Due date for final paper: Monday December 3rd at 4:00 pm in my office (Rm. 4428 Biosciences) or my mailbox in the main Department of Biology office. Remember to afix your graded outline to you paper.
Tutorial Peer Evaluation Sheets | HERE |
Handout for Group Phylogenetics Exercise provided | HERE |
Guidelines for Critical Review outline | HERE |
Phylogenetics Project Peer Evaluation Sheets | HERE |
Marking Rubric for Critical Review | HERE |
Biology 440 Laboratory
|Week starting …||Activity|
|Mon. Sept. 10||Introduction, overview of lab goals, assignment to student groups, and assignment of papers for individual tutorials.|
|Mon. Sept. 17||Open Lab. Preparing for your individual presentations. Bring questions about your articles|
|Mon. Sept. 24||Student Individual Tutorials. Groups A, B and C.|
|Mon. Oct. 1||Student Individual Tutorials. Groups A, B and C.|
|Mon. Oct. 8||No labs. Please do meet to chat about your phylogenetic project possibilities.|
|Mon. Oct. 15||Student Individual Tutorials. Groups D, E, and F.|
|Mon. Oct. 22||Student Individual Tutorials. Groups D, E, and F.|
|Mon. Oct. 29||Phylogenetics practicum.
|Mon. Nov. 5||Open lab for work on group phylogenetics projects.|
|Mon. Nov. 12||Oral presentation of group phylogenetic proposals (see below). All groups. Note that the outline for your critical review is due Monday October 29th at 4:00 pm|
|Mon. Nov. 19||Presentations for Phylogenetics Group Exercise. Groups A, B and C.|
|Mon. Nov. 26||Presentations for Phylogenetics Group Exercise. Groups D, E and F.|
Individual Tutorial (worth 15% of your final grade): A key objective of this course is to illuminate major issues in speciation and macroevolution by exploring recent primary literature. We thus ask each student to read a peer-reviewed journal article (selected in the first lab period, with student names to be posted below) and present the major findings in a brief (15 minute + 5 minutes of questions) oral presentation. The subjects of these articles relate roughly to the order of topics presented in lecture. Note that you should read these articles thoroughly soon after you choose them so that you may come to the second week’s sessions armed with questions.
The presentations based on this article should include a clear summation of the context and importance of the research undertaken (i.e. how does it fit onto the broader framework of understanding biodiversity origins and overarching evolutionary patterns), a concise statement of the objectives and methods used to address them, and a succinct statement of the major findings of the paper. You will wish to read some of the antecedent papers cited by the authors, or other papers by the same authors to augment your insights. Remember to start broadly and NOT with “My paper is by …” or “The title of my paper is …” Time limits will be strictly enforced so that we do not run late (i.e. practice your presentation at least once before coming to class). Presentations should include approximately 15 PowerPoint slides.
A few pointers for the PowerPoint slides:
- Do not include an outline slide at the outset. I know that other professors will have required you to include one but I find them superfluous. Rather include a slide or two that provide the BIG PICTURE context of the kinds of knowledge deficits that the study you are presenting seeks to fill.
- Use larger font (e.g. 24 pt.) and be consistent across overheads,
- Use point form and a telegraphic prose style (i.e. do not make us read or listen to you read verbatim large tracts of text on the overheads unless it is a dramatic recitation of some giant in the field that farmers a question),
- In lists of points/items, limit the number to 5 or 6 maximum,
- Do not simply cut and paste tables – redo them so that they are legible and relate directly to the points that you most want to make AND highlight the elements that you wish the audience to understand,
- Make sure all figures and tables have legible, appropriately sized text, and ensure that figures have all relevant axes labeled,
- Use the entire slide (e.g. do not squish some small text off to one edge or side of the slide, make your figures big when possible),
- Similarly with figures, make sure that they are clear and that axes labels are legible,
- Avoid using cutesy-wootesy cartoons or figures as they imply lack of seriousness of purpose,
- Do not feel compelled to present/reproduce everything in the article – present only that which you feel best illuminates the central themes. Remember also that you can read and include additional information from other articles (either ones that you find or that are cited in your focal article), as this may provide perspective and broader context. Indeed some briefer articles can only really be understood by reading one or two others by the same author(s).
- Do not provide a literature cited slide at the end as no one will have time to read it. Include citations on the relevant, individual slides.
Click | HERE | to access a pdf version of the TUTORIAL MARKING SHEETS required for each presentation.
We provide some ideas for emphases in your presentation in parentheses after the article title but these are simply suggestions that you need not (and should not) slavishly adhere to. As we imply above, you are encouraged to 1. add to or enrich these themes, and 2. read other related articles to facilitate your understanding and presentation. Below in the second and third columns, I will paste your names after we have decided. Click on the links to go to the relevant journal web sites.
Phylogenetics Group Exercise (worth 25% of your final grade):
In the first lab period we divided you into groups of 3-5 students for purposes of this group phylogenetics project.
Overview. Easily obtained molecular data, an ever-expanding tool chest of phylogentic methods and software, and readily-accessible, high-performance personal computers and now the advent of cloud computing have revolutionized our ability to evaluate the evolutionary affinities of groups of taxa. The purpose of this exercise is to introduce some of the basic issues of molecular phylogenetics, provide practical (albeit brief) experience in phylogeny estimation, and to illustrate how phylogenetics can be used to address specific hypotheses. In consultation with me and your TA, Danielle, I would like each group to propose a hypothesis (e.g. biogeographical, adaptive, gene duplication) for a select group of organisms (e.g. HIV, ranid frogs, ratite birds) for which suitable DNA sequence exists (i.e. evolving at an appropriate rate and available in Genbank or other reliable source). Obviously if sequences exist in Genbank then there is a good chance that they have been used in a publication; however, I wish for each group to derive an evolutionary tree from first principles.
During labs in the week starting November 6th, you will as a group present your hypothesis and ideas for analysis in class. This is to be a constructive session of discussions on how you may best go about addressing your hypothesis. (Worth 5%)
Each research group will select approximately 40-50 homologous sequences (with at least one outgroup taxon) and copy each of them into a text file in FASTA format. We will then create a DNA alignment using the program CLUSTALX or other alignment program We will save this in a Phylip or nexus format text file which can then be ported into other programs for phylogenetic analysis (e.g. MrBayes, BEAST). Not to worry – I will provide more information and guidance in the lab and we will walk through some of the basic phylogenetic analyses together (i.e. we will sit down with your file at a series of scheduled meetings and work through some of these analyses). Presentations illustrating your findings will be 20 minutes (max.) in length with about 5-10 minutes of questions to follow. Preparatory work, phyloegentic analyses, and presentations should be apportioned equally among all group members (how you do this is up to you).
Schedule for Findings from the Phylogenetics Computer Lab:
Week starting … November 19 Groups A, B & C
Week starting … November 26 Groups D, E & F
Handout for Group Phylogenetics Exercise provided | HERE |
Term paper (outline worth 10%; term paper worth 30%): This will be critical review of a major topic in speciation and macroevolution that is to be chosen in consultation with me or your TAs. Begin with a paragraph broadly stating what the major issues or controversies are and how they relate to speciation or macroevolution, and then in subsequent paragraphs focus more on the specifics of your chosen topic. At the end of the Introduction clearly state the objectives of your review. For the remainder of the review explore your subject, its theoretical underpinnings, and the empirical data that support or refute your views. Use subtitles to help organize your review. Use Trends in Ecology and Evolution as your template (including for format of references). Your paper should be 10-12 pages double-spaced 12 pt. font (not including references and figures). The Literature Cited section should include at least 10-15 research articles from the primary literature.
We would like you to provide an outline of your term paper (2 pages pt. form, divided into the sections that you will use in your paper). This is due on Monday October 30th by 4:00 pm and is worth 10% of your final grade.
Due date for final paper (30% of your final grade): Monday December 3rd at 4:00 pm in my office (Rm. 4428 Biosciences). Late reports lose 5 marks (out of a total of 25) for each 24 hours (or part thereof) they are overdue. Any concerns regarding this due date must be addressed to Dr. Lougheed, not your TA, BEFORE THE PAPER IS DUE.
A note on plagiarism: Plagiarism means “… to steal from the writings or ideas of another” (Chambers Dictionary. Larousse 1996). This definition does not capture all of the subtlety of the term. Obviously plagairism encompasses directly copying from other sources (and including fellow students’ papers) without due acknowledgement (and quotation marks or other suitable demarcation) but it also includes using an idea or opinion, reproducing a figure or a table (even when altered), citing statistics without giving appropriate credit. Even paraphrasing without suitable recognition of the source or author is considered plagiarism. Consequences of plagiarism can be substantial – see the Arts & Science calendar.