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

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.

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

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. This paper will be selected by the course instructors, and a link to it 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.

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.


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) P1: Morgan Napier
P2: Qiaoshan Lin
D1: Austin Spence
D2: Mike Stankov

Th Sept 8 (L)
Tu Sept 13 (P/D)
Experimental Evolution (eukaryotes) (EJ) P1: Jacob Kasper
P2: Amy LaFountain

Th Sept 15 (L)
Tu Sept 20 (P/D)
Adaptation and Speciation 1 (EJ) P1: Kevin Bieger
D1: Amy LaFountain
D2: Qiaoshan Lin

Th Sept 22 (L)
Tu Sept 27 (P/D)
Adaptation and Speciation 2 (EJ) P1: Matt Sasaki
P2: Tim Pullen
D1: Tanner Matson
D2: Jacob Kasper

Th Sept 29 (L)
Tu Oct 4 (P/D)
Adaptation and Speciation 3 (YY) P1: Tanner Matson
D1: Matt Sasaki
D2: Tim Pullen

Th Oct 6 (L)
Tu Oct 11 (P/D)
Diversification Patterns and Processes (EJ) P1: Vandana Gurung

Th Oct 13 (L)
Tu Oct 18 (P/D)
Novelty 1 (YY) P1:
D1: Kevin Bieger
D2: Vandana Gurung

Th Oct 20 (L)
Tu Oct 25 (P/D)
Novelty 2 (EJ) P1:

Th Oct 27 (L)
Tu Nov 1 (P/D)
Novelty 3 (YY) P1:

Th Nov 3 (L)
Tu Nov 8 (P/D)
Evolution in Action: Domestication and Agriculture (YY) P1:

Th Nov 10 (L)
Tu Nov 15 (P/D)
Evolution in Action: Humans as Unintentional Agents of Selection (EJ) P1: Jacob Kasper

Th Nov 17 (L)
Tu Nov 29 (P/D)
Applications of Evolutionary Thinking: Medicine (YY) P1:

Th Dec 1 (L)
Tu Dec 6 (P/D)
Applications of Evolutionary Thinking: Conservation (EJ) P1:

Th Dec 8 Wrap-up P1:
Final Exam Period Preproposal Review Panel NA NA