSTOR Allen, GA., and JA Antos. 1993. Sex ratio variation in the dioecious shrub Oemleria cerasiformis. American Naturalist 141: 537-553.
JSTOR Antos, JA, and GA Allen. 1990. A comparison of reproductive effort in the dioecious shrub Oemleria cerasiformis using nitrogen, energy and biomass as currencies. American Midland Naturalist. 124: 254-262.
AFS Courses Server Antos, JA, and GA Allen. 1990. Habitat relationships of the Pacific Coast shrub Oemleria cerasiformis (Rosaceae). Madroño 37: 249-260.
JSTOR Antos, JA, and GA Allen. 1994. Biomass allocation among reproductive structures in the dioecious shrub Oemleria cerasiformis - a functional interpretation. Journal of Ecology 82: 21-29.
JSTOR Antos, JA, and GA Allen. 1999. Patterns of reproductive effort in male and female shrubs of Oemleria cerasiformis: a 6-year study. Journal of Ecology 87:77-84.

 

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WEEK 7: Fern Reproductive Biology


 

Water Sprite
Homepage
Researchers at the University of Tennessee have been working to establish the fern species Ceratopteris richardii, the water sprite, as a new model-organism for teaching and research. They have established a website that provides a great deal of information about the biology of the water sprite, methods for its culture, and the kinds of research projects that are possible with this species.

 

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