| WEEK & DATE | TOPIC | REQUIRED READING | SUGGESTED READING |
| Week 1A 1/19/10 | Intro, phylogeny primer | Delsuc et al. Nat Reviews Gen. 2005.Phylogenomics & the Reconstruction of the Tree of Life. | Harrison & Langdale. A step by step guide to phylogeny reconstruction |
| Week 1B1/21/10 | Anatomy of a genome project | Metzker.Nat Reviews Gen. 2006.Sequencing technologies - the next generation. | |
| Week 2A1/26/10 | PAPER DISCUSSION | Clark et al. Nature. 2007. Evolution of genes and genomes on the Drosophila phylogeny. | |
| Week 2B1/28/10 | Orthology, paralogy, and gene history | Koonin.Annu Rev Gen. 2005. Orthologs, Paralogs, and Evolutionary Genomics | |
| Ortlund et al. 2007.Crystal structure of an ancient protein:evolution by conformational epistasis | |||
| Week 3A2/2/10 | Evolution of new gene functions | Lynch & Conery.Science 2000.The evolutionary fate and consequences of duplicate genes. | Bailey & Eichler. Nat Reviews Gen. 2006.Primate segmental duplications: crucibles of evolution, diversity and disease |
| Week 3B2/4/10 | PAPER DISCUSSION | PAPER:Zhou et al. 2008, Genome Research | Hittenger & Carroll. Nature. 2007.Gene duplication and the adaptive evolution of a classic genetic switch. |
| Week 4A2/9/10 | Whole genome duplication (Dana Wohlbach, guest lecturer) | Semom & Wolfe.2007.Consequences of genome duplication. | Van de Peer.Nat. Reviews Gen. 2009.The evolutionary significance of ancient genome duplications. |
| Week 4B2/11/10 | PAPER DISCUSSION | PAPER:Aury et al. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia | |
| Week 5A2/16/10 | Lateral gene transfer and the bacterial species concept (Nicole Perna, guest lecturer) | tbd | |
| Week 5B2/18/10 | PAPER DISCUSSION | tbd | |
| Week 6A2/23/10 | Molecular evolution - Part I | Nielsen. Annu Rev Genet. 2005.Molecular signatures of natural selection. | |
| Week 6B2/25/10 | PAPER DISCUSSION | Fay, Wycoff, Wu.Nature. 2002. Testing the neutral theory of molecular evolution with genomic data from Drosophila. | |
| Smith & Eyre-Walker.Nature. 2002.Adaptive protein evolution in Drosophila. | |||
| Week 7A3/2/10 | Molecular evolution - Part II:genome-wide scans | Stinchcombe & Hoekstra.Heredity. 2007.Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits | |
| Week 7B3/4/10 | PAPER DISCUSSION | Sabeti et al. 2007.Nature.Genome-wide detection and characterization of positive selection in human populations | |
| Week 8A3/9/10 | QTL mapping (Karl Broman, guest lecturer) | tbd | |
| Week 8B3/11/10 | PAPER DISCUSSION | tbd | |
| Week 9A3/16/10 | Evolution of gene expression | Rifkin et al. 2003.Nat Gen. Evolution of gene expression in the Drosophila melanogaster subgroup | Pall et al. Nat Gen Reviews 2006. An integrated view of protein evolution. |
| Week 9B3/18/10 | PAPER DISCUSSION | Denver et al. 2005.The transcriptional consequences of mutation and natural selection in Cenorhabditis elegans | |
| Week 10A3/23/10 | eQTL mapping & the cis-trans debate | Rockman & Kruglyak. Nat Reviews Gen 2006. Genetics of global gene expression. ** OR ** Gilad eQTL review | Brem et al. Science. 2002Genetic dissection of transcriptional regulation in budding yeast. |
| Wittkopp et al. Nat Gen. 2008.Regulatory changes underlying expression differences within and between Drosophila species. | |||
| Week 10B3/25/10 | PAPER DISCUSSION | Tirosh et al. Science 2009 A yeast hybrid provides insight into the evolution of gene expression regulation. | |
| Week 11A4/6/10 | Evolution of cis-regulation - Part I | Ludwig et al. Nature 2000.Evidence for stabilizing selection in a eukaryotic enhancer element. | |
| Week 11B4/8/10 | PAPER DISCUSSION | Kim et al. 2009. PLoS Gen. Evolution of Regulatory Sequences in 12 Drosophila species | |
| Berman 2002 PNAS. | |||
| Week 12A4/13/10 | Evolution of cis-regulation - Part II | ||
| Week 12B4/15/10 | PAPER DISCUSSION | Tsong Nature 2006. Evolution of alternative transcriptional circuits with identical logic. | |
| Week 13A4/20/10 | Evolution of cis-regulation - Part III | ||
| Week 13B4/22/10 | PAPER DISCUSSION | Rubin paper - mammalian stuff | |
| Week 14A4/27/10 | Evolutionary proteomics & systems biology | ||
| Week 14B4/29/10 | PAPER DISCUSSION | tbd | |
| Week 15A5/4/10 | Final wrap-up, remaining questions | ||
| Week 15B5/6/10 | PAPER DISCUSSION | Clark et al. Nature. 2007. Evolution of genes and genomes on the Drosophila phylogeny. | |