Difference between revisions of "EEB 5449 Fall 2018"
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− | | Th. Oct. 25 (L) <br> Tu. Oct. 30 (P/D)|| Genome Evolution (YY) ||P1: Susan McEvoy<br> P2: Kyle Drake<br> ||D1: Alex Trouern-Trend<br> D2: Matt Brandt<br> ||P1: <br> P2: <br> D: <br> | + | | Th. Oct. 25 (L) <br> Tu. Oct. 30 (P/D)|| Genome Evolution (YY) ||P1: Susan McEvoy<br> P2: Kyle Drake<br> ||D1: Alex Trouern-Trend<br> D2: Matt Brandt<br> ||P1: <br> P2: <br> D: [https://www.nature.com.ezproxy.lib.uconn.edu/articles/s41467-018-04344-z Vogel et al. 2018] <br> |
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Revision as of 16:24, 26 October 2018
EEB 5449, Fall 2018
Evolution
Meeting Time: Tuesdays and Thursdays, 9:30-10:45 am, TLS171b (Bamford room)
Contents
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 be signed up for 1 presentation and 1 discussion slot. If you're not, let us know. 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. 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.
Deadlines
Weekly | Reaction paper based on discussion readings |
Thursday, Oct. 25 | Preproposal topic approved |
Monday, Nov. 26, 5 pm | Preproposal due |
Final Exam time (TBD) | Take-home final due |
Course grade
Presentation | 10% |
Discussions | 25% |
Preproposal | 50% (40% written preproposal; 10% preproposal presentation) |
Take-home final exam | 15% |
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 |
NA | NA | |
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 |
NA | NA | |
Th. Sept. 6 (L) Tu. Sept. 11 (P/D) |
Experimental Evolution (microbes) (YY) | P: Alex Trouern-Trend |
D1: Yuan D2: Jockusch |
P: 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 |
P1: Kang et al. 2016 |
Th. Sept. 20 (L) Tu. Sept. 25 (P/D) |
Adaptation and Speciation 1 (EJ)
Funk et al. 2006 comparative analysis of ecological speciation; Kilias et al. 1980 experimental ecological speciation; STICKLEBACKS: Marques et al. 2016 stickleback lake-stream parallel divergence; Behm et al. 2010 collapse of the Enos Lake ecomorphs; Marques et al. 2017 early steps in ecomorph divergence; Stuart et al. 2017: test of lake-stream parallelism |
P1: Eliza Grames P2: Kayla Morin |
D1: Andrew Stillman D2: Amanda Hewes |
P1: Van Bocxlaer 2017 |
Th. Sept. 27 (L) Tu. Oct. 2 (P/D) Oct. 2, Presentation and Discussion in TLS 153 today |
Adaptation and Speciation 2 (YY) | P1: Charlie Brown |
D1: Mark Stukel D2: Kes Lippert |
|
Th. Oct. 4 (L) Tu. Oct. 9 (P/D) |
Diversification Patterns and Processes (EJ)
Lecture Examples: Alfaro et al. 2009 vertebrate rate shifts; Farrell 1998 beetle phytophagy; Ellis and Oakley 2016 sexual selection; Madriñan et al. 2013 paramo; Givnish et al. 2016 orchids; et al. 2012 cichlids 1; Meier et al. 2017 cichlids2 |
P1: Mark Stukel P2: Marat Vasilenko |
D1: Charlie Brown D2: Jack Phillips |
P1: Owen et al. 2017 |
Th. Oct. 11 (L) Tu. Oct. 16 (P/D) |
Novelty 1 (YY) | P1: Amanda Hewes |
D1: Lucas Myers D2: Johnny Bator |
P1: Moriyama et al. 2016 |
Th. Oct. 18 (L) Tu. Oct. 23 (P/D) |
Novelty 2 (EJ)
Drosophila: Gompel et al. 2005; Werren et al. 2010; Koshikawa et al. 2015; Heliconius: Reed et al. 2011; Heliconius Genome Consortium 2012; Wallbank et al. 2016; Bates: Bates 1862 shortened version of classic mimicry paper |
P1: Kes Lippert P2: Jack Phillips |
D1: Susan McEvoy D2: Marat Vasilenko |
P1: Jandzik et al. 2015 |
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 |
P1: P2: D: Vogel et al. 2018 |
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 D3: Katie Weeks |
P1: P2: D: |
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 |
P1: P2: D: |
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 |
P1: P2: D: |
Th. Nov. 29 (L) |
Applications of Evolutionary Thinking: Medicine (YY) | NA | NA | |
Tu. Dec. 4 | Proposal Presentations | P1: P2: P3: P4: |
NA | |
Th. Dec. 6 | Proposal Presentations | P1: P2: P3: P4: |
NA | |
Final Exam period, Tu Dec. 11, 3:30-5:30 pm (or later?) | Proposal Presentations | NA | NA |