Difference between revisions of "EEB 5449 Fall 2018"

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| Th. Sept. 6 (L) <br> Tu. Sept. 11 (P/D)|| Experimental Evolution (microbes) (YY) ||P1: Alex Trouern-Trend<br> P2: <br>  ||D1: Yuan <br> D2: Jockusch<br>  ||P1: <br> P2: <br> D: <br>
| Th. Sept. 6 (L) <br> Tu. Sept. 11 (P/D)|| Experimental Evolution (microbes) (YY) ||P1: Alex Trouern-Trend<br> P2: <br>  ||D1: Yuan <br> D2: Jockusch<br>  ||P1: [http://ezproxy.lib.uconn.edu/login?url=https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.13895 Marchetti et al. 2017] <br> P2: <br> D: [https://www.nature.com/articles/s41467-018-04778-5.pdf  Clerissi et al. 2018] <br>

Revision as of 01:54, 8 September 2018

EEB 5449, Fall 2018
Meeting Time: Tuesdays and Thursdays, 9:30-10:45 am, TLS171b (Bamford room)


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.


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 in the first half of the course (through Novelty 1/Oct. 18). If you have access to EEBedia, please sign yourself up directly. If not, send Yaowu or Elizabeth some information about your preferences, and we'll sign you up. We will need to triple up for one session, so if the topic you really want is full, ask for it anyway. Those of you who are signing up now can also help yourselves to first pick (also 1 presentation & 1 discussion) for the second half of the course.

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


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

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. 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 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 will be handed in each week. 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. 25, and are encouraged to begin discussing your ideas with us well in advance of this. The final preproposal is due by Monday Nov. 26 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.


WeeklyReaction paper based on discussion readings
Thursday, Oct. 25Preproposal topic approved
Monday, Nov. 26, 5 pmPreproposal due
Final Exam time (TBD) Take-home final due

Course grade

Preproposal50% (40% written preproposal; 10% preproposal presentation)
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. 28 Overview & Evolution review 1 (EJ) NA NA
Th Aug. 30 Evolution review 2 (EJ)

Darwin and Wallace 1858
Bumpus 1899 winter storm selects on sparrows
Pugesek and Tomer 1996 reanalysis of Bumpus
Campbell-Staton et al. 2017 winter storm selects on lizards
Fishman and Saunders 2008 meiotic drive in Mimulus

Tu Sept. 4 Evolution review 3 (YY)

A NYT piece about Carl Woese: https://www.nytimes.com/2018/08/13/magazine/evolution-gene-microbiology.html
Woese & Fox, 1977 Three domains of life
Crick 1958 On protein synthesis
Hug et al. 2016 The tree of life 40 years later
Larsen et al. 2017 Pie of life
Burki 2014 Eukaryotic tree of life

Th. Sept. 6 (L)
Tu. Sept. 11 (P/D)
Experimental Evolution (microbes) (YY) P1: Alex Trouern-Trend
D1: Yuan
D2: Jockusch
P1: Marchetti et al. 2017
D: Clerissi et al. 2018
Th. Sept. 13 (L)
Tu. Sept. 18 (P/D)
Experimental Evolution (eukaryotes) (EJ) P1: Matt Brandt
P2: Andrew Stillman
D1: Jockusch
D2: Yuan
Th. Sept. 20 (L)
Tu. Sept. 25 (P/D)
Adaptation and Speciation 1 (EJ) P1: Eliza Grames
P2: Kayla Morin
D1: Andrew Stillman
D2: Amanda Hewes
Th. Sept. 27 (L)
Tu. Oct. 2 (P/D)
Oct. 2, Bamford room not available
Adaptation and Speciation 2 (YY) P1: Charlie Brown
P2: Marat Vasilenko
D1: Jack Phillips
D2: Kes Lippert
Th. Oct. 4 (L)
Tu. Oct. 9 (P/D)
Diversification Patterns and Processes (EJ) P1: Mark Stukel
D1: Charlie Brown
D2: Mark Stukel
Th. Oct. 11 (L)
Tu. Oct. 16 (P/D)
Novelty 1 (YY) P1: Amanda Hewes
D1: Lucas Myers
D2: Johnny Bator 
Th. Oct. 18 (L)
Tu. Oct. 23 (P/D)
Novelty 2 (EJ) P1: Kes Lippert
P2: Jack Phillips
D1: Susan McEvoy
D2: Marat Vasilenko
Th. Oct. 25 (L)
Tu. Oct. 30 (P/D)
Genome Evolution (YY) P1: Susan McEvoy
P2: Kyle Drake
D1: Alex Trouern-Trend
D2: Matt Brandt
Th. Nov. 1 (L)
Tu. Nov. 6 (P/D)
Evolution in Action: Humans as Unintentional Agents of Selection (EJ) P1: Dipanjana Dalui
P2: Lucas Myers
D1: Claire Bailey
D2: Kayla Morin
Th. Nov. 8 (L)
Tu. Nov. 13 (P/D)
Evolution in Action: Domestication and Agriculture (YY) P1: Claire Bailey
P2: Laura Cunningham
D1: Kyle Drake
D2: Dipanjana Dalui
Th. Nov. 15 (L)
Tu. Nov. 27 (P/D)
Applications of Evolutionary Thinking: Conservation (EJ) P1: Johnny Bator 
P2: Katie Weeks
D1: Eliza Grames
D2: Laura Cunningham
Th. Nov. 29 (L)
Applications of Evolutionary Thinking: Medicine (YY) NA NA
Tu. Dec. 4 Proposal Presentations P1:
Th. Dec. 6 Proposal Presentations P1:
Final Exam period (TBA) Proposal Presentations NA NA