Evolutionary Developmental Biology

EEB 333

Fall 2007

Course schedule

Don't get confused by the order.  Presentation papers are for Tuesday and discussion papers for Thursday.

Dec. 6:  The developmental basis of phenotypic plasticity (Dave)

Discussion Papers

Grether, G. F. 2005. Environmental change, phenotypic plasticity, and genetic compensation. American Naturalist 166: E115-E123. [pdf]

Suzuki, Y. and H. F. Nijhout. 2008. Genetic basis of adaptive evolution of a polyphenism by genetic accommodation. Journal of Evolutionary Biology. [pdf]

Kontiainen, P., J. E. Brommer, P. Karell and H. Pietiainen. 2008. Heritability, plasticity and canalization of Ural owl egg size in a cyclic environment. Journal of Evolutionary Biology. [pdf]


Dec 4:  Project Presentations II (Carrie, Beth, Frank)

Background Papers

Gavrilets, S.  1997.  Evolution and speciation on holey adaptive landscapes.  Trends in Ecology & Evolution 12:307-312. [pdf]

Davidson, E.H., Erwin, D.H. 2006. Gene Regulatory Networks and the Evolution of Animal Body Plans. Science 311:796-800. [pdf]

Levine, J.D.  2004. Sharing time on the Fly. Current Opinion in Cell Biology 16:210-216 [pdf]

Nov. 29:  Student Presentations I (Maxi, Dave, Diego)

Background Papers

Emlen DJ, Corley Lavine L, Ewen-Campen B. 2007.  On the origin and evolutionary diversification of beetle horns. Proc Natl Acad Sci USA 104 Suppl 1:8661-8. [pdf]

Roman J, Darling JA.  2007.  Paradox lost: genetic diversity and the success of aquatic invasions. Trends Ecol Evol. 22(9):454-64. [pdf]

Grant, P. R., Grant, B. R. and Abzhanov, A. 2006. A developing paradigm for the development. of bird beaks. Biological Journal of the Linnean Society 86:17-22. [pdf]

Nov. 13-15:  Evolvability (Maxi)

Discussion Papers

Hendrikse, J. L., T. E. Parsons and B. Hallgrímsson. 2007. Evolvability as the proper focus of evolutionary developmental biology. Evolution & Development 9: 393–401. [pdf]

Carey, C. C., K. F. Gorman and S. Rutherford. 2006. Modularity and intrinsic evolvability of Hsp90-buffered change. PLoS ONE 1: e76. [pdf]

Bloom, J. D., S. T. Labthavikul, C. R. Otey and F. H. Arnold. 2006. Protein stability promotes evolvability. Proceedings of the National Academy of Sciences USA 103: 5869-5874. [pdf]

Questions for Discussion 12

Nov. 6-8:  Developmental modules (Carrie)

Discussion Papers

Storz, B. L. and J. Travis. 2007. Temporally dissociated, trait-specific modifications underlie phenotypic polyphenism in Spea multiplicata tadpoles, which suggests modularity. TSW Development & Embryology 2: 60-71. [pdf]

Wang, Z. and J. Zhang. 2007. In search of the biological significance of modular structures in protein networks. PLoS Computational Biology 3: e107. [pdf]

Berg, R. L. 1960. The ecological significance of correlation pleiades. Evolution 14: 171-180. [pdf]

Don't forget that we'll also be discussing Pigliucci (2007).

Questions for Discussion 11

Oct. 30-Nov. 1:  RNA silencing and other mechanisms of gene regulation (Diego)

Discussion Papers

Liu B, Chen Z, Song X, Liu C, Cui X, Zhao X, Fang J, Xu W, Zhang H, Wang X, Chu C, Deng X, Xue Y, Cao X. (2007). Oryza sativa Dicer-like4 Reveals a Key Role for Small Interfering RNA Silencing in Plant Development. Plant Cell, in press. [pdf]

Wolf, J. B. and Hager, R. (2006). A Maternal-Offspring Coadaptation Theory for the Evolution of Genomic Imprinting. PLoS Biology 4, e380. [pdf]

Pigliucci, M. (2007). Do we need an extended evolutionary synthesis? Evolution (OnlineEarly Articles). [pdf]

Questions for Discussion 10


Oct. 23-25:  Developmental network structure:  significance of topology (Beth)

Discussion Papers

Siegal ML, Promislow DE, Bergman A.  2007.  Functional and evolutionary inference in gene networks: does topology matter? Genetica 129(1):83-103. [pdf]

Ma W, Lai L, Ouyang Q, Tang C. 2006.  Robustness and modular design of the Drosophila segment polarity network.
Mol Syst Biol. 2:70. [pdf]

Cooper TF, Morby AP, Gunn A, Schneider D. 2006.  Effect of random and hub gene disruptions on environmental and mutational robustness in Escherichia coli.  BMC Genomics 7:237. [pdf]

Questions for Discussion 9

Lecture examples

segment polarity network

von Dassow G, Meir E, Munro EM, Odell GM.   2000.  The segment polarity network is a robust developmental module.  Nature 406(6792):188-92. [pdf]

von Dassow G, Odell GM.  2002.  Design and constraints of the Drosophila segment polarity module: robust spatial patterning emerges from intertwined cell state switches.  J Exp Zool. 294(3):179-215. [pdf]

Albert R, Othmer HG.  2003.  The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster.  J Theor Biol. 223(1):1-18. [pdf]

Ingolia NT.  2004.  Topology and robustness in the Drosophila segment polarity network.  PLoS Biol. 2(6):e123. [pdf]

evolution of robustness 
Proulx SR, Nuzhdin S, Promislow DE.  2007.  Direct selection on genetic robustness revealed in the yeast transcriptome.  PLoS ONE 2(9):e911. [pdf]

Siegal ML, Bergman A. 2002.  Waddington's canalization revisited: developmental stability and evolution.  Proc Natl Acad Sci USA 99(16):10528-32. [pdf]

Wilke CO, Wang JL, Ofria C, Lenski RE, Adami C.  2001.  Evolution of digital organisms at high mutation rates leads to survival of the flattest.
Nature 412(6844):331-3. [pdf]

Elena SF, Wilke CO, Ofria C, Lenski RE.2007.  Effects of population size and mutation rate on the evolution of mutational robustness.  Evolution 61(3):666-74. [pdf]

Sanjuán R, Cuevas JM, Furió V, Holmes EC, Moya A.  2007.  Selection for robustness in mutagenized RNA viruses.  PLoS Genet. 3(6):e93. [pdf]


Oct. 16-18:  Evolution of developmental pathways (Frank)

Discussion Papers

Rockman MV, Wray GA.  2002. Abundant raw material for cis-regulatory evolution in humans. Mol Biol Evol. 19(11):1991-2004. [pdf]

Landry CR, Wittkopp PJ, Taubes CH, Ranz JM, Clark AG, Hartl DL.  2005.  Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila.  Genetics 171(4):1813-22. [pdf]

Tanay A, Regev A, Shamir R.  2005.  Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci USA. 102(20):7203-8. [pdf]

Questions for Discussion 8

Lecture examples

eve regulation
Janssens H, Hou S, Jaeger J, Kim AR, Myasnikova E, Sharp D, Reinitz J.  2006.  Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene.  Nat Genet. 38(10):1159-65. [pdf]

Ludwig MZ, Bergman C, Patel NH, Kreitman M. 2000.  Evidence for stabilizing selection in a eukaryotic enhancer element.  Nature 403(6769):564-7. [pdf]

Ludwig MZ, Palsson A, Alekseeva E, Bergman CM, Nathan J, Kreitman M. 2005.  Functional evolution of a cis-regulatory module.  PLoS Biol. 3(4):e93. [pdf]

Ludwig MZ, Patel NH, Kreitman M.  1998.  Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.  Development 125(5):949-58. [pdf]

Arnosti DN, Barolo S, Levine M, Small S.  1996.  The eve stripe 2 enhancer employs multiple modes of transcriptional synergy.  Development 122(1):205-14. [pdf]

evolution of bicoid and long germ development
McGregor AP. 2006.  Wasps, beetles and the beginning of the ends.  Bioessays 28(7):683-6. [pdf]

Schroder R. 2003.  The genes orthodenticle and hunchback substitute for bicoid in the beetle Tribolium.  Nature 422(6932):621-5. [pdf]

Lynch JA, Brent AE, Leaf DS, Pultz MA, Desplan C.  2006.  Localized maternal orthodenticle patterns anterior and posterior in the long germ wasp Nasonia.  Nature 439(7077):728-32. [pdf]



Oct. 9-11:  Developmental constraints and evolution (Frank)

Discussion Papers

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 [pdf]
  
Kavanagh KD, Evans AR, Jernvall J. 2007.  Predicting evolutionary patterns of mammalian teeth from development.  Nature 449(7161):427-32. [pdf]

K. Schwenk and G. P. Wagner. 2004. The relativism of constraints on phenotypic evolution. Pp. 390-408 in Phenotypic Integration.  Studying the Ecology and Evolution of Complex Phenotypes.  M. Pigliucci and K. Preston, eds. Oxford University Press, Oxford. [contact me if you don't have a copy]

Questions for Discussion 7

Lecture examples

Brakefield PM, Roskam JC. 2006.  Exploring evolutionary constraints is a task for an integrative evolutionary biology.  Am Nat. 168 Suppl 6:S4-13. [pdf]

Beldade P, Koops K, Brakefield PM. 2002.  Developmental constraints versus flexibility in morphological evolution.  Nature 416(6883):844-7. [pdf]

Beldade P, Koops K, Brakefield PM.  2002.  Modularity, individuality, and evo-devo in butterfly wings.  Proc Natl Acad Sci USA 99(22):14262-7. [pdf]

Beldade P, Brakefield PM.  2003.  The difficulty of agreeing about constraints.  Evol Dev. 5(2):119-20. [pdf]

Arthur W.  2003.  Developmental constraint and natural selection.  Evol Dev. 5(2):117-8. [pdf]

Prusinkiewicz P, Erasmus Y, Lane B, Harder LD, Coen E.  2007.  Evolution and development of inflorescence architectures. Science 316(5830):1452-6. [pdf]

Arthur W.  2002.  The interaction between developmental bias and natural selection: from centipede segments to a general hypothesis.  Heredity 89(4):239-46. [pdf]

Oct. 2-4:  Development and homology (Dave)

Discussion Papers

Wagner GP.  2007.  The developmental genetics of homology.  Nat Rev Genet. 8(6):473-9. [pdf]

Hall BK.  2007.  Homoplasy and homology: dichotomy or continuum?  J Hum Evol. 52(5):473-9. [pdf]

Butler AB, Saidel WM.  2000.  Defining sameness: historical, biological, and generative homology.  Bioessays 22(9):846-53. [pdf]

I hope these aren't quite as inscrutable as last week's choices were!

Sept. 25-27:  What does development reveal about homoplasy? (Suegene)

Discussion Papers

Harrison CJ, Corley SB, Moylan EC, Alexander DL, Scotland RW, Langdale JA.  2005.  Independent recruitment of a conserved developmental mechanism during leaf evolution.  Nature 434(7032):509-14. [pdf]

Wake DB.  1991.  Homoplasy: The result of natural selection, or evidence of design limitations?  The American Naturalist 138:543-567. [pdf]

Jaramillo MA, Manos PS, Zimmer EA. 2004. Phylogenetic relationships of the perianth-less Piperales: reconstructing the evolution of floral development. International Journal of Plant Sciences 165(3): 403-416. [pdf]

Lecture examples

Sticklebacks
Taylor EB, Boughman JW, Groenenboom M, Sniatynski M, Schluter D, Gow JL. 2006.  Speciation in reverse: morphological and genetic evidence of the collapse of a three-spined stickleback (Gasterosteus aculeatus) species pair. Mol Ecol. 15(2):343-55. [pdf]

Marchinko KB, Schluter D.  2007.  Parallel evolution by correlated response: lateral plate reduction in threespine stickleback.
Evolution 61(5):1084-90. [pdf]

Knecht AK, Hosemann KE, Kingsley DM.  2007.  Constraints on utilization of the EDA-signaling pathway in threespine stickleback evolution.  Evol Dev. 9(2):141-54. [pdf]

Colosimo PF, Hosemann KE, Balabhadra S, Villarreal G Jr, Dickson M, Grimwood J, Schmutz J, Myers RM, Schluter D, Kingsley DM.  2005. Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles.  Science 307(5717):1928-33. [pdf]

Cresko WA, Amores A, Wilson C, Murphy J, Currey M, Phillips P, Bell MA, Kimmel CB, Postlethwait JH. 2004.  Parallel genetic basis for repeated evolution of armor loss in Alaskan threespine stickleback populations.  Proc Natl Acad Sci USA 101(16):6050-5. [pdf]

Peichel CL, Nereng KS, Ohgi KA, Cole BL, Colosimo PF, Buerkle CA, Schluter D, Kingsley DM.  2001.  The genetic architecture of divergence between threespine stickleback species.  Nature 414(6866):901-5. [pdf]

Salamander limbs
Shubin N, Wake DB, Crawford AJ.  1995.  Morphological Vvion in the limbs of Taricha granulosa (Caudata: Salamandridae): Evolutionary and phylogenetic implications.  Evolution 49:874-884 [pdf]

Alberch P, Gale EA.  1985.  A developmental analysis of an evolutionary trend: digital reduction in amphibians.  Evolution 39:8-23. [pdf]

Drosophila wing spots
Prud'homme B, Gompel N, Rokas A, Kassner VA, Williams TM, Yeh SD, True JR, Carroll SB.  2006.  Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene.  Nature 440(7087):1050-3. [pdf]

Gompel N, Prud'homme B, Wittkopp PJ, Kassner VA, Carroll SB.  2005.  Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila.  Nature 433(7025):481-7. [pdf]

Hegde SN, Chethan BK, Krishna MS.  2005.  Mating success of males with and without wing patch in Drosophila biarmipes.
Indian J Exp Biol. 43(10):902-9.

Courtship videos for D. biarmipes and D. tristis


Sept. 18-20:  Morphological novelty (Diego)

Discussion Papers

Müller, G. B. and S. A. Newman. 2005. The innovation triad: An EvoDevo agenda. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution 304B: 487-503. [pdf]

McGregor, A. P., V. Orgogozo, I. Delon, J. Zanet, D. G. Srinivasan, F. Payre and D. L. Stern. 2007. Morphological evolution through multiple cis-regulatory mutations at a single gene. Nature 448: 587-590. [pdf]

Shigetani, Y., F. Sugahara and S. Kuratani. 2005. A new evolutionary scenario for the vertebrate jaw. BioEssays 27: 331-338. [pdf]

Questions for Discussion 4

 

Sept. 11-13:  Novelty at the molecular level (Beth)

Discussion Papers

Wapinski, I., A. Pfeffer, N. Friedman and A. Regev. 2007. Natural history and evolutionary principles of gene duplication in fungi. Nature 449: 54-61. [pdf]

Duarte, J. M., L. Cui, P. K. Wall, Q. Zhang, X. Zhang, et al. 2006. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Molecular Biology and Evolution 23: 469-478. [pdf]

Rodríguez-Trelles, F., R. Tarrío and F. J. Ayala. 2003. Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene. Proceedings of the National Academy of Sciences USA 100: 13413-13417. [pdf]

Questions for Discussion 3

Guan Y, Dunham MJ, Troyanskaya OG. 2007.  Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics. 175(2):933-43. [pdf]  This papers appears to directly conflict with Wapinski et al. in its conclusions about whole genome vs. segmental duplication events.

References on the origin of molecular novelties [doc]

(see below, after first week, for sneak preview of Sept. 20 papers)


Sept. 4-6:  The molecular building blocks of development (Maxi and Carrie)

Discussion Papers

Wray GA.  2007.  The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet. 8(3):206-16. [pdf]

Hoekstra HE, Coyne JA. 2007.  The locus of evolution: evo devo and the genetics of adaptation. Evolution 61(5):995-1016. [pdf]

Questions for Discussion 2

Examples discussed in lecture

References for examples discussed in lecture [doc]


Aug. 28-30:  Overview of evolutionary developmental biology (Elizabeth and Carl)

Discussion Papers
Wagner, G. P., C-H. Chiu, and M. Laubichler. 2000. Developmental evolution as a mechanistic science: the inference from developmental mechanisms to evolutionary processes. American Zoologist 40: 819-831. [pdf]
 
Breuker, C.J., V. Debat, and C.P. Klingenberg.  2006.  Functional evo-devo.  TREE 21:488-492. [pdf]
 
Raff, R. A. 2000. Evo-devo: the evolution of a new discipline. Nature Reviews Genetics 1: 74-79. [pdf]

         Questions for Discussion 1


Examples discussed in lecture

Hughes, C. L. and T. C. Kaufman.  2002.  Hox genes and the evolution of the arthropod body plan.  Evolution and Development 4:459-499. [pdf]

Hoekstra H.E.  2006.  Genetics, development and evolution of adaptive pigmentation in vertebrates.  Heredity 97(3):222-34. [pdf]

Further reading on lecture examples
Slack JM. 2002.  Conrad Hal Waddington: the last Renaissance biologist? Nat Rev Genet. 3(11):889-95. [pdf]

Panfilio KA, Akam M.  2007.   A comparison of Hox3 and Zen protein coding sequences in taxa that span the Hox3/zen divergence. Dev Genes Evol. 217(4):323-9. [pdf]

Papillon D., Telford M.J.  2007.  Evolution of Hox3 and ftz in arthropods: insights from the crustacean Daphnia pulex. Dev Genes Evol. 217(4):315-22. [pdf]

Hughes, C. L., P. L. Liu, and T. C. Kaufman.  2004.  Expression patterns of the rogue Hox genes Hox3/zen and fushi tarazu in the apterygote insect Thermobia domestica.  Evolution and Development 6: 393-401. [pdf]

Stauber, M., A. Prell, and U. Schmidt-Ott.  2002.  A single Hox3 gene with composite bicoid and zerknullt expression characteristics in non-Cyclorrhaphan flies.  Proc Natl Acad Sci U S A 99: 274-9. [pdf]

Damen, W. G. and D. Tautz.  1998.  A Hox class 3 orthologue from the spider Cupiennius salei is expressed in a Hox-gene-like fashion.  Dev Genes Evol. 208: 586-90. [pdf]

Rosenblum, E. B., H. E. Hoekstra, and M. W. Nachman.  2004.  Adaptive reptile color variation and the evolution of the Mc1r gene.  Evolution 58:1794-808. [pdf]

Makova, K. and H. Norton.  2005.  Worldwide polymorphism at the MC1R locus and normal pigmentation variation in humans.  Peptides: 26:1901-1908. [pdf]

Nachman, M. W., H. E. Hoekstra, and S. L. D'Agostino.  2003.  The genetic basis of adaptive melanism in pocket mice.  Proceedings of the National Academy of Sciences USA 100:5268-5273. [pdf]

Hoekstra, H. E. and M. W. Nachman.  2003.  Different genes underlie adaptive melanism in different populations of rock pocket mice.  Mol. Ecol.12:1185-94. [pdf]
 
Steiner C.C., Weber J.N., Hoekstra H.E. 2007.  Adaptive Variation in Beach Mice Produced by Two Interacting Pigmentation Genes. PLoS Biol. 14;5(9):e219 [pdf]


Nov. 20-22:  Thanksgiving break


Dec. 11:  Final exam due