http://hydrodictyon.eeb.uconn.edu/eebedia/api.php?action=feedcontributions&user=Elizabeth+Clark&feedformat=atomEEBedia - User contributions [en]2024-03-28T20:18:19ZUser contributionsMediaWiki 1.25.2http://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=EEB_5449_Fall_2016&diff=36398EEB 5449 Fall 20162016-10-07T02:14:25Z<p>Elizabeth Clark: /* Topics and Readings */</p>
<hr />
<div><span style="font-size: x-large">EEB 5449, Fall 2016</span><br><br />
<span style="font-size: large">''Evolution''</span><br><br />
<span style="font-size: small">'''Meeting Time: Tuesdays and Thursdays, 9:30-10:45 am, TLS171B, Bamford Room)'''<br><br />
<br />
==Description==<br />
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. <br> <br><br />
<br />
==Instructors==<br />
<br />
'''[mailto:elizabeth.jockusch@uconn.edu Dr. Elizabeth Jockusch]'''<br><br />
Office: Biology/Pharmacy 305B<br><br />
Phone: (860) 486-4452<br><br />
Office hours: by appointment<br><br><br />
<br />
'''[mailto:yaowu.yuan@uconn.edu Dr. Yaowu Yuan]'''<br><br />
Office: Biology/Pharmacy 300A<br><br />
Phone: (860) 486-3469<br><br />
Office hours: by appointment<br><br />
<br><br />
<br />
==Announcements and Handouts==<br />
<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 directly. If not, send Yaowu or Elizabeth some information about your preferences, and we'll sign you up. We will need to triple up for one session, so if the topic you really want is full, ask for it anyway. Those of you who are signing up now can also help yourselves to first pick (also 1 presentation & 1 discussion) for the second half of the course.<br><br />
<br><br />
<br />
<b>Discussion leaders</b>: 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.<br><br />
<br><br />
<b>Editing EEBedia</b>: To post discussion questions and links to papers, you will need to edit the EEBedia site [this page] directly. [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Help:Contents Here's] some helpful information for those of you new to EEBedia.<br><br />
<br><br />
<br />
<b>Posting papers on EEBedia</b>: 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 (<b><nowiki>http://ezproxy.lib.uconn.edu/login?url=http://</nowiki></b>) followed by the web address for the paper. Be sure to test it! Include basic citation information as the displayed text.<br><br />
<br><br />
<br />
<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><br />
<br><br />
<br />
<b>Textbook</b>: 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:<br />
*Bergstrom and Dugatkin, Evolution<br />
*Freeman and Herron, Evolutionary Analysis<br />
*Futuyma, Evolution<br />
*Zimmer and Emlen, Evolution, Making Sense of Life<br><br><br />
<br />
==Resources==<br />
[http://darwin-online.org.uk Darwin's complete writings]<br><br />
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Classic_Works_in_Evolutionary_Biology—The_List_With_Links Classic Papers in Evolutionary Biology]<br><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><br />
<br><br />
<br />
==Expectations and Grading== <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> <br />
<br />
<b>Presentations</b>: Each student will give two presentations about papers from the primary literature, selected in consultation with the instructors. Each presenter should post a link to their paper on EEBedia by the Friday before the presentation. All students are expected to look at these papers briefly and come prepared to ask questions. More information about presentation preparation is available [https://drive.google.com/open?id=0B-wU9Sg5Mrvhdm5DZkRpN0poNjA here]. <br><br><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><br />
<br />
<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><br />
<br />
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><br />
1. "Conceptual Framework" or "Objectives" or "Specific Aims"<br><br />
2. "Rationale and Significance" or "Background"<br><br />
3. "Research Question(s)" or "Hypotheses"<br><br />
4. "Research Approach" or "Experimental Plan"<br><br />
5. "Broader Impacts"<br><br />
<br />
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> <br />
<br />
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><br />
<br />
<br />
<br />
<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><br />
<br />
"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><br />
'''Intellectual Merit:''' The Intellectual Merit criterion encompasses the potential to advance knowledge; and<br><br />
'''Broader Impacts:''' The Broader Impacts criterion encompasses the potential to benefit society and contribute to the achievement of specific, desired societal outcomes.<br><br />
<br />
The following elements should be considered in the review for both criteria:<br><br />
1. What is the potential for the proposed activity to<br><br />
a. Advance knowledge and understanding within its own field or across different fields (Intellectual Merit); and<br><br />
b. Benefit society or advance desired societal outcomes (Broader Impacts)?<br><br />
2. To what extent do the proposed activities suggest and explore creative, original, or potentially transformative concepts?<br><br />
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><br />
4. How well qualified is the individual, team, or organization to conduct the proposed activities?<br><br />
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><br />
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,<br />
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."<br />
<br />
===Deadlines===<br />
<table><br />
<tr><br />
<td>Weekly</td><td>Reaction paper based on discussion readings</td><br />
</tr><br />
<tr><br />
<td>Thursday, Oct. 25</td><td>Preproposal topic approved</td><br />
</tr><br />
<tr><br />
<td>Monday, Nov. 28, 5 pm</td><td>Preproposal due</td><br />
</tr><br />
<tr><br />
<td>Friday, December 9</td><td>Preproposal reviews due</td><br />
</tr><br />
<tr><br />
</table><br />
<br><br />
===Course grade===<br />
<table><br />
<tr><br />
<td>Presentations</td><td>20%</td><br />
</tr><br />
<tr><br />
<td>Discussions</td><td>20%</td><br />
</tr><br />
<tr><br />
<td>Preproposal</td><td>50%</td><br />
</tr><br />
<tr><br />
<td>Panel reviews</td><td>10%</td><br />
</tr><br />
</table><br />
<br><br />
<br />
==Topics and Readings==<br />
{| border="1" cellpadding="1"<br />
!style="background:#F0F9E8;" width="125"|Dates<br />
<br />
!style="background:#BAE4BC;" width="300"|Lecture<br />
!style="background:#7BCCC4;" width="185"|Presenters<br />
!style="background:#43A2CA;" width="185"|Discussion Leaders<br />
!style="background:#0868AC;" width="300"|<font color="#FFFFFF">Papers</font><br />
<br />
|- <br />
| Tu Aug. 30 || Overview || NA || NA ||<br><br />
<br />
|- <br />
| 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]<br />
<br />
|- <br />
| 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><br />
<br />
|- <br />
| 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><br />
<br />
|- <br />
| 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><br />
<br />
|- <br />
| 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><br />
<br />
|- <br />
| Th Oct 6 (L) <br> Tu Oct 11 (P/D) || Diversification Patterns and Processes (EJ) || P1: Austin Spence <br> P2: Eileen Schaub || D1: Genevieve Nuttall <br> D2: Ellie Clark <br>D3: Jacob Kasper <br> || P1: <br> P2: <br> D:[http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/280/1756/20122820 Joy 2013] <br><br />
<br />
|- <br />
| Th Oct 13 (L) <br> Tu Oct 18 (P/D) || Novelty 1 (YY) || P1: Sarah Hurley <br> P2: Ellie Clark || D1: Kevin Bieger<br> D2: Vandana Gurung|| P1:<br> P2: <br> D:<br><br />
<br />
|- <br />
| Th Oct 20 (L) <br> Tu Oct 25 (P/D) || Novelty 2 (EJ) || P1: Eileen Schaub <br> P2: Mike Stankov || D1: Morgan Napier <br> D2:|| P1: <br> P2: <br> D:<br><br />
<br />
|- <br />
| Th Oct 27 (L) <br> Tu Nov 1 (P/D) || Novelty 3 (YY) || P1: Amy LaFountain <br> P2: Tim Pullen || D1: Matt Sasaki <br> D2:Vandana Gurung || P1: <br> P2: <br> D:<br><br />
<br />
|- <br />
| Th Nov 3 (L) <br> Tu Nov 8 (P/D) || Evolution in Action: Domestication and Agriculture (YY) || P1: Tanner Matson<br> P2: Qiaoshan Lin<br> || D1: Lisa Terlova <br> D2: Amy LaFountain || P1: <br> P2: <br> D:<br><br />
<br />
|- <br />
| Th Nov 10 (L) <br> Tu Nov 15 (P/D) || Evolution in Action: Humans as Unintentional Agents of Selection (EJ) || P1: Jacob Kasper<br> P2: Kevin Bieger || D1: Sarah Hurley<br> D2: Tim Pullen|| P1: <br> P2: <br> D:<br><br />
<br />
|- <br />
| 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:|| P1: <br> P2: <br> D:<br><br />
<br />
|- <br />
| 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:|| P1: <br> P2: <br> D:<br><br />
<br />
|- <br />
| Th Dec 8 || Wrap-up || P1: Lisa Terlova <br> P2: Morgan Napier<br> P3: Genevieve Nuttall <br> P4: Austin Spence|| N/A || <br><br />
<br />
|- <br />
| Final Exam Period || Preproposal Review Panel || NA || NA||<br></div>Elizabeth Clarkhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=EEB_5449_Fall_2016&diff=36397EEB 5449 Fall 20162016-10-07T02:13:40Z<p>Elizabeth Clark: /* Topics and Readings */</p>
<hr />
<div><span style="font-size: x-large">EEB 5449, Fall 2016</span><br><br />
<span style="font-size: large">''Evolution''</span><br><br />
<span style="font-size: small">'''Meeting Time: Tuesdays and Thursdays, 9:30-10:45 am, TLS171B, Bamford Room)'''<br><br />
<br />
==Description==<br />
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. <br> <br><br />
<br />
==Instructors==<br />
<br />
'''[mailto:elizabeth.jockusch@uconn.edu Dr. Elizabeth Jockusch]'''<br><br />
Office: Biology/Pharmacy 305B<br><br />
Phone: (860) 486-4452<br><br />
Office hours: by appointment<br><br><br />
<br />
'''[mailto:yaowu.yuan@uconn.edu Dr. Yaowu Yuan]'''<br><br />
Office: Biology/Pharmacy 300A<br><br />
Phone: (860) 486-3469<br><br />
Office hours: by appointment<br><br />
<br><br />
<br />
==Announcements and Handouts==<br />
<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 directly. If not, send Yaowu or Elizabeth some information about your preferences, and we'll sign you up. We will need to triple up for one session, so if the topic you really want is full, ask for it anyway. Those of you who are signing up now can also help yourselves to first pick (also 1 presentation & 1 discussion) for the second half of the course.<br><br />
<br><br />
<br />
<b>Discussion leaders</b>: 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.<br><br />
<br><br />
<b>Editing EEBedia</b>: To post discussion questions and links to papers, you will need to edit the EEBedia site [this page] directly. [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Help:Contents Here's] some helpful information for those of you new to EEBedia.<br><br />
<br><br />
<br />
<b>Posting papers on EEBedia</b>: 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 (<b><nowiki>http://ezproxy.lib.uconn.edu/login?url=http://</nowiki></b>) followed by the web address for the paper. Be sure to test it! Include basic citation information as the displayed text.<br><br />
<br><br />
<br />
<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><br />
<br><br />
<br />
<b>Textbook</b>: 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:<br />
*Bergstrom and Dugatkin, Evolution<br />
*Freeman and Herron, Evolutionary Analysis<br />
*Futuyma, Evolution<br />
*Zimmer and Emlen, Evolution, Making Sense of Life<br><br><br />
<br />
==Resources==<br />
[http://darwin-online.org.uk Darwin's complete writings]<br><br />
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Classic_Works_in_Evolutionary_Biology—The_List_With_Links Classic Papers in Evolutionary Biology]<br><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><br />
<br><br />
<br />
==Expectations and Grading== <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> <br />
<br />
<b>Presentations</b>: Each student will give two presentations about papers from the primary literature, selected in consultation with the instructors. Each presenter should post a link to their paper on EEBedia by the Friday before the presentation. All students are expected to look at these papers briefly and come prepared to ask questions. More information about presentation preparation is available [https://drive.google.com/open?id=0B-wU9Sg5Mrvhdm5DZkRpN0poNjA here]. <br><br><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><br />
<br />
<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><br />
<br />
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><br />
1. "Conceptual Framework" or "Objectives" or "Specific Aims"<br><br />
2. "Rationale and Significance" or "Background"<br><br />
3. "Research Question(s)" or "Hypotheses"<br><br />
4. "Research Approach" or "Experimental Plan"<br><br />
5. "Broader Impacts"<br><br />
<br />
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> <br />
<br />
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><br />
<br />
<br />
<br />
<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><br />
<br />
"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><br />
'''Intellectual Merit:''' The Intellectual Merit criterion encompasses the potential to advance knowledge; and<br><br />
'''Broader Impacts:''' The Broader Impacts criterion encompasses the potential to benefit society and contribute to the achievement of specific, desired societal outcomes.<br><br />
<br />
The following elements should be considered in the review for both criteria:<br><br />
1. What is the potential for the proposed activity to<br><br />
a. Advance knowledge and understanding within its own field or across different fields (Intellectual Merit); and<br><br />
b. Benefit society or advance desired societal outcomes (Broader Impacts)?<br><br />
2. To what extent do the proposed activities suggest and explore creative, original, or potentially transformative concepts?<br><br />
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><br />
4. How well qualified is the individual, team, or organization to conduct the proposed activities?<br><br />
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><br />
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,<br />
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."<br />
<br />
===Deadlines===<br />
<table><br />
<tr><br />
<td>Weekly</td><td>Reaction paper based on discussion readings</td><br />
</tr><br />
<tr><br />
<td>Thursday, Oct. 25</td><td>Preproposal topic approved</td><br />
</tr><br />
<tr><br />
<td>Monday, Nov. 28, 5 pm</td><td>Preproposal due</td><br />
</tr><br />
<tr><br />
<td>Friday, December 9</td><td>Preproposal reviews due</td><br />
</tr><br />
<tr><br />
</table><br />
<br><br />
===Course grade===<br />
<table><br />
<tr><br />
<td>Presentations</td><td>20%</td><br />
</tr><br />
<tr><br />
<td>Discussions</td><td>20%</td><br />
</tr><br />
<tr><br />
<td>Preproposal</td><td>50%</td><br />
</tr><br />
<tr><br />
<td>Panel reviews</td><td>10%</td><br />
</tr><br />
</table><br />
<br><br />
<br />
==Topics and Readings==<br />
{| border="1" cellpadding="1"<br />
!style="background:#F0F9E8;" width="125"|Dates<br />
<br />
!style="background:#BAE4BC;" width="300"|Lecture<br />
!style="background:#7BCCC4;" width="185"|Presenters<br />
!style="background:#43A2CA;" width="185"|Discussion Leaders<br />
!style="background:#0868AC;" width="300"|<font color="#FFFFFF">Papers</font><br />
<br />
|- <br />
| Tu Aug. 30 || Overview || NA || NA ||<br><br />
<br />
|- <br />
| 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]<br />
<br />
|- <br />
| 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><br />
<br />
|- <br />
| 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><br />
<br />
|- <br />
| 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><br />
<br />
|- <br />
| 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><br />
<br />
|- <br />
| Th Oct 6 (L) <br> Tu Oct 11 (P/D) || Diversification Patterns and Processes (EJ) || P1: Austin Spence <br> P2: Eileen Schaub || D1: Genevieve Nuttall <br> D2: Ellie Clark <br>D3: Jacob Kasper <br> || P1: <br> P2: <br> D:[http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/280/1756/20122820 Joy 2013] <br><br />
<br />
|- <br />
| Th Oct 13 (L) <br> Tu Oct 18 (P/D) || Novelty 1 (YY) || P1: Sarah Hurley <br> P2: Ellie Clark || D1: Kevin Bieger<br> D2: Vandana Gurung|| P1:<br> P2: <br> D:<br><br />
<br />
|- <br />
| Th Oct 20 (L) <br> Tu Oct 25 (P/D) || Novelty 2 (EJ) || P1: Eileen Schaub <br> P2: Mike Stankov || D1: Morgan Napier <br> D2:|| P1: <br> P2: <br> D:<br><br />
<br />
|- <br />
| Th Oct 27 (L) <br> Tu Nov 1 (P/D) || Novelty 3 (YY) || P1: Amy LaFountain <br> P2: Tim Pullen || D1: Matt Sasaki <br> D2:Vandana Gurung || P1: <br> P2: <br> D:<br><br />
<br />
|- <br />
| Th Nov 3 (L) <br> Tu Nov 8 (P/D) || Evolution in Action: Domestication and Agriculture (YY) || P1: Tanner Matson<br> P2: Qiaoshan Lin<br> || D1: Lisa Terlova <br> D2: Amy LaFountain || P1: <br> P2: <br> D:<br><br />
<br />
|- <br />
| Th Nov 10 (L) <br> Tu Nov 15 (P/D) || Evolution in Action: Humans as Unintentional Agents of Selection (EJ) || P1: Jacob Kasper<br> P2: Kevin Bieger || D1: Sarah Hurley<br> D2: Tim Pullen|| P1: <br> P2: <br> D:<br><br />
<br />
|- <br />
| 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:|| P1: <br> P2: <br> D:<br><br />
<br />
|- <br />
| 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:|| P1: <br> P2: <br> D:<br><br />
<br />
|- <br />
| Th Dec 8 || Wrap-up || P1: Lisa Terlova <br> P2: Morgan Napier<br> P3: Genevieve Nuttall <br> P4: Austin Spence|| N/A || <br><br />
<br />
|- <br />
| Final Exam Period || Preproposal Review Panel || NA || NA||<br></div>Elizabeth Clarkhttp://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=EEB_5449_Fall_2016&diff=36064EEB 5449 Fall 20162016-09-08T01:25:09Z<p>Elizabeth Clark: /* Topics and Readings */</p>
<hr />
<div><span style="font-size: x-large">EEB 5449, Fall 2016</span><br><br />
<span style="font-size: large">''Evolution''</span><br><br />
<span style="font-size: small">'''Meeting Time: Tuesdays and Thursdays, 9:30-10:45 am, TLS171B, Bamford Room)'''<br><br />
<br />
==Description==<br />
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. <br> <br><br />
<br />
==Instructors==<br />
<br />
'''[mailto:elizabeth.jockusch@uconn.edu Dr. Elizabeth Jockusch]'''<br><br />
Office: Biology/Pharmacy 305B<br><br />
Phone: (860) 486-4452<br><br />
Office hours: by appointment<br><br><br />
<br />
'''[mailto:yaowu.yuan@uconn.edu Dr. Yaowu Yuan]'''<br><br />
Office: Biology/Pharmacy 300A<br><br />
Phone: (860) 486-3469<br><br />
Office hours: by appointment<br><br />
<br><br />
<br />
==Announcements and Handouts==<br />
<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 directly. If not, send Yaowu or Elizabeth some information about your preferences, and we'll sign you up. We will need to triple up for one session, so if the topic you really want is full, ask for it anyway. Those of you who are signing up now can also help yourselves to first pick (also 1 presentation & 1 discussion) for the second half of the course.<br><br />
<br><br />
<br />
<b>Discussion leaders</b>: 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.<br><br />
<br><br />
<b>Editing EEBedia</b>: To post discussion questions and links to papers, you will need to edit the EEBedia site [this page] directly. [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Help:Contents Here's] some helpful information for those of you new to EEBedia.<br><br />
<br><br />
<br />
<b>Posting papers on EEBedia</b>: 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 (<b><nowiki>http://ezproxy.lib.uconn.edu/login?url=http://</nowiki></b>) followed by the web address for the paper. Be sure to test it! Include basic citation information as the displayed text.<br><br />
<br><br />
<br />
<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><br />
<br><br />
<br />
<b>Textbook</b>: 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:<br />
*Bergstrom and Dugatkin, Evolution<br />
*Freeman and Herron, Evolutionary Analysis<br />
*Futuyma, Evolution<br />
*Zimmer and Emlen, Evolution, Making Sense of Life<br><br><br />
<br />
==Resources==<br />
[http://darwin-online.org.uk Darwin's complete writings]<br><br />
[http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Classic_Works_in_Evolutionary_Biology—The_List_With_Links Classic Papers in Evolutionary Biology]<br><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><br />
<br><br />
<br />
==Expectations and Grading== <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> <br />
<br />
<b>Presentations</b>: Each student will give two presentations about papers from the primary literature, selected in consultation with the instructors. Each presenter should post a link to their paper on EEBedia by the Friday before the presentation. All students are expected to look at these papers briefly and come prepared to ask questions. More information about presentation preparation is available [https://drive.google.com/open?id=0B-wU9Sg5Mrvhdm5DZkRpN0poNjA here]. <br><br><br />
<br />
<b>Discussions</b>: Each week, we will discuss in depth one paper from the primary literature. This paper will be selected by the course instructors, and a link to it will be posted on EEBedia by the Friday before the discussion. We expect everyone to participate actively in the discussion. Two students will guide the discussion, based on a list of questions they write and distribute in advance. To help prepare for discussions, all students should write a brief (<1 page) reaction piece to the weekly readings, highlighting your thoughts about the readings, connections between them or questions raised by them. (Note: this reaction piece should *not* summarize the contents of the paper.) This will be handed in each week. Discussion grades will be based on a combination of discussion participation, reaction pieces, effectiveness at leading discussions, questions during presentations.<br><br><br />
<br />
<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><br><br />
<br />
<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. <br><br><br />
<br />
===Deadlines===<br />
<table><br />
<tr><br />
<td>Weekly</td><td>Reaction paper based on discussion readings</td><br />
</tr><br />
<tr><br />
<td>Thursday, Oct. 25</td><td>Preproposal topic approved</td><br />
</tr><br />
<tr><br />
<td>Monday, Nov. 28, 5 pm</td><td>Preproposal due</td><br />
</tr><br />
<tr><br />
<td>Friday, December 9</td><td>Preproposal reviews due</td><br />
</tr><br />
<tr><br />
</table><br />
<br><br />
===Course grade===<br />
<table><br />
<tr><br />
<td>Presentations</td><td>20%</td><br />
</tr><br />
<tr><br />
<td>Discussions</td><td>20%</td><br />
</tr><br />
<tr><br />
<td>Preproposal</td><td>50%</td><br />
</tr><br />
<tr><br />
<td>Panel reviews</td><td>10%</td><br />
</tr><br />
</table><br />
<br><br />
<br />
==Topics and Readings==<br />
{| border="1" cellpadding="1"<br />
!style="background:#F0F9E8;" width="125"|Dates<br />
<br />
!style="background:#BAE4BC;" width="300"|Lecture<br />
!style="background:#7BCCC4;" width="185"|Presenters<br />
!style="background:#43A2CA;" width="185"|Discussion Leaders<br />
!style="background:#0868AC;" width="300"|<font color="#FFFFFF">Papers</font><br />
<br />
|- <br />
| Tu Aug. 30 || Overview || NA || NA ||<br><br />
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|- <br />
| 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]<br />
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| Th Sept 8 (L) <br> Tu Sept 13 (P/D) || Experimental Evolution (eukaryotes) (EJ) || P1: Jacob Kasper <br> P2: Amy LaFountain || D1: Sarah Hurley <br> D2: Lisa Terlova|| P1: <br> P2: <br> D:<br><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: <br> P2: <br> D:<br><br />
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| Th Sept 22 (L) <br> Tu Sept 27 (P/D) || Adaptation and Speciation 2 (EJ) || P1: Matt Sasaki<br> P2: Tim Pullen || D1: Tanner Matson <br> D2: Jacob Kasper|| P1: <br> P2: <br> D:<br><br />
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| Th Sept 29 (L) <br> Tu Oct 4 (P/D) || Adaptation and Speciation 3 (YY) || P1: Tanner Matson<br> P2: Vandana Gurung|| D1: Matt Sasaki<br> D2: Tim Pullen|| P1: <br> P2: <br> D:<br><br />
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| Th Oct 6 (L) <br> Tu Oct 11 (P/D) || Diversification Patterns and Processes (EJ) || P1: Austin Spence <br> P2: || D1: Genevieve Nuttall <br> D2: Ellie Clark|| P1: <br> P2: <br> D:<br><br />
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| Th Oct 13 (L) <br> Tu Oct 18 (P/D) || Novelty 1 (YY) || P1: Sarah Hurley <br> P2: Ellie Clark || D1: Kevin Bieger<br> D2: Vandana Gurung|| P1:<br> P2: <br> D:<br><br />
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| Th Oct 20 (L) <br> Tu Oct 25 (P/D) || Novelty 2 (EJ) || P1: <br> P2: || D1: <br> D2:|| P1: <br> P2: <br> D:<br><br />
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| Th Oct 27 (L) <br> Tu Nov 1 (P/D) || Novelty 3 (YY) || P1: Amy LaFountain <br> P2: || D1: Matt Sasaki <br> D2:|| P1: <br> P2: <br> D:<br><br />
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| Th Nov 3 (L) <br> Tu Nov 8 (P/D) || Evolution in Action: Domestication and Agriculture (YY) || P1: <br> P2: || D1: Lisa Terlova <br> D2:|| P1: <br> P2: <br> D:<br><br />
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| Th Nov 10 (L) <br> Tu Nov 15 (P/D) || Evolution in Action: Humans as Unintentional Agents of Selection (EJ) || P1: Jacob Kasper<br> P2: || D1: Sarah Hurley<br> D2:|| P1: <br> P2: <br> D:<br><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: || D1: <br> D2:|| P1: <br> P2: <br> D:<br><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: <br> D2:|| P1: <br> P2: <br> D:<br><br />
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| Th Dec 8 || Wrap-up || P1: <br> P2: || N/A || <br><br />
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| Final Exam Period || Preproposal Review Panel || NA || NA||<br></div>Elizabeth Clark