Evo Devo Fall2011

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(Nov. 15: Discussion: Evolvability --- Lecture: Morphospace)
(Nov. 15: Discussion: Evolvability --- Lecture: Morphospace)
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<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> 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>Pavlicev, M., J. M. Cheverud, et al. 2011. Evolution of adaptive phenotypic variation patterns by direct selection for evolvability. Proceedings of the Royal Society B-Biological Sciences 278: 1903-1912.  [http://rspb.royalsocietypublishing.org/content/278/1713/1903.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>

Revision as of 18:44, 14 November 2011

EEB 5333, Fall 2011
Evolutionary Developmental Biology
Meeting Time: Tuesdays, 12:30-3:15 pm, Bamford Room (TLS 171B)



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.


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

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. 


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

Aug. 30: Overview of evolutionary developmental biology

Books & Sources in Evolutionary Developmental Biology
References related to lecture material

  • Hughes CL, Kaufman TC. 2002. Hox genes and the evolution of the arthropod body plan. Evol Dev. 4:459-499. link
  • Hughes CL, Liu PZ, Kaufman TC. 2004. Expression patterns of the rogue Hox genes Hox3/zen and fushi tarazu in the apterygote insect Thermobia domestica. Evol Dev. 6(6):393-401. link
  • Papillon D, Telford MJ. 2007. Evolution of Hox3 and ftz in arthropods: insights from the crustacean Daphnia pulex. Dev Genes Evol. 217(4):315-22. link
  • Rafiqi AM, Lemke S, Ferguson S, Stauber M, Schmidt-Ott U. 2008. Evolutionary origin of the amnioserosa in cyclorrhaphan flies correlates with spatial and temporal expression changes of zen. Proc Natl Acad Sci U S A. 105(1):234-9. link
  • Rafiqi AM, Lemke S, Schmidt-Ott U. 2010. Postgastrular zen expression is required to develop distinct amniotic and serosal epithelia in the scuttle fly Megaselia. Dev Biol. 341(1):282-90. link
  • Rosenblum EB, Hoekstra HE, Nachman MW. 2004. Adaptive reptile color variation and the evolution of the Mc1r gene. Evolution. 2004 Aug;58(8):1794-808. link
  • Rosenblum EB, Römpler H, Schöneberg T, Hoekstra HE. 2010. Molecular and functional basis of phenotypic convergence in white lizards at White Sands. Proc Natl Acad Sci U S A. 107(5):2113-7. link

Sept. 6: The molecular building blocks of development

Discussion Questions Pdficon small.gif
Discussion Readings

  • Brakefield PM. 2011. Evodevo and accounting for Darwin's endless forms. Philos Trans R Soc Lond B Biol Sci. 366: 2069-75. link
  • Müller GB. 2007. Evo-devo: extending the evolutionary synthesis. Nat Rev Genet. 8(12):943-9. 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]

Sept. 13: Small RNAs: another layer of gene regulation

Discussion Leader: Colin Carlson
Discussion Questions.

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

  • 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. link
  • 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. link
  • Lynch VJ, Wagner GP. 2008. Resurrecting the role of transcription factor change in developmental evolution. Evolution 62(9):2131-54. link

Sept. 20: Development and homoplasy

Discussion Leader: Elizabeth
Discussion Questions Pdficon small.gif
Discussion Readings

  • 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. link
  • Loh YH, Yi SV, Streelman JT. 2011. Evolution of microRNAs and the diversification of species. Genome Biol Evol. 3:55-65. link
  • Wu CI, Shen Y, Tang T. 2009. Evolution under canalization and the dual roles of microRNAs: a hypothesis. Genome Res. 19(5):734-43. link

Sept. 27: Evolution of developmental networks

Discussion Leader: Jessie Rack

Discussion Readings :Pdficon small.gifDiscussion Questions 9_27.pdf

  • Gompel N, Prud'homme B. 2009. The causes of repeated genetic evolution. Dev Biol. 332(1):36-47. link
  • 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. link
  • 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. link

Oct. 4: Development and homology

Discussion Leader: Frank Smith

  • 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. link
  • Poelwijk FJ, de Vos MG, Tans SJ. 2011. Tradeoffs and optimality in the evolution of gene regulation. Cell 146(3):350-2. link
  • 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. link

Oct. 11: Developmental constraints and evolution

Discussion Leader: Jon Velotta

  • Shubin N, Tabin C, Carroll S. 2009. Deep homology and the origins of evolutionary novelty. Nature. 2009457(7231):818-23. link
  • 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. link
  • Van Valen LM. 1982. Homology and causes. Journal of Morphology 173: 305-312. link

Oct. 18: Discussion: Constraints --- Lecture: Modularity

Discussion Leader: Brigette Zacharczenko

  • 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 link
  • Salazar-Ciudad I, Jernvall J. 2010. A computational model of teeth and the developmental origins of morphological variation. Nature 464(7288):583-6. link
  • 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. link
  • Don't forget the paper for Carl's lecture!

Oct. 25: Discussion: Modularity --- Lecture: Robustness and canalization

Discussion Leader: Carl

  • 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. link
  • 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
  • Goswami, A. and P. D. Polly. 2010. The influence of modularity on cranial morphological disparity in Carnivora and Primates (Mammalia). PLoS ONE 5: e9517. link

Nov. 1: Discussion: Robustness and canalization --- Lecture: Plasticity

Discussion Leader: Jessie Rack

  • 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. link
  • 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. link
  • Milton, C. C., C. M. Ulane, et al. 2006. Control of canalization and evolvability by Hsp90. PLoS ONE 1: e75. link

Nov. 8: Discussion: Plasticity --- Lecture: Evolvability

Discussion Leader: Jon Velotta

  • Beldade, P., A. R. A. Mateus, et al. 2011. Evolution and molecular mechanisms of adaptive developmental plasticity. Molecular Ecology 20: 1347-1363. link
  • McGuigan, K., N. Nishimura, et al. 2011. Cryptic genetic variation and body size evolution in threespine stickleback. Evolution 65: 1203-1211. link
  • 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. link

Nov. 15: Discussion: Evolvability --- Lecture: Morphospace

Discussion Leader: Brigette Zacharczenko

  • Woods, R. J., J. E. Barrick, et al. 2011. Second-order selection for evolvability in a large Escherichia coli population. Science 331: 1433-1436. link
  • 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. link

Nov. 22: Thanksgiving Break

Nov. 29: Discussion: Morphospace --- Lecture: Novelty

Discussion Leader: Colin Carlson

Dec. 6: Project presentations

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