Difference between revisions of "EEB5449 Fall 2022"

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|- Lecture 1 <https://drive.google.com/file/d/1tZXSuS67dU0FA9dowW036gzI8nXpaa9e/view?usp=sharing slides>
 
| Th Sept. 1 (L)|| Evolution review 2 (EJ)<br>
 
| Th Sept. 1 (L)|| Evolution review 2 (EJ)<br>
  

Revision as of 14:57, 31 August 2022

EEB 5449, Fall 2022
Evolution
Meeting Time: Tuesdays and Thursdays, 11-12:15
Course meets in person in TLS171B


Description

This is an advanced course that explores the patterns and mechanisms of biological evolution (from molecules to organisms to ecosystems) and the applications of evolutionary principles in other branches of Biology and Medicine. Class periods will include discussion and critical analysis of primary literature.

Instructors

Dr. Elizabeth Jockusch
Office: Biology/Pharmacy 305B
Phone: (860) 486-4452
Office hours: by appointment

Dr. Yaowu Yuan
Office: Biology/Pharmacy 300A
Phone: (860) 486-3469
Office hours: by appointment

Announcements and Handouts

Presentation & discussion sign-up: Everyone should sign up for 1 presentation and 1 discussion slot. If you're not able to access EEBedia, let us know your preferences. There are a few extra presentation slots; feel free to switch into one, so long as it doesn't leave a day with no presentations. It's also fine to swap slots, so long as you find someone to swap with. Just make the change on EEBedia (or contact one of us if you don't have editing access.)

Discussion leaders: Please post a pdf with discussion questions on the course website prior to the discussion. In the ideal world, this would happen no later than Sunday night of the week you will lead discussion.

Editing EEBedia: To post discussion questions and links to papers, you will need to edit the EEBedia site [this page] directly. Here's some helpful information for those of you new to EEBedia.

Posting papers on EEBedia: Presenters should post a link to their chosen paper by the end of Friday the week before the presentation. Do NOT post the pdf, as this would be a copyright violation in some cases (and bloats the material stored on EEBedia). This link goes in the last column of the Topics and Readings table and should include the exproxy prefix (http://ezproxy.lib.uconn.edu/login?url=http://) followed by the web address for the paper. Be sure to test it! Include basic citation information as the displayed text.

Accessing papers from off campus: Access to some resources is through subscriptions paid for by the UConn libraries. If you try to access these resources from off-campus, you may encounter a subscription page that asks you to pay an inordinate sum. If this happens, there are two ways to authenticate yourself as a UConn user. You can either configure UConn's VPN client (see instructions here) or login with ezproxy (full instructions here); the short version of the latter is that you just need to paste the following http://ezproxy.lib.uconn.edu/login?url=http:// at the beginning of the link you are trying to access. (second http:// depends on whether your browser enters that automatically.) For both methods, you will need to login with your netid and password.

Textbook: Although no specific textbook readings are required, we highly recommend that you use one of the major Evolution textbooks as a companion for this course. It will be helpful both to refresh your knowledge of core topics and to gain additional background by reading relevant sections whenever the lecture focuses on topics you are relatively unfamiliar with. There are multiple good options:

  • Bergstrom and Dugatkin, Evolution
  • Freeman and Herron, Evolutionary Analysis
  • Futuyma, Evolution
  • Zimmer and Emlen, Evolution, Making Sense of Life

Resources

Darwin's complete writings
Classic Papers in Evolutionary Biology
Dobzhanksy-Nothing in Biology Makes Sense Except in the Light of Evolution: often quoted, less often read
Presentation feedback form

Expectations and Grading

This course has a mixed lecture/discussion format. In general, Thursdays will be used for lectures that provide an overview and background information. Tuesdays will be dedicated to student presentations and student-led discussion of readings from the primary literature.

Presentation: Each student will give 1 presentation about a recent paper from the primary literature, selected in consultation with the instructors. (In general, any paper published in the last two years will count as recent; we are also open to being convinced that an older paper is more appropriate.)All students are expected to look at these papers briefly before class and come prepared to ask questions.
Presenter responsibilities are as follows:

  • Week before the presentation: discuss choice of paper with EJ or YY (whoever is giving the associated lecture), who must approve the choice
  • Friday before the presentation: post a link to the selected paper on EEBedia
  • Monday before the presentation: meet with EJ or YY to review a draft of your presentation, and revise as necessary

More information about presentation preparation is available here.

Discussions: Each week, we will discuss in depth one recent paper from the primary literature. Two students will lead each discussion. We expect everyone to participate actively in the discussion. To help prepare for discussions, all students should write a brief (<1 page) reaction piece to the weekly readings, highlighting your thoughts about the readings, connections between them or questions raised by them. (Note: this reaction piece should *not* summarize the contents of the paper.) This is due by email to the instructor who gave the associated lecture BEFORE the beginning of discussion. Everyone should also think about the discussion questions in advance. Discussion grades will be based on a combination of discussion participation, reaction pieces, effectiveness at leading discussions, and questions during presentations.
Discussion leader responsibilities are as follows:

  • week before: discuss paper options with EJ or YY (whoever is giving the associated lecture), who must approve the choice
  • Friday before the discussion: post a link to the selected paper on EEBedia
  • Monday before the discussion: distribute list of discussion questions


Preproposal: Each student will write an NSF-style preproposal on a research project of your choice that is related to evolution. You will also give a 15 minute presentation on your project. Ideally, your project will be closely connected to your own research interests, and also integrate multiple topics covered in class. You should receive written approval for your preproposal topic no later than Thursday, Oct. 20, and are encouraged to begin discussing your ideas with us well in advance of this. The final preproposal is due by Monday Nov. 28 at 5 pm. Presentations will be scheduled for the last week of class and the final exam period. More information on the preproposal assignment is available here.

Take-home final: We will distribute a take-home final exam the last week of class. We anticipate that there will be a choice of questions, and that you will be asked to write a maximum of 2 pages applying what you have learned in this class to answer one of these questions. You may not discuss the questions or your answers with other students, but you may use resources such as your course notes, textbooks and the primary literature.

Deadlines

WeeklyReaction paper based on discussion readings
Thursday, Oct. 20Preproposal topic approved
Monday, Nov. 28, 5 pmPreproposal due
Friday, Dec. 9, 5 pmPreproposal panel reviews due
Final Exam time (TBD) Take-home final due

Course grade

Presentation10%
Discussions25%
Preproposal40% (30% written preproposal; 10% preproposal presentation)
Preproposal panel10%
Take-home final exam15%

Course Policies

Disabilities: The University of Connecticut is committed to protecting the rights of individuals with disabilities and assuring that the learning environment is accessible. If you anticipate or experience physical or academic barriers based on disability or pregnancy, please let us know immediately so that we can discuss options. Students who require accommodations should contact the Center for Students with Disabilities, Wilbur Cross Building Room 204, (860) 486-2020.

Topics and Readings

Dates Lecture Presenters Discussion Leaders Papers
Tu Aug 30 (L) Overview & Evolution review 1 (EJ)
NA NA
Th Sept. 1 (L) Evolution review 2 (EJ)

Darwin's writings all of them, for free online!

NA NA
Tu Sept. 6 (L) Evolution review 3 (YY) NA NA
Th. Sept. 8 (L)
Tu. Sept. 13 (P/D)
Evolution in action: experimental evolution (YY)

P1:
P2:

D1:

D2:

P1: author-year

P2: author-year
D: author-year

Th. Sept. 15 (L)
Tu. Sept. 20 (P/D)
Evolution in action: humans as selective agents (EJ)

P1:
P2:

D1:

D2:

P1: author-year

P2: author-year
D: author-year

Th. Sept. 22 (L)
Tu. Sept. 27 (P/D)
Adaptation in varying environments (EJ)

P1:
P2:

D1:

D2:

P1: author-year

P2: author-year
D: author-year

Th.Sept. 29 (L)
Tu. Oct. 4 (P/D)
Adaptation and speciation 2 (YY)

P1:
P2:

D1:

D2:

P1: author-year

P2: author-year
D: author-year

Th. Oct. 6 (L)
Tu. Oct. 11 (P/D)
Diversification patterns and processes (EJ)

P1:
P2:

D1:

D2:

P1: author-year

P2: author-year
D: author-year

Th. Oct. 13 (L)
Tu. Oct. 18 (P/D)
Extinction (EJ)

P1:
P2:

D1:

D2:

P1: author-year

P2: author-year
D: author-year

Th. Oct. 20 (L)
Tu. Oct. 25 (P/D)
Developmental mechanisms of phenotypic evolution (YY)

P1:
P2:

D1:

D2:

P1: author-year

P2: author-year
D: author-year

Th. Oct. 27 (L)
Tu. Nov. 1 (P/D)
Novelty (YY)

P1:
P2:

D1:

D2:

P1: author-year

P2: author-year
D: author-year

Th. Nov. 3 (L)
Tu. Nov. 8 (P/D)
Genome evolution (YY)

P1:
P2:

D1:

D2:

P1: author-year

P2: author-year
D: author-year

Th. Nov. 10 (L)
Tu. Nov. 12 (P/D)
Applications of evolutionary thinking in conservation (EJ)

P1:
P2:

D1:

D2:

P1: author-year

P2: author-year
D: author-year

Th. Nov. 17 (L)
Evolutionary Medicine (YY)

P1:
P2:

D1:

D2:

P1: author-year

P2: author-year
D: author-year

Tu. Nov. 29 Proposal Presentations

P1:
P2:
P3:
P4:
P5:

NA P1: Article

P2: Article
P3: Article
P4: Article
P5: Article

Th. Dec. 1 Proposal Presentations

P1:
P2:
P3:
P4:
P5:

NA P1: Article

P2: Article
P3: Article
P4: Article
P5: Article

Tu. Dec. 6 Proposal Presentations

P1:
P2:
P3:
P4:
P5:

NA P1: Article

P2: Article
P3: Article
P4: Article
P5: Article

Th. Dec. 8 Proposal Presentations

P1:
P2:
P3:
P4:
P5:

NA P1: Article

P2: Article
P3: Article
P4: Article
P5: Article


Final Exam period, time TBD Peer Review Panel NA NA