EEB 5859: Graduate Seminar

Fall 2013 – Genetics, Development, and Evolution of Phenotypic Diversity.

Meeting Time: Wednesday 2:00 pm; Meeting Room: BioPharm 303

bullets_tri_purple   Motivation: If you have ever been amazed by the beauty and diversity of the color, shape, size of butterflies, seashells, coral reef fishes, tropical birds, flowers, just to name a few, and have ever wondered how these “endless forms most beautiful and most wonderful” have arisen and evolved, this seminar may help to satisfy your curiosity.

 bullets_tri_purple   Conceptual Framework: Our conceptual framework to understand the evolution of phenotypic diversity include three major components: (i) the genetic basis that prescribes phenotypic variation; (ii) the developmental process through which gene products change phenotypes; and, (iii) the ecological consequence (or adaptive significance) of alternative phenotypes in their natural habitat. Throughout this seminar we will emphasize the critical role of genetics in linking “Evo-Devo”, which has so far focused on developmental patterning and re-patterning as an individual process, with the “Modern Synthesis” that deals with allele frequency change as a population process.

bullets_tri_purple   Major Questions:  We think addressing the following questions is the key to understanding phenotypic evolution: Is the phenotypic variation under investigation caused by few (or single) genes of large effect or many genes of small effect? What is the causal gene(s)? Are there usually “hotspot” genes chosen by evolution to generate similar phenotypes over and over again? Can we predict which genes represent “hotspots” based on their positions in the developmental pathway/network? What are the causal mutations? Are there many mutations with small effect or few mutations with large effect underlying the causal gene? Are the causal mutations from standing variation or de novo mutations? Are the causal mutations located to cis-elements or coding DNA? How do different allelic variants produce phenotypic difference during development? Are the derived alleles fixed by selection or drift? If by selection what’s the selecting agent? Are the derived alleles dominant or recessive? Do the empirical results confer to the theoretical prediction of “Haldane’s sieve”? We will start from first principles and make logic inferences to answer these questions, and then will critically evaluate a number of empirical study systems and see whether the experimental evidence support or refute our logic inferences.

 bullets_tri_purple   A Few Recommended Books:

Enrico Coen (1999): The Art of Genes – How Organisms Make Themselves.
S. B. Carroll, J. Grenier, S. Weatherbee (2004): From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design, 2nd Edition.
Sean B. Carroll (2006): Endless Forms Most Beautiful: The New Science of Evo Devo.
David L. Stern (2010): Evolution, Development, and the Predictable Genome.
Wallace Arthur (2011): Evolution: A Developmental Approach.

Week 1 (Aug. 28): Organizational meeting

Week 2 (Sep. 04): Questions, Predictions, and Emperical Study Systems

Sommer R.J. 2009. The future of evo-devo: model systems and evolutionary theory. Nat Rev Genet.10(6):416-422. [link]
Stern D.L., Orgogozo V. 2009. Is Genetic Evolution Predictable? Science. 323: 746-751. [link]
Carroll S.B. 2008. Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution. Cell. 134: 25-36. [link]

Week 3 (Sep. 11): Mimulus flower color (Yaowu)

Schemske D.W., Bradshaw H.D.Jr. 1999. Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus). PNAS. 96: 11910-11915. [link]
Bradshaw H.D.Jr., Schemske D.W. 2003. Allele substitution at a flower colour locus produces a pollinator shift in monkeyflowers. Nature. 426: 176-178. [link]
Yuan et al. 2013. Genetic Dissection of a Major Anthocyanin QTL Contributing to Pollinator-Mediated Reproductive Isolation Between Sister Species of Mimulus. Genetics. 194: 255-263. [link]

Week 4 (Sep. 18): Deer mice coat color (Sarah)

Catherine et al. 2009. On the Origin and Spread of an Adaptive Allele in Deer Mice. Science. 325: 1095-1098. [link]
Kingsley et al. 2009. Melanism in Peromyscus Is Caused by Independent Mutations in Agouti. PLOS One. 4(7): e6435. [link]
Catherine et al. 2013. Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene. Science. 339: 1312-1316. [link]

Week 5 (Sep. 25): Drosophila larval trichome patterning (Yaowu)

Sucena E., Stern D.L. 2000. Divergence of larval morphology between Drosophila sechellia and its sibling species caused by cis-regulatory evolution of ovo/shaven-baby. PNAS. 97: 4530-4534. [link]
McGregor et al. 2007. Morphological evolution through multiple cis-regulatory mutations at a single gene. Nature. 448: 587-590. [link]
Frankel et al. 2011. Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature. 474: 598-603. [link]

Week 6 (Oct. 02): Helicolius butterfly wing pattern mimicry (Cera)

Reed et al. 2011. optix Drives the Repeated Convergent Evolution of ButterflyWing Pattern Mimicry. Science. 333: 1137-1141. [link]

Week 7 (Oct. 09): Drosophila wing pigmentation (Tim)

Gompel et al. 2005.Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature. 433: 481-487. [link]
Werner et al. 2010. Generation of a novel wing colour pattern by the Wingless morphogen. Nature. 464: 1143-1148. [link]
Arnoult et al. 2013. Emergence and Diversification of Fly Pigmentation Through Evolution of a Gene Regulatory Module. Science. 339: 1423-1426. [link]

Week 9 (Oct. 23): Stickleback lateral plate reduction (Mike)

Colosimo et al. 2005.Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles. Science. 307: 1929-1933. [link]
Barrett et al. 2009. Environment Specific Pleiotropy Facilitates Divergence at the Ectodysplasin Locus in Threespine Stickleback. Evolution. 63: 2831-2837. [link]
Jones et al. 2012.The genomic basis of adaptive evolution in threespine sticklebacks. Nature. 484: 55-61. [link]

Week 10 (Oct. 30): Stickleback pelvic spine reduction (Elizabeth)

Shapiro et al. 2004. Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature. 428: 717-723. [link]
Chan et al. 2010. Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science. 327: 302-305. [link]

Week 11 (Nov. 06): Arabidopsis trichome density (Dustin)

Handley et al. 2005. Variation in trichome density and resistance against a specialist insect herbivore in natural populations of Arabidopsis thaliana. Ecological Entomology. 30: 284-292. [link]
Symonds et al. 2011. Natural Allelic Variation Defines a Role for ATMYC1: Trichome Cell Fate Determination. PLoS Genetics. 7: e10020695. [link]
Bloomer et al. 2011. Natural variation in GL1 and its effects on trichome density in Arabidopsis thaliana. Molecular Ecology. 21: 3501–3515. [link]

Week 12 (Nov. 13): Phlox flower color and Nasonia wing size (Carl and Yaowu)

Hopkins, R., D. A. Levin, and M. D. Rausher. 2011. Molecular signatures of selection on reproductive character displacement of flower color in Phlox drummondii. Evolution 66: 469-485.  [link]
Loehlin et al. 2011. Non-Coding Changes Cause Sex-Specific Wing Size Differences between Closely Related Species of Nasonia. PLoS Genetics. 6: e000821. [link]
Loehlin, D. L., and Werren, J.H. 2012. Evolution of Shape by Multiple Regulatory Changes to a Growth Gene. Science. 335: 943–947. [link]