EEB5449 Fall 2020

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EEB 5449, Fall 2020
Evolution
Meeting Time: Tuesdays and Thursdays, 11-12:15
Access information for online meetings will be sent by email


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 able to access EEBedia, let us know your preferences. 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. (In general, any paper published in the last two years will count as recent; we are also open to being convinced that an older paper is more appropriate.)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 recent 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 is due by email to the instructor who gave the associated lecture BEFORE the beginning of discussion. 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. 22, and are encouraged to begin discussing your ideas with us well in advance of this. The final preproposal is due by Monday Nov. 30 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

WeeklyReaction paper based on discussion readings
Thursday, Oct. 22Preproposal topic approved
Monday, Nov. 30, 5 pmPreproposal due
Final Exam time (TBD) Take-home final due

Course grade

Presentation10%
Discussions25%
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 Sept. 1 (L) Overview & Evolution review 1 (EJ)
Lecture 1 slides
NA NA
Th Sept. 3 (L) Evolution review 2 (EJ)
Lecture 2 slides

Darwin and Wallace 1858
Bumpus 1899 winter storm selects on sparrows
Donihue et al. 2020 hurricanes select on Anolis (lizards)
Eldakar et al. 2010 group selection in waterstriders
Darwin's writings all of them, for free online!

NA NA
Tu Sept. 8 (L) Evolution review 3 (YY)

Diversity of Life slides
Carl Woese
Crick 1958 On Protein Synthesis
Eme et al. 2017 Archaea and the origin of eukaryotes
Burki et al. 2020 The New Tree of Eukaryotes

NA NA
Th. Sept. 10 (L)
Tu. Sept. 15 (P/D)
Evolution in action: experimental evolution (YY)

Experimental Evolution

P1: Christian Polania
P2: Zachary Muscavitch

D1: Amanda Pastore

D2: Swapna Subramanian

P1: Alseth et al. 2019

P2: Herron et al. 2019
D: Beltran et al. 2020

Th. Sept. 17 (L)
Tu. Sept. 22 (P/D)
Evolution in action: humans as selective agents (EJ)

Lecture slides
Lecture examples
Winchell et al. 2016 Urban Anolis
Kern and Langerhans 2018 Urban fish
Purugganan 2019 Plant domestication review

P1: Cindy Barreto

P2: Vidya Vuruputoor

D1: Elizabeth

D2: Yaowu

P1: Caizergues et al. 2018

P2: Adu‐Yeboah, Patricia, et al. 2020
D: Zheng et al. 2020

Th. Sept. 24 (L)
Tu. Sept. 29 (P/D)
Adaptation in varying environments (EJ)

Lecture slides
Lecture examples
Dobzhansky 1943 Temporal fluctuations
Bergland et al. 2014 Seasonal SNPs
Van Valen 1973 Red Queen
Ehrlich and Raven 1964 butterfly-plant coevolution
Brockhurst et al. 2014 Red Queen Review

P1: Nick Van Gilder

P2: Anne Washington

D1: Vidya Vuruputoor

D2: Cindy Barreto

P1: Hague et al. 2020

P2: Nielsen and Kingsolver 2020
D: Kaur et al. 2019

Th. Oct. 1 (L)
Tu. Oct. 6 (P/D)
Adaptation and speciation 2 (YY) Lecture slides

P1: Hongfei Chen
P2: NA

D1: Zachary Muscavitch

D2: Kara Heilemann

P1: McGee et al. 2020

P2: NA
D: Bracewell et al. 2018

Th. Oct. 8 (L)
Tu. Oct. 13 (P/D)
Diversification patterns and processes (EJ)

Lecture slides
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; Wagner et al. 2012 cichlids 1; McGee et al. 2020 cichlids2

P1: Ben Townson

P2: Laura Bizzarri

D1: Kris Anderson

D2: Noorpreet Kaur

P1: Villastrigo et al. 2020

P2: Serrano-Serrano et al. 2017
D: Han et al. 2019

Th. Oct. 15 (L)
Tu. Oct. 20 (P/D)
Extinction (EJ)

Lecture slides

P1: Amanda Deguire

P2: Michael LaScaleia

D1: Ben Townson

D2: Anne Washington

P1: Pires et al. 2017

P2: Suggit et al. 2018
D:Lowery and Fraass 2019

Th. Oct. 22 (L)
Tu. Oct. 27 (P/D)
Developmental mechanisms of phenotypic evolution (YY)

Lecture slides

P1: Amanda Pastore

P2: NA

D1: Hongfei Chen

D2: Christian Polania

P1: Reed et al. 2020

P2: NA
D: Fuqua et al. 2020

Th. Oct. 29 (L)
Tu. Nov. 3 (P/D)
Novelty (YY)

P1: Douglas Stephan
P2: Kara Heilemann

D1: Laura Bizzarri

D2: Michael LaScaleia

P1: Article

P2: Article
D: Article

Th. Nov. 5 (L)
Tu. Nov. 10 (P/D)
Genome evolution (YY)

P1: Noorpreet Kaur
P2: Kris Anderson

D1: Grace Vaziri

D2: Douglas Stephan

P1: Article

P2: Article
D: Article

Th. Nov. 12 (L)
Tu. Nov. 17 (P/D)
Applications of evolutionary thinking in conservation (EJ)

P1: Swapna Subramanian
P2: Grace Vaziri

D1: Amanda Deguire

D2: Nick Van Gilder

P1: Article

P2: Article
D: Article

Th. Nov. 19 (L)
Evolutionary Medicine (YY)

P1: NA
P2: NA

D1: NA

D2: NA

P1: Article

P2: Article
D: Article

Tu. Dec. 1 Proposal Presentations

P1: Name
P2: Name
P3: Name
P4: Name
P5: Name

NA P1: Article

P2: Article
P3: Article
P4: Article
P5: Article

Th. Dec. 3 Proposal Presentations

P1: Name
P2: Name
P3: Name
P4: Name
P5: Name

NA P1: Article

P2: Article
P3: Article
P4: Article
P5: Article


Final Exam period, TBA Proposal Presentations

P1: Name
P2: Name
P3: Name
P4: Name
P5: Name
P6: Name
P7: Name
P8: Name
P9: Name

NA P1: Article

P2: Article
P3: Article
P4: Article
P5: Article
P6: Article
P7: Article
P8: Article
P9: Article