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 seven to ten pages, not counting bibliography and appendices.
Select your topic carefully! Aim to analyze about eight in group 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 (with out-group) and annotated bibliography: 5%; due 4/3.
- Character list and taxon-character matrix: 5%; due 4/19
- Preliminary draft of results: 5%; due 4/26
- Final write-up: 20%; due 5/10
NOTE: The first three components receive full credit if you turn them in completed. I will be pointing out errors in them that I expect you to correct in the final write-up. If you don't correct mistakes that I indicate in your earlier drafts, I will then deduct a bunch of points. If any of the early components are not turned in on time (without some prior arrangement with me) you lose all points for it and forfeit any chance to get them back. NOTE: All preliminary work will be integrated into the final paper!
First, indicate the following:
- The name of the group of organisms you are going to be looking at. Provide both a common and scientific name E.G.: "I will be examining the phylogeny of Lutrinae - the otters."
- Your reasons for being interested in it.
- An annotated bibliography of literature on your group.
- The identity of your out-group taxon (provide both common and Scientific names) and a justification for its use. E.G.: "The outgroup Neovison vison - the American mink is chosen because it is a well-known member of Mustelinae - generally regarded as the sister taxon of Lutrinae (ref) and because it lacks ecological adaptations that would indicate the presence of many uniquely derived character states.
- A list of in-group taxa, providing both scientific and common names. E.G.: Lontra canadensis, the North American River Otter.
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:
- Background information on published research into the phylogeny of the group you have chosen.
- Information with which to justify your outgroup choice
- Morphological character information for your taxon-character matrix.
TAXON-CHARACTER MATRIX AND CHARACTER LIST: This is really two assignments in one:
- Character list: Prepare a text or doc file with a full list of the characters that you have identified and are scoring your taxa for. This should be turned in as a print out. It should have the following format:
0) Character name: (0) ancestral state; (1) derived state.
- Number your characters starting with character "0." This will make your life easier when you perform your analysis
- Use simple telegraphic descriptions, not paragraphs. There are other places for that.
So a sample of a short character list might look like this:
0) Whatchamajiggies: (0) absent; (1) present.
1) Thingamabob: (0) absent; (1) present.
2) Dorsal spine height: (0) less than two times antero-posterior length; (1) greater than or equal to two times antero-posterior length.
The purpose of this is to verify that your character list is well in hand. You are, of course, encouraged to continue to expand and modify your list as you continue your research.
- Taxon-character matrix: Prepare your matrix as you did in homework 3, only this time do it as an Excel spreadsheet in which:
- Each row represents a taxon
- Each column represents a character
- Characters should be:
- "0" for ancestral
- "1" for derived
- "?" for unscorable (either because unknown or meaningless.)
'Your name here'
- In the second line, between apostrophes, name your matrix.
- In the third line, give the number of characters and the number of taxa separated by a space.
- Use any name for taxa as long as they are fewer than 32 characters and have no spaces, quotation marks, apostrophes, or dash marks. (Keep it simple)
- The last line should be a semicolon.
- Give me a printout
- e-mail a .txt file to me.
But note: Any character that is phylogenetically uninformative (in-group taxa all have the same state, or only a single taxon shows derived state) should be eliminated.
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:
- Your output file.
- The version of your input file (i.e. your matrix) that you actually used.
- A separate .doc file in which you provide a synopsis of your results:
- the number of trees you recovered
- a picture of either:
- your single most parsimonious tree
- the strict consensus of your trees if you recovered two most parsimonious trees
- The strict and majority-rule trees if you recovered three or more trees.
- A simple list of derived character states that diagnose each clade (monophyletic group) recovered in all of your most parsimonious trees. If you obtained more than one tree, then I only want synapomorphies for the clades appearing in your consensus.
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.
- ABSTRACT: A brief telegraphic synopsis of your entire paper, emphasizing the conclusions
- INTRODUCTION: Plainly describe the evolutionary question you seek to answer. (E.g. What is the evolutionary tree of chamaeleons?) Indicate why it should be considered interesting or relevant to ongoing research. Provide a summary, based on your library search, of related published research to date.
- INCLUDED TAXA: List the ingroup taxa and briefly explain why you chose to include them. (This may be because they are particularly significant, of because of the availablility of data, for instance.) List the outgroup taxon or taxa used, and indicate why you thought they were appropriate choices.
- CHARACTERS: List and discuss each character, with all of its possible states. A typical format would be:
1) Thingamabob: (0) absent; (1) present.
From then on, you can simply refer to this as "character 1."
- METHODS: Describe how you did your analysis. Give enough information that the reader could take your matrix and replicate you result. Be sure to mention:
- The number of taxa and characters in the matrix.
- The name of the software used to compile the matrix and run the analysis (TnT 1.5beta).
- The type of computer you used.
- Which search algorithm you used (traditional).
For better or for worse, it is customary to use passive voice for this, thus you often read stuff like:
".....The phylogenetic analysis of potatoheads was performed on a Macintosh G4 computer using the heuristic search mode of TnT 1.5beta....."
- RESULTS: Synopsize your results. If you get a single most parsimonious tree, describe it. If you get a set of most parsimonious trees, describe:
- the consensus result that you prefer (say strict or majority-rule).
- a list and discussion of synapomorphies diagnosing recovered clades. Please don't just list "derived states for characters x, y, z, etc." The list should, minimally:
- Refer to taxa by name
- Refer both to character number and text description
- Should not require the reader to refer to other information to make sense
Node 10 (budgies, cockatiels)
(2) Tail feathers: (0) short -> (1) long.
(5) Personalities: (1) surly -> (0) cute.
- major points of disagreement between the trees.
- Please attach a copy of your output file as an appendix.
You can obtain a screen-shot of the TnT tree window, that can be trimmed and embedded in the text. Don't overdo this. A consensus tree and no more than two alternative trees are useful. (Indeed, the consensus will probably be enough in most cases.) If you want to make more, make them appendices.
- DISCUSSION: Now, give free reign to your creativity. Tell the reader what is interesting or significant in your result within the general context of Earth and Life history. Possibilities include:
- comparison and contrast of your result with those of other workers. Possible reasons for differences.
- an interesting history of a groups' attainment of an ecological specialization
- an interesting story of the history of its geographic dispersal.
- Maybe it resolves a previously intractible phylogenetic issue, or vindicates or refutes your decision to consider only a particular kind of data.
If your results are poorly resolved, you should try to identify why.
- Maybe you simply don't have enough data to achieve resolution
- Maybe there are one or two problematic wild-card taxa in your matrix that cause a great deal of homoplasy.
- Maybe your collection of trees cluster around two major topologies, with minor variations.
- CONCLUSIONS: Summarize your major conclusions and indicate directions for future work. What is your personal appraisal of your result? Do you trust it? If not, why not? If you had had more time and access to more information, what kind of data would you have liked to have included?
- ACKNOWLEDGEMENTS: Acknowledge any individual or institution who went out of their way to help you.
- BIBLIOGRAPHY: Your text should contain normal citations. For each citation in the text, be sure a corresponding bibliographic reference is present (and vice versa). For a standard scientific citation and bibliography format, visit my guide to the Council of Scientific Editors (CSE) bibliographic style. (Note, this format is easier to use than the ones favored by liberal arts departments. Hurray!)
Be sure to cite TNT using the following language:
Goloboff, Pablo A, James S. Farris, Kevin C Nixon. 2008, TNT, a free program for phylogenetic analysis. Cladistics 24: 774–786 doi:10.1111/j.1096-0031.2008.00217.x
- APPENDICES: Attach any ancillary information that might be useful here. This might include:
- images of your set of most parsimonious trees, if useful.
- A printout of your data matrix and output file should definitely be included as an appendix.
- Illustrations of your taxa, if possible.
- Failure to employ proper CSE-stle references in body text and bibliography.
- Incorrect taxonomic grammar. Common errors:
- Common names should be lower-case. E.G.: "human."
- Linnean binomial scientific names should be in italics with the first element capitalized and the second lower-case. E.G.: "Homo sapiens
- Padding and repetition. (Grrrrr!)
- Avoidance of proper monophyletic group names. E.G. If you are writing about sea horses and their kin, refer to them as "members of Syngnathidae" (note capitalization) or as "syngnathids" - the informal equivalent. (Note lower-case)
- Indications that you don't understand your cladograms. E.G.: The first lineage to branch in your in-group is not more closely related to the outgroup.
- And above all: apologizing for your results.
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.)
- University of Maryland: Electronic Journals
- Cambridge Journals Online
- Wiley Interscience
- Science magazine
If you are working on any kind of mammal:
- Walker, Ernest P. 1981. Walker's Mammals of the World QL703.W222 1983
- Charles G. Sibley and Jon E. Ahlquist. 1990. Phylogeny and classification of birds : a study in molecular evolution. QL696.5.S53 1990.
- Shannon J. Hackett, et al., 2008. A phylogenomic study of birds reveals their evolutionary history. Science. Vol. 320 no. 5884 pp. 1763-1768 DOI:10.1126/science.1157704
- Jacques A. Gauthier, Maureen Kearney, Jessica Anderson Maisano, Olivier Rieppel, and Adam D.B. Behlke. 2012. Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record. Bulletin of the Peabody Museum of Natural History 53(1):3-308.
- Romer, Alfred Sherwood. 1966. Vertebrate paleontology. QE841.R6 1966. (Expecially good for mammals.)
- Carroll, Robert. 1988. Vertebrate Paleontology and Evolution. Not in UMD Library, but you can borrow and photocopy Merck's copy.
The perfect source for paleontological references:
A few journals to be aware of: (Many have on-line versions)
- The Auk (for ornithology)
- Biological Journal of the Linnean Society
- Journal of Herpetology
- Journal of Morphology
- Journal of Paleontology
- Journal of Vertebrate Paleontology
- Philosophical Transactions of the Royal Society of London
- PLOS One (Public Library of Science)
- Proceedings of the National Academy of Sciences
- Systematic Biology
- Zoological Journal of the Linnean Society
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.