Project Assignment

Perform a phylogenetic analysis: of the evolutionary history of a group of vertebrates of your choosing, using the analytic techniques that you have learned in class plus digital methods that we will cover soon, and present your results as a scientific paper. Your write-up should be roughly six to eight pages, not counting bibliography and appendices.

Select your topic carefully! Aim to analyze about eight taxa. Be sure to select an appropriate outgroup. It is good to have at least three times as many characters as taxa. Select a group for which you can score characters easily, either from information you get in the library or on the web, or from physical examination of specimens. (E.G., mammals tend to be hard to score without looking at internal anatomy whereas reptiles and fish have many unambiguous external structures that allow easy scoring.) Be sure to consult with me about your selection and research.

GRADING: To make sure everyone is on track, we will break this up into a series of steps, each of which will be graded separately:

TAXON LIST AND ANNOTATED BIBLIOGRAPHY: A two-part assignment:

First, indicate the following:

Owing to the nature of the project, which is a cross between a proof-of-concept type lab exercise and a research paper, we relax the normal restrictions on the kind of resources you may use to allow sources like reputable on-line resources and field guides. You will need to obtain three general types of information from your references, however:

TAXON-CHARACTER MATRIX AND CHARACTER LIST: This is really two assignments in one:

PRELIMINARY DRAFT OF RESULTS: You will perform your analysis using T.N.T., "T.N.T." (aka "the New Technologies"). You will definitely want the menu-interface PC version of the application. (An intimidating command-line only version exists for the Mac.) This can be downloaded for free from http://www.lillo.org.ar/phylogeny/tnt/. Scroll to the "download" section and click "Win (menu interface)." The licensing agreement that appears when you first use it merely requires that you not disseminate your copy and that you cite it in any publication that may result from your research using it. On the same web page, you can also download a PowerPoint tutorial from the link in the "documentation" paragraph. This is intended for high-level users of phylogenetic software, but some of it will be useful to you. Merck has written a simple guide to T.N.T. that is available here.

Turn in the following by e-mail:

Don't overdo this. It is a verification of your ability to use the software.

THE FINAL WRITE-UP: SCOPE: The text of your research should be roughly six to ten unpadded double-spaced pages. This does not count figures and appendices. I suggest you take the format given below as a default.

FORMAT: This template is a good general pattern. You may modify it in any way you like as the needs of your particular subject matter and analysis dictate, however if you are puzzled about how to organize your write-up, use this as a default. It shouldn't steer you wrong.

Typically, the results of a phylogenetic analysis are presented with trim, spare prose. People generally do not sit down and read these things from start to finish. They want to be able quickly to find the information they need. THEREFORE, DO NOT PAD! Better that your write-up be slightly short.

Things that will cost you points in the final paper:

Useful Research References for HONR219d projects

The following references are likely to be useful to your project research. Remember, with each one you should be seeking to build up your bibliography. General information on evolutionary history:

Access to on-line journals: (For these, be sure to use a UMD account to take advantage of UMD library on-line subscriptions.)

If you are working on any kind of mammal:

If you are working on any kind of bird:

If you are working on any kind of squamate:

For Paleontology background: (Note: Both written from Linnean perspective.)

The perfect source for paleontological references:

A few journals to be aware of: (Many have on-line versions)

Note: Amateur resources like Wikipedia are a very good place to START your literature search, but they won't fly in your bibliography. All bibliographic references must be to print material, the on-line versions of print journals, and the web sites of qualified experts and expert organizations.