Evo Devo Fall2013

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(Week 3 (Sept. 10/12): The molecular building blocks of development (CS))
(Topics and Readings)
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<b>Discussion leaders</b>: Please email a pdf with discussion questions to the faculty member in charge.  In the ideal world, this would happen no later than Tuesday night of the week you will present.<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>
 
<br>
 
<br>
  
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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.
 
<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.
 
  [https://vpn.uconn.edu/content/63/16/,DanaInfo=jxb.oxfordjournals.org+5741.full.pdf+html link]
 
  [https://vpn.uconn.edu/content/63/16/,DanaInfo=jxb.oxfordjournals.org+5741.full.pdf+html link]
  <br> <br>
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  <br>  
</ul>
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Discussion Questions: {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2013_Discussion3Questions.pdf}}  <br>
Discussion Questions: {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/DiscussionQuestions_Week_3.pdf}}  <br>
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<br>
 
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===Week 4 (Sept. 17/19): Evolution of developmental networks (CS)===
 
===Week 4 (Sept. 17/19): Evolution of developmental networks (CS)===
 
<font color="#FF3300"><b>Reminder:</b></font> Talk to Carl or Elizabeth about your proposed project this week!<br>
 
<font color="#FF3300"><b>Reminder:</b></font> Talk to Carl or Elizabeth about your proposed project this week!<br>
 
Discussion Leader: Carl<br>
 
Discussion Leader: Carl<br>
Discussion Readings:<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.
 +
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:<br>
 
Discussion Questions:<br>
  
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Discussion Leader: Nora<br>
 
Discussion Leader: Nora<br>
 
Discussion Readings:<br>
 
Discussion Readings:<br>
 +
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
 +
<br>
 +
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:<br>
 
Discussion Questions:<br>
  
 
===Week 6 (Oct. 1/3): Homoplasy (CS)===
 
===Week 6 (Oct. 1/3): Homoplasy (CS)===
 
Discussion Leader: Carl<br>
 
Discussion Leader: Carl<br>
 +
Background reading for Tuesday: <br>
 +
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
 +
<br><br>
 
Discussion Readings:<br>
 
Discussion Readings:<br>
 +
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
 +
<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>
 
Discussion Questions:<br>
 
Discussion Questions:<br>
  
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Discussion Leader: Dister<br>
 
Discussion Leader: Dister<br>
 
Discussion Readings:<br>
 
Discussion Readings:<br>
Discussion Questions:<br>
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<ul>
 +
<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>
 +
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. [http://ezproxy.lib.uconn.edu/login?url=http://www.nature.com/nature/journal/v500/n7463/full/nature12336.html link]</li>
 +
<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!
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</ul>
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Discussion Questions: {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2013_Discussion7Questions.pdf}}<br>
  
 
===Week 8 (Oct. 15/17): Novelty (EJ)===
 
===Week 8 (Oct. 15/17): Novelty (EJ)===
 
Discussion Leader: Nasim<br>
 
Discussion Leader: Nasim<br>
 
Discussion Readings:<br>
 
Discussion Readings:<br>
Discussion Questions:<br>
+
<ul>
 
+
<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>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>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>
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</ul>
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Discussion Questions: {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2013_Discussion8Questions.pdf}}  <br>
 
===Week 9 (Oct. 22/24): Morphospace (CS)===
 
===Week 9 (Oct. 22/24): Morphospace (CS)===
 
Discussion Leader: class<br>
 
Discussion Leader: class<br>

Revision as of 23:35, 16 October 2013

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

Contents

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:
    Discussion Questions:

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

    Discussion Leader: Wei
    Discussion Readings:
    Discussion Questions:

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

    Discussion Leader: Tim
    Discussion Readings:
    Discussion Questions:

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

    Discussion Leader: Ellen
    Discussion Readings:
    Discussion Questions:

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

    Discussion Leader: Elizabeth
    Discussion Readings:
    Discussion Questions:
    Reminder: Project papers are due on Monday, Nov. 25!

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

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

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