EEB 5449 Fall 2016

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EEB 5449, Fall 2016
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 ( 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

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.

Presentations: Each student will give two presentations about papers from the primary literature, selected in consultation with the instructors. Each presenter should post a link to their paper on EEBedia by the Friday before the presentation. All students are expected to look at these papers briefly and come prepared to ask questions. More information about presentation preparation is available here.

Discussions: Each week, we will discuss in depth one paper from the primary literature. The discussion leaders should let the course instructors know if they have ideas for a paper or would like suggestions. A link to the paper will be posted on EEBedia by the Friday before the discussion. We expect everyone to participate actively in the discussion. Two students will guide the discussion, based on a list of questions they write and distribute in advance. 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. Discussion grades will be based on a combination of discussion participation, reaction pieces, effectiveness at leading discussions, questions during presentations.

Preproposal: Each student will write an NSF-style preproposal on a topic of your choice that is related to evolution. 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 project no later than Thursday, Oct. 25, and are encouraged to begin discussing your ideas with the course instructors well in advance of this. The final preproposal is due by Monday Nov. 28 at 5 pm.

The Preproposal is limited to four pages (not including References) and, in addition to the title and your name, should include the following 5 sub-sections (per NSF preproposal guidelines):
1. "Conceptual Framework" or "Objectives" or "Specific Aims"
2. "Rationale and Significance" or "Background"
3. "Research Question(s)" or "Hypotheses"
4. "Research Approach" or "Experimental Plan"
5. "Broader Impacts"

There is no specific requirements for the length of each sub-section. But a good balance could be something like: Section 1, 1/4-1/3 pages; Section 2: 1/2-2/3 pages; Section 3: 1/3-2/3 pages; Section 4: 1.5-2 pages (including figures); Section 5: 1/2-2/3 pages. Before writing the preproposal, you should also familiarize yourself with the Review Criteria as listed in the next section

References Cited are limited to 3 pages. You can use a standard journal style for the reference format. Fonts should be "Arial 10-11" or "Times New Roman 11-12".

Preproposal Panel Review: Each student will be assigned three preproposals to review. We will meet during the final exam period to conduct an NSF-style panel review of the full set of proposals. Here are the Review Criteria extracted from the NSF preproposal guidelines:

"When evaluating NSF proposals, reviewers will be asked to consider what the proposers want to do, why they want to do it, how they plan to do it, how they will know if they succeed, and what benefits could accrue if the project is successful. These issues apply both to the technical aspects of the proposal and the way in which the project may make broader contributions. To that end, reviewers will be asked to evaluate all proposals against two criteria:
Intellectual Merit: The Intellectual Merit criterion encompasses the potential to advance knowledge; and
Broader Impacts: The Broader Impacts criterion encompasses the potential to benefit society and contribute to the achievement of specific, desired societal outcomes.

The following elements should be considered in the review for both criteria:
1. What is the potential for the proposed activity to
a. Advance knowledge and understanding within its own field or across different fields (Intellectual Merit); and
b. Benefit society or advance desired societal outcomes (Broader Impacts)?
2. To what extent do the proposed activities suggest and explore creative, original, or potentially transformative concepts?
3. Is the plan for carrying out the proposed activities well-reasoned, well-organized, and based on a sound rationale? Does the plan incorporate a mechanism to assess success?
4. How well qualified is the individual, team, or organization to conduct the proposed activities?
5. Are there adequate resources available to the PI (either at the home organization or through collaborations) to carry out the proposed activities?

Broader impacts may be accomplished through the research itself, through the activities that are directly related to specific research projects, or through activities that are supported by, but are complementary to, the project. NSF values the advancement of scientific knowledge and activities that contribute to achievement of societally relevant outcomes. Such outcomes include, but are not limited to: full participation of women, persons with disabilities, and underrepresented minorities in science, technology, engineering, and mathematics (STEM); improved STEM education and educator development at any level; increased public scientific literacy and public engagement with science and technology; improved well-being of individuals in society; development of a diverse, globally competitive STEM workforce; increased partnerships between academia, industry, and others; improved national security; increased economic competitiveness of the United States; and enhanced infrastructure for research and education."


WeeklyReaction paper based on discussion readings
Thursday, Oct. 25Preproposal topic approved
Monday, Nov. 28, 5 pmPreproposal due
Friday, December 9Preproposal reviews due

Course grade

Panel reviews10%

Topics and Readings

Dates Lecture Presenters Discussion Leaders Papers
Tu Aug. 30 Overview NA NA
Th Sept 1 (L)
Tu Sept 6 (P/D)
Experimental Evolution (microbes) (YY)
Further Readings: Lenski interview
The Man Who Bottled Evolution
Suggested Papers: Tenaillon et al. 2016 Phillips et al., 2016 Lindsey et al., 2013 Plucain et al., 2013
P1: Morgan Napier
P2: Qiaoshan Lin
D1: Austin Spence
D2: Mike Stankov
P1: King et al. 2016
P2: Tenaillon et al. 2016
D: Maddamsetti et al. 2015
Th Sept 8 (L)
Tu Sept 13 (P/D)
Experimental Evolution (eukaryotes) (EJ)
Classic Papers: Endler 1980 Muller 1932 Review: Kawecki et al. 2012 Lecture examples: Goddard et al. 2005 Becks and Agrawal 2012
P1: Jacob Kasper
P2: Amy LaFountain
D1: Sarah Hurley
D2: Lisa Terlova
P1: Fraser et al. 2015
P2: Helliwell et al. 2015
D: Castillo et al., 2015
Th Sept 15 (L)
Tu Sept 20 (P/D)
Adaptation and Speciation 1 (EJ) P1: Kevin Bieger
P2: Genevieve Nuttall
D1: Amy LaFountain
D2: Qiaoshan Lin
P1: Comeault et al. 2015
P2: Burri et al. 2015
D: Stankowski et al. 2015
Th Sept 22 (L)
Tu Sept 27 (P/D)
Adaptation and Speciation 2 (EJ)
Classics: Coyne and Orr (1989) Grant and Grant 1992 Reviews: Ritchie 2007 Abbott et al. 2013 Lecture Examples: Brideau et al. 2006 Turner and Hare 2014 Heliconius Genome Consurtium 2012 Recent: Marques et al. 2016 Lamichhaney et al. 2015 Smith et al. 2016
P1: Matt Sasaki
P2: Tim Pullen
D1: Tanner Matson
D2: Morgan Napier
P1: Picq et al. 2015
P2: Pfennig et al. 2015
D: Smith et al. 2016
Th Sept 29 (L)
Tu Oct 4 (P/D)
Adaptation and Speciation 3 (YY)
Suggested Papers: Arnold et al. 2016Grossenbacher et al. 2014
P1: Tanner Matson
P2: Vandana Gurung
D1: Matt Sasaki
D2: Tim Pullen
P1: Filchak et al. 2000
P2: Xu et al. 2015
D: MacLeod et al. 2015
Th Oct 6 (L)
Tu Oct 11 (P/D)
Diversification Patterns and Processes (EJ) P1: Austin Spence
P2: Eileen Schaub
D1: Genevieve Nuttall
D2: Ellie Clark
D3: Jacob Kasper
P1: Blom et al. 2016
P2: Schwery et al. 2015
D:Joy 2013
Th Oct 13 (L)
Tu Oct 18 (P/D)
Novelty 1 (YY)
Suggested Papers: Stansbury & Moczek, 2014.Grossenbacher et al. 2014
P1: Sarah Hurley
P2: Ellie Clark
D1: Kevin Bieger
D2: Vandana Gurung
Th Oct 20 (L)
Tu Oct 25 (P/D)
Novelty 2 (EJ) P1: Eileen Schaub
P2: Mike Stankov
D1: Morgan Napier
Th Oct 27 (L)
Tu Nov 1 (P/D)
Novelty 3 (YY) P1: Amy LaFountain
P2: Tim Pullen
D1: Matt Sasaki
D2:Vandana Gurung
Th Nov 3 (L)
Tu Nov 8 (P/D)
Evolution in Action: Domestication and Agriculture (YY) P1: Tanner Matson
P2: Qiaoshan Lin
D1: Lisa Terlova
D2: Amy LaFountain
Th Nov 10 (L)
Tu Nov 15 (P/D)
Evolution in Action: Humans as Unintentional Agents of Selection (EJ) P1: Jacob Kasper
P2: Kevin Bieger
D1: Sarah Hurley
D2: Tim Pullen
Th Nov 17 (L)
Tu Nov 29 (P/D)
Applications of Evolutionary Thinking: Medicine (YY) P1: Lisa Terlova
P2: Vandana Gurung
D1: Qiaoshan Lin
D2: Austin Spence
Th Dec 1 (L)
Tu Dec 6 (P/D)
Applications of Evolutionary Thinking: Conservation (EJ) P1: Matt Sasaki
P2: Sarah Hurley
D1: Mike Stankov
Th Dec 8 Wrap-up P1: Lisa Terlova
P2: Morgan Napier
P3: Genevieve Nuttall
P4: Austin Spence
Final Exam Period Preproposal Review Panel NA NA