Difference between revisions of "Evo Devo Fall2011"

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EEB 5333, Fall 2011
Evolutionary Developmental Biology
Meeting Time: Tuesdays, 12:30-3:15 pm, room TBA

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

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

Course grade

Topics and Readings

Aug. 30: Overview of evolutionary developmental biology

Books & Sources in Evolutionary Developmental Biology Books & Sources in Evolutionary Developmental Biology

The Classics
Goldschmidt, R. B. 1940. The Material Basis of Evolution. New Haven, CT, Yale University Press. 
Schmalhausen, I. I. 1949. Factors of Evolution. Philadelphia, PA, Blakiston.
Waddington, C. H. 1957. The Strategy of the Genes. London, Allen & Unwin.
de Beer, G. R. 1958. Embryos and Ancestors. Oxford, Clarendon Press.
Bonner, J. T. 1958. The Evolution of Development. Cambridge, Cambridge University Press.
Berrill, N. J. 1961. Growth, Development, and Pattern. San Francisco, W.H. Freeman.
Whyte, L. L. 1965. Internal Factors in Evolution. New York, Braziller.
Rendel, J. M. 1967. Canalisation and Gene Control. London, Logos Press.
Gould, S. J. 1977. Ontogeny and Phylogeny. Cambridge, MA, Belknap Press.
Riedl, R. 1978. Order in Living Organisms. New York, John Wiley and Sons.

The New Wave
Bonner, J. T., Ed. 1982. Evolution and Development: Report of the Dahlem Workshop on Evolution and Development. Berlin, Springer-Verlag.
Buss, L. W. 1987. The Evolution of Individuality. Princeton, Princeton University Press.
Arthur, W. 1988. A Theory of the Evolution of Development. New York, John Wiley & Sons.
Bonner, J. T. 1988. The Evolution of Complexity by Means of Natural Selection. Princeton, NJ, Princeton University Press.
Thomson, K. S. 1988. Morphogenesis and Evolution. New York, NY, Oxford University Press.
Hall, B. K. 1992. Evolutionary Developmental Biology, Chapman and Hall.
Rollo, C. D. 1994. Phenotypes: Their Epigenetics, Ecology and Evolution. London, Chapman and Hall.
Raff, R. A. 1996. The shape of life: genes, development, and the evolution of animal form. Chicago, IL, University of Chicago Press.
Arthur, W. 1997. The Origin of Animal Body Plans: A Study in Evolutionary Developmental Biology. Cambridge, UK, Cambridge University Press.
Gerhart, J. and M. Kirschner. 1997. Cells, Embryos, and Evolution. Malden, MA, Blackwell Science.
Hall, B. K. 1998. Evolutionary Developmental Biology, 2nd ed. London, Chapman and Hall.
Schlichting, C. D. and M. Pigliucci. 1998. Phenotypic Evolution: A Reaction Norm Perspective. Sunderland, MA, Sinauer Associates.
Coen, E. 1999. The Art of Genes - How Organisms Make Themselves. Oxford, Oxford University Press.
Carroll, S. B., J. K. Grenier and S. D. Weatherbee. 2001. From DNA to Diversity. London, Blackwell Science. (2nd  edition 2004)
Davidson, E. H. 2001. Genomic Regulatory Systems: Development and Evolution. San Diego, Academic Press.
Levinton, J. S. 2001. Genetics, paleontology, and macroevolution. Cambridge, UK, Cambridge University Press.
Pigliucci, M. 2001. Phenotypic Plasticity: Beyond Nature and Nurture. Baltimore, MD, Johns Hopkins University Press.
Wilkins, A. S. 2002. The Evolution of Developmental Pathways. Sunderland, MA, Sinauer Associates.
West-Eberhard, M. J. 2003. Developmental Plasticity and Evolution. New York, Oxford University Press.
Arthur, W. 2004. Biased Embryos and Evolution. Cambridge, Cambridge University Press.

Robert, J. S. 2004. Embryology, Epigenesis and Evolution: Taking Development Seriously. Cambridge, UK, Cambridge University Press.
Wagner, A. 2005. Robustness and Evolvability in Living Systems. Princeton, NJ, Princeton University Press.
Gerhart, J.C. and M.W. Kirschner. 2005. The Plausibility of Life: Resolving Darwin's Dilemma. New Haven, CT. Yale University Press. 
Carroll, S. B. 2006. Endless Forms Most Beautiful: The New Science of Evo Devo, W.W. Norton.
Davidson, E. H. 2006. The Regulatory Genome.  Gene Regulatory Networks in Development and Evolution. San Diego, Academic Press/Elsevier.
Amundson, R. 2007. The Changing Role of the Embryo in Evolutionary Thought: Roots of Evo-Devo. Cambridge University Press.
McGhee, G. R. 2007. The Geometry of Evolution: Adaptive Landscapes and Theoretical Morphospaces Cambridge, UK, Cambridge University Press.
Gilbert, S. F. and D. Epel. 2009. Ecological Developmental Biology: Integrating Epigenetics, Medicine, and Evolution. Sunderland, MA, Sinauer Associates.
Minelli, A. 2009. The Development of Animal Form: Ontogeny, Morphology, and Evolution. Forms of Becoming: The Evolutionary Biology of Development, Cambridge University Press.
Gilbert, S. F. 2010. Developmental Biology. 9th ed. Sunderland, MA, Sinauer Associates.
Piersma, T. and J. A. van Gils. 2011. The Flexible Phenotype: A Body-Centred Integration of Ecology, Physiology, and Behaviour, Oxford University Press.
Stern, D. L. 2010. Evolution, Development, and the Predictable Genome, Roberts & Company Publishers.
Arthur, W. 2011. Evolution: A Developmental Approach, Wiley-Blackwell. (undergrad text)
Bateson, P. and P. Gluckman. 2011. Plasticity, Robustness, Development and Evolution, Cambridge University Press.	
Wagner, A. 2011. The Origins of Evolutionary Innovations: A Theory of Transformative Change in Living Systems, Oxford University Press.

Edited volumes
Nitecki, M. H., Ed. 1990. Evolutionary Innovations. Chicago, University of Chicago Press.
Sanderson, M. J. and L. Hufford, Eds. 1996. Homoplasy: the recurrence of similarity in evolution. San Diego, CA, Academic Press, Inc.
Oyama, S., P. E. Griffiths and R. D. Gray, Eds. 2001. Cycles of Contingency: Developmental Systems and Evolution. Cambridge, MA, MIT Press.
Zelditch, M. L., Ed. 2001. Beyond Heterochrony: The Evolution of Development. New York, John Wiley & Sons.	
Cronk, Q. C. B., R. M. Bateman and J. A. Hawkins, Eds. 2002. Developmental Genetics and Plant Evolution, Taylor and Francis.
Crutchfield, J. P. and P. Schuster, Eds. 2002. Evolutionary Dynamics: Exploring the Interplay of Selection, Accident, Neutrality, and Function. New York, Oxford University Press.
Minugh-Purvis, N. and K. J. McNamara, Eds. 2002. Human Evolution Through Developmental Change. Baltimore, Johns Hopkins University Press.
Hall, B. K. and W. M. Olson, Eds. 2003. Keywords and Concepts in Evolutionary Developmental Biology. Cambridge, MA, Harvard University Press.
Müller, G. B. and S. A. Newman, Eds. 2003. Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology. Cambridge, MA, MIT Press.
DeWitt, T. J. and S. E. Scheiner, Eds. 2004. Phenotypic Plasticity. Functional and Conceptual Approaches. New York, Oxford University Press.
Hall, B. K., R. D. Pearson and G. B. Müller, Eds. 2004. Environment, Development, and Evolution: Toward a Synthesis. Cambridge, MA, MIT Press.
Pigliucci, M. and K. Preston, Eds. 2004. Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes. Oxford, UK, Oxford University Press.
Schlosser, G. and G. P. Wagner, Eds. 2004. Modularity in Development and Evolution. Chicago, IL, University of Chicago Press.
Callebaut, W. and D. Rasskin-Gutman, Eds. 2005. Modularity. Understanding the Development and Evolution of Natural Complex Systems. Boston, MIT Press.
Schlosser, G., W. Callebaut, et al., Eds. 2005. Amphibian variations: the role of modules in mosaic evolution.
Hallgrímsson, B. and B. K. Hall, Eds. 2005. Variation: A Central Concept in Biology, Academic Press.
Laubichler, M. and J. Maienschein, Eds. 2007. From Embryology to Evo-Devo: A History of Developmental Evolution. Cambridge, MA, MIT Press.
Sansom, R. and R. Brandon, Eds. 2007. Integrating Evolution and Development: From Theory to Practice, MIT Press.
Minelli, A. and G. Fusco, Eds. 2008. Evolving Pathways: Key Themes in Evolutionary Developmental Biology Cambridge University Press.
Whitman, D. and T. N. Ananthakrishnan, Eds. 2009. Phenotypic Plasticity of Insects. Enfield, NH, Science Publishers.
Hallgrimsson, B. and B. K. Hall, Eds. 2011. Epigenetics: Linking Genotype and Phenotype in Development and Evolution, University of California Press.
Pigliucci, M. and G. B. Müller, Eds. 2010. Evolution — the Extended Synthesis The MIT Press.
Bell, M. A., D. J. Futuyma, W. F. Eanes and J. S. Levinton. 2011. Evolution Since Darwin: The First 150 Years. Sunderland, MA, Sinauer Associates.

Sept. 6: The molecular building blocks of development

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

Sept. 20: Development and homoplasy

Sept. 27: Development and homology

Oct. 4: Evolution of developmental networks

Oct. 11: Developmental constraints and evolution

Oct. 18: Developmental modules

Oct. 25: Robustness and canalization

Nov. 2: Evolvability

Nov. 9: Novelty

Nov. 16: Morphospace

Nov. 22: Thanksgiving Break

Nov. 29: EcoEvoDevo

Dec. 6: Project presentations