WEEK DATE |
TOPIC |
REQUIRED READING |
SUGGESTED READING |
| Click for ppt & pdfs 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 1B 1/21/10 |
Anatomy of a genome project | Metzker.Nat Reviews Gen.
2006.Sequencing technologies -
the next generation. |
|
| Week 2A 1/26/10 |
PAPER DISCUSSION | Clark et al. Nature. 2007. Evolution of genes and genomes on
the Drosophila phylogeny. |
|
| Week 2B 1/28/10 |
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 3A 2/2/10 |
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 3B 2/4/10 |
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 4A 2/9/10 |
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 4B 2/11/10 |
PAPER DISCUSSION | PAPER:Aury et al. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia | |
| Week 5A 2/16/10 |
Lateral gene transfer and the bacterial species concept (Nicole Perna, guest lecturer) | tbd | |
Week 5B 2/18/10 |
PAPER DISCUSSION | tbd | |
Week 6A 2/23/10 |
Molecular evolution - Part I | Nielsen. Annu Rev Genet. 2005.Molecular signatures of natural selection. | |
Week 6B 2/25/10 |
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 7A 3/2/10 |
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 7B 3/4/10 |
PAPER DISCUSSION | Sabeti et al. 2007.Nature.Genome-wide detection and characterization of positive selection in human populations | |
| Week 8A 3/9/10 |
QTL mapping (Karl Broman, guest lecturer) | tbd | |
Week 8B 3/11/10 |
PAPER DISCUSSION | Colosimo et al. 2004. PLoS Biol. The genetic architecture of parallel armor plate reduction in threespine sticklebacks. |
|
Week 9A 3/16/10 |
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 9B 3/18/10 |
PAPER DISCUSSION | Denver et al. 2005.The transcriptional consequences of mutation and natural selection in Cenorhabditis elegans | |
Week 10A 3/23/10 |
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 10B 3/25/10 |
PAPER DISCUSSION | Tirosh et al. Science 2009 A yeast hybrid provides insight into the evolution of gene expression regulation. | |
Week 11A 4/6/10 |
Evolution of cis-regulation - Part I | Ludwig et al. Nature 2000.Evidence for stabilizing selection in a eukaryotic enhancer element. | |
Week 11B 4/8/10 |
PAPER DISCUSSION | Moses et al. PLoS Comp Bio. 2006. Large-scale turnover of functional transcription factor binding sites in Drosophila. |
|
| Week 12A 4/13/10 |
Evolution of cis-regulation - Part II | tbd | |
Week 12B 4/15/10 |
PAPER DISCUSSION | Tsong Nature 2006. Evolution of alternative transcriptional circuits with identical logic. | |
| Week 13A 4/20/10 |
Evolution of cis-regulation - Part III | tbd | |
Week 13B 4/22/10 |
PAPER DISCUSSION | Rubin paper - mammalian stuff | |
Week 14A 4/27/10 |
Evolutionary proteomics & systems biology | ||
Week 14B 4/29/10 |
PAPER DISCUSSION | tbd | |
Week 15A 5/4/10 |
Final wrap-up, remaining questions | ||
Week 15B 5/6/10 |
PAPER DISCUSSION | Clark et al. Nature. 2007. Evolution of genes and genomes on the Drosophila phylogeny. | |