Difference between revisions of "EEB5449 Fall 2020"

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(Created page with "<span style="font-size: x-large">EEB 5449, Fall 2018</span><br> <span style="font-size: large">''Evolution''</span><br> <span style="font-size: small">'''Meeting Time: Tuesday...")
 
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<span style="font-size: x-large">EEB 5449, Fall 2018</span><br>
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<span style="font-size: x-large">EEB 5449, Fall 2020</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, TLS171b (Bamford room)'''<br>
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<span style="font-size: small">'''Meeting Time: Tuesdays and Thursdays, 11-12:15'''<br>
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<span style="font-size: small">'''In-person meetings will take place in Gant South 119'''<br>
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<span style="font-size: small">'''Access information for online meetings will be sent by email'''<br>
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==Description==
 
==Description==
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==Announcements and Handouts==
 
==Announcements and Handouts==
<b>Presentation & discussion sign-up</b>: 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.)<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 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.)<br>
 
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<br>
  
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More information about presentation preparation is available [https://drive.google.com/open?id=0B-wU9Sg5Mrvhdm5DZkRpN0poNjA here].<br><br>
 
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.  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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<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 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.<br>
 
<u>Discussion leader responsibilities are as follows</u>:
 
<u>Discussion leader responsibilities are as follows</u>:
 
*week before: discuss paper options with EJ or YY (whoever is giving the associated lecture), who must approve the choice
 
*week before: discuss paper options with EJ or YY (whoever is giving the associated lecture), who must approve the choice
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<br>
 
<br>
  
<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>
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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. 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 [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/EEB5449_Preproposal here].<br><br>
  
 
<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>
 
<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>
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</tr>
 
</tr>
 
<tr>
 
<tr>
<td>Thursday, Oct. 25</td><td>Preproposal topic approved</td>
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<td>Thursday, Oct. 22</td><td>Preproposal topic approved</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
<td>Monday, Nov. 26, 5 pm</td><td>Preproposal due</td>
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<td>Monday, Nov. 30, 5 pm</td><td>Preproposal due</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
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|-  
 
|-  
| Tu Aug. 28 || Overview & Evolution review 1 (EJ)|| NA || NA ||<br>
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| Tu Sept. 1, GS119 || Overview & Evolution review 1 (EJ)|| NA || NA ||<br>
  
 
|-  
 
|-  
| Th Aug. 30 || Evolution review 2 (EJ)<br>
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| Th Sept. 3, GS119 || Evolution review 2 (EJ)|| NA || NA ||<br>
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/j.1096-3642.1858.tb02500.x Darwin and Wallace 1858]<br>
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[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>
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[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>
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|-  
 
|-  
|Tu Sept. 4 || Evolution review 3 (YY) <br>
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|Tu Sept. 8, online || Evolution review 3 (YY) || NA || NA ||<br>
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>
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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>
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| Th. Sept. 10 (L, online) <br> Tu. Sept. 15 (P/D, online)|| Evolution in action: experimental Evolution (YY) ||
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P1: Name <br>
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P2: Name <br> 
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||D1: Name<br>  
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D2: Name<br>   
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||P1: Article<br>
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P2: Article<br>  
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D: Article<br>
  
 
|-  
 
|-  
| 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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| Th. Sept. 17 (L, GS119) <br>Tu. Sept. 22 (P/D, online)|| Evolution in action: humans as selective agents (EJ) ||
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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P1: Name <br>
P2: [http://ezproxy.lib.uconn.edu/login?url=https://www.nature.com/articles/ncomms14691.pdf  Gervasi et al. 2017] <br>
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P2: Name <br>   
D: [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/evo.12815 Castillo et al. 2015]<br>
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||D1: Name<br>  
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D2: Name<br>   
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||P1: Article<br>  
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P2: Article<br>  
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D: Article<br>
  
 
|-  
 
|-  
| Th. Sept. 20 (L) <br> Tu. Sept. 25 (P/D)|| Adaptation and Speciation 1 (EJ)
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| Th. Sept. 24 (L, GS119) <br> Tu. Sept. 29 (P/D, online)|| Adaptation and speciation 1 ||
[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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P1: Name <br>
[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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P2: Name <br>   
[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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||D1: Name<br>  
[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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D2: Name<br>   
[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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||P1: Article<br>  
[http://redpath-staff.mcgill.ca/hendry/Stuart2017NEE1,0158.pdf Stuart et al. 2017]: test of lake-stream parallelism
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P2: Article<br>  
||P1: Eliza Grames <br> P2: Kayla Morin<br>  ||D1: Andrew Stillman<br> D2: Amanda Hewes<br>  ||
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D: Article<br>
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>
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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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| Th. Oct. 1 (L, online) <br> Tu. Oct. 6 (P/D,online) <br> || Adaptation and speciation 2 (YY) ||
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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P1: Name <br>
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>
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P2: Name <br> 
 
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||D1: Name<br>  
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D2: Name<br>   
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||P1: Article<br>
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P2: Article<br>  
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D: Article<br>
 
|-  
 
|-  
| Th. Oct. 4 (L) <br> Tu. Oct. 9 (P/D)|| Diversification Patterns and Processes (EJ)  
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| Th. Oct. 8 (L, GS119) <br> Tu. Oct. 13 (P/D, online)|| Diversification patterns and processes (EJ) ||
'''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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P1: Name <br>
[http://ezproxy.lib.uconn.edu/login?url=http://science.sciencemag.org/content/281/5376/555.full Farrell 1998] beetle phytophagy;
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P2: Name <br>   
[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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||D1: Name<br>  
[https://doi-org.ezproxy.lib.uconn.edu/10.3389/fgene.2013.00192 Madriñan et al. 2013] paramo;
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D2: Name<br>   
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1098/rspb.2015.1553 Givnish et al. 2016] orchids;
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||P1: Article<br>  
[https://doi-org.ezproxy.lib.uconn.edu/10.1038/nature11144Wagner et al. 2012] cichlids 1;
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P2: Article<br>  
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/ncomms14363 Meier et al. 2017] cichlids2
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D: Article<br>
||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]]
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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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| Th. Oct. 15 (L, GS119) <br> Tu. Oct. 20 (P/D, online)|| Extinction (EJ) ||
P1: [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/ncomms10397 Moriyama et al. 2016]<br>  
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P1: Name <br>
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]]
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P2: Name <br> 
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||D1: Name<br>  
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D2: Name<br>
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||P1: Article<br>
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P2: Article<br>  
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D: Article<br>
  
 
|-  
 
|-  
| Th. Oct. 18 (L) <br> Tu. Oct. 23 (P/D)|| Novelty 2 (EJ)
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| Th. Oct. 22 (L, online) <br> Tu. Oct. 27 (P/D, online)||Developmental mechanisms of phenotypic integration  ||
'''<i>Drosophila</i>''': [http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/nature03235 Gompel et al. 2005];
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P1: Name <br>
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/nature08896 Werren et al. 2010];
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P2: Name <br>   
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1073/pnas.1509022112 Koshikawa et al. 2015];
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||D1: Name<br>  
'''<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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D2: Name<br>   
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/nature11041 Heliconius Genome Consortium 2012];
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||P1: Article<br>  
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1371/journal.pbio.1002353 Wallbank et al. 2016];
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P2: Article<br>  
'''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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D: Article<br>
||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>
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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. 29 (L, online) <br> Tu. Nov. 3 (P/D, online)|| Novelty (YY)||
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P1: Name <br>
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P2: Name <br>   
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||D1: Name<br>  
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D2: Name<br>   
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||P1: Article<br>  
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P2: Article<br>  
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D: Article<br>
  
 
|-  
 
|-  
| Th. Nov. 1 (L) <br> Tu. Nov. 6 (P/D)|| Evolution in Action: Humans as Unintentional Agents of Selection (EJ)  
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| Th. Nov. 5 (L, online) <br> Tu. Nov. 10 (P/D, online)||Genome evolution (YY) ||
'''Lecture examples'''
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P1: Name <br>
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/evo.12925 Winchell et al. 2016] Urban ''Anolis'';
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P2: Name <br>   
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1126/science.1257008 Stuart et al. 2014] Introduced ''Anolis'';
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||D1: Name<br>  
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/gcb.14115 Kern and Langerhans 2018] Urban fish;
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D2: Name<br>
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1007/s10592-006-9202-1 Noël et al. 2007] Salamander drift;
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||P1: Article<br>  
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1073/pnas.0708446105 Cheptou et al. 2008] Seed dispersal
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P2: Article<br>  
||P1: Dipanjana Dalui<br> P2: Lucas Myers<br>  ||D1: Claire Bailey<br> D2: Kayla Morin<br> D3: Katie Weeks <br> ||
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D: Article<br>
P1: [http://ezproxy.lib.uconn.edu/login?url=https://www.nature.com/articles/srep31957 Carvalho et al. 2016] <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. 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. 12 (L, GS119) <br> Tu. Nov. 17 (P/D, online)|| Applications of evolutionary thinking in conservation (EJ) ||
 
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P1: Name <br>
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P2: Name <br>   
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||D1: Name<br>  
 +
D2: Name<br>   
 +
||P1: Article<br>  
 +
P2: Article<br>  
 +
D: Article<br>
 
|-  
 
|-  
| Th. Nov. 15 (L) <br> Tu. Nov. 27 (P/D)|| Applications of Evolutionary Thinking: Conservation (EJ)  
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| Th. Nov. 19 (L, online) <br>|| Evolutionary Medicine (YY) ||
'''Lecture examples'''
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P1: NA<br>
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1038/33136 Saccheri et al. 1998] Metapopulation extinction risk;
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P2: NA <br>   
[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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||D1: NA<br>  
[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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D2: NA<br>   
[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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||P1: Article<br>  
[http://ezproxy.lib.uconn.edu/login?url=https://doi.org/10.1111/mec.13139 Frankham 2015] Genetic rescue meta-analysis;
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P2: Article<br>  
[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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D: Article<br>
[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. 29 (L) <br>|| Applications of Evolutionary Thinking: Medicine (YY) || NA || NA ||<br>
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| Tu. Dec. 1 || Proposal Presentations ||  
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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. 3||
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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>
 
  
 
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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>
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| Final Exam period, TBA|| Proposal Presentations ||  
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P9: Name<br>|| NA ||<br>

Revision as of 15:02, 25 August 2020

EEB 5449, Fall 2020
Evolution
Meeting Time: Tuesdays and Thursdays, 11-12:15
In-person meetings will take place in Gant South 119
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. 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 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, GS119 Overview & Evolution review 1 (EJ) NA NA
Th Sept. 3, GS119 Evolution review 2 (EJ) NA NA
Tu Sept. 8, online Evolution review 3 (YY) NA NA
Th. Sept. 10 (L, online)
Tu. Sept. 15 (P/D, online)
Evolution in action: experimental Evolution (YY)

P1: Name
P2: Name

D1: Name

D2: Name

P1: Article

P2: Article
D: Article

Th. Sept. 17 (L, GS119)
Tu. Sept. 22 (P/D, online)
Evolution in action: humans as selective agents (EJ)

P1: Name
P2: Name

D1: Name

D2: Name

P1: Article

P2: Article
D: Article

Th. Sept. 24 (L, GS119)
Tu. Sept. 29 (P/D, online)
Adaptation and speciation 1

P1: Name
P2: Name

D1: Name

D2: Name

P1: Article

P2: Article
D: Article

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

P1: Name
P2: Name

D1: Name

D2: Name

P1: Article

P2: Article
D: Article

Th. Oct. 8 (L, GS119)
Tu. Oct. 13 (P/D, online)
Diversification patterns and processes (EJ)

P1: Name
P2: Name

D1: Name

D2: Name

P1: Article

P2: Article
D: Article

Th. Oct. 15 (L, GS119)
Tu. Oct. 20 (P/D, online)
Extinction (EJ)

P1: Name
P2: Name

D1: Name

D2: Name

P1: Article

P2: Article
D: Article

Th. Oct. 22 (L, online)
Tu. Oct. 27 (P/D, online)
Developmental mechanisms of phenotypic integration

P1: Name
P2: Name

D1: Name

D2: Name

P1: Article

P2: Article
D: Article

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

P1: Name
P2: Name

D1: Name

D2: Name

P1: Article

P2: Article
D: Article

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

P1: Name
P2: Name

D1: Name

D2: Name

P1: Article

P2: Article
D: Article

Th. Nov. 12 (L, GS119)
Tu. Nov. 17 (P/D, online)
Applications of evolutionary thinking in conservation (EJ)

P1: Name
P2: Name

D1: Name

D2: Name

P1: Article

P2: Article
D: Article

Th. Nov. 19 (L, online)
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 ||

Th. Dec. 3

P1: Name
P2: Name
P3: Name
P4: Name
P5: Name
|| NA ||


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 ||