Final Project Guidelines for EEOB 563 (2023)

The final project will consist of a paper and a presentation. You’ll develop them in several steps.

Step 1. Project outline on GitHub

March 23.

Prepare a one-page summary of your project. Include a short introduction, main questions, proposed methods, and source(s) of data. Create a GitHub repository for your final project; add the project outline. Email me the address of the repository and be ready to present your idea in class.

Step 2. Submit your paper for a peer review

April 20

Conduct all phylogenetic analyses

You are not limited to the software we used in class, but note that available GUI solutions (e.g., Mega, BioEdit, Geneious) are usually limited in terms of options and will not be able to run on Nova.

Write your paper.

The paper should be in the format of a typical research article with the Introduction, Methods, Results, and Discussion sections.
The length will vary depending on the project topic, but you should aim for ~5 double-spaced pages (not including figures and references).
Here is some experts’ advise on producing a first-class paper. Because the focus of the class is on phylogenetics, your phylogenetic analysis will carry most of the weight for this project. However, to get the full grade, I expect you to ask (and at least attempt to answer) some additional questions based on phylogenetic trees that you’ve inferred (e.g., correlated evolution, natural selection, testing different topologies, molecular clock analysis, etc.).

Submit your paper for a peer review.

You will be given email addresses of two other students in the class. Please send them the link to your public GitHub repository that contains both your ms. and your data (make sure to place them in their own folders). In turn, you will receive links to two repositories to review. When you receive a link, first fork the repository, then clone the forked repository on your computer and save your review inside it.

Step 3. Return written reviews to the authors

April 25

Provide a kind of review you would like to receive. If you haven’t done it already, fork the repository that contains the paper you reviewed and clone it on your computer. Add your review to the repository, push it to GitHub and submit a Pull request (use Google or ask on Slack, if you need more info!) Accept the pull requests of your reviewers and start working on the final version of your paper.

Step 3. Submit the final version of your paper

April 30 @11:59pm

Incorporate reviewers’ comments into the final version of the ms.
Submit the address of your repository on Canvas.

Step 4. Presentations

May 2, 4

Prepare a presentation of your project in the PowerPoint/Keynote format.
Plan for a 15 minutes presentation and ~5 minutes for questions and discussion. The presentation order will be determined randomly and posted on the website.

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