EEB 5449 Fall 2018

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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 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 ( 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 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
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.


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:
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) 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
P2: Gervasi et al. 2017
D: Castillo et al. 2015

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
P2: Riddle et al. 2018
D: Nwankwo et al. 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

P1: Zhang et al. 2015
D: Comeault & Matute 2018

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
P2: Jackson et al. 2017
D: Laenen et al. 2016
File:Discussion Questions.pdf

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
D: Levis et al. 2018
File:Levis et al. 2018 Questions.pdf

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
P2: Glassford et al. 2015
D: Paps et al. 2018

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: Plomion et al. 2018
P2: Barckmann et al. 2018
D: Vogel et al. 2018
Th. Nov. 1 (L)
Tu. Nov. 6 (P/D)
Evolution in Action: Humans as Unintentional Agents of Selection (EJ)

Lecture examples Winchell et al. 2016 Urban Anolis; Stuart et al. 2014 Introduced Anolis; Kern and Langerhans 2018 Urban fish; Noël et al. 2007 Salamander drift; Cheptou et al. 2008 Seed dispersal

P1: Dipanjana Dalui
P2: Lucas Myers
D1: Claire Bailey
D2: Kayla Morin
D3: Katie Weeks

P1: Carvalho et al. 2016
P2: Major et al. 2017
D: Brans et al. 2018
File:Questions for Brans et al. (2018) Discussion.pdf

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: Wang et al. 2016
P2: Wu et al. 2018
D:Gallone et al. 2016
Th. Nov. 15 (L)
Tu. Nov. 27 (P/D)
Applications of Evolutionary Thinking: Conservation (EJ)

Lecture examples Saccheri et al. 1998 Metapopulation extinction risk; Rogers and Slatkin 2018 Mammoth mutational meltdown; Palkopoulou et al. 2015 Mammoth demography; Epps et al. 2005 Bighorn sheep fragmentation; Frankham 2015 Genetic rescue meta-analysis; Gilbert-Norton et al. 2010 Corridor meta-analysis; Kelly and Phillips 2018 Quoll genetic rescue

P1: Johnny Bator 
P2: Katie Weeks
D1: Eliza Grames
D2: Laura Cunningham
P2: Hinton et al. 2018
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, Tu Dec. 11, 3:30-5:30 pm (or later?) Proposal Presentations NA NA