Difference between revisions of "EEB 5449 Fall 2018"

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<span style="font-size: x-large">EEB 5449, Fall 2018</span><br>
 
<span style="font-size: x-large">EEB 5449, Fall 2018</span><br>
 
<span style="font-size: large">''Evolution''</span><br>
 
<span style="font-size: large">''Evolution''</span><br>
<span style="font-size: small">'''Meeting Time: Tuesdays and Thursdays, 9:30-10:45 am, XXXXXX'''<br>
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<span style="font-size: small">'''Meeting Time: Tuesdays and Thursdays, 9:30-10:45 am, TLS171b (Bamford room)'''<br>
  
 
==Description==
 
==Description==
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==Announcements and Handouts==
 
==Announcements and Handouts==
<b>Presentation & discussion sign-up</b>: 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 directlyIf 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 anywayThose 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.<br>
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<b>Presentation & discussion sign-up</b>: Everyone should be signed up for 1 presentation and 1 discussion slot.  If you're not, let us knowThere 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 withJust make the change on EEBedia (or contact one of us if you don't have editing access.)<br>
 
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<br>
 
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<b>Accessing papers from off campus</b>: 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 ([http://remoteaccess.uconn.edu/vpn-overview/connect-via-vpn-client-2/ see instructions here]) or login with ezproxy ([http://classguides.lib.uconn.edu/EZProxy full instructions here]); the short version of the latter is that you just need to paste the following <b><nowiki>http://ezproxy.lib.uconn.edu/login?url=http://</nowiki></b> 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.<br>
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<b>Accessing papers from off campus</b>: 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 ([http://remoteaccess.uconn.edu/vpn-overview/connect-via-vpn-client-2/ see instructions here]) or login with ezproxy ([https://helpcenter.uconn.edu/2017/11/15/using-ezproxy/ full instructions here]); the short version of the latter is that you just need to paste the following <b><nowiki>http://ezproxy.lib.uconn.edu/login?url=http://</nowiki></b> 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.<br>
 
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<br>
  
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[http://darwin-online.org.uk Darwin's complete writings]<br>
 
[http://darwin-online.org.uk Darwin's complete writings]<br>
 
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Classic_Works_in_Evolutionary_Biology—The_List_With_Links Classic Papers in Evolutionary Biology]<br>
 
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Classic_Works_in_Evolutionary_Biology—The_List_With_Links Classic Papers in Evolutionary Biology]<br>
[http://ezproxy.lib.uconn.edu/login?url=http://http://www.jstor.org/stable/4444260 Dobzhanksy-Nothing in Biology Makes Sense Except in the Light of Evolution]: often quoted, less often read<br>
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[http://ezproxy.lib.uconn.edu/login?url=http://www.jstor.org/stable/4444260 Dobzhanksy-Nothing in Biology Makes Sense Except in the Light of Evolution]: often quoted, less often read<br>
 +
[https://docs.google.com/forms/d/e/1FAIpQLSe8Y-FpE4N25mZnnYurc1tCHs17jxFOSsUfCi0ew4PcYkXxew/viewform Presentation feedback form]
 
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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.<br><br>   
 
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.<br><br>   
  
<b>Presentations</b>: Each student will give XXX 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 [https://drive.google.com/open?id=0B-wU9Sg5Mrvhdm5DZkRpN0poNjA here]. <br><br>
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<b>Presentation</b>: Each student will give 1 presentation about a recent paper from the primary literature, selected in consultation with the instructors. <u>All students</u> are expected to look at these papers briefly before class and come prepared to ask questions.<br>
 +
<u>Presenter responsibilities are as follows</u>:
 +
*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
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More information about presentation preparation is available [https://drive.google.com/open?id=0B-wU9Sg5Mrvhdm5DZkRpN0poNjA here].<br><br>
  
<b>Discussions</b>:  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.<br><br>
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<b>Discussions</b>:  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.<br>
 
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<u>Discussion leader responsibilities are as follows</u>:
<b>Preproposal</b>: 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.<br>
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*week before: discuss paper options with EJ or YY (whoever is giving the associated lecture), who must approve the choice
 
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*Friday before the discussion: post a link to the selected paper on EEBedia
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):<br>
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*Monday before the discussion: distribute list of discussion questions
1. "Conceptual Framework" or "Objectives" or "Specific Aims"<br>
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<br>
2. "Rationale and Significance" or "Background"<br>
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3. "Research Question(s)" or "Hypotheses"<br>
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4. "Research Approach" or "Experimental Plan"<br>
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5. "Broader Impacts"<br>
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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<br> 
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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".<br>
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<b>Preproposal Panel Review</b>: 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: <br>
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"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:<br>
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<b>Preproposal</b>: 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 [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB5449_Preproposal here].<br><br>
 '''Intellectual Merit:''' The Intellectual Merit criterion encompasses the potential to advance knowledge; and<br>
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 '''Broader Impacts:''' The Broader Impacts criterion encompasses the potential to benefit society and contribute to the achievement of specific, desired societal outcomes.<br>
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The following elements should be considered in the review for both criteria:<br>
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<b>Take-home final</b>: 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. <br><br>
1. What is the potential for the proposed activity to<br>
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a. Advance knowledge and understanding within its own field or across different fields (Intellectual Merit); and<br>
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b. Benefit society or advance desired societal outcomes (Broader Impacts)?<br>
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2. To what extent do the proposed activities suggest and explore creative, original, or potentially transformative concepts?<br>
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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?<br>
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4. How well qualified is the individual, team, or organization to conduct the proposed activities?<br>
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5. Are there adequate resources available to the PI (either at the home organization or through collaborations) to carry out the proposed activities?<br><br>
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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,
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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."
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===Deadlines===
 
===Deadlines===
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</tr>
 
</tr>
 
<tr>
 
<tr>
<td>Monday, Nov. 28, 5 pm</td><td>Preproposal due</td>
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<td>Monday, Nov. 26, 5 pm</td><td>Preproposal due</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
<td>Friday, December 9</td><td>Preproposal reviews due</td>
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<td>Final Exam time (TBD) </td><td>Take-home final due</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
 
</table>
 
</table>
<br>
 
 
===Course grade===
 
===Course grade===
 
<table>
 
<table>
 
<tr>
 
<tr>
<td>Presentation</td><td>15%</td>
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<td>Presentation</td><td>10%</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
<td>Discussions</td><td>20%</td>
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<td>Discussions</td><td>25%</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
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</tr>
 
</tr>
 
<tr>
 
<tr>
<td>Take-home final exam question</td><td>15%</td>
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<td>Take-home final exam</td><td>15%</td>
 
</tr>
 
</tr>
 
</table>
 
</table>
<br>
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==Course Policies==
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<b>Disabilities</b>: 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 [http://csd.uconn.edu/ Center for Students with Disabilities], Wilbur Cross Building Room 204, (860) 486-2020.<br><br>
  
 
==Topics and Readings==
 
==Topics and Readings==
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|-  
 
|-  
| Tu Aug. 28 || Overview || NA || NA ||<br>
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| Tu Aug. 28 || Overview & Evolution review 1 (EJ)|| NA || NA ||<br>
  
 
|-  
 
|-  
| Th Aug. 30 (L) <br> Tu Sept. 4 (P/D) || Overview || NA || NA ||<br>
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| Th Aug. 30 || Evolution review 2 (EJ)<br>
 +
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/j.1096-3642.1858.tb02500.x Darwin and Wallace 1858]<br>
 +
[http://ezproxy.lib.uconn.edu/login?url=https://www.jstor.org/stable/1626985 Bumpus 1899] winter storm selects on sparrows<br>
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1007/BF01237725 Pugesek and Tomer 1996] reanalysis of Bumpus<br>
 +
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1126/science.aam5512 Campbell-Staton et al. 2017] winter storm selects on lizards<br>
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1126/science.1161406 Fishman and Saunders 2008] meiotic drive in <i>Mimulus</i><br>
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|| NA || NA ||<br>
  
 
|-  
 
|-  
| Th. Sept. 6 (L) <br> Tu. Sept. 11|| Overview || NA || NA ||<br>
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|Tu Sept. 4 || Evolution review 3 (YY) <br>
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A NYT piece about Carl Woese: https://www.nytimes.com/2018/08/13/magazine/evolution-gene-microbiology.html <br>
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[http://ezproxy.lib.uconn.edu/login?url=http://www.pnas.org/content/74/11/5088 Woese & Fox, 1977] Three domains of life<br>
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[https://profiles.nlm.nih.gov/ps/access/scbbzy.pdf Crick 1958] On protein synthesis<br>
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[http://ezproxy.lib.uconn.edu/login?url=https://www.nature.com/articles/nmicrobiol201648 Hug et al. 2016] The tree of life 40 years later<br>
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[http://ezproxy.lib.uconn.edu/login?url=https://www.journals.uchicago.edu/doi/10.1086/693564 Larsen et al. 2017] Pie of life <br>
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[http://ezproxy.lib.uconn.edu/login?url=http://cshperspectives.cshlp.org/content/6/5/a016147 Burki 2014] Eukaryotic tree of life <br>
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|| NA || NA ||<br>
  
 
|-  
 
|-  
| Th. Sept. 13 (L) <br>Tu. Sept. 18 || Overview || NA || NA ||<br>
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| Th. Sept. 6 (L) <br> Tu. Sept. 11 (P/D)|| Experimental Evolution (microbes) (YY) ||P: Alex Trouern-Trend<br>  ||D1: Yuan <br> D2: Jockusch<br>  ||P: [http://ezproxy.lib.uconn.edu/login?url=https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.13895 Marchetti et al. 2017] <br>  D: [https://www.nature.com/articles/s41467-018-04778-5.pdf  Clerissi et al. 2018] <br>
  
 
|-  
 
|-  
| Th. Sept. 20 (L) <br> Tu. Sept. 25|| Overview || NA || NA ||<br>
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| Th. Sept. 13 (L) <br>Tu. Sept. 18 (P/D)|| Experimental Evolution (eukaryotes) (EJ) ||P1: Matt Brandt<br> P2: Andrew Stillman<br>  ||D1: Jockusch<br> D2: Yuan<br>  ||
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P1:  [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1186/s12864-016-2556-y Kang et al. 2016]<br>
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P2:  [http://ezproxy.lib.uconn.edu/login?url=https://www.nature.com/articles/ncomms14691.pdf  Gervasi et al. 2017] <br> 
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D: [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/evo.12815 Castillo et al. 2015]<br>
  
 
|-  
 
|-  
| Th. Sept. 27 (L) <br>|| Overview || NA || NA ||<br>
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| Th. Sept. 20 (L) <br> Tu. Sept. 25 (P/D)|| Adaptation and Speciation 1 (EJ)
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1073/pnas.0508653103 Funk et al. 2006] comparative analysis of ecological speciation;
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/j.1558-5646.1980.tb04012.x Kilias et al. 1980] experimental ecological speciation; STICKLEBACKS:
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1371/journal.pgen.1005887 Marques et al. 2016] stickleback lake-stream parallel divergence;
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1086/648559 Behm et al. 2010] collapse of the Enos Lake ecomorphs;
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/mec.13774 Marques et al. 2017] early steps in ecomorph divergence;
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[http://redpath-staff.mcgill.ca/hendry/Stuart2017NEE1,0158.pdf Stuart et al. 2017]: test of lake-stream parallelism
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||P1: Eliza Grames <br> P2: Kayla Morin<br>  ||D1: Andrew Stillman<br> D2: Amanda Hewes<br>  ||
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P1: [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1098/rspb.2017.1494 Van Bocxlaer 2017]<br>
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P2: [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/nature26136 Riddle et al. 2018]<br>
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D: [http://ezproxy.lib.uconn.edu/login?url=https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.3673 Nwankwo et al. 2017]<br>
  
 
|-  
 
|-  
| Tu. Oct. 2 || Overview || NA || NA ||<br>
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| Th. Sept. 27 (L) <br> Tu. Oct. 2 (P/D) <br> <b>Oct. 2, Presentation and Discussion in TLS 153 today</b>|| Adaptation and Speciation 2 (YY) ||P1: Charlie Brown<br> ||D1: Mark Stukel<br> D2: Kes Lippert<br>  ||
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P1: [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1098/rspb.2015.1649 Zhang et al. 2015]<br>
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D: [http://ezproxy.lib.uconn.edu/login?url=http://www.pnas.org/content/pnas/early/2018/09/11/1809685115.full.pdf  Comeault & Matute 2018] <br>
  
 
|-  
 
|-  
| Th. Oct. 4 (L) <br>|| Overview || NA || NA ||<br>
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| Th. Oct. 4 (L) <br> Tu. Oct. 9 (P/D)|| Diversification Patterns and Processes (EJ)
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'''Lecture Examples''': [http://ezproxy.lib.uconn.edu/login?url=http://www.pnas.org/content/106/32/13410.full Alfaro et al. 2009] vertebrate rate shifts;
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[http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/281/5376/555.full Farrell 1998] beetle phytophagy;
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1016/j.cub.2016.05.043 Ellis and Oakley 2016] sexual selection;
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[https://doi-org.ezproxy.lib.uconn.edu/10.3389/fgene.2013.00192 Madriñan et al. 2013] paramo;
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1098/rspb.2015.1553 Givnish et al. 2016] orchids;
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[https://doi-org.ezproxy.lib.uconn.edu/10.1038/nature11144Wagner et al. 2012] cichlids 1;
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/ncomms14363 Meier et al. 2017] cichlids2
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||P1: Mark Stukel<br> P2: Marat Vasilenko<br>  ||D1: Charlie Brown<br> D2: Jack Phillips<br>  ||
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P1: [http://ezproxy.lib.uconn.edu/login?url=https://academic.oup.com/sysbio/article/66/4/569/2957003 Owen et al. 2017] <br>
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P2: [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/evo.13212 Jackson et al. 2017]<br>
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D: [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/nph.13835 Laenen et al. 2016]<br> [[File:Discussion_Questions.pdf]]
  
 
|-  
 
|-  
| Tu. Oct. 9 || Overview || NA || NA ||<br>
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| Th. Oct. 11 (L) <br> Tu. Oct. 16 (P/D)|| Novelty 1 (YY) ||P1: Amanda Hewes<br> ||D1: Lucas Myers<br> D2: Johnny Bator <br> ||
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P1: [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/ncomms10397 Moriyama et al. 2016]<br>  
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D: [http://labs.bio.unc.edu/pfennig/LabSite/Research_files/2018_Nature_Ecology_%26_Evolution.pdf Levis et al. 2018]<br> [[File:Levis_et_al._2018_Questions.pdf]]
  
 
|-  
 
|-  
| Th. Oct. 11 (L) <br>|| Overview || NA || NA ||<br>
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| Th. Oct. 18 (L) <br> Tu. Oct. 23 (P/D)|| Novelty 2 (EJ)
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'''<i>Drosophila</i>''': [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/nature03235 Gompel et al. 2005];
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/nature08896 Werren et al. 2010];
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1073/pnas.1509022112 Koshikawa et al. 2015];
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'''<i>Heliconius</i>''': [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1126/science.1208227 Reed et al. 2011];
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/nature11041 Heliconius Genome Consortium 2012];
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1371/journal.pbio.1002353 Wallbank et al. 2016];
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'''Bates''': [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/j.1095-8312.1981.tb01842.x Bates 1862] shortened version of classic mimicry paper
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||P1: Kes Lippert<br> P2: Jack Phillips<br>  ||D1: Susan McEvoy<br> D2: Marat Vasilenko<br>  ||
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P1: [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/nature14000 Jandzik et al. 2015]<br>
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P2: [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1016/j.devcel.2015.08.005 Glassford et al. 2015]<br>
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D: [http://www.nature.com.ezproxy.lib.uconn.edu/articles/s41467-018-04136-5 Paps et al. 2018]<br>
  
 
|-  
 
|-  
| Tu. Oct. 16 || Overview || NA || NA ||<br>
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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: [http://www.nature.com.ezproxy.lib.uconn.edu/articles/s41477-018-0172-3 Plomion et al. 2018]<br> P2: [https://academic.oup.com/nar/article/46/18/9524/5078797 Barckmann et al. 2018]<br> D: [https://www.nature.com/articles/s41467-018-04344-z Vogel et al. 2018] <br>
  
 
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| Th. Oct. 18 (L) <br>|| Overview || NA || NA ||<br>
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| Th. Nov. 1 (L) <br> Tu. Nov. 6 (P/D)|| Evolution in Action: Humans as Unintentional Agents of Selection (EJ)  
 
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'''Lecture examples'''
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/evo.12925 Winchell et al. 2016] Urban ''Anolis'';
| Tu. Oct. 23 || Overview || NA || NA ||<br>
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1126/science.1257008 Stuart et al. 2014] Introduced ''Anolis'';
 
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/gcb.14115 Kern and Langerhans 2018] Urban fish;
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1007/s10592-006-9202-1 Noël et al. 2007] Salamander drift;
| Th. Oct. 25 (L) <br>|| Overview || NA || NA ||<br>
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1073/pnas.0708446105 Cheptou et al. 2008] Seed dispersal
 
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||P1: Dipanjana Dalui<br> P2: Lucas Myers<br>  ||D1: Claire Bailey<br> D2: Kayla Morin<br> D3: Katie Weeks <br> ||
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P1: [http://ezproxy.lib.uconn.edu/login?url=https://www.nature.com/articles/srep31957 Carvalho et al. 2016] <br>
| Tu. Oct. 30 || Overview || NA || NA ||<br>
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P2: [http://ezproxy.lib.uconn.edu/login?url=https://onlinelibrary.wiley.com/doi/full/10.1111/eva.12584 Major et al. 2017]<br>  
 
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D: [http://rspb.royalsocietypublishing.org.ezproxy.lib.uconn.edu/content/285/1883/20180169 Brans et al. 2018]<br>[[File:Questions_for_Brans_et_al._(2018)_Discussion.pdf]] <br>
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| Th. Nov. 1 (L) <br>|| Overview || NA || NA ||<br>
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| Tu. Nov. 6 || Overview || NA || NA ||<br>
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| Th. Nov. 8 (L) <br>|| Overview || NA || NA ||<br>
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| Tu. Nov. 13 || Overview || NA || NA ||<br>
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| Th. Nov. 15 (L) <br>|| Overview || NA || NA ||<br>
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| Tu. Nov. 20 || THANKSGIVING BREAK || NA || NA ||<br>
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| Th. Nov. 22 || THANKSGIVING || NA || NA ||<br>
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| Tu. Nov. 27 || Overview || NA || NA ||<br>
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| Th. Nov. 29 (L) <br>|| Overview || NA || NA ||<br>
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| Tu. Dec. 4 || Overview || NA || NA ||<br>
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| Th. Dec. 6 (L) <br>|| Overview || NA || NA ||<br>
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| Th Sept 1 (L) <br> Tu Sept 6 (P/D) || Experimental Evolution (microbes) (YY)<br> '''Further Readings:''' [https://evolution-institute.org/article/evolutionary-biologys-master-craftsman-an-interview-with-richard-lenski/ Lenski interview]<br>[http://science.sciencemag.org/content/342/6160/790 The Man Who Bottled Evolution] <br> '''Suggested Papers:''' [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v536/n7615/pdf/nature18959.pdf Tenaillon et al. 2016] [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/evo.12849/epdf Phillips et al., 2016] [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v494/n7438/pdf/nature11879.pdf Lindsey et al., 2013] [http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/sci/343/6177/1366.full.pdf Plucain et al., 2013]|| P1:  Morgan Napier<br> P2: Qiaoshan Lin ||  D1:  Austin Spence<br> D2: Mike Stankov|| P1: [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/ismej/journal/v10/n8/full/ismej2015259a.html King et al. 2016] <br> P2: [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v536/n7615/pdf/nature18959.pdf Tenaillon et al. 2016] <br> D: [http://ezproxy.lib.uconn.edu/login?url=http://www.genetics.org/content/genetics/200/2/619.full.pdf Maddamsetti et al. 2015]
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| Th Sept 8 (L) <br> Tu Sept 13 (P/D) || Experimental Evolution (eukaryotes) (EJ)<br><b>Classic Papers:</b> [http://ezproxy.lib.uconn.edu/login?url=https://www.jstor.org/stable/2408316 Endler 1980] [http://ezproxy.lib.uconn.edu/login?url=https://www.jstor.org/stable/2456922 Muller 1932] <b>Review:</b> [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencedirect.com/science/article/pii/S0169534712001425 Kawecki et al. 2012] <b>Lecture examples: </b>[http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v434/n7033/full/nature03405.html Goddard et al. 2005] [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001317 Becks and Agrawal 2012]|| P1:  Jacob Kasper <br> P2: Amy LaFountain ||  D1: Sarah Hurley <br> D2: Lisa Terlova|| P1: [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/wol1/doi/10.1111/mec.13022/full Fraser et al. 2015] <br> P2: [http://www.nature.com/ismej/journal/v9/n6/full/ismej2014230a.html Helliwell et al. 2015] <br> D: [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/evo.12815/full Castillo et al., 2015]<br>
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| Th Sept 15 (L) <br> Tu Sept 20 (P/D) || Adaptation and Speciation 1 (EJ) || P1:  Kevin Bieger<br> P2: Genevieve Nuttall  ||  D1: Amy LaFountain<br> D2: Qiaoshan Lin|| P1: [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencedirect.com/science/article/pii/S0960982215006612 Comeault et al. 2015]<br> P2: [http://ezproxy.lib.uconn.edu/login?url=http://genome.cshlp.org/content/25/11/1656.long Burri et al. 2015]<br> D: [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/evo.12807/full Stankowski et al. 2015]<br>
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| Th Sept 22 (L) <br> Tu Sept 27 (P/D) || Adaptation and Speciation 2 (EJ) <br><b>Classics:</b> [http://ezproxy.lib.uconn.edu/login?url=http://www.jstor.org/stable/2409213 Coyne and Orr (1989)] [http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/256/5054/193.long Grant and Grant 1992] <b>Reviews:</b> [http://ezproxy.lib.uconn.edu/login?url=http://www.annualreviews.org/doi/full/10.1146/annurev.ecolsys.38.091206.095733 Ritchie 2007] [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2012.02599.x/full Abbott et al. 2013] <b>Lecture Examples:</b> [http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/314/5803/1292.long Brideau et al. 2006] [http://ezproxy.lib.uconn.edu/login?url=https://elifesciences.org/content/3/e02504 Turner and Hare 2014] [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v487/n7405/full/nature11041.html Heliconius Genome Consurtium 2012] <b>Recent:</b> [http://ezproxy.lib.uconn.edu/login?url=http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005887 Marques et al. 2016] [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v518/n7539/abs/nature14181.html Lamichhaney et al. 2015] [http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/283/1835/20160821 Smith et al. 2016] || P1: Matt Sasaki<br> P2: Tim Pullen ||  D1: Tanner Matson <br> D2: Morgan Napier|| P1: [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1002/ece3.2028/abstract Picq et al. 2015] <br> P2: [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/evo.12624/full Pfennig et al. 2015]<br> D: [http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/283/1835/20160821 Smith et al. 2016] <br>
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| Th Sept 29 (L) <br> Tu Oct 4 (P/D) || Adaptation and Speciation 3 (YY)<br> '''Suggested Papers:''' [http://ezproxy.lib.uconn.edu/login?url=http://www.pnas.org/content/113/29/8320.full Arnold et al. 2016][http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/wol1/doi/10.1111/evo.12355/full Grossenbacher et al. 2014]|| P1: Tanner Matson<br> P2: Vandana Gurung|| D1: Matt Sasaki<br> D2: Tim Pullen|| P1: [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v407/n6805/full/407739a0.html Filchak et al. 2000]<br> P2: [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1002/ece3.1378/epdf Xu et al. 2015]<br> D: [http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/282/1809/20150425.full MacLeod et al. 2015]<br>
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| Th Oct 6 (L) <br> Tu Oct 11 (P/D) || Diversification Patterns and Processes (EJ) <br>'''Classic''': [http://www.johnboccio.com/courses/SOC26/Bak-Sneppan/02_Raup.pdf Raup and Sepkoski 1982] [http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/281/5376/555.full Farrell 1998] '''Lecture Examples''': [http://ezproxy.lib.uconn.edu/login?url=http://www.pnas.org/content/106/32/13410.full Alfaro et al. 2009] [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1890/0012-9658(2006)87%5b2468:GVITDR%5d2.0.CO%3b2/full Ricklefs 2006] [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v487/n7407/full/nature11144.html Wagner et al. 2012] [http://ezproxy.lib.uconn.edu/login?url=http://journal.frontiersin.org/article/10.3389/fgene.2013.00192/full Madriñan et al. 2016] '''Recommended''': [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/articles/ncomms12384?WT.feed_name=subjects_evolutionary-genetics Nevado et al. 2016]|| P1: Austin Spence <br> P2: Eileen Schaub  ||  D1:  Genevieve Nuttall <br> D2: Ellie Clark <br>D3: Jacob Kasper <br> || P1: [http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/283/1832/20160181 Blom et al. 2016] <br> P2: [http://onlinelibrary.wiley.com.ezproxy.lib.uconn.edu/doi/10.1111/nph.13234/full Schwery et al. 2015] <br> D: [http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/280/1756/20122820  Joy 2013] <br>
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| Th Oct 13 (L) <br> Tu Oct 18 (P/D) || Novelty 1 (YY)<br>'''Suggested Papers:''' [http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/royprsb/281/1782/20133333.full.pdf Stansbury & Moczek, 2014.][http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/338/6105/384.full.pdf+html Nasvall et al. 2012][http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005721 Ruiz-Orera et al. 2015.] [http://ezproxy.lib.uconn.edu/login?url=http://www.plantphysiol.org/content/early/2016/07/05/pp.16.00779.full.pdf Zhao et al. 2016]|| P1: Sarah Hurley <br> P2: Ellie Clark ||  D1:  Kevin Bieger<br> D2: Vandana Gurung|| P1: [http://link.springer.com.ezproxy.lib.uconn.edu/article/10.1007/s00427-007-0147-2 Baratte et al. 2007]<br> P2: [http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/royprsb/281/1782/20133333.full.pdf Stansbury & Moczek, 2014.]<br> D: [http://www.pnas.org/content/104/42/16714.long Busch & Zachgo 2007]<br>
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| Th Oct 20 (L) <br> Tu Oct 25 (P/D) || Novelty 2 (EJ) <br>'''cis-regulatory review:''' [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencedirect.com/science/article/pii/S0168952512001473 Yáñez-Cuna et al. 2013] '''Lecture examples:''' [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v433/n7025/full/nature03235.html Gompel et al. 2005] [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v464/n7292/full/nature08896.html Werner et al. 2010] [http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/339/6126/1423.long Arnoult et al. 2013] '''Recommended:''' [http://ezproxy.lib.uconn.edu/login?url=http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002893 Oliver et al. 2012] [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencedirect.com/science/article/pii/S0960982216307898 Dowell et al. 2016] [http://ezproxy.lib.uconn.edu/login?url=http://evodevojournal.biomedcentral.com/articles/10.1186/2041-9139-5-7 Martin et al. 2014] [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/articles/ncomms6149 Santos et al. 2014] [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencedirect.com/science/article/pii/S221112471401105X Lynch et al. 2015] || P1: Eileen Schaub  <br> P2: Mike Stankov  ||  D1:  Morgan Napier <br> D2: Kevin Bieger|| P1: [http://www.amjbot.org/content/98/6/923.long Hemingway et al. 2011] <br> P2: [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencedirect.com/science/article/pii/S0960982216307898 Dowell et al. 2016]<br> D: [http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/339/6126/1423.full Arnoult et al. 2013]<br>
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| Th Oct 27 (L) <br>  Tu Nov 1 (P/D) || Novelty 3 (YY) <br> '''Papers worth detailed reading:''' [http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/165/3891/349.full.pdf Britten & Davidson 1969] [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nrg/journal/v9/n5/pdf/nrg2337.pdf Feschotte 2008][http://ezproxy.lib.uconn.edu/login?url=http://www.cell.com/cell-reports/pdf/S2211-1247(14)01105-X.pdf Lynch et al. 2015] || P1:  Amy LaFountain <br> P2: Tim Pullen ||  D1: Matt Sasaki <br> D2:Vandana Gurung <br> D3: Ellie Clark || P1: [http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/282/1803/20142778 Yant et al. 2015] <br> P2: [http://labs.bio.unc.edu/pfennig/LabSite/Photos_files/2016_Am%20Nat.pdf Allf et al. 2016] <br> D: [http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/282/1798/20142272.short Nichols et al. 2014] <br>
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| Th Nov 3 (L) <br> Tu Nov 8 (P/D) || Evolution in Action: Humans as Unintentional Agents of Selection (EJ) <br> '''Reviews:''' [http://ezproxy.lib.uconn.edu/login?url=http://www.annualreviews.org/doi/full/10.1146/annurev-ecolsys-112414-054339 Heino et al. 2015] [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/ele.12262/full Moran and Alexander 2014] [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/nph.14004/full Vallejo-Marín and Hiscock 2016] [http://ezproxy.lib.uconn.edu/login?url=http://link.springer.com/article/10.1007/s13280-014-0547-2 Donihue and Lambert 2015] '''Lecture Examples:''' [http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/299/5613/1738 Heath et al. 2003] [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2005.02794.x/full Taylor et al. 2006] [http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/340/6136/1086.full?sid=2e0bdecd-9e5b-4f4a-ac0a-6a8b4f7b9f20 Galetti et al. 2013] [http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/346/6208/463.full Stuart et al. 2014] '''Recommended:''' [http://ezproxy.lib.uconn.edu/login?url=http://www.pnas.org/content/105/10/3796.full Cheptou et al. 2008] [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/evo.12925/full Winchell et al. 2016] [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/wol1/doi/10.1111/mec.13405/full Roy et al. 2015] || P1: Jacob Kasper<br> P2: Kevin Bieger || D1: Sarah Hurley<br> D2: Tim Pullen<br> D3: Tanner Matson|| P1: [http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/279/1743/3870.full Kovach et al. 2012]<br> P2: [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/evo.12925/full Winchell et al. 2016]<br> D: [http://ezproxy.lib.uconn.edu/login?url=http://www.pnas.org/content/105/10/3796.full Cheptou et al. 2008]<br>
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| Th. Nov. 8 (L) <br> Tu. Nov. 13 (P/D)|| Evolution in Action: Domestication and Agriculture (YY) ||P1: Claire Bailey<br> P2: Laura Cunningham<br>  ||D1: Kyle Drake<br> D2: Dipanjana Dalui<br> ||P1: [https://www.nature.com/articles/cr201644.pdf Wang et al. 2016]<br> P2: [https://www.nature.com/articles/nature25447 Wu et al. 2018]<br> D:[https://www.cell.com/action/showPdf?pii=S0092-8674%2816%2931071-6 Gallone et al. 2016] <br>
  
 
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| Th Nov 10 (L) <br> Tu Nov 15 (P/D) || Evolution in Action: Domestication and Agriculture (YY) || P1: Tanner Matson<br> P2: Qiaoshan Lin<br> || D1: Lisa Terlova  <br> D2: Amy LaFountain <br> D3: Eileen Schaub || P1: [http://ezproxy.lib.uconn.edu/login?url=http://link.springer.com/article/10.1007/s11692-013-9262-3 Maselli et al. 2014]<br> P2: [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/ng/journal/v48/n9/pdf/ng.3633.pdf Meyer et al. 2016]<br> D: [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2008.00373.x/full Guillemin et al. 2008]<br>
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| Th. Nov. 15 (L) <br> Tu. Nov. 27 (P/D)|| Applications of Evolutionary Thinking: Conservation (EJ)  
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'''Lecture examples'''
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/33136 Saccheri et al. 1998] Metapopulation extinction risk;
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1371/journal.pgen.1006601 Rogers and Slatkin 2018] Mammoth mutational meltdown;
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1016/j.cub.2015.04.007 Palkopoulou et al. 2015] Mammoth demography;
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/j.1461-0248.2005.00804.x Epps et al. 2005] Bighorn sheep fragmentation;
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/mec.13139 Frankham 2015] Genetic rescue meta-analysis;
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/j.1523-1739.2010.01450.x Gilbert-Norton et al. 2010] Corridor meta-analysis;
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[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/cobi.13149 Kelly and Phillips 2018] Quoll genetic rescue
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||P1: Johnny Bator <br> P2: Katie Weeks<br> ||D1: Eliza Grames<br> D2: Laura Cunningham<br> ||
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P1: [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1007/s10592-017-0939-5 Hendricks et al. 2017]<br>  
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P2: [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1002/ece3.3950 Hinton et al. 2018] <br>  
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D: [http://ezproxy.lib.uconn.edu/login?url=https://doi-org.ezproxy.lib.uconn.edu/10.1007/s10592-018-1050-2 Liu et al. 2018] <br>
  
 
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| Th Nov 17 (L) <br> Tu Nov 29 (P/D) || Applications of Evolutionary Thinking: Medicine (YY) || P1: Lisa Terlova  <br> P2: Vandana Gurung  || D1:  Qiaoshan Lin<br> D2: Austin Spence<br> D3: Jacob Kasper|| P1:[https://www-ncbi-nlm-nih-gov.ezproxy.lib.uconn.edu/pmc/articles/PMC4660033/pdf/emss-65989.pdf Ortmann et al. 2015] <br> P2: [http://onlinelibrary.wiley.com/wol1/doi/10.1111/j.1558-5646.2010.01142.x/full Lahdenpera et al. 2010] <br> D: [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencedirect.com/science/article/pii/S0966842X15000165 Day et al. 2015]<br>
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| Th. Nov. 29 (L) <br>|| Applications of Evolutionary Thinking: Medicine (YY) || NA || NA ||<br>
  
 
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| Th Dec 1 (L) <br> Tu Dec 6 (P/D) || Applications of Evolutionary Thinking: Conservation (EJ) || P1: Matt Sasaki <br> P2: Sarah Hurley ||  D1:  Mike Stankov<br> D2: Genevieve Nuttall <br> D3: Eileen Schaub|| P1: [http://ezproxy.lib.uconn.edu/login?url=http://link.springer.com/article/10.1007/s10592-015-0776-3/fulltext.html Stockwell et al. 2016]<br> P2: [http://onlinelibrary.wiley.com.ezproxy.lib.uconn.edu/doi/10.1111/acv.12159/full Mowry et al. 2014] <br> D: [http://ezproxy.lib.uconn.edu/login?url=http://www.pnas.org/content/112/8/2307.full van Oppen et al. 2015]<br>
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| Tu. Dec. 4 || Proposal Presentations || P1: Alex <br> P2: Andrew<br> P3: Eliza<br> P4: Kayla<br> P5: Matt<br> || NA ||<br>
  
 
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| Th Dec 8 || Wrap-up || P1: Lisa Terlova (EJ)<br> P2: Morgan Napier (EJ)<br> P3: Genevieve Nuttall (YY)<br> P4: Austin Spence (YY)<br> P5: Ellie Clark (EJ)<br> P6: Mike Stankov (YY)|| N/A || P1: [http://www.pnas.org/content/111/18/6672.full.pdf?with-ds=yes Li et al. 2014] <br> P2: [http://ezproxy.lib.uconn.edu/login?url=http://http://press.endocrine.org/doi/full/10.1210/jc.2014-2703 Casarini and Brigante 2014]<br> P3: [https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-016-0786-x Harrington et al. 2016]<br> P4: [http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/354/6310/336 Natarajan et al. 2016]<br> P5: [http://ezproxy.lib.uconn.edu/login?url=http://http://www.amjbot.org/content/102/5/805.full Wu et al. 2015] <br>
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| Th. Dec. 6|| Proposal Presentations || P1: Amanda<br> P2: Charlie<br> P3: Claire<br> P4: Jack<br>P5: Marat<br> || NA ||<br>
P6: [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/articles/ncomms12384 Nevado et al. 2016]<br>
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| Tu Dec 13<br> (Final Exam Period) ||<span style="font-size: small"><font color="#FF3300"> '''3:30-5:30 pm''' </font></span>Preproposal Review Panel || NA || NA||<br>
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| Final Exam period, Tu Dec. 11, 3:30-6 pm|| Proposal Presentations || P1: Dipanjana<br> P2: Johnny<br> P3: Katie<br> P4: Kes<br> P5: Kyle<br> || P6: Laura<br> P7: Lucas<br> P8: Mark<br> P9: Susan<br> ||<br>

Latest revision as of 15:26, 25 November 2018

EEB 5449, Fall 2018
Evolution
Meeting Time: Tuesdays and Thursdays, 9:30-10:45 am, TLS171b (Bamford room)

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

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

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 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

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
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

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
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

P1: Hendricks et al. 2017
P2: Hinton et al. 2018
D: Liu et al. 2018

Th. Nov. 29 (L)
Applications of Evolutionary Thinking: Medicine (YY) NA NA
Tu. Dec. 4 Proposal Presentations P1: Alex
P2: Andrew
P3: Eliza
P4: Kayla
P5: Matt
NA
Th. Dec. 6 Proposal Presentations P1: Amanda
P2: Charlie
P3: Claire
P4: Jack
P5: Marat
NA
Final Exam period, Tu Dec. 11, 3:30-6 pm Proposal Presentations P1: Dipanjana
P2: Johnny
P3: Katie
P4: Kes
P5: Kyle
P6: Laura
P7: Lucas
P8: Mark
P9: Susan