Difference between revisions of "Evo Devo Fall2013"

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(Topics and Readings)
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===Week 1 (Aug. 27/29):  Overview of evolutionary developmental biology===
 
===Week 1 (Aug. 27/29):  Overview of evolutionary developmental biology===
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Discussion Leader:<br>
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Discussion Readings:<br>
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Discussion Questions:<br>
  
 
===Week 2 (Sept. 3/5):  The molecular building blocks of development===
 
===Week 2 (Sept. 3/5):  The molecular building blocks of development===
Discussion Questions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2011_Discussion1Questions.pdf}}  <br>
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Discussion Leader:<br>
Discussion Readings<br>
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Discussion Readings:<br>
<ul>
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Discussion Questions:<br>
<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>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>
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</ul>
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<br>
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===Week 3 (Sept. 10/12): Small RNAs: another layer of gene regulation===
 
===Week 3 (Sept. 10/12): Small RNAs: another layer of gene regulation===
Discussion Leader: Colin Carlson<br>
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Discussion Leader:<br>
Discussion Questions.<br>
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Discussion Readings:<br>
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Discussion Questions:<br>
  
General questions of interest:
 
• So just what the bloody hell is a small RNA? (Fig. 1)
 
• 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?
 
 
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:
 
- How does this paper disagree with previous literature (eg. Sticklebacks)? What are the implications for:
 
o Said previous studies?
 
o Overall perspective?
 
o Our interpretation of this study’s quality?
 
- In Fig. 5 why does the pattern reverse for the all-mutation data?
 
- “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?)
 
 
Hare:
 
- What’s going on in Figure 2?
 
- Figures 1 & 6: What do they represent? How do they differ? Is this a clear format in which to present data?
 
- “A handful of isolated case studies support our findings.” – Again, does this make the paper groundbreaking, or dubious?
 
- “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?)
 
- For fun… Does Figure 7 reek of Microsoft Excel? What does this tell us about the effort required to publish in PLoS?
 
 
 
 
Discussion Readings<br>
 
<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>
 
<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 Genet.  4(6):e1000106. [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000106 link]</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>
 
</ul>
 
<br>
 
 
===Week 4 (Sept. 17/19):  Development and homoplasy===
 
===Week 4 (Sept. 17/19):  Development and homoplasy===
Discussion Leader: Elizabeth<br>
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Discussion Leader:<br>
Discussion Questions {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/evodevo/EEB5333_Fall2011_Discussion3Questions.pdf}}  <br>
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Discussion Readings:<br>
Discussion Readings<br>
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Discussion Questions:<br>
<ul>
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<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>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>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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</ul>
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<br>
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===Week 5 (Sept. 24/26): Evolution of developmental networks===
 
===Week 5 (Sept. 24/26): Evolution of developmental networks===
Discussion Leader: Jessie Rack
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Discussion Leader:<br>
 
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Discussion Readings:<br>
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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Discussion Questions:<br>
<ul>
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<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>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>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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</ul>
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<br>
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===Week 6 (Oct. 1/3):  Development and homology===
 
===Week 6 (Oct. 1/3):  Development and homology===
Discussion Leader: Frank Smith
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Discussion Leader:<br>
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Discussion Readings:<br>
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Discussion Questions:<br>
  
<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>
 
<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>
 
<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>
 
</ul>
 
<br>
 
 
===Week 7 (Oct. 8/10) :  Developmental constraints and evolution===
 
===Week 7 (Oct. 8/10) :  Developmental constraints and evolution===
Discussion Leader: Jon Velotta
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Discussion Leader:<br>
<ul>
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Discussion Readings:<br>
<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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Discussion Questions:<br>
<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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<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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</ul>
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<br>
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===Week 8 (Oct. 15/17): Modularity===
 
===Week 8 (Oct. 15/17): Modularity===
Discussion Leader: Brigette Zacharczenko
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Discussion Leader:<br>
<ul>
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Discussion Readings:<br>
<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>
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Discussion Questions:<br>
<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>
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<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>
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Don't forget the paper for Carl's lecture!
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</ul>
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<br>
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===Week 9 (Oct. 22/24): Robustness and canalization===
 
===Week 9 (Oct. 22/24): Robustness and canalization===
Discussion Leader: Carl
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Discussion Leader:<br>
 
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Discussion Readings:<br>
<ul>
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Discussion Questions:<br>
<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.
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[http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2010.02040.x/abstract;jsessionid=7BA3E3E8FD8B21217A51BF1E3838A97D.d02t01 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.
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[http://www.pnas.org/content/108/10/4057 link]</li>
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<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.
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[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0009517 link]</li>
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</ul>
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<br>
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===Week 10 (Oct. 29/31): Plasticity ===
 
===Week 10 (Oct. 29/31): Plasticity ===
Discussion Leader: Jessie Rack
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Discussion Leader:<br>
 
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Discussion Readings:<br>
<ul>
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Discussion Questions:<br>
<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.
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[http://www.pnas.org/content/104/34/13717.abstract?etoc link]</li>
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<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.
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[http://www.jstor.org/stable/10.1086/603639 link]</li>
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<li>Milton, C. C., C. M. Ulane, et al. 2006. Control of canalization and evolvability by Hsp90. PLoS ONE 1: e75.
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[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000075 link]</li>
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</ul>
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<br>
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===Week 11 (Nov. 5/7): Evolvability===
 
===Week 11 (Nov. 5/7): Evolvability===
Discussion Leader: Jon Velotta
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Discussion Leader:<br>
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Discussion Readings:<br>
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Discussion Questions:<br>
  
<ul>
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===Week 13 (Nov. 19/21): Novelty===
<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>
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Discussion Leader:<br>
<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>
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Discussion Readings:<br>
<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.
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Discussion Questions:<br>
[http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2011.02370.x/abstract link]</li>
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</ul>
 
<br>
 
 
===Week 12 (Nov. 12/14): Morphospace ===
 
Discussion Leader: Brigette Zacharczenko
 
<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>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>
 
 
 
</ul>
 
<br>
 
 
===Week 13 (Nov. 19/21): Novelty===
 
 
===Week 14 (Nov. 26/28): Happy Thanksgiving!===
 
===Week 14 (Nov. 26/28): Happy Thanksgiving!===
Discussion Leader: Colin Carlson
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Discussion Leader:<br>
 
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Discussion Readings:<br>
<ul>
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Discussion Questions:<br>
<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.
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[http://beheco.oxfordjournals.org/content/22/5/1042 link]</li>
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<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>
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<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.
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[http://onlinelibrary.wiley.com/doi/10.1111/j.1439-0469.2009.00527.x/abstract link]</li>
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</ul>
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<br>
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===Week 15 (Dec. 3/5): Project Presentations ===
 
===Week 15 (Dec. 3/5): Project Presentations ===
 
[[Category:EEB Courses]]
 
[[Category:EEB Courses]]

Revision as of 17:28, 16 July 2013

EEB 5333, Fall 2013
Evolutionary Developmental Biology
Meeting Time: Tuesdays, 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


Handouts and Announcements

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 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.
 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, Oct. 28Term paper topic approved
Thursday, Dec. 1Independent project paper due
Dec. 6-8Independent project presentations
Tuesday, Dec. 13Final exam due


Course grade

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


Topics and Readings

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

Discussion Leader:
Discussion Readings:
Discussion Questions:

Week 2 (Sept. 3/5): The molecular building blocks of development

Discussion Leader:
Discussion Readings:
Discussion Questions:

Week 3 (Sept. 10/12): Small RNAs: another layer of gene regulation

Discussion Leader:
Discussion Readings:
Discussion Questions:

Week 4 (Sept. 17/19): Development and homoplasy

Discussion Leader:
Discussion Readings:
Discussion Questions:

Week 5 (Sept. 24/26): Evolution of developmental networks

Discussion Leader:
Discussion Readings:
Discussion Questions:

Week 6 (Oct. 1/3): Development and homology

Discussion Leader:
Discussion Readings:
Discussion Questions:

Week 7 (Oct. 8/10) : Developmental constraints and evolution

Discussion Leader:
Discussion Readings:
Discussion Questions:

Week 8 (Oct. 15/17): Modularity

Discussion Leader:
Discussion Readings:
Discussion Questions:

Week 9 (Oct. 22/24): Robustness and canalization

Discussion Leader:
Discussion Readings:
Discussion Questions:

Week 10 (Oct. 29/31): Plasticity

Discussion Leader:
Discussion Readings:
Discussion Questions:

Week 11 (Nov. 5/7): Evolvability

Discussion Leader:
Discussion Readings:
Discussion Questions:

Week 13 (Nov. 19/21): Novelty

Discussion Leader:
Discussion Readings:
Discussion Questions:

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

Discussion Leader:
Discussion Readings:
Discussion Questions:

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