Difference between revisions of "Evo Devo Fall2013"

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<span style="font-size: x-large">EEB 5333, Fall 2013</span><br>
 
<span style="font-size: x-large">EEB 5333, Fall 2013</span><br>
 
<span style="font-size: large">''Evolutionary Developmental Biology''</span><br>
 
<span style="font-size: large">''Evolutionary Developmental Biology''</span><br>
<span style="font-size: small">'''Meeting Time: Tuesdays, 2:00-3:15 pm, Bamford Room (TLS 171B)'''<br>
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<span style="font-size: small">'''Meeting Time: Tuesdays and Thursdays, 2:00-3:15 pm, Bamford Room (TLS 171B)'''<br>
  
 
==Description==
 
==Description==
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Office hours: by appointment<br>
 
Office hours: by appointment<br>
  
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==Announcements and Handouts==
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It's time to begin the conversations about project topics.  We'd like everyone to have a topic approved by Sept. 20.  You can initiate conversations with us by email or in person.  Cera, Nora, Ellen, Wei: your primary contact is Carl.  Dister, Nasim, Jeff, Tim: your primary contact is Elizabeth.<br>
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<br>
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<b>Discussion leaders</b>: Please email a pdf with discussion questions to both Elizabeth and Carl.  In the ideal world, this would happen no later than Tuesday night of the week you will present.  we will post it on the website.<br>
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<br>
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[http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0f/Evodevo_Sources.pdf Books & Sources in Evolutionary Developmental Biology]<br>
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<br>
  
 
==Expectations and Grading==
 
==Expectations and Grading==
 
This course has a mixed lecture/discussion format.  In general, Tuesdays will be used for lectures that provide an overview and background information.  Thursdays will be dedicated to student-led discussion based on reading from the literature.  We expect everyone to participate actively in the class.  In order to help prepare for discussions, you should write a brief (<1 page) reaction piece to each set of readings, highlighting your thoughts about the readings, connections between them or questions raised by them.  This will be handed in each week.  Responsibility for leading the discussions will rotate. 
  
 
This course has a mixed lecture/discussion format.  In general, Tuesdays will be used for lectures that provide an overview and background information.  Thursdays will be dedicated to student-led discussion based on reading from the literature.  We expect everyone to participate actively in the class.  In order to help prepare for discussions, you should write a brief (<1 page) reaction piece to each set of readings, highlighting your thoughts about the readings, connections between them or questions raised by them.  This will be handed in each week.  Responsibility for leading the discussions will rotate. 
  
You are required to complete an independent project on a topic of your choice.  Appropriate topics will integrate diverse data types or theoretical models and empirical information, and allow you to explore a particular example or concept in greater depth.  You should discuss your choice of topics with one of us no later than Friday, October 28. The last week of class will be devoted to presentations and discussions based on these projects. You will be in charge of assigning a paper relevant to your presentation.

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You are expected to complete an independent project on a topic of your choice.  Ideally, your topic will be closely connected to your own research interests, and also integrate multiple topics covered in class .  You should discuss your choice of topics with one of us no later than Friday, Sept. 20. To help you stay on track, an outline and relevant references are due on Tuesday, Oct. 8.  The final project paper is due by Monday Nov. 25, and the last week of class will be devoted to presentations and discussions based on these projects.
 
There will be one take-home exam due the day of the Final Exam. It will consist of one or several essay questions that will ask you to integrate the knowledge that you have acquired during the course. 
  
 
There will be one take-home exam due the day of the Final Exam. It will consist of one or several essay questions that will ask you to integrate the knowledge that you have acquired during the course. 
  
  
 
<br>
 
<br>
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===Deadlines===
 
===Deadlines===
 
<table>
 
<table>
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</tr>
 
</tr>
 
<tr>
 
<tr>
<td>Friday, Oct. 28</td><td>Term paper topic approved</td>
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<td>Friday, Sept. 20</td><td>Project topic approved</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
<td>Thursday, Dec. 1</td><td>Independent project paper due</td>
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<td>Tuesday, Oct. 8</td><td>Project outline and references due</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
<td>Dec. 6-8</td><td>Independent project presentations</td>
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<td>Monday, Nov. 25</td><td>Project paper due</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
<td>Tuesday, Dec. 13</td><td>Final exam due</td>
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<td>Dec. 3-5</td><td>Project presentations</td>
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</tr>
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<tr>
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<td>Tuesday, Dec. 10</td><td>Final exam due</td>
 
</tr>
 
</tr>
 
</table>
 
</table>
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</tr>
 
</tr>
 
<tr>
 
<tr>
<td>Individual project</td><td>40%, based on presentation (15%) and paper (25%)</td>
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<td>Independent project</td><td>40%, based on presentation (15%) and paper (25%)</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
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===Aug. 27:  Overview of evolutionary developmental biology===
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===Week 1 (Aug. 27/29):  Overview of evolutionary developmental biology (EJ)===
[http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0f/Evodevo_Sources.pdf Books & Sources in Evolutionary Developmental Biology]<br>
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Discussion Leader: Elizabeth<br>
 
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Discussion Readings:<br>
===Sept. 6:  The molecular building blocks of development===
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Discussion Questions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2011_Discussion1Questions.pdf}}  <br>
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Discussion Readings<br>
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<ul>
 
<ul>
<li>Brakefield PM. 2011. Evodevo and accounting for Darwin's endless forms. Philos Trans R Soc Lond B Biol Sci. 366: 2069-75. [http://www.nature.com/nrg/journal/v8/n12/full/nrg2219.html link]</li>
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<li>Moczek AP. 2012. The nature of nurture and the future of evodevo: toward a theory of developmental evolution. Int. Comp. Biol. 52:108-119. [http://ezproxy.lib.uconn.edu/login?url=http://icb.oxfordjournals.org/content/52/1/108.long link]</li>
<li>Müller GB. 2007. Evo-devo: extending the evolutionary synthesis. Nat Rev Genet. 8(12):943-9. [http://rstb.royalsocietypublishing.org/content/366/1574/2069.long link]</li>
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<li>Wray GA. 2010. Embryos and evolution: 150 years of reciprocal illumination.  Pp. 215-239 In Bell MA, Futuyma DJ, Eanes WF, Levinton JS, Evolution since Darwin: The First 150 Years. Sinauer Associates, Sunderland MA. [EJ will provide copies]</li>
 
<li>Wray GA. 2010. Embryos and evolution: 150 years of reciprocal illumination.  Pp. 215-239 In Bell MA, Futuyma DJ, Eanes WF, Levinton JS, Evolution since Darwin: The First 150 Years. Sinauer Associates, Sunderland MA. [EJ will provide copies]</li>
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If time permits (I know there's not much this week!), I'd also encourage you to read this:
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<li>Müller GB. 2007. Evo-devo: extending the evolutionary synthesis. Nat Rev Genet. 8(12):943-9. [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nrg/journal/v8/n12/full/nrg2219.html link]</li>
 
</ul>
 
</ul>
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Discussion Questions: {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2013_Discussion1Questions.pdf}}  <br>
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===Week 2 (Sept. 3/5): Morphological and molecular patterns (EJ)===
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Discussion Leader: Jeff<br>
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Discussion Readings: The developmental hourglass and the phylotypic stage<br>
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<ul>
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<li>Quint M, Drost HG, Gabel A, Ullrich KK, Bönn M, Grosse I. 2012. A transcriptomic hourglass in plant embryogenesis. Nature 490(7418):98-101.[http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v490/n7418/full/nature11394.html link]</li>
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<li>Irie N, Kuratani S. 2011. Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis.
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Nat Commun. 2:248. [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/ncomms/journal/v2/n3/full/ncomms1248.html link]</li>
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<li>Xiangjun Tian, Joan E. Strassmann and David C. Queller. 2013. Dictyostelium Development Shows a Novel Pattern of Evolutionary Conservation. Mol. Biol. Evol. 30:977-984. [http://ezproxy.lib.uconn.edu/login?url=http://mbe.oxfordjournals.org/content/30/4/977.full link]</li>
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[http://embryo.asu.edu/pages/slime-mold-development-video-john-tyler-bonner Slime molds in action!]
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</ul>
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Discussion Questions: {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2013_Discussion2Questions.pdf}}  <br>
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===Week 3 (Sept. 10/12): The molecular building blocks of development (CS)===
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Discussion Leader: Cera<br>
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Discussion Readings:<br>
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<li>Hoekstra, H. E. and J. A. Coyne. 2007. The locus of evolution: evo devo and the genetics of adaptation. Evolution 61:995-1016. [http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2007.00105.x/abstract;jsessionid=A6CE2F975795DC863F781C3AEF0AC936.d04t01 link]
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<li>Carroll, S. B. 2008. EvoDevo and an Expanding Evolutionary Synthesis: a genetic theory of morphological evolution. Cell 134:25-36.
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[https://vpn.uconn.edu/science/article/pii/,DanaInfo=www.sciencedirect.com+S0092867408008179 link]
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<li>Wessinger, C. A. and M. D. Rausher. 2012. Lessons from flower colour evolution on targets of selection. Journal of Experimental Botany 63:5741-5749.
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[https://vpn.uconn.edu/content/63/16/,DanaInfo=jxb.oxfordjournals.org+5741.full.pdf+html link]
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<br>
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Discussion Questions: {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2013_Discussion3Questions.pdf}}  <br>
 
<br>
 
<br>
===Sept. 13: Small RNAs: another layer of gene regulation===
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===Week 4 (Sept. 17/19): Evolution of developmental networks (CS)===
Discussion Leader: Colin Carlson<br>
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<font color="#FF3300"><b>Reminder:</b></font> Talk to Carl or Elizabeth about your proposed project this week!<br>
Discussion Questions.<br>
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Discussion Leader: Carl<br>
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Discussion Readings:<br>Lowe, C. B., M. Kellis, et al. 2011. Three periods of regulatory innovation during vertebrate evolution. Science 333: 1019-1024.
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10.1126/science.1202702
  
General questions of interest:
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Chae, L., I. Lee, et al. 2012. Towards understanding how molecular networks evolve in plants. Current Opinion in Plant Biology 15: 177-184.
• So just what the bloody hell is a small RNA? (Fig. 1)
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10.1016/j.pbi.2012.01.006
• Hare and Frankel both use Drosophila as the study organism – not an uncommon choice, but how representative is Drosophila as a model of genetic evolution? How broadly can the results be generalized?
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Lynch:
 
- Is this paper something which could ever be made accessible to the public? (eg. “As a consequence of the modular structure of cis-regulatory regions, the effect of mutations that alter a single cis-regulatory element will be restricted to particular places and times and not globally affect gene expression, that is, not alter expression in every tissue in which a particular gene is expressed.”)
 
- What is the ultimate point of this paper? (e.g. is it that last sentence, “Thus, the evolution of transcription factor proteins themselves, and not just their binding sites, plays an active role in the evolution of development.”)
 
  
Frankel:
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Discussion Questions:<br>
- How does this paper disagree with previous literature (eg. Sticklebacks)? What are the implications for:
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o Said previous studies?
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o Overall perspective?
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o Our interpretation of this study’s quality?
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- In Fig. 5 why does the pattern reverse for the all-mutation data?
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- “Widespread deletion of cis-regulatory DNA may thus reduce the evolutionary potential of existing enhancers.” – What are the implications for evolvability and genetic potential? (Hopeful monsters?)
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Hare:
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===Week 5 (Sept. 24/26): Homology (CS)===
- What’s going on in Figure 2?
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Discussion Leader: Nora<br>
- Figures 1 & 6: What do they represent? How do they differ? Is this a clear format in which to present data?
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Discussion Readings:<br>
- “A handful of isolated case studies support our findings.” – Again, does this make the paper groundbreaking, or dubious?
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Gillis, J. A., M. S. Modrell, et al. 2013. Developmental evidence for serial homology of the vertebrate jaw and gill arch skeleton. Nature Communications 4. 
- “we note that insertions and deletions are a major source of sequence variation in Drosophila,” – who here was shocked to learn insertions and deletions could possibly be contributing to sequence variation? (Serious question: How much does this contribution vary, lineage by lineage? Is this something worth spending serious time studying?)
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10.1038/ncomms2429
- For fun… Does Figure 7 reek of Microsoft Excel? What does this tell us about the effort required to publish in PLoS?
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<br>
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Sharma, V., B. N. Tripathi, et al. 2012. Organ-wise homologies of stipule, leaf and inflorescence between Pisum sativum genetic variants, Delonix regia and Caesalpinia bonduc indicate parallel evolution of morphogenetic regulation. Plant Systematics and Evolution 298: 1167-1175. 
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10.1007/s00606-012-0612-x
  
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Discussion Questions:<br>
  
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===Week 6 (Oct. 1/3): Homoplasy (CS)===
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Discussion Leader: Carl<br>
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Background reading for Tuesday: <br>
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Arendt, J. and D. Reznick. 2008. Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation? Trends in Ecology & Evolution 23: 26-32.  10.1016/j.tree.2007.09.011
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<br><br>
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Discussion Readings:<br>
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Zhang, R., C. C. Guo, et al. 2013. Disruption of the petal identity gene APETALA3-3 is highly correlated with loss of petals within the buttercup family (Ranunculaceae). Proceedings of the National Academy of Sciences of the United States of America 110: 5074-5079. 10.1073/pnas.1219690110
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<br><br>Muschick, M., A. Indermaur, et al. 2012. Convergent evolution within an adaptive radiation of cichlid fishes. Current Biology 22: 2362-2368.    10.1016/j.cub.2012.10.048
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<br><br>
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Discussion Questions:<br>
  
Discussion Readings<br>
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===Week 7 (Oct. 8/10): Constraints (EJ)===
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<font color="#FF3300"><b>Reminder:</b></font> Project outlines and references due on Tuesday!<br>
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Discussion Leader: Dister<br>
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Discussion Readings:<br>
 
<ul>
 
<ul>
<li>Frankel N, Erezyilmaz DF, McGregor AP, Wang S, Payre F, Stern DL. 2011. Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature 474(7353):598-603. [http://www.nature.com/nature/journal/v474/n7353/full/nature10200.html link]</li>
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<li>Chitwood DH, Headland LR, Ranjan A, Martinez CC, Braybrook SA, Koenig DP, Kuhlemeier C, Smith RS, Sinha NR. 2012. Leaf asymmetry as a developmental constraint imposed by auxin-dependent phyllotactic patterning. Plant Cell 24(6):2318-27. [http://ezproxy.lib.uconn.edu/login?url=http://www.plantcell.org/content/24/6/2318.long link]</li>
<li>Hare EE, Peterson BK, Iyer VN, Meier R, Eisen MB. 2007. Sepsid ''even-skipped'' enhancers are functionally conserved in ''Drosophila'' despite lack of sequence conservation. PLoS Genet4(6):e1000106. [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000106 link]</li>
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<li>
<li>Lynch VJ, Wagner GP. 2008. Resurrecting the role of transcription factor change in developmental evolution. Evolution 62(9):2131-54. [http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2008.00440.x/full link]</li>
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de Bakker MA, Fowler DA, den Oude K, Dondorp EM, Navas MC, Horbanczuk JO, Sire JY, Szczerbińska D, Richardson MK. 2013. Digit loss in archosaur evolution and the interplay between selection and constraintsNature 500(7463):445-8. [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v500/n7463/full/nature12336.html link]</li>
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<li>Salazar-Ciudad I, Marín-Riera M. 2013. Adaptive dynamics under development-based genotype-phenotype maps. Nature 497:361-4. [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v497/n7449/full/nature12142.html link]</li>
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Highly recommended: read the [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v497/n7449/full/nature12099.html News and Views] first!
 
</ul>
 
</ul>
<br>
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===Sept. 20:  Development and homoplasy===
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Discussion Questions{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2013_Discussion7Questions.pdf}}<br>
Discussion Leader: Elizabeth<br>
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Discussion Questions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2011_Discussion3Questions.pdf}} <br>
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===Week 8 (Oct. 15/17): Novelty (EJ)===
Discussion Readings<br>
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Discussion Leader: Nasim<br>
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Discussion Readings:<br>
 
<ul>
 
<ul>
<li>Christodoulou F, Raible F, Tomer R, Simakov O, Trachana K, Klaus S, Snyman H, Hannon GJ, Bork P, Arendt D. 2010. Ancient animal microRNAs and the evolution of tissue identity. Nature 463(7284):1084-8. [http://www.nature.com/nature/journal/v463/n7284/full/nature08744.html link]</li>
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<li>Rebeiz M, Jikomes N, Kassner VA, Carroll SB. 2011. Evolutionary origin of a novel gene expression pattern through co-option of the latent activities of existing regulatory sequences. Proc Natl Acad Sci 108(25):10036-43. [http://ezproxy.lib.uconn.edu/login?url=http://www.pnas.org/content/108/25/10036.full link]</li>
<li>Loh YH, Yi SV, Streelman JT. 2011. Evolution of microRNAs and the diversification of species. Genome Biol Evol. 3:55-65. [http://gbe.oxfordjournals.org/content/3/55.long link]</li>
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<li>Sharma B, Kramer E. 2013. Sub- and neo-functionalization of APETALA3 paralogs have contributed to the evolution of novel floral organ identity in Aquilegia (columbine, Ranunculaceae). New Phytol. 197(3):949-57. [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/nph.12078/full link]</li>
<li>Wu CI, Shen Y, Tang T. 2009. Evolution under canalization and the dual roles of microRNAs: a hypothesis. Genome Res. 19(5):734-43. [http://genome.cshlp.org/content/19/5/734.long link]</li>
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<li>Oliver JC, Tong XL, Gall LF, Piel WH, Monteiro A. 2012. A single origin for nymphalid butterfly eyespots followed by widespread loss of associated gene expression. PLoS Genet. 8(8):e1002893. [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002893 link]</li>
 
</ul>
 
</ul>
<br>
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Discussion Questions: {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2013_Discussion8Questions.pdf}} <br>
 
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===Week 9 (Oct. 22/24): Morphospace (CS)===
===Sept. 27: Evolution of developmental networks===
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Discussion Leader: class<br>
Discussion Leader: Jessie Rack
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Discussion Readings:<br>
 
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Discussion Readings :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/limnology/restricted/Discussion%20Questions%209_27.pdf}}Discussion Questions 9_27.pdf<br>
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<ul>
 
<ul>
<li>Gompel N, Prud'homme B. 2009. The causes of repeated genetic evolution. Dev Biol. 332(1):36-47. [http://www.sciencedirect.com/science/article/pii/S001216060900565X link]</li>
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<li> Bennett & Goswami. 2013. Statistical support for the hypothesis of developmental constraint in marsupial skull evolution. BMC Biology 11: 52.</li>
<li>Cooley AM, Modliszewski JL, Rommel ML, Willis JH. 2011. Gene duplication in ''Mimulus'' underlies parallel floral evolution via independent trans-regulatory changes. Curr Biol. 21(8):700-4. [http://www.sciencedirect.com/science/article/pii/S0960982211003009 link]</li>
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<li>Arbour & Lopez-Fernandez. 2013. Ecological variation in South American geophagine cichlids arose during an early burst of adaptive morphological and functional evolution. Proceedings of the Royal Society B-Biological Sciences 280: 20130849.</li>
<li>Reed RD, Papa R, Martin A, Hines HM, Counterman BA, Pardo-Diaz C, Jiggins CD, Chamberlain NL, Kronforst MR,Chen R, Halder G, Nijhout HF, McMillan WO. 2011. ''optix'' drives the repeated convergent evolution of butterfly wing pattern mimicry. Science 333(6046):1137-41. [http://www.sciencemag.org/content/333/6046/1137.full link]</li>
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<li>Roelants et al. 2011. Anuran radiations and the evolution of tadpole morphospace. Proceedings of the National Academy of Sciences USA 108: 8731-8736. 10.1073/pnas.1100633108</li>
 
</ul>
 
</ul>
<br>
 
  
===Oct. 4:  Development and homology===
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Discussion Questions:<br>
Discussion Leader: Frank Smith
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===Week 10 (Oct. 29/31): Modularity (EJ)===
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Discussion Leader: Wei<br>
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Discussion Readings:<br>
 
<ul>
 
<ul>
<li>Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. 2011. Three periods of regulatory innovation during vertebrate evolution. Science. 2011 333(6045):946-7. [http://www.sciencemag.org/content/333/6045/1019.short link]</li>
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<li>Mallarino, R., P. R. Grant, et al. 2011. Two developmental modules establish 3D beak-shape variation in Darwin's finches. Proceedings of the National Academy of Sciences USA 108:4057-4062.
<li>Poelwijk FJ, de Vos MG, Tans SJ. 2011. Tradeoffs and optimality in the evolution of gene regulation. Cell 146(3):350-2. [http://www.sciencedirect.com/science/article/pii/S0092867411007100 link]</li>
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[http://ezproxy.lib.uconn.edu/login?url=http://www.pnas.org/content/108/10/4057 link]</li>
<li> McLean CY, Reno PL, Pollen AA, Bassan AI, Capellini TD, Guenther C, Indjeian VB, Lim X, Menke DB, Schaar BT, Wenger AM, Bejerano G, Kingsley DM. 2011. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471(7337):216-9. [http://www.nature.com/nature/journal/v471/n7337/abs/nature09774.html link]</li>
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<li>Parsons KJ, Márquez E, Albertson RC. 2012. Constraint and opportunity: the genetic basis and evolution of modularity in the cichlid mandible. Am Nat. 179(1):64-78.
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[http://ezproxy.lib.uconn.edu/login?url=http://www.jstor.org/stable/10.1086/663200 link]</li>
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<li>Clune J, Mouret JB, Lipson H. 2013. The evolutionary origins of modularity. Proc Biol Sci. B 280(1755):20122863.  
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[http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/280/1755/20122863.long link]</li>
 
</ul>
 
</ul>
<br>
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Discussion Questions: {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2013_Discussion10Questions.pdf}}  <br>
===Oct. 11: Developmental constraints and evolution===
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Discussion Leader: Jon Velotta
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===Week 11 (Nov. 5/7): Robustness and plasticity (CS)===
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Discussion Leader: Tim<br>
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Discussion Readings:<br>
 
<ul>
 
<ul>
<li>Shubin N, Tabin C, Carroll S. 2009. Deep homology and the origins of evolutionary novelty. Nature. 2009457(7231):818-23. [http://www.nature.com/nature/journal/v457/n7231/full/nature07891.html link]</li>
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<li>Scoville, A. G. and M. Pfrender. 2010. Phenotypic plasticity facilitates recurrent rapid adaptation to introduced predators. Proceedings of the National Academy of Sciences of the United States of America 107: 4260-4263. 10.1073/pnas.0912748107.
<li>Young RL, Wagner GP. 2011. Why ontogenetic homology criteria can be misleading: lessons from digit identity transformations. J Exp Zool B Mol Dev Evol. 316B(3):165-70. [http://onlinelibrary.wiley.com/doi/10.1002/jez.b.21396/full link]</li>
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[http://ezproxy.lib.uconn.edu/login?url=http://www.pnas.org/content/107/9/4260.full link]</li>
<li>Van Valen LM. 1982. Homology and causes. Journal of Morphology 173: 305-312. [http://onlinelibrary.wiley.com/doi/10.1002/jmor.1051730307/abstract link]</li>
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<li>Gunter HM, Fan S, Xiong F, Franchini P, Fruciano C, Meyer A. 2013. Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish. Mol Ecol. 22(17):4516-31.
 +
[http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/mec.12417/full link] </li>
 +
<li>Sgrò CM, Wegener B, Hoffmann AA. 2010. A naturally occurring variant of Hsp90 that is associated with decanalization. Proc Biol Sci. 77(1690):2049-57.
 +
[http://ezproxy.lib.uconn.edu/login?url=http://rspb.royalsocietypublishing.org/content/277/1690/2049.long link]</li>
 
</ul>
 
</ul>
<br>
+
Discussion Questions:<br>
  
===Oct. 18: Discussion: Constraints  ---  Lecture: Modularity===
+
===Week 12 (Nov. 12/14): Evolvability (EJ)===
Discussion Leader: Brigette Zacharczenko
+
Discussion Leader: Ellen<br>
 +
Discussion Readings:<br>
 
<ul>
 
<ul>
<li>Maynard Smith J; R. Burian; S. Kauffman; P. Alberch; J. Campbell; B. Goodwin; R. Lande; D. Raup; L. Wolpert.  1985.  Developmental constraints and evolution: A perspective from the Mountain Lake Conference on development and evolution. Q. Rev. Biol. 60:265-287 [http://www.jstor.org/stable/2828504 link]</li>
+
<li>Woods RJ, Barrick JE, Cooper TF, Shrestha U, Kauth MR, Lenski RE. 2011. Second-order selection for evolvability in a large Escherichia coli population. Science 331(6023):1433-6. [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencemag.org/content/331/6023/1433.long link]</li>
<li>Salazar-Ciudad I, Jernvall J. 2010. A computational model of teeth and the developmental origins of morphological variation. Nature 464(7288):583-6. [http://www.nature.com/nature/journal/v464/n7288/full/nature08838.html link]</li>
+
<li>Garfield DA, Runcie DE, Babbitt CC, Haygood R, Nielsen WJ, Wray GA. 2013. The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network. PLoS Biol 11(10): e1001696. [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001696 link]</li>
<li>Renaud S, Auffray JC, Michaux J. 2006. Conserved phenotypic variation patterns, evolution along lines of least resistance, and departure due to selection in fossil rodents. Evolution 60(8):1701-17. [http://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2006.tb00514.x/pdf link]</li>
+
<li>Rabosky DL, Santini F, Eastman J, Smith SA, Sidlauskas B, Chang J, Alfaro ME. 2013. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nat Commun. 4:1958. [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/ncomms/2013/130606/ncomms2958/full/ncomms2958.html link]</li>
Don't forget the paper for Carl's lecture!
+
 
</ul>
 
</ul>
<br>
+
Discussion Questions: {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2013_Discussion12Questions.pdf}}  <br>
 
+
===Oct. 25: Discussion: Modularity ---  Lecture: Robustness and canalization===
+
Discussion Leader: Carl
+
  
 +
===Week 13 (Nov. 19/21): Case studies (EJ) and heterochrony (CS)===
 +
Discussion Leader: Class--email a question to Elizabeth<br>
 +
Discussion Readings: Let'st just focus on the future, instead of case studies.  So forget about Arnoult et al. (with apologies to those of you who have already read it).<br>
 
<ul>
 
<ul>
<li>Bissell, E. K. and P. K. Diggle. 2010. Modular genetic architecture of floral morphology in Nicotiana: quantitative genetic and comparative phenotypic approaches to floral integration. Journal of Evolutionary Biology 23: 1744-1758.
+
<li>Irschick DJ, Albertson RC, Brennan P, Podos J, Johnson NA, Patek S, Dumont E. 2013. Evo-devo beyond morphology: from genes to resource use. Trends Ecol Evol. 28(5):267-73. [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencedirect.com/science/article/pii/S0169534712003151 link]</li>
[http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2010.02040.x/abstract;jsessionid=7BA3E3E8FD8B21217A51BF1E3838A97D.d02t01 link]</li>
+
<li>Parsons KJ, Albertson RC. 2013. Unifying and generalizing the two strands of evo-devo. Trends Ecol Evol. 28(10):584-91. [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencedirect.com/science/article/pii/S0169534713001675 link]</li>
<li>Mallarino, R., P. R. Grant, et al. 2011. Two developmental modules establish 3D beak-shape variation in Darwin's finches. Proceedings of the National Academy of Sciences USA 108: 4057-4062.
+
[http://www.pnas.org/content/108/10/4057 link]</li>
+
<li>Goswami, A. and P. D. Polly. 2010. The influence of modularity on cranial morphological disparity in Carnivora and Primates (Mammalia). PLoS ONE 5: e9517.
+
[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0009517 link]</li>
+
 
+
 
</ul>
 
</ul>
<br>
+
Optional Reading for those interested in micro-evo-devo:
 
+
===Nov. 1:  Discussion: Robustness and canalization --- Lecture: Plasticity ===
+
Discussion Leader: Jessie Rack
+
 
+
 
<ul>
 
<ul>
<li>Hall, M. C., I. Dworkin, et al. 2007. Genetics of microenvironmental canalization in Arabidopsis thaliana. Proceedings of the National Academy of Sciences USA 104: 13717-13722.
+
<li>Nunes MD, Arif S, Schlötterer C, McGregor AP. 2013. A perspective on micro-evo-devo: progress and potential. Genetics 195(3):625-34. [http://ezproxy.lib.uconn.edu/login?url=http://www.genetics.org/content/195/3/625.long link]</li>
[http://www.pnas.org/content/104/34/13717.abstract?etoc link]</li>
+
<li>Edgell, T. C., B. R. Lynch, et al. 2009. Experimental evidence for the rapid evolution of behavioral canalization in natural populations. American Naturalist 174: 434-440.
+
[http://www.jstor.org/stable/10.1086/603639 link]</li>
+
<li>Milton, C. C., C. M. Ulane, et al. 2006. Control of canalization and evolvability by Hsp90. PLoS ONE 1: e75.
+
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000075 link]</li>
+
 
+
 
</ul>
 
</ul>
<br>
+
Discussion Questions: {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2013_Discussion13Questions.pdf}}  <br>
 +
<font color="#FF3300"><b>Reminder:</b></font> Project papers are due on Monday, Nov. 25!<br><br>
  
===Nov. 8: Discussion: Plasticity ---  Lecture: Evolvability===
+
===Week 14 (Nov. 26/28): Happy Thanksgiving!===
Discussion Leader: Jon Velotta
+
  
<ul>
+
===Week 15 (Dec. 3/5): Project Presentations ===
<li> Beldade, P., A. R. A. Mateus, et al. 2011. Evolution and molecular mechanisms of adaptive developmental plasticity. Molecular Ecology 20: 1347-1363. [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2011.05016.x/abstract link]</li>
+
[[Category:EEB Courses]]
<li>McGuigan, K., N. Nishimura, et al. 2011. Cryptic genetic variation and body size evolution in threespine stickleback. Evolution 65: 1203-1211. [http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2010.01195.x/abstract link]</li>
+
<li>Kulkarni, S. S., I. Gomez-Mestre, et al. 2011. Evolutionary reduction of developmental plasticity in desert spadefoot toads. Journal of Evolutionary Biology 24: 2445–2455.
+
[http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2011.02370.x/abstract link]</li>
+
 
+
</ul>
+
<br>
+
  
===Nov. 15: Discussion: Evolvability --- Lecture: Morphospace ===
+
Here's the presentation order. Of course, any swap that is mutually agreeable to you is fine with us.  Talks should be 15 min., with 5 min. for questions. Please add your title and suggest a background reading. (Dister and Wei: email that information and we'll add it for you).<br><br>
Discussion Leader: Brigette Zacharczenko
+
<b>Tuesday, December 3</b>
 
<ul>
 
<ul>
<li> Woods, R. J., J. E. Barrick, et al. 2011. Second-order selection for evolvability in a large Escherichia coli population. Science 331: 1433-1436. [http://www.sciencemag.org/content/331/6023/1433.full link]</li>
+
<li>Cera: How does development evolve under selection for signaling morphology? [http://www.biomedcentral.com.ezproxy.lib.uconn.edu/1471-2148/13/158 suggested reading]</li>
<li>Young, N. M., G. P. Wagner, et al. 2010. Development and the evolvability of human limbs. Proceedings of the National Academy of Sciences of the United States of America 107: 3400-3405. [http://www.pnas.org/content/107/8/3400 link]</li>
+
<li>Ellen: The evolution of developmental plasticity in the introduced range of an invasive species [http://www.jstor.org/stable/2463217 suggested reading]</li>
 
+
<li>Wei: The origin, development and evolution of plant apomixes [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1002/9780470015902.a0002035.pub2/full link]</li>
 
+
<li>Jeff: Diadromy: why & how. Suggested reading: [http://www.jstor.org/stable/1700892 link]</li>
 
</ul>
 
</ul>
<br>
 
 
===Nov. 22:  Thanksgiving Break===
 
===Nov. 29: Discussion: Morphospace --- Lecture: Novelty===
 
Discussion Leader: Colin Carlson
 
  
 +
<b>Thursday, December 5</b>
 
<ul>
 
<ul>
<li> Stoddard, M. C. and R. O. Prum. 2011. How colorful are birds? Evolution of the avian plumage color gamut. Behavioral Ecology 22: 1042-1052.
+
<li>Nora: Identifying plant functional trait novelty via transgressive segregation [http://ezproxy.lib.uconn.edu/login?url=http://link.springer.com/article/10.1007/s11692-012-9209-0/fulltext.html link]</li>
[http://beheco.oxfordjournals.org/content/22/5/1042 link]</li>
+
<li>Nasim: Neoteny in dwarf males of <i>Groutella Steere </i> [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencedirect.com/science/article/pii/S1433831911000151 link]</li>
<li>Roelants; K.; A. Haas; et al. 2011. Anuran radiations and the evolution of tadpole morphospace. Proceedings of the National Academy of Sciences USA 108: 8731-8736. [http://www.pnas.org/content/108/21/8731 link]</li>
+
<li>Dister: Arbuscular Mycorrhizal: Symbiosis and the Development of Embryophytes [http://ezproxy.lib.uconn.edu/login?url=http://www.sciencedirect.com/science/article/pii/S1369526606001786 link]</li>
<li>Renaud, S. and J. C. Auffray. 2010. Adaptation and plasticity in insular evolution of the house mouse mandible. Journal of Zoological Systematics and Evolutionary Research 48: 138-150.
+
<li>Tim: Petal spot development in th Beetle Daisy [http://ezproxy.lib.uconn.edu/login?url=http://onlinelibrary.wiley.com/doi/10.1111/nph.12112/full link]</li>
[http://onlinelibrary.wiley.com/doi/10.1111/j.1439-0469.2009.00527.x/abstract link]</li>
+
 
+
 
</ul>
 
</ul>
<br>
 
 
===Dec. 6: Project presentations===
 
[[Category:EEB Courses]]
 

Latest revision as of 16:48, 3 December 2013

EEB 5333, Fall 2013
Evolutionary Developmental Biology
Meeting Time: Tuesdays and Thursdays, 2:00-3:15 pm, Bamford Room (TLS 171B)

Description

This is an advanced course that explores the interface between evolutionary biology and developmental biology. In addition to considering how developmental pathways evolve, and the developmental basis of phenotypic evolution, we will ask what novel insights emerge from a synthesis of these fields. Major topics to be considered include the following: developmental constraints, homology, plasticity, novelty and evolvability.

Instructors

Dr. Elizabeth Jockusch
Office: Biology/Pharmacy 305B
Phone: (860) 486-4452
Office hours: by appointment

Dr. Carl Schlichting
Office: Torrey Life Sciences 366
Phone: (860) 486-4056
Office hours: by appointment


Announcements and Handouts

It's time to begin the conversations about project topics. We'd like everyone to have a topic approved by Sept. 20. You can initiate conversations with us by email or in person. Cera, Nora, Ellen, Wei: your primary contact is Carl. Dister, Nasim, Jeff, Tim: your primary contact is Elizabeth.

Discussion leaders: Please email a pdf with discussion questions to both Elizabeth and Carl. In the ideal world, this would happen no later than Tuesday night of the week you will present. we will post it on the website.

Books & Sources in Evolutionary Developmental Biology


Expectations and Grading

This course has a mixed lecture/discussion format. In general, Tuesdays will be used for lectures that provide an overview and background information. Thursdays will be dedicated to student-led discussion based on reading from the literature. We expect everyone to participate actively in the class. In order to help prepare for discussions, you should write a brief (<1 page) reaction piece to each set of readings, highlighting your thoughts about the readings, connections between them or questions raised by them. This will be handed in each week. Responsibility for leading the discussions will rotate. 
 You are expected to complete an independent project on a topic of your choice. Ideally, your topic will be closely connected to your own research interests, and also integrate multiple topics covered in class . You should discuss your choice of topics with one of us no later than Friday, Sept. 20. To help you stay on track, an outline and relevant references are due on Tuesday, Oct. 8. The final project paper is due by Monday Nov. 25, and the last week of class will be devoted to presentations and discussions based on these projects. There will be one take-home exam due the day of the Final Exam. It will consist of one or several essay questions that will ask you to integrate the knowledge that you have acquired during the course. 



Deadlines

WeeklyDiscussion pieces
Friday, Sept. 20Project topic approved
Tuesday, Oct. 8Project outline and references due
Monday, Nov. 25Project paper due
Dec. 3-5Project presentations
Tuesday, Dec. 10Final exam due


Course grade

Discussions35%, including participation, leading discussion, and reaction pieces
Independent project40%, based on presentation (15%) and paper (25%)
Final exam25%


Topics and Readings

Week 1 (Aug. 27/29): Overview of evolutionary developmental biology (EJ)

Discussion Leader: Elizabeth
Discussion Readings:

  • Moczek AP. 2012. The nature of nurture and the future of evodevo: toward a theory of developmental evolution. Int. Comp. Biol. 52:108-119. link
  • Wray GA. 2010. Embryos and evolution: 150 years of reciprocal illumination. Pp. 215-239 In Bell MA, Futuyma DJ, Eanes WF, Levinton JS, Evolution since Darwin: The First 150 Years. Sinauer Associates, Sunderland MA. [EJ will provide copies]
  • If time permits (I know there's not much this week!), I'd also encourage you to read this:

  • Müller GB. 2007. Evo-devo: extending the evolutionary synthesis. Nat Rev Genet. 8(12):943-9. link

Discussion Questions: Pdficon small.gif

Week 2 (Sept. 3/5): Morphological and molecular patterns (EJ)

Discussion Leader: Jeff
Discussion Readings: The developmental hourglass and the phylotypic stage

  • Quint M, Drost HG, Gabel A, Ullrich KK, Bönn M, Grosse I. 2012. A transcriptomic hourglass in plant embryogenesis. Nature 490(7418):98-101.link
  • Irie N, Kuratani S. 2011. Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis. Nat Commun. 2:248. link
  • Xiangjun Tian, Joan E. Strassmann and David C. Queller. 2013. Dictyostelium Development Shows a Novel Pattern of Evolutionary Conservation. Mol. Biol. Evol. 30:977-984. link
  • Slime molds in action!

Discussion Questions: Pdficon small.gif

Week 3 (Sept. 10/12): The molecular building blocks of development (CS)

Discussion Leader: Cera
Discussion Readings:

  • Hoekstra, H. E. and J. A. Coyne. 2007. The locus of evolution: evo devo and the genetics of adaptation. Evolution 61:995-1016. link
  • Carroll, S. B. 2008. EvoDevo and an Expanding Evolutionary Synthesis: a genetic theory of morphological evolution. Cell 134:25-36. link
  • Wessinger, C. A. and M. D. Rausher. 2012. Lessons from flower colour evolution on targets of selection. Journal of Experimental Botany 63:5741-5749. link
    Discussion Questions: Pdficon small.gif

    Week 4 (Sept. 17/19): Evolution of developmental networks (CS)

    Reminder: Talk to Carl or Elizabeth about your proposed project this week!
    Discussion Leader: Carl
    Discussion Readings:
    Lowe, C. B., M. Kellis, et al. 2011. Three periods of regulatory innovation during vertebrate evolution. Science 333: 1019-1024. 10.1126/science.1202702

    Chae, L., I. Lee, et al. 2012. Towards understanding how molecular networks evolve in plants. Current Opinion in Plant Biology 15: 177-184. 10.1016/j.pbi.2012.01.006


    Discussion Questions:

    Week 5 (Sept. 24/26): Homology (CS)

    Discussion Leader: Nora
    Discussion Readings:
    Gillis, J. A., M. S. Modrell, et al. 2013. Developmental evidence for serial homology of the vertebrate jaw and gill arch skeleton. Nature Communications 4. 10.1038/ncomms2429
    Sharma, V., B. N. Tripathi, et al. 2012. Organ-wise homologies of stipule, leaf and inflorescence between Pisum sativum genetic variants, Delonix regia and Caesalpinia bonduc indicate parallel evolution of morphogenetic regulation. Plant Systematics and Evolution 298: 1167-1175. 10.1007/s00606-012-0612-x

    Discussion Questions:

    Week 6 (Oct. 1/3): Homoplasy (CS)

    Discussion Leader: Carl
    Background reading for Tuesday:
    Arendt, J. and D. Reznick. 2008. Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation? Trends in Ecology & Evolution 23: 26-32. 10.1016/j.tree.2007.09.011

    Discussion Readings:
    Zhang, R., C. C. Guo, et al. 2013. Disruption of the petal identity gene APETALA3-3 is highly correlated with loss of petals within the buttercup family (Ranunculaceae). Proceedings of the National Academy of Sciences of the United States of America 110: 5074-5079. 10.1073/pnas.1219690110

    Muschick, M., A. Indermaur, et al. 2012. Convergent evolution within an adaptive radiation of cichlid fishes. Current Biology 22: 2362-2368. 10.1016/j.cub.2012.10.048

    Discussion Questions:

    Week 7 (Oct. 8/10): Constraints (EJ)

    Reminder: Project outlines and references due on Tuesday!
    Discussion Leader: Dister
    Discussion Readings:

    • Chitwood DH, Headland LR, Ranjan A, Martinez CC, Braybrook SA, Koenig DP, Kuhlemeier C, Smith RS, Sinha NR. 2012. Leaf asymmetry as a developmental constraint imposed by auxin-dependent phyllotactic patterning. Plant Cell 24(6):2318-27. link
    • de Bakker MA, Fowler DA, den Oude K, Dondorp EM, Navas MC, Horbanczuk JO, Sire JY, Szczerbińska D, Richardson MK. 2013. Digit loss in archosaur evolution and the interplay between selection and constraints. Nature 500(7463):445-8. link
    • Salazar-Ciudad I, Marín-Riera M. 2013. Adaptive dynamics under development-based genotype-phenotype maps. Nature 497:361-4. link
    • Highly recommended: read the News and Views first!

    Discussion Questions: Pdficon small.gif

    Week 8 (Oct. 15/17): Novelty (EJ)

    Discussion Leader: Nasim
    Discussion Readings:

    • Rebeiz M, Jikomes N, Kassner VA, Carroll SB. 2011. Evolutionary origin of a novel gene expression pattern through co-option of the latent activities of existing regulatory sequences. Proc Natl Acad Sci 108(25):10036-43. link
    • Sharma B, Kramer E. 2013. Sub- and neo-functionalization of APETALA3 paralogs have contributed to the evolution of novel floral organ identity in Aquilegia (columbine, Ranunculaceae). New Phytol. 197(3):949-57. link
    • Oliver JC, Tong XL, Gall LF, Piel WH, Monteiro A. 2012. A single origin for nymphalid butterfly eyespots followed by widespread loss of associated gene expression. PLoS Genet. 8(8):e1002893. link

    Discussion Questions: Pdficon small.gif

    Week 9 (Oct. 22/24): Morphospace (CS)

    Discussion Leader: class
    Discussion Readings:

    • Bennett & Goswami. 2013. Statistical support for the hypothesis of developmental constraint in marsupial skull evolution. BMC Biology 11: 52.
    • Arbour & Lopez-Fernandez. 2013. Ecological variation in South American geophagine cichlids arose during an early burst of adaptive morphological and functional evolution. Proceedings of the Royal Society B-Biological Sciences 280: 20130849.
    • Roelants et al. 2011. Anuran radiations and the evolution of tadpole morphospace. Proceedings of the National Academy of Sciences USA 108: 8731-8736. 10.1073/pnas.1100633108

    Discussion Questions:

    Week 10 (Oct. 29/31): Modularity (EJ)

    Discussion Leader: Wei
    Discussion Readings:

    • Mallarino, R., P. R. Grant, et al. 2011. Two developmental modules establish 3D beak-shape variation in Darwin's finches. Proceedings of the National Academy of Sciences USA 108:4057-4062. link
    • Parsons KJ, Márquez E, Albertson RC. 2012. Constraint and opportunity: the genetic basis and evolution of modularity in the cichlid mandible. Am Nat. 179(1):64-78. link
    • Clune J, Mouret JB, Lipson H. 2013. The evolutionary origins of modularity. Proc Biol Sci. B 280(1755):20122863. link

    Discussion Questions: Pdficon small.gif

    Week 11 (Nov. 5/7): Robustness and plasticity (CS)

    Discussion Leader: Tim
    Discussion Readings:

    • Scoville, A. G. and M. Pfrender. 2010. Phenotypic plasticity facilitates recurrent rapid adaptation to introduced predators. Proceedings of the National Academy of Sciences of the United States of America 107: 4260-4263. 10.1073/pnas.0912748107. link
    • Gunter HM, Fan S, Xiong F, Franchini P, Fruciano C, Meyer A. 2013. Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish. Mol Ecol. 22(17):4516-31. link
    • Sgrò CM, Wegener B, Hoffmann AA. 2010. A naturally occurring variant of Hsp90 that is associated with decanalization. Proc Biol Sci. 77(1690):2049-57. link

    Discussion Questions:

    Week 12 (Nov. 12/14): Evolvability (EJ)

    Discussion Leader: Ellen
    Discussion Readings:

    • Woods RJ, Barrick JE, Cooper TF, Shrestha U, Kauth MR, Lenski RE. 2011. Second-order selection for evolvability in a large Escherichia coli population. Science 331(6023):1433-6. link
    • Garfield DA, Runcie DE, Babbitt CC, Haygood R, Nielsen WJ, Wray GA. 2013. The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network. PLoS Biol 11(10): e1001696. link
    • Rabosky DL, Santini F, Eastman J, Smith SA, Sidlauskas B, Chang J, Alfaro ME. 2013. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nat Commun. 4:1958. link

    Discussion Questions: Pdficon small.gif

    Week 13 (Nov. 19/21): Case studies (EJ) and heterochrony (CS)

    Discussion Leader: Class--email a question to Elizabeth
    Discussion Readings: Let'st just focus on the future, instead of case studies. So forget about Arnoult et al. (with apologies to those of you who have already read it).

    • Irschick DJ, Albertson RC, Brennan P, Podos J, Johnson NA, Patek S, Dumont E. 2013. Evo-devo beyond morphology: from genes to resource use. Trends Ecol Evol. 28(5):267-73. link
    • Parsons KJ, Albertson RC. 2013. Unifying and generalizing the two strands of evo-devo. Trends Ecol Evol. 28(10):584-91. link

    Optional Reading for those interested in micro-evo-devo:

    • Nunes MD, Arif S, Schlötterer C, McGregor AP. 2013. A perspective on micro-evo-devo: progress and potential. Genetics 195(3):625-34. link

    Discussion Questions: Pdficon small.gif
    Reminder: Project papers are due on Monday, Nov. 25!

    Week 14 (Nov. 26/28): Happy Thanksgiving!

    Week 15 (Dec. 3/5): Project Presentations

    Here's the presentation order. Of course, any swap that is mutually agreeable to you is fine with us. Talks should be 15 min., with 5 min. for questions. Please add your title and suggest a background reading. (Dister and Wei: email that information and we'll add it for you).

    Tuesday, December 3

    • Cera: How does development evolve under selection for signaling morphology? suggested reading
    • Ellen: The evolution of developmental plasticity in the introduced range of an invasive species suggested reading
    • Wei: The origin, development and evolution of plant apomixes link
    • Jeff: Diadromy: why & how. Suggested reading: link

    Thursday, December 5

    • Nora: Identifying plant functional trait novelty via transgressive segregation link
    • Nasim: Neoteny in dwarf males of Groutella Steere link
    • Dister: Arbuscular Mycorrhizal: Symbiosis and the Development of Embryophytes link
    • Tim: Petal spot development in th Beetle Daisy link